Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009617.1 Hibiscus syriacus cultivar Beakdansim tig00117005_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: 3386631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 16
Found at i:498915 original size:23 final size:22
Alignment explanation
Indices: 498867--498915 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
498857 TTAGAATGTC
498867 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
498888 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
498911 AAGGA
1 AAGGA
498916 AAAATGTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:499864 original size:31 final size:31
Alignment explanation
Indices: 499826--499936 Score: 143
Period size: 31 Copynumber: 3.6 Consensus size: 31
499816 GGGTCGAGGG
* *
499826 TTTACCTATGTTCTTTGGGACATATATACTA
1 TTTACCTATGTTCTTCGGGACATATAGACTA
* *
499857 TTTACCTATGTTCTTCGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATAGACTA
* *
499888 TTTACCTATGTTCTTCGGGATATATGGACTGA
1 TTTACCTATGTTCTTCGGGACATATAGACT-A
*
499920 -TTACCTAGGTTCTTCGG
1 TTTACCTATGTTCTTCGG
499937 AATCTATGGA
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATAGACTA
Found at i:499924 original size:62 final size:62
Alignment explanation
Indices: 499825--499949 Score: 164
Period size: 62 Copynumber: 2.0 Consensus size: 62
499815 AGGGTCGAGG
* * * *
499825 GTTTACCTATGTTCTTTGGGACATATATACTATTTACCTATGTTCTTCGGGA-CATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATAGACTATTTACCTAGGTTCTTCGGAATC-TATGGACT
* *
499887 GTTTACCTATGTTCTTCGGGATATATGGACTGA-TTACCTAGGTTCTTCGGAATCTATGGACT
1 GTTTACCTATGTTCTTCGGGACATATAGACT-ATTTACCTAGGTTCTTCGGAATCTATGGACT
499949 G
1 G
499950 GTCCTTCGGG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
62 53 0.96
63 2 0.04
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATAGACTATTTACCTAGGTTCTTCGGAATCTATGGACT
Found at i:499945 original size:31 final size:31
Alignment explanation
Indices: 499827--499949 Score: 135
Period size: 31 Copynumber: 4.0 Consensus size: 31
499817 GGTCGAGGGT
* **
499827 TTACCTATGTTCTTTGGGA-CATATATACT-A
1 TTACCTATGTTCTTCGGGATC-TATGGACTGA
*
499857 TTTACCTATGTTCTTCGGGA-CATATGGACTGT
1 -TTACCTATGTTCTTCGGGATC-TATGGACTGA
*
499889 TTACCTATGTTCTTCGGGATATATGGACTGA
1 TTACCTATGTTCTTCGGGATCTATGGACTGA
* *
499920 TTACCTAGGTTCTTCGGAATCTATGGACTG
1 TTACCTATGTTCTTCGGGATCTATGGACTG
499950 GTCCTTCGGG
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
31 81 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGATCTATGGACTGA
Found at i:503217 original size:23 final size:22
Alignment explanation
Indices: 503169--503217 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
503159 ACAGAATGTC
503169 AAGG-GGGAACCGATACCCCTA
1 AAGGAGGGAACCGATACCCCTA
* *
503190 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGA-TACCCCTA
503213 AAGGA
1 AAGGA
503218 AAAATGTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 9 0.39
23 11 0.48
ACGTcount: A:0.33, C:0.29, G:0.29, T:0.10
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCTA
Found at i:504191 original size:31 final size:31
Alignment explanation
Indices: 504117--504301 Score: 277
Period size: 31 Copynumber: 6.0 Consensus size: 31
504107 AGGGTCGAGG
*
504117 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
504148 G-TTACCTA-GTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
504177 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
504208 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
504239 GTTTACCTATGTTCTTCGGGACATATGGAAT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
504270 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
504301 G
1 G
504302 GTCCTTCGGG
Statistics
Matches: 141, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
29 20 0.14
30 14 0.10
31 106 0.75
32 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:508961 original size:37 final size:37
Alignment explanation
Indices: 508918--509025 Score: 144
Period size: 37 Copynumber: 2.9 Consensus size: 37
508908 AGAATAACGT
* * *
508918 TAGAGTTTTACTAGGATTCGAGCTCTTAAAAATAAGA
1 TAGAGTTTTACTATGATTCGAACTCCTAAAAATAAGA
* *
508955 TAGAGTTTTACTATGACTCGAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCGAACTCCTAAAAATAAGA
* * *
508992 TAAAGTTATACTATGATTCAAACTCCTAAAAATA
1 TAGAGTTTTACTATGATTCGAACTCCTAAAAATA
509026 TGATCTACAA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCGAACTCCTAAAAATAAGA
Found at i:509647 original size:4 final size:4
Alignment explanation
Indices: 509638--509814 Score: 73
Period size: 4 Copynumber: 42.5 Consensus size: 4
509628 TTTTTATGCT
* * *
509638 TTTA TTTA TTATA TATA TATTA -TT- TTTA TTTG TTTA TTTTA TTTG TTTA
1 TTTA TTTA TT-TA TTTA T-TTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA
* *
509687 TTTTA TTTA TATA TTT- TTTA TTCT- TTT- TTTA TATA TTT- TTTA TTTA
1 -TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * *
509733 TTTTA CTTA CTAA TTTA TCTTTA CTTTC TTTA TCTTA TCT- TTTA TTTAA
1 -TTTA TTTA TTTA TTTA --TTTA -TTTA TTTA T-TTA TTTA TTTA TTT-A
509782 TTTA TTT- TTCTCA TTTAA TTTTA TTTA TTTA TT
1 TTTA TTTA TT-T-A TTT-A -TTTA TTTA TTTA TT
509815 ATTCTACATT
Statistics
Matches: 134, Mismatches: 19, Indels: 40
0.69 0.10 0.21
Matches are distributed among these distances:
3 18 0.13
4 74 0.55
5 33 0.25
6 9 0.07
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:509678 original size:37 final size:36
Alignment explanation
Indices: 509570--509731 Score: 102
Period size: 37 Copynumber: 4.4 Consensus size: 36
509560 AGATTACATA
* * * * *
509570 TATATATATGTTATTTTTTATTATCTGTTTTATTAAT
1 TATATATATATTA-TTTTTATTTTTTATTTTATTTAT
*
509607 T-TATATATATATATTTACTATTTTTTATGCTTTTATTTAT
1 TATATATATAT-TATTT-TTATTTTTTA---TTTTATTTAT
*
509647 TATATATATATTATTTTTATTTGTTTATTTTATTTGT
1 TATATATATATTATTTTTATTT-TTTATTTTATTTAT
* * *
509684 T-TAT-TTTATT-TATATATTTTTTATTCTT-TTT-T
1 TATATATATATTATTTTTATTTTTTATT-TTATTTAT
* *
509716 TATATATTTTTTATTT
1 TATATATATATTATTT
509732 ATTTTACTTA
Statistics
Matches: 101, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
32 2 0.02
33 12 0.12
34 14 0.14
35 7 0.07
36 14 0.14
37 19 0.19
39 5 0.05
40 19 0.19
41 9 0.09
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (36 bp):
TATATATATATTATTTTTATTTTTTATTTTATTTAT
Found at i:509687 original size:41 final size:38
Alignment explanation
Indices: 509567--509713 Score: 109
Period size: 41 Copynumber: 3.6 Consensus size: 38
509557 TTTAGATTAC
*
509567 ATATATATATATGTTATT-TTTTATTAT-CTGTTTTATTAATTT
1 ATATATATATAT-TT-TTATTTT-TTATGC--TTTTATTTA-TT
*
509609 ATATATATATATTTACTATTTTTTATGCTTTTATTTATT
1 ATATATATATATTT-TTATTTTTTATGCTTTTATTTATT
** *
509648 ATATATATATTATTTTTATTTGTTTATTTTATTTGTTTATT
1 ATATATATA-TATTTTTATTT-TTTATGCT-TTTATTTATT
* *
509689 TTATTTATATATTTTTTATTCTTTT
1 ATATATATATA-TTTTTATT-TTTT
509714 TTTATATATT
Statistics
Matches: 90, Mismatches: 8, Indels: 15
0.80 0.07 0.13
Matches are distributed among these distances:
39 16 0.18
40 21 0.23
41 35 0.39
42 18 0.20
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (38 bp):
ATATATATATATTTTTATTTTTTATGCTTTTATTTATT
Found at i:509701 original size:13 final size:13
Alignment explanation
Indices: 509638--509814 Score: 88
Period size: 13 Copynumber: 13.8 Consensus size: 13
509628 TTTTTATGCT
*
509638 TTTATTTATTATA
1 TTTATTTATTTTA
*
509651 TATATATTATTTTTA
1 TTTAT-TTA-TTTTA
*
509666 TTTGTTTATTTTA
1 TTTATTTATTTTA
*
509679 TTTGTTTATTTTA
1 TTTATTTATTTTA
*
509692 TTTATATA-TTT-
1 TTTATTTATTTTA
*
509703 TTTA-TTCTTTT-
1 TTTATTTATTTTA
*
509714 TTTATATA-TTT-
1 TTTATTTATTTTA
509725 TTTATTTATTTTA
1 TTTATTTATTTTA
509738 CTTACTAATTTATCTTTA
1 -TT--T-ATTTAT-TTTA
* *
509756 CTTTCTTTATCTTA
1 -TTTATTTATTTTA
* *
509770 TCT-TTTATTTAA
1 TTTATTTATTTTA
*
509782 TTTATTT-TTCTCA
1 TTTATTTATT-TTA
509795 TTTA---ATTTTA
1 TTTATTTATTTTA
509805 TTTATTTATT
1 TTTATTTATT
509815 ATTCTACATT
Statistics
Matches: 128, Mismatches: 19, Indels: 34
0.71 0.10 0.19
Matches are distributed among these distances:
10 7 0.05
11 23 0.18
12 18 0.14
13 42 0.33
14 11 0.09
15 12 0.09
16 2 0.02
17 6 0.05
18 7 0.05
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.71
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:509717 original size:22 final size:23
Alignment explanation
Indices: 509687--509730 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
509677 TATTTGTTTA
509687 TTTTATTTATATATTTTTTATTC
1 TTTTATTTATATATTTTTTATTC
509710 TTTT-TTTATATATTTTTTATT
1 TTTTATTTATATATTTTTTATT
509731 TATTTTACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTATTTATATATTTTTTATTC
Found at i:509733 original size:41 final size:43
Alignment explanation
Indices: 509567--509735 Score: 122
Period size: 42 Copynumber: 4.0 Consensus size: 43
509557 TTTAGATTAC
* * * *
509567 ATATATA-TATATGTTATTT-TTTATTATCTGTTTTATTAATTT
1 ATATATATTAT-TTTTATTTGTTTATTATATTTTTTATTTATTT
* * **
509609 ATATATA-TATATTTACTAT-TTT-TTAT-GCTTTTATTTATTAT
1 ATATATATTATTTTTA-TTTGTTTATTATATTTTTTATTTATT-T
*
509650 ATATATATTATTTTTATTTGTTTATTTTATTTGTTTATTTTATTT
1 ATATATATTATTTTTATTTGTTTATTATATTT-TTTA-TTTATTT
* *
509695 ATATAT-TT-TTTATTCTTTTTTTA-TATATTTTTTATTTATTT
1 ATATATATTATTT-TTATTTGTTTATTATATTTTTTATTTATTT
509736 TACTTACTAA
Statistics
Matches: 104, Mismatches: 14, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
40 10 0.10
41 24 0.23
42 29 0.28
43 12 0.12
44 12 0.12
45 11 0.11
46 6 0.06
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.69
Consensus pattern (43 bp):
ATATATATTATTTTTATTTGTTTATTATATTTTTTATTTATTT
Found at i:509736 original size:9 final size:9
Alignment explanation
Indices: 509637--509811 Score: 55
Period size: 9 Copynumber: 19.3 Consensus size: 9
509627 TTTTTTATGC
509637 TTTTATTTA
1 TTTTATTTA
* *
509646 TTATATATA
1 TTTTATTTA
* *
509655 TATTATTTT
1 TTTTATTTA
*
509664 TATTTGTTTA
1 T-TTTATTTA
509674 TTTTATTT-
1 TTTTATTTA
*
509682 GTTTATTT-
1 TTTTATTTA
*
509690 TATTTATATA
1 T-TTTATTTA
509700 -TTT-TTTA
1 TTTTATTTA
509707 TTCTT-TTT-
1 TT-TTATTTA
*
509715 TTATATATT-
1 TTTTAT-TTA
509724 TTTTATTTA
1 TTTTATTTA
*
509733 TTTTACTTA
1 TTTTATTTA
* *
509742 -CTAATTTA
1 TTTTATTTA
509750 TCTTTACTTT-
1 T-TTTA-TTTA
*
509760 CTTTATCTTA
1 TTTTAT-TTA
509770 TCTTTTATTTA
1 --TTTTATTTA
*
509781 ATTTATTT-
1 TTTTATTTA
*
509789 TTCTCATTTAA
1 TT-TTATTT-A
509800 TTTTATTTA
1 TTTTATTTA
509809 TTT
1 TTT
509812 ATTATTCTAC
Statistics
Matches: 120, Mismatches: 28, Indels: 36
0.65 0.15 0.20
Matches are distributed among these distances:
7 4 0.03
8 23 0.19
9 67 0.56
10 13 0.11
11 8 0.07
12 5 0.04
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.71
Consensus pattern (9 bp):
TTTTATTTA
Found at i:509819 original size:27 final size:29
Alignment explanation
Indices: 509772--509825 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
509762 TTATCTTATC
*
509772 TTTTATTTAATTTATTTTTCT-CATTTAA
1 TTTTATTTAATTTATTATTCTACATTTAA
509800 TTTTATTT-ATTTATTATTCTACATTT
1 TTTTATTTAATTTATTATTCTACATTT
509826 TTATCTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (29 bp):
TTTTATTTAATTTATTATTCTACATTTAA
Found at i:515623 original size:28 final size:28
Alignment explanation
Indices: 515583--515640 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
515573 ATTTTCACCT
515583 AACTAAATTGATGTAAGCAATGACATCA
1 AACTAAATTGATGTAAGCAATGACATCA
515611 AACTAAATTGATGTAAGCAATGACATCA
1 AACTAAATTGATGTAAGCAATGACATCA
515639 AA
1 AA
515641 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (28 bp):
AACTAAATTGATGTAAGCAATGACATCA
Found at i:520299 original size:29 final size:29
Alignment explanation
Indices: 520257--520315 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
520247 ATTTTCACCT
520257 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
520286 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
520315 A
1 A
520316 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:529798 original size:21 final size:21
Alignment explanation
Indices: 529772--530195 Score: 265
Period size: 21 Copynumber: 21.1 Consensus size: 21
529762 CAACTCGATT
529772 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
** *
529793 TTGCGATTTTCCAA-AT----
1 TTGCGATAGTCCAAGTTCGCG
* * *
529809 TTACGTTAGTCCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCG
**
529828 TTGCGATAGTCCAAGTTTACG
1 TTGCGATAGTCCAAGTTCGCG
* **
529849 TTGAGATAGTTGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* ** *
529870 TTGCAATTTTCCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCG
*
529889 TTGCGATAGTCCAAGTTCACG
1 TTGCGATAGTCCAAGTTCGCG
** * *
529910 TTGCGATTTTACAAATT--CG
1 TTGCGATAGTCCAAGTTCGCG
** *
529929 TTGCGATAGTAGAAGTTCGGG
1 TTGCGATAGTCCAAGTTCGCG
* *
529950 TTGCAATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
** * *
529971 TTGCGATTTTTCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCG
* *
529990 TTGCGATATTCCAAGTTCACG
1 TTGCGATAGTCCAAGTTCGCG
** * *
530011 TTGCGATTTTTCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCG
* *
530030 TTGCGATAATCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
** *
530051 TTGCGATTTTCCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCG
* *
530070 TTGCTATAGTCCAAGTTCGTG
1 TTGCGATAGTCCAAGTTCGCG
*
530091 TTGCGATAGTCCAAGTTCGTG
1 TTGCGATAGTCCAAGTTCGCG
*
530112 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* *
530133 TTGCGATAGTCGAAATTCGCG
1 TTGCGATAGTCCAAGTTCGCG
** *
530154 TTGCGATTTTCCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCG
*
530173 TTGCGATAGTCCAAGTTCACG
1 TTGCGATAGTCCAAGTTCGCG
530194 TT
1 TT
530196 CGAAGTTCGC
Statistics
Matches: 311, Mismatches: 75, Indels: 34
0.74 0.18 0.08
Matches are distributed among these distances:
16 10 0.03
17 1 0.00
19 105 0.34
20 1 0.00
21 194 0.62
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCG
Found at i:529898 original size:40 final size:40
Alignment explanation
Indices: 529847--529956 Score: 148
Period size: 40 Copynumber: 2.8 Consensus size: 40
529837 TCCAAGTTTA
* * *
529847 CGTTGAGATAGTTGAAGTTCGCGTTGCAATTTTCCAAATT
1 CGTTGCGATAGTAGAAGTTCGCGTTGCAATTTTACAAATT
** * *
529887 CGTTGCGATAGTCCAAGTTCACGTTGCGATTTTACAAATT
1 CGTTGCGATAGTAGAAGTTCGCGTTGCAATTTTACAAATT
*
529927 CGTTGCGATAGTAGAAGTTCGGGTTGCAAT
1 CGTTGCGATAGTAGAAGTTCGCGTTGCAAT
529957 AGTCGAAGTT
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.35
Consensus pattern (40 bp):
CGTTGCGATAGTAGAAGTTCGCGTTGCAATTTTACAAATT
Found at i:529953 original size:61 final size:61
Alignment explanation
Indices: 529772--530375 Score: 383
Period size: 61 Copynumber: 10.1 Consensus size: 61
529762 CAACTCGATT
* * *
529772 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAA-T--TTACGTTAGTCCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
** * * * * * ** *
529828 TTGCGATAGTCCAAGTTTACGTTGAGATAGTT-GAAGTTCGCGTTGCAATTTTCCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCGTTGCGAT-TTTCCAAATT--CGTTGCGATAGTCCAAGTTCGCG
* * ** *
529889 TTGCGATAGTCCAAGTTCACGTTGCGATTTTACAAATTCGTTGCGATAGTAGAAGTTCGGG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
* * * * *
529950 TTGCAATAGTCGAAGTTCGCGTTGCGATTTTTCAAATTCGTTGCGATATTCCAAGTTCACG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
** * * ** * * ** *
530011 TTGCGATTTTTCAAATT--CGTTGCGATAATCGAAGTTCGCGTTGCGATTTTCCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT--CGTTGCGATAGTCCAAGTTCGCG
* * ** * *
530070 TTGCTATAGTCCAAGTTCGTGTTGCGATAGTCCAAGTTCGTGTTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTC--GTTGCGATAGTCCAAGTTCGCG
* * *
530133 TTGCGATAGTCGAAATTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCACG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
* * *
530194 TT-C----G---AAGTTCGCGTTGCGATTTTCAAAATTCGTTGCGATAGTCTAAGTTCACG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
** * ** *
530247 TTGCGATTTTCCAAATT--CGTTGCGATAGTCCAAGTTCGTGTTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTC--GTTGCGATAGTCCAAGTTCGCG
** * ** * * * **
530308 TTGCGATTTTCCAAATT--CGTTGCGATAGTCCAAGTTCACGTTGCGATAATCGAAGTTCGTA
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT--CGTTGCGATAGTCCAAGTTCGCG
530369 TTGCGAT
1 TTGCGAT
530376 TTTTCAAATT
Statistics
Matches: 438, Mismatches: 81, Indels: 53
0.77 0.14 0.09
Matches are distributed among these distances:
53 48 0.11
54 1 0.00
56 28 0.06
57 3 0.01
59 58 0.13
60 3 0.01
61 262 0.60
63 35 0.08
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (61 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
Found at i:530006 original size:40 final size:40
Alignment explanation
Indices: 529949--530423 Score: 412
Period size: 40 Copynumber: 11.9 Consensus size: 40
529939 AGAAGTTCGG
* * *
529949 GTTGCAATAGTCGAAGTTCGCGTTGCGATTTTTCAAATTC
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTC
* * *
529989 GTTGCGATATTCCAAGTTCACGTTGCGATTTTTCAAATTC
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTC
* *
530029 GTTGCGATAATCGAAGTTCGCGTTGCGATTTTCCAAATTC
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTC
* * ** *
530069 GTTGCTATAGTCCAAGTTCGTGTTGCGATAGTCCAAGTTC
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTC
* ** *
530109 GTGTTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAATTCGC
1 --GTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT--C
** * ** *
530153 GTTGCGATTTTCCAAATT--CGTTGCGATAGTCCAAGTTC
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTC
* * *
530191 ---ACG-T--TCGAAGTTCGCGTTGCGATTTTCAAAATTC
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTC
* *
530225 GTTGCGATAGTCTAAGTTCACGTTGCGATTTTCCAAATTC
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTC
* ** *
530265 GTTGCGATAGTCCAAGTTCGTGTTGCGATAGTCCAAGTTCGC
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT--C
** * ** *
530307 GTTGCGATTTTCCAAATT--CGTTGCGATAGTCCAAGTTCAC
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT--C
* * ** *
530347 GTTGCGATAATCGAAGTTCGTATTGCGATTTTTCAAATTC
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTC
*
530387 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAA
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAA
530424 ATCGCAACGA
Statistics
Matches: 357, Mismatches: 62, Indels: 32
0.79 0.14 0.07
Matches are distributed among these distances:
32 6 0.02
34 17 0.05
35 2 0.01
37 2 0.01
38 2 0.01
40 250 0.70
42 77 0.22
44 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (40 bp):
GTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTC
Found at i:530223 original size:53 final size:53
Alignment explanation
Indices: 530142--530248 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
530132 GTTGCGATAG
*
530142 TCGAAATTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCACGT
1 TCGAAATTCGCGTTGCGATTTTCAAAATTCGTTGCGATAGTCCAAGTTCACGT
* *
530195 TCGAAGTTCGCGTTGCGATTTTCAAAATTCGTTGCGATAGTCTAAGTTCACGT
1 TCGAAATTCGCGTTGCGATTTTCAAAATTCGTTGCGATAGTCCAAGTTCACGT
530248 T
1 T
530249 GCGATTTTCC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (53 bp):
TCGAAATTCGCGTTGCGATTTTCAAAATTCGTTGCGATAGTCCAAGTTCACGT
Found at i:530250 original size:21 final size:20
Alignment explanation
Indices: 530224--530415 Score: 158
Period size: 21 Copynumber: 9.4 Consensus size: 20
530214 TTTCAAAATT
*
530224 CGTTGCGATAGTCTAAGTTC
1 CGTTGCGATAGTCCAAGTTC
** *
530244 ACGTTGCGATTTTCCAAATT-
1 -CGTTGCGATAGTCCAAGTTC
530264 CGTTGCGATAGTCCAAGTTC
1 CGTTGCGATAGTCCAAGTTC
*
530284 GTGTTGCGATAGTCCAAGTTC
1 -CGTTGCGATAGTCCAAGTTC
** *
530305 GCGTTGCGATTTTCCAAATT-
1 -CGTTGCGATAGTCCAAGTTC
530325 CGTTGCGATAGTCCAAGTTC
1 CGTTGCGATAGTCCAAGTTC
* *
530345 ACGTTGCGATAATCGAAGTT-
1 -CGTTGCGATAGTCCAAGTTC
** * *
530365 CGTATTGCGATTTTTCAAATT-
1 CG--TTGCGATAGTCCAAGTTC
*
530386 CGTTGCGATAGTCGAAGTTC
1 CGTTGCGATAGTCCAAGTTC
530406 GCGTTGCGAT
1 -CGTTGCGAT
530416 TTTCCAAAAT
Statistics
Matches: 136, Mismatches: 27, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
19 46 0.34
21 90 0.66
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCCAAGTTC
Found at i:530253 original size:196 final size:194
Alignment explanation
Indices: 530002--530354 Score: 555
Period size: 196 Copynumber: 1.8 Consensus size: 194
529992 GCGATATTCC
*
530002 AAGTTCACGTTGCGATTTTTCAAATTCGTTGCGATAATCGAAGTTCGCGTTGCGATTTTCCAAAT
1 AAGTTCACGTTGCGATTTTTCAAATTCGTTGCGATAATCGAAGTTCACGTTGCGATTTTCCAAAT
* * * *
530067 TCGTTGCTATAGTCCAAGTTCGTGTTGCGATAGTCCAAGTTCGTGTTGCGATAGTCGAAGTTCGC
66 TCGTTGCGATAGTCCAAGTTCGTGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAATT--C
* *
530132 GTTGCGATAGTCGAAATTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTC
129 GTTGCGATAGTCCAAATTCACGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTC
530197 G
194 G
* * *
530198 AAGTTCGCGTTGCGA-TTTTCAAAATTCGTTGCGATAGTCTAAGTTCACGTTGCGATTTTCCAAA
1 AAGTTCACGTTGCGATTTTTC-AAATTCGTTGCGATAATCGAAGTTCACGTTGCGATTTTCCAAA
**
530262 TTCGTTGCGATAGTCCAAGTTCGTGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
65 TTCGTTGCGATAGTCCAAGTTCGTGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAATTCG
*
530327 TTGCGATAGTCCAAGTTCACGTTGCGAT
130 TTGCGATAGTCCAAATTCACGTTGCGAT
530355 AATCGAAGTT
Statistics
Matches: 143, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
194 27 0.19
195 5 0.03
196 111 0.78
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (194 bp):
AAGTTCACGTTGCGATTTTTCAAATTCGTTGCGATAATCGAAGTTCACGTTGCGATTTTCCAAAT
TCGTTGCGATAGTCCAAGTTCGTGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAATTCGT
TGCGATAGTCCAAATTCACGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTCG
Found at i:530260 original size:74 final size:73
Alignment explanation
Indices: 530121--530349 Score: 208
Period size: 74 Copynumber: 3.0 Consensus size: 73
530111 GTTGCGATAG
* **
530121 TCGAAGTTCGCGTTGCGATAGTCGAAATTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCA
1 TCGAAGTTCGCGTTGCGATAGTCAAAATTC-CGTTGCGATAGTCCAAATTCGTTGCGATAGTCCA
530186 AGTTCACGT
65 AGTTCACGT
** * * **
530195 TCGAAGTTCGCGTTGCGATTTTCAAAATT-CGTTGCGATAGTCTAAGTTCACGTTGCGATTTTCC
1 TCGAAGTTCGCGTTGCGATAGTCAAAATTCCGTTGCGATAGTCCAAATT--CGTTGCGATAGTCC
* *
530259 AAATTCGTTGCGAT
64 AAGTTC---ACG-T
* * * * **
530273 AGTCCAAGTTCGTGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTC
1 --TCGAAGTTCGCGTTGCGATAGTCAAAATTC-CGTTGCGATAGTCCAAATTCGTTGCGATAGTC
530338 CAAGTTCACGT
63 CAAGTTCACGT
530349 T
1 T
530350 GCGATAATCG
Statistics
Matches: 120, Mismatches: 25, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
72 15 0.12
74 44 0.37
76 1 0.01
77 4 0.03
78 1 0.01
80 40 0.33
82 15 0.12
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (73 bp):
TCGAAGTTCGCGTTGCGATAGTCAAAATTCCGTTGCGATAGTCCAAATTCGTTGCGATAGTCCAA
GTTCACGT
Found at i:530376 original size:61 final size:61
Alignment explanation
Indices: 529988--530415 Score: 394
Period size: 61 Copynumber: 7.1 Consensus size: 61
529978 TTTTCAAATT
* * * * *
529988 CGTTGCGATATTCCAAGTTCACGTTGCGATTTTTCAAATTCGTTGCGATAATCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCG
** * * ** *
530049 CGTTGCGATTTTCCAAATT--CGTTGCTATAGTCCAAGTTCGTGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTC--GTTGCGATAGTCCAAGTTCG
* * ** * ** *
530110 TGTTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAATTCGCGTTGCGATTTTCCAAATT--
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT--CGTTGCGATAGTCCAAGTTCG
* ** * ** * *
530171 CGTTGCGATAGTCCAAGTTCACGTT-CGAAGTT-C----GCGTTGCGATTTTCAAAATT--
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCG
* *
530224 CGTTGCGATAGTCTAAGTTCACGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCG
* *
530285 TGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCA
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCG
* * ** * *
530346 CGTTGCGATAATCGAAGTTCGTATTGCGATTTTTCAAATTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCG
530407 CGTTGCGAT
1 CGTTGCGAT
530416 TTTCCAAAAT
Statistics
Matches: 304, Mismatches: 49, Indels: 28
0.80 0.13 0.07
Matches are distributed among these distances:
53 42 0.14
54 5 0.02
55 1 0.00
59 30 0.10
60 4 0.01
61 190 0.62
63 31 0.10
65 1 0.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (61 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCG
Found at i:530420 original size:101 final size:99
Alignment explanation
Indices: 529818--530423 Score: 587
Period size: 101 Copynumber: 6.1 Consensus size: 99
529808 TTTACGTTAG
* * * * * * **
529818 TCCAAATTCGTTGCGATAGTCCAAGTTTACGTTGAGATAGTT-GAAGTTCGCGTTGCAATTTTCC
1 TCCAAATTCGTTGCGATAGTCGAAGTTCACGTTGCGATA-TTCCAAATT--CGTTGCGATAGTCC
*
529882 AAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATTT
63 AAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTT
* * ** * * * * ** *
529919 TACAAATTCGTTGCGATAGTAGAAGTTCGGGTTGCAATAGTCGAAGTTCGCGTTGCGATTTTTCA
1 TCCAAATTCGTTGCGATAGTCGAAGTTCACGTTGCGATATTCCAAATT--CGTTGCGATAGTCCA
* *
529984 AATTCGTTGCGATATTCCAAGTTCACGTTGCGATTT
64 AATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTT
* * * * * *
530020 TTCAAATTCGTTGCGATAATCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCTATAGTCCAAG
1 TCCAAATTCGTTGCGATAGTCGAAGTTCACGTTGCGATATTCCAAATTCGTTGCGATAGTCCAAA
* **
530085 TTCGTGTTGCGATAGTCCAAGTTCGTGTTGCGATAG
66 TTC--GTTGCGATAGTCCAAGTTCGCGTTGCGATTT
* * * * *
530121 TCGAAGTTCGCGTTGCGATAGTCGAAATTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCA
1 TCCAAATT--CGTTGCGATAGTCGAAGTTCACGTTGCGATATTCCAAATTCGTTGCGATAGTCCA
* * *
530186 AGTTC---ACG-T--TCGAAGTTCGCGTTGCGATTT
64 AATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTT
* * * *
530216 TCAAAATTCGTTGCGATAGTCTAAGTTCACGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAG
1 TCCAAATTCGTTGCGATAGTCGAAGTTCACGTTGCGATATTCCAAATTCGTTGCGATAGTCCAAA
530281 TTCGTGTTGCGATAGTCCAAGTTCGCGTTGCGATTT
66 TTC--GTTGCGATAGTCCAAGTTCGCGTTGCGATTT
* * * * ** *
530317 TCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATAATCGAAGTTCGTATTGCGATTTTTCA
1 TCCAAATTCGTTGCGATAGTCGAAGTTCACGTTGCGATATTCCAAATTCG--TTGCGATAGTCCA
*
530382 AATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTT
64 AATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTT
530418 TCCAAA
1 TCCAAA
530424 ATCGCAACGA
Statistics
Matches: 430, Mismatches: 60, Indels: 30
0.83 0.12 0.06
Matches are distributed among these distances:
93 57 0.13
95 23 0.05
97 1 0.00
98 4 0.01
99 16 0.04
100 1 0.00
101 257 0.60
103 71 0.17
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (99 bp):
TCCAAATTCGTTGCGATAGTCGAAGTTCACGTTGCGATATTCCAAATTCGTTGCGATAGTCCAAA
TTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTT
Found at i:530849 original size:18 final size:19
Alignment explanation
Indices: 530822--530910 Score: 63
Period size: 19 Copynumber: 4.4 Consensus size: 19
530812 TTATTTTGGA
530822 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
*
530841 TTTTT-ACTATTGCAACAACAC
1 TTTTTCACTA-T-C-GCAACAC
*
530862 GTTTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* * *
530884 ATTTTAACTATCACAACAC
1 TTTTTCACTATCGCAACAC
530903 ATTTTTCA
1 -TTTTTCA
530911 AAATCATGTT
Statistics
Matches: 53, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
18 4 0.08
19 17 0.32
20 6 0.11
21 10 0.19
22 11 0.21
23 1 0.02
24 1 0.02
25 3 0.06
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.37
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:530900 original size:41 final size:43
Alignment explanation
Indices: 530832--530912 Score: 114
Period size: 41 Copynumber: 1.9 Consensus size: 43
530822 TTTTTCACTA
* *
530832 TCGCAACACTTTTTACTATTGCAACAACACGTTTTTCAAACTC
1 TCGCAACACTTTTAACTATTGCAACAACACATTTTTCAAACTC
530875 TCGCAACACATTTTAACTA-T-C-ACAACACATTTTTCAAA
1 TCGCAACAC-TTTTAACTATTGCAACAACACATTTTTCAAA
530913 ATCATGTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 16 0.46
42 1 0.03
43 10 0.29
44 8 0.23
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (43 bp):
TCGCAACACTTTTAACTATTGCAACAACACATTTTTCAAACTC
Found at i:532974 original size:20 final size:19
Alignment explanation
Indices: 532949--533010 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
532939 AATTCACAAC
532949 GCGATTTTAGTTTTCGCGTT
1 GCGATTTTA-TTTTCGCGTT
* *
532969 GCGATTTTCTTTTTGGCGTT
1 GCGATTTT-ATTTTCGCGTT
* *
532989 GCGAATTTCATTTTCGTGTT
1 GCG-ATTTTATTTTCGCGTT
533009 GC
1 GC
533011 AAATTTAAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 30 0.88
21 4 0.12
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (19 bp):
GCGATTTTATTTTCGCGTT
Found at i:533002 original size:21 final size:20
Alignment explanation
Indices: 532959--533016 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
532949 GCGATTTTAG
*
532959 TTTTCGCGTTGCGATTTTCT
1 TTTTCGCGTTGCGAATTTCT
* *
532979 TTTTGGCGTTGCGAATTTCA
1 TTTTCGCGTTGCGAATTTCT
* *
532999 TTTTCGTGTTGCAAATTT
1 TTTTCGCGTTGCGAATTT
533017 AAGTTTCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.52
Consensus pattern (20 bp):
TTTTCGCGTTGCGAATTTCT
Found at i:534705 original size:42 final size:42
Alignment explanation
Indices: 534522--534704 Score: 242
Period size: 42 Copynumber: 4.4 Consensus size: 42
534512 CCCCCCACTT
* * * *
534522 CGAGAGCTATCACCTGATCGGGCCGATTCTACAACTCGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACAACTAGACAC
* * * * *
534564 CGAAAGTCATCACATGATCGAGCCGATTCTACAACTCGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACAACTAGACAC
* *
534606 CGAGAGCCATCACATGATCGAGCCGATTATACACCTAGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACAACTAGACAC
*
534648 CGAGAGCCATCACCTAATCGAGCCGATTATAC-ACTTAGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACAAC-TAGACAC
534690 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
534705 ATTCCATCAT
Statistics
Matches: 127, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
41 1 0.01
42 126 0.99
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCGATTATACAACTAGACAC
Found at i:534908 original size:21 final size:21
Alignment explanation
Indices: 534884--534937 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
534874 TGGTGCATGG
534884 CGTGATGAGGTA-CGATA-TTTA
1 CGTGATGAGGTATC--TACTTTA
*
534905 CGTGGTGAGGTATCTACTTTA
1 CGTGATGAGGTATCTACTTTA
534926 CGTGATGAGGTA
1 CGTGATGAGGTA
534938 GCCGCTCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.24, C:0.11, G:0.31, T:0.33
Consensus pattern (21 bp):
CGTGATGAGGTATCTACTTTA
Found at i:535069 original size:4 final size:4
Alignment explanation
Indices: 535060--535105 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
535050 TTTTTTGGCA
* * * *
535060 TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
535106 TTAGCGGCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:535287 original size:21 final size:21
Alignment explanation
Indices: 535238--535391 Score: 71
Period size: 21 Copynumber: 7.3 Consensus size: 21
535228 AAAGAAGCTC
* * *
535238 GATCCACATACCATTGTTTAG
1 GATCCACCTCCCATTGTTCAG
535259 GATCCACCTCCCATTGTTCAG
1 GATCCACCTCCCATTGTTCAG
* ** * *
535280 GATTCACCTGTCATCGTTCAA
1 GATCCACCTCCCATTGTTCAG
*** * * *
535301 GAGGTACCTCTCATCGTTCAA
1 GATCCACCTCCCATTGTTCAG
*
535322 GAGGCC-CCTCCC-TTCGTTCAG
1 GA-TCCACCTCCCATT-GTTCAG
* * * *
535343 AAGGCC-CCTTCCATCGTTCAG
1 GA-TCCACCTCCCATTGTTCAG
**
535364 GATCCACCTCCCACCGTTCAG
1 GATCCACCTCCCATTGTTCAG
535385 GATCCAC
1 GATCCAC
535392 ATGGCATACT
Statistics
Matches: 105, Mismatches: 24, Indels: 8
0.77 0.18 0.06
Matches are distributed among these distances:
20 3 0.03
21 100 0.95
22 2 0.02
ACGTcount: A:0.21, C:0.36, G:0.17, T:0.27
Consensus pattern (21 bp):
GATCCACCTCCCATTGTTCAG
Found at i:537003 original size:20 final size:20
Alignment explanation
Indices: 536980--537043 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
536970 CGAATTCGAT
*
536980 TTTCGTGTTGCAAATTTGAC
1 TTTCGCGTTGCAAATTTGAC
*** *
537000 TTTCGCAACGCGAATTTGAC
1 TTTCGCGTTGCAAATTTGAC
537020 TTTCGCGTTGCAAATTTGAC
1 TTTCGCGTTGCAAATTTGAC
537040 TTTC
1 TTTC
537044 AATTCAAGGC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (20 bp):
TTTCGCGTTGCAAATTTGAC
Found at i:539241 original size:34 final size:34
Alignment explanation
Indices: 539195--539269 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
539185 TGATACGAAT
*
539195 AACTTTTGTGTAACAATCAACTGCTATCTTTACC
1 AACTCTTGTGTAACAATCAACTGCTATCTTTACC
539229 AACTCTTGTGTAACAATCAACTGCTATCTTTACC
1 AACTCTTGTGTAACAATCAACTGCTATCTTTACC
539263 AACTCTT
1 AACTCTT
539270 CTTCCCGTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (34 bp):
AACTCTTGTGTAACAATCAACTGCTATCTTTACC
Found at i:540364 original size:14 final size:15
Alignment explanation
Indices: 540328--540365 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
540318 GAAATCATTG
540328 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
540343 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
540358 AAAAATTA
1 AAAAATTA
540366 GAGATGGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:540547 original size:20 final size:19
Alignment explanation
Indices: 540503--540590 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 19
540493 CAAAACATCT
*
540503 GTGTTGCGAAAATAAAAGC
1 GTGTTGCGAAAATAAAATC
* *
540522 -TGTTGCGAAATTAAAATTT
1 GTGTTGCGAAAATAAAA-TC
*
540541 GTGTTGCG-AATTCGAAAATC
1 GTGTTGCGAAAAT--AAAATC
* *
540561 GAGTTGCGAAAACAAAATTC
1 GTGTTGCGAAAATAAAA-TC
540581 GTGTTGCGAA
1 GTGTTGCGAA
540591 TTTGGAAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
18 15 0.27
19 8 0.15
20 26 0.47
21 6 0.11
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.28
Consensus pattern (19 bp):
GTGTTGCGAAAATAAAATC
Found at i:540578 original size:40 final size:41
Alignment explanation
Indices: 540523--540611 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 41
540513 AATAAAAGCT
** *
540523 GTTGCGAAATTAAAATTTGTGTTGCGAA-TTCGAAAATCGA
1 GTTGCGAAAACAAAATTCGTGTTGCGAATTTCGAAAATCGA
* *
540563 GTTGCGAAAACAAAATTCGTGTTGCGAATTTGGAAAATCGC
1 GTTGCGAAAACAAAATTCGTGTTGCGAATTTCGAAAATCGA
*
540604 GTTACGAA
1 GTTGCGAA
540612 TTTGGAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 25 0.60
41 17 0.40
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (41 bp):
GTTGCGAAAACAAAATTCGTGTTGCGAATTTCGAAAATCGA
Found at i:540612 original size:21 final size:21
Alignment explanation
Indices: 540587--540632 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
540577 ATTCGTGTTG
540587 CGAATTTGGAAAATCGCGTTA
1 CGAATTTGGAAAATCGCGTTA
*
540608 CGAATTTGGAAAATCGCGTTG
1 CGAATTTGGAAAATCGCGTTA
540629 CGAA
1 CGAA
540633 AAAGAAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (21 bp):
CGAATTTGGAAAATCGCGTTA
Found at i:540680 original size:20 final size:20
Alignment explanation
Indices: 540657--540698 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
540647 TGCGCTTTCA
*
540657 GAAACTGAGTTGCGAATTTG
1 GAAACTGAGTTGCGAAATTG
*
540677 GAAACTGTGTTGCGAAATTG
1 GAAACTGAGTTGCGAAATTG
540697 GA
1 GA
540699 GTTCGTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (20 bp):
GAAACTGAGTTGCGAAATTG
Found at i:542997 original size:20 final size:20
Alignment explanation
Indices: 542972--543032 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
542962 AACCCTTACA
**
542972 AATATCAAGTAGAAGCAAGC
1 AATATCAAACAGAAGCAAGC
*
542992 AATATCAAACAGAAGCAAAC
1 AATATCAAACAGAAGCAAGC
* * * *
543012 AACATAAAACAAAATCAAGC
1 AATATCAAACAGAAGCAAGC
543032 A
1 A
543033 GAATCAAGCA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.59, C:0.18, G:0.11, T:0.11
Consensus pattern (20 bp):
AATATCAAACAGAAGCAAGC
Found at i:545875 original size:26 final size:26
Alignment explanation
Indices: 545818--545877 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
545808 TCTTTCAATT
*
545818 AATATATATGTTTATATTAATAAATT
1 AATATATATGTTTATATTAATAAATG
*
545844 AATATATA-GTTTATATATACT-AATG
1 AATATATATGTTTATAT-TAATAAATG
545869 AACTATATA
1 AA-TATATA
545878 ATATATAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 13 0.43
26 17 0.57
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (26 bp):
AATATATATGTTTATATTAATAAATG
Found at i:545880 original size:33 final size:33
Alignment explanation
Indices: 545843--546084 Score: 259
Period size: 33 Copynumber: 7.4 Consensus size: 33
545833 ATTAATAAAT
545843 TAATATATAGTTTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
* *
545876 TAATATATAGTTTGTATATAC-----CA-TATA
1 TAATATATAGTTTATATATACTAATGAACTATA
* *
545903 CAA-A-ATAGGTTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
*
545934 TAATATATAGTTTATATATACTAATAAACTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
545967 TAATATATAGTTTATATATACTAATGAACTATATA
1 TAATATATAGTTTATATATACTAATGAAC--TATA
* * *
546002 TAATGTATAGTTTATATATACGATAT-AGTCTATA
1 TAATATATAGTTTATATATACTA-ATGA-ACTATA
* * *
546036 TATGTTATATAGTTTATATATACTAATAAATTATA
1 TA--ATATATAGTTTATATATACTAATGAACTATA
*
546071 TAATGTATAGTTTA
1 TAATATATAGTTTA
546085 GGGTTTAGGA
Statistics
Matches: 174, Mismatches: 20, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
25 13 0.07
26 1 0.01
27 6 0.03
28 1 0.01
30 1 0.01
31 6 0.03
32 1 0.01
33 83 0.48
34 6 0.03
35 34 0.20
36 22 0.13
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (33 bp):
TAATATATAGTTTATATATACTAATGAACTATA
Found at i:545922 original size:58 final size:60
Alignment explanation
Indices: 545844--546084 Score: 234
Period size: 58 Copynumber: 3.8 Consensus size: 60
545834 TTAATAAATT
* *
545844 AATATATAGTTTATATATACTAATGAACTATATAATATATAGTTTGTATATACCATATAC
1 AATATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACAATATAC
*
545904 AA-A-ATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATAAACTATA
1 AATATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATAC-----AA-TATA
*
545967 T
60 C
*
545968 AATATATAGTTTATATATACTAATGAACTATATATAATGTATAGTTTATATATACGATATAGTCT
1 AATATATAGTTTATATATACTAATGAAC--TATATAATATATAGTTTATATATAC-A-ATA---T
*
546033 AT
59 AC
* * *
546035 ATATGTTATATAGTTTATATATACTAATAAATTATATAATGTATAGTTTA
1 A-A---TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTA
546085 GGGTTTAGGA
Statistics
Matches: 154, Mismatches: 9, Indels: 27
0.81 0.05 0.14
Matches are distributed among these distances:
58 46 0.30
59 1 0.01
60 2 0.01
63 1 0.01
64 9 0.06
65 2 0.01
66 22 0.14
67 4 0.03
68 25 0.16
69 18 0.12
71 24 0.16
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (60 bp):
AATATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACAATATAC
Found at i:546109 original size:71 final size:71
Alignment explanation
Indices: 545907--546085 Score: 219
Period size: 69 Copynumber: 2.6 Consensus size: 71
545897 CATATACAAA
* * * * * **
545907 ATAGGTTATATATACTAATG-AA-CTATATAATATATAGTTTATATATACTA-ATAAACTATATA
1 ATAGTTTATATATACTAATGAAATATATATAATGTATAGTTTAGATATACGATATAGTCTATATA
*
545969 --ATAT
66 TGTTAT
* *
545973 ATAGTTTATATATACTAATGAACTATATATAATGTATAGTTTATATATACGATATAGTCTATATA
1 ATAGTTTATATATACTAATGAAATATATATAATGTATAGTTTAGATATACGATATAGTCTATATA
546038 TGTTAT
66 TGTTAT
546044 ATAGTTTATATATACTAAT-AAAT-TATATAATGTATAGTTTAG
1 ATAGTTTATATATACTAATGAAATATATATAATGTATAGTTTAG
546086 GGTTTAGGAT
Statistics
Matches: 98, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
66 19 0.19
67 1 0.01
68 25 0.26
69 28 0.29
70 3 0.03
71 22 0.22
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (71 bp):
ATAGTTTATATATACTAATGAAATATATATAATGTATAGTTTAGATATACGATATAGTCTATATA
TGTTAT
Found at i:546178 original size:20 final size:20
Alignment explanation
Indices: 546140--546192 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
546130 ACTATATAGT
* *
546140 ATATATAGTTTATCTATATA
1 ATATATAGTATATCAATATA
*
546160 ATATATAGTATATGAATATA
1 ATATATAGTATATCAATATA
546180 A-ACTATAGTATAT
1 ATA-TATAGTATAT
546193 ATATAGGTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (20 bp):
ATATATAGTATATCAATATA
Found at i:546262 original size:50 final size:51
Alignment explanation
Indices: 546161--546280 Score: 188
Period size: 50 Copynumber: 2.4 Consensus size: 51
546151 ATCTATATAA
*
546161 TATATAGTATATGAATATAAACTATAGTATATATATAGGTCATATGTAAAC
1 TATATAGTATATAAATATAAACTATAGTATATATATAGGTCATATGTAAAC
* *
546212 TATATAGTATATAAATATCAACTATA-TATATATATATGTCATATGTAAAC
1 TATATAGTATATAAATATAAACTATAGTATATATATAGGTCATATGTAAAC
* *
546262 TATATAGTTTATATATATA
1 TATATAGTATATAAATATA
546281 GTTCATATGT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 39 0.62
51 24 0.38
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (51 bp):
TATATAGTATATAAATATAAACTATAGTATATATATAGGTCATATGTAAAC
Found at i:546275 original size:20 final size:19
Alignment explanation
Indices: 546252--546368 Score: 84
Period size: 18 Copynumber: 6.2 Consensus size: 19
546242 TATATATGTC
546252 ATATGTAAACTATATAGTTT
1 ATATGTAAACT-TATAGTTT
* * * **
546272 ATATATATAGTTCATATGTAA
1 ATATGTAAACTT-ATA-GTTT
546293 ATAT-T-AAC-TATAGTTT
1 ATATGTAAACTTATAGTTT
546309 ATATGTAAAC-TATAG-TT
1 ATATGTAAACTTATAGTTT
*
546326 AGTATATAAACTATATAGTTT
1 A-TATGTAAACT-TATAGTTT
*
546347 ATATGTAAAC-TATAGTTC
1 ATATGTAAACTTATAGTTT
546365 ATAT
1 ATAT
546369 ATATATATAA
Statistics
Matches: 77, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
16 6 0.08
17 7 0.09
18 28 0.36
19 2 0.03
20 25 0.32
21 9 0.12
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (19 bp):
ATATGTAAACTTATAGTTT
Found at i:546370 original size:20 final size:18
Alignment explanation
Indices: 546298--546368 Score: 90
Period size: 18 Copynumber: 3.8 Consensus size: 18
546288 TGTAAATATT
546298 AACTATAGTTTATATGTA
1 AACTATAGTTTATATGTA
*
546316 AACTATAG-TTAGTATATA
1 AACTATAGTTTA-TATGTA
546334 AACTATATAGTTTATATGTA
1 AAC--TATAGTTTATATGTA
*
546354 AACTATAGTTCATAT
1 AACTATAGTTTATAT
546369 ATATATATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
17 3 0.07
18 27 0.59
20 13 0.28
21 3 0.07
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (18 bp):
AACTATAGTTTATATGTA
Found at i:546379 original size:24 final size:23
Alignment explanation
Indices: 546347--546436 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 23
546337 TATATAGTTT
*
546347 ATATGTAAACTATAGTTCATATATA
1 ATATATAAACTATAGTT-ATATA-A
546372 TATATAAATAAACTATAGTTTATATAA
1 -ATAT--ATAAACTATAG-TTATATAA
546399 ATAGTATAAA-TATAG-TATATAA
1 ATA-TATAAACTATAGTTATATAA
*
546421 ATATATAAATTATAGT
1 ATATATAAACTATAGT
546437 ATGTGTTTAT
Statistics
Matches: 57, Mismatches: 1, Indels: 15
0.78 0.01 0.21
Matches are distributed among these distances:
21 6 0.11
22 15 0.26
24 5 0.09
25 5 0.09
26 7 0.12
27 2 0.04
28 15 0.26
29 2 0.04
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (23 bp):
ATATATAAACTATAGTTATATAA
Found at i:546385 original size:28 final size:29
Alignment explanation
Indices: 546352--546410 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
546342 AGTTTATATG
*
546352 TAAACTATAGTTCATATATATA-TATAAA
1 TAAACTATAGTTCATATAAATAGTATAAA
*
546380 TAAACTATAGTTTATATAAATAGTATAAA
1 TAAACTATAGTTCATATAAATAGTATAAA
546409 TA
1 TA
546411 TAGTATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (29 bp):
TAAACTATAGTTCATATAAATAGTATAAA
Found at i:546520 original size:22 final size:22
Alignment explanation
Indices: 546479--546542 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 22
546469 TCCTAAACCC
* *
546479 TAAACCATATAATATATATATATA
1 TAAACTATATAATTTATAT-TA-A
*
546503 TAAACTATATAGTTTATATTAA
1 TAAACTATATAATTTATATTAA
546525 TAAACTATATAATTTATA
1 TAAACTATATAATTTATA
546543 CAATATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 18 0.50
23 2 0.06
24 16 0.44
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAACTATATAATTTATATTAA
Found at i:546717 original size:2 final size:2
Alignment explanation
Indices: 546712--546763 Score: 61
Period size: 2 Copynumber: 25.5 Consensus size: 2
546702 GTTTATACTT
* *
546712 TA TA TA -A TA TA TA TA TA TA TA TA AA CTA TA TA GTT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
546755 TA TA TA TA T
1 TA TA TA TA T
546764 TGGTTGTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
1 1 0.02
2 40 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:547201 original size:202 final size:201
Alignment explanation
Indices: 546788--547590 Score: 887
Period size: 202 Copynumber: 3.8 Consensus size: 201
546778 TTTTCTCAAT
* * * *
546788 TTATTACTTATTTTTATTTATT-AATTGGTCCATAATTTTTTAAATGAGTATAATTTAGTA-TAT
1 TTATTACTTATTTATATTT-TTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACT-T
* * *
546851 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTTTTTTGTTATTTAA
64 TTTTGTATTAATTTCAACCTC-AAATTTAAAATTATTTCGATTTGA------TTTTG-TGTGT-G
** * * *
546916 TATATTTTTATTTTTATTTGTAATTT-GTATTTTTTCAATTTAGTCCTCCAAATTTTATTTGCAC
120 TATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCAT
546980 CTGAAATTGACCCATAC
185 CTGAAATTGACCCATAC
*
546997 TTATTACTTATTTATATTTTTAAATTGGCCCGTAACTTTTTAAATGGGTATAATTTAGTACTTTT
1 TTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTT
*
547062 TTGTATTAATTTCAACCTCAAAGTTTAAAATTATTTTGATTTGATTTTGTGTGTGTATATTTAAA
66 TTGTATTAATTTCAACCTCAAA-TTTAAAATTATTTCGATTTGATTTTGTGTGTGTATATTTAAA
547127 TTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGA
130 TTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGA
547192 CCCATAC
195 CCCATAC
* * *
547199 TTATTACTTATTTTTATTTTTAAATTGACCCATAACTTTTTAAATAGGTATAATTTAGTAC-TTT
1 TTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTT
* *
547263 TTGAATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCTAATCAATGTGTGTTGTT
66 TTGTATTAATTTCAACCTCA-AATTTAAAATTATTTCGATTTGAT--T--T---TGTGTG-TG--
* * *
547328 TAATTTATATAAATTTTTATTTGTAATTTCATATTTGTTTAATTTATTCCTCCAAATTTTATTTG
120 T-A--TATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTG
* * *
547393 CATATGAAATTGATCTATAC
182 CATCTGAAATTGACCCATAC
* * * *
547413 TTATTACTTAATTCTAT-TTTTTTATTTGGCCCATAACTTTTTAAATGGGTATAATTTATTATTT
1 TTATTACTT-ATT-TATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
* * * *
547477 TTTTGTATTAATTTCAACCTCACAACTTAAAATCATTTCAAGTTGATCCCTCATCAATGTGTGTT
64 TTTTGTATTAATTTCAACCTCA-AATTTAAAATTATTTCGATTTGAT---T--T---TGTGTG-T
547542 GTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
119 G--T-A--TATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
547591 ATTCTTAAAT
Statistics
Matches: 529, Mismatches: 43, Indels: 36
0.87 0.07 0.06
Matches are distributed among these distances:
201 66 0.12
202 114 0.22
203 6 0.01
205 1 0.00
208 11 0.02
209 96 0.18
210 1 0.00
211 1 0.00
212 1 0.00
214 83 0.16
215 42 0.08
216 44 0.08
217 63 0.12
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (201 bp):
TTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTT
TTGTATTAATTTCAACCTCAAATTTAAAATTATTTCGATTTGATTTTGTGTGTGTATATTTAAAT
TTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGAC
CCATAC
Found at i:550361 original size:16 final size:16
Alignment explanation
Indices: 550336--550369 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
550326 CATATCAAGA
*
550336 ACACTTTAAGAAGATG
1 ACACTCTAAGAAGATG
550352 ACACTCTAAGAAGATG
1 ACACTCTAAGAAGATG
550368 AC
1 AC
550370 TACATTATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.21
Consensus pattern (16 bp):
ACACTCTAAGAAGATG
Found at i:552005 original size:23 final size:24
Alignment explanation
Indices: 551963--552007 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
551953 GAGAGCCCTC
*
551963 AAAATATTTGAAATTAAGATTTAT
1 AAAATATTTCAAATTAAGATTTAT
*
551987 AAAATA-TTCAAATTTAGATTT
1 AAAATATTTCAAATTAAGATTT
552008 TGACCTGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (24 bp):
AAAATATTTCAAATTAAGATTTAT
Found at i:555619 original size:20 final size:20
Alignment explanation
Indices: 555568--555623 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
555558 AATTATTATT
* *
555568 TTTTA-TATTTTTAAATTAA
1 TTTTATTATTTTCATATTAA
* *
555587 ATTAATT-TTTTCATATTAA
1 TTTTATTATTTTCATATTAA
555606 TTTTATTATTTTCATATT
1 TTTTATTATTTTCATATT
555624 TCTAAATTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTATTATTTTCATATTAA
Found at i:555671 original size:26 final size:25
Alignment explanation
Indices: 555619--555671 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
555609 TATTATTTTC
* * * *
555619 ATATTTCTAAATTAAATGTATATTT
1 ATATTTCTAAAGTAAATATAAAATT
555644 ATATTTCTAAAAGTAAATATAAAATT
1 ATATTTCT-AAAGTAAATATAAAATT
555670 AT
1 AT
555672 GATTATTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (25 bp):
ATATTTCTAAAGTAAATATAAAATT
Found at i:556906 original size:16 final size:16
Alignment explanation
Indices: 556885--556919 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
556875 TAAAATGATT
*
556885 AATGTTGAATGGTTTA
1 AATGTTGAATGATTTA
556901 AATGTTGAATGATTTA
1 AATGTTGAATGATTTA
556917 AAT
1 AAT
556920 AGAGGTGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (16 bp):
AATGTTGAATGATTTA
Found at i:558516 original size:12 final size:12
Alignment explanation
Indices: 558499--558530 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
558489 GAGTTATAAC
558499 AGTGTTGGCCTA
1 AGTGTTGGCCTA
558511 AGTGTTGGCCTA
1 AGTGTTGGCCTA
558523 AGTAGTTG
1 AGT-GTTG
558531 AGAATCAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.19, C:0.12, G:0.34, T:0.34
Consensus pattern (12 bp):
AGTGTTGGCCTA
Found at i:559155 original size:18 final size:18
Alignment explanation
Indices: 559132--559174 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
559122 AAATATTTTC
559132 TATTATATTA-TAATAATT
1 TATTATATTATTAA-AATT
* *
559150 TATTATTTTATTAAATTT
1 TATTATATTATTAAAATT
559168 TATTATA
1 TATTATA
559175 CTAATTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTATATTATTAAAATT
Found at i:561514 original size:24 final size:25
Alignment explanation
Indices: 561487--561536 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
561477 TTTATCTTTG
561487 AGCTAAACTTA-TAATATTTTA-AGA
1 AGCTAAACTTATTAA-ATTTTACAGA
*
561511 AGCTAAATTTATTAAATTTTACAGA
1 AGCTAAACTTATTAAATTTTACAGA
561536 A
1 A
561537 TATAAAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (25 bp):
AGCTAAACTTATTAAATTTTACAGA
Found at i:562370 original size:33 final size:33
Alignment explanation
Indices: 562283--562401 Score: 168
Period size: 33 Copynumber: 3.5 Consensus size: 33
562273 CTTTATTTTT
*
562283 TTCGGGTCAGGTCGGG-TTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
562315 TTCGGGTCGAGTCGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTC--G--GGTCGGGTTTTTTTAAGTGTGATA
* *
562352 TTCGGGTCGGGTCGGGTTTGTTTAAGTGTGGTA
1 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
562385 TTCGGGTCGGGTCGGGT
1 TTCGGGTCGGGTCGGGT
562402 CGGGTTCGGG
Statistics
Matches: 79, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
32 8 0.10
33 39 0.49
35 1 0.01
36 7 0.09
37 24 0.30
ACGTcount: A:0.11, C:0.11, G:0.39, T:0.39
Consensus pattern (33 bp):
TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
Found at i:562498 original size:2 final size:2
Alignment explanation
Indices: 562491--562549 Score: 67
Period size: 2 Copynumber: 32.0 Consensus size: 2
562481 AATACCCCTC
562491 TA TA TA TA TA TA TA TA TA T- TA TA TA TA T- TCA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
562531 TA T- TA TA TA T- TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
562550 AATAAGATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
1 6 0.12
2 43 0.86
3 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:562515 original size:17 final size:17
Alignment explanation
Indices: 562493--562549 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
562483 TACCCCTCTA
562493 TATATATATATATATAT
1 TATATATATATATATAT
562510 TATATATAT-TCATATAT
1 TATATATATAT-ATATAT
562527 TATATAT-TATATAT-T
1 TATATATATATATATAT
*
562542 AATATATA
1 TATATATA
562550 AATAAGATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
15 7 0.19
16 6 0.17
17 23 0.64
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:562998 original size:16 final size:17
Alignment explanation
Indices: 562961--563000 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
562951 TATGAAATTG
*
562961 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
*
562978 GATTCCAATTCC-CATA
1 GATTCCAATTCCTCACA
562994 GATTCCA
1 GATTCCA
563001 CTTCTCTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:563666 original size:7 final size:7
Alignment explanation
Indices: 563654--563686 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
563644 TTCAAGGTTA
563654 GCCCAAC
1 GCCCAAC
563661 GCCCAAC
1 GCCCAAC
563668 GCCCAAC
1 GCCCAAC
*
563675 GCCCAAT
1 GCCCAAC
563682 GCCCA
1 GCCCA
563687 TTTCATGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.27, C:0.55, G:0.15, T:0.03
Consensus pattern (7 bp):
GCCCAAC
Found at i:565481 original size:23 final size:23
Alignment explanation
Indices: 565437--565484 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
565427 CTCAATCAAT
* * *
565437 AGCTTCTAGAAGGTCTAGTCAGC
1 AGCTTCTAGAAGATCCAATCAGC
565460 AGCTTCTAGAAGATCCAATCAGC
1 AGCTTCTAGAAGATCCAATCAGC
565483 AG
1 AG
565485 TGACGTGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (23 bp):
AGCTTCTAGAAGATCCAATCAGC
Found at i:566890 original size:94 final size:93
Alignment explanation
Indices: 566730--566917 Score: 367
Period size: 94 Copynumber: 2.0 Consensus size: 93
566720 TAAAAAAATA
566730 GAGGCTATCACTCCCGAAGATTTCAGCCTATTTCGTTGGTAGGTAGTTTATATAAAATCGTGGCT
1 GAGGCTATCACTCCCGAAGATTTCAGCCTATTTCGTTGGTAGGTAGTTTATATAAAATCGTGGCT
566795 CGTGTTTTGGCAAGACGGATGGCTAGTT
66 CGTGTTTTGGCAAGACGGATGGCTAGTT
566823 GAGGCTATCACTCCCGAAGATTTCAAGCCTATTTCGTTGGTAGGTAGTTTATATAAAATCGTGGC
1 GAGGCTATCACTCCCGAAGATTTC-AGCCTATTTCGTTGGTAGGTAGTTTATATAAAATCGTGGC
566888 TCGTGTTTTGGCAAGACGGATGGCTAGTT
65 TCGTGTTTTGGCAAGACGGATGGCTAGTT
566917 G
1 G
566918 TATGGGAGAA
Statistics
Matches: 94, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
93 24 0.26
94 70 0.74
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (93 bp):
GAGGCTATCACTCCCGAAGATTTCAGCCTATTTCGTTGGTAGGTAGTTTATATAAAATCGTGGCT
CGTGTTTTGGCAAGACGGATGGCTAGTT
Found at i:569056 original size:25 final size:23
Alignment explanation
Indices: 569022--569083 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 23
569012 TCTGCTTCTT
569022 GTTTTCCTTGTTTCATTTCTTGCCG
1 GTTTTCCTTGTTTCATTT-TT-CCG
* *
569047 GTTTTCCTTGTTTCGTTTTTTCG
1 GTTTTCCTTGTTTCATTTTTCCG
569070 G-TTTCCTTGTTTCA
1 GTTTTCCTTGTTTCA
569084 GCACAACAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 12 0.35
23 3 0.09
24 2 0.06
25 17 0.50
ACGTcount: A:0.03, C:0.21, G:0.16, T:0.60
Consensus pattern (23 bp):
GTTTTCCTTGTTTCATTTTTCCG
Found at i:575368 original size:35 final size:35
Alignment explanation
Indices: 575322--575392 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 35
575312 AAAGAAATGC
575322 ACATTTGCAAAATGA-AAACTT-TCTTACAAACATAT
1 ACATTTGCAAAAT-ATAAA-TTGTCTTACAAACATAT
575357 ACATTTGCAAAATATAAATTGTCTTACAAACATAT
1 ACATTTGCAAAATATAAATTGTCTTACAAACATAT
575392 A
1 A
575393 AATTCTATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
34 3 0.09
35 31 0.91
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.32
Consensus pattern (35 bp):
ACATTTGCAAAATATAAATTGTCTTACAAACATAT
Found at i:591910 original size:3 final size:3
Alignment explanation
Indices: 591904--591950 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
591894 GTTGTTGTTG
591904 TTA TTA TTA 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 TTA TTA TTA TT
591951 TATAGAATCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:594813 original size:40 final size:40
Alignment explanation
Indices: 594766--594855 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
594756 AGTTATAAGG
* * *
594766 GTATCGATACTGCAGAGTAGGTATCTATACTATAAGGCCA
1 GTATCGATACTACAAAGTAGATATCTATACTATAAGGCCA
* *
594806 TTATCGATACTACAAAGTAGATATCTATACTGTAAGGCCA
1 GTATCGATACTACAAAGTAGATATCTATACTATAAGGCCA
594846 GTATCGATAC
1 GTATCGATAC
594856 CAAAGGTATG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (40 bp):
GTATCGATACTACAAAGTAGATATCTATACTATAAGGCCA
Found at i:594850 original size:20 final size:20
Alignment explanation
Indices: 594786--594855 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
594776 TGCAGAGTAG
*
594786 GTATCTATACTATAAGGCCA
1 GTATCGATACTATAAGGCCA
* * * *
594806 TTATCGATACTACAAAG-TA
1 GTATCGATACTATAAGGCCA
* *
594825 GATATCTATACTGTAAGGCCA
1 G-TATCGATACTATAAGGCCA
594846 GTATCGATAC
1 GTATCGATAC
594856 CAAAGGTATG
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
19 1 0.03
20 33 0.92
21 2 0.06
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACTATAAGGCCA
Found at i:608471 original size:21 final size:25
Alignment explanation
Indices: 608447--608496 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 25
608437 TGATTTGAAT
608447 TTTAATGA-TTA-GTAAT-A-ATGA
1 TTTAATGATTTATGTAATCATATGA
608468 TTTAATGATTTATGTAATCATATGA
1 TTTAATGATTTATGTAATCATATGA
608493 TTTA
1 TTTA
608497 TTAATAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.32
22 3 0.12
23 5 0.20
24 1 0.04
25 8 0.32
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (25 bp):
TTTAATGATTTATGTAATCATATGA
Found at i:608545 original size:8 final size:8
Alignment explanation
Indices: 608462--608525 Score: 53
Period size: 8 Copynumber: 8.1 Consensus size: 8
608452 TGATTAGTAA
608462 TAATGATT
1 TAATGATT
608470 TAATGATT
1 TAATGATT
*
608478 T-ATGTAAT
1 TAATG-ATT
*
608486 CATATGATT
1 TA-ATGATT
* *
608495 T-ATTA-A
1 TAATGATT
608501 TAATGATT
1 TAATGATT
608509 TAATGATT
1 TAATGATT
608517 TAATGATT
1 TAATGATT
608525 T
1 T
608526 GATACTAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
6 1 0.02
7 9 0.21
8 28 0.65
9 2 0.05
10 3 0.07
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.50
Consensus pattern (8 bp):
TAATGATT
Found at i:608575 original size:22 final size:23
Alignment explanation
Indices: 608489--608830 Score: 83
Period size: 22 Copynumber: 15.3 Consensus size: 23
608479 ATGTAATCAT
*
608489 ATGATTTATTAATAATGAT-TTA
1 ATGATTTATTAATAATGATAATA
* * * *
608511 ATGATTTAATGAT-TTGATACTA
1 ATGATTTATTAATAATGATAATA
* *
608533 ATAATTTAATAATAATTTGATAATA
1 ATGATTTATTAATAA--TGATAATA
608558 ATGA-TTATTAATAATGATTTGAATTTTA
1 ATGATTTATTAATAATGA--T-AA---TA
* *
608586 ATGATTTAATAATAATGAT-TTA
1 ATGATTTATTAATAATGATAATA
* *
608608 ATGATTTA-T-GT-A--ATCAT-
1 ATGATTTATTAATAATGATAATA
*
608625 ATGATTTATTAATAATGAT-TTA
1 ATGATTTATTAATAATGATAATA
* * * *
608647 ATGATTTA--AGT-GTAATCAT-
1 ATGATTTATTAATAATGATAATA
*
608666 ATGATTTATTAATAATGAT--TCG
1 ATGATTTATTAATAATGATAAT-A
* * * *
608688 ATGATTTAATGAT-TTGATACTA
1 ATGATTTATTAATAATGATAATA
* * *
608710 ATAATTTAATAATGATTTGATAATA
1 ATGATTTATTAAT-A-ATGATAATA
608735 ATGA-TTATTAATAATGATTTGAATTTTA
1 ATGATTTATTAATAATGA--T-AA---TA
* *
608763 ATGATTTAATAATAAT-AT-TTA
1 ATGATTTATTAATAATGATAATA
*
608784 ATGATTTA-T-GTAAT--T-AT-
1 ATGATTTATTAATAATGATAATA
*
608801 ATGATTTATTAATAATGAT-TTA
1 ATGATTTATTAATAATGATAATA
608823 ATGATTTA
1 ATGATTTA
608831 AGTGTAATCA
Statistics
Matches: 240, Mismatches: 39, Indels: 82
0.66 0.11 0.23
Matches are distributed among these distances:
17 18 0.08
18 5 0.02
19 21 0.09
20 7 0.03
21 24 0.10
22 83 0.35
23 2 0.01
24 18 0.08
25 25 0.10
26 1 0.00
27 1 0.00
28 13 0.05
29 22 0.09
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.47
Consensus pattern (23 bp):
ATGATTTATTAATAATGATAATA
Found at i:608589 original size:15 final size:14
Alignment explanation
Indices: 608431--609059 Score: 234
Period size: 14 Copynumber: 46.4 Consensus size: 14
608421 GCATTTGTAC
608431 TAATAATGATTTGAA
1 TAATAATGATTT-AA
** *
608446 TTTTAATGA-TTAG
1 TAATAATGATTTAA
608459 TAATAATGATTTAA
1 TAATAATGATTTAA
* * *
608473 TGAT--TTATGTAA
1 TAATAATGATTTAA
* *
608485 TCAT-ATGATTTAT
1 TAATAATGATTTAA
608498 TAATAATGATTTAA
1 TAATAATGATTTAA
* *
608512 TGATTTAATGATTTGA
1 T-A-ATAATGATTTAA
* *
608528 TACTAATAATTTAA
1 TAATAATGATTTAA
*
608542 TAAT-A--ATTTGA
1 TAATAATGATTTAA
*
608553 TAATAATGA-TTAT
1 TAATAATGATTTAA
608566 TAATAATGATTTGAA
1 TAATAATGATTT-AA
**
608581 TTTTAATGATTTAA
1 TAATAATGATTTAA
608595 TAATAATGATTTAA
1 TAATAATGATTTAA
* * *
608609 TGAT--TTATGTAA
1 TAATAATGATTTAA
* *
608621 TCAT-ATGATTTAT
1 TAATAATGATTTAA
608634 TAATAATGATTTAA
1 TAATAATGATTTAA
* *
608648 TGATTTAA-G-TGTAA
1 T-A-ATAATGATTTAA
* *
608662 TCAT-ATGATTTAT
1 TAATAATGATTTAA
**
608675 TAATAATGATTCGA
1 TAATAATGATTTAA
* *
608689 TGATTTAATGATTTGA
1 T-A-ATAATGATTTAA
* *
608705 TACTAAT-AATT--
1 TAATAATGATTTAA
*
608716 TAATAATGATTTGA
1 TAATAATGATTTAA
*
608730 TAATAATGA-TTAT
1 TAATAATGATTTAA
608743 TAATAATGATTTGAA
1 TAATAATGATTT-AA
**
608758 TTTTAATGATTTAA
1 TAATAATGATTTAA
608772 TAATAAT-ATTTAA
1 TAATAATGATTTAA
* * *
608785 TGAT--TTATGTAA
1 TAATAATGATTTAA
* *
608797 TTAT-ATGATTTAT
1 TAATAATGATTTAA
608810 TAATAATGATTTAA
1 TAATAATGATTTAA
* *
608824 TGATTTAA-G-TGTAA
1 T-A-ATAATGATTTAA
* * *
608838 TCAT-ATAATTTAT
1 TAATAATGATTTAA
* *
608851 TAATAATAATTCAA
1 TAATAATGATTTAA
* *
608865 TGATTTAATGATTTGA
1 T-A-ATAATGATTTAA
* *
608881 TACTAAT-AATT--
1 TAATAATGATTTAA
*
608892 TAATAATGATTTGA
1 TAATAATGATTTAA
* *
608906 TAATAAT-AATTAT
1 TAATAATGATTTAA
608919 TAATAATGATTTGAA
1 TAATAATGATTT-AA
** *
608934 TTTTAATGA-TTAG
1 TAATAATGATTTAA
608947 TAATAATGATTTAA
1 TAATAATGATTTAA
* * *
608961 TGAT--TTATGTAA
1 TAATAATGATTTAA
* *
608973 TCAT-ATGATTTAT
1 TAATAATGATTTAA
608986 TAATAATGATTTAA
1 TAATAATGATTTAA
* *
609000 TGATTTAATGATTTGA
1 T-A-ATAATGATTTAA
* * *
609016 TACTACT-AATT--
1 TAATAATGATTTAA
*
609027 TAATAATGATTTGA
1 TAATAATGATTTAA
*
609041 TAACAATGATTT-A
1 TAATAATGATTTAA
609054 TAATAA
1 TAATAA
609060 ATTTGTAGAT
Statistics
Matches: 450, Mismatches: 117, Indels: 96
0.68 0.18 0.14
Matches are distributed among these distances:
11 29 0.06
12 48 0.11
13 117 0.26
14 159 0.35
15 49 0.11
16 48 0.11
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.46
Consensus pattern (14 bp):
TAATAATGATTTAA
Found at i:608595 original size:8 final size:8
Alignment explanation
Indices: 608569--608655 Score: 53
Period size: 8 Copynumber: 11.4 Consensus size: 8
608559 TGATTATTAA
608569 TAATGATT
1 TAATGATT
608577 TGAAT--TT
1 T-AATGATT
608584 TAATGATT
1 TAATGATT
*
608592 TAAT-A-A
1 TAATGATT
608598 TAATGATT
1 TAATGATT
608606 TAATGATT
1 TAATGATT
*
608614 T-ATGTAAT
1 TAATG-ATT
*
608622 CATATGATT
1 TA-ATGATT
* *
608631 T-ATTA-A
1 TAATGATT
608637 TAATGATT
1 TAATGATT
608645 TAATGATT
1 TAATGATT
608653 TAA
1 TAA
608656 GTGTAATCAT
Statistics
Matches: 59, Mismatches: 10, Indels: 20
0.66 0.11 0.22
Matches are distributed among these distances:
6 8 0.14
7 14 0.24
8 29 0.49
9 5 0.08
10 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.48
Consensus pattern (8 bp):
TAATGATT
Found at i:608673 original size:41 final size:40
Alignment explanation
Indices: 608586--608698 Score: 183
Period size: 41 Copynumber: 2.8 Consensus size: 40
608576 TTGAATTTTA
*
608586 ATGATTTAATAATAATGATTTAATGATTT-ATGTAATCAT
1 ATGATTTATTAATAATGATTTAATGATTTAATGTAATCAT
608625 ATGATTTATTAATAATGATTTAATGATTTAAGTGTAATCAT
1 ATGATTTATTAATAATGATTTAATGATTTAA-TGTAATCAT
**
608666 ATGATTTATTAATAATGATTCGATGATTTAATG
1 ATGATTTATTAATAATGATTTAATGATTTAATG
608699 ATTTGATACT
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
39 28 0.41
40 3 0.04
41 38 0.55
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.46
Consensus pattern (40 bp):
ATGATTTATTAATAATGATTTAATGATTTAATGTAATCAT
Found at i:608725 original size:25 final size:25
Alignment explanation
Indices: 608694--609057 Score: 121
Period size: 25 Copynumber: 14.2 Consensus size: 25
608684 TTCGATGATT
*
608694 TAATGATTTGATACTAATAATTTAA
1 TAATGATTTGATAATAATAATTTAA
*
608719 TAATGATTTGATAATAATGATTATTAA
1 TAATGATTTGATAATAAT-AAT-TTAA
** *
608746 TAATGATTTGAATTTTAATGATTTAA
1 TAATGATTTG-ATAATAATAATTTAA
* * * *
608772 TAATAATATT--TAATGATTTATGTAA
1 TAATGAT-TTGATAAT-AATAATTTAA
*
608797 TTATATGATTT-ATTAATAATGA-TT--
1 -TA-ATGATTTGA-TAATAATAATTTAA
* * * *
608821 TAATGATTTAAGT-GTAATCATATAA
1 TAATGATTTGA-TAATAATAATTTAA
* *
608846 T--TTA-TTAATAATAATTCAATGATT--
1 TAATGATTTGATAATAA-T-AAT--TTAA
*
608870 TAATGATTTGATACTAATAATTTAA
1 TAATGATTTGATAATAATAATTTAA
608895 TAATGATTTGATAATAATAATTATTAA
1 TAATGATTTGATAATAATAA-T-TTAA
** *
608922 TAATGATTTGAATTTTAATGATTAGTAA
1 TAATGATTTG-ATAATAATAATT--TAA
* * * *
608950 TAATGATTTAATGAT--TTATGTAA
1 TAATGATTTGATAATAATAATTTAA
*
608973 TCATATGATTT-ATTAATAATGATTTAATGA
1 T-A-ATGATTTGA-TAATAATAATTT-A--A
* *
609003 TTTAATGATTTGATACTACTAATTTAA
1 --TAATGATTTGATAATAATAATTTAA
* *
609030 TAATGATTTGATAACAATGATTT-A
1 TAATGATTTGATAATAATAATTTAA
609054 TAAT
1 TAAT
609058 AAATTTGTAG
Statistics
Matches: 254, Mismatches: 46, Indels: 79
0.67 0.12 0.21
Matches are distributed among these distances:
21 1 0.00
22 19 0.07
23 14 0.06
24 12 0.05
25 79 0.31
26 23 0.09
27 55 0.22
28 30 0.12
29 1 0.00
30 17 0.07
31 2 0.01
32 1 0.00
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (25 bp):
TAATGATTTGATAATAATAATTTAA
Found at i:608772 original size:8 final size:8
Alignment explanation
Indices: 608746--609013 Score: 54
Period size: 8 Copynumber: 34.1 Consensus size: 8
608736 TGATTATTAA
608746 TAATGATT
1 TAATGATT
608754 TGAAT--TT
1 T-AATGATT
608761 TAATGATT
1 TAATGATT
*
608769 TAAT-A-A
1 TAATGATT
608775 TAAT-ATT
1 TAATGATT
608782 TAATGATT
1 TAATGATT
*
608790 T-ATGTAAT
1 TAATG-ATT
608798 TATATGATT
1 TA-ATGATT
* *
608807 T-ATTA-A
1 TAATGATT
608813 TAATGATT
1 TAATGATT
608821 TAATGATT
1 TAATGATT
*
608829 TAA-G-TG
1 TAATGATT
* *
608835 TAATCATA
1 TAATGATT
*
608843 TAATTTATT
1 TAA-TGATT
*
608852 AATAATAATT
1 --TAATGATT
*
608862 CAATGATT
1 TAATGATT
608870 TAATGATT
1 TAATGATT
* *
608878 TGAT-A-C
1 TAATGATT
*
608884 TAATAATTT
1 TAATGA-TT
608893 AATAATGATT
1 --TAATGATT
* * *
608903 TGATAATAA
1 TAATGAT-T
*
608912 TAATTATT
1 TAATGATT
608920 AATAATGATT
1 --TAATGATT
608930 TGAAT--TT
1 T-AATGATT
608937 TAATGA-T
1 TAATGATT
* *
608944 TAGT-A-A
1 TAATGATT
608950 TAATGATT
1 TAATGATT
608958 TAATGATT
1 TAATGATT
*
608966 T-ATGTAAT
1 TAATG-ATT
*
608974 CATATGATT
1 TA-ATGATT
* *
608983 T-ATTA-A
1 TAATGATT
608989 TAATGATT
1 TAATGATT
608997 TAATGATT
1 TAATGATT
609005 TAATGATT
1 TAATGATT
609013 T
1 T
609014 GATACTACTA
Statistics
Matches: 186, Mismatches: 41, Indels: 66
0.63 0.14 0.23
Matches are distributed among these distances:
6 24 0.13
7 37 0.20
8 79 0.42
9 19 0.10
10 19 0.10
11 8 0.04
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (8 bp):
TAATGATT
Found at i:608779 original size:67 final size:67
Alignment explanation
Indices: 608625--608831 Score: 217
Period size: 67 Copynumber: 3.0 Consensus size: 67
608615 ATGTAATCAT
* * * *
608625 ATGATTTATTAATAATGATTTAATGATTTAAGTGTAATCATATGATTTATTAATAATGATTCGAT
1 ATGATTTAATAATAAT-ATTTAATAATTT-A-TGTAATTATATGATTTATTAATAATGATTTGAT
608690 GATTTA
63 -ATTTA
* *
608696 ATGATTTGATACTAATAATTTAATAATGATT-TGATAA-TA-ATGA-TTATTAATAATGATTTGA
1 ATGATTTAATAATAAT-ATTTAATAAT--TTATG-TAATTATATGATTTATTAATAATGATTTGA
608757 -ATTTTA
62 TA-TTTA
* *
608763 ATGATTTAATAATAATATTTAATGATTTATGTAATTATATGATTTATTAATAATGATTTAATGAT
1 ATGATTTAATAATAATATTTAATAATTTATGTAATTATATGATTTATTAATAATGATTTGAT-AT
608828 TTA
65 TTA
608831 A
1 A
608832 GTGTAATCAT
Statistics
Matches: 115, Mismatches: 11, Indels: 23
0.77 0.07 0.15
Matches are distributed among these distances:
64 5 0.04
65 4 0.03
66 14 0.12
67 35 0.30
68 22 0.19
69 5 0.04
70 3 0.03
71 25 0.22
73 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.47
Consensus pattern (67 bp):
ATGATTTAATAATAATATTTAATAATTTATGTAATTATATGATTTATTAATAATGATTTGATATT
TA
Found at i:608837 original size:41 final size:39
Alignment explanation
Indices: 608763--608874 Score: 154
Period size: 41 Copynumber: 2.8 Consensus size: 39
608753 TTGAATTTTA
* *
608763 ATGATTTAATAATAATATTTAATGATTT-ATGTAATTAT
1 ATGATTTATTAATAATATTTAATGATTTAATGTAATCAT
608801 ATGATTTATTAATAATGATTTAATGATTTAAGTGTAATCAT
1 ATGATTTATTAATAAT-ATTTAATGATTTAA-TGTAATCAT
* *
608842 ATAATTTATTAATAATAATTCAATGATTTAATG
1 ATGATTTATTAATAAT-ATTTAATGATTTAATG
608875 ATTTGATACT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
38 15 0.23
39 12 0.18
40 3 0.05
41 36 0.55
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (39 bp):
ATGATTTATTAATAATATTTAATGATTTAATGTAATCAT
Found at i:608876 original size:176 final size:177
Alignment explanation
Indices: 608451--609007 Score: 998
Period size: 176 Copynumber: 3.2 Consensus size: 177
608441 TTGAATTTTA
* *
608451 ATGA-TTAGTAATAATGATTTAATGATTT-A-TGTAATCATATGATTTATTAATAATGATTTAAT
1 ATGATTTATTAATAATGATTTAATGATTTAAGTGTAATCATATGATTTATTAATAATGATTCAAT
*
608513 GATTTAATGATTTGATACTAATAATTTAATAATAATTTGATAATAATGATTATTAATAATGATTT
66 GATTTAATGATTTGATACTAATAATTTAATAATGATTTGATAATAATGATTATTAATAATGATTT
608578 GAATTTTAATGATTTAATAATAATGATTTAATGATTTATGTAATCAT
131 GAATTTTAATGATTTAATAATAATGATTTAATGATTTATGTAATCAT
*
608625 ATGATTTATTAATAATGATTTAATGATTTAAGTGTAATCATATGATTTATTAATAATGATTCGAT
1 ATGATTTATTAATAATGATTTAATGATTTAAGTGTAATCATATGATTTATTAATAATGATTCAAT
608690 GATTTAATGATTTGATACTAATAATTTAATAATGATTTGATAATAATGATTATTAATAATGATTT
66 GATTTAATGATTTGATACTAATAATTTAATAATGATTTGATAATAATGATTATTAATAATGATTT
*
608755 GAATTTTAATGATTTAATAATAAT-ATTTAATGATTTATGTAATTAT
131 GAATTTTAATGATTTAATAATAATGATTTAATGATTTATGTAATCAT
* *
608801 ATGATTTATTAATAATGATTTAATGATTTAAGTGTAATCATATAATTTATTAATAATAATTCAAT
1 ATGATTTATTAATAATGATTTAATGATTTAAGTGTAATCATATGATTTATTAATAATGATTCAAT
*
608866 GATTTAATGATTTGATACTAATAATTTAATAATGATTTGATAATAATAATTATTAATAATGATTT
66 GATTTAATGATTTGATACTAATAATTTAATAATGATTTGATAATAATGATTATTAATAATGATTT
*
608931 GAATTTTAATGA-TTAGTAATAATGATTTAATGATTTATGTAATCAT
131 GAATTTTAATGATTTAATAATAATGATTTAATGATTTATGTAATCAT
608977 ATGATTTATTAATAATGATTTAATGATTTAA
1 ATGATTTATTAATAATGATTTAATGATTTAA
609008 TGATTTGATA
Statistics
Matches: 368, Mismatches: 11, Indels: 6
0.96 0.03 0.02
Matches are distributed among these distances:
174 4 0.01
175 33 0.09
176 212 0.58
177 119 0.32
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (177 bp):
ATGATTTATTAATAATGATTTAATGATTTAAGTGTAATCATATGATTTATTAATAATGATTCAAT
GATTTAATGATTTGATACTAATAATTTAATAATGATTTGATAATAATGATTATTAATAATGATTT
GAATTTTAATGATTTAATAATAATGATTTAATGATTTATGTAATCAT
Found at i:608960 original size:21 final size:25
Alignment explanation
Indices: 608935--608984 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 25
608925 TGATTTGAAT
608935 TTTAATGA-TTA-GTAAT-A-ATGA
1 TTTAATGATTTATGTAATCATATGA
608956 TTTAATGATTTATGTAATCATATGA
1 TTTAATGATTTATGTAATCATATGA
608981 TTTA
1 TTTA
608985 TTAATAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.32
22 3 0.12
23 5 0.20
24 1 0.04
25 8 0.32
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (25 bp):
TTTAATGATTTATGTAATCATATGA
Found at i:608982 original size:17 final size:14
Alignment explanation
Indices: 608958--608998 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 14
608948 AATAATGATT
608958 TAATGATTTATGTAA
1 TAATGATTTAT-TAA
608973 TCATATGATTTATTAA
1 T-A-ATGATTTATTAA
608989 TAATGATTTA
1 TAATGATTTA
608999 ATGATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.33
15 2 0.08
16 5 0.21
17 9 0.38
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (14 bp):
TAATGATTTATTAA
Found at i:609059 original size:135 final size:138
Alignment explanation
Indices: 608801--609047 Score: 419
Period size: 135 Copynumber: 1.8 Consensus size: 138
608791 ATGTAATTAT
*
608801 ATGATTTATTAATAATGATTTAATGATTTAAGTGTAATCATATAATTTATTAATAATAATTCAAT
1 ATGATTTAGTAATAATGATTTAATGATTTAAGTGTAATCATATAATTTATTAATAATAATTCAAT
*
608866 GATTTAATGATTTGATACTAATAATTTAATAATGATTTGATAATAATAATTATTAATAATGATTT
66 GATTTAATGATTTGATACTAATAATTTAATAATGATTTGATAACAATAATTATTAATAATGATTT
608931 GAATTTTA
131 GAATTTTA
* * *
608939 ATGA-TTAGTAATAATGATTTAATGATTT-A-TGTAATCATATGATTTATTAATAATGATTTAAT
1 ATGATTTAGTAATAATGATTTAATGATTTAAGTGTAATCATATAATTTATTAATAATAATTCAAT
*
609001 GATTTAATGATTTGATACTACTAATTTAATAATGATTTGATAACAAT
66 GATTTAATGATTTGATACTAATAATTTAATAATGATTTGATAACAAT
609048 GATTTATAAT
Statistics
Matches: 103, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
135 75 0.73
136 1 0.01
137 23 0.22
138 4 0.04
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.46
Consensus pattern (138 bp):
ATGATTTAGTAATAATGATTTAATGATTTAAGTGTAATCATATAATTTATTAATAATAATTCAAT
GATTTAATGATTTGATACTAATAATTTAATAATGATTTGATAACAATAATTATTAATAATGATTT
GAATTTTA
Found at i:609076 original size:27 final size:27
Alignment explanation
Indices: 609046--609101 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
609036 TTTGATAACA
*
609046 ATGATTTATAATAAATTTGTAGATTAT
1 ATGATTTATAATAAATTCGTAGATTAT
609073 ATGATTTATAATAAATTCGTAGATTAT
1 ATGATTTATAATAAATTCGTAGATTAT
609100 AT
1 AT
609102 TATATTCGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (27 bp):
ATGATTTATAATAAATTCGTAGATTAT
Found at i:609413 original size:11 final size:11
Alignment explanation
Indices: 609399--609441 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
609389 CTAATGATTT
*
609399 ATTAATAATTA
1 ATTATTAATTA
609410 ATTATTTAA-TA
1 ATTA-TTAATTA
*
609421 ATTATTGATTA
1 ATTATTAATTA
609432 ATTATTAATT
1 ATTATTAATT
609442 TAATGATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 3 0.11
11 21 0.78
12 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (11 bp):
ATTATTAATTA
Found at i:609416 original size:18 final size:18
Alignment explanation
Indices: 609390--609440 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
609380 AAATGATTAC
*
609390 TAATGATTTATTAATAAT
1 TAATTATTTATTAATAAT
* *
609408 TAATTATTTAATAATTAT
1 TAATTATTTATTAATAAT
* *
609426 TGATTAATTATTAAT
1 TAATTATTTATTAAT
609441 TTAATGATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (18 bp):
TAATTATTTATTAATAAT
Found at i:625226 original size:4 final size:4
Alignment explanation
Indices: 625217--625245 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
625207 AATAAAAATT
625217 GGGA GGGA GGGA GGGA GGGA GGGA GGGA G
1 GGGA GGGA GGGA GGGA GGGA GGGA GGGA G
625246 TAGTAAATTA
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:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (4 bp):
GGGA
Found at i:626190 original size:6 final size:6
Alignment explanation
Indices: 626179--626206 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
626169 TTTATTGGCG
626179 AAAATT AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAA
626207 AATTCAATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:626539 original size:34 final size:32
Alignment explanation
Indices: 626501--626611 Score: 150
Period size: 33 Copynumber: 3.3 Consensus size: 32
626491 AGTCTTACTT
* *
626501 GGACTCAAAATGCTTCGGTTTTAGTGTTTCAATA
1 GGACTC-AAATACTT-GGTTTTAGTGTTTTAATA
*
626535 GGACTCAAATACGTGGGTTTTAGTGTTTTAATA
1 GGACTCAAATAC-TTGGTTTTAGTGTTTTAATA
*
626568 TGACTCAAATACGTTGGTTTTAGTGTTTTAATA
1 GGACTCAAATAC-TTGGTTTTAGTGTTTTAATA
626601 GGACTCAAATA
1 GGACTCAAATA
626612 AGTTGATTTA
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
33 63 0.90
34 7 0.10
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.39
Consensus pattern (32 bp):
GGACTCAAATACTTGGTTTTAGTGTTTTAATA
Found at i:626558 original size:33 final size:33
Alignment explanation
Indices: 626517--626611 Score: 163
Period size: 33 Copynumber: 2.9 Consensus size: 33
626507 AAAATGCTTC
*
626517 GGTTTTAGTGTTTCAATAGGACTCAAATACGTG
1 GGTTTTAGTGTTTTAATAGGACTCAAATACGTG
* *
626550 GGTTTTAGTGTTTTAATATGACTCAAATACGTT
1 GGTTTTAGTGTTTTAATAGGACTCAAATACGTG
626583 GGTTTTAGTGTTTTAATAGGACTCAAATA
1 GGTTTTAGTGTTTTAATAGGACTCAAATA
626612 AGTTGATTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.41
Consensus pattern (33 bp):
GGTTTTAGTGTTTTAATAGGACTCAAATACGTG
Found at i:626684 original size:3 final size:3
Alignment explanation
Indices: 626670--626728 Score: 70
Period size: 3 Copynumber: 19.7 Consensus size: 3
626660 GGTCTGCAAA
626670 AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT
626715 ATAT AAT -AT AAT AA
1 A-AT AAT AAT AAT AA
626729 AATGTTTTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 5 0.10
3 38 0.75
4 8 0.16
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:626713 original size:29 final size:28
Alignment explanation
Indices: 626670--626728 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
626660 GGTCTGCAAA
626670 AATAATAAAATAAT-AATAATAATAATAAT
1 AATAATAAAATAATAAAT-ATAAT-ATAAT
626699 AATAAT-AAATAAATAAATATAATATAAT
1 AATAATAAAAT-AATAAATATAATATAAT
626727 AA
1 AA
626729 AATGTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 11 0.39
29 14 0.50
30 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (28 bp):
AATAATAAAATAATAAATATAATATAAT
Found at i:627216 original size:84 final size:80
Alignment explanation
Indices: 627078--627338 Score: 319
Period size: 84 Copynumber: 3.2 Consensus size: 80
627068 AATGAAATCA
* * * *
627078 AACTCGAAGCTCTTTGGCAGATAACCCTTCT-TGCCTTGAGCTATGCTACAAATGATGGTGCCTT
1 AACTCGAAGGTCTTTGGCAGATAACCCTTCTAT-CCTTGAGTTATGCT-GAAATGAT-GTGCCAT
*
627142 TG-AGCTGAGTGGAGTCG
63 TGAAGCTGAGTGTAGTCG
627159 AACTCGAAGGTCTTTGGTGACAGATAACCCTTCTATCCTTGAGTTATGCTGTAAATGATGTGCCA
1 AACTCGAAGGTCTTT-G-G-CAGATAACCCTTCTATCCTTGAGTTATGCTG-AAATGATGTGCCA
* *
627224 TTGAAGCTGAGTGTAATCT
62 TTGAAGCTGAGTGTAGTCG
* * * ** * *
627243 AACTCGAGGGTCTTTGGCGGATAACCCTTCTAGCCTTGAGTTATATTGAAATGATGTGCCCTCGA
1 AACTCGAAGGTCTTTGGCAGATAACCCTTCTATCCTTGAGTTATGCTGAAATGATGTGCCATTGA
627308 AGCTGAGTGTAGTCG
66 AGCTGAGTGTAGTCG
627323 AACTCGAAGGTCTTTG
1 AACTCGAAGGTCTTTG
627339 TGTTTCAAGA
Statistics
Matches: 157, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
80 43 0.27
81 41 0.26
82 2 0.01
83 10 0.06
84 60 0.38
85 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (80 bp):
AACTCGAAGGTCTTTGGCAGATAACCCTTCTATCCTTGAGTTATGCTGAAATGATGTGCCATTGA
AGCTGAGTGTAGTCG
Found at i:627410 original size:34 final size:34
Alignment explanation
Indices: 627335--627457 Score: 194
Period size: 34 Copynumber: 3.6 Consensus size: 34
627325 CTCGAAGGTC
627335 TTTGTGTTTCAAGAGAAAC-ATTTTCAAAGGTTTTTT
1 TTTGTGTTTCAAGAGAAACGA-TTTCAAAGG--TTTT
*
627371 TTTGTGTTTCGAGAGAAACGATTTCAAAGGTTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
627405 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
*
627439 TTTGTGTTTCATGAGAAAC
1 TTTGTGTTTCAAGAGAAAC
627458 TATCTCCAGG
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
34 55 0.66
36 27 0.33
37 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (34 bp):
TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
Found at i:627592 original size:36 final size:36
Alignment explanation
Indices: 627510--628417 Score: 651
Period size: 36 Copynumber: 25.1 Consensus size: 36
627500 CAAAGATCAG
*
627510 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
627547 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
627583 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
627620 AGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
627656 TGTTTCAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
*
627685 TGTTTCAACG-GAAATTGTCTCAAGAGAGACAAAATT
1 TGTTTCAA-GAGAAACTGTCTCAAGAGAGACAAAATT
*
627721 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGAAAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC------AAAATT
*
627763 TATTTCAAGAGAAACTGTCTCAAGAGAGACAAAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTC-A-AGAG----AGACAAAATT
*
627805 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
627842 AGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
627878 TGTTT-AATGTA-AAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAA-G-AGAAAC-TGTCTCAAGAGAGACAAAATT
* *
627907 TGTTCCAATG-GAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAA-GAGAAACTGTCTCAAGAGAGACAAAATT
*
627943 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
627979 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * ****
628016 TGTTT--TGAGTAAATTAGTCTCAAGCGAGACGACCCCT
1 TGTTTCAAGAG-AAACT-GTCTCAAGAGAGAC-AAAATT
* *
628053 TGTTTCAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
*
628082 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
628118 TGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAGAAAAAAAT
1 TGTTTCAAGAGAAACTGTCTCAAG--AG----AGACAAAATT
*
628160 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTC-A-AGAG----AGACAAAATT
* *
628202 TGTTTCAAGAGAAATTGTCTCAAGAGTGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
628239 AGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
628275 TGTTT-AATGTA-AAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAA-G-AGAAAC-TGTCTCAAGAGAGACAAAATT
* *
628304 TGTTCCAATG-GAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAA-GAGAAACTGTCTCAAGAGAGACAAAATT
* *
628340 TATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
628376 TATTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
628413 TGTTT
1 TGTTT
628418 TGAGTAAATT
Statistics
Matches: 709, Mismatches: 82, Indels: 160
0.75 0.09 0.17
Matches are distributed among these distances:
28 10 0.01
29 58 0.08
30 15 0.02
31 4 0.01
32 8 0.01
33 6 0.01
34 2 0.00
35 14 0.02
36 283 0.40
37 167 0.24
38 8 0.01
39 2 0.00
40 8 0.01
41 2 0.00
42 110 0.16
43 2 0.00
44 6 0.01
48 4 0.01
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:627762 original size:42 final size:41
Alignment explanation
Indices: 627683--627874 Score: 206
Period size: 42 Copynumber: 4.9 Consensus size: 41
627673 ATTCAAAGAT
*
627683 TTTGTTTCAACG-GAAATTGTCTCAAGAGAGAC-----AAAA
1 TTTGTTTCAA-GAGAAACTGTCTCAAGAGAGACAAAGAAAAA
*
627719 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGAAAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAG-AAAAA
*
627761 TTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGA-AAAA
* *
627803 TTTGTTTCAAGAGAAACTATCTCAAGAGAGAC----AAAAC
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGAAAAA
* * * *
627840 TTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
627875 ATTTGTTTAA
Statistics
Matches: 134, Mismatches: 11, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
35 1 0.01
36 29 0.22
37 30 0.22
38 1 0.01
41 1 0.01
42 72 0.54
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.23
Consensus pattern (41 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGAAAAA
Found at i:627930 original size:222 final size:217
Alignment explanation
Indices: 627510--628011 Score: 786
Period size: 222 Copynumber: 2.3 Consensus size: 217
627500 CAAAGATCAG
* * *
627510 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTC-A-AGAG
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAG
*
627573 ----AGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAA
66 ACAAAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAA
* *
627634 CTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAACGGAAA
131 CTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTCCAACGGAAA
* *
627699 TTGTCTCAAGAGAGACAAAATT
196 CTATCTCAAGAGAGACAAAATT
*
627721 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGAAAAAATTTATTTCAAGAGAAACTGTCTCAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-----AAAAATTTGTTTCAAGAGAAACTGTCTCAA
627786 GAGAGACAAAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAA
61 GAGAGACAAAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAA
*
627851 AGAAACTGTCTCAAGGGAGACAAAATTTGTTT-AATGTAAAACATATTCAAAGATTTTGTTCCAA
126 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAA-GGAAAACATATTCAAAGATTTTGTTCCAA
*
627915 TGGAAACTATCTCAAGAGAGACAAAATT
190 CGGAAACTATCTCAAGAGAGACAAAATT
*
627943 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAG
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAG
628007 ACAAA
66 ACAAA
628012 ATTTTGTTTT
Statistics
Matches: 266, Mismatches: 13, Indels: 19
0.89 0.04 0.06
Matches are distributed among these distances:
211 28 0.11
216 63 0.24
217 1 0.00
218 4 0.02
221 2 0.01
222 168 0.63
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (217 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAG
ACAAAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAA
CTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTCCAACGGAAA
CTATCTCAAGAGAGACAAAATT
Found at i:628117 original size:175 final size:174
Alignment explanation
Indices: 627719--628192 Score: 540
Period size: 175 Copynumber: 2.6 Consensus size: 174
627709 AGAGACAAAA
* *
627719 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGAAAAAATTTATTTCAAGAGAAACTGTCTC
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC------AAAATTTGTTTCAAGGGAAACTGTCTC
*
627784 AAGAGAGACAAAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCA
60 -A-AGAG---AAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT-CA
* * *
627849 AAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTAATGTAAAACATATTCAAAGAT
119 AAAGAAACTGTCTCAAGCGAGACAAAACTTGTTTAATGGAAAACATATTCAAAGAT
* * *
627905 TTTGTTCCAATGGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAG-
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
* * * *** *
627969 AGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTTGTT-TTGAGTAAATTAG
66 AGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCAAAAG-AAACT-G
***
628033 TCTCAAGCGAGACGACCCCTTGTTTCAA-GGAAAACATATTCAAAGAT
129 TCTCAAGCGAGAC-AAAACTTGTTT-AATGGAAAACATATTCAAAGAT
628080 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAG--A
* * *
628145 GACAAAGAAAAAAATTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAA
64 G---AAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
628193 GACAAAATTT
Statistics
Matches: 252, Mismatches: 26, Indels: 25
0.83 0.09 0.08
Matches are distributed among these distances:
172 2 0.01
173 4 0.02
174 60 0.24
175 84 0.33
176 2 0.01
177 2 0.01
178 4 0.02
179 1 0.00
180 25 0.10
181 39 0.15
186 29 0.12
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.26
Consensus pattern (174 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
AGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCAAAAGAAACTGTC
TCAAGCGAGACAAAACTTGTTTAATGGAAAACATATTCAAAGAT
Found at i:628133 original size:397 final size:397
Alignment explanation
Indices: 627452--628455 Score: 1615
Period size: 397 Copynumber: 2.5 Consensus size: 397
627442 GTGTTTCATG
* * * ** *
627452 AGAAACTATCTCCAGGGAGGCAAAATTTTGTTTCAA-G-AGAAACATATTCAAAGATCAGTGTTT
1 AGAAACTGTCTCAAGGGAGACAAAA-TTTGTTT-AATGTA-AAACATATTCAAAGAT-TTTGTTC
* * *
627515 CAA-GAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
62 CAATG-GAAACTATCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* * * *** *
627579 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAG-AAACT-GTCTCA
125 AATTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTTGTT--TTGAGTAAATTAGTCTCA
* *** *
627642 AGGGAGACGA-AATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAACGGAAATTGTCTC
188 AGCGAGACGACCCCTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAACGGAAACTGTCTC
* *
627706 AAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGAAAAAATTTATTTCAA
253 AAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAGAAAAAAATTATTTCAA
627771 GAGAAACTGTCTCAAGAGAGACAAAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACA
318 GAGAAACTGTCTCAAGAGAGACAAAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACA
627836 AAACTTAGTTCCAAA
383 AAACTTAGTTCCAAA
627851 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTAATGTAAAACATATTCAAAGATTTTGTTCCAAT
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTAATGTAAAACATATTCAAAGATTTTGTTCCAAT
627916 GGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
66 GGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
627981 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTTGTTTTGAGTAAATTAGTCTCAAGCGAGAC
131 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTTGTTTTGAGTAAATTAGTCTCAAGCGAGAC
*
628046 GACCCCTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
196 GACCCCTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAACGGAAACTGTCTCAAGAGAGA
* *
628111 CAAAATTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAGAAAAAAATTGTTTTAAGAGAAACT
261 CAAAATTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAGAAAAAAATTATTTCAAGAGAAACT
* * *
628176 GTCTCAAGAGAGACAAAGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGTGACAAAACTTAG
326 GTCTCAAGAGAGACAAAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAG
628241 TTCCAAA
391 TTCCAAA
628248 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTAATGTAAAACATATTCAAAGATTTTGTTCCAAT
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTAATGTAAAACATATTCAAAGATTTTGTTCCAAT
* *
628313 GGAAACTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
66 GGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
628378 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTTGTTTTGAGTAAATTAGTCTCAAGCGAGAC
131 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTTGTTTTGAGTAAATTAGTCTCAAGCGAGAC
628443 GACCCCTTGTTTC
196 GACCCCTTGTTTC
628456 TAGAGAAACA
Statistics
Matches: 568, Mismatches: 31, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
394 2 0.00
395 4 0.01
396 90 0.16
397 424 0.75
398 25 0.04
399 23 0.04
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.26
Consensus pattern (397 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTGTTTAATGTAAAACATATTCAAAGATTTTGTTCCAAT
GGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
TTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTTGTTTTGAGTAAATTAGTCTCAAGCGAGAC
GACCCCTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAACGGAAACTGTCTCAAGAGAGA
CAAAATTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAGAAAAAAATTATTTCAAGAGAAACT
GTCTCAAGAGAGACAAAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAG
TTCCAAA
Found at i:628227 original size:42 final size:42
Alignment explanation
Indices: 628080--628271 Score: 199
Period size: 42 Copynumber: 4.8 Consensus size: 42
628070 ATTCAAAGAT
*
628080 TTTGTTTCAAGGGAAACTGTCTC-A-AGAG----AGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGACAAAA
* * *
628116 TTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAGAAAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGACAAAA
* *
628158 ATTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGACAAAA
* *
628200 TTTGTTTCAAGAGAAATTGTCTCAAGAGTGACAAA-AC----
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGACAAAA
* * * *
628237 TTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
628272 ATTTGTTTAA
Statistics
Matches: 133, Mismatches: 17, Indels: 11
0.83 0.11 0.07
Matches are distributed among these distances:
36 23 0.17
37 30 0.23
38 3 0.02
41 2 0.02
42 75 0.56
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (42 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGACAAAA
Found at i:628348 original size:222 final size:223
Alignment explanation
Indices: 627969--628372 Score: 591
Period size: 222 Copynumber: 1.8 Consensus size: 223
627959 GTCTCAAGAG
* * *** *
627969 AGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTTGTTTTGAGTAAATTAGT
1 AGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTAGTTAAAAGTAAACTAGT
*** * *
628034 CTCAAGCGAGACGACCCCTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAGGGAAACTG
66 CTCAAGCGAGACGAAAACTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTCCAAGGGAAACTA
*
628099 TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAGAAAAAAATTGTT
131 TCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAAAGACAAAGAAAAAAATTGTT
628164 TTAAGAGAAACTGTCTCAAGAGAGACAA
196 TTAAGAGAAACTGTCTCAAGAGAGACAA
*
628192 AGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGTGACAAAACTTAGTTCCAAAAG-AAACT-
1 AGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTAGTT--AAAAGTAAACTA
* * * *
628255 GTCTCAAGGGAGAC-AAAATTTGTTT-AATGTAAAACATATTCAAAGATTTTGTTCCAATGGAAA
64 GTCTCAAGCGAGACGAAAACTTGTTTCAA-GGAAAACATATTCAAAGATTTTGTTCCAAGGGAAA
*
628318 CTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAA
128 CTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAAAGACAAA
628373 ATTTATTTCA
Statistics
Matches: 160, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
221 2 0.01
222 91 0.57
223 61 0.38
224 4 0.03
225 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (223 bp):
AGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTAGTTAAAAGTAAACTAGT
CTCAAGCGAGACGAAAACTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTCCAAGGGAAACTA
TCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAAAGACAAAGAAAAAAATTGTT
TTAAGAGAAACTGTCTCAAGAGAGACAA
Found at i:628385 original size:21 final size:21
Alignment explanation
Indices: 628323--628387 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
628313 GGAAACTATC
628323 TCAAGAGAGACAAAATTTATT
1 TCAAGAGAGACAAAATTTATT
* * *
628344 TCAAG-G-G---AAA-CTGTC
1 TCAAGAGAGACAAAATTTATT
628359 TCAAGAGAGACAAAATTTATT
1 TCAAGAGAGACAAAATTTATT
628380 TCAAGAGA
1 TCAAGAGA
628388 AATTGTCTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 7 0.22
16 4 0.12
17 1 0.03
19 1 0.03
20 4 0.12
21 15 0.47
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTATT
Found at i:628427 original size:36 final size:34
Alignment explanation
Indices: 628321--628442 Score: 127
Period size: 36 Copynumber: 3.4 Consensus size: 34
628311 ATGGAAACTA
* * *
628321 TCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTG
1 TCTCAAGAGAGACAAAATTT-TTT-TAGAGAAATTG
*
628357 TCTCAAGAGAGACAAAATTTATTTCAAGAGAAATTG
1 TCTCAAGAGAGACAAAATTT-TTT-TAGAGAAATTG
*
628393 TCTCAAGAGAGACAAAATTTTGTTTTGAGTAAATTAG
1 TCTCAAGAGAGACAAAATTTT-TTTAGAG-AAATT-G
*
628430 TCTCAAGCGAGAC
1 TCTCAAGAGAGAC
628443 GACCCCTTGT
Statistics
Matches: 78, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
35 4 0.05
36 61 0.78
37 13 0.17
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (34 bp):
TCTCAAGAGAGACAAAATTTTTTTAGAGAAATTG
Found at i:628670 original size:42 final size:43
Alignment explanation
Indices: 628597--628723 Score: 150
Period size: 42 Copynumber: 3.0 Consensus size: 43
628587 ACTTCATTGG
* * * *
628597 GCACGATATCCTTCTTCGTGAAGTTGAAATCGTGGATGGTTGA
1 GCACGATATCCTCCGTCATGGAGTTGAAATCGTGGATGGTTGA
* *
628640 GCATGATATCCTCCGTCATGGAG-TGAAATCGTGGAT-TTATGA
1 GCACGATATCCTCCGTCATGGAGTTGAAATCGTGGATGGT-TGA
** *
628682 TTACGATGTCCTCCGTCATGGAGTTGAAATCGTGGATGGTTG
1 GCACGATATCCTCCGTCATGGAGTTGAAATCGTGGATGGTTG
628724 CTTCGTTGTG
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 1 0.01
42 35 0.50
43 33 0.47
44 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (43 bp):
GCACGATATCCTCCGTCATGGAGTTGAAATCGTGGATGGTTGA
Found at i:631764 original size:36 final size:36
Alignment explanation
Indices: 631714--631784 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
631704 AAGTATTGAT
*
631714 ATGTTTTTTGTACTTGTTCCAAAAAGTCTCGAATGG
1 ATGTTTTTTATACTTGTTCCAAAAAGTCTCGAATGG
* *
631750 ATGTTTTTTATACTTGTTCCAAAAATTCTTGAATG
1 ATGTTTTTTATACTTGTTCCAAAAAGTCTCGAATG
631785 ACTACATCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (36 bp):
ATGTTTTTTATACTTGTTCCAAAAAGTCTCGAATGG
Found at i:633600 original size:34 final size:33
Alignment explanation
Indices: 633562--633670 Score: 114
Period size: 33 Copynumber: 3.3 Consensus size: 33
633552 AATCCTACTT
*
633562 GGACTCAAAATGCTTCGGTTTTAGTGTTTCAATA
1 GGACTCAAAATACTT-GGTTTTAGTGTTTCAATA
* *
633596 GGACTC-AAATACATGGGGTTTAGTGTTTCAATA
1 GGACTCAAAATAC-TTGGTTTTAGTGTTTCAATA
* * * *
633629 TGACT-TAAATACGTTGGTTTTTGTGTTTTAATA
1 GGACTCAAAATAC-TTGGTTTTAGTGTTTCAATA
633662 GGACTCAAA
1 GGACTCAAA
633671 TAGGTTGATT
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
33 52 0.85
34 9 0.15
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (33 bp):
GGACTCAAAATACTTGGTTTTAGTGTTTCAATA
Found at i:633623 original size:33 final size:33
Alignment explanation
Indices: 633581--633672 Score: 121
Period size: 33 Copynumber: 2.8 Consensus size: 33
633571 ATGCTTCGGT
633581 TTTAGTGTTTCAATAGGACTCAAATACATGGGG
1 TTTAGTGTTTCAATAGGACTCAAATACATGGGG
* * * * *
633614 TTTAGTGTTTCAATATGACTTAAATACGTTGGT
1 TTTAGTGTTTCAATAGGACTCAAATACATGGGG
* *
633647 TTTTGTGTTTTAATAGGACTCAAATA
1 TTTAGTGTTTCAATAGGACTCAAATA
633673 GGTTGATTCA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (33 bp):
TTTAGTGTTTCAATAGGACTCAAATACATGGGG
Found at i:633774 original size:25 final size:21
Alignment explanation
Indices: 633731--633780 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
633721 GGCCTGCAAA
*
633731 AATAATAAAAGAAAAAAATATT
1 AATAATAAAAAAAAAAAATA-T
633753 AATAATAAATAAATAAATAAATAT
1 AATAATAAA-AAA-AAA-AAATAT
633777 AATA
1 AATA
633781 TAATATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 9 0.38
23 2 0.08
24 8 0.33
25 5 0.21
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (21 bp):
AATAATAAAAAAAAAAAATAT
Found at i:635936 original size:33 final size:31
Alignment explanation
Indices: 635894--635980 Score: 115
Period size: 33 Copynumber: 2.8 Consensus size: 31
635884 AGTTGGTAAG
635894 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAA--TA
*
635927 TTGGAAATTTCATCTTGGTTAGTGGCCAATA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAATA
* *
635958 TTGGAAAATTC-T-TTGGTAGGTGG
1 TTGGAAATTTCATCTTGGTTGGTGG
635981 TCAAACTTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.18
30 1 0.02
31 12 0.24
33 28 0.56
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.39
Consensus pattern (31 bp):
TTGGAAATTTCATCTTGGTTGGTGGCCAATA
Found at i:635963 original size:31 final size:32
Alignment explanation
Indices: 635894--635964 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 32
635884 AGTTGGTAAG
*
635894 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTAGTGGCCAAC-TA
635927 TTGGAAATTTCATCTTGGTTAGTGGCCAA-TA
1 TTGGAAATTTCATCTTGGTTAGTGGCCAACTA
635958 TTGGAAA
1 TTGGAAA
635965 ATTCTTTGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
31 9 0.24
33 28 0.76
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (32 bp):
TTGGAAATTTCATCTTGGTTAGTGGCCAACTA
Found at i:640663 original size:29 final size:32
Alignment explanation
Indices: 640584--640674 Score: 125
Period size: 33 Copynumber: 2.9 Consensus size: 32
640574 AGTTAGCAAG
*
640584 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAAC-TA
*
640617 TTGGAAACTTCATCTTGGTTGGTGGCCAAC-A
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTA
*
640648 TTGGAAAATTC-T-TTGGTAGGTGGCCAA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAA
640675 ACTTTGAACA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
29 14 0.25
30 1 0.02
31 11 0.20
33 29 0.53
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.35
Consensus pattern (32 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTA
Found at i:648603 original size:23 final size:22
Alignment explanation
Indices: 648565--648732 Score: 63
Period size: 25 Copynumber: 6.9 Consensus size: 22
648555 AAAAGGTAAG
* *
648565 AAAT-AAATAAATAAATTAATT
1 AAATAAAATAAAAAAATAAATT
*
648586 AATTAAAATGAAAAAAATAAATT
1 AAATAAAAT-AAAAAAATAAATT
**
648609 AAATAAAAGATAAGACAAAGA-AAACA
1 AAAT-AAA-ATAA-A-AAA-ATAAATT
648635 AAGATAAAATAGTAAGTAAAATAAA-T
1 AA-ATAAAATA--AA--AAAATAAATT
*
648661 AAATAAAATATTAAAATATATATATAT
1 AAATAAAATA--AAAA-A-ATAAAT-T
* *
648688 ATATATAAATAAAACAAATAAATA
1 AAATA-AAATAAAA-AAATAAATT
*
648712 AAATAATAATAAAAAAGTAAA
1 AAATAA-AATAAAAAAATAAA
648733 AATAATATAT
Statistics
Matches: 113, Mismatches: 15, Indels: 36
0.69 0.09 0.22
Matches are distributed among these distances:
21 3 0.03
22 4 0.04
23 23 0.20
24 17 0.15
25 26 0.23
26 19 0.17
27 16 0.14
28 5 0.04
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (22 bp):
AAATAAAATAAAAAAATAAATT
Found at i:648723 original size:61 final size:60
Alignment explanation
Indices: 648651--648777 Score: 164
Period size: 63 Copynumber: 2.0 Consensus size: 60
648641 AAATAGTAAG
* *
648651 TAAAATAAATAAATAAAATATTAAAATATATATATATATATATAAATAAAACAAATAAATAAAA
1 TAAAATAAAAAAATAAAA-A-TAATATATATATATATATA-ATAAATAAAA-AAATAAATAAAA
* * *
648715 TAATAATAAAAAAGTAAAAATAATATATATATATATATAATAAATAAAAACATAAAAAAAA
1 TAA-AATAAAAAAATAAAAATAATATATATATATATATAATAAATAAAAAAATAAATAAAA
648776 TA
1 TA
648778 GTATATATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
61 12 0.21
62 10 0.18
63 18 0.32
64 4 0.07
65 13 0.23
ACGTcount: A:0.69, C:0.02, G:0.01, T:0.28
Consensus pattern (60 bp):
TAAAATAAAAAAATAAAAATAATATATATATATATATAATAAATAAAAAAATAAATAAAA
Done.