Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001162.1 Hibiscus syriacus cultivar Beakdansim tig00002317_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: 1560963
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 9
Found at i:622238 original size:116 final size:117
Alignment explanation
Indices: 621991--622242 Score: 282
Period size: 116 Copynumber: 2.2 Consensus size: 117
621981 CAGTGAAAAG
* * * *
621991 GTTCATATTGAGAAGAAC-CAATTCGACAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCAATCCGACAAGGGAGAAAAAGTTCATAATAAGAAGAACTTGTTCA
* * * * ** *
622055 ACTTTGTTCGATTTCATCACAGAAGAAGGTATATCAACATTTCCAGTAGAGA
66 ACCTTGGTCGATTCCATCACAGAAGAAGGGATATCAACATCACCAGGAGAGA
*
622107 GTTCATAATGAGAAGAACTC-ATCCGATAAGGGAGAAAAAGTTCATAATAAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCAATCCGACAAGGGAGAAAAAGTTCATAATAAGAAGAACTTGTTCA
* ***
622171 ACCTTGGT-GATTCCATCACATAATGAAGTGGA-AT-GGTATCACCAGCGAG-GA
66 ACCTTGGTCGATTCCATCACAGAA-GAAG-GGATATCAACATCACCAG-GAGAGA
622222 GTTCATAATGAGGAAGAACTC
1 GTTCATAATGA-GAAGAACTC
622243 GTTCGATCAG
Statistics
Matches: 115, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
115 32 0.28
116 80 0.70
117 3 0.03
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (117 bp):
GTTCATAATGAGAAGAACTCAATCCGACAAGGGAGAAAAAGTTCATAATAAGAAGAACTTGTTCA
ACCTTGGTCGATTCCATCACAGAAGAAGGGATATCAACATCACCAGGAGAGA
Found at i:624809 original size:9 final size:9
Alignment explanation
Indices: 624795--624829 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
624785 CCGACTCTTC
624795 TTCTTCTCT
1 TTCTTCTCT
*
624804 TTCTTCTTT
1 TTCTTCTCT
624813 TTCTTCTCCT
1 TTCTTCT-CT
624823 TTCTTCT
1 TTCTTCT
624830 TTGCGCAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (9 bp):
TTCTTCTCT
Found at i:624816 original size:18 final size:19
Alignment explanation
Indices: 624790--624831 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
624780 TTTGACCGAC
*
624790 TCTTCTTCTTCT-CTTTCT
1 TCTTTTTCTTCTCCTTTCT
624808 TCTTTTTCTTCTCCTTTCT
1 TCTTTTTCTTCTCCTTTCT
624827 TCTTT
1 TCTTT
624832 GCGCAAGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (19 bp):
TCTTTTTCTTCTCCTTTCT
Found at i:625847 original size:12 final size:12
Alignment explanation
Indices: 625830--625861 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
625820 AAGAACTTGG
625830 TAGAAAGAATTT
1 TAGAAAGAATTT
625842 TAGAAAGAATTT
1 TAGAAAGAATTT
625854 TAGAAAGA
1 TAGAAAGA
625862 TCTTAAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (12 bp):
TAGAAAGAATTT
Found at i:626700 original size:30 final size:30
Alignment explanation
Indices: 626666--626725 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
626656 AAAGGATGAA
* *
626666 GAAAAGAAGGAATTAGGTAGCTGGAAATTT
1 GAAAAGAAGGAATTAGATAGCTAGAAATTT
*
626696 GAAAAGAAGGAATTAGATTGCTAGAAATTT
1 GAAAAGAAGGAATTAGATAGCTAGAAATTT
626726 TAGAATGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.45, C:0.03, G:0.27, T:0.25
Consensus pattern (30 bp):
GAAAAGAAGGAATTAGATAGCTAGAAATTT
Found at i:631626 original size:39 final size:39
Alignment explanation
Indices: 631572--631662 Score: 173
Period size: 39 Copynumber: 2.3 Consensus size: 39
631562 TATTTCGAGT
*
631572 TCGAGTTGAACTTGATAATTTTTAGTTCGTGAGTTTGAG
1 TCGAGTTGAGCTTGATAATTTTTAGTTCGTGAGTTTGAG
631611 TCGAGTTGAGCTTGATAATTTTTAGTTCGTGAGTTTGAG
1 TCGAGTTGAGCTTGATAATTTTTAGTTCGTGAGTTTGAG
631650 TCGAGTTGAGCTT
1 TCGAGTTGAGCTT
631663 ACTTTTAAAG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.21, C:0.09, G:0.27, T:0.43
Consensus pattern (39 bp):
TCGAGTTGAGCTTGATAATTTTTAGTTCGTGAGTTTGAG
Found at i:634525 original size:14 final size:14
Alignment explanation
Indices: 634508--634584 Score: 71
Period size: 14 Copynumber: 6.1 Consensus size: 14
634498 CGTTATATTT
634508 GTTTATTTATGTTC
1 GTTTATTTATGTTC
*
634522 GTTTA---A-GTTT
1 GTTTATTTATGTTC
634532 GTTTATTTATGTTC
1 GTTTATTTATGTTC
*
634546 ----ATTTATGTTT
1 GTTTATTTATGTTC
*
634556 GTTCATTTATGTTC
1 GTTTATTTATGTTC
634570 GTTTATTTATGTTC
1 GTTTATTTATGTTC
634584 G
1 G
634585 AACAAAGGGA
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
10 17 0.34
11 1 0.02
13 1 0.02
14 31 0.62
ACGTcount: A:0.16, C:0.06, G:0.16, T:0.62
Consensus pattern (14 bp):
GTTTATTTATGTTC
Found at i:634575 original size:24 final size:24
Alignment explanation
Indices: 634492--634583 Score: 116
Period size: 24 Copynumber: 3.9 Consensus size: 24
634482 CATTCAATTA
* *
634492 TATGTTCG-TTATATTTGTTTATT
1 TATGTTCGTTTATGTTTGTTCATT
* *
634515 TATGTTCGTTTAAGTTTGTTTATT
1 TATGTTCGTTTATGTTTGTTCATT
*
634539 TATGTTCATTTATGTTTGTTCATT
1 TATGTTCGTTTATGTTTGTTCATT
634563 TATGTTCGTTTAT-TTATGTTC
1 TATGTTCGTTTATGTT-TGTTC
634584 GAACAAAGGG
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.16
24 51 0.84
ACGTcount: A:0.16, C:0.07, G:0.14, T:0.63
Consensus pattern (24 bp):
TATGTTCGTTTATGTTTGTTCATT
Found at i:634861 original size:10 final size:10
Alignment explanation
Indices: 634846--635003 Score: 91
Period size: 10 Copynumber: 14.1 Consensus size: 10
634836 ATTTTTGTGT
634846 TGTTCGTTTA
1 TGTTCGTTTA
*
634856 TGTTCGGTTA
1 TGTTCGTTTA
634866 TTGTATTCGTTTA
1 -TG--TTCGTTTA
*
634879 TGTTCATTTATTA
1 TGTTC--GT-TTA
*
634892 TGTTCATTTA
1 TGTTCGTTTA
*
634902 TGTTCGTTCGTTTG
1 ---T-GTTCGTTTA
634916 TGTTCGTTTA
1 TGTTCGTTTA
*
634926 TGTTCATTTATTA
1 TGTTC--GT-TTA
634939 TGTTCGTTTA
1 TGTTCGTTTA
*
634949 TGTTCGTTCGTTTG
1 ---T-GTTCGTTTA
634963 TGTTCGTTTA
1 TGTTCGTTTA
*
634973 CGTTCGTTTA
1 TGTTCGTTTA
*
634983 TGTTCATTTA
1 TGTTCGTTTA
634993 TGTTCGTTTA
1 TGTTCGTTTA
635003 T
1 T
635004 CATTTAAATG
Statistics
Matches: 116, Mismatches: 15, Indels: 34
0.70 0.09 0.21
Matches are distributed among these distances:
10 66 0.57
11 6 0.05
12 4 0.03
13 25 0.22
14 15 0.13
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:634878 original size:23 final size:23
Alignment explanation
Indices: 634846--634997 Score: 125
Period size: 23 Copynumber: 6.7 Consensus size: 23
634836 ATTTTTGTGT
* *
634846 TGTTCGTTTATGTTCGGTTATTG
1 TGTTCGTTTATGTTCAGTTATTA
* *
634869 TATTCGTTTATGTTCATTTATTA
1 TGTTCGTTTATGTTCAGTTATTA
* * *
634892 TGTTCATTTATGTTC-GTTCGTTTG
1 TGTTCGTTTATGTTCAGTT--ATTA
*
634916 TGTTCGTTTATGTTCATTTATTA
1 TGTTCGTTTATGTTCAGTTATTA
* *
634939 TGTTCGTTTATGTTC-GTTCGTTTG
1 TGTTCGTTTATGTTCAGTT--ATTA
*
634963 TGTTCGTTTACGTTC-G-T-TTA
1 TGTTCGTTTATGTTCAGTTATTA
*
634983 TGTTCATTTATGTTC
1 TGTTCGTTTATGTTC
634998 GTTTATCATT
Statistics
Matches: 104, Mismatches: 20, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
20 15 0.14
22 4 0.04
23 50 0.48
24 33 0.32
25 2 0.02
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.59
Consensus pattern (23 bp):
TGTTCGTTTATGTTCAGTTATTA
Found at i:634892 original size:13 final size:13
Alignment explanation
Indices: 634876--634902 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
634866 TTGTATTCGT
634876 TTATGTTCATTTA
1 TTATGTTCATTTA
634889 TTATGTTCATTTA
1 TTATGTTCATTTA
634902 T
1 T
634903 GTTCGTTCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (13 bp):
TTATGTTCATTTA
Found at i:634932 original size:47 final size:47
Alignment explanation
Indices: 634866--635000 Score: 213
Period size: 47 Copynumber: 2.9 Consensus size: 47
634856 TGTTCGGTTA
*
634866 TTGTATTCGTTTATGTTCATTTATTATGTTCATTTATGTTCGTTCGT
1 TTGTGTTCGTTTATGTTCATTTATTATGTTCATTTATGTTCGTTCGT
*
634913 TTGTGTTCGTTTATGTTCATTTATTATGTTCGTTTATGTTCGTTCGT
1 TTGTGTTCGTTTATGTTCATTTATTATGTTCATTTATGTTCGTTCGT
* *
634960 TTGTGTTCGTTTACGTTC--GT-TTATGTTCATTTATGTTCGTT
1 TTGTGTTCGTTTATGTTCATTTATTATGTTCATTTATGTTCGTT
635001 TATCATTTAA
Statistics
Matches: 83, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
44 20 0.24
45 1 0.01
47 62 0.75
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.59
Consensus pattern (47 bp):
TTGTGTTCGTTTATGTTCATTTATTATGTTCATTTATGTTCGTTCGT
Found at i:634959 original size:14 final size:14
Alignment explanation
Indices: 634940--634970 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
634930 CATTTATTAT
634940 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
634954 GTTCGTTTGTGTTC
1 GTTCGTTTATGTTC
634968 GTT
1 GTT
634971 TACGTTCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.13, G:0.26, T:0.58
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:635093 original size:16 final size:15
Alignment explanation
Indices: 635072--635101 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
635062 TTTTGGTTTA
635072 TTCGTTTATGTTATTG
1 TTCGTTTAT-TTATTG
635088 TTCGTTTATTTATT
1 TTCGTTTATTTATT
635102 AAATGAACGA
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:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (15 bp):
TTCGTTTATTTATTG
Found at i:635931 original size:28 final size:28
Alignment explanation
Indices: 635898--635968 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
635888 GAATATAGGA
635898 CAGAGGGGTACACAAGGAATTGGCATCG
1 CAGAGGGGTACACAAGGAATTGGCATCG
*
635926 TAGAGGGGTACACAAGGAATTGGCATCG
1 CAGAGGGGTACACAAGGAATTGGCATCG
635954 CAGAGGGG--CACAAGG
1 CAGAGGGGTACACAAGG
635969 GCGTGGCTCG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
26 7 0.17
28 34 0.83
ACGTcount: A:0.32, C:0.17, G:0.38, T:0.13
Consensus pattern (28 bp):
CAGAGGGGTACACAAGGAATTGGCATCG
Found at i:636118 original size:23 final size:24
Alignment explanation
Indices: 636092--636144 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 24
636082 TTACTAACCC
*
636092 CTAACTT-CTAACTTATTAACATA
1 CTAACTTGCTAACTTACTAACATA
* **
636115 CTAA-TTGCTAATTTACTAATTTA
1 CTAACTTGCTAACTTACTAACATA
636138 CTAACTT
1 CTAACTT
636145 TTTATTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 2 0.08
23 20 0.83
24 2 0.08
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.43
Consensus pattern (24 bp):
CTAACTTGCTAACTTACTAACATA
Found at i:636624 original size:34 final size:30
Alignment explanation
Indices: 636586--636654 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
636576 TTGATATAAC
636586 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
636620 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
636649 AATTTA
1 AATTTA
636655 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:636665 original size:29 final size:30
Alignment explanation
Indices: 636595--636654 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
636585 CAATTTAAGG
636595 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
636626 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
636655 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:636760 original size:21 final size:21
Alignment explanation
Indices: 636734--636790 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
636724 AGGGTGTCAA
*
636734 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTAC
*
636755 AGTGCATCCATGCATCCCTAC
1 AGTGCATCCATGCACCCCTAC
636776 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
636791 TCCATTTCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.39, G:0.18, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:636835 original size:20 final size:20
Alignment explanation
Indices: 636810--636884 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
636800 AATGCACTTA
636810 GTGCATCGATGCATCCTGAT
1 GTGCATCGATGCATCCTGAT
** *
636830 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTGAT
*
636851 GTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCCTGAT
*
636871 GTGCATCCATGCAT
1 GTGCATCGATGCAT
636885 GAAGGCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 30 0.64
21 17 0.36
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGAT
Found at i:636855 original size:41 final size:41
Alignment explanation
Indices: 636810--636892 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
636800 AATGCACTTA
*
636810 GTGCATCGATGCATCCTGATGTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCCTGATGTGCATCCATGCATCAAGGCT
* *
636851 GTGCATCGATGCATCCTGTTGTGCATCCATGCATGAAGGCT
1 GTGCATCGATGCATCCTGATGTGCATCCATGCATCAAGGCT
636892 G
1 G
636893 CAACAGCTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGATGTGCATCCATGCATCAAGGCT
Found at i:640117 original size:34 final size:30
Alignment explanation
Indices: 640079--640147 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
640069 TTGATATAAC
640079 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTA
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTA
*
640113 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTA
640142 AATTTA
1 AATTTA
640148 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 9 0.27
30 12 0.36
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTA
Found at i:640158 original size:29 final size:30
Alignment explanation
Indices: 640088--640147 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
640078 CAATTTAAGG
640088 CAAAATGGTTTTTGGACTTGAATTAAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTAAATTTA
*
640119 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTAAATTTA
640148 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 12 0.43
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTAAATTTA
Found at i:640253 original size:21 final size:21
Alignment explanation
Indices: 640227--640283 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
640217 AGGGTGTCAA
640227 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
* * *
640248 AGTGCATCTATGAATCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
640269 AGTTCATCCATGCAC
1 AGTGCATCCATGCAC
640284 TCCATTTCGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:640348 original size:21 final size:20
Alignment explanation
Indices: 640303--640398 Score: 93
Period size: 21 Copynumber: 4.7 Consensus size: 20
640293 AATGCACTTA
**
640303 GTGCATCGATGCATCCTGAT
1 GTGCATCGATGCATCAGGAT
*
640323 GTGCATCGATGCATCAAGGTT
1 GTGCATCGATGCATC-AGGAT
*
640344 GTGCATCGATGCATCTAGGCT
1 GTGCATCGATGCATC-AGGAT
* ** *
640365 GTGCATAGATGCATCCTGCT
1 GTGCATCGATGCATCAGGAT
*
640385 GTGCATCCATGCAT
1 GTGCATCGATGCAT
640399 GAAGGCTGCA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 30 0.46
21 35 0.54
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCAGGAT
Found at i:640388 original size:41 final size:41
Alignment explanation
Indices: 640303--640398 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
640293 AATGCACTTA
* *
640303 GTGCATCGATGCATCCTGATGTGCATCGATGCATCAAGGTT
1 GTGCATCGATGCATCCTGATGTGCATAGATGCATCAAGGCT
* **
640344 GTGCATCGATGCAT-CTAGGCTGTGCATAGATGCATC-CTGCT
1 GTGCATCGATGCATCCT--GATGTGCATAGATGCATCAAGGCT
*
640385 GTGCATCCATGCAT
1 GTGCATCGATGCAT
640399 GAAGGCTGCA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 2 0.04
41 29 0.62
42 16 0.34
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGATGTGCATAGATGCATCAAGGCT
Found at i:640803 original size:34 final size:32
Alignment explanation
Indices: 640764--640833 Score: 77
Period size: 34 Copynumber: 2.1 Consensus size: 32
640754 TTTTGTAAAG
* * *
640764 GGGAAATGTTATAGCTTATCCCGTATAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCGGA-AAAA-CTA
* *
640798 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
640830 GGGA
1 GGGA
640834 GTTGTAAGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 7 0.23
33 4 0.13
34 20 0.65
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
Found at i:641442 original size:2 final size:2
Alignment explanation
Indices: 641428--641475 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
641418 TATCTTTCGA
*
641428 AT AT AT -T AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
641469 AT AT AT A
1 AT AT AT A
641476 ATTTATTACA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:642454 original size:19 final size:18
Alignment explanation
Indices: 642432--642475 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
642422 AAAAGGTAAG
* *
642432 AAATAAATAAATAAAATT
1 AAATAAAGAAAAAAAATT
*
642450 AAAATGAAGAAAAAAAATT
1 -AAATAAAGAAAAAAAATT
642469 AAATAAA
1 AAATAAA
642476 AGATAAGATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (18 bp):
AAATAAAGAAAAAAAATT
Found at i:642603 original size:2 final size:2
Alignment explanation
Indices: 642596--642705 Score: 65
Period size: 2 Copynumber: 58.5 Consensus size: 2
642586 AGTGAAAATA
* *
642596 AT AT AT AT AT AT AT AT AT AT AT AA AT AGT AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * * * *
642639 AA AT -T A- AT A- AA AT -T AT -T A- AT AA AA AA AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
642674 AT AT AT AT AT A- AT CT AA AA 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
642706 CTAAAGTAAA
Statistics
Matches: 86, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
1 8 0.09
2 76 0.88
3 2 0.02
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (2 bp):
AT
Found at i:642718 original size:25 final size:23
Alignment explanation
Indices: 642604--642717 Score: 89
Period size: 21 Copynumber: 5.0 Consensus size: 23
642594 TAATATATAT
**
642604 ATATATATATATATAAA-TAGTA
1 ATATATATATATATAAACTAAAA
*
642626 A-ATATATATATATAAATTAATAA
1 ATATATATATATATAAACTAA-AA
*
642649 A-AT-TAT-TA-ATAAA-AAAATA
1 ATATATATATATATAAACTAAA-A
642668 ATATATATATATATATAATCTAAAA
1 ATATATATATATATA-AA-CTAAAA
*
642693 ATATATATATATACTAAAGTAAAA
1 ATATATATATATA-TAAACTAAAA
642717 A
1 A
642718 AGAAAATGCA
Statistics
Matches: 76, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
18 1 0.01
19 4 0.05
20 7 0.09
21 20 0.26
22 8 0.11
23 7 0.09
24 8 0.11
25 16 0.21
26 5 0.07
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (23 bp):
ATATATATATATATAAACTAAAA
Found at i:645032 original size:67 final size:65
Alignment explanation
Indices: 644916--645089 Score: 217
Period size: 65 Copynumber: 2.6 Consensus size: 65
644906 AAGATATCTG
* * * * *
644916 TTGTTTCATGA-AAACGGCCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATAT-GAAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAATAAAT-TCAAAGA
644979 TTT
64 -TT
*
644982 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
645047 T
65 T
* * *
645048 TTGTTTAAAGAGAAACTGTCTCAAGAGAGACGAAATTTGTTT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTT
645090 CAAGAGAGAC
Statistics
Matches: 96, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
65 38 0.40
66 5 0.05
67 33 0.34
68 20 0.21
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:645164 original size:123 final size:123
Alignment explanation
Indices: 644993--645216 Score: 340
Period size: 123 Copynumber: 1.8 Consensus size: 123
644983 GTGTTTCAAG
* ** * * *
644993 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTAAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTAAAG
*
645058 AGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAGACAAAACTTAGTTCCAAA
66 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAGACAAAACTTAGTTCCAAA
* * * *
645116 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAATAAAACATATTCAAATAATTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTAAAG
*
645181 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG
66 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG
645217 GGAAACTGTC
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
123 89 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (123 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTAAAG
AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAGACAAAACTTAGTTCCAAA
Found at i:645215 original size:36 final size:36
Alignment explanation
Indices: 645168--645359 Score: 184
Period size: 36 Copynumber: 5.5 Consensus size: 36
645158 ATATTCAAAT
645168 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
645204 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGA
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* * * *
645240 AATTTATTTCAAGTGAAA-TGTTTTC-A-A-TG----
1 AATTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAA
** * * *
645269 TTTTTATTTCAAGAGAAACTGTCTCAAGGGAGACAA
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* * *
645305 AATTTTGTTTAAAGGGAAACTATCTCAAGATAGACAA
1 AA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
645342 AATTCGTTTCAAGGGAAA
1 AATTTGTTTCAAGGGAAA
645360 TGTTTTCAAT
Statistics
Matches: 125, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
29 18 0.14
30 3 0.02
32 1 0.01
33 1 0.01
34 1 0.01
35 3 0.02
36 68 0.54
37 30 0.24
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (36 bp):
AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
Found at i:645237 original size:101 final size:101
Alignment explanation
Indices: 645089--645446 Score: 396
Period size: 102 Copynumber: 3.5 Consensus size: 101
645079 GAAATTTGTT
* * * * * *
645089 TCAAGAGAGACAAAACTTAGTTCCAAA-AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAT
1 TCAAGAGAGACAAAACTTTGTT-TAAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGT
* ** * * *
645153 AAAACATATTCAAATAATTTGTTTCAAGGGAAACTGTC
65 GAAATGTTTTC-AATATTTTGTTTCAAGAGAAACTGTC
* * * *
645191 TCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTATTTCAAGTG
1 TCAAGAGAGACAAAACTTTGTTTAAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGTG
* *
645255 AAATGTTTTCAATGTTTTTATTTCAAGAGAAACTGTC
66 AAATGTTTTCAAT-ATTTTGTTTCAAGAGAAACTGTC
* * * * *
645292 TCAAGGGAGACAAAATTTTGTTTAAAGGGAAACTATCTCAAGATAGACAAAATTCGTTTCAAGGG
1 TCAAGAGAGACAAAACTTTGTTTAAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGTG
* *
645357 AAATGTTTTCAATGTTTATGTTTCAAGATAAACTGTC
66 AAATGTTTTCAATATTT-TGTTTCAAGAGAAACTGTC
* * * * *
645394 TCAAGGGAGACAATATTTTGTTTAAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TCAAGAGAGACAAAACTTTGTTTAAAGGGAAACTATCTCAAGAGAGACAAAAT
645447 CTTCTTTTTA
Statistics
Matches: 221, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
100 5 0.02
101 80 0.36
102 136 0.62
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (101 bp):
TCAAGAGAGACAAAACTTTGTTTAAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGTG
AAATGTTTTCAATATTTTGTTTCAAGAGAAACTGTC
Found at i:645333 original size:37 final size:36
Alignment explanation
Indices: 645283--645359 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 36
645273 TATTTCAAGA
* * *
645283 GAAACTGTCTCAAGGGAGACAAAATTTTGTTTAAAGG
1 GAAACTATCTCAAGAGAGACAAAA-TTCGTTTAAAGG
* *
645320 GAAACTATCTCAAGATAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGAGAGACAAAATTCGTTTAAAGG
645356 GAAA
1 GAAA
645360 TGTTTTCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
36 14 0.40
37 21 0.60
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.25
Consensus pattern (36 bp):
GAAACTATCTCAAGAGAGACAAAATTCGTTTAAAGG
Found at i:645360 original size:102 final size:102
Alignment explanation
Indices: 645174--645446 Score: 404
Period size: 102 Copynumber: 2.7 Consensus size: 102
645164 AAATAATTTG
* * * *
645174 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTAAAGGGAAACTATCTCAAGAGAGAC
* * * *
645238 GAAATTTATTTCAAGTGAAATGTTTTCAATGTTTTTA
66 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATA
*
645275 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTAAAGGGAAACTATCTCAAGATAGAC
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTAAAGGGAAACTATCTCAAGAGAGAC
* *
645340 AAAATTCGTTTCAAGGGAAATGTTTTCAATGTTTATG
66 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATA
* * * *
645377 TTTCAAGATAAACTGTCTCAAGGGAGACAATATTTTGTTTAAAGGGAAACTATCTCAAGCGAGAT
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTAAAGGGAAACTATCTCAAGAGAGAC
645442 AAAAT
66 AAAAT
645447 CTTCTTTTTA
Statistics
Matches: 155, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 30 0.19
102 125 0.81
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.31
Consensus pattern (102 bp):
TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTAAAGGGAAACTATCTCAAGAGAGAC
AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATA
Found at i:647116 original size:13 final size:13
Alignment explanation
Indices: 647087--647141 Score: 51
Period size: 13 Copynumber: 4.0 Consensus size: 13
647077 GTCTTCTTCA
647087 ATTTTC-CTTTGTT
1 ATTTTCTCTTT-TT
647100 -TTTTCTCTTTTT
1 ATTTTCTCTTTTT
647112 ATTTTCTCTTTGCTTTT
1 ATTTTCTC--T--TTTT
647129 ATTTTCTCTTTTT
1 ATTTTCTCTTTTT
647142 GTTCTGATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
12 7 0.19
13 15 0.42
15 2 0.06
17 12 0.33
ACGTcount: A:0.05, C:0.16, G:0.04, T:0.75
Consensus pattern (13 bp):
ATTTTCTCTTTTT
Found at i:651231 original size:7 final size:7
Alignment explanation
Indices: 651209--651246 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
651199 AATTAACACC
651209 TTTTGCA
1 TTTTGCA
651216 -TTTGCA
1 TTTTGCA
*
651222 TTTTGTA
1 TTTTGCA
651229 TTTTGCA
1 TTTTGCA
*
651236 TCTTGCA
1 TTTTGCA
651243 TTTT
1 TTTT
651247 TGCGTTTGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (7 bp):
TTTTGCA
Found at i:658849 original size:18 final size:18
Alignment explanation
Indices: 658826--658885 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
658816 ATGTATTACA
658826 TGATAATGATATTGATAT
1 TGATAATGATATTGATAT
**
658844 TGATAATGATAGAGATCA-
1 TGATAATGATATTGAT-AT
* * *
658862 CGATAATGATGTTGATGT
1 TGATAATGATATTGATAT
658880 TGATAA
1 TGATAA
658886 GGATGGTATA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
18 31 0.97
19 1 0.03
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37
Consensus pattern (18 bp):
TGATAATGATATTGATAT
Found at i:659823 original size:116 final size:116
Alignment explanation
Indices: 659619--659972 Score: 485
Period size: 116 Copynumber: 3.1 Consensus size: 116
659609 AGATAGACCA
* * * * *
659619 AACATTTCAAGTGGAAGGGTTCATAATAAAAAGAATTCATTTGATGAGAGAGAAGAAGTTCCTAA
1 AACATTTCCAGTGGAAGGGTTCATAATGAGAAGAACTCATTTGATGAGGGAGAAGAAGTTCCTAA
* *
659684 TGAGAAGAACTTGTTCAACCTTGGCTCATCTATAACAGAAGGAGTTGGATC
66 TGAGAAGAACTTGTTCAACCTTGGCTCATCCATCACAGAAGGAGTTGGATC
*
659735 AACATTTCCAGTGGAAGGGTTCATAATGAGAAGAACTCATTTGATGAGGGAGAAGAAATTCCTAA
1 AACATTTCCAGTGGAAGGGTTCATAATGAGAAGAACTCATTTGATGAGGGAGAAGAAGTTCCTAA
* * *
659800 TGAGAAGAACTTGTTCTACCTTGGCTCGTCCATCACAGAAGGAGGTGGATC
66 TGAGAAGAACTTGTTCAACCTTGGCTCATCCATCACAGAAGGAGTTGGATC
* * * * * * ** * *
659851 AACACTTT-CAATGAAATGATTCATAGTGAGAAGAACTCGTCCGATGGGGGAGAAGAAGTTCATA
1 AACA-TTTCCAGTGGAAGGGTTCATAATGAGAAGAACTCATTTGATGAGGGAGAAGAAGTTCCTA
* *
659915 ATGAGAAGAACTTGTTCAATCTTGGCTCATCCATCACATAAGGAGTTGGATC
65 ATGAGAAGAACTTGTTCAACCTTGGCTCATCCATCACAGAAGGAGTTGGATC
659967 AACATT
1 AACATT
659973 ATCTCACTGA
Statistics
Matches: 210, Mismatches: 27, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
115 2 0.01
116 205 0.98
117 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.26
Consensus pattern (116 bp):
AACATTTCCAGTGGAAGGGTTCATAATGAGAAGAACTCATTTGATGAGGGAGAAGAAGTTCCTAA
TGAGAAGAACTTGTTCAACCTTGGCTCATCCATCACAGAAGGAGTTGGATC
Found at i:660537 original size:44 final size:43
Alignment explanation
Indices: 660345--660537 Score: 122
Period size: 44 Copynumber: 4.4 Consensus size: 43
660335 ATTGTTTTCT
* * * * *
660345 TTTTGCTAGATTTCT-TCAAATAAGGAGTTAGACCATCATCAATC
1 TTTTGCTAGA-TTCTATCACATAAGGAGTTGGATCAACATC-ACC
* * * * * *
660389 TTTTGTTCGATTCCATCACAGAAGGAGGTCGATCAACATGC-CC
1 TTTTGCTAGATTCTATCACATAAGGAGTTGGATCAACAT-CACC
* * * * **
660432 TTTTTCTCAG-TTCCATCACATAAAGAGTTGGAGCAACATTTCC
1 TTTTGCT-AGATTCTATCACATAAGGAGTTGGATCAACATCACC
* * *
660475 ATTCTGTTCGATTCTATCACATAAGGAGTTGGATCAACATCACTC
1 -TTTTGCTAGATTCTATCACATAAGGAGTTGGATCAACATCAC-C
*
660520 TTTTGCTAGATTTTATCA
1 TTTTGCTAGATTCTATCA
660538 TAGAATGAGG
Statistics
Matches: 110, Mismatches: 32, Indels: 14
0.71 0.21 0.09
Matches are distributed among these distances:
43 36 0.33
44 72 0.65
45 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (43 bp):
TTTTGCTAGATTCTATCACATAAGGAGTTGGATCAACATCACC
Found at i:660557 original size:353 final size:350
Alignment explanation
Indices: 659838--660675 Score: 994
Period size: 353 Copynumber: 2.4 Consensus size: 350
659828 TCCATCACAG
* * * * * * * *
659838 AAGGAGGTGGATCAACACTT-TCAATGAAATGATTCATAGTGAGAAGAACTCGTCCGATGGGGGA
1 AAGGAGGTGGATCAACA-TTCCCAATAAAAAGGTTCATAATAAGAAGAACTCGTTCGATGAGGGA
* *
659902 GAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTGGCTCATCCATCACATAAGGAGTTGGATC
65 GAAAAAGTTCATAATGAGAAGAACTTGTTCAATCTTGGCTCATCCATCACACAAGGAGTTGGATC
* * * * *
659967 AACATTATCTCACTGAATATTGTTTTTTTCCTAGATTCTATCACATAATGAGTTGGATCATCATC
130 AACATTATCTCACTGAAGATTGTTTTTTTCCTAGATTCTATCAAATAAGGAGTTAGACCATCATC
* * *
660032 ACTCTTTTGTTCGATTCCATAACAGAAAAAGGTGGATCAACATGCCTTTTTGCTCGGTTCCATCA
195 AATCTTTTGTTCGATTCCATAACAGAAAAAGGTCGATCAACATGCCTTTTTGCTCAGTTCCATCA
* * * * * *
660097 TATAAGTAGTTAGCCCAGCATCACCATTTTGCTCGATTTCATCACATAAGGAATTAGATCATCGT
260 CATAAGTAGTTAGACCAACATCACCATTCTGCTCGATTTCATCACATAAGGAATTAGATCAACAT
*
660162 CACTTTTTTGCTAGATTTTATCATAA
325 CACTCTTTTGCTAGATTTTATCATAA
* * *
660188 AAGGAGGTGGATCAACATTCCTAATAAAAAGGTTTATAATAAGAAAAACTCGTTCGATGAGGGAG
1 AAGGAGGTGGATCAACATTCCCAATAAAAAGGTTCATAATAAGAAGAACTCGTTCGATGAGGGAG
*
660253 AAAAAGTTCATAATGAGAAGAACTTGTTTAA-CATTGGCTCATCCATCACACAAGGAGTTGGAT-
66 AAAAAGTTCATAATGAGAAGAACTTGTTCAATC-TTGGCTCATCCATCACACAAGGAGTTGGATC
* *
660316 AAGCATTATCTCACTGGAGATTGTTTTCTTTTTGCTAGATTTCT-TCAAATAAGGAGTTAGACCA
130 AA-CATTATCTCACTGAAGATTG--TT-TTTTTCCTAGA-TTCTATCAAATAAGGAGTTAGACCA
* **
660380 TCATCAATCTTTTGTTCGATTCCATCACAGAAGGAGGTCGATCAACATGCCCTTTTT-CTCAGTT
190 TCATCAATCTTTTGTTCGATTCCATAACAGAAAAAGGTCGATCAACATG-CCTTTTTGCTCAGTT
* * ** * * *
660444 CCATCACATAAAG-AGTTGGAGCAACATTTCCATTCTGTTCGA-TTCTATCACATAAGGAGTTGG
254 CCATCACAT-AAGTAGTTAGACCAACATCACCATTCTGCTCGATTTC-ATCACATAAGGAATTAG
*
660507 ATCAACATCACTCTTTTGCTAGATTTTATCATAG
317 ATCAACATCACTCTTTTGCTAGATTTTATCATAA
* * ** *
660541 AATGAGGTGTATCAACATTCCCAATTGAAAGGTTCATAATGAGAAGAACTCG-TCTGATGAGGGA
1 AAGGAGGTGGATCAACATTCCCAATAAAAAGGTTCATAATAAGAAGAACTCGTTC-GATGAGGGA
* * * * * * * *
660605 GAATAAGTTCCTAATGAGAAGATA-TTGTTCCACCTTGGAT-ATTCCATCACAGAATGAGGTGGA
65 GAAAAAGTTCATAATGAGAAGA-ACTTGTTCAATCTTGGCTCA-TCCATCACACAAGGAGTTGGA
660668 TCAACATT
128 TCAACATT
660676 TCTAGTGGTA
Statistics
Matches: 415, Mismatches: 58, Indels: 27
0.83 0.12 0.05
Matches are distributed among these distances:
349 5 0.01
350 127 0.31
352 8 0.02
353 257 0.62
354 18 0.04
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (350 bp):
AAGGAGGTGGATCAACATTCCCAATAAAAAGGTTCATAATAAGAAGAACTCGTTCGATGAGGGAG
AAAAAGTTCATAATGAGAAGAACTTGTTCAATCTTGGCTCATCCATCACACAAGGAGTTGGATCA
ACATTATCTCACTGAAGATTGTTTTTTTCCTAGATTCTATCAAATAAGGAGTTAGACCATCATCA
ATCTTTTGTTCGATTCCATAACAGAAAAAGGTCGATCAACATGCCTTTTTGCTCAGTTCCATCAC
ATAAGTAGTTAGACCAACATCACCATTCTGCTCGATTTCATCACATAAGGAATTAGATCAACATC
ACTCTTTTGCTAGATTTTATCATAA
Found at i:661341 original size:3 final size:3
Alignment explanation
Indices: 661333--661370 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
661323 TTTTTATGTT
661333 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
661371 TGTGCTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:661968 original size:55 final size:54
Alignment explanation
Indices: 661834--661958 Score: 151
Period size: 55 Copynumber: 2.3 Consensus size: 54
661824 TTACGATGAG
* * *
661834 ATGTATCGATACACTACTTGATGTATCGATATACCCCCAACATCGAATGCATTT
1 ATGTACCGATACACTACTTGATGTATCAATACACCCCCAACATCGAATGCATTT
* * * * * *
661888 AGTGTACCGATATAATCCTTAATGTATTAATACACCCCCAATATCGAATGCATTTT
1 A-TGTACCGATACACTACTTGATGTATCAATACACCCCCAACATCGAATGCA-TTT
661944 ATGTACCGATACACT
1 ATGTACCGATACACT
661959 GTCTGATGTA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
54 1 0.02
55 53 0.91
56 4 0.07
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (54 bp):
ATGTACCGATACACTACTTGATGTATCAATACACCCCCAACATCGAATGCATTT
Found at i:667755 original size:21 final size:20
Alignment explanation
Indices: 667710--667785 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 20
667700 TTGTGCACAT
667710 TGTATCGATACACCCT-TGCTA-
1 TGTATCGATACA--CTATG-TAG
667731 TGTATCGATACACTATGATAG
1 TGTATCGATACACTATG-TAG
* *
667752 TGTATCGATAGACTATGCAG
1 TGTATCGATACACTATGTAG
*
667772 TGTACCGATACACT
1 TGTATCGATACACT
667786 CGTCGGGTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 18 0.38
21 28 0.58
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (20 bp):
TGTATCGATACACTATGTAG
Found at i:667775 original size:20 final size:21
Alignment explanation
Indices: 667731--667785 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
667721 ACCCTTGCTA
*
667731 TGTATCGATACACTATGATAG
1 TGTATCGATACACTATGACAG
*
667752 TGTATCGATAGACTATG-CAG
1 TGTATCGATACACTATGACAG
*
667772 TGTACCGATACACT
1 TGTATCGATACACT
667786 CGTCGGGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (21 bp):
TGTATCGATACACTATGACAG
Found at i:668273 original size:12 final size:13
Alignment explanation
Indices: 668244--668276 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
668234 GTATTATAAT
*
668244 TTTTCAAACATTG
1 TTTTCAAACATAG
668257 TTTTCAAA-ATAG
1 TTTTCAAACATAG
668269 TTTTCAAA
1 TTTTCAAA
668277 TATTGCCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:668318 original size:3 final size:3
Alignment explanation
Indices: 668312--668359 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
668302 TCATTTCGTT
* *
668312 TTA TTA TTA TTA TTA TTA ATA TTA GTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
668360 AATAAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:669704 original size:3 final size:3
Alignment explanation
Indices: 669691--669747 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
669681 TTATTTGCAA
*
669691 TAT TAT T-T TAT TAT TAT TAT T-T T-T TAT TGT T-T TAAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
*
669733 T-T CAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
669748 TATAAAAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
2 9 0.20
3 35 0.76
4 2 0.04
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:669707 original size:11 final size:11
Alignment explanation
Indices: 669691--669744 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
669681 TTATTTGCAA
669691 TATTATT-TTAT
1 TATTATTATT-T
669702 TATTATTATTT
1 TATTATTATTT
*
669713 T-TTATTGTTT
1 TATTATTATTT
669723 TAATTATTATTT
1 T-ATTATTATTT
*
669735 CATTATTATT
1 TATTATTATT
669745 ATTTATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 9 0.24
11 18 0.49
12 10 0.27
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (11 bp):
TATTATTATTT
Found at i:669711 original size:48 final size:47
Alignment explanation
Indices: 669654--669744 Score: 112
Period size: 48 Copynumber: 1.9 Consensus size: 47
669644 TTTAATACTA
*
669654 TATTTTTATTTCCTT-TTATTTTAATCATTATTTGCAATATTATTTTAT
1 TATTATTATTT-CTTATTATTTTAATCATTATTT-CAATATTATTTTAT
* * * *
669702 TATTATTATTTTTTATTGTTTTAATTATTATTTCATTATTATT
1 TATTATTATTTCTTATTATTTTAATCATTATTTCAATATTATT
669745 ATTTATAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
47 11 0.30
48 26 0.70
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.67
Consensus pattern (47 bp):
TATTATTATTTCTTATTATTTTAATCATTATTTCAATATTATTTTAT
Found at i:669766 original size:2 final size:2
Alignment explanation
Indices: 669759--669806 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
669749 ATAAAAATAA
*
669759 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AA AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
669799 AT AT AT AT
1 AT AT AT AT
669807 TTTTTTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:670090 original size:17 final size:17
Alignment explanation
Indices: 670068--670105 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
670058 ATATTTTATT
670068 TATATTTTATATATAAA
1 TATATTTTATATATAAA
* *
670085 TATATTTTTTATATAAT
1 TATATTTTATATATAAA
670102 TATA
1 TATA
670106 ACTTTGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTTATATATAAA
Found at i:677649 original size:114 final size:114
Alignment explanation
Indices: 677485--677822 Score: 525
Period size: 114 Copynumber: 3.0 Consensus size: 114
677475 GTGCCATGTT
* *
677485 CTCATGGTAGAAATAAGGAGGCCCAATATCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATGGTAGAAATAAGGAGGCCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
677550 ATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATTTG
66 ATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATTTG
*
677599 CTCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATGGTAGAAATAAGGAGGCCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
677664 ATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATTTG
66 ATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATTTG
* * * *
677713 CTCATAGTACAAATAAAGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATGGTAGAAATAAGGAGGCCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * * * * * * *
677778 GTTCGATAGGAAC-CACAGAACCAATCATTGGAATTAAAAGATGAA
66 ATTTGGTATGAACTC-CAAAATCAATCATTGGATTTGAAAGATGAA
677823 CTGCATGACC
Statistics
Matches: 208, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
113 1 0.00
114 207 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (114 bp):
CTCATGGTAGAAATAAGGAGGCCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
ATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATTTG
Found at i:680398 original size:22 final size:22
Alignment explanation
Indices: 680367--680421 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
680357 ATCTGCACTC
680367 TTCAAAGATGATAGACTCCT-TT
1 TTCAAAGATGATAGA-TCCTCTT
* *
680389 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATCCTCTT
680411 TTCAAAGATGA
1 TTCAAAGATGA
680422 AAGCTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 3 0.10
22 26 0.90
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGATCCTCTT
Found at i:681423 original size:77 final size:76
Alignment explanation
Indices: 681268--681823 Score: 959
Period size: 76 Copynumber: 7.3 Consensus size: 76
681258 CTATTTCCCA
** *
681268 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTATGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
681333 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
681344 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGAAGTTTTTTGATGTTTACA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
681409 AAGCCTTAGGGT
65 AAGCCTTAGGGT
* * *
681421 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTTTATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG-CTTTTTGATGTTTTCA
681486 AAGCCTTAGGGT
65 AAGCCTTAGGGT
681498 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
681563 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
681574 CATCTGTAAGTCCTTTAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
681639 AGCCTTAGGGT
66 AGCCTTAGGGT
681650 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
681715 AGCCTTAGGGT
66 AGCCTTAGGGT
*
681726 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTAGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
681791 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
681802 TATCTGTAAGACCTACAGTGCA
1 CATCTGTAAGTCCTTCAGTGCA
681824 ATATAATAAG
Statistics
Matches: 459, Mismatches: 19, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
76 315 0.69
77 144 0.31
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:682011 original size:3 final size:3
Alignment explanation
Indices: 682005--682046 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
681995 TCATTTCGTT
* *
682005 TTA TTA TTA TTA TTA TTA ATA TTA GTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
682047 AATAAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:683386 original size:3 final size:3
Alignment explanation
Indices: 683373--683437 Score: 61
Period size: 3 Copynumber: 23.3 Consensus size: 3
683363 TTATTTGCAA
*
683373 TAT TAT T-T TAT TAT TAT TAT T-T T-T TAT TGT T-T TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
*
683415 T-T CAT TAT TAT TAT T-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
683438 TATAAAATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
2 11 0.21
3 39 0.74
4 3 0.06
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:683386 original size:8 final size:8
Alignment explanation
Indices: 683373--683438 Score: 65
Period size: 8 Copynumber: 9.0 Consensus size: 8
683363 TTATTTGCAA
683373 TATTATTT
1 TATTATTT
683381 TATTA--T
1 TATTATTT
683387 TATTATTT
1 TATTATTT
683395 T-TTATTGT
1 TATTATT-T
683403 T-TTA-TT
1 TATTATTT
683409 TATTATTT
1 TATTATTT
*
683417 CATTA--T
1 TATTATTT
683423 TATTATTT
1 TATTATTT
683431 TATTATTT
1 TATTATTT
683439 ATAAAATAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
6 13 0.27
7 9 0.18
8 27 0.55
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (8 bp):
TATTATTT
Found at i:683405 original size:10 final size:10
Alignment explanation
Indices: 683386--683438 Score: 52
Period size: 11 Copynumber: 4.9 Consensus size: 10
683376 TATTTTATTA
683386 TTATTATTTT
1 TTATTATTTT
*
683396 TTATTGTTTTAT
1 TTATT-ATTT-T
*
683408 TTATTATTTCA
1 TTATTATTT-T
683419 TTATTATTATT
1 TTATTATT-TT
683430 TTATTATTT
1 TTATTATTT
683439 ATAAAATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 6 0.17
11 22 0.63
12 7 0.20
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (10 bp):
TTATTATTTT
Found at i:683414 original size:22 final size:22
Alignment explanation
Indices: 683374--683438 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
683364 TATTTGCAAT
683374 ATTATT-TTATTATTATTATTT-
1 ATTATTATTATT-TTATTATTTC
* * *
683395 TTTATTGTTTTATTTATTATTTC
1 ATTATTATTAT-TTTATTATTTC
683418 ATTATTATTATTTTATTATTT
1 ATTATTATTATTTTATTATTT
683439 ATAAAATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 5 0.14
22 22 0.61
23 9 0.25
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (22 bp):
ATTATTATTATTTTATTATTTC
Found at i:683463 original size:17 final size:16
Alignment explanation
Indices: 683438--683473 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
683428 TTTTATTATT
683438 TATAAAATAAATATATA
1 TATAAAATAAATA-ATA
*
683455 TATATAATAAATAATA
1 TATAAAATAAATAATA
683471 TAT
1 TAT
683474 TTTTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TATAAAATAAATAATA
Found at i:683757 original size:17 final size:17
Alignment explanation
Indices: 683735--683772 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
683725 ATATTTTATT
683735 TATATTTTATATATAAA
1 TATATTTTATATATAAA
* *
683752 TATATTTTTTATATAAT
1 TATATTTTATATATAAA
683769 TATA
1 TATA
683773 ACTTTGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTTATATATAAA
Found at i:686315 original size:55 final size:54
Alignment explanation
Indices: 686203--686347 Score: 193
Period size: 55 Copynumber: 2.6 Consensus size: 54
686193 TACAATGAGA
* *
686203 TGTATCGATACACTACTTGATGTATCGATACA-ACCCAACATCGAATGCATTTAG
1 TGTACCGATACACT-CTTGATGTATCGATACACCCCCAACATCGAATGCATTTAG
* * *
686257 TGTACTGATACACTCCTTGATATATCGATACACCCCCAACATCGAATGCATTTTG
1 TGTACCGATACACT-CTTGATGTATCGATACACCCCCAACATCGAATGCATTTAG
* *
686312 TGTACCGATACACTGTCTGATGTACCGATACACCCC
1 TGTACCGATACACTCT-TGATGTATCGATACACCCC
686348 TGGCTCAGGA
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
54 29 0.37
55 50 0.63
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (54 bp):
TGTACCGATACACTCTTGATGTATCGATACACCCCCAACATCGAATGCATTTAG
Found at i:686905 original size:52 final size:52
Alignment explanation
Indices: 686826--686941 Score: 223
Period size: 52 Copynumber: 2.2 Consensus size: 52
686816 CCCAGGGGGT
686826 ACCGATTCCCCCCTTATATAACGGTCGAAATATTTGAATTTTACACTTAGGGA
1 ACCGATT-CCCCCTTATATAACGGTCGAAATATTTGAATTTTACACTTAGGGA
686879 ACCGATTCCCCCTTATATAACGGTCGAAATATTTGAATTTTACACTTAGGGA
1 ACCGATTCCCCCTTATATAACGGTCGAAATATTTGAATTTTACACTTAGGGA
686931 ACCGATTCCCC
1 ACCGATTCCCC
686942 ATAGGGGGTA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 56 0.89
53 7 0.11
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (52 bp):
ACCGATTCCCCCTTATATAACGGTCGAAATATTTGAATTTTACACTTAGGGA
Found at i:692323 original size:21 final size:21
Alignment explanation
Indices: 692297--692336 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
692287 CCCCCTTTGA
*
692297 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
692318 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
692337 TGGGGTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:698289 original size:76 final size:76
Alignment explanation
Indices: 698193--698350 Score: 244
Period size: 76 Copynumber: 2.1 Consensus size: 76
698183 TGATTTAAAA
* *
698193 AAAATAGTTGGATAACAAAAACAAAAACACAAGAATAGGTGGGTGACCAAATAGGCAATTTATCA
1 AAAATAGTTGGATAACAAAAACAAAAACACAAGAATAGGTGGATGACCAAATAGACAATTTATCA
*
698258 TTAATTAAGTT
66 TTAACTAAGTT
* * * * *
698269 AAAATAGTTGGATAATAAAAATAAAAACACGATAATAGGTTGATGACCAAATAGACAATTTATCA
1 AAAATAGTTGGATAACAAAAACAAAAACACAAGAATAGGTGGATGACCAAATAGACAATTTATCA
698334 TTAACTAAGTT
66 TTAACTAAGTT
698345 AAAATA
1 AAAATA
698351 CTATAAAAGT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.25
Consensus pattern (76 bp):
AAAATAGTTGGATAACAAAAACAAAAACACAAGAATAGGTGGATGACCAAATAGACAATTTATCA
TTAACTAAGTT
Found at i:698628 original size:51 final size:51
Alignment explanation
Indices: 698564--698666 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
698554 TTTTGAAATT
*
698564 TTAAAATTTTTATATATTTTAATTTTTTATGTATTATTCTTTTTAGAAAAA
1 TTAAAATTATTATATATTTTAATTTTTTATGTATTATTCTTTTTAGAAAAA
698615 TTAAAATTATTATATATTTTAATTTTTTATGTATTATTCTTTTTAGAAAAA
1 TTAAAATTATTATATATTTTAATTTTTTATGTATTATTCTTTTTAGAAAAA
698666 T
1 T
698667 CTTATTTTTG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (51 bp):
TTAAAATTATTATATATTTTAATTTTTTATGTATTATTCTTTTTAGAAAAA
Found at i:699842 original size:2 final size:2
Alignment explanation
Indices: 699835--699930 Score: 192
Period size: 2 Copynumber: 48.0 Consensus size: 2
699825 AATAAATAAG
699835 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
699877 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
699919 AT AT AT AT AT AT
1 AT AT AT AT AT AT
699931 GTAAATAAAA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 94 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:703151 original size:22 final size:22
Alignment explanation
Indices: 703123--703166 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
703113 ATACTGTTCC
703123 ATCTGAAAGTGGTTCACAAAAG
1 ATCTGAAAGTGGTTCACAAAAG
703145 ATCTGAAAGTGGTTCACAAAAG
1 ATCTGAAAGTGGTTCACAAAAG
703167 TAGGTCAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.23
Consensus pattern (22 bp):
ATCTGAAAGTGGTTCACAAAAG
Found at i:704519 original size:23 final size:21
Alignment explanation
Indices: 704483--704525 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
704473 AAATAAAAAA
*
704483 AATAAAAAATAATAATATAGT
1 AATAAAAAATAATAAGATAGT
704504 AATAATAAAATAAATAAGATAG
1 AATAA-AAAAT-AATAAGATAG
704526 ATAAATAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 5 0.26
23 9 0.47
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (21 bp):
AATAAAAAATAATAAGATAGT
Found at i:706351 original size:84 final size:84
Alignment explanation
Indices: 706254--706490 Score: 332
Period size: 84 Copynumber: 2.8 Consensus size: 84
706244 GATAGATAGC
* * * *
706254 CCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATTGAACTTGCAG
1 CCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAG
*
706319 GTCTTTT-GTTGGCAGATAA
66 GT-TTTTGGTTGGCAAATAA
* * * * * * *
706338 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAACTGAGCGTAGTCAAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAG
*
706403 GTTTTTGGTTGGCAAATAG
66 GTTTTTGGTTGGCAAATAA
*
706422 CCCTTCTTGCCTTGAGCTATGTTGTAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAG
706487 GTTT
66 GTTT
706491 GGTGTTTCAA
Statistics
Matches: 131, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
83 4 0.03
84 127 0.97
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (84 bp):
CCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAG
GTTTTTGGTTGGCAAATAA
Found at i:706857 original size:101 final size:101
Alignment explanation
Indices: 706736--706988 Score: 294
Period size: 101 Copynumber: 2.4 Consensus size: 101
706726 AGAGATAAAA
* *
706736 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAAATTGTCTCAAGGGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAAACTGTCTCAAGAGA
*
706801 GACGAAATATGTTTCAAGGAAAACATATTTAAAGAT
66 GACAAAATATGTTTCAAGGAAAACATATTTAAAGAT
* **
706837 TTTGTTTCAA-AGGAAACTGTCTCAAGAGAGGCAAAATTTGTTTCAAGGGAAACTGTCTCAAGAG
1 TTTGTTTCAAGA-GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAAACTGTCTCAAGAG
* * * * * *
706901 AGACAAAATTTGTTTCAAGGGAAA-TTGTCTCAAGAGAGACAAAA
65 AGACAAAATATGTTTCAAGGAAAACATAT-T-TA-A-AG----AT
706945 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTT
706989 TGAGTAAATT
Statistics
Matches: 128, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
100 3 0.02
101 79 0.62
102 1 0.01
103 1 0.01
104 2 0.02
108 34 0.27
109 8 0.06
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.28
Consensus pattern (101 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAAACTGTCTCAAGAGA
GACAAAATATGTTTCAAGGAAAACATATTTAAAGAT
Found at i:706882 original size:21 final size:21
Alignment explanation
Indices: 706858--706958 Score: 73
Period size: 21 Copynumber: 5.4 Consensus size: 21
706848 GGAAACTGTC
706858 TCAAGAGAGGCAAAATTTGTT
1 TCAAGAGAGGCAAAATTTGTT
* *
706879 TC-A-AG-GG--AAA-CTGTC
1 TCAAGAGAGGCAAAATTTGTT
*
706894 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGGCAAAATTTGTT
*
706915 TC-A-AG-GG--AAA-TTGTC
1 TCAAGAGAGGCAAAATTTGTT
*
706930 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGGCAAAATTTGTT
706951 TCAAGAGA
1 TCAAGAGA
706959 AACTGTCTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 24
0.64 0.10 0.26
Matches are distributed among these distances:
15 11 0.19
16 8 0.14
17 4 0.07
18 5 0.08
19 4 0.07
20 8 0.14
21 19 0.32
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.26
Consensus pattern (21 bp):
TCAAGAGAGGCAAAATTTGTT
Found at i:706899 original size:137 final size:138
Alignment explanation
Indices: 706593--706960 Score: 427
Period size: 137 Copynumber: 2.6 Consensus size: 138
706583 CAAAGGTTGG
* * ** *
706593 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAAATTGTCTCAAGAGAGA
* ** * * * ** *
706658 CAAAATTTGTTTTTAGAG-AAAC-TGTCTCAAGAGAGACAAAACTTTGTTTTGAGGGAAACTGTC
66 CAAAATATGTTTCAAGAGAAAACATAT-T-TA-A-AG-----ATTTTGTTTCAAAGGAAACTGTC
*
706721 TCAAAAGAGATAAAATT
122 TCAAAAGAGACAAAATT
*
706738 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAAATTGTCTCAAGGGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAAATTGTCTCAAGAGAGA
* *
706803 CGAAATATGTTTCAAG-GAAAACATATTTAAAGATTTTGTTTCAAAGGAAACTGTCTCAAGAGAG
66 CAAAATATGTTTCAAGAGAAAACATATTTAAAGATTTTGTTTCAAAGGAAACTGTCTCAAAAGAG
*
706867 GCAAAATT
131 ACAAAATT
* **
706875 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAAATTGTCTCAAGAGAGA
*
706940 CAAAATTTGTTTCAAGAGAAA
66 CAAAATATGTTTCAAGAGAAA
706961 CTGTCTCAAG
Statistics
Matches: 195, Mismatches: 25, Indels: 13
0.84 0.11 0.06
Matches are distributed among these distances:
137 108 0.55
138 4 0.02
142 2 0.01
143 1 0.01
144 2 0.01
145 76 0.39
146 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.27
Consensus pattern (138 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAAATTGTCTCAAGAGAGA
CAAAATATGTTTCAAGAGAAAACATATTTAAAGATTTTGTTTCAAAGGAAACTGTCTCAAAAGAG
ACAAAATT
Found at i:707007 original size:37 final size:36
Alignment explanation
Indices: 706593--706988 Score: 484
Period size: 36 Copynumber: 11.1 Consensus size: 36
706583 CAAAGGTTGG
**
706593 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
706629 TATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** *
706665 TGTTTTTAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
** * *
706702 TGTTTTGAGGGAAACTGTCTCAAAAGAGATAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
706738 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
706774 TGTTTCAAAAGAAATTGTCTCAAGGGAGACGAAATA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * * *
706810 TGTTTCAAGGAAAACATAT-T-TA-A-AG----ATTT
1 TGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAATT
* *
706839 TGTTTCAAAGGAAACTGTCTCAAGAGAGGCAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
706875 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
706911 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
706947 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
706984 TGTTT
1 TGTTT
706989 TGAGTAAATT
Statistics
Matches: 309, Mismatches: 40, Indels: 21
0.84 0.11 0.06
Matches are distributed among these distances:
28 2 0.01
29 16 0.05
30 1 0.00
31 1 0.00
32 2 0.01
33 2 0.01
35 1 0.00
36 243 0.79
37 41 0.13
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:711133 original size:23 final size:24
Alignment explanation
Indices: 711071--711138 Score: 79
Period size: 22 Copynumber: 2.9 Consensus size: 24
711061 TTGTTAGATT
*
711071 ATAAAATAAAAAATATA-TAAAAA
1 ATAAAATAAATAATATAGTAAAAA
*
711094 ATAAAA-AAATAATATAGT-AATA
1 ATAAAATAAATAATATAGTAAAAA
*
711116 ATAAAATAAATAAGATAGATAAA
1 ATAAAATAAATAATATAG-TAAA
711139 TAAGGATACA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
22 18 0.47
23 17 0.45
24 1 0.03
25 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (24 bp):
ATAAAATAAATAATATAGTAAAAA
Found at i:718492 original size:18 final size:18
Alignment explanation
Indices: 718449--718486 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
718439 GTGAAGTATG
*
718449 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
718467 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
718485 AA
1 AA
718487 GTGTGTAAGG
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:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:722076 original size:55 final size:55
Alignment explanation
Indices: 721992--722095 Score: 208
Period size: 55 Copynumber: 1.9 Consensus size: 55
721982 ATAACCTTGT
721992 TAGAAAGAACAAGAGCAATGTTGAGGGATGCAAGCCTAGAAAAATCATTTTGGGC
1 TAGAAAGAACAAGAGCAATGTTGAGGGATGCAAGCCTAGAAAAATCATTTTGGGC
722047 TAGAAAGAACAAGAGCAATGTTGAGGGATGCAAGCCTAGAAAAATCATT
1 TAGAAAGAACAAGAGCAATGTTGAGGGATGCAAGCCTAGAAAAATCATT
722096 CTAGGCAGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.42, C:0.12, G:0.26, T:0.19
Consensus pattern (55 bp):
TAGAAAGAACAAGAGCAATGTTGAGGGATGCAAGCCTAGAAAAATCATTTTGGGC
Found at i:729306 original size:3 final size:3
Alignment explanation
Indices: 729298--729374 Score: 109
Period size: 3 Copynumber: 25.7 Consensus size: 3
729288 TTTAATAAAT
* *
729298 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** *
729346 TAA TAA GGA TAA TAA TAT TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
729375 TGGATAAAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:729381 original size:12 final size:12
Alignment explanation
Indices: 729318--729381 Score: 67
Period size: 12 Copynumber: 5.3 Consensus size: 12
729308 AATAATAATA
729318 ATAATAATAAT-G
1 ATAATAAT-ATGG
**
729330 ATAATAATATTA
1 ATAATAATATGG
*
729342 ATAATAATAAGG
1 ATAATAATATGG
**
729354 ATAATAATATTA
1 ATAATAATATGG
729366 ATAATAATATGG
1 ATAATAATATGG
729378 ATAA
1 ATAA
729382 AAAAATTTAG
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
11 2 0.05
12 40 0.95
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (12 bp):
ATAATAATATGG
Found at i:729822 original size:113 final size:113
Alignment explanation
Indices: 729624--730171 Score: 821
Period size: 113 Copynumber: 4.8 Consensus size: 113
729614 TCTTGATGAG
*
729624 TTCTTCTCATTATGAACTT-TCTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTAC-C
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTC
* * * *
729687 TGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
64 TGGAAAAGCTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAAA
729737 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
729802 GAAAAGATGATTCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAAA
* *
729850 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * * * *
729915 GCAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAG
66 GAAAAGCTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAAA
*
729963 TTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* **
730028 GAAAAGCTGATCCATCGAATGATGGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAAA
* *
730076 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
730141 GAAAAGCTGTTCCATCAAATGATGGATTCAA
66 GAAAAGCTGATCCATCAAATGATGGATTCAA
730172 ATCTTTGCTA
Statistics
Matches: 391, Mismatches: 42, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
112 1 0.00
113 389 0.99
114 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGCTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAAA
Found at i:730827 original size:82 final size:82
Alignment explanation
Indices: 730690--730951 Score: 463
Period size: 82 Copynumber: 3.2 Consensus size: 82
730680 TTTACTATGA
* * * *
730690 GCAAATTCATCTTCCAAATTCAATGATTGTTCT-ATCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGAATGTTCTGCT-AAACCAGGTCAGATAACTCAAAGAACAC
730754 TTCCAGAAGATGCTATTG
65 TTCCAGAAGATGCTATTG
730772 GCAAATTCATCTTCCAAATTCAATGAATGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGAATGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
730837 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
730854 GCAAATTCATCTTCCAAATTCAATGAATGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGAATGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
730919 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
*
730936 GTAAATTCATCTTCCA
1 GCAAATTCATCTTCCA
730952 TTTAATGTTT
Statistics
Matches: 174, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
82 173 0.99
83 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (82 bp):
GCAAATTCATCTTCCAAATTCAATGAATGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTG
Found at i:732096 original size:18 final size:17
Alignment explanation
Indices: 732073--732166 Score: 90
Period size: 18 Copynumber: 5.4 Consensus size: 17
732063 CCTTGACCCC
732073 TTTTCTTTTTCTTCTCTT
1 TTTTCTTTTTCTT-TCTT
732091 TTTTCTATTTTCCATTT-TT
1 TTTTCT-TTTT-C-TTTCTT
732110 TTTTC-TTTTCTTTTCTT
1 TTTTCTTTTTC-TTTCTT
732127 TTTT-TCTTTTCTTTC--
1 TTTTCT-TTTTCTTTCTT
732142 TTTTCTTTTTCTTTTCTT
1 TTTTCTTTTTC-TTTCTT
732160 TTTTCTT
1 TTTTCTT
732167 CAAGCATAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 20
0.76 0.01 0.23
Matches are distributed among these distances:
15 9 0.14
16 9 0.14
17 14 0.22
18 18 0.28
19 11 0.17
20 2 0.03
21 2 0.03
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTCTTTTTCTTTCTT
Found at i:732118 original size:5 final size:5
Alignment explanation
Indices: 732105--732161 Score: 75
Period size: 5 Copynumber: 11.8 Consensus size: 5
732095 CTATTTTCCA
*
732105 TTTTT TTTTC TTTTC TTTTC -TTT- TTTTC TTTTC -TTTC TTTTC TTTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC
732153 TTTTC TTTT
1 TTTTC TTTT
732162 TTCTTCAAGC
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
4 10 0.21
5 32 0.68
6 5 0.11
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTC
Found at i:732151 original size:38 final size:38
Alignment explanation
Indices: 732073--732166 Score: 113
Period size: 38 Copynumber: 2.5 Consensus size: 38
732063 CCTTGACCCC
*
732073 TTTTCTTTT-TCTTCTCTTTTTTCTATTTTCCATTTTT
1 TTTTCTTTTCTTTTCTCTTTTTTCTATTTTCCATTTTT
* *
732110 TTTTCTTTTCTTTTCT-TTTTTTCTTTTCTTTC-TTTTCT
1 TTTTCTTTTCTTTTCTCTTTTTTCTATT-TTCCATTTT-T
*
732148 TTTTCTTTTCTTTTTTCTT
1 TTTTCTTTTCTTTTCTCTT
732167 CAAGCATAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
37 23 0.47
38 24 0.49
39 2 0.04
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (38 bp):
TTTTCTTTTCTTTTCTCTTTTTTCTATTTTCCATTTTT
Found at i:744500 original size:12 final size:12
Alignment explanation
Indices: 744483--744507 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
744473 TCTTTTCCGT
744483 TCTCTGTTTTTC
1 TCTCTGTTTTTC
744495 TCTCTGTTTTTC
1 TCTCTGTTTTTC
744507 T
1 T
744508 GTTCCTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.24, G:0.08, T:0.68
Consensus pattern (12 bp):
TCTCTGTTTTTC
Found at i:744984 original size:3 final size:3
Alignment explanation
Indices: 744976--745064 Score: 133
Period size: 3 Copynumber: 29.7 Consensus size: 3
744966 TTTAATAAAT
* *
744976 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** *
745024 TAA TAA TAA TAA GGA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
745065 TGGATAAAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:753194 original size:105 final size:105
Alignment explanation
Indices: 753084--753776 Score: 1179
Period size: 105 Copynumber: 6.6 Consensus size: 105
753074 TTTGTCACAT
* * * *
753084 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTCGATTCACCTCCTTCTGGGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
753149 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
753189 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
*
753254 GGAACATACTCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
*
753294 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
753359 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
*
753399 GAGTTATTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
*
753464 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
* * *
753504 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTAAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* * *
753569 GGAACAAGTTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
* * *
753609 GAGTTCTTCTTATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* * *
753674 GGAATAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
* * *
753714 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGGTCACCTCCTTCTGTGGTGGATTTGA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGA
753777 TTGTTGTTGA
Statistics
Matches: 564, Mismatches: 24, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 564 1.00
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
Found at i:754710 original size:8 final size:8
Alignment explanation
Indices: 754699--754774 Score: 106
Period size: 8 Copynumber: 10.0 Consensus size: 8
754689 TTCTTTTTTC
754699 TTTTCATT
1 TTTTCATT
754707 TTTTCATT
1 TTTTCATT
754715 TTTTCA-T
1 TTTTCATT
754722 TTTTCATT
1 TTTTCATT
*
754730 TTTTTATT
1 TTTTCATT
754738 TTTT-ATT
1 TTTTCATT
754745 TTTT-A-T
1 TTTTCATT
*
754751 TTTTCACT
1 TTTTCATT
754759 TTTTCATT
1 TTTTCATT
754767 TTTTCATT
1 TTTTCATT
754775 CATTCTCTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
6 5 0.08
7 16 0.25
8 42 0.67
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTCATT
Found at i:754717 original size:15 final size:15
Alignment explanation
Indices: 754699--754774 Score: 100
Period size: 15 Copynumber: 5.0 Consensus size: 15
754689 TTCTTTTTTC
754699 TTTTCATTTTTTCATT
1 TTTTCA-TTTTTCATT
754715 TTTTCATTTTTCATT
1 TTTTCATTTTTCATT
* *
754730 TTTTTATTTTTTATT
1 TTTTCATTTTTCATT
*
754745 TTTT-ATTTTTCACT
1 TTTTCATTTTTCATT
754759 TTTTCATTTTTTCATT
1 TTTTCA-TTTTTCATT
754775 CATTCTCTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
14 12 0.23
15 27 0.51
16 14 0.26
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCATTTTTCATT
Found at i:754768 original size:7 final size:7
Alignment explanation
Indices: 754686--754774 Score: 83
Period size: 7 Copynumber: 12.3 Consensus size: 7
754676 CGAACCCTCC
*
754686 TTTTTCT
1 TTTTTCA
754693 TTTTTC-
1 TTTTTCA
754699 -TTTTCA
1 TTTTTCA
754705 TTTTTTCA
1 -TTTTTCA
754713 TTTTTTCA
1 -TTTTTCA
754721 TTTTTCA
1 TTTTTCA
*
754728 TTTTTTTA
1 -TTTTTCA
*
754736 TTTTTTA
1 TTTTTCA
*
754743 TTTTTTA
1 TTTTTCA
754750 TTTTTCA
1 TTTTTCA
754757 CTTTTTCA
1 -TTTTTCA
754765 TTTTTTCA
1 -TTTTTCA
754773 TT
1 TT
754775 CATTCTCTTT
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
5 5 0.07
7 35 0.47
8 34 0.46
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTCA
Found at i:754791 original size:37 final size:35
Alignment explanation
Indices: 754686--754793 Score: 103
Period size: 37 Copynumber: 3.0 Consensus size: 35
754676 CGAACCCTCC
* *
754686 TTTTTC-TTTTTTCTTTTCATT-TTTTCATTTTTTCA
1 TTTTTCATTTTTTC-ATTCATTATTTT-TTTTTTTCA
* **
754721 TTTTTCATTTTTTTATTTTTTATTTTTTATTTTTCA
1 TTTTTCATTTTTTCATTCATTATTTTTT-TTTTTCA
*
754757 CTTTTTCATTTTTTCATTCATTCTCTTTTTTTTTTCA
1 -TTTTTCATTTTTTCATTCATTAT-TTTTTTTTTTCA
754794 AGTATAGTAC
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
35 11 0.19
36 17 0.29
37 26 0.44
38 5 0.08
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (35 bp):
TTTTTCATTTTTTCATTCATTATTTTTTTTTTTCA
Found at i:758307 original size:14 final size:14
Alignment explanation
Indices: 758288--758314 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
758278 AAATGAATGT
758288 AAAGAATGAAGAAC
1 AAAGAATGAAGAAC
758302 AAAGAATGAAGAA
1 AAAGAATGAAGAA
758315 TGAAAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.04, G:0.22, T:0.07
Consensus pattern (14 bp):
AAAGAATGAAGAAC
Found at i:761993 original size:30 final size:30
Alignment explanation
Indices: 761952--762018 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
761942 CTTTCTCAAT
761952 ACGTTCCAATTTGTCGTCCATCTTCTTACTC
1 ACGTT-CAATTTGTCGTCCATCTTCTTACTC
761983 ACGTTCAATTTGTCGTCCATCTTCTTACTC
1 ACGTTCAATTTGTCGTCCATCTTCTTACTC
762013 ACGTTC
1 ACGTTC
762019 CTGGTATAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 31 0.86
31 5 0.14
ACGTcount: A:0.16, C:0.31, G:0.10, T:0.42
Consensus pattern (30 bp):
ACGTTCAATTTGTCGTCCATCTTCTTACTC
Found at i:777424 original size:62 final size:63
Alignment explanation
Indices: 777340--777459 Score: 158
Period size: 62 Copynumber: 1.9 Consensus size: 63
777330 TATGTGTTGT
* *
777340 TTTTTTAACTTTGAATATTAAAAGATAAT-TATATACT-TTTGAATA-TTTAAAATTAAAATAAT
1 TTTTTTAACTTTGAATAATAAAAG-GAATATATAT-CTATTT-AATATTTTAAAATTAAAATAAT
777402 A
63 A
*
777403 TTTTTTAA-TTTGAATAATAAAAGGAATATATATCTATTTAATATTTTAAATTTAAAA
1 TTTTTTAACTTTGAATAATAAAAGGAATATATATCTATTTAATATTTTAAAATTAAAA
777460 GATAATGTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
61 9 0.18
62 34 0.67
63 8 0.16
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.47
Consensus pattern (63 bp):
TTTTTTAACTTTGAATAATAAAAGGAATATATATCTATTTAATATTTTAAAATTAAAATAATA
Found at i:781337 original size:18 final size:21
Alignment explanation
Indices: 781290--781337 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
781280 AGGGTATGTA
781290 AAATAAATAAATGAAATATTTG
1 AAATAAATAAATGAAATA-TTG
781312 AAATAAATAAAT-AAATA-TG
1 AAATAAATAAATGAAATATTG
781331 AAA-AAAT
1 AAATAAAT
781338 TTAAAGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.15
19 5 0.19
21 5 0.19
22 12 0.46
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (21 bp):
AAATAAATAAATGAAATATTG
Found at i:783687 original size:24 final size:24
Alignment explanation
Indices: 783660--783728 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
783650 AACCTGCTTT
*
783660 AGTAGAGGCAGACTGATCTTGCTC
1 AGTAGAGGCAGACTGTTCTTGCTC
* * * *
783684 AGTAGAGACAGATTGTTCTTGTTG
1 AGTAGAGGCAGACTGTTCTTGCTC
* *
783708 AGAAGAGGCAAACTGTTCTTG
1 AGTAGAGGCAGACTGTTCTTG
783729 TTGAGAGGAG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (24 bp):
AGTAGAGGCAGACTGTTCTTGCTC
Found at i:789595 original size:59 final size:59
Alignment explanation
Indices: 789529--789640 Score: 181
Period size: 59 Copynumber: 1.9 Consensus size: 59
789519 TGATTAACAA
* *
789529 AAACTTAAAGGACTAAAATAGCACAAATAGAAACTTTG-AGGACCAAAATAGAAAAATAG
1 AAACTTAAAAGACTAAAATAGCAAAAATAGAAAC-TTGAAGGACCAAAATAGAAAAATAG
*
789588 AAACTTAAAAGACTAAAATAGCAAAAATAGAAACTTGAAGGACTAAAATAGAA
1 AAACTTAAAAGACTAAAATAGCAAAAATAGAAACTTGAAGGACCAAAATAGAA
789641 CAAACAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
58 3 0.06
59 46 0.94
ACGTcount: A:0.58, C:0.11, G:0.14, T:0.17
Consensus pattern (59 bp):
AAACTTAAAAGACTAAAATAGCAAAAATAGAAACTTGAAGGACCAAAATAGAAAAATAG
Found at i:789605 original size:29 final size:30
Alignment explanation
Indices: 789529--789638 Score: 159
Period size: 30 Copynumber: 3.7 Consensus size: 30
789519 TGATTAACAA
*
789529 AAACTTAAAGGACTAAAATAGCACAAATAG
1 AAACTTAAAGGACTAAAATAGCAAAAATAG
** *
789559 AAACTTTGAGGACCAAAATAG-AAAAATAG
1 AAACTTAAAGGACTAAAATAGCAAAAATAG
*
789588 AAACTTAAAAGACTAAAATAGCAAAAATAG
1 AAACTTAAAGGACTAAAATAGCAAAAATAG
*
789618 AAACTTGAAGGACTAAAATAG
1 AAACTTAAAGGACTAAAATAG
789639 AACAAACAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
29 24 0.35
30 45 0.65
ACGTcount: A:0.57, C:0.11, G:0.15, T:0.17
Consensus pattern (30 bp):
AAACTTAAAGGACTAAAATAGCAAAAATAG
Found at i:789659 original size:30 final size:29
Alignment explanation
Indices: 789528--789659 Score: 122
Period size: 30 Copynumber: 4.4 Consensus size: 29
789518 ATGATTAACA
*
789528 AAAACTTAAAGGACTAAAATAGCACAAATAG
1 AAAA-TTAAAGGACTAAAATAG-AAAAATAG
* ** *
789559 AAACTTTGAGGACCAAAATAGAAAAATAG
1 AAAATTAAAGGACTAAAATAGAAAAATAG
* *
789588 AAACTTAAAAGACTAAAATAGCAAAAATAG
1 AAAATTAAAGGACTAAAATAG-AAAAATAG
* * *
789618 AAACTTGAAGGACTAAAATAGAACAAACA-
1 AAAATTAAAGGACTAAAATAGAA-AAATAG
789647 AAAATGTAAAGGA
1 AAAAT-TAAAGGA
789660 TTGAATCATA
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
29 30 0.36
30 51 0.61
31 3 0.04
ACGTcount: A:0.59, C:0.11, G:0.14, T:0.16
Consensus pattern (29 bp):
AAAATTAAAGGACTAAAATAGAAAAATAG
Found at i:791549 original size:134 final size:134
Alignment explanation
Indices: 791332--791669 Score: 446
Period size: 134 Copynumber: 2.5 Consensus size: 134
791322 TGTCTGGTCG
* * * * * * * * *
791332 TCTAAGGGTGGCACGACTCTTACTTGGTGAGGAGATATGGTCGGTGGATGACACGGCTCATACGT
1 TCTAGGGGTGACACGGCTCCTACATGATGAGGAGGTATGGTCGGGGGATGACACGGTTCATACGT
* * *
791397 GATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCGATGAGGACGGCTG
66 GATGAAGAGTACTGGCCATCTTTAGGAAGGGTGATAACAAGGTTCCTACGCGATGAGGACGACTG
791462 GTTA
131 GTTA
* * *
791466 TCTAGGGGTGACACGGCTCCTACATGATGAGGAGGTTTGGTCGGGGGATGACACGATTCCTACGT
1 TCTAGGGGTGACACGGCTCCTACATGATGAGGAGGTATGGTCGGGGGATGACACGGTTCATACGT
* *
791531 GATGAAGACG-ACAT-GCCATCTTTAGGAAGGGTGATAACAAGGTTCCTACGTGATGAGGACGAT
66 GATGAAGA-GTAC-TGGCCATCTTTAGGAAGGGTGATAACAAGGTTCCTACGCGATGAGGACGAC
791594 TGGTTA
129 TGGTTA
* ** * *
791600 TCTAGGGGTGACATGGCTCCTATGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCTTACGT
1 TCTAGGGGTGACACGGCTCCTACATGATGAGGAGGTATGGTCGGGGGATGACACGGTTCATACGT
791665 GATGA
66 GATGA
791670 GGATGATAAA
Statistics
Matches: 179, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
134 177 0.99
135 2 0.01
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.25
Consensus pattern (134 bp):
TCTAGGGGTGACACGGCTCCTACATGATGAGGAGGTATGGTCGGGGGATGACACGGTTCATACGT
GATGAAGAGTACTGGCCATCTTTAGGAAGGGTGATAACAAGGTTCCTACGCGATGAGGACGACTG
GTTA
Found at i:793254 original size:12 final size:13
Alignment explanation
Indices: 793226--793271 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
793216 CTTTTCTTTC
*
793226 TTTCTTTTGTTTTT
1 TTTC-TTTGATTTT
793240 TTTCTTTGATTTT
1 TTTCTTTGATTTT
793253 TTTCTTTGATTTT
1 TTTCTTTGATTTT
*
793266 TCTCTT
1 TTTCTT
793272 ATTTGCTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 26 0.87
14 4 0.13
ACGTcount: A:0.04, C:0.11, G:0.07, T:0.78
Consensus pattern (13 bp):
TTTCTTTGATTTT
Found at i:795685 original size:17 final size:17
Alignment explanation
Indices: 795645--795686 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
795635 TTGATAAAAC
*
795645 TCATACAAATAATAAAT
1 TCATACGAATAATAAAT
795662 TCATACGAATAATAAAT
1 TCATACGAATAATAAAT
*
795679 TCTTACGA
1 TCATACGA
795687 GAGTAAAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (17 bp):
TCATACGAATAATAAAT
Found at i:796911 original size:57 final size:59
Alignment explanation
Indices: 796846--796976 Score: 160
Period size: 57 Copynumber: 2.2 Consensus size: 59
796836 TGATTAACAG
* * *
796846 AAACTTAAAGGATTAAAATAGCACAAACGGAAACTTTG-AGGACCAAAATAGC-AAA-AA
1 AAACTTAAAGGACTAAAATAGCAAAAACAGAAAC-TTGAAGGACCAAAATAGCAAAATAA
* * *
796903 AAACTTAAAGAACTAAAATAGCAAAAATAGAAACTTGAAGGACTAAAATAGCATAAATAA
1 AAACTTAAAGGACTAAAATAGCAAAAACAGAAACTTGAAGGACCAAAATAGCA-AAATAA
*
796963 AAATTTAAAGGACT
1 AAACTTAAAGGACT
796977 GAATCATAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
56 3 0.05
57 42 0.68
59 3 0.05
60 14 0.23
ACGTcount: A:0.56, C:0.11, G:0.14, T:0.18
Consensus pattern (59 bp):
AAACTTAAAGGACTAAAATAGCAAAAACAGAAACTTGAAGGACCAAAATAGCAAAATAA
Found at i:796961 original size:30 final size:29
Alignment explanation
Indices: 796844--796976 Score: 135
Period size: 30 Copynumber: 4.6 Consensus size: 29
796834 TATGATTAAC
* *
796844 AGAAACTTAAAGGATTAAAATAGCACAAAC
1 AGAAACTTAAAGGACTAAAATAGCA-AAAT
* ** *
796874 GGAAACTTTGAGGACCAAAATAGCAAAA-
1 AGAAACTTAAAGGACTAAAATAGCAAAAT
*
796902 A-AAACTTAAAGAACTAAAATAGCAAAAAT
1 AGAAACTTAAAGGACTAAAATAGC-AAAAT
*
796931 AGAAACTTGAAGGACTAAAATAGCATAAAT
1 AGAAACTTAAAGGACTAAAATAGCA-AAAT
* *
796961 AAAAATTTAAAGGACT
1 AGAAACTTAAAGGACT
796977 GAATCATAAA
Statistics
Matches: 84, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
27 18 0.21
28 4 0.05
29 5 0.06
30 57 0.68
ACGTcount: A:0.56, C:0.11, G:0.14, T:0.18
Consensus pattern (29 bp):
AGAAACTTAAAGGACTAAAATAGCAAAAT
Found at i:797535 original size:14 final size:14
Alignment explanation
Indices: 797516--797551 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
797506 CGCCTGAAGT
*
797516 AGAGAGAGGAAGAG
1 AGAGAGAGGAAGAA
*
797530 AGAGAGAGGGAGAA
1 AGAGAGAGGAAGAA
797544 AGAGAGAG
1 AGAGAGAG
797552 CTCCAGAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (14 bp):
AGAGAGAGGAAGAA
Found at i:802298 original size:18 final size:19
Alignment explanation
Indices: 802264--802337 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
802254 ATGATGGGAT
802264 GGTACCGATACCCCCCATA
1 GGTACCGATACCCCCCATA
*
802283 GGTATCGATA-CCCCCATGCAA
1 GGTACCGATACCCCCCAT---A
* *
802304 TGGTACCGATACCCCTCAGGA
1 -GGTACCGATACCCCCCA-TA
*
802325 GGTACTGATACCC
1 GGTACCGATACCC
802338 TTAGACATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
18 7 0.16
19 9 0.20
20 12 0.27
21 2 0.05
22 9 0.20
23 5 0.11
ACGTcount: A:0.26, C:0.35, G:0.20, T:0.19
Consensus pattern (19 bp):
GGTACCGATACCCCCCATA
Found at i:802313 original size:22 final size:18
Alignment explanation
Indices: 802262--802318 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 18
802252 GAATGATGGG
802262 ATGGTACCGATACCCCCC
1 ATGGTACCGATACCCCCC
*
802280 ATAGGTATCGATACCCCCATGC
1 AT-GGTACCGATACCCCC---C
802302 AATGGTACCGATACCCC
1 -ATGGTACCGATACCCC
802319 TCAGGAGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 2 0.06
19 14 0.44
22 14 0.44
23 2 0.06
ACGTcount: A:0.26, C:0.37, G:0.18, T:0.19
Consensus pattern (18 bp):
ATGGTACCGATACCCCCC
Found at i:808140 original size:23 final size:22
Alignment explanation
Indices: 808091--808190 Score: 116
Period size: 23 Copynumber: 4.5 Consensus size: 22
808081 TGTGCATAAA
* *
808091 GTATCGATACCCCTTAT-ACAG
1 GTATCGATACCCCTTTTAATAG
808112 GTATCGATACCCCTTTTGAATAG
1 GTATCGATACCCCTTTT-AATAG
* *
808135 GTATCGATACCCC-TTGAATAT
1 GTATCGATACCCCTTTTAATAG
808156 GTATCGATACCCCCTTTTAAT-G
1 GTATCGATA-CCCCTTTTAATAG
808178 TGTATCGATACCC
1 -GTATCGATACCC
808191 TCCTGATCGT
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
21 29 0.43
22 9 0.13
23 30 0.44
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (22 bp):
GTATCGATACCCCTTTTAATAG
Found at i:808144 original size:44 final size:44
Alignment explanation
Indices: 808091--808213 Score: 139
Period size: 44 Copynumber: 2.8 Consensus size: 44
808081 TGTGCATAAA
808091 GTATCGATACCCCTT-ATACAGGTATCGATA-CCCCTTTTGAATAG-
1 GTATCGATACCCCTTGA-ACAGGTATCGATACCCCCTTTT-AAT-GT
* *
808135 GTATCGATACCCCTTGAATATGTATCGATACCCCCTTTTAATGT
1 GTATCGATACCCCTTGAACAGGTATCGATACCCCCTTTTAATGT
* *
808179 GTATCGATACCCTCCTGATC--GTATCGATACCCCCT
1 GTATCGATACCC-CTTGAACAGGTATCGATACCCCCT
808214 GTCGGGTTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
43 16 0.23
44 41 0.59
45 13 0.19
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (44 bp):
GTATCGATACCCCTTGAACAGGTATCGATACCCCCTTTTAATGT
Found at i:808191 original size:21 final size:21
Alignment explanation
Indices: 808091--808190 Score: 105
Period size: 21 Copynumber: 4.6 Consensus size: 21
808081 TGTGCATAAA
*
808091 GTATCGATACCCCTTATACA-G
1 GTATCGATACCCCTTTTA-ATG
808112 GTATCGATACCCCTTTTGAATAG
1 GTATCGATACCCCTTTT-AAT-G
* *
808135 GTATCGATACCCC-TTGAATAT
1 GTATCGATACCCCTTTTAAT-G
808156 GTATCGATACCCCCTTTTAATG
1 GTATCGATA-CCCCTTTTAATG
808178 TGTATCGATACCC
1 -GTATCGATACCC
808191 TCCTGATCGT
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
21 30 0.44
22 10 0.15
23 28 0.41
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (21 bp):
GTATCGATACCCCTTTTAATG
Found at i:813669 original size:21 final size:21
Alignment explanation
Indices: 813625--813727 Score: 113
Period size: 21 Copynumber: 5.0 Consensus size: 21
813615 GGCACTGAAA
*
813625 ATTGTCCCGAAGAACCAC--T
1 ATTGTCCCGAAGGACCACTGT
* * *
813644 A-TGTCTCGTAGGATCACTGT
1 ATTGTCCCGAAGGACCACTGT
813664 ATTGTCCCGAAGGACCACTGT
1 ATTGTCCCGAAGGACCACTGT
*
813685 ATTGTCCCGAAAGACCACTGT
1 ATTGTCCCGAAGGACCACTGT
* * *
813706 ATTATCCAGAAGGACCATTGT
1 ATTGTCCCGAAGGACCACTGT
813727 A
1 A
813728 ACCCTCGACT
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
18 12 0.17
19 1 0.01
20 2 0.03
21 54 0.78
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.26
Consensus pattern (21 bp):
ATTGTCCCGAAGGACCACTGT
Found at i:814997 original size:18 final size:18
Alignment explanation
Indices: 814959--814997 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
814949 TCAATTCGTA
***
814959 TTTAATTTTTTATTTTTT
1 TTTAATTTTTTATTACAT
814977 TTTAATTTTTTATTACAT
1 TTTAATTTTTTATTACAT
814995 TTT
1 TTT
814998 TTATTATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTAATTTTTTATTACAT
Found at i:815014 original size:25 final size:23
Alignment explanation
Indices: 814970--815016 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
814960 TTAATTTTTT
* *
814970 ATTTTTTTTTAATTTTTTATTAC
1 ATTTTTTATTAATTTATTATTAC
814993 ATTTTTTATTATATATTATTATTA
1 ATTTTTTATTA-AT-TTATTATTA
815017 TTATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 2 0.10
25 8 0.40
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTTTTATTAATTTATTATTAC
Found at i:815039 original size:4 final size:4
Alignment explanation
Indices: 814957--815052 Score: 53
Period size: 4 Copynumber: 24.2 Consensus size: 4
814947 ATTCAATTCG
*
814957 TATT TAATT T-TT TATT T-TT T-TT TAATT T-TT TATT ACATT T-TT TATT
1 TATT T-ATT TATT TATT TATT TATT T-ATT TATT TATT -TATT TATT TATT
* * *
815003 ATATAT TA-T TA-T TATT ATATA TATA TATA TATT TATT TATT TATT TATT
1 -TAT-T TATT TATT TATT -TATT TATT TATT TATT TATT TATT TATT TATT
815052 T
1 T
815053 TATTCTATAT
Statistics
Matches: 77, Mismatches: 4, Indels: 22
0.75 0.04 0.21
Matches are distributed among these distances:
3 21 0.27
4 37 0.48
5 18 0.23
6 1 0.01
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (4 bp):
TATT
Found at i:815363 original size:18 final size:18
Alignment explanation
Indices: 815301--815363 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
815291 ATCTACCTTT
*
815301 TTTATTTCTT-TTTTTA-
1 TTTATTTATTCTTTTTAC
* *
815317 TTT-TTCATTCTTATTTCC
1 TTTATTTATTCTT-TTTAC
815335 TTTATTTTATTCTTTTTAC
1 TTTA-TTTATTCTTTTTAC
815354 TTTATTTATT
1 TTTATTTATT
815364 TTCTTTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
15 4 0.11
16 5 0.14
17 3 0.08
18 9 0.24
19 8 0.22
20 8 0.22
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTATTTATTCTTTTTAC
Found at i:815367 original size:20 final size:19
Alignment explanation
Indices: 815313--815371 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
815303 TATTTCTTTT
*
815313 TTTATTTTTCATTCTTATTTCC
1 TTTA-TTTT-ATTCTT-TTTAC
815335 TTTATTTTATTCTTTTTAC
1 TTTATTTTATTCTTTTTAC
*
815354 TTTATTTATTTTCTTTTT
1 TTTATTT-TATTCTTTTT
815372 TAACGTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.32
20 15 0.44
21 4 0.12
22 4 0.12
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTATTTTATTCTTTTTAC
Found at i:816238 original size:21 final size:19
Alignment explanation
Indices: 816205--816248 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
816195 ACTTTTCATT
*
816205 TTTTCTTTCATCATTTATTTA
1 TTTTATTTCATCA-TT-TTTA
*
816226 TTTTATTTTATCATTTTTA
1 TTTTATTTCATCATTTTTA
816245 TTTT
1 TTTT
816249 GCTAACATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 2 0.10
21 11 0.52
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTATTTCATCATTTTTA
Done.