Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008122.1 Hibiscus syriacus cultivar Beakdansim tig00110676_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: 2511854
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:2024275 original size:2 final size:2
Alignment explanation
Indices: 2024268--2024298 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2024258 GTTTATACTT
2024268 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 T
2024299 TAGAACTAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2025244 original size:4 final size:4
Alignment explanation
Indices: 2025235--2025278 Score: 79
Period size: 4 Copynumber: 11.0 Consensus size: 4
2025225 AGCCATGATA
*
2025235 TATG TATG TATG TATG TATT TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2025279 GCTAGTTTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:2029301 original size:17 final size:17
Alignment explanation
Indices: 2029263--2029309 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
2029253 GTAATCTATA
*
2029263 TTATTT-TTTTATATTG
1 TTATTTATTTTCTATTG
*
2029279 TATATTTATTTTCTTTTG
1 T-TATTTATTTTCTATTG
2029297 TTATTTGATTTTC
1 TTATTT-ATTTTC
2029310 GATAAGTCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 10 0.38
18 15 0.58
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.72
Consensus pattern (17 bp):
TTATTTATTTTCTATTG
Found at i:2031172 original size:26 final size:27
Alignment explanation
Indices: 2031115--2031178 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
2031105 CCAAAATTAT
* *
2031115 GATTGAGAAACAAAATCCCAAAATCAC
1 GATTGAGAAACAAAACCCCAAAAACAC
*
2031142 AATTGAGAAAC-AAACCCCAAAAACAC
1 GATTGAGAAACAAAACCCCAAAAACAC
*
2031168 GATTGACAAAC
1 GATTGAGAAAC
2031179 TCTCCTAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 22 0.69
27 10 0.31
ACGTcount: A:0.53, C:0.23, G:0.11, T:0.12
Consensus pattern (27 bp):
GATTGAGAAACAAAACCCCAAAAACAC
Found at i:2032008 original size:30 final size:30
Alignment explanation
Indices: 2031970--2032059 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
2031960 TGGATTCATG
2031970 GATCAAATTGATATTTTATATAAAATTTAGA
1 GATCAAATT-ATATTTTATATAAAATTTAGA
* * *
2032001 G-TTAAATTAATATTTTATGTAAAGTTTA-A
1 GATCAAATT-ATATTTTATATAAAATTTAGA
* *
2032030 GATCAAATTACTATTCTATCTAAAATTTAG
1 GATCAAATTA-TATTTTATATAAAATTTAG
2032060 GAATTAAGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
29 3 0.06
30 44 0.92
31 1 0.02
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (30 bp):
GATCAAATTATATTTTATATAAAATTTAGA
Found at i:2049996 original size:9 final size:8
Alignment explanation
Indices: 2049974--2050062 Score: 53
Period size: 9 Copynumber: 11.0 Consensus size: 8
2049964 CGAACCCGAA
*
2049974 AATATTAT
1 AATATAAT
2049982 ATATATAATT
1 A-ATATAA-T
2049992 AATATAA-
1 AATATAAT
2049999 AATATAA-
1 AATATAAT
*
2050006 AATATTAT
1 AATATAAT
2050014 ATATATAATT
1 A-ATATAA-T
*
2050024 AATATAAAA
1 AATAT-AAT
2050033 AATATAA-
1 AATATAAT
*
2050040 AATATTAT
1 AATATAAT
2050048 -ATAT-AT
1 AATATAAT
2050054 ATATATAAT
1 A-ATATAAT
2050063 CGGGTCGGGG
Statistics
Matches: 66, Mismatches: 5, Indels: 19
0.73 0.06 0.21
Matches are distributed among these distances:
6 2 0.03
7 23 0.35
8 8 0.12
9 27 0.41
10 6 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
AATATAAT
Found at i:2050002 original size:7 final size:7
Alignment explanation
Indices: 2049992--2050044 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
2049982 ATATATAATT
2049992 AATATAA
1 AATATAA
2049999 AATATAA
1 AATATAA
*
2050006 AATATTA
1 AATATAA
* *
2050013 TATATAT
1 AATATAA
2050020 AAT-TAA
1 AATATAA
* *
2050026 TATAAAA
1 AATATAA
2050033 AATATAA
1 AATATAA
2050040 AATAT
1 AATAT
2050045 TATATATATA
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
6 4 0.11
7 31 0.89
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AATATAA
Found at i:2050008 original size:32 final size:33
Alignment explanation
Indices: 2049972--2050054 Score: 150
Period size: 32 Copynumber: 2.5 Consensus size: 33
2049962 CCCGAACCCG
2049972 AAAATATTATATATATAATTAATAT-AAAATAT
1 AAAATATTATATATATAATTAATATAAAAATAT
2050004 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATAT-AAAAATAT
2050038 AAAATATTATATATATA
1 AAAATATTATATATATA
2050055 TATATAATCG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
32 25 0.51
34 24 0.49
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (33 bp):
AAAATATTATATATATAATTAATATAAAAATAT
Found at i:2050142 original size:2 final size:2
Alignment explanation
Indices: 2050135--2050183 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2050125 TGTTTGACTT
2050135 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
2050177 TA TA TA T
1 TA TA TA T
2050184 GGGTTAAGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2050709 original size:21 final size:21
Alignment explanation
Indices: 2050685--2050724 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2050675 ATCTTTTATT
*
2050685 TTTTTCGAAC-TTTTGTTTAGG
1 TTTTTC-AACATTTTATTTAGG
2050706 TTTTTCAACATTTTATTTA
1 TTTTTCAACATTTTATTTA
2050725 TATGTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (21 bp):
TTTTTCAACATTTTATTTAGG
Found at i:2052183 original size:12 final size:12
Alignment explanation
Indices: 2052168--2052192 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2052158 TTTTTAAAAT
2052168 AATAAAATATTA
1 AATAAAATATTA
2052180 AATAAAATATTA
1 AATAAAATATTA
2052192 A
1 A
2052193 TTACTTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATAAAATATTA
Found at i:2055501 original size:36 final size:36
Alignment explanation
Indices: 2055461--2055537 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
2055451 GACTCGACTT
2055461 GAAAGTTCACGAG-TCTAAAATTATCAAACTTGATTC
1 GAAAGTTCACGAGCT-TAAAATTATCAAACTTGATTC
** * *
2055497 GAAAGTTTGCGAGCTTAAAATTTTCAAATTTGATTC
1 GAAAGTTCACGAGCTTAAAATTATCAAACTTGATTC
2055533 GAAAG
1 GAAAG
2055538 CTTGAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
36 35 0.97
37 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (36 bp):
GAAAGTTCACGAGCTTAAAATTATCAAACTTGATTC
Found at i:2069479 original size:17 final size:17
Alignment explanation
Indices: 2069444--2069481 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2069434 TACAAAATTT
*
2069444 ATTAAAAAAATATATAA
1 ATTAAAAAAATAGATAA
2069461 ATTAAAAATAATAGA-AA
1 ATTAAAAA-AATAGATAA
2069478 ATTA
1 ATTA
2069482 TATTAAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
ATTAAAAAAATAGATAA
Found at i:2073621 original size:60 final size:61
Alignment explanation
Indices: 2073571--2073687 Score: 150
Period size: 61 Copynumber: 1.9 Consensus size: 61
2073561 ATTATTGGGT
*
2073571 ATTACT-TTATTAAGT-GTATCGACTATCAAAACTTACAAAATGGTCATCTGACTATTGAAC
1 ATTACTATTATTAAGTCCT-TCGACTATCAAAACTTACAAAATGGTCATCTGACTATTGAAC
* * * *
2073631 ATTATTATTTTTAAGTCCTTCGACTATTAAAAGTTACAAAATGGTCATGC-GACTATT
1 ATTACTATTATTAAGTCCTTCGACTATCAAAACTTACAAAATGGTCAT-CTGACTATT
2073688 CATTATGTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
60 5 0.10
61 42 0.86
62 2 0.04
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (61 bp):
ATTACTATTATTAAGTCCTTCGACTATCAAAACTTACAAAATGGTCATCTGACTATTGAAC
Found at i:2081508 original size:30 final size:30
Alignment explanation
Indices: 2081437--2081509 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
2081427 AAAATGTAGG
*
2081437 TTTTG-AAAGTTTAATGGCTAAAATATAAA
1 TTTTGAAAAGTTTAAGGGCTAAAATATAAA
* *
2081466 CTTTGTAAAAGTTTAGGGGCTAAAA-ATATAA
1 TTTTG-AAAAGTTTAAGGGCTAAAATATA-AA
2081497 TTTTGAAAAGTTT
1 TTTTGAAAAGTTT
2081510 TATATTTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 4 0.11
30 11 0.30
31 22 0.59
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAGTTTAAGGGCTAAAATATAAA
Found at i:2082012 original size:29 final size:30
Alignment explanation
Indices: 2081960--2082050 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 30
2081950 CAAATTTTGG
* **
2081960 TTAGTGACTAAAATATAGGTTTTG-AAAGT
1 TTAGTGGCTAAAATATAAATTTTGAAAAGT
* *
2081989 TTAGTGGCTAAAATATAAACTTTGTAATAG-
1 TTAGTGGCTAAAATATAAATTTTG-AAAAGT
*
2082019 TTAGGGGCTAAAA-ATATAATTTTGAAAAGT
1 TTAGTGGCTAAAATATA-AATTTTGAAAAGT
2082049 TT
1 TT
2082051 TATATTTTAG
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
29 27 0.54
30 20 0.40
31 3 0.06
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.37
Consensus pattern (30 bp):
TTAGTGGCTAAAATATAAATTTTGAAAAGT
Found at i:2083777 original size:38 final size:31
Alignment explanation
Indices: 2083696--2083777 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
2083686 AGGGAAGGAT
*
2083696 ATATATATTTTTCGGGTCGAATCAATGGATG
1 ATATATATTTTTCGGGTCGAATCAATGGACG
*
2083727 ATATATAATTTTCGGGTCGGATTGGATTCAAGTGGACG
1 ATATATATTTTTCGGGTC-GA----A-TCAA-TGGACG
2083765 ATATATATTTTTC
1 ATATATATTTTTC
2083778 AAGCTGGATC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
31 17 0.41
32 2 0.05
36 1 0.02
37 4 0.10
38 17 0.41
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (31 bp):
ATATATATTTTTCGGGTCGAATCAATGGACG
Found at i:2088591 original size:23 final size:23
Alignment explanation
Indices: 2088543--2088592 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
2088533 ATCATGACTA
* *
2088543 TTCATGAAAAATAATTAAGTCTT
1 TTCATAAAAAATAATTAAGTCAT
**
2088566 TTCATAAAAAATAATTATTTCAT
1 TTCATAAAAAATAATTAAGTCAT
2088589 TTCA
1 TTCA
2088593 CTCTAAAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (23 bp):
TTCATAAAAAATAATTAAGTCAT
Found at i:2089796 original size:3 final size:3
Alignment explanation
Indices: 2089788--2089813 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2089778 TAACAACTAA
2089788 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2089814 GATCTTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2093081 original size:60 final size:60
Alignment explanation
Indices: 2092983--2093108 Score: 209
Period size: 60 Copynumber: 2.1 Consensus size: 60
2092973 GAGACCTCAA
* *
2092983 GAAT-AACAACAATACTTCATGTTCTTTGAGTAAAATTAAAGGTTAAAATTCTGGTTTTT
1 GAATGAACAACAATACTTCAGGTTCTTTGAGTAAAATTAAAGGTTAAAATTCTGATTTTT
* *
2093042 GAATGAACAACAATACTTCAGGTTCTTTGAGTAAGATTAAAGGTTCAAATTCTGATTTTT
1 GAATGAACAACAATACTTCAGGTTCTTTGAGTAAAATTAAAGGTTAAAATTCTGATTTTT
2093102 GAATGAA
1 GAATGAA
2093109 AAAAATTAGA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 4 0.06
60 58 0.94
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (60 bp):
GAATGAACAACAATACTTCAGGTTCTTTGAGTAAAATTAAAGGTTAAAATTCTGATTTTT
Found at i:2101592 original size:16 final size:15
Alignment explanation
Indices: 2101565--2101617 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 15
2101555 AATATTTATT
2101565 TTTATATAAATTAAAA
1 TTTAT-TAAATTAAAA
2101581 TATTATTAAATTAAAA
1 T-TTATTAAATTAAAA
2101597 TTATATTAAATATATAAA
1 TT-TATTAAAT-TA-AAA
2101615 TTT
1 TTT
2101618 TAAGAAAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
15 1 0.03
16 20 0.61
17 7 0.21
18 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTATTAAATTAAAA
Found at i:2103603 original size:3 final size:3
Alignment explanation
Indices: 2103595--2103652 Score: 66
Period size: 3 Copynumber: 18.7 Consensus size: 3
2103585 AGTGTGCGTG
2103595 AGA AGA AGA AG- AGA ATGA ATGA AGA AGA AGA AG- AGA ATGA AGGA AGA
1 AGA AGA AGA AGA AGA A-GA A-GA AGA AGA AGA AGA AGA A-GA A-GA AGA
2103642 AGA AGA AGA AG
1 AGA AGA AGA AG
2103653 CTGCCACATC
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
2 4 0.08
3 33 0.66
4 13 0.26
ACGTcount: A:0.60, C:0.00, G:0.34, T:0.05
Consensus pattern (3 bp):
AGA
Found at i:2103620 original size:16 final size:15
Alignment explanation
Indices: 2103595--2103650 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 15
2103585 AGTGTGCGTG
2103595 AGAA-GAAGAAGAGA
1 AGAATGAAGAAGAGA
2103609 ATGAATGAAGAAGAAGA
1 A-GAATGAAGAAG-AGA
2103626 AG-A-GAATGAAG-GA
1 AGAATGAA-GAAGAGA
2103639 AGAA-GAAGAAGA
1 AGAATGAAGAAGA
2103651 AGCTGCCACA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 8 0.22
14 8 0.22
15 8 0.22
16 8 0.22
17 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.34, T:0.05
Consensus pattern (15 bp):
AGAATGAAGAAGAGA
Found at i:2103623 original size:25 final size:22
Alignment explanation
Indices: 2103595--2103650 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
2103585 AGTGTGCGTG
*
2103595 AGAAGAAGAAGAGAATGAATGA
1 AGAAGAAGAAGAGAATGAAGGA
2103617 AGAAGAAGAAGAGAATGAAGGA
1 AGAAGAAGAAGAGAATGAAGGA
2103639 AGAAGAAGAAGA
1 AGAAGAAGAAGA
2103651 AGCTGCCACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.34, T:0.05
Consensus pattern (22 bp):
AGAAGAAGAAGAGAATGAAGGA
Found at i:2103901 original size:26 final size:26
Alignment explanation
Indices: 2103872--2103950 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
2103862 GTACAAATAT
2103872 AATCATTCAAATTCAAAAACTCCTAA
1 AATCATTCAAATTCAAAAACTCCTAA
* * *
2103898 AATCACTTTATGACT-AAAAA-----AA
1 AATCA-TTCA-AATTCAAAAACTCCTAA
2103920 AATCATTCAAATTCAAAAACTCCTAA
1 AATCATTCAAATTCAAAAACTCCTAA
2103946 AATCA
1 AATCA
2103951 CTTTATGACT
Statistics
Matches: 39, Mismatches: 6, Indels: 16
0.64 0.10 0.26
Matches are distributed among these distances:
20 2 0.05
21 8 0.21
22 7 0.18
26 12 0.31
27 8 0.21
28 2 0.05
ACGTcount: A:0.52, C:0.20, G:0.01, T:0.27
Consensus pattern (26 bp):
AATCATTCAAATTCAAAAACTCCTAA
Found at i:2103921 original size:22 final size:22
Alignment explanation
Indices: 2103896--2103972 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
2103886 AAAAACTCCT
2103896 AAAATCACTTTATGACTAAAAA
1 AAAATCACTTTATGACTAAAAA
* * *
2103918 AAAATCA-TTCA-AATTCAAAAA
1 AAAATCACTTTATGACT-AAAAA
2103939 CTCCTAAAATCACTTTATGACTAAAAA
1 -----AAAATCACTTTATGACTAAAAA
2103966 AAAATCA
1 AAAATCA
2103973 TTACACCTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 16
0.65 0.10 0.25
Matches are distributed among these distances:
20 2 0.05
21 8 0.20
22 14 0.34
26 7 0.17
27 8 0.20
28 2 0.05
ACGTcount: A:0.55, C:0.17, G:0.03, T:0.26
Consensus pattern (22 bp):
AAAATCACTTTATGACTAAAAA
Found at i:2103924 original size:48 final size:48
Alignment explanation
Indices: 2103872--2103974 Score: 206
Period size: 48 Copynumber: 2.1 Consensus size: 48
2103862 GTACAAATAT
2103872 AATCATTCAAATTCAAAAACTCCTAAAATCACTTTATGACTAAAAAAA
1 AATCATTCAAATTCAAAAACTCCTAAAATCACTTTATGACTAAAAAAA
2103920 AATCATTCAAATTCAAAAACTCCTAAAATCACTTTATGACTAAAAAAA
1 AATCATTCAAATTCAAAAACTCCTAAAATCACTTTATGACTAAAAAAA
2103968 AATCATT
1 AATCATT
2103975 ACACCTCTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.28
Consensus pattern (48 bp):
AATCATTCAAATTCAAAAACTCCTAAAATCACTTTATGACTAAAAAAA
Found at i:2106900 original size:60 final size:60
Alignment explanation
Indices: 2106833--2106949 Score: 173
Period size: 60 Copynumber: 1.9 Consensus size: 60
2106823 ATAGTCGGGT
*
2106833 GACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGTAACA-CTCTATAGTTGAAA
1 GACCATTTTGTAACTTTTAATAATCGAGGGACTCAACAAAGTAACATCT-TATAGTTGAAA
* * * *
2106893 GACCATTTTGTAACTTTTAATAATCGATGGACTTAATAAAGTAATATCTTATAGTTG
1 GACCATTTTGTAACTTTTAATAATCGAGGGACTCAACAAAGTAACATCTTATAGTTG
2106950 GGGACCATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
60 49 0.96
61 2 0.04
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAATCGAGGGACTCAACAAAGTAACATCTTATAGTTGAAA
Found at i:2108165 original size:31 final size:32
Alignment explanation
Indices: 2108129--2108211 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
2108119 CCTAACATTT
2108129 ACTTTTTGTTTTATTTTAGTACC-CGCCGTTA
1 ACTTTTTGTTTTATTTTAGTACCACGCCGTTA
* * * * *
2108160 GCTTTTTATTTCATTTTAGTACCATGCTGTTA
1 ACTTTTTGTTTTATTTTAGTACCACGCCGTTA
*
2108192 ACTTTCTGTTTTCATTTTAG
1 ACTTTTTGTTTT-ATTTTAG
2108212 CACCTAAATT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 20 0.49
32 14 0.34
33 7 0.17
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.54
Consensus pattern (32 bp):
ACTTTTTGTTTTATTTTAGTACCACGCCGTTA
Found at i:2110716 original size:23 final size:24
Alignment explanation
Indices: 2110671--2110718 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
2110661 ATCCTACAGC
*
2110671 ATCCTAAAAGTTTTAACATTTTTT
1 ATCCTAAAACTTTTAACATTTTTT
2110695 ATCCT-AAACTTTTAA-ATCTTTTT
1 ATCCTAAAACTTTTAACAT-TTTTT
2110718 A
1 A
2110719 ATTTAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 2 0.09
23 15 0.68
24 5 0.23
ACGTcount: A:0.33, C:0.15, G:0.02, T:0.50
Consensus pattern (24 bp):
ATCCTAAAACTTTTAACATTTTTT
Found at i:2113725 original size:15 final size:17
Alignment explanation
Indices: 2113695--2113726 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2113685 CCATGACATA
2113695 ATATCATTGAGGAATGC
1 ATATCATTGAGGAATGC
2113712 ATATCA-TG-GGAATGC
1 ATATCATTGAGGAATGC
2113727 TTTGGGGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.28
Consensus pattern (17 bp):
ATATCATTGAGGAATGC
Found at i:2125768 original size:60 final size:60
Alignment explanation
Indices: 2125687--2125802 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
2125677 ATGGTCCCCG
* * * *
2125687 GACTATAGGATGTTATTTTGTTGAGTC-CTCTGATTATTAAAAGTTACAAAATGGTCTTTC
1 GACTATAGGACGTTACTTTGTTGAGTCATTC-GACTATTAAAAGTTACAAAATGGTCTTTC
* *
2125747 GACTATAGGACGTTGCTTTGTTGAGTCATTCGACTATTAGAAGTTACAAAATGGTC
1 GACTATAGGACGTTACTTTGTTGAGTCATTCGACTATTAAAAGTTACAAAATGGTC
2125803 ACCCAATGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 47 0.96
61 2 0.04
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (60 bp):
GACTATAGGACGTTACTTTGTTGAGTCATTCGACTATTAAAAGTTACAAAATGGTCTTTC
Found at i:2126136 original size:60 final size:60
Alignment explanation
Indices: 2126012--2126124 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
2126002 AACATAATGA
* * *
2126012 ATAGTCGGGTGACCATTTTGTAACTTCTAATAGTCGATGGACTTAACAAAGCAACGTCCT
1 ATAGTCGGGTGACCATTTTGTAACTTCTAATAGTCAATGGACTTAACAAAACAACATCCT
*
2126072 ATAGTCGGAG-GACCATTTTGTAACTTTTAATAGTCAAAT-GA-TTCAACAAAACA
1 ATAGTCGG-GTGACCATTTTGTAACTTCTAATAGTC-AATGGACTT-AACAAAACA
2126125 TTATGCTATA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
59 2 0.04
60 42 0.89
61 3 0.06
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (60 bp):
ATAGTCGGGTGACCATTTTGTAACTTCTAATAGTCAATGGACTTAACAAAACAACATCCT
Found at i:2127353 original size:29 final size:31
Alignment explanation
Indices: 2127316--2127390 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 31
2127306 TAGGCGTTAC
* *
2127316 ATCATTTATACCATTAAAATTTTA-ATTT-T
1 ATCAATTATACCATTAAAATTTGATATTTGT
* * * *
2127345 ATCAATTATAACACTAAACTTTGATTTTTGT
1 ATCAATTATACCATTAAAATTTGATATTTGT
*
2127376 TTCAATTATACCATT
1 ATCAATTATACCATT
2127391 GGCCGTTAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
29 19 0.54
30 3 0.09
31 13 0.37
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.48
Consensus pattern (31 bp):
ATCAATTATACCATTAAAATTTGATATTTGT
Found at i:2130128 original size:2 final size:2
Alignment explanation
Indices: 2130121--2130148 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2130111 TAATATTATC
2130121 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
2130149 GTTTTTTTAA
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:2146032 original size:20 final size:20
Alignment explanation
Indices: 2145944--2146060 Score: 76
Period size: 21 Copynumber: 5.7 Consensus size: 20
2145934 ATCAGTTTCC
* *
2145944 AAAATCGTAACGCGATTATTG
1 AAAATCGCAACGCGAATA-TG
*
2145965 AAAATCGCAATGCGATAGTAT-
1 AAAATCGCAACGCGA-A-TATG
* ** * * *
2145986 AAATTCGCATTGCGATTTTCA
1 AAAATCGCAACGCGAATAT-G
2146007 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGAATATG
* *
2146027 AAAATCGCAACGCGAACA-C
1 AAAATCGCAACGCGAATATG
2146046 ATAAATCGCAACGCG
1 A-AAATCGCAACGCG
2146061 TATCCGTAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
19 3 0.04
20 30 0.39
21 40 0.53
22 1 0.01
23 2 0.03
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATG
Found at i:2146050 original size:62 final size:60
Alignment explanation
Indices: 2145885--2146056 Score: 163
Period size: 61 Copynumber: 2.9 Consensus size: 60
2145875 AATGACCAAC
* * * * *
2145885 AAAATCGCAACGCGAA-ATAAAAATCGCAACGCGATCCCCA-GAATCGCAAATCAGTTTCC
1 AAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACATAAATCGC-AATCAGTTTCA
* * * ** * *
2145944 AAAATCGTAACGCGATTATTGAAAATCGCAATGCGATA-GTATAAATTCGCATTGCGATTTTCA
1 AAAATCGCAACGCGAATA-TGAAAATCGCAACGCGATACACATAAA-TCGCAAT-C-AGTTTCA
2146007 AAAATCGCAACGCGAATATGAAAATCGCAACGCGA-ACACATAAATCGCAA
1 AAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACATAAATCGCAA
2146057 CGCGTATCCG
Statistics
Matches: 89, Mismatches: 17, Indels: 12
0.75 0.14 0.10
Matches are distributed among these distances:
59 14 0.16
60 2 0.02
61 26 0.29
62 26 0.29
63 21 0.24
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (60 bp):
AAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACATAAATCGCAATCAGTTTCA
Found at i:2146070 original size:20 final size:20
Alignment explanation
Indices: 2146008--2146237 Score: 232
Period size: 20 Copynumber: 11.5 Consensus size: 20
2145998 CGATTTTCAA
* ** *
2146008 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
2146028 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
2146048 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2146068 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
2146088 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
2146108 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2146128 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2146148 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
2146168 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
2146188 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
2146208 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
2146228 AAATCACAAC
1 AAATCGCAAC
2146238 ACTGAAATTT
Statistics
Matches: 176, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 172 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:2147158 original size:12 final size:12
Alignment explanation
Indices: 2147141--2147165 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2147131 ATATAATCCT
2147141 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2147153 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2147165 G
1 G
2147166 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2147862 original size:14 final size:14
Alignment explanation
Indices: 2147843--2147899 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2147833 GCGAAATGAA
*
2147843 AATCGCAACGACAG
1 AATCGCAACGAAAG
2147857 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
2147874 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
2147890 AATCGCAACG
1 AATCGCAACG
2147900 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:2147870 original size:33 final size:33
Alignment explanation
Indices: 2147824--2147916 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2147814 GCGAAACCAA
*
2147824 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
2147857 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2147890 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2147917 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:2147881 original size:19 final size:19
Alignment explanation
Indices: 2147787--2147921 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
2147777 TAGTTTACTT
* *
2147787 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2147807 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2147826 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2147845 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
2147859 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2147878 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
2147892 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2147911 TCGCAATGCGA
1 TCGCAACGCGA
2147922 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:2147939 original size:19 final size:19
Alignment explanation
Indices: 2147917--2148045 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2147907 AAAATCGCAA
2147917 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2147936 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2147950 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2147969 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2147983 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2148002 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2148021 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2148041 TGCGA
1 TGCGA
2148046 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2147959 original size:33 final size:33
Alignment explanation
Indices: 2147917--2148008 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2147907 AAAATCGCAA
2147917 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
2147950 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
2147983 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2148009 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2148209 original size:93 final size:93
Alignment explanation
Indices: 2148093--2148561 Score: 904
Period size: 93 Copynumber: 5.1 Consensus size: 93
2148083 ATGGATTGCA
*
2148093 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATATTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2148157 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2148185 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2148250 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2148278 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2148343 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2148371 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
2148436 TAGCAGAATTGGCAGCAATCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2148464 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
2148529 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2148557 TTACT
1 TTACT
2148562 AAGCAATCTA
Statistics
Matches: 372, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 368 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2149408 original size:21 final size:22
Alignment explanation
Indices: 2149366--2149409 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
2149356 ATAATAACAA
*
2149366 AATTAGTAATTGTTAAATAATT
1 AATTAGTAATTGTTAAAAAATT
2149388 AATTA-TAATT-TTAGAAAAATT
1 AATTAGTAATTGTTA-AAAAATT
2149409 A
1 A
2149410 TATAGAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 3 0.15
21 12 0.60
22 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (22 bp):
AATTAGTAATTGTTAAAAAATT
Found at i:2150304 original size:19 final size:19
Alignment explanation
Indices: 2150280--2150363 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
2150270 GCAACGAGAG
*
2150280 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
2150299 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2150318 AATCGCAA--CG--AT-AG
1 AATCGCAACGCGAAATGAA
2150332 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2150351 AATCGCAATGCGA
1 AATCGCAACGCGA
2150364 TTTTGGTTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 9 0.16
15 2 0.04
16 2 0.04
17 2 0.04
18 2 0.04
19 39 0.70
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2150320 original size:52 final size:52
Alignment explanation
Indices: 2150258--2150363 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
2150248 TCTTTTGGTT
*
2150258 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGACAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
* *
2150310 GAAATGAAAATCGCAACGATAGAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
2150362 GA
1 GA
2150364 TTTTGGTTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (52 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:2150394 original size:14 final size:14
Alignment explanation
Indices: 2150375--2150431 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2150365 TTTGGTTTCG
2150375 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2150389 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2150408 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2150422 CGTTGCGATT
1 CGTTGCGATT
2150432 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2150407 original size:33 final size:33
Alignment explanation
Indices: 2150359--2150439 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
2150349 AAAATCGCAA
**
2150359 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2150392 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2150425 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
2150440 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2150442 original size:21 final size:21
Alignment explanation
Indices: 2150416--2150491 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
2150406 CGCGTTGCGA
2150416 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
2150437 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
2150457 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
2150478 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
2150492 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2150472 original size:41 final size:41
Alignment explanation
Indices: 2150415--2150492 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
2150405 TCGCGTTGCG
*
2150415 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
2150456 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
2150493 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:2150613 original size:33 final size:33
Alignment explanation
Indices: 2150571--2150641 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2150561 AATACTAACT
*
2150571 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
2150604 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
2150637 TGAAA
1 TGAAA
2150642 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:2150876 original size:23 final size:22
Alignment explanation
Indices: 2150823--2150878 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
2150813 TGGTTGTGAG
**
2150823 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
2150845 GGAAATCTTCGGAGATGGGGGAC
1 GGATTTCTTCGGAGAT-GGGGAC
2150868 GGATTTCTTCG
1 GGATTTCTTCG
2150879 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.20, C:0.16, G:0.41, T:0.23
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:2151052 original size:20 final size:20
Alignment explanation
Indices: 2151027--2151177 Score: 187
Period size: 20 Copynumber: 7.5 Consensus size: 20
2151017 TTAAATATCA
2151027 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
2151047 CGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACG
* **
2151067 CATTGCGATTTACCCATACG
1 CGTTGCGATTTACGGATACG
*
2151087 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
2151107 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
2151127 CGTTGCGATTTATGTG-TTCG
1 CGTTGCGATTTACG-GATACG
* ** *
2151147 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGGATACG
2151167 CGTTGCGATTT
1 CGTTGCGATTT
2151178 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
20 112 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:2151194 original size:21 final size:21
Alignment explanation
Indices: 2151164--2151246 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
2151154 ATTTTCATAT
*
2151164 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
2151185 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
2151206 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
2151227 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
2151247 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:2151237 original size:42 final size:43
Alignment explanation
Indices: 2151144--2151242 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
2151134 ATTTATGTGT
* *
2151144 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
2151185 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
2151227 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
2151243 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:2156408 original size:27 final size:28
Alignment explanation
Indices: 2156351--2156408 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
2156341 CTATACTGGT
* *
2156351 ATTTTAAACTTAATATTAATTAAATGAG
1 ATTTTAAACTTAATAATAATTAAATAAG
* *
2156379 ATTTTAAATTTAATAAT-GTTAAATAAG
1 ATTTTAAACTTAATAATAATTAAATAAG
2156406 ATT
1 ATT
2156409 ACAATCTGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (28 bp):
ATTTTAAACTTAATAATAATTAAATAAG
Found at i:2161430 original size:12 final size:12
Alignment explanation
Indices: 2161413--2161437 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2161403 CATATTACAA
2161413 AATTATATATAT
1 AATTATATATAT
2161425 AATTATATATAT
1 AATTATATATAT
2161437 A
1 A
2161438 TAGAGAGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTATATATAT
Found at i:2167311 original size:21 final size:20
Alignment explanation
Indices: 2167226--2167382 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
2167216 AATGACCAAT
** *
2167226 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
2167245 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
2167265 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
2167285 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
2167306 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
2167327 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * *
2167348 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
2167368 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
2167383 ACACATAAAT
Statistics
Matches: 104, Mismatches: 28, Indels: 11
0.73 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:2167411 original size:20 final size:20
Alignment explanation
Indices: 2167349--2167593 Score: 246
Period size: 20 Copynumber: 12.2 Consensus size: 20
2167339 CGATTTTCCA
* ** *
2167349 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
2167369 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
2167389 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2167409 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
2167429 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
2167449 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2167469 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2167489 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
2167509 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
2167529 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
*
2167549 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
2167569 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
2167589 AAATC
1 AAATC
2167594 CGGTAGGGCA
Statistics
Matches: 192, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 188 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:2168344 original size:24 final size:24
Alignment explanation
Indices: 2168305--2168351 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2168295 AAATTTGGTC
2168305 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2168329 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2168352 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:2168543 original size:12 final size:12
Alignment explanation
Indices: 2168526--2168550 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2168516 ATATAATCCT
2168526 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2168538 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2168550 G
1 G
2168551 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2169005 original size:18 final size:18
Alignment explanation
Indices: 2168982--2169019 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2168972 TGGCAGGGTG
2168982 ATGGCTAATCTAAGTGAA
1 ATGGCTAATCTAAGTGAA
2169000 ATGGCTAATCTAAGTGAA
1 ATGGCTAATCTAAGTGAA
2169018 AT
1 AT
2169020 TACGAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (18 bp):
ATGGCTAATCTAAGTGAA
Found at i:2170709 original size:14 final size:14
Alignment explanation
Indices: 2170690--2170778 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
2170680 TTGAAATGAA
2170690 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2170704 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
2170723 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2170737 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2170756 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2170770 AATCGCAAC
1 AATCGCAAC
2170779 ACGAAATGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 29 0.48
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.33
ACGTcount: A:0.44, C:0.24, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2170727 original size:33 final size:33
Alignment explanation
Indices: 2170682--2170796 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
2170672 TCTTTGGGTT
2170682 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
2170715 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
2170748 GAAATGAAAATCGCAACGAGAGAATCGCAACAC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2170781 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2170797 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.47, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2170728 original size:19 final size:19
Alignment explanation
Indices: 2170704--2170801 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
2170694 GCAACGAGAG
*
2170704 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
2170723 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
2170737 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2170756 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
2170770 AATCGCAACACGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2170789 AATCGCAATGCGA
1 AATCGCAACGCGA
2170802 TTTTGGTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2170832 original size:14 final size:14
Alignment explanation
Indices: 2170813--2170869 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2170803 TTTGGTTTCG
2170813 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2170827 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2170846 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2170860 CGTTGCGATT
1 CGTTGCGATT
2170870 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2170845 original size:33 final size:33
Alignment explanation
Indices: 2170797--2170877 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
2170787 AAAATCGCAA
**
2170797 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2170830 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2170863 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
2170878 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2170900 original size:20 final size:20
Alignment explanation
Indices: 2170853--2170909 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
2170843 TCGCGTTGCG
***
2170853 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACAGTC
2170873 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGACAGTC
2170894 ATTCTCTCGTTGCGAC
1 ATTCTCTCGTTGCGAC
2170910 TCTTCTGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.12, C:0.28, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACAGTC
Found at i:2171435 original size:20 final size:20
Alignment explanation
Indices: 2171408--2171600 Score: 228
Period size: 20 Copynumber: 9.7 Consensus size: 20
2171398 CTTTAAATAT
*
2171408 CGCGTTGCGATTTACGGATT
1 CGCGTTGCGATTTACGGATA
*
2171428 CTCGTTGCGATTTACGGATTA
1 CGCGTTGCGATTTACGGA-TA
*
2171449 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2171468 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
2171488 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
2171508 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2171528 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2171548 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2171568 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2171588 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2171601 TGGAAAATCG
Statistics
Matches: 150, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 146 0.97
21 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2171617 original size:21 final size:21
Alignment explanation
Indices: 2171587--2171669 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
2171577 ATTTTCATAT
*
2171587 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
2171608 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
2171629 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
2171650 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
2171670 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:2171660 original size:42 final size:43
Alignment explanation
Indices: 2171567--2171665 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
2171557 ATTTATGTGT
* *
2171567 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
2171608 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
2171650 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
2171666 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:2174028 original size:60 final size:60
Alignment explanation
Indices: 2173951--2174063 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
2173941 AACTTATCCC
* *
2173951 CGATTATATGATATTACTTTATTAAGTCTA-TCAACTATTAAAAGTTATAAAATGATCATT
1 CGATTATATGATATTACTGTATTAAGT-TATTCAACTATTAAAAGTTACAAAATGATCATT
* * *
2174011 CGATTATA-GATTGTTACTGTATTGAGTTATTCGACTATTAAAAGTTACAAAAT
1 CGATTATATGA-TATTACTGTATTAAGTTATTCAACTATTAAAAGTTACAAAAT
2174064 AATAGTCTGA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 4 0.09
60 42 0.91
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.41
Consensus pattern (60 bp):
CGATTATATGATATTACTGTATTAAGTTATTCAACTATTAAAAGTTACAAAATGATCATT
Found at i:2178245 original size:19 final size:20
Alignment explanation
Indices: 2178221--2178259 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2178211 CGTGTGAACC
2178221 GTCGGTTCAC-ACCGGTTTT
1 GTCGGTTCACAACCGGTTTT
*
2178240 GTCGGTTCCCAACCGGTTTT
1 GTCGGTTCACAACCGGTTTT
2178260 TTAGCGGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.10, C:0.28, G:0.26, T:0.36
Consensus pattern (20 bp):
GTCGGTTCACAACCGGTTTT
Found at i:2181535 original size:17 final size:18
Alignment explanation
Indices: 2181513--2181550 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 18
2181503 CAAAATTAGA
2181513 ACAATTTAAAT-CAATAT
1 ACAATTTAAATACAATAT
2181530 ACAATTTAAATAACAATAT
1 ACAATTTAAAT-ACAATAT
2181549 AC
1 AC
2181551 GTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.58
19 8 0.42
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (18 bp):
ACAATTTAAATACAATAT
Found at i:2181936 original size:49 final size:49
Alignment explanation
Indices: 2181553--2181909 Score: 624
Period size: 49 Copynumber: 7.3 Consensus size: 49
2181543 CAATATACGT
** *
2181553 AAAATAATATATAAAATCTAGAATAACTTAAATATAAAGCAATCTAGAC
1 AAAATAATATATAAAATCTAGAATAACTTAAATAGCAAGCAATCTACAC
* *
2181602 AAAATAATATATAAAATCTAGAATAACTTAAATATCAAGCAATCTATAC
1 AAAATAATATATAAAATCTAGAATAACTTAAATAGCAAGCAATCTACAC
*
2181651 AAAATAATATATAAAATCTAGAATAACTTAAATAGCAAGCAATCTATAC
1 AAAATAATATATAAAATCTAGAATAACTTAAATAGCAAGCAATCTACAC
*
2181700 AAAATAATAAATAAAATCTAGAATAACTTAAATAGCAAGCAATCTACAC
1 AAAATAATATATAAAATCTAGAATAACTTAAATAGCAAGCAATCTACAC
*
2181749 AAAATAATATATAAAATCTAGAATAACTTAAACAGCAAGCAATCTACAC
1 AAAATAATATATAAAATCTAGAATAACTTAAATAGCAAGCAATCTACAC
2181798 AAAATAATATATAAAATCTAGAATAACTTAAATAGCAAGCAATCTACAC
1 AAAATAATATATAAAATCTAGAATAACTTAAATAGCAAGCAATCTACAC
* *
2181847 TAAATAATATATAAAATCTAGAATAACTTAAATAGCAAGCAATCCACAC
1 AAAATAATATATAAAATCTAGAATAACTTAAATAGCAAGCAATCTACAC
2181896 AAAATAATATATAA
1 AAAATAATATATAA
2181910 GCCGTAGAAT
Statistics
Matches: 297, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 297 1.00
ACGTcount: A:0.56, C:0.13, G:0.06, T:0.25
Consensus pattern (49 bp):
AAAATAATATATAAAATCTAGAATAACTTAAATAGCAAGCAATCTACAC
Found at i:2190761 original size:34 final size:34
Alignment explanation
Indices: 2190718--2190802 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
2190708 TATGATTGAT
2190718 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
2190752 CTCTCGGCGTCTTCAGTTGGATTCTTCGTAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
2190786 ATCTCGGCGTCTTCAGT
1 CTCTCGGCGTCTTCAGT
2190803 GCTGTGCATG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (34 bp):
CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
Found at i:2190856 original size:22 final size:22
Alignment explanation
Indices: 2190831--2190887 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
2190821 CGTGAGAAAT
2190831 CACGGGTTCTGCAAGGAGAGAG
1 CACGGGTTCTGCAAGGAGAGAG
2190853 CACGGGTTCTGCAAGGAGAGAG
1 CACGGGTTCTGCAAGGAGAGAG
*
2190875 CACGGGTCCTGCA
1 CACGGGTTCTGCA
2190888 GGGCTGCACG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.25, C:0.23, G:0.39, T:0.14
Consensus pattern (22 bp):
CACGGGTTCTGCAAGGAGAGAG
Found at i:2191678 original size:171 final size:173
Alignment explanation
Indices: 2191392--2191749 Score: 569
Period size: 172 Copynumber: 2.1 Consensus size: 173
2191382 TTGTAAAGTT
* * *
2191392 TTAGGGACCATTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGCTAT
1 TTAGGGATCATTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATTAAAAGTTGCTAT
*
2191457 ACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTAGAAAGAATTTA-AAATTTA-T
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
*
2191520 GGATTAAATTGCTAACTTTGAAAATGTTGAGAACCAAATAGTAA
131 -GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
* * * *
2191564 TTAGGGATCGTTTTGCAAAATTTGAGGAATTTAAGAAATTAGAGTAAATTA-TAAAAGTTGGTAT
1 TTAGGGATCATTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATTAAAAGTTGCTAT
* *
2191628 ACTATGCTTGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
* *
2191693 GATTAAATTGCAAAGTTTGAAAATGTTGAGAAGCAAATAGTAA
131 GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
2191736 TTAGGGATCATTTT
1 TTAGGGATCATTTT
2191750 ATACTTGATG
Statistics
Matches: 170, Mismatches: 14, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
171 64 0.38
172 105 0.62
173 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37
Consensus pattern (173 bp):
TTAGGGATCATTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATTAAAAGTTGCTAT
ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
Found at i:2194076 original size:37 final size:37
Alignment explanation
Indices: 2194026--2194400 Score: 510
Period size: 37 Copynumber: 10.0 Consensus size: 37
2194016 CATTAAAATT
*
2194026 AAGTAATTATTATTAAATTATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
2194063 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAA--ATTAAATCATTA
* *
2194102 AAGTAATTATTATTAAAGCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
2194139 AAGTAATTATTATTAAATC------ATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
*
2194170 AAATAATTATTATTAAATCATTAAATCATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAA--ATTAAATCATTA
*
2194209 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTAA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATT-A
* *
2194247 ATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTA
1 A--AGT-AA-TT--ATTATTAAATCATTAAAATTAAATCATTA
*
2194290 AAGTAATTATTATTAAATCACTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
*
2194327 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* *
2194364 AAGTAATTATTATTAAATCATTAAAGTTAAATAATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
2194401 TATTTAAATC
Statistics
Matches: 304, Mismatches: 17, Indels: 34
0.86 0.05 0.10
Matches are distributed among these distances:
31 29 0.10
37 161 0.53
38 2 0.01
39 74 0.24
40 4 0.01
41 4 0.01
42 2 0.01
43 2 0.01
44 26 0.09
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (37 bp):
AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
Found at i:2194238 original size:14 final size:14
Alignment explanation
Indices: 2193983--2194442 Score: 199
Period size: 14 Copynumber: 34.7 Consensus size: 14
2193973 TCAGTAAATA
2193983 TAAATCATTAAAGT
1 TAAATCATTAAAGT
* * * *
2193997 CAAGTAATTATTA-T
1 TAAATCATTA-AAGT
*
2194011 TAAATCATTAAAAT
1 TAAATCATTAAAGT
* * *
2194025 TAAGTAATTATTA-T
1 TAAATCATTA-AAGT
* *
2194039 TAAATTATTAAAAT
1 TAAATCATTAAAGT
2194053 TAAATCATTAAAG-
1 TAAATCATTAAAGT
*
2194066 T-AATTATT--A-T
1 TAAATCATTAAAGT
*
2194076 TAAATCATTAAATCAT
1 TAAATCATTAAA--GT
2194092 TAAATCATTAAAG-
1 TAAATCATTAAAGT
*
2194105 T-AATTATT--A-T
1 TAAATCATTAAAGT
*
2194115 TAAAGCATTAAAGT
1 TAAATCATTAAAGT
2194129 TAAATCATTAAAG-
1 TAAATCATTAAAGT
*
2194142 T-AATTATT--A-T
1 TAAATCATTAAAGT
*
2194152 TAAATCATTAAATCAT
1 TAAATCATTAAA--GT
* *
2194168 TAAAATAATTATTA-T
1 T-AAATCATTA-AAGT
*
2194183 TAAATCATTAAATCAT
1 TAAATCATTAAA--GT
2194199 TAAATCATTAAAG-
1 TAAATCATTAAAGT
*
2194212 T-AATTATT--A-T
1 TAAATCATTAAAGT
2194222 TAAATCATTAAAGT
1 TAAATCATTAAAGT
*
2194236 TAAATCATTAAATCAT
1 TAAATCATTAAA--GT
* *
2194252 TAAA--GTTAAATCAT
1 TAAATCATTAAA--GT
*
2194266 TAAATCATTAAAAT
1 TAAATCATTAAAGT
2194280 TAAATCATTAAAG-
1 TAAATCATTAAAGT
*
2194293 T-AATTATT--A-T
1 TAAATCATTAAAGT
* *
2194303 TAAATCACTAAAAT
1 TAAATCATTAAAGT
2194317 TAAATCATTAAAG-
1 TAAATCATTAAAGT
*
2194330 T-AATTATT--A-T
1 TAAATCATTAAAGT
2194340 TAAATCATTAAAGT
1 TAAATCATTAAAGT
2194354 TAAATCATTAAAG-
1 TAAATCATTAAAGT
*
2194367 T-AATTATT--A-T
1 TAAATCATTAAAGT
2194377 TAAATCATTAAAGT
1 TAAATCATTAAAGT
* * *
2194391 TAAATAATTATATT
1 TAAATCATTAAAGT
2194405 TAAATCATTAAAGT
1 TAAATCATTAAAGT
* *
2194419 TAAATAATTAAATT
1 TAAATCATTAAAGT
*
2194433 TAAATAATTA
1 TAAATCATTA
2194443 TTATTAAATA
Statistics
Matches: 341, Mismatches: 53, Indels: 104
0.68 0.11 0.21
Matches are distributed among these distances:
10 14 0.04
11 40 0.12
12 42 0.12
13 17 0.05
14 177 0.52
15 4 0.01
16 38 0.11
17 8 0.02
18 1 0.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (14 bp):
TAAATCATTAAAGT
Found at i:2194360 original size:74 final size:73
Alignment explanation
Indices: 2194242--2194451 Score: 270
Period size: 74 Copynumber: 2.9 Consensus size: 73
2194232 AAGTTAAATC
2194242 ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA
1 ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA
2194307 TCACTAAA
66 TCACTAAA
* *
2194315 ATTAAATCATTAAAG-TAATTATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTA
1 ATTAAATCATTAAAGTTAA--ATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTA
*
2194379 AATCATTAAA
64 AATCACTAAA
* * * * *
2194389 GTTAAATAATTATATTTAAATCATTAAAGT--TAAATAATTAAAT--TTAAA-TAATTATTATTA
1 ATTAAATCATTAAAGTTAAATCATTAAA-TCATTAA-AATTAAATCATTAAAGTAATTATTATTA
2194449 AAT
64 AAT
2194452 ATGTACTCGA
Statistics
Matches: 122, Mismatches: 10, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
70 15 0.12
71 5 0.04
72 6 0.05
73 30 0.25
74 63 0.52
75 3 0.02
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.40
Consensus pattern (73 bp):
ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA
TCACTAAA
Found at i:2194431 original size:8 final size:8
Alignment explanation
Indices: 2194009--2194416 Score: 217
Period size: 8 Copynumber: 54.8 Consensus size: 8
2193999 AGTAATTATT
2194009 ATTAAATC
1 ATTAAATC
2194017 ATTAAA--
1 ATTAAATC
* *
2194023 ATTAAGTA
1 ATTAAATC
*
2194031 ATT--ATT
1 ATTAAATC
*
2194037 ATTAAATT
1 ATTAAATC
2194045 ATTAAA--
1 ATTAAATC
2194051 ATTAAATC
1 ATTAAATC
*
2194059 ATTAAAGTA
1 ATTAAA-TC
*
2194068 ATT--ATT
1 ATTAAATC
2194074 ATTAAATC
1 ATTAAATC
2194082 ATTAAATC
1 ATTAAATC
2194090 ATTAAATC
1 ATTAAATC
*
2194098 ATTAAAGTA
1 ATTAAA-TC
*
2194107 ATT--ATT
1 ATTAAATC
*
2194113 ATTAAAGC
1 ATTAAATC
2194121 ATTAAA--
1 ATTAAATC
*
2194127 GTTAAATC
1 ATTAAATC
*
2194135 ATTAAAGTA
1 ATTAAA-TC
*
2194144 ATT--ATT
1 ATTAAATC
2194150 ATTAAATC
1 ATTAAATC
2194158 ATTAAATC
1 ATTAAATC
*
2194166 ATTAAAATA
1 ATT-AAATC
*
2194175 ATT--ATT
1 ATTAAATC
2194181 ATTAAATC
1 ATTAAATC
2194189 ATTAAATC
1 ATTAAATC
2194197 ATTAAATC
1 ATTAAATC
*
2194205 ATTAAAGTA
1 ATTAAA-TC
*
2194214 ATT--ATT
1 ATTAAATC
2194220 ATTAAATC
1 ATTAAATC
2194228 ATTAAA--
1 ATTAAATC
*
2194234 GTTAAATC
1 ATTAAATC
2194242 ATTAAATC
1 ATTAAATC
2194250 ATTAAA--
1 ATTAAATC
*
2194256 GTTAAATC
1 ATTAAATC
2194264 ATTAAATC
1 ATTAAATC
2194272 ATTAAA--
1 ATTAAATC
2194278 ATTAAATC
1 ATTAAATC
*
2194286 ATTAAAGTA
1 ATTAAA-TC
*
2194295 ATT--ATT
1 ATTAAATC
2194301 ATTAAATC
1 ATTAAATC
*
2194309 ACTAAA--
1 ATTAAATC
2194315 ATTAAATC
1 ATTAAATC
*
2194323 ATTAAAGTA
1 ATTAAA-TC
*
2194332 ATT--ATT
1 ATTAAATC
2194338 ATTAAATC
1 ATTAAATC
2194346 ATTAAA--
1 ATTAAATC
*
2194352 GTTAAATC
1 ATTAAATC
*
2194360 ATTAAAGTA
1 ATTAAA-TC
*
2194369 ATT--ATT
1 ATTAAATC
2194375 ATTAAATC
1 ATTAAATC
2194383 ATTAAA--
1 ATTAAATC
* *
2194389 GTTAAATA
1 ATTAAATC
*
2194397 ATTATAT-
1 ATTAAATC
2194404 -TTAAATC
1 ATTAAATC
2194411 ATTAAA
1 ATTAAA
2194417 GTTAAATAAT
Statistics
Matches: 312, Mismatches: 42, Indels: 92
0.70 0.09 0.21
Matches are distributed among these distances:
6 89 0.29
7 7 0.02
8 181 0.58
9 35 0.11
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (8 bp):
ATTAAATC
Found at i:2197282 original size:18 final size:17
Alignment explanation
Indices: 2197259--2197292 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
2197249 AAATTATTAG
2197259 TCTCACGCTTCAGACGAA
1 TCTCACGCTTC-GACGAA
2197277 TCTCACGCTTCGACGA
1 TCTCACGCTTCGACGA
2197293 CAAACAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (17 bp):
TCTCACGCTTCGACGAA
Found at i:2197748 original size:110 final size:110
Alignment explanation
Indices: 2197559--2197778 Score: 415
Period size: 110 Copynumber: 2.0 Consensus size: 110
2197549 AGATTCCCGC
2197559 CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCAGAAGACGCCG
1 CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCAGAAGACGCCG
*
2197624 AGAGATCCTACAGTCCAATTGCTTGAAGACGCCGAGCATTCCCAT
66 AGAGATCCTACAGTCCAATTGCTTGAAGACACCGAGCATTCCCAT
2197669 CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCAGAAGACGCCG
1 CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCAGAAGACGCCG
2197734 AGAGATCCCT-CAGTCCAATTGCTTGAAGACACCGAGCATTCCCAT
66 AGAGAT-CCTACAGTCCAATTGCTTGAAGACACCGAGCATTCCCAT
2197779 AGTGTCATAA
Statistics
Matches: 108, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
110 105 0.97
111 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.25, T:0.18
Consensus pattern (110 bp):
CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCAGAAGACGCCG
AGAGATCCTACAGTCCAATTGCTTGAAGACACCGAGCATTCCCAT
Found at i:2197874 original size:43 final size:43
Alignment explanation
Indices: 2197813--2197900 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
2197803 AGAAAGCAAT
*
2197813 CATGGAAAAATTAACCCTAAAAACGTCGAGATATCCAAAGAAC
1 CATGGAAAAATTAACCCTAAAAACGCCGAGATATCCAAAGAAC
2197856 CATGGAAAAATTAACCCTAAAAACGCCGAGATATCCAAAGAAC
1 CATGGAAAAATTAACCCTAAAAACGCCGAGATATCCAAAGAAC
2197899 CA
1 CA
2197901 CTTGAAGCAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.49, C:0.23, G:0.14, T:0.15
Consensus pattern (43 bp):
CATGGAAAAATTAACCCTAAAAACGCCGAGATATCCAAAGAAC
Found at i:2199083 original size:63 final size:63
Alignment explanation
Indices: 2199008--2199135 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 63
2198998 TGTTTGAAAG
* *
2199008 TAACAACGATACATATCATTAAAACATGATTTTATCATATCCTAATTAGTACGTTAAAATCCA
1 TAACAACAATACATATCATTAAAACATGATTTTATCATATCCTAATTAATACGTTAAAATCCA
2199071 TAACAACAATACATATCATTAAAACATGATTTTATCATATCCTAATTAATACGTTAAAATCCA
1 TAACAACAATACATATCATTAAAACATGATTTTATCATATCCTAATTAATACGTTAAAATCCA
2199134 TA
1 TA
2199136 CGAACACTGA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.34
Consensus pattern (63 bp):
TAACAACAATACATATCATTAAAACATGATTTTATCATATCCTAATTAATACGTTAAAATCCA
Found at i:2201408 original size:3 final size:3
Alignment explanation
Indices: 2201400--2201439 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2201390 CTCTCATTCA
2201400 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
2201440 TTTGTTTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:2206655 original size:27 final size:28
Alignment explanation
Indices: 2206614--2206682 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
2206604 CAATTAAATA
* ** *
2206614 CTAAACCCTAAACCTTAAATTTTAGACT
1 CTAAACACTAAACCTTAAATCATAAACT
2206642 CTAAACAC-AAACCTTAAATCATAAACT
1 CTAAACACTAAACCTTAAATCATAAACT
2206669 CTAAAC-CTTAAACC
1 CTAAACAC-TAAACC
2206683 ATTCTTACAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 1 0.03
27 22 0.63
28 12 0.34
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.26
Consensus pattern (28 bp):
CTAAACACTAAACCTTAAATCATAAACT
Found at i:2207707 original size:31 final size:31
Alignment explanation
Indices: 2207671--2207745 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
2207661 AAATAGAAAA
2207671 TTTAGGTACTAAAATTGACCAAAACTAATAG
1 TTTAGGTACTAAAATTGACCAAAACTAATAG
*
2207702 TTTAGGTATTAAAATTGACCAAAACTAATAG
1 TTTAGGTACTAAAATTGACCAAAACTAATAG
2207733 TTTAGGTACTAAA
1 TTTAGGTACTAAA
2207746 TGTGTAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (31 bp):
TTTAGGTACTAAAATTGACCAAAACTAATAG
Found at i:2212607 original size:17 final size:17
Alignment explanation
Indices: 2212585--2212623 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2212575 TCTCCTGAAA
*
2212585 ATTTTATATTCTTT-TAT
1 ATTTTAAATT-TTTCTAT
2212602 ATTTTAAATTTTTCTAT
1 ATTTTAAATTTTTCTAT
2212619 ATTTT
1 ATTTT
2212624 TTTATTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTAAATTTTTCTAT
Found at i:2212660 original size:26 final size:26
Alignment explanation
Indices: 2212626--2212686 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
2212616 TATATTTTTT
* *
2212626 TATTGATAATTTATTTTATCTTTTAAAA
1 TATT-ATAATTT-TATTATCTTCTAAAA
*
2212654 T-TTATAATTTTATTCTCTTCTAAAA
1 TATTATAATTTTATTATCTTCTAAAA
2212679 TATTATAA
1 TATTATAA
2212687 ATTTCTCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 13 0.45
26 13 0.45
27 2 0.07
28 1 0.03
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (26 bp):
TATTATAATTTTATTATCTTCTAAAA
Found at i:2212695 original size:25 final size:25
Alignment explanation
Indices: 2212644--2212697 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
2212634 ATTTATTTTA
* * *
2212644 TCTTTTAAAATTTATAATTTTATTC
1 TCTTCTAAAATTTATAAATTTACTC
2212669 TCTTCTAAAATATTATAAATTT-CTC
1 TCTTCTAAAAT-TTATAAATTTACTC
2212694 TCTT
1 TCTT
2212698 AACATAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (25 bp):
TCTTCTAAAATTTATAAATTTACTC
Found at i:2217461 original size:14 final size:15
Alignment explanation
Indices: 2217432--2217463 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2217422 AAATAATTAA
2217432 AATAATATATTTTAT
1 AATAATATATTTTAT
2217447 AATAATATA-TTTAT
1 AATAATATATTTTAT
2217461 AAT
1 AAT
2217464 TACTTATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:2217521 original size:42 final size:40
Alignment explanation
Indices: 2217447--2217548 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 40
2217437 TATATTTTAT
* *
2217447 AATAATATA-TTTATAATTACTTATTACATTTTAAACAATTAA
1 AATAATATATTTTATAA-TAATTATTACATTTT-AACAACT-A
* *
2217489 AATAATATATTTTATAATAATT-TTATATTTTTAATAACTA
1 AATAATATATTTTATAATAATTATTACA-TTTTAACAACTA
2217529 AATAATATATTTTAATAATA
1 AATAATATATTTT-ATAATA
2217549 TAAAATAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 14 0.26
41 15 0.28
42 17 0.32
43 7 0.13
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (40 bp):
AATAATATATTTTATAATAATTATTACATTTTAACAACTA
Found at i:2217525 original size:20 final size:20
Alignment explanation
Indices: 2217488--2217548 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
2217478 TAAACAATTA
2217488 AAATAATATATTTT-ATAAT
1 AAATAATATATTTTAATAAT
**
2217507 -AATTTTATATTTTTAATAACT
1 AAATAATATA-TTTTAATAA-T
2217528 AAATAATATATTTTAATAAT
1 AAATAATATATTTTAATAAT
2217548 A
1 A
2217549 TAAAATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 7 0.21
19 4 0.12
20 6 0.18
21 10 0.29
22 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATAATATATTTTAATAAT
Found at i:2217542 original size:40 final size:42
Alignment explanation
Indices: 2217447--2217548 Score: 120
Period size: 41 Copynumber: 2.5 Consensus size: 42
2217437 TATATTTTAT
* *
2217447 AATAATATA-TTTATAATTACTTATTACATTTTAAACAATTAA
1 AATAATATATTTTATAA-TAATTATTACATTTTAAACAACTAA
* * *
2217489 AATAATATATTTTATAATAATT-TTATATTTTTAATAACT-A
1 AATAATATATTTTATAATAATTATTACATTTTAAACAACTAA
2217529 AATAATATATTTTAATAATA
1 AATAATATATTTT-ATAATA
2217549 TAAAATAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
40 14 0.26
41 19 0.36
42 13 0.25
43 7 0.13
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (42 bp):
AATAATATATTTTATAATAATTATTACATTTTAAACAACTAA
Found at i:2221938 original size:74 final size:73
Alignment explanation
Indices: 2221846--2221999 Score: 166
Period size: 74 Copynumber: 2.1 Consensus size: 73
2221836 TAAATTAAGC
* * * * *
2221846 ATTTAGCATATAAGCTATCACTTTT-GATCCGTTTTAATATATAAACTTTCAGTTTTTTCAAAAT
1 ATTTAGTACATAAACTATCACTTTTAG-TCCGTTTTAATATATAAA-TTTAAATTTTTTCAAAAT
* *
2221910 CATATCTAAT
64 AATACCTAAT
* * * * * *
2221920 GTTTAGTACATAAACTATCAGTTTTAGTCTGTTTTAGTATTTAAATTTAAATTTTTTTAAAATAA
1 ATTTAGTACATAAACTATCACTTTTAGTCCGTTTTAATATATAAATTTAAATTTTTTCAAAATAA
2221985 TACCTAAT
66 TACCTAAT
2221993 ATTTAGT
1 ATTTAGT
2222000 TTTTGTTTCA
Statistics
Matches: 65, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
73 29 0.45
74 35 0.54
75 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (73 bp):
ATTTAGTACATAAACTATCACTTTTAGTCCGTTTTAATATATAAATTTAAATTTTTTCAAAATAA
TACCTAAT
Found at i:2226830 original size:30 final size:30
Alignment explanation
Indices: 2226792--2226871 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 30
2226782 ATGTTTAAAA
* * *
2226792 TATTACAAATTGATCATTAATATTATCGTT
1 TATTACAAAATGATCACTAACATTATCGTT
* *
2226822 TCTTACAAAATGGTCACTAACATTATCGTT
1 TATTACAAAATGATCACTAACATTATCGTT
*
2226852 TATTATAAAATGATCACTAA
1 TATTACAAAATGATCACTAA
2226872 AAATTAACAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (30 bp):
TATTACAAAATGATCACTAACATTATCGTT
Found at i:2228145 original size:16 final size:16
Alignment explanation
Indices: 2228124--2228156 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2228114 TCTCTCGTTT
2228124 ACCTGCTTGTTGGGTG
1 ACCTGCTTGTTGGGTG
2228140 ACCTGCTTGTTGGGTG
1 ACCTGCTTGTTGGGTG
2228156 A
1 A
2228157 AGGTTGCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.18, G:0.36, T:0.36
Consensus pattern (16 bp):
ACCTGCTTGTTGGGTG
Found at i:2229097 original size:39 final size:38
Alignment explanation
Indices: 2229021--2229098 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 38
2229011 AACAAGATGC
*
2229021 CGCTATATATACATCTTATTGCGGCGTTTGATTTAAGAA
1 CGCTATATATACATCTTATTGCGGCATTT-ATTTAAGAA
* *
2229060 CGCTACTATATTCATCTTGTTGCGGCATTT-TTCTAAGAA
1 CGCTA-TATATACATCTTATTGCGGCATTTATT-TAAGAA
2229099 ACGTCACTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 2 0.06
39 11 0.32
40 21 0.62
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.40
Consensus pattern (38 bp):
CGCTATATATACATCTTATTGCGGCATTTATTTAAGAA
Found at i:2232953 original size:12 final size:12
Alignment explanation
Indices: 2232938--2232976 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
2232928 AATTACATAT
2232938 ATATTTATAAAA
1 ATATTTATAAAA
2232950 ATATTTATAAAA
1 ATATTTATAAAA
2232962 ATATATT-TAAAA
1 ATAT-TTATAAAA
2232974 ATA
1 ATA
2232977 ATTTTTGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 24 0.92
13 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATTTATAAAA
Found at i:2232953 original size:14 final size:14
Alignment explanation
Indices: 2232936--2232974 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
2232926 TTAATTACAT
2232936 ATATATTTAT-AAA
1 ATATATTTATAAAA
2232949 A-ATATTTATAAAA
1 ATATATTTATAAAA
2232962 ATATATTTA-AAAA
1 ATATATTTATAAAA
2232975 TAATTTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.33
13 9 0.38
14 7 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATTTATAAAA
Found at i:2244746 original size:19 final size:19
Alignment explanation
Indices: 2244701--2244753 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
2244691 AGAATGTTTA
*
2244701 AAAGTATAAATACTTATAT
1 AAAGTATCAATACTTATAT
2244720 AAAGTATCAATACTTATAT
1 AAAGTATCAATACTTATAT
*
2244739 AAAGTATCAAAACTT
1 AAAGTATCAATACTT
2244754 TTGCAGGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (19 bp):
AAAGTATCAATACTTATAT
Found at i:2249095 original size:56 final size:56
Alignment explanation
Indices: 2248938--2249526 Score: 381
Period size: 51 Copynumber: 11.1 Consensus size: 56
2248928 AGGATAAATG
* * **
2248938 AGACTTGAAACATCTTCAA-ATGACGAG-CCTGCTCCCTATTCCTTCAG-GAAGTATA
1 AGACTCGAAAAATCTTCAATAAAACGAGTCC-GCTCCCTATTCCTTCAGAG-AGTATA
** * * * * *
2248993 AGACTCGAGCAATCTTC-ATAAAATGTGTCTGCTCTCTATTCATTCAGAGAGTATA
1 AGACTCGAAAAATCTTCAATAAAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATA
* * *
2249048 AGACTTGAATAATCTTCAATAAAACGAGTCCGCTCTCTATTCCTTCAGAGAGTAT-
1 AGACTCGAAAAATCTTCAATAAAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATA
*
2249103 AGAACTCGAAAAATCTTCAATAAAACGAGTCCGCTCTCTATTCCTTCAGAGAGTAT-
1 AG-ACTCGAAAAATCTTCAATAAAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATA
*
2249159 AGAACTCGAAAAATCTTCAAT-AAAC-AGGTCCACTCCCTATTCCTTCAGAGAGTATA
1 AG-ACTCGAAAAATCTTCAATAAAACGA-GTCCGCTCCCTATTCCTTCAGAGAGTATA
* * * **
2249215 GGACTC----AATCTTTAA-CAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTCGAAAAATCTTCAATAAAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATA
* * ** ** * *
2249266 GGACTC----AATCCTCAA-CGAACTTGTCCGCTCTCTATTCATTCAGAGAGTATA
1 AGACTCGAAAAATCTTCAATAAAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATA
* ** **
2249317 GGACTC----AATCTTCAA-CGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTCGAAAAATCTTCAATAAAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATA
* ** ** *
2249368 GGACTC----AATCTTCAA-CGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATA
1 AGACTCGAAAAATCTTCAATAAAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATA
* ** ** *
2249419 GGACTC----AATCTTCAA-CGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATA
1 AGACTCGAAAAATCTTCAATAAAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATA
* ** ** * *
2249470 GGACTC----AATCTTCAA-CGAACTTGTCCGCTCTCTATTCATTCAGAGAGTATA
1 AGACTCGAAAAATCTTCAATAAAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATA
*
2249521 GGACTC
1 AGACTC
2249527 AATCTTCAAC
Statistics
Matches: 489, Mismatches: 36, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
51 291 0.60
54 2 0.00
55 88 0.18
56 108 0.22
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (56 bp):
AGACTCGAAAAATCTTCAATAAAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATA
Found at i:2249250 original size:51 final size:51
Alignment explanation
Indices: 2249075--2249536 Score: 645
Period size: 51 Copynumber: 8.9 Consensus size: 51
2249065 AATAAAACGA
* * ** **
2249075 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAAACGA
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAA-CGAACTT
* * ** **
2249131 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAG
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACGAACTT
* * *
2249186 GTCCACTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTTAACAAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
2249237 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCCTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
* *
2249288 GTCCGCTCTCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
2249339 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
2249390 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
2249441 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
* *
2249492 GTCCGCTCTCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
2249537 AAACGAATTT
Statistics
Matches: 385, Mismatches: 21, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
51 301 0.78
55 36 0.09
56 48 0.12
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (51 bp):
GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:2250703 original size:26 final size:27
Alignment explanation
Indices: 2250668--2250735 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 27
2250658 TTGAACCCTC
*
2250668 CTTTTATTTCTCTTTTTTCAC-TTTTCT
1 CTTTTTTTTC-CTTTTTTCACTTTTTCT
* *
2250695 -TTTTTTTTCCATTTTTCTCTTTTTCT
1 CTTTTTTTTCCTTTTTTCACTTTTTCT
2250721 CTTATTTTTTCCTTT
1 CTT-TTTTTTCCTTT
2250736 CGTTTTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
25 8 0.24
26 14 0.41
27 2 0.06
28 10 0.29
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.74
Consensus pattern (27 bp):
CTTTTTTTTCCTTTTTTCACTTTTTCT
Found at i:2250720 original size:42 final size:41
Alignment explanation
Indices: 2250674--2250790 Score: 105
Period size: 42 Copynumber: 2.7 Consensus size: 41
2250664 CCTCCTTTTA
2250674 TTTCTCTTTTTTCACTTTTCTTTTTTTTTCCAT-TTTTCTCTT
1 TTTCTCTTTTTTC-CTTTTCTTTTTTTTTCCATATTTT-TCTT
* *
2250716 TTTCTCTTATTT--TTTCCTTTCGTTTTTTCCATCATTTTTCTT
1 TTTCTCTTTTTTCCTTTTCTTT--TTTTTTCCAT-ATTTTTCTT
*
2250758 TTTCTCATTTTTTCTTCTTTTCTCTTTTATTTC
1 TTTCTC-TTTTTTC--CTTTTCT-TTTTTTTTC
2250791 TTCTTTAAGC
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
39 7 0.12
41 10 0.17
42 21 0.35
43 9 0.15
46 6 0.10
47 5 0.08
48 2 0.03
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.72
Consensus pattern (41 bp):
TTTCTCTTTTTTCCTTTTCTTTTTTTTTCCATATTTTTCTT
Found at i:2250775 original size:19 final size:19
Alignment explanation
Indices: 2250674--2250796 Score: 68
Period size: 18 Copynumber: 6.5 Consensus size: 19
2250664 CCTCCTTTTA
2250674 TTTC-TCTTTTT-TCACTTT
1 TTTCTTCTTTTTCTCA-TTT
2250692 TCTT-TT-TTTTTC-CA-TT
1 T-TTCTTCTTTTTCTCATTT
2250708 TTTC-TCTTTTTCTCTTATTT
1 TTTCTTCTTTTTCTC--ATTT
**
2250728 TTTCCTTTCGTTTTT-TCCATCA
1 TTT-C-TTC-TTTTTCT-CATTT
2250750 TTT-TTCTTTTTCTCATTT
1 TTTCTTCTTTTTCTCATTT
*
2250768 TTTCTTC-TTTTCTCTTTT
1 TTTCTTCTTTTTCTCATTT
2250786 ATTTCTTCTTT
1 -TTTCTTCTTT
2250797 AAGCAAAATA
Statistics
Matches: 82, Mismatches: 5, Indels: 34
0.68 0.04 0.28
Matches are distributed among these distances:
15 3 0.04
16 9 0.11
17 1 0.01
18 29 0.35
19 18 0.22
20 7 0.09
21 1 0.01
22 5 0.06
23 3 0.04
24 6 0.07
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.72
Consensus pattern (19 bp):
TTTCTTCTTTTTCTCATTT
Found at i:2264352 original size:17 final size:16
Alignment explanation
Indices: 2264330--2264380 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 16
2264320 AAAAAAAATA
2264330 TATATATAATATAAGTT
1 TATATATAATATAA-TT
2264347 TATATATAA-ACTATATT
1 TATATATAATA-TA-ATT
2264364 TATATATAACTATAATT
1 TATATATAA-TATAATT
2264381 ATTATAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.03
17 25 0.83
18 3 0.10
19 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (16 bp):
TATATATAATATAATT
Found at i:2264352 original size:19 final size:17
Alignment explanation
Indices: 2264345--2264387 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
2264335 ATAATATAAG
2264345 TTTATATATAAACTATA
1 TTTATATATAAACTATA
2264362 TTTATATAT-AACTATA
1 TTTATATATAAACTATA
*
2264378 ATTAT-TATAA
1 TTTATATATAA
2264388 GTTATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 3 0.12
16 12 0.50
17 9 0.38
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTATATATAAACTATA
Found at i:2264386 original size:17 final size:17
Alignment explanation
Indices: 2264332--2264386 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
2264322 AAAAAATATA
2264332 TATATAA-TATAAGTT-T
1 TATATAACTATAA-TTAT
*
2264348 ATATATAAACTATATTTA-
1 -TATAT-AACTATAATTAT
2264366 TATATAACTATAATTAT
1 TATATAACTATAATTAT
2264383 TATA
1 TATA
2264387 AGTTATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 10 0.31
17 14 0.44
18 4 0.12
19 4 0.12
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (17 bp):
TATATAACTATAATTAT
Found at i:2264707 original size:5 final size:5
Alignment explanation
Indices: 2264699--2264724 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2264689 TTTTATTATT
2264699 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
2264725 TTCTAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:2264906 original size:15 final size:15
Alignment explanation
Indices: 2264873--2264911 Score: 64
Period size: 13 Copynumber: 2.7 Consensus size: 15
2264863 CCATCCCTAA
2264873 TATAAACTATATATG
1 TATAAACTATATATG
2264888 --TAAACTATATATG
1 TATAAACTATATATG
2264901 TATAAACTATA
1 TATAAACTATA
2264912 AAAAGTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 13 0.59
15 9 0.41
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (15 bp):
TATAAACTATATATG
Found at i:2265072 original size:19 final size:19
Alignment explanation
Indices: 2265048--2265109 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
2265038 TTTTATTTGG
2265048 GAATTTAGAGGGAAATTGA
1 GAATTTAGAGGGAAATTGA
*
2265067 GAATTTAGAGGG-AATAGAA
1 GAATTTAGAGGGAAATTG-A
* *
2265086 AAATTTGGAGGGAAATTGA
1 GAATTTAGAGGGAAATTGA
2265105 GAATT
1 GAATT
2265110 GAGATTTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 4 0.11
19 28 0.78
20 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.26
Consensus pattern (19 bp):
GAATTTAGAGGGAAATTGA
Found at i:2265339 original size:15 final size:16
Alignment explanation
Indices: 2265310--2265342 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2265300 TGTATGTATG
2265310 TATGTATATAACTATA
1 TATGTATATAACTATA
2265326 TATGTATA-AACTATA
1 TATGTATATAACTATA
2265341 TA
1 TA
2265343 AAATATATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (16 bp):
TATGTATATAACTATA
Found at i:2265433 original size:2 final size:2
Alignment explanation
Indices: 2265426--2265461 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2265416 AATCTATAAA
2265426 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2265462 AACACTATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2265726 original size:7 final size:7
Alignment explanation
Indices: 2265714--2265748 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
2265704 TTATAGAAAT
2265714 CCTAAAC
1 CCTAAAC
2265721 CCTAAAC
1 CCTAAAC
*
2265728 CCTAAAT
1 CCTAAAC
*
2265735 CATAAAC
1 CCTAAAC
2265742 CCTAAAC
1 CCTAAAC
2265749 TATAGTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (7 bp):
CCTAAAC
Found at i:2265816 original size:2 final size:2
Alignment explanation
Indices: 2265804--2265875 Score: 73
Period size: 2 Copynumber: 37.5 Consensus size: 2
2265794 ATTTATATTA
* *
2265804 AT AT A- AT AT AT AT AT AT TT AT GT AT A- ACT A- AT AT A- AGT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT
2265843 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2265876 AACACTATGC
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
1 5 0.08
2 52 0.88
3 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Done.