Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 32 of 311
Found at i:9098991 original size:3 final size:3
Alignment explanation
Indices: 9098983--9099380 Score: 168
Period size: 3 Copynumber: 135.0 Consensus size: 3
9098973 TTAATTTTAA
* * * * * * *
9098983 TAT TAT TAT TGT TAT TAT TAG TAA TAT TAT TTT TAT AAT TTT TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * * * *
9099031 TAT TAG TAC TAT TTT CTAT TTT TAC TGT TGT TAT TAA TAG CA- TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
9099076 TAT TAT TCAT ATAT TAT TAT TTT CTAT T-T TTT TAT TAT CAT TAT TGT
1 TAT TAT T-AT -TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
* *
9099123 TAA CA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CT-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * * * *
9099167 CTA- TAT TTT TAT TAT TAG TAT TAT T-T CAT TAT TAT TAT ATGT TAC
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
* * * *
9099212 TAT TA- CAT TCAT TAT TTT TAT T-T T-T TAT TAA TAT TAT TAT TAC
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
9099255 TAT TAT TAT TTT TAT TTT TAT T-T T-T TA- TAC TAT AAT TA- TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
9099298 TCT T-T TAT GT-T TAT CAT TAT TCT TAT TAT TAT T-T CT-T TA- TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
* * * *
9099340 TAT TGT CAT TAT TAGCT TAT CAT TAT TAT TAT AAT TAT TAT
1 TAT TAT TAT TAT TA--T TAT TAT TAT TAT TAT TAT TAT TAT
9099381 AATACTTTCC
Statistics
Matches: 293, Mismatches: 75, Indels: 54
0.69 0.18 0.13
Matches are distributed among these distances:
2 29 0.10
3 245 0.84
4 15 0.05
5 4 0.01
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:9104808 original size:9 final size:9
Alignment explanation
Indices: 9104787--9104820 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
9104777 TATTTTATAA
9104787 TTTTTAAA-
1 TTTTTAAAT
9104795 TTTTTAAAT
1 TTTTTAAAT
*
9104804 TTTTTGAAT
1 TTTTTAAAT
9104813 TTTTTAAA
1 TTTTTAAA
9104821 ATATTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:9115321 original size:19 final size:19
Alignment explanation
Indices: 9115297--9115337 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
9115287 TGAAAATTTG
*
9115297 AAATCTCTCAAAACCTTCA
1 AAATCTCCCAAAACCTTCA
9115316 AAATCTCCCAAAACCTTCA
1 AAATCTCCCAAAACCTTCA
9115335 AAA
1 AAA
9115338 ATATCATAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (19 bp):
AAATCTCCCAAAACCTTCA
Found at i:9115858 original size:19 final size:19
Alignment explanation
Indices: 9115836--9115874 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
9115826 TTAACTGTAA
*
9115836 TTTATTGCTGTAAATTATT
1 TTTATTACTGTAAATTATT
*
9115855 TTTATTACTGTAATTTATT
1 TTTATTACTGTAAATTATT
9115874 T
1 T
9115875 AGTTTAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.62
Consensus pattern (19 bp):
TTTATTACTGTAAATTATT
Found at i:9117560 original size:16 final size:16
Alignment explanation
Indices: 9117539--9117571 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
9117529 AGATAGAGTG
9117539 CAAGAAGATGTTGTGT
1 CAAGAAGATGTTGTGT
9117555 CAAGAAGATGTTGTGT
1 CAAGAAGATGTTGTGT
9117571 C
1 C
9117572 TTGATGTTTG
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:0.30, C:0.09, G:0.30, T:0.30
Consensus pattern (16 bp):
CAAGAAGATGTTGTGT
Found at i:9118731 original size:22 final size:23
Alignment explanation
Indices: 9118700--9118744 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
9118690 TGAAAGGTAT
*
9118700 CTTACTATCTTATTC-TTT-TTAA
1 CTTACAATC-TATTCATTTGTTAA
9118722 CTTACAATCTATTCATTTGTTAA
1 CTTACAATCTATTCATTTGTTAA
9118745 TATTATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.27, C:0.18, G:0.02, T:0.53
Consensus pattern (23 bp):
CTTACAATCTATTCATTTGTTAA
Found at i:9118775 original size:18 final size:15
Alignment explanation
Indices: 9118754--9118810 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 15
9118744 ATATTATTTG
9118754 ATTTTTTTAAATGCGTAT
1 ATTTTTTTAAAT--GT-T
9118772 ATTTTTATTAAATGTT
1 ATTTTT-TTAAATGTT
9118788 ATTTTTTTACACATG-T
1 ATTTTTTTA-A-ATGTT
9118804 ATTTTTT
1 ATTTTTT
9118811 GTAGGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
15 3 0.08
16 16 0.44
17 5 0.14
18 6 0.17
19 6 0.17
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.61
Consensus pattern (15 bp):
ATTTTTTTAAATGTT
Found at i:9119137 original size:9 final size:9
Alignment explanation
Indices: 9119123--9119156 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
9119113 TTTTGTTTTT
9119123 GTTAATTCA
1 GTTAATTCA
9119132 GTTAATTCA
1 GTTAATTCA
9119141 GTTAATTCA
1 GTTAATTCA
9119150 GTTAATT
1 GTTAATT
9119157 TGGTTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (9 bp):
GTTAATTCA
Found at i:9119510 original size:26 final size:26
Alignment explanation
Indices: 9119481--9119530 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
9119471 TCTTACAATA
*
9119481 GATTAA-ATCTAGCATGGGATATAATT
1 GATTAATAT-TAGCATGGGAGATAATT
9119507 GATTAATATTAGCATGGGAGATAA
1 GATTAATATTAGCATGGGAGATAA
9119531 GCTTCAGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (26 bp):
GATTAATATTAGCATGGGAGATAATT
Found at i:9123465 original size:42 final size:42
Alignment explanation
Indices: 9123398--9123479 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
9123388 ATGAGTTTCC
* * *
9123398 GTTTAACCCTAATGGGTTTCAATTCAGCTATTTTGAGCTTTA
1 GTTTAACCCTAACGGGTTTCAATTCAACTATTATGAGCTTTA
* *
9123440 GTTTAACCCTTACGGGTTTTC-ATTCAACTCTTATGAGCTT
1 GTTTAACCCTAACGGG-TTTCAATTCAACTATTATGAGCTT
9123480 CCGTTCAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 30 0.88
43 4 0.12
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.43
Consensus pattern (42 bp):
GTTTAACCCTAACGGGTTTCAATTCAACTATTATGAGCTTTA
Found at i:9125999 original size:40 final size:40
Alignment explanation
Indices: 9125910--9126006 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
9125900 AAAGATATTT
* * * **
9125910 GGCACTAAGTGTGCGATTGAAACTAGCTTTGGCTATTTGG
1 GGCACTAAGTGTGCGATTGAAACTAGCTTCGACTATATAA
* * * *
9125950 GGCATTAAGTGTGCGATTTAAATTATCTTCGACTATATAA
1 GGCACTAAGTGTGCGATTGAAACTAGCTTCGACTATATAA
9125990 GGCACTAAGTGTGCGAT
1 GGCACTAAGTGTGCGAT
9126007 ACTAACTTAG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (40 bp):
GGCACTAAGTGTGCGATTGAAACTAGCTTCGACTATATAA
Found at i:9132846 original size:4 final size:4
Alignment explanation
Indices: 9132837--9132865 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
9132827 AGAAAACGTG
9132837 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
9132866 TAGAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:9133695 original size:47 final size:47
Alignment explanation
Indices: 9133631--9133741 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
9133621 GACATTGAGT
* *
9133631 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTATTC
* * *
9133678 CGATGAAGTACTCTGTGTACTATAATGTTAAAGTTCCGGATTTATTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTATTC
9133725 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
9133742 CTTATCCCGG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 51 0.93
48 4 0.07
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTATTC
Found at i:9137909 original size:45 final size:45
Alignment explanation
Indices: 9137805--9137973 Score: 144
Period size: 45 Copynumber: 3.7 Consensus size: 45
9137795 AGTTCGCACG
* * * * * * *
9137805 TATAAGTCTGCCATATCTATAAATTTTCTTCTCTAAATTCGCA-A
1 TATAAGTCTACCATATCTATGAATCTTCTTCTATGAAGTCACATA
* * * * *
9137849 GTATAAGACCACCATAACTATGAATCTGCTTCTATGAA-TCTGCATA
1 -TATAAGTCTACCATATCTATGAATCTTCTTCTATGAAGTC-ACATA
* * ** *
9137895 TATAAGTTTGCCATATCTATGAATCTTCTTAAATGAAGTCACATT
1 TATAAGTCTACCATATCTATGAATCTTCTTCTATGAAGTCACATA
9137940 TATAAGTCTACCATATCTATGAATTCTTCTTCTA
1 TATAAGTCTACCATATCTATGAA-TCTTCTTCTA
9137974 CGAGTTCACA
Statistics
Matches: 97, Mismatches: 23, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
44 2 0.02
45 84 0.87
46 11 0.11
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (45 bp):
TATAAGTCTACCATATCTATGAATCTTCTTCTATGAAGTCACATA
Found at i:9138668 original size:13 final size:13
Alignment explanation
Indices: 9138650--9138675 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9138640 TGCTGATAGT
9138650 TGAAATCTCAAAG
1 TGAAATCTCAAAG
9138663 TGAAATCTCAAAG
1 TGAAATCTCAAAG
9138676 GGTGATAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
TGAAATCTCAAAG
Found at i:9138689 original size:35 final size:35
Alignment explanation
Indices: 9138643--9138713 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
9138633 TTGCATATGC
9138643 TGATAGTTGAAATCTCAAAGTGAAATCTCAAAGGG
1 TGATAGTTGAAATCTCAAAGTGAAATCTCAAAGGG
9138678 TGATAGTTGAAATCTCAAAGTGAAATCTCAAAGGG
1 TGATAGTTGAAATCTCAAAGTGAAATCTCAAAGGG
9138713 T
1 T
9138714 CAATCATTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (35 bp):
TGATAGTTGAAATCTCAAAGTGAAATCTCAAAGGG
Found at i:9138703 original size:13 final size:13
Alignment explanation
Indices: 9138685--9138710 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9138675 GGGTGATAGT
9138685 TGAAATCTCAAAG
1 TGAAATCTCAAAG
9138698 TGAAATCTCAAAG
1 TGAAATCTCAAAG
9138711 GGTCAATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
TGAAATCTCAAAG
Found at i:9139546 original size:43 final size:43
Alignment explanation
Indices: 9139499--9139587 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 43
9139489 TAAACCCAAA
9139499 AAAAAAAAAAT-TTATTTGCTTCAAAATTAAAAATAAAACAATT
1 AAAAAAAAAATCTTATTTGCTTCAAAA-TAAAAATAAAACAATT
*** * *
9139542 AAAAATGTATTCTTATTTGCTTTAAAATAAAAATAAAACAATT
1 AAAAAAAAAATCTTATTTGCTTCAAAATAAAAATAAAACAATT
9139585 AAA
1 AAA
9139588 TTAGATTTAG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 26 0.65
44 14 0.35
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (43 bp):
AAAAAAAAAATCTTATTTGCTTCAAAATAAAAATAAAACAATT
Found at i:9142885 original size:17 final size:19
Alignment explanation
Indices: 9142863--9142899 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
9142853 TAAAAAAATG
9142863 ATTTTTTAT-ATTTT-ATA
1 ATTTTTTATAATTTTAATA
9142880 A-TTTTTATAATTTTAATA
1 ATTTTTTATAATTTTAATA
9142898 AT
1 AT
9142900 AATAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
16 7 0.41
17 6 0.35
18 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTTTATAATTTTAATA
Found at i:9142898 original size:18 final size:18
Alignment explanation
Indices: 9142865--9142931 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 18
9142855 AAAAAATGAT
9142865 TTTTTAT-ATTTT-ATAA
1 TTTTTATAATTTTAATAA
9142881 TTTTTATAATTTTAATAA
1 TTTTTATAATTTTAATAA
** *
9142899 TAATAATAAATTATTTAATAA
1 TTTTTAT-AA-T-TTTAATAA
9142920 TTTTTA-AATTTT
1 TTTTTATAATTTT
9142932 TAACTATGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
16 7 0.17
17 8 0.20
18 9 0.22
19 4 0.10
20 1 0.03
21 11 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTTATAATTTTAATAA
Found at i:9142933 original size:18 final size:18
Alignment explanation
Indices: 9142873--9142934 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
9142863 ATTTTTTATA
9142873 TTTT-ATAATTTTTATAA-
1 TTTTAATAATTTTTA-AAT
**
9142890 TTTTAATAATAATAATAAAT
1 TTTTAATAAT--TTTTAAAT
9142910 TATTTAATAATTTTTAAAT
1 T-TTTAATAATTTTTAAAT
9142929 TTTTAA
1 TTTTAA
9142935 CTATGAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
17 4 0.11
18 10 0.28
19 9 0.25
20 4 0.11
21 9 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAATAATTTTTAAAT
Found at i:9147187 original size:20 final size:20
Alignment explanation
Indices: 9147164--9147221 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
9147154 TACCCCTAAC
9147164 TGCACTCTGGTGCCCCTGAT
1 TGCACTCTGGTGCCCCTGAT
* * *
9147184 TGCACACTCGTGCTCCTGAT
1 TGCACTCTGGTGCCCCTGAT
*
9147204 TGCACTTTGGTGCCCCTG
1 TGCACTCTGGTGCCCCTG
9147222 TTTTTCCATG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.10, C:0.34, G:0.24, T:0.31
Consensus pattern (20 bp):
TGCACTCTGGTGCCCCTGAT
Found at i:9148149 original size:54 final size:54
Alignment explanation
Indices: 9148027--9148149 Score: 122
Period size: 54 Copynumber: 2.3 Consensus size: 54
9148017 CTATGTGTCT
* * * *
9148027 CAAGTCAGTGAGTTACACGGGCTAGCACACGGCCTGCGACATGGCCGTTTGAGC
1 CAAGTCAGTGAGTTACAAGGGCTAGCACACGGCCTGCGACACGGCCGTATGAAC
* *** * * * *
9148081 CAAGTTAAAAAGTTACAAGGGCTAGCATA-GAGTCTGTGACACGGTCGTATGAAC
1 CAAGTCAGTGAGTTACAAGGGCTAGCACACG-GCCTGCGACACGGCCGTATGAAC
9148135 CAAGTCAGTGAGTTA
1 CAAGTCAGTGAGTTA
9148150 TACAATCTAT
Statistics
Matches: 52, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
53 1 0.02
54 51 0.98
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.21
Consensus pattern (54 bp):
CAAGTCAGTGAGTTACAAGGGCTAGCACACGGCCTGCGACACGGCCGTATGAAC
Found at i:9150867 original size:21 final size:21
Alignment explanation
Indices: 9150841--9150923 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 21
9150831 TGATCAGTAG
*
9150841 ACGACACATAAAGTGCCTAAA
1 ACGACACACAAAGTGCCTAAA
* * * *
9150862 ACGACACACGAGGTGCCTGAC
1 ACGACACACAAAGTGCCTAAA
* *
9150883 ACGACACACGAGGTGCCTGAAA
1 ACGACACACAAAGTGCCT-AAA
* *
9150905 TATGACACATAAAGTGCCT
1 -ACGACACACAAAGTGCCT
9150924 GATCGGTAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
21 34 0.69
22 1 0.02
23 14 0.29
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.14
Consensus pattern (21 bp):
ACGACACACAAAGTGCCTAAA
Found at i:9150913 original size:23 final size:21
Alignment explanation
Indices: 9150853--9150902 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
9150843 GACACATAAA
* *
9150853 GTGCCTAAAACGACACACGAG
1 GTGCCTGACACGACACACGAG
9150874 GTGCCTGACACGACACACGAG
1 GTGCCTGACACGACACACGAG
9150895 GTGCCTGA
1 GTGCCTGA
9150903 AATATGACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.30, G:0.28, T:0.12
Consensus pattern (21 bp):
GTGCCTGACACGACACACGAG
Found at i:9151269 original size:21 final size:21
Alignment explanation
Indices: 9151240--9151280 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
9151230 AAAAAAGAAA
9151240 AAAAGAAAAAACCTAACCCCC
1 AAAAGAAAAAACCTAACCCCC
9151261 AAAA-AAAAAACCTAACCCCC
1 AAAAGAAAAAACCTAACCCCC
9151281 CCCAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.59, C:0.34, G:0.02, T:0.05
Consensus pattern (21 bp):
AAAAGAAAAAACCTAACCCCC
Found at i:9152086 original size:11 final size:11
Alignment explanation
Indices: 9152070--9152099 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
9152060 GTATATATTG
9152070 TATATATTATA
1 TATATATTATA
*
9152081 TTTATATTATA
1 TATATATTATA
9152092 TATATATT
1 TATATATT
9152100 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:9152154 original size:21 final size:23
Alignment explanation
Indices: 9152128--9152170 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
9152118 ATACTTCTTG
*
9152128 TATATT-TC-CATGTATATACTT
1 TATATTGTCTCATGTACATACTT
9152149 TATATTGTCTCATGTACATACT
1 TATATTGTCTCATGTACATACT
9152171 CCGAAATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 2 0.11
23 11 0.58
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (23 bp):
TATATTGTCTCATGTACATACTT
Found at i:9155842 original size:19 final size:19
Alignment explanation
Indices: 9155818--9155862 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
9155808 AGTTGTTCAA
9155818 TTATCAGATGAAGCCAAAG
1 TTATCAGATGAAGCCAAAG
*
9155837 TTATCAGATGAAGCCGAAG
1 TTATCAGATGAAGCCAAAG
*
9155856 TTCTCAG
1 TTATCAG
9155863 TTGCCAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (19 bp):
TTATCAGATGAAGCCAAAG
Found at i:9164588 original size:72 final size:73
Alignment explanation
Indices: 9164379--9164797 Score: 621
Period size: 72 Copynumber: 5.7 Consensus size: 73
9164369 TGATGTTTTT
*
9164379 ATTTCTG-TTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 ATTTCTGTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
9164443 GTAATTTCA
65 GTAATTTCA
* **
9164452 ATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
1 ATTTCTGTT-TTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
9164517 GTAATTTCA
65 GTAATTTCA
* * ** * *
9164526 ATTTCTGTTTTC-AAAATTCAACTCATATTGCAAGAAATGAGTTGAGCCTCAAGACATGCTGAGG
1 ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
* *
9164590 TATTTTAA
66 TAATTTCA
*
9164598 ATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
1 ATTTCTG-TTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
*
9164663 GGTAATTTAA
64 GGTAATTTCA
*
9164673 ATTTCTGTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTC-GAGACACGCTGAG
1 ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG-GACACGCTGAG
9164736 GTAATTTCA
65 GTAATTTCA
*
9164745 ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
9164798 ATCACACATG
Statistics
Matches: 314, Mismatches: 24, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
71 1 0.00
72 128 0.41
73 50 0.16
74 74 0.24
75 61 0.19
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (73 bp):
ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
TAATTTCA
Found at i:9164646 original size:147 final size:147
Alignment explanation
Indices: 9164379--9164797 Score: 639
Period size: 147 Copynumber: 2.9 Consensus size: 147
9164369 TGATGTTTTT
* *
9164379 ATTTCTG-TTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 ATTTCTGTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAG
* **
9164443 GTAATTTCAATTTCTGTTGTT-AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG
64 GTAATTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
*
9164507 ACACGCTGAGGTAATTTCA
129 ACACGCTGAGGTAATTTAA
* * ** *
9164526 ATTTCTGTTTTCAAAATTCAACTCATATTGCAAGAAATGAGTTGAGCCTCAAGACATGCTGAGGT
1 ATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGT
* * *
9164591 ATTTTAAATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
66 AATTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
9164656 ACGCTGAGGTAATTTAA
131 ACGCTGAGGTAATTTAA
* *
9164673 ATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGAGACACGCTGAGGT
1 ATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGT
*
9164738 AATTTCAATTTCTG-TTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
66 AATTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
9164798 ATCACACATG
Statistics
Matches: 245, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
145 40 0.16
146 66 0.27
147 135 0.55
148 4 0.02
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (147 bp):
ATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGT
AATTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
ACGCTGAGGTAATTTAA
Found at i:9165726 original size:28 final size:27
Alignment explanation
Indices: 9165649--9165731 Score: 80
Period size: 28 Copynumber: 3.1 Consensus size: 27
9165639 AGCCCTCCCC
** *
9165649 AAAA-AAAAACCTAACCCCC-CCAAGA
1 AAAAGAAAAACCTAACCCCCAAAAAAA
***
9165674 AAAAGAAAAAACCTAACCAAAAAAAAAA
1 AAAAG-AAAAACCTAACCCCCAAAAAAA
9165702 GAAAAGAAAAACCTAACCCCCAAAAAAA
1 -AAAAGAAAAACCTAACCCCCAAAAAAA
9165730 AA
1 AA
9165732 CCAAGAAACC
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
25 4 0.09
27 14 0.31
28 22 0.49
29 5 0.11
ACGTcount: A:0.67, C:0.24, G:0.05, T:0.04
Consensus pattern (27 bp):
AAAAGAAAAACCTAACCCCCAAAAAAA
Found at i:9166052 original size:11 final size:12
Alignment explanation
Indices: 9166030--9166080 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
9166020 TATATACATC
9166030 ATAATAAAAAAT
1 ATAATAAAAAAT
9166042 ATAATAAAAATAT
1 ATAATAAAAA-AT
*
9166055 ATATACAAAACAAAT
1 ATA-A-TAAA-AAAT
9166070 ATAA-AAAAAAT
1 ATAATAAAAAAT
9166081 TACCTTTTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
11 4 0.12
12 13 0.38
13 5 0.15
14 2 0.06
15 8 0.24
16 2 0.06
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAATAAAAAAT
Found at i:9166201 original size:11 final size:12
Alignment explanation
Indices: 9166167--9166204 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
9166157 CTGGCCGAAT
* *
9166167 TTCCCTTCCCCC
1 TTCCCTTCTCTC
9166179 TTCCCTTCTCTC
1 TTCCCTTCTCTC
9166191 TTCCC-TCTCTC
1 TTCCCTTCTCTC
9166202 TTC
1 TTC
9166205 TTTTTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (12 bp):
TTCCCTTCTCTC
Found at i:9166520 original size:11 final size:11
Alignment explanation
Indices: 9166502--9166531 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
9166492 GTGTCTATTG
9166502 TATATATTATA
1 TATATATTATA
*
9166513 TTTATATTATA
1 TATATATTATA
9166524 TATATATT
1 TATATATT
9166532 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:9166942 original size:16 final size:15
Alignment explanation
Indices: 9166918--9166952 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
9166908 TAATTATTAT
9166918 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
9166934 TATTTTAATATTTTA
1 TATTCTAATATTTTA
9166949 TATT
1 TATT
9166953 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:9172255 original size:27 final size:27
Alignment explanation
Indices: 9172207--9172365 Score: 175
Period size: 27 Copynumber: 5.9 Consensus size: 27
9172197 GCGAGACTGC
* *
9172207 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
*
9172234 CAGATATTGTGGCGGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
*
9172260 CAGATTTATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
9172287 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
9172314 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
9172341 CAGATATTTGTGGCATAGCCACCAG
1 CAGATA-TTGTGGCAGAGCCACCAG
9172366 GACGCTTCCT
Statistics
Matches: 114, Mismatches: 10, Indels: 16
0.81 0.07 0.11
Matches are distributed among these distances:
26 9 0.08
27 102 0.89
28 3 0.03
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:9172366 original size:54 final size:53
Alignment explanation
Indices: 9172225--9172368 Score: 225
Period size: 54 Copynumber: 2.7 Consensus size: 53
9172215 GTGACGAAGT
** * *
9172225 CACCAGATACAGATATTGTGGCGGAGCCACCAGAACAGATTTATGTGGCAGAGC
1 CACCAGAT-CAGATATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
9172279 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGAT-ATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
9172333 CACCAGATCAGATATTTGTGGCATAGCCACCAGGAC
1 CACCAGATCAGATA-TTGTGGCATAGCCACCAGGAC
9172369 GCTTCCTCCA
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
53 6 0.07
54 78 0.93
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.19
Consensus pattern (53 bp):
CACCAGATCAGATATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
Found at i:9173710 original size:27 final size:27
Alignment explanation
Indices: 9173662--9173820 Score: 166
Period size: 27 Copynumber: 5.9 Consensus size: 27
9173652 GCGAGGCTGC
* *
9173662 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
*
9173689 CAGATATTGTGGCGGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
*
9173715 CAGATTTATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
9173742 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
9173769 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
9173796 CAGATATTTGTGGTATAGCCACCAG
1 CAGATA-TTGTGGCAGAGCCACCAG
9173821 GACGCTTCCT
Statistics
Matches: 113, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
26 9 0.08
27 101 0.89
28 3 0.03
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:9173821 original size:54 final size:53
Alignment explanation
Indices: 9173680--9173823 Score: 216
Period size: 54 Copynumber: 2.7 Consensus size: 53
9173670 GTGACGAAGT
** * *
9173680 CACCAGATACAGATATTGTGGCGGAGCCACCAGAACAGATTTATGTGGCAGAGC
1 CACCAGAT-CAGATATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
9173734 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGAT-ATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
*
9173788 CACCAGATCAGATATTTGTGGTATAGCCACCAGGAC
1 CACCAGATCAGATA-TTGTGGCATAGCCACCAGGAC
9173824 GCTTCCTCCA
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
53 6 0.07
54 77 0.93
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (53 bp):
CACCAGATCAGATATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
Found at i:9188993 original size:19 final size:20
Alignment explanation
Indices: 9188952--9188993 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
9188942 ATTATTTGAG
*
9188952 TTTGAGCTTAGTATAATATA
1 TTTGAGCTTAGAATAATATA
*
9188972 TTTGAGTTTAGAATAA-ATA
1 TTTGAGCTTAGAATAATATA
9188991 TTT
1 TTT
9188994 TAAAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (20 bp):
TTTGAGCTTAGAATAATATA
Found at i:9200385 original size:51 final size:50
Alignment explanation
Indices: 9200330--9200489 Score: 248
Period size: 51 Copynumber: 3.2 Consensus size: 50
9200320 TTAATCACAT
9200330 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
* *
9200381 TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTATCAT
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCAC
* * *
9200431 TTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
*
9200482 TTGTCACT
1 TTATCACT
9200490 GATCAGAAGT
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
50 46 0.46
51 55 0.54
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (50 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCAC
Found at i:9204090 original size:24 final size:24
Alignment explanation
Indices: 9204054--9204111 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
9204044 CCACCGTCTC
*
9204054 TGTC-TCAAGTTTAGCTCTTTCTG
1 TGTCATCAAATTTAGCTCTTTCTG
9204077 TGTCATCAAATTTAGCTCTTTCTG
1 TGTCATCAAATTTAGCTCTTTCTG
9204101 TGTCATCAAAT
1 TGTCATCAAAT
9204112 ATTTCAGACT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 4 0.12
24 29 0.88
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.45
Consensus pattern (24 bp):
TGTCATCAAATTTAGCTCTTTCTG
Found at i:9207691 original size:15 final size:16
Alignment explanation
Indices: 9207671--9207703 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
9207661 TATATATTTT
9207671 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
9207686 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
9207703 T
1 T
9207704 ATAACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:9207789 original size:22 final size:22
Alignment explanation
Indices: 9207750--9207808 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
9207740 GTTTTAAGAA
*
9207750 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
9207771 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
9207793 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
9207809 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:9207825 original size:26 final size:24
Alignment explanation
Indices: 9207779--9207827 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
9207769 ATTTGTTTTA
*
9207779 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
9207803 ATATTTGATTTATTATATTTTTAAA
1 ATATTT-ATTT-TTATATTTTTAAA
9207828 ATTTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 4 0.18
26 12 0.55
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:9207838 original size:25 final size:26
Alignment explanation
Indices: 9207782--9207839 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
9207772 TGTTTTAATA
*
9207782 TTTATTT-TTATGTTTTTAAATATAT
1 TTTATTTATTATATTTTTAAATATAT
* *
9207807 TTGATTTATTATATTTTTAAA-ATTT
1 TTTATTTATTATATTTTTAAATATAT
9207832 TTTATTTA
1 TTTATTTA
9207840 ATGAAATAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 16 0.57
26 12 0.43
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (26 bp):
TTTATTTATTATATTTTTAAATATAT
Found at i:9212038 original size:13 final size:14
Alignment explanation
Indices: 9212022--9212057 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
9212012 CAATCTCATA
9212022 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
9212035 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
9212048 TCTC-ATTTCA
1 TCTCAATTTCA
9212058 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:9212047 original size:18 final size:19
Alignment explanation
Indices: 9212009--9212049 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
9211999 TGGTTCATGT
9212009 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
9212028 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
9212046 TTTC
1 TTTC
9212050 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:9212239 original size:39 final size:38
Alignment explanation
Indices: 9212172--9212306 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
9212162 ACCAATATGG
* * *
9212172 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
9212211 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
9212249 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
9212290 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
9212307 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:9212571 original size:18 final size:19
Alignment explanation
Indices: 9212545--9212583 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
9212535 TTTCAATTCA
9212545 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
9212564 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
9212582 AT
1 AT
9212584 CTATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:9213906 original size:5 final size:5
Alignment explanation
Indices: 9213896--9213952 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
9213886 TTACTTATTT
* *
9213896 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
9213944 ATAT- ATATA
1 ATATA ATATA
9213953 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:9213912 original size:12 final size:12
Alignment explanation
Indices: 9213895--9213950 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
9213885 TTTACTTATT
9213895 TATATAATATAA
1 TATATAATATAA
9213907 TATATAATATAATA
1 TATATAATAT-A-A
9213921 TACTATAATATAA
1 TA-TATAATATAA
*
9213934 TA-ATAATTTAA
1 TATATAATATAA
9213945 TATATA
1 TATATA
9213951 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:9213965 original size:26 final size:26
Alignment explanation
Indices: 9213897--9213952 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
9213887 TACTTATTTA
*
9213897 TATAATATAATATATAATATAATATAC
1 TATAATATAACA-ATAATATAATATAC
* *
9213924 TATAATATAATAATAATTTAATATA-
1 TATAATATAACAATAATATAATATAC
9213949 TATA
1 TATA
9213953 TTTTAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAACAATAATATAATATAC
Found at i:9215687 original size:25 final size:22
Alignment explanation
Indices: 9215645--9215707 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
9215635 ACGAACACCT
* *
9215645 AAAAACCTAGAAATTTAAAAATAG
1 AAAAACCCA-AAAATTAAAAA-AG
*
9215669 AAAAACCTCCAAAAATTAAAAAAT
1 AAAAA-C-CCAAAAATTAAAAAAG
9215693 AAAAACCCAAAAATT
1 AAAAACCCAAAAATT
9215708 TAAATTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 9 0.26
23 1 0.03
24 11 0.32
25 11 0.32
26 2 0.06
ACGTcount: A:0.65, C:0.14, G:0.03, T:0.17
Consensus pattern (22 bp):
AAAAACCCAAAAATTAAAAAAG
Found at i:9216858 original size:18 final size:17
Alignment explanation
Indices: 9216837--9216883 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
9216827 AATTTTATTC
*
9216837 TTATAATTTTTTTATAAT
1 TTAT-ATTTTTTTATAAA
*
9216855 TTATATGTTTTTTCTAAA
1 TTATAT-TTTTTTATAAA
9216873 TTATATTTTTT
1 TTATATTTTTT
9216884 CTAAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (17 bp):
TTATATTTTTTTATAAA
Found at i:9217585 original size:20 final size:19
Alignment explanation
Indices: 9217560--9217617 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
9217550 TTGGAGTTTA
9217560 AATTGAGTTAAACAACAAAT
1 AATTGAGTTAAACAA-AAAT
*
9217580 AATTGATTTAAACAAAAAT
1 AATTGAGTTAAACAAAAAT
* * *
9217599 GAATCGATTTGAACAAAAA
1 -AATTGAGTTAAACAAAAA
9217618 AAGAATCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 4 0.12
20 30 0.88
ACGTcount: A:0.55, C:0.09, G:0.10, T:0.26
Consensus pattern (19 bp):
AATTGAGTTAAACAAAAAT
Found at i:9217623 original size:21 final size:20
Alignment explanation
Indices: 9217567--9217624 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
9217557 TTAAATTGAG
* * *
9217567 TTAAACAACAAATAATTGAT
1 TTAAACAAAAAAGAATCGAT
*
9217587 TTAAACAAAAATGAATCGAT
1 TTAAACAAAAAAGAATCGAT
*
9217607 TTGAACAAAAAAAGAATC
1 TTAAAC-AAAAAAGAATC
9217625 AATTCAACAG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
20 21 0.68
21 10 0.32
ACGTcount: A:0.57, C:0.10, G:0.09, T:0.24
Consensus pattern (20 bp):
TTAAACAAAAAAGAATCGAT
Found at i:9217918 original size:14 final size:15
Alignment explanation
Indices: 9217899--9217933 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
9217889 TTTAATTTTC
9217899 AAAATTTCAAAAA-A
1 AAAATTTCAAAAATA
*
9217913 AAAATTTTAAAAATA
1 AAAATTTCAAAAATA
9217928 AAAATT
1 AAAATT
9217934 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATTTCAAAAATA
Found at i:9217963 original size:30 final size:31
Alignment explanation
Indices: 9217929--9218030 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
9217919 TTAAAAATAA
*
9217929 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
9217959 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
9217989 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
9218019 AAATTTCATTTT
1 AAATTTCATTTT
9218031 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:9218313 original size:10 final size:10
Alignment explanation
Indices: 9218294--9218343 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
9218284 TTTTTCGAAG
*
9218294 GAAAAAAGAA
1 GAAAAGAGAA
9218304 GAAAAGAGAA
1 GAAAAGAGAA
9218314 GAAAAGAGAA
1 GAAAAGAGAA
* *
9218324 -AGAGGAGAA
1 GAAAAGAGAA
9218333 GAAAAGA-AA
1 GAAAAGAGAA
9218342 GA
1 GA
9218344 GTACCGGCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:9218344 original size:17 final size:19
Alignment explanation
Indices: 9218297--9218339 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
9218287 TTCGAAGGAA
9218297 AAAAGAAGAAA-A-GAGAAG
1 AAAAG-AGAAAGAGGAGAAG
9218315 AAAAGAGAAAGAGGAGAAG
1 AAAAGAGAAAGAGGAGAAG
9218334 AAAAGA
1 AAAAGA
9218340 AAGAGTACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAGAGGAGAAG
Found at i:9218415 original size:3 final size:3
Alignment explanation
Indices: 9218409--9218440 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
9218399 GTGTAGGAGG
9218409 AGA AGA AGA AGA AGA AGA AGAA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA A
9218441 AGAAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:9218435 original size:10 final size:10
Alignment explanation
Indices: 9218411--9218444 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
9218401 GTAGGAGGAG
9218411 AAGAAGAAG-
1 AAGAAGAAGA
9218420 AAGAAGAAGA
1 AAGAAGAAGA
9218430 AAGAAGAAGA
1 AAGAAGAAGA
9218440 AAGAA
1 AAGAA
9218445 AAAAAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (10 bp):
AAGAAGAAGA
Found at i:9218649 original size:14 final size:15
Alignment explanation
Indices: 9218610--9218650 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
9218600 AAACCAAAGC
9218610 AAAAAAAAGCAGCCCA
1 AAAAAAAAG-AGCCCA
9218626 AAAAGAAAAG-GCCCA
1 AAAA-AAAAGAGCCCA
9218641 AAAAAAAAGA
1 AAAAAAAAGA
9218651 AAAAACAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 5 0.22
15 9 0.39
16 4 0.17
17 5 0.22
ACGTcount: A:0.68, C:0.17, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAGCCCA
Found at i:9218792 original size:23 final size:23
Alignment explanation
Indices: 9218762--9218864 Score: 81
Period size: 23 Copynumber: 4.5 Consensus size: 23
9218752 AGCAGGCCAG
9218762 GAAAAAAAGAGAGAAAGAAGAAA
1 GAAAAAAAGAGAGAAAGAAGAAA
*
9218785 GAAAAAAAGAAAG-AAGAA-AAA
1 GAAAAAAAGAGAGAAAGAAGAAA
* * *
9218806 -AAGAAAAGAGAAAAAAAGGAAAAAA
1 GAA-AAAA-AGAGAGAAA-GAAGAAA
*
9218831 GAAGAAAAA-AGAAGAAAAAAGAAA
1 GAA-AAAAAGAG-AGAAAGAAGAAA
9218855 -AAAAAAAGAG
1 GAAAAAAAGAG
9218865 TTTCAATTCG
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
20 2 0.03
21 7 0.11
22 15 0.23
23 18 0.27
24 9 0.14
25 8 0.12
26 7 0.11
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (23 bp):
GAAAAAAAGAGAGAAAGAAGAAA
Found at i:9218793 original size:15 final size:14
Alignment explanation
Indices: 9218765--9218861 Score: 92
Period size: 15 Copynumber: 6.8 Consensus size: 14
9218755 AGGCCAGGAA
* *
9218765 AAAAAGAGAGAAAG
1 AAAAAGAAAAAAAG
9218779 AAGAAAGAAAAAAAG
1 AA-AAAGAAAAAAAG
9218794 AAAGAAGAAAAAAAG
1 AAA-AAGAAAAAAAG
9218809 AAAAGAGAAAAAAAGG
1 AAAA-AGAAAAAAA-G
*
9218825 AAAAAAGAAGAAAA-
1 -AAAAAGAAAAAAAG
*
9218839 AAGAAG-AAAAAAG
1 AAAAAGAAAAAAAG
9218852 AAAAA-AAAAA
1 AAAAAGAAAAA
9218862 GAGTTTCAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
12 5 0.07
13 13 0.19
14 4 0.06
15 35 0.50
16 9 0.13
17 4 0.06
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:9218805 original size:16 final size:16
Alignment explanation
Indices: 9218786--9218859 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 16
9218776 AAGAAGAAAG
9218786 AAAAAAAGAAAGAAG-
1 AAAAAAAGAAAGAAGA
9218801 AAAAAAAGAAA-AGAGAA
1 AAAAAAAGAAAGA-AG-A
*
9218818 AAAAAGGAAAAAAGAAGA
1 AAAAA--AAGAAAGAAGA
*
9218836 AAAAAGAAGAAAAAAGA
1 AAAAA-AAGAAAGAAGA
9218853 AAAAAAA
1 AAAAAAA
9218860 AAGAGTTTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
14 1 0.02
15 13 0.26
16 2 0.04
17 20 0.40
18 6 0.12
19 7 0.14
20 1 0.02
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAGAAGA
Found at i:9218829 original size:10 final size:10
Alignment explanation
Indices: 9218764--9218863 Score: 86
Period size: 10 Copynumber: 10.1 Consensus size: 10
9218754 CAGGCCAGGA
9218764 AAAAAAGAGAG
1 AAAAAAGA-AG
*
9218775 AAAGAAGAAAG
1 AAAAAAG-AAG
9218786 AAAAAAAGAAAG
1 -AAAAAAG-AAG
9218798 AAGAAAA-AA-
1 AA-AAAAGAAG
*
9218807 AGAAAAG-AG
1 AAAAAAGAAG
*
9218816 AAAAAA-AGG
1 AAAAAAGAAG
9218825 AAAAAAGAAG
1 AAAAAAGAAG
9218835 AAAAAAGAAG
1 AAAAAAGAAG
9218845 AAAAAAGAA-
1 AAAAAAGAAG
9218854 AAAAAA-AAG
1 AAAAAAGAAG
9218863 A
1 A
9218864 GTTTCAATTC
Statistics
Matches: 75, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
8 7 0.09
9 20 0.27
10 23 0.31
11 10 0.13
12 15 0.20
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:9218854 original size:7 final size:7
Alignment explanation
Indices: 9218764--9218861 Score: 83
Period size: 7 Copynumber: 13.6 Consensus size: 7
9218754 CAGGCCAGGA
9218764 AAAAAAG
1 AAAAAAG
*
9218771 AGAGAAAG
1 A-AAAAAG
*
9218779 AAGAAAG
1 AAAAAAG
9218786 AAAAAAAG
1 -AAAAAAG
*
9218794 AAAGAAG
1 AAAAAAG
9218801 AAAAAAAG
1 -AAAAAAG
*
9218809 AAAAGAG
1 AAAAAAG
9218816 AAAAAAAGG
1 -AAAAAA-G
9218825 AAAAAAG
1 AAAAAAG
*
9218832 AAGAAA-
1 AAAAAAG
*
9218838 AAAGAAG
1 AAAAAAG
9218845 AAAAAAG
1 AAAAAAG
9218852 AAAAAA-
1 AAAAAAG
9218858 AAAA
1 AAAA
9218862 GAGTTTCAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
6 8 0.11
7 37 0.49
8 29 0.39
9 1 0.01
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:9218859 original size:38 final size:36
Alignment explanation
Indices: 9218764--9218861 Score: 119
Period size: 34 Copynumber: 2.8 Consensus size: 36
9218754 CAGGCCAGGA
* * *
9218764 AAAAAAGAGAGAAAGAAGAAAGAAAAAAAGAAAGAAG
1 AAAAAAGA-AGAAAAAAGAAAAAAAAAAAAAAAGAAG
* **
9218801 -AAAAA-AAGAAAAGAGAAAAAAAGGAAAAAAGAAG
1 AAAAAAGAAGAAAAAAGAAAAAAAAAAAAAAAGAAG
9218835 AAAAAAGAAGAAAAAAGAAAAAAAAAA
1 AAAAAAGAAGAAAAAAGAAAAAAAAAA
9218862 GAGTTTCAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
34 22 0.44
35 6 0.12
36 22 0.44
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (36 bp):
AAAAAAGAAGAAAAAAGAAAAAAAAAAAAAAAGAAG
Found at i:9219220 original size:20 final size:21
Alignment explanation
Indices: 9219183--9219221 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
9219173 AAAAAATATT
*
9219183 AAAAAAAAGTCTCATATTTAC
1 AAAAAAAAATCTCATATTTAC
*
9219204 AAAAAAAAATTTC-TATTT
1 AAAAAAAAATCTCATATTT
9219222 TTCAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (21 bp):
AAAAAAAAATCTCATATTTAC
Found at i:9219268 original size:21 final size:21
Alignment explanation
Indices: 9219229--9219267 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9219219 TTTTTCAAAA
9219229 TTTCTCGTGCCTTCAAAAATT
1 TTTCTCGTGCCTTCAAAAATT
*
9219250 TTTCTCGTG-TTTCAAAAA
1 TTTCTCGTGCCTTCAAAAA
9219268 AAATATATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.44
Consensus pattern (21 bp):
TTTCTCGTGCCTTCAAAAATT
Found at i:9219518 original size:18 final size:17
Alignment explanation
Indices: 9219444--9219606 Score: 159
Period size: 17 Copynumber: 9.4 Consensus size: 17
9219434 ATCTATTTTC
* *
9219444 CAAAATTTTTAGTGTCTT
1 CAAAAATTTTCGTGT-TT
*
9219462 CTAAAAATTTTTGTGTTT
1 C-AAAAATTTTCGTGTTT
9219480 CAAAAATTTTCGT-TTT
1 CAAAAATTTTCGTGTTT
*
9219496 CAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTT
9219513 CAAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
* *
9219531 CAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTT
** *
9219548 CAAAAATCCTCTTGTTTT
1 CAAAAATTTTCGTG-TTT
9219566 CAAAAA-TTTCGGTGTTT
1 CAAAAATTTTC-GTGTTT
**
9219583 TGAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
9219601 CAAAAA
1 CAAAAA
9219607 AAAAATCTCG
Statistics
Matches: 119, Mismatches: 19, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
16 15 0.13
17 51 0.43
18 41 0.34
19 12 0.10
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (17 bp):
CAAAAATTTTCGTGTTT
Found at i:9219606 original size:35 final size:34
Alignment explanation
Indices: 9219444--9219606 Score: 168
Period size: 35 Copynumber: 4.7 Consensus size: 34
9219434 ATCTATTTTC
* * * *
9219444 CAAAATTTTTAGTGTCTTCTAAAAATTTTTGTGTTT
1 CAAAAATTTTCGTGTTTTC-AAAAA-TTTCGTGTTT
9219480 CAAAAATTTTC--GTTTTCAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTT-CGTGTTT
* *
9219513 CAAAAATTTTCGTGTTTTCAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTTTCAAAA-ATTTCGTGTTT
** *
9219548 CAAAAATCCTCTTGTTTTCAAAAATTTCGGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTC-GTGTTT
**
9219583 TGAAAATTTTCGTGTTTTCAAAAA
1 CAAAAATTTTCGTGTTTTCAAAAA
9219607 AAAAATCTCG
Statistics
Matches: 106, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
32 3 0.03
33 22 0.21
34 9 0.08
35 60 0.57
36 12 0.11
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (34 bp):
CAAAAATTTTCGTGTTTTCAAAAATTTCGTGTTT
Found at i:9219621 original size:39 final size:38
Alignment explanation
Indices: 9219567--9219693 Score: 106
Period size: 39 Copynumber: 3.4 Consensus size: 38
9219557 TCTTGTTTTC
*
9219567 AAAAATTTCGGTGTTTTGAAAATTTTCGTGTTTTCAAAAA
1 AAAAATCTC-GTGTTTT-AAAATTTTCGTGTTTTCAAAAA
*
9219607 AAAAATCTCGTGTTTCATAAATTTT-G-GTTTT---AAA
1 AAAAATCTCGTGTTTTA-AAATTTTCGTGTTTTCAAAAA
* * *
9219641 AAAAAT-T-ATGTCTTAAAATTCTCGTGTTTTCAAAACA
1 AAAAATCTCGTGTTTTAAAATTTTCGTGTTTTCAAAA-A
*
9219678 AGAAATTCTCGTGTTT
1 A-AAAATCTCGTGTTT
9219694 CAATCGGATC
Statistics
Matches: 68, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
31 6 0.09
32 6 0.09
33 6 0.09
34 9 0.13
36 2 0.03
37 7 0.10
38 6 0.09
39 14 0.21
40 12 0.18
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (38 bp):
AAAAATCTCGTGTTTTAAAATTTTCGTGTTTTCAAAAA
Found at i:9231984 original size:74 final size:72
Alignment explanation
Indices: 9231908--9232593 Score: 946
Period size: 72 Copynumber: 9.6 Consensus size: 72
9231898 CTGTTTCAAA
*
9231908 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
*
9231973 TGTTGTC
66 TGTTTTC
*
9231980 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGATAATTTC-AT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG-TAATTTCAAT
9232044 TTCTGTTTTC
63 TTCTGTTTTC
*
9232054 --AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
9232117 TGTTTTC
66 TGTTTTC
* * ** * * *
9232124 AAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT-A-TTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
9232187 TGTCTTTC
66 TGT-TTTC
*
9232195 AAAAAATCAACTCATACTGC-AGAGGTGAGTTGAG-CTCA-GACACGCTGAGGTAATTTCAATTT
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
9232257 CTGTTGTT-
65 CTGTT-TTC
** * *
9232265 --AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
9232328 TGTTTTC
66 TGTTTTC
* ** * * * * *
9232335 AAAATTCAACTCATATTGCGAGAAATGAGTTAAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
9232400 TGTTTTTC
66 TG-TTTTC
* **
9232408 AAAAAATCAACTCATATTGAGAGAGGTGAGTTGAGCCTTGGGACACGCTGAGGTAATTTCAATTT
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
9232473 CTGTTTTC
65 CTGTTTTC
9232481 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GAGACACGCTGAGGTAATTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG-GACACGCTGAGGTAATTTCAATTT
9232545 CTGTTTTC
65 CTGTTTTC
*
9232553 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
9232594 ATCACACATG
Statistics
Matches: 551, Mismatches: 41, Indels: 40
0.87 0.06 0.06
Matches are distributed among these distances:
67 16 0.03
68 12 0.02
69 25 0.05
70 106 0.19
71 31 0.06
72 189 0.34
73 47 0.09
74 118 0.21
75 7 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (72 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
TGTTTTC
Found at i:9232274 original size:211 final size:212
Alignment explanation
Indices: 9231908--9232588 Score: 983
Period size: 211 Copynumber: 3.2 Consensus size: 212
9231898 CTGTTTCAAA
* ** * *
9231908 AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGT-ATTTCAATTTT
*
9231973 TGTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGATAA
65 TGTTTTC-AAAAAATCAACTCATATTGC-AGAGGTGAGTTGAGCCTC-GGACACGCTGAGG-TAA
*
9232038 TTTC-ATTTCTGTTTTCAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGA
126 TTTCAATTTCTGTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGA
9232102 GGTAATTTCAATTTCTGTTTTC
191 GGTAATTTCAATTTCTGTTTTC
* * *
9232124 AAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTA-TTCAATTTTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTCAATTTTT
* *
9232188 GTCTTTCAAAAAATCAACTCATACTGCAGAGGTGAGTTGAG-CTCAGACACGCTGAGGTAATTTC
66 GT-TTTCAAAAAATCAACTCATATTGCAGAGGTGAGTTGAGCCTCGGACACGCTGAGGTAATTTC
** * *
9232252 AATTTCTGTTGTT-AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACATGCTGAGGT
130 AATTTCTGTT-TTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGT
*
9232316 AATTTCAATTTTTGTTTTC
194 AATTTCAATTTCTGTTTTC
* * *
9232335 AAAATTCAACTCATATTGCGAGAAATGAGTTAAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTA-TTTCAATTTT
* *
9232400 TGTTTTTCAAAAAATCAACTCATATTGAGAGAGGTGAGTTGAGCCTTGGGACACGCTGAGGTAAT
65 TG-TTTTCAAAAAATCAACTCATATTG-CAGAGGTGAGTTGAGCC-TCGGACACGCTGAGGTAAT
*
9232465 TTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACGCTG
127 TTCAATTTCTGTTTT--AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTG
9232530 AGGTAATTTCAATTTCTGTTTTC
190 AGGTAATTTCAATTTCTGTTTTC
**
9232553 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 -AAAAATCAACTCATATTGCGAGAAATGAGTTGAGC
9232589 TTCAGATCAC
Statistics
Matches: 418, Mismatches: 34, Indels: 23
0.88 0.07 0.05
Matches are distributed among these distances:
210 7 0.02
211 136 0.33
212 5 0.01
213 47 0.11
214 45 0.11
215 7 0.02
216 76 0.18
218 64 0.15
219 31 0.07
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (212 bp):
AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTCAATTTTT
GTTTTCAAAAAATCAACTCATATTGCAGAGGTGAGTTGAGCCTCGGACACGCTGAGGTAATTTCA
ATTTCTGTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAA
TTTCAATTTCTGTTTTC
Found at i:9233509 original size:32 final size:31
Alignment explanation
Indices: 9233440--9233510 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
9233430 TTAAGCCCTC
*
9233440 CCAAAAAAAAACCTAACCCAAAAAAAAAGAA
1 CCAAGAAAAAACCTAACCCAAAAAAAAAGAA
** *
9233471 AAAAGAAAAAACCTAACCCCCCAAAAAAAA-AA
1 CCAAGAAAAAACCTAA--CCCAAAAAAAAAGAA
9233503 CCAAGAAA
1 CCAAGAAA
9233511 CCTTAGCCAC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
31 13 0.41
32 8 0.25
33 11 0.34
ACGTcount: A:0.69, C:0.24, G:0.04, T:0.03
Consensus pattern (31 bp):
CCAAGAAAAAACCTAACCCAAAAAAAAAGAA
Found at i:9233761 original size:13 final size:13
Alignment explanation
Indices: 9233743--9233767 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9233733 ATTTTACTCT
9233743 TTTTTTATTTTTA
1 TTTTTTATTTTTA
9233756 TTTTTTATTTTT
1 TTTTTTATTTTT
9233768 TTTCCTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:9233853 original size:11 final size:12
Alignment explanation
Indices: 9233818--9233855 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
9233808 AAAAGATATA
*
9233818 ATAAAAATATAT
1 ATAAAAATAAAT
9233830 ATACAAAATAAAT
1 ATA-AAAATAAAT
9233843 ATAAAAA-AAAT
1 ATAAAAATAAAT
9233854 AT
1 AT
9233856 TACCTTTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 6 0.25
12 7 0.29
13 11 0.46
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (12 bp):
ATAAAAATAAAT
Found at i:9234295 original size:11 final size:11
Alignment explanation
Indices: 9234264--9234306 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
9234254 AGTTTTTATC
*
9234264 ATATGTATA-T
1 ATATATATATT
*
9234274 ATGTATATATT
1 ATATATATATT
*
9234285 ATATTTATATT
1 ATATATATATT
9234296 ATATATATATT
1 ATATATATATT
9234307 CTTAATGTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 7 0.26
11 20 0.74
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (11 bp):
ATATATATATT
Found at i:9234361 original size:21 final size:23
Alignment explanation
Indices: 9234335--9234377 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
9234325 ATACTTCTTG
*
9234335 TATATT-TC-CATGTATATACTT
1 TATATTGTCTCATGTACATACTT
9234356 TATATTGTCTCATGTACATACT
1 TATATTGTCTCATGTACATACT
9234378 CCGAAATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 2 0.11
23 11 0.58
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (23 bp):
TATATTGTCTCATGTACATACTT
Found at i:9234716 original size:16 final size:15
Alignment explanation
Indices: 9234692--9234726 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
9234682 TAATTATTAT
9234692 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
9234708 TATTTTAATATTTTA
1 TATTCTAATATTTTA
9234723 TATT
1 TATT
9234727 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:9235556 original size:15 final size:15
Alignment explanation
Indices: 9235531--9235573 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
9235521 TCATATATAT
9235531 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
9235547 TATAAATTCAATCAA
1 TATAAATTCAATCAA
*
9235562 TATAATTTCAAT
1 TATAAATTCAAT
9235574 AAATTCATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.40
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:9235971 original size:51 final size:51
Alignment explanation
Indices: 9235890--9235999 Score: 177
Period size: 51 Copynumber: 2.2 Consensus size: 51
9235880 TTCTTCGTAC
*
9235890 TTCATCCGGAATTATTACTTTATTGTTCTAGCTTCAACAAGAACTTCATAT
1 TTCATCCGGAATTATTACTTTATTGCTCTAGCTTCAACAAGAACTTCATAT
* *
9235941 TTCATCCGG-ATATATTACTTTATTGCTCTAGTTTCAACAAGAGCTTCATAT
1 TTCATCCGGAAT-TATTACTTTATTGCTCTAGCTTCAACAAGAACTTCATAT
9235992 TTCATCCG
1 TTCATCCG
9236000 AATAACTTAG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 2 0.04
51 53 0.96
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (51 bp):
TTCATCCGGAATTATTACTTTATTGCTCTAGCTTCAACAAGAACTTCATAT
Found at i:9240880 original size:20 final size:20
Alignment explanation
Indices: 9240855--9240893 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
9240845 ATTAAGTGGA
9240855 TTTAATATT-GTCATATTTTT
1 TTTAATATTCGT-ATATTTTT
9240875 TTTAATATTCGTATATTTT
1 TTTAATATTCGTATATTTT
9240894 AATATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTAATATTCGTATATTTTT
Found at i:9249865 original size:38 final size:38
Alignment explanation
Indices: 9249793--9249872 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 38
9249783 ATGAGATGAT
*
9249793 ATAT-TATAAGATATGTTCTAACATGAAATTTGATATG
1 ATATGTATAAGATATGTTCTAACATGAAATCTGATATG
* *
9249830 ATATGTATAAGATATGTTTTGAA-ATGGAATCTGATATG
1 ATATGTATAAGATATGTTCT-AACATGAAATCTGATATG
*
9249868 CTATG
1 ATATG
9249873 ATACGTTCTG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 4 0.11
38 31 0.84
39 2 0.05
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (38 bp):
ATATGTATAAGATATGTTCTAACATGAAATCTGATATG
Found at i:9254832 original size:26 final size:26
Alignment explanation
Indices: 9254801--9254906 Score: 110
Period size: 26 Copynumber: 4.2 Consensus size: 26
9254791 CTTATGAGTA
**
9254801 TCCCGA-TAAATGGCTCTTCACGAGCT
1 TCCCGATTAAA-GGCTCTTCGTGAGCT
* *
9254827 TCCCGATTAAAGGCTTTTTGTGAGCT
1 TCCCGATTAAAGGCTCTTCGTGAGCT
* * *
9254853 TCCCTATTAAATGCTCTTTGTGAGCT
1 TCCCGATTAAAGGCTCTTCGTGAGCT
*
9254879 TCCCG-TTAAAGGTTCTTCG-GAGCT
1 TCCCGATTAAAGGCTCTTCGTGAGCT
9254903 TCCC
1 TCCC
9254907 AATATTGGCT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
24 9 0.13
25 11 0.16
26 44 0.65
27 4 0.06
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (26 bp):
TCCCGATTAAAGGCTCTTCGTGAGCT
Found at i:9269534 original size:22 final size:21
Alignment explanation
Indices: 9269500--9269540 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
9269490 GTCCTTCCAT
* *
9269500 TTTTTTATGATTTTCAATTAG
1 TTTTTTAAGATTTTAAATTAG
9269521 TTTTTTAAGTATTTTAAATT
1 TTTTTTAAG-ATTTTAAATT
9269541 GGCCCTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.63
Consensus pattern (21 bp):
TTTTTTAAGATTTTAAATTAG
Found at i:9269931 original size:19 final size:20
Alignment explanation
Indices: 9269907--9269944 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9269897 ATTATTAATA
9269907 ATTATT-TTTTTAAAACATT
1 ATTATTATTTTTAAAACATT
*
9269926 ATTATTATTTTTAATACAT
1 ATTATTATTTTTAAAACAT
9269945 GCATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTATTATTTTTAAAACATT
Found at i:9270290 original size:12 final size:12
Alignment explanation
Indices: 9270273--9270335 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
9270263 CTCTCTGTAT
9270273 TTACTTATATTA
1 TTACTTATATTA
9270285 TTACTTATATTA
1 TTACTTATATTA
*
9270297 TTA-TTGCTATTA
1 TTACTT-ATATTA
*
9270309 TCA-TTATGATTTA
1 TTACTTAT-A-TTA
9270322 TTACTT-TATTA
1 TTACTTATATTA
9270333 TTA
1 TTA
9270336 TCATTATTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
11 9 0.21
12 26 0.60
13 6 0.14
14 2 0.05
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (12 bp):
TTACTTATATTA
Found at i:9270298 original size:3 final size:3
Alignment explanation
Indices: 9270280--9270371 Score: 55
Period size: 3 Copynumber: 31.0 Consensus size: 3
9270270 TATTTACTTA
** * * *
9270280 TAT TAT TACT TA- TAT TAT TAT TGC TAT TAT CAT TAT GATT TAT TAC
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* * ** *
9270326 T-T TAT TAT TAT CAT TAT TAC TGC AAT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9270372 ATTTTTACTC
Statistics
Matches: 66, Mismatches: 18, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
2 5 0.08
3 56 0.85
4 5 0.08
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:9274838 original size:18 final size:19
Alignment explanation
Indices: 9274815--9274850 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9274805 AGGCTGTATG
9274815 TGTAAA-ATATTTATTTTA
1 TGTAAAGATATTTATTTTA
*
9274833 TGTAAAGATATTTGTTTT
1 TGTAAAGATATTTATTTT
9274851 TTAGTAGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (19 bp):
TGTAAAGATATTTATTTTA
Found at i:9282987 original size:50 final size:50
Alignment explanation
Indices: 9282908--9283093 Score: 183
Period size: 50 Copynumber: 3.8 Consensus size: 50
9282898 TGGTAAAACT
*
9282908 GCAAATCTTATAC-CCCTAAAGTTGCAGTGG-GTCAGATTGAAGTTACCATA
1 GCAAATCTTAT-CTCCCTAAAGTTGCAGTGGAG-CAGATTAAAGTTACCATA
* *
9282958 GCAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGTTACCATG
1 GCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGTTACCATA
* ** * * *
9283008 GCGAATCTTATCTCCCCGAAGTTACAATGGAGCAAATTAAAG----C-TA
1 GCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGTTACCATA
* *
9283053 -TAAATCTTATCTCCCTGAAA-TTGTAGTGGAGCAGATTAAAG
1 GCAAATCTTATCTCCCT-AAAGTTGCAGTGGAGCAGATTAAAG
9283094 CTATAAATCT
Statistics
Matches: 114, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
44 30 0.26
45 3 0.03
46 1 0.01
49 1 0.01
50 78 0.68
51 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (50 bp):
GCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGTTACCATA
Found at i:9283445 original size:44 final size:44
Alignment explanation
Indices: 9282903--9283443 Score: 360
Period size: 44 Copynumber: 12.0 Consensus size: 44
9282893 CATATTGGTA
* *
9282903 AAACTGCAAATCTTATAC-CCCTAAAGTTGCAGTGG-GTCAGATTG
1 AAACTACAAATCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATTG
* *
9282947 AAGTTACCATAGCAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATT-
1 AA---A-C-TA-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG
* * * * *
9282996 AAAGTTACCATGGCGAATCTTATCTCCCCGAAGTTACAATGGAGCAAATT-
1 AAA-CTA-CA-----AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG
* * *
9283046 AAAGCTATAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATT-
1 AAA-CTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG
* * * * *
9283090 AAAGCTATAAATCTTTTCTCCCTGAAGATGCAGTAGAGTGAGA-TG
1 AAA-CTACAAATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTG
* * * * *
9283135 AAACAACGAATCTTATCTCCCTAAAGTTGCAATTGAGCAGATTG
1 AAACTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG
* * * * * *
9283179 AAACTACAAATTTTATCTTCCTGAATTTGCAATGCAGTAGATTG
1 AAACTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG
* * * ** * *
9283223 AAAATATAAATCTTATCT-CCTGAAGATATAGTAGAGTGAGA-TG
1 AAACTACAAATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTG
* * * * *
9283266 AAACAACGAATCTTATCTCCCTAAAGTTGTAGTTGAGCAGATTG
1 AAACTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG
* * * *
9283310 AAACTACAAATCTTATCTCCCTAAAATTGCATTGGAGTAGATTG
1 AAACTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG
* * ** * *
9283354 AAACTACAAATCTTATTTTCCTGAAGTTATAGTAGAGCTGATTG
1 AAACTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG
* ** **
9283398 AAGCTATTAATCTTATCTTTCTGAAGTTGCAGTGGAGCAGATTG
1 AAACTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG
9283442 AA
1 AA
9283444 GCGATAATCC
Statistics
Matches: 389, Mismatches: 89, Indels: 38
0.75 0.17 0.07
Matches are distributed among these distances:
43 33 0.08
44 270 0.69
45 10 0.03
46 1 0.00
47 1 0.00
48 1 0.00
49 5 0.01
50 67 0.17
51 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (44 bp):
AAACTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG
Found at i:9283472 original size:132 final size:131
Alignment explanation
Indices: 9283009--9283443 Score: 408
Period size: 132 Copynumber: 3.3 Consensus size: 131
9282999 GTTACCATGG
** * * * * * * *
9283009 CGAATCTTATCTCCCCGAAGTTACAATGGAGCAAATT-AAAGCTATAAATCTTATCTCCCTGAAA
1 CGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAA-CGACAAATCCTATCTCCCTAAAA
* * * * * * * **
9283073 TTGTAGTGGAGCAGATT-AAAGCTATAAATCTTTTCTCCCTGAAGATGCAGTAGAGTGAGATGAA
65 TTGCAATGCAGTAGATTGAAA-ATACAAATCTTATCT-CCTGAAGATATAGTAGAGTGAGATGAA
9283137 ACAA
128 ACAA
* * * ** * * *
9283141 CGAATCTTATCTCCCTAAAGTTGCAATTGAGCAGATTGAAACTACAAATTTTATCTTCCTGAATT
1 CGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAACGACAAATCCTATCTCCCTAAAAT
*
9283206 TGCAATGCAGTAGATTGAAAATATAAATCTTATCTCCTGAAGATATAGTAGAGTGAGATGAAACA
66 TGCAATGCAGTAGATTGAAAATACAAATCTTATCTCCTGAAGATATAGTAGAGTGAGATGAAACA
9283271 A
131 A
* * * *
9283272 CGAATCTTATCTCCCTAAAGTTGTAGTTGAGCAGATTGAAACTACAAATCTTATCTCCCTAAAAT
1 CGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAACGACAAATCCTATCTCCCTAAAAT
* * * * * * *
9283337 TGCATTGGAGTAGATTGAAACTACAAATCTTATTTTCCTGAAGTTATAGTAGAGCTGA-TTGAAG
66 TGCAATGCAGTAGATTGAAAATACAAATCTTA-TCTCCTGAAGATATAGTAGAG-TGAGATGAAA
*
9283401 CTA
129 CAA
** ** *
9283404 TTAATCTTATCTTTCTGAAGTTGCAGTGGAGCAGATTGAA
1 CGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAA
9283444 GCGATAATCC
Statistics
Matches: 260, Mismatches: 39, Indels: 8
0.85 0.13 0.03
Matches are distributed among these distances:
131 116 0.45
132 135 0.52
133 9 0.03
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Consensus pattern (131 bp):
CGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAACGACAAATCCTATCTCCCTAAAAT
TGCAATGCAGTAGATTGAAAATACAAATCTTATCTCCTGAAGATATAGTAGAGTGAGATGAAACA
A
Found at i:9285041 original size:3 final size:3
Alignment explanation
Indices: 9285035--9285093 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
9285025 TTGTTGTTTG
* * * * **
9285035 TAT TAT TTT TAT TAT TAT CAT CAT TAT TAT TAT TATT TAT TTT TCC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
9285081 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
9285094 TAATTAGTAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:9293838 original size:45 final size:45
Alignment explanation
Indices: 9293783--9293908 Score: 148
Period size: 45 Copynumber: 2.8 Consensus size: 45
9293773 ATTCGCTTTA
* * * *
9293783 TTTTGTTGTGTACCCATAGCCATAGGCGGATTCCATGTACAGTGT
1 TTTTGCTGTGTATCCATAGCCATAGGCAGATTCCATCTACAGTGT
* * *
9293828 TTTTGCTGTGTATCCACAGCCATAGGCAGATTCCATCTGCGGTGT
1 TTTTGCTGTGTATCCATAGCCATAGGCAGATTCCATCTACAGTGT
* * *
9293873 TTTTACTGTGTGTCCATAGCCATTGGCAG-TT-CATCT
1 TTTTGCTGTGTATCCATAGCCATAGGCAGATTCCATCT
9293909 GCAAACCATT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
43 5 0.07
44 2 0.03
45 63 0.90
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (45 bp):
TTTTGCTGTGTATCCATAGCCATAGGCAGATTCCATCTACAGTGT
Found at i:9296844 original size:16 final size:19
Alignment explanation
Indices: 9296796--9296851 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 19
9296786 TTTAGTCATA
9296796 TAATAAATTATTAATATAAT
1 TAATAAATTATTAATAT-AT
9296816 TAATATAATTTATT-AT-T-T
1 TAATA-AA-TTATTAATATAT
9296834 TAATAAATTATTTAATAT
1 TAATAAATTA-TTAATAT
9296852 TTCAATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.10
17 4 0.13
18 8 0.26
19 1 0.03
20 6 0.19
21 4 0.13
22 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATAAATTATTAATATAT
Found at i:9296877 original size:13 final size:14
Alignment explanation
Indices: 9296861--9296902 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
9296851 TTTCAATTTT
9296861 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
9296874 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
9296889 ATTTTAAATAATAT
1 ATTTT-AATAATAT
9296903 TCTTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:9296887 original size:16 final size:16
Alignment explanation
Indices: 9296865--9296901 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
9296855 AATTTTATTT
9296865 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
9296882 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
9296897 TAATA
1 TAATA
9296902 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:9297037 original size:26 final size:27
Alignment explanation
Indices: 9297008--9297062 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
9296998 CTCTTCACAA
*
9297008 ATTTGC-AATTTAGTCTCTGTACTTTT
1 ATTTGCAAATTTAGTCTCTCTACTTTT
*
9297034 ATTTTCAAGAATTTAGTCTCTCTACTTTT
1 ATTTGC-A-AATTTAGTCTCTCTACTTTT
9297063 CAGATTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.21
29 19 0.79
ACGTcount: A:0.22, C:0.16, G:0.09, T:0.53
Consensus pattern (27 bp):
ATTTGCAAATTTAGTCTCTCTACTTTT
Found at i:9301018 original size:72 final size:72
Alignment explanation
Indices: 9300863--9301018 Score: 170
Period size: 72 Copynumber: 2.2 Consensus size: 72
9300853 TTTTATGATT
* * * * *
9300863 GATGGCTTGAG-TCCAGCATATGTTACGGATTCTTTGAAGGTTGTGTAAGCAACATCTAATCATT
1 GATGGCTTGAGATCCAGCATATGTTACGGATTCTCTAAAGCTTGTGTAAGAAACATCAAATCATT
* *
9300927 ATTTATT
66 ATCTATA
* * * * * * *
9300934 GATGTCTCGAGATCTAGCATGTGTTGCGGATTCTCTAAAGCTTGTGTGAGAAACATCAAATTATT
1 GATGGCTTGAGATCCAGCATATGTTACGGATTCTCTAAAGCTTGTGTAAGAAACATCAAATCATT
*
9300999 CTCTATA
66 ATCTATA
9301006 GATGGCTTGAGAT
1 GATGGCTTGAGAT
9301019 TCAACACTTA
Statistics
Matches: 67, Mismatches: 17, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
71 9 0.13
72 58 0.87
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (72 bp):
GATGGCTTGAGATCCAGCATATGTTACGGATTCTCTAAAGCTTGTGTAAGAAACATCAAATCATT
ATCTATA
Found at i:9307155 original size:48 final size:48
Alignment explanation
Indices: 9307083--9307464 Score: 326
Period size: 48 Copynumber: 8.0 Consensus size: 48
9307073 AGGGTAAATT
* * * * *
9307083 GCCGATGCCATGTCCTAGATATGGTCTTACACTGGCTCACATGTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAG
* * * *** *
9307131 GCCGATGCCATGTCCCAGACATGGTCTTACATTAGCCCTCGCCTCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAG
** * * * ** **
9307179 GCTAATACCATGTCCCAGACATGATTTTACACTAGCTTTCATA-CTGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATC-AAG
* * * *
9307227 GCTGATGCCATGCCCCA-AGCATGGTCTTACACTAGCACACATATCAAT
1 GCCGATGCCATGTCCCAGA-CATGGTCTTACACTAGCTCACATATCAAG
* * * *
9307275 GCCGATGCCATATCCCAGACATGGTCTTACACTGGCTCTCATAAT-ATG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCAAG
* * *
9307323 GTCGATGCCATGTCCCAGTCATGGTCTTACACTAG-TACACATATCAAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCT-CACATATCAAG
* * * *
9307371 ACCGATGCCATGTCCCAGATATGGTCTTACACTAGCTCTCATA--ATG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAG
* *
9307417 TGACTGATGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCA
1 -G-CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCA
9307465 CTCAATTGTC
Statistics
Matches: 259, Mismatches: 63, Indels: 22
0.75 0.18 0.06
Matches are distributed among these distances:
46 1 0.00
47 5 0.02
48 247 0.95
49 5 0.02
50 1 0.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAG
Found at i:9307254 original size:96 final size:96
Alignment explanation
Indices: 9307082--9307464 Score: 439
Period size: 96 Copynumber: 4.0 Consensus size: 96
9307072 GAGGGTAAAT
* * * * * * *
9307082 TGCCGATGCCATGTCCTAGATATGGTCTTACACTGGCTCACAT-GTCGAGGCCGATGCCATGTCC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAT-GTGGCTGATGCCATGTCC
* * * ***
9307146 CAGACATGGTCTTACATTAGCCCTCGCCTCAA
65 CAGACATGGTCTTACACTAGCACACATATCAA
** * * * * * *
9307178 TGCTAATACCATGTCCCAGACATGATTTTACACTAGCTTTCATACTGTGGCTGATGCCATGCCCC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGGCTGATGCCATGTCCC
9307243 A-AGCATGGTCTTACACTAGCACACATATCAA
66 AGA-CATGGTCTTACACTAGCACACATATCAA
* * *
9307274 TGCCGATGCCATATCCCAGACATGGTCTTACACTGGCTCTCATAATATGG-TCGATGCCATGTCC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGGCT-GATGCCATGTCC
* *
9307338 CAGTCATGGTCTTACACTAGTACACATATCAA
65 CAGACATGGTCTTACACTAGCACACATATCAA
** * *
9307370 CACCGATGCCATGTCCCAGATATGGTCTTACACTAGCTCTCATAATGTGACTGATGCCATGTCCC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGGCTGATGCCATGTCCC
*
9307435 AGACATGGTCTTACACTAGCGCACATATCA
66 AGACATGGTCTTACACTAGCACACATATCA
9307465 CTCAATTGTC
Statistics
Matches: 239, Mismatches: 43, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
95 2 0.01
96 235 0.98
97 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (96 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGGCTGATGCCATGTCCC
AGACATGGTCTTACACTAGCACACATATCAA
Found at i:9313202 original size:16 final size:15
Alignment explanation
Indices: 9313181--9313219 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
9313171 AACCTTAAGC
9313181 TTTCTTTTTACTTTTT
1 TTTCTTTTTA-TTTTT
9313197 TTTCTTTTTTATTTTT
1 TTTC-TTTTTATTTTT
*
9313213 CTTCTTT
1 TTTCTTT
9313220 GGTTGCTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 12 0.57
17 6 0.29
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTCTTTTTATTTTT
Found at i:9315057 original size:27 final size:27
Alignment explanation
Indices: 9315026--9315081 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
9315016 CTTCTTCAAA
9315026 TAGTGAACATTATGAAACCCTTTTGAT
1 TAGTGAACATTATGAAACCCTTTTGAT
9315053 TAGTGAACATTATGAAACCCTTTTGAT
1 TAGTGAACATTATGAAACCCTTTTGAT
9315080 TA
1 TA
9315082 CTTTCACTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (27 bp):
TAGTGAACATTATGAAACCCTTTTGAT
Found at i:9316794 original size:3 final size:3
Alignment explanation
Indices: 9316786--9316838 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
9316776 ATATGATCCT
* *
9316786 TTC TTC TTC TTC TTC TTC TT- TTGC TTT TTC TTT TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC
*
9316831 TCC TTC TT
1 TTC TTC TT
9316839 TTAATTTATG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:9317518 original size:5 final size:5
Alignment explanation
Indices: 9317508--9317584 Score: 136
Period size: 5 Copynumber: 15.4 Consensus size: 5
9317498 ATTTCTCGTA
* *
9317508 TATAT TATAT TATAT TATAC TATAC TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
9317558 TATAT TATAT TATAT TATAT TATAT TA
1 TATAT TATAT TATAT TATAT TATAT TA
9317585 CAAGGTTGTA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 70 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:9320211 original size:59 final size:60
Alignment explanation
Indices: 9320143--9320256 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 60
9320133 ACATTTTTTC
*
9320143 TTAATTTGGTACTTAAACTTAACACTTTTT-CTTAAATTAGTATTTAATCTTTTTGGAGT
1 TTAATTTGGTACTTAAACTTAACACTTTTTACTTAAATTAGTACTTAATCTTTTTGGAGT
* * * * * *
9320202 TTAATTTGGTACTTGAACTTGACTCTTTTTATTTAATTTGGTACTTAATCTTTTT
1 TTAATTTGGTACTTAAACTTAACACTTTTTACTTAAATTAGTACTTAATCTTTTT
9320257 TTTTTGTTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 27 0.57
60 20 0.43
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.54
Consensus pattern (60 bp):
TTAATTTGGTACTTAAACTTAACACTTTTTACTTAAATTAGTACTTAATCTTTTTGGAGT
Found at i:9329589 original size:13 final size:13
Alignment explanation
Indices: 9329571--9329620 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
9329561 TTCCCGAAAG
9329571 TTATTTTTTAATT
1 TTATTTTTTAATT
*
9329584 TTATTTTTGTAAAAT
1 TTATTTTT-T-AATT
* *
9329599 TTAATTTTTAATC
1 TTATTTTTTAATT
9329612 TTATTTTTT
1 TTATTTTTT
9329621 TTTTGTAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 18 0.60
14 2 0.07
15 10 0.33
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (13 bp):
TTATTTTTTAATT
Found at i:9336628 original size:27 final size:27
Alignment explanation
Indices: 9336598--9336670 Score: 76
Period size: 32 Copynumber: 2.5 Consensus size: 27
9336588 TGTCTTGAAT
9336598 TTGTTAGGTATTGATTATGTTTTAAGC
1 TTGTTAGGTATTGATTATGTTTTAAGC
*
9336625 TTGTTAGATATTGGATTTATTATGTTTTAAGC
1 TTGTTAGGTATT-G----ATTATGTTTTAAGC
9336657 TTGTT-GGATATTGA
1 TTGTTAGG-TATTGA
9336671 AATGATTGAC
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
27 12 0.32
28 1 0.03
31 2 0.05
32 23 0.61
ACGTcount: A:0.23, C:0.03, G:0.22, T:0.52
Consensus pattern (27 bp):
TTGTTAGGTATTGATTATGTTTTAAGC
Found at i:9358089 original size:47 final size:47
Alignment explanation
Indices: 9358020--9358114 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
9358010 TACTAGGCTC
9358020 AACACGTTTAAAAAAAGACCTTATATTTTGTCCAAGCTCATTTGTTG
1 AACACGTTTAAAAAAAGACCTTATATTTTGTCCAAGCTCATTTGTTG
9358067 AACACGTTTAAAAAAAGACCTTATATTTTGTCCAAGCTCATTTGTTG
1 AACACGTTTAAAAAAAGACCTTATATTTTGTCCAAGCTCATTTGTTG
9358114 A
1 A
9358115 GTCCATATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.36
Consensus pattern (47 bp):
AACACGTTTAAAAAAAGACCTTATATTTTGTCCAAGCTCATTTGTTG
Found at i:9363958 original size:30 final size:30
Alignment explanation
Indices: 9363923--9363986 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
9363913 CAAAACAGGT
* *
9363923 TGAGAAGATTGTAGGGTTGATGAAGGTGCA
1 TGAGAAGATTGGACGGTTGATGAAGGTGCA
*
9363953 TGAGAAGATTGGACTGTTGATGAAGGTGCA
1 TGAGAAGATTGGACGGTTGATGAAGGTGCA
9363983 TGAG
1 TGAG
9363987 CTGTCAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.05, G:0.39, T:0.27
Consensus pattern (30 bp):
TGAGAAGATTGGACGGTTGATGAAGGTGCA
Found at i:9368032 original size:24 final size:28
Alignment explanation
Indices: 9367978--9368032 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
9367968 CATAATTTTT
* *
9367978 TAATTAAACTAATAATTATGTTTTCGTA
1 TAATTAAACAAATAATTATGTTTTCGAA
9368006 TAATTAAA-AAATAA-TAT-TTTTC-AA
1 TAATTAAACAAATAATTATGTTTTCGAA
9368030 TAA
1 TAA
9368033 AATTGTAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 4 0.16
25 5 0.20
26 3 0.12
27 5 0.20
28 8 0.32
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (28 bp):
TAATTAAACAAATAATTATGTTTTCGAA
Found at i:9388642 original size:13 final size:13
Alignment explanation
Indices: 9388624--9388648 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9388614 TATATGATAT
9388624 GTGTGAAAATTTC
1 GTGTGAAAATTTC
9388637 GTGTGAAAATTT
1 GTGTGAAAATTT
9388649 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:9392500 original size:23 final size:23
Alignment explanation
Indices: 9392474--9392519 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
9392464 TTAACCAATT
9392474 TAAAATGAGTTACAACTGTCAAA
1 TAAAATGAGTTACAACTGTCAAA
9392497 TAAAATGAGTTACAACTGTCAAA
1 TAAAATGAGTTACAACTGTCAAA
9392520 AGGAGAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (23 bp):
TAAAATGAGTTACAACTGTCAAA
Found at i:9395464 original size:18 final size:18
Alignment explanation
Indices: 9395441--9395477 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
9395431 CTTGGCCCAT
*
9395441 TGTAGTAACAGTAATCAG
1 TGTAGTAACAGTAAACAG
*
9395459 TGTAGTAATAGTAAACAG
1 TGTAGTAACAGTAAACAG
9395477 T
1 T
9395478 ATGCAAATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
TGTAGTAACAGTAAACAG
Found at i:9395884 original size:27 final size:27
Alignment explanation
Indices: 9395826--9395925 Score: 105
Period size: 27 Copynumber: 3.7 Consensus size: 27
9395816 GGGTAAGCAG
* *
9395826 TCATTTTACCTTATAAGGGCAAAACCAA
1 TCATTTTACCTCATAAGGGCAAAA-AAA
***
9395854 -CATTTTACCTCATAAGGGCAAAATTG
1 TCATTTTACCTCATAAGGGCAAAAAAA
* *
9395880 TCATTTTATCACATAAGGGCAAAAAAA
1 TCATTTTACCTCATAAGGGCAAAAAAA
9395907 TCATTTT-CTCTCATAAGGG
1 TCATTTTAC-CTCATAAGGG
9395926 TTCAGGTACG
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (27 bp):
TCATTTTACCTCATAAGGGCAAAAAAA
Done.