Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009029.1 Hibiscus syriacus cultivar Beakdansim tig00112429_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: 496945
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 1 of 3
Found at i:374 original size:184 final size:185
Alignment explanation
Indices: 65--438 Score: 693
Period size: 184 Copynumber: 2.0 Consensus size: 185
55 TAGATTGCTT
65 AGTAAATTGTTTCGGTTGCTGCCAATTCTGCTAAACTGGTATTCTTTAACACTGTGAAATAGTAT
1 AGTAAATTGTTTCGGTTGCTGCCAATTCTGCTAAACTGGTATTCTTTAACACTGTGAAATAGTAT
130 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTTGCTGCCAATTCTGCTAAACTG
66 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTTGCTGCCAATTCTGCTAAACTG
195 TGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
249 AGTAAATT-TGTTC-GTTGCTGCC-ATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTGT-TTCGGTTGCTGCCAATTCTGCTAAACTG-GTATTCTTTAACACTGTGAAATAGT
311 ATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTTGCTGCCAATTCTGCTAAA
64 A-TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTTGCTGCCAATTCTGCTAAA
376 CTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
128 CTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
434 AGTAA
1 AGTAA
439 TTTATCCATT
Statistics
Matches: 186, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
182 14 0.08
183 36 0.19
184 101 0.54
185 35 0.19
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (185 bp):
AGTAAATTGTTTCGGTTGCTGCCAATTCTGCTAAACTGGTATTCTTTAACACTGTGAAATAGTAT
TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:408 original size:94 final size:93
Alignment explanation
Indices: 65--438 Score: 679
Period size: 94 Copynumber: 4.1 Consensus size: 93
55 TAGATTGCTT
65 AGTAAA-TTGTTTCGGTTGCTGCCAATTCTGCTAAACTG-GTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTTG-TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
128 A-TTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
156 AGTAAATTTGTTCGGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-T
1 AGTAAATTTGTTCGG-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
220 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
249 AGTAAATTTGTTC-GTTGCTGCC-ATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
312 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
340 AGTAAATTTGTTCGGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTTGTTCGG-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
405 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
434 AGTAA
1 AGTAA
439 TTTATCCATT
Statistics
Matches: 275, Mismatches: 0, Indels: 13
0.95 0.00 0.05
Matches are distributed among these distances:
90 38 0.14
91 62 0.23
92 30 0.11
93 71 0.26
94 74 0.27
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:522 original size:19 final size:19
Alignment explanation
Indices: 482--610 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
472 TAGTTTACTT
* *
482 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
502 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
521 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
540 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
554 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
573 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
587 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
606 TCGCA
1 TCGCA
611 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:561 original size:33 final size:32
Alignment explanation
Indices: 518--610 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
508 CGCGAAACCA
**
518 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
550 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
583 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
611 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:608 original size:52 final size:52
Alignment explanation
Indices: 482--610 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
472 TAGTTTACTT
**
482 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
534 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
587 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
611 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:628 original size:19 final size:19
Alignment explanation
Indices: 606--739 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
596 GAAACCAAAA
*
606 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
625 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
641 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
658 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
674 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
691 TCGCGTTGCGATTTT-GGT
1 TCGCGTTGCGATTTTCATT
*
709 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
729 TCGTGTTGCGA
1 TCGCGTTGCGA
740 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
18 16 0.17
19 29 0.31
20 11 0.12
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:647 original size:14 final size:14
Alignment explanation
Indices: 628--684 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
618 TTTCATTTCG
628 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
642 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
659 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
675 CGTTGCGATT
1 CGTTGCGATT
685 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:653 original size:33 final size:33
Alignment explanation
Indices: 611--739 Score: 168
Period size: 33 Copynumber: 3.8 Consensus size: 33
601 CAAAATCGCA
611 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
* *
644 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
*
677 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCT--TT--CG
* *
714 TTGCGATTTTAAGTTTCGTGTTGCGA
1 TTGCGATTTTCA-TTTCGCGTTGCGA
740 AAGTAAACTA
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
33 58 0.69
35 1 0.01
37 13 0.15
38 12 0.14
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:2590 original size:37 final size:37
Alignment explanation
Indices: 2548--2618 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
2538 AATTGATTGT
*
2548 TTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
2585 TTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTGATTGTTTAATTGATTTGTAAAAGATGATT
2619 TGTAAAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.30, C:0.01, G:0.17, T:0.52
Consensus pattern (37 bp):
TTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:2617 original size:14 final size:14
Alignment explanation
Indices: 2600--2635 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2590 ATTGTTTAAT
2600 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2614 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2628 TGATTTGT
1 TGATTTGT
2636 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2758 original size:19 final size:19
Alignment explanation
Indices: 2742--2843 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2732 AAAAATGACT
2742 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2761 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2780 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2794 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2813 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2833 ATCGCAATGCG
1 ATCGCAATGCG
2844 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2896 original size:19 final size:19
Alignment explanation
Indices: 2872--3178 Score: 358
Period size: 19 Copynumber: 17.4 Consensus size: 19
2862 GATTATCTCG
2872 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2891 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2910 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
2924 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2943 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2962 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
2981 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
3000 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
3015 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3033 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3052 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3066 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3085 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3104 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3118 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3138 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
3152 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
3171 TTGCGATT
1 TTGCGATT
3179 GTATTTTCCG
Statistics
Matches: 249, Mismatches: 13, Indels: 52
0.79 0.04 0.17
Matches are distributed among these distances:
14 32 0.13
15 2 0.01
16 31 0.12
17 28 0.11
18 5 0.02
19 139 0.56
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2947 original size:71 final size:71
Alignment explanation
Indices: 2872--3111 Score: 355
Period size: 71 Copynumber: 3.4 Consensus size: 71
2862 GATTATCTCG
2872 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
2937 TTCGCA
66 TTCGCA
* *
2943 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
* *
3006 TT-ATGTCG-G
61 TTCATTTCGCA
*
3015 TT-CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
3079 TTCGCA
66 TTCGCA
3085 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
3112 CTCTCGTTGC
Statistics
Matches: 150, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
66 6 0.04
68 6 0.04
69 7 0.05
70 2 0.01
71 107 0.71
72 2 0.01
73 7 0.05
74 7 0.05
76 6 0.04
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:3031 original size:142 final size:136
Alignment explanation
Indices: 2840--3178 Score: 504
Period size: 142 Copynumber: 2.4 Consensus size: 136
2830 AAAATCGCAA
2840 TGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTT-TAATTTCGCATTGCGATTAT-TCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
*
2904 TTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
64 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-
*
2969 TTTCATTTCGTAT
128 -TTC-TCTCG--T
2982 TGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTTTAATTTCGCATTGCGATTAT-TC-GTTGCGATTTTCATTTCGCATTGCGATTTTCAT
3046 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
64 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
3111 TCTCTCGT
129 TCTCTCGT
* * *
3119 TGCGATTTTCATTTCCGCATTGCGATT-TTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTAATTT-CGCATTGCGATTATTC--GTTGCGATTTTCATTTCGCATTGCGATT
3179 GTATTTTCCG
Statistics
Matches: 185, Mismatches: 7, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
136 2 0.01
137 18 0.10
138 34 0.18
139 4 0.02
140 3 0.02
142 118 0.64
143 6 0.03
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (136 bp):
TGCGATTTTAATTTCGCATTGCGATTATTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTC
TCTCGT
Found at i:3117 original size:52 final size:52
Alignment explanation
Indices: 2872--3150 Score: 354
Period size: 52 Copynumber: 5.2 Consensus size: 52
2862 GATTATCTCG
*
2872 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
2924 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
2981 TTGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
3033 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
3085 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
3138 TTGCGATTTTCAT
1 TTGCGATTTTCAT
3151 GTTGGGATTT
Statistics
Matches: 212, Mismatches: 7, Indels: 15
0.91 0.03 0.06
Matches are distributed among these distances:
51 3 0.01
52 152 0.72
53 19 0.09
54 6 0.03
55 8 0.04
57 24 0.11
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:5499 original size:12 final size:12
Alignment explanation
Indices: 5482--5506 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5472 TTCTTCGGGA
5482 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5494 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5506 C
1 C
5507 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:5715 original size:24 final size:24
Alignment explanation
Indices: 5681--5727 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5671 CTGAAACATC
5681 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
5705 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
5728 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:6428 original size:20 final size:20
Alignment explanation
Indices: 6400--6768 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
6390 AAATTTCAGT
* * * *
6400 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
6420 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
6440 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
6460 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
6480 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6500 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
6520 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
6540 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6560 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6580 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
6600 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
6620 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6640 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
6660 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
6680 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
6700 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
6720 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
6740 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
6760 GTTGCGATT
1 GTTGCGATT
6769 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:7251 original size:18 final size:16
Alignment explanation
Indices: 7216--7246 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7206 AACTATAGGG
7216 TATTATATTGTTAAAT
1 TATTATATTGTTAAAT
*
7232 TATTTTATTGTTAAA
1 TATTATATTGTTAAA
7247 AATTAGAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
TATTATATTGTTAAAT
Found at i:7856 original size:30 final size:29
Alignment explanation
Indices: 7820--7877 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
7810 AGTGTTAGCC
7820 GTAGGTCGCCATGC-CTTTCCGGGCGACCTT
1 GTAGGTCGCCATGCAC--TCCGGGCGACCTT
7850 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
7878 AGCCTTGCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 12 0.44
30 14 0.52
31 1 0.04
ACGTcount: A:0.12, C:0.34, G:0.31, T:0.22
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:7965 original size:23 final size:23
Alignment explanation
Indices: 7935--7983 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
7925 GCGACCTACC
7935 CTCGCTCGGCTGCCCTTGCATAG
1 CTCGCTCGGCTGCCCTTGCATAG
7958 CTCGCTCGGCTGCCCTTGCATAG
1 CTCGCTCGGCTGCCCTTGCATAG
7981 CTC
1 CTC
7984 ATTCGGATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.08, C:0.41, G:0.24, T:0.27
Consensus pattern (23 bp):
CTCGCTCGGCTGCCCTTGCATAG
Found at i:7989 original size:23 final size:23
Alignment explanation
Indices: 7939--7989 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
7929 CCTACCCTCG
*
7939 CTCGGCTGCCCTTGCATAGCTCG
1 CTCGGCTGCCCTTGCATAGCTCA
7962 CTCGGCTGCCCTTGCATAGCTCA
1 CTCGGCTGCCCTTGCATAGCTCA
*
7985 TTCGG
1 CTCGG
7990 ATGGCCTCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.10, C:0.37, G:0.25, T:0.27
Consensus pattern (23 bp):
CTCGGCTGCCCTTGCATAGCTCA
Found at i:8014 original size:24 final size:24
Alignment explanation
Indices: 7986--8040 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
7976 CATAGCTCAT
7986 TCGGATGGCCTCGGTCAGAT-GCTC
1 TCGGATGGCCTCGGTCAGATGGC-C
* *
8010 TCGGATAGCCTCGGTCGGATGGCC
1 TCGGATGGCCTCGGTCAGATGGCC
8034 TCGGATG
1 TCGGATG
8041 CCCAGCGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.13, C:0.27, G:0.36, T:0.24
Consensus pattern (24 bp):
TCGGATGGCCTCGGTCAGATGGCC
Found at i:8027 original size:14 final size:14
Alignment explanation
Indices: 7986--8037 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
7976 CATAGCTCAT
7986 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
*
8000 TCAGAT-G-CTC--
1 TCGGATGGCCTCGG
*
8010 TCGGATAGCCTCGG
1 TCGGATGGCCTCGG
8024 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
8038 ATGCCCAGCG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 5 0.16
11 1 0.03
12 6 0.19
13 1 0.03
14 18 0.58
ACGTcount: A:0.12, C:0.29, G:0.37, T:0.23
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:8117 original size:29 final size:29
Alignment explanation
Indices: 8080--8195 Score: 196
Period size: 29 Copynumber: 4.0 Consensus size: 29
8070 GCTATCTCTT
* * *
8080 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGGTCGCCCGGAAGGCATGGCGACCTA
8109 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGGTCGCCCGGAAGGCATGGCGACCTA
*
8138 GTAGGTCGCCCGGAAGGCATGACGACCTA
1 GTAGGTCGCCCGGAAGGCATGGCGACCTA
8167 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGGTCGCCCGGAAGGCATGGCGACCTA
8196 CGGCCAACAC
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 82 1.00
ACGTcount: A:0.22, C:0.28, G:0.36, T:0.14
Consensus pattern (29 bp):
GTAGGTCGCCCGGAAGGCATGGCGACCTA
Found at i:8927 original size:21 final size:24
Alignment explanation
Indices: 8902--8945 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
8892 TATAAAATTG
8902 AAAAT-AT-AAATTTT-TTTTAAT
1 AAAATGATAAAATTTTATTTTAAT
*
8923 AAAATGGTAAAATTTTATTTTAA
1 AAAATGATAAAATTTTATTTTAA
8946 CTCCGGAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 1 0.05
23 7 0.37
24 6 0.32
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (24 bp):
AAAATGATAAAATTTTATTTTAAT
Found at i:8943 original size:28 final size:28
Alignment explanation
Indices: 8877--8935 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
8867 TCATAAAGTT
* *
8877 TATATAATTTTTTTTTATAAAATTGAAAA
1 TATA-AATTTTTTTTAATAAAATGGAAAA
8906 TATAAATTTTTTTTAATAAAATGGTAAAA
1 TATAAATTTTTTTTAATAAAATGG-AAAA
8935 T
1 T
8936 TTTATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (28 bp):
TATAAATTTTTTTTAATAAAATGGAAAA
Found at i:9640 original size:18 final size:17
Alignment explanation
Indices: 9613--9651 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
9603 TCATATTTAT
*
9613 TTATATAAAATATAATA
1 TTATATAAAAAATAATA
9630 TTATATAAAAAAATAATA
1 TTATAT-AAAAAATAATA
9648 TTAT
1 TTAT
9652 GATCTTGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTATATAAAAAATAATA
Found at i:12910 original size:2 final size:2
Alignment explanation
Indices: 12903--12943 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
12893 AGCCCTTTAC
12903 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C- CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12944 TTTTTATCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:13231 original size:18 final size:19
Alignment explanation
Indices: 13208--13252 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
13198 TTTACTGAAT
*
13208 ATAAAATTATTAGT-GAGA
1 ATAAAATTATTACTAGAGA
*
13226 ATAAAA-AATTACTAGAGA
1 ATAAAATTATTACTAGAGA
13244 ATAAAATTA
1 ATAAAATTA
13253 ATGGGAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 5 0.23
18 16 0.73
19 1 0.05
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.29
Consensus pattern (19 bp):
ATAAAATTATTACTAGAGA
Found at i:14246 original size:573 final size:573
Alignment explanation
Indices: 13158--14306 Score: 1989
Period size: 573 Copynumber: 2.0 Consensus size: 573
13148 ATATTATAGA
* * *
13158 GAATGATTGAGCAGTGGGTTGAAAATTATTCAACGTTTGATTTACTGAATATAAAATTATTAGTG
1 GAATGATTGAGCAGTGGGTTGAAAATTATTCAACGTTTGATTCACGGAATATAAAATTATCAGTG
* *
13223 AGAATAAAAAATTACTAGAGAATAAAATTAATGGGAATATTATATTTTGTGTTTGGTTGGTTTAG
66 AGAATAAAAAATTACAAGAGAATAAAATTAATAGGAATATTATATTTTGTGTTTGGTTGGTTTAG
* * *
13288 CAGGAATGTAAAATTATCGTGTTTGGTTAAAGAAATAAATGATTATTGGAATGCATATTTGACCA
131 CAGGAATGTAAAATTACCGTGTTTGGTTAAAGAAATAAAAGATTATTAGAATGCATATTTGACCA
13353 AACTACCTTTATTATATATTTATATAATATTACAAATTGTAAAATTTTATATATTTTCTTTAAAA
196 AACTACCTTTATTATATATTTATATAATATTACAAATTGTAAAATTTTATATATTTTCTTTAAAA
13418 AATTAAATTCATAATATTTATATAAATTTTTTACAAAATTAAAAATATAAAAAATGTTTAATGAA
261 AATTAAATTCATAATATTTATATAAATTTTTTACAAAATTAAAAATATAAAAAATGTTTAATGAA
*
13483 AGGGTAAATTTTTTTAACCCCTGAACTTCATATAAAATTTTAATTATAGATTTTTTTTTGTAAAT
326 AGGGTAAATTTTTTTAACACCTGAACTTCATATAAAATTTTAATTATAGATTTTTTTTTGTAAAT
* *
13548 CTAAAATAATTTAAGGGTAAAATTGTAATTTAACATTTGTAAAATTTTTATTATTCAATGATAGA
391 CTAAAATAATTTAAGGATAAAATTGTAATTTAACATTTGTAAAATTTTTATTATTCAATGACAGA
13613 AGAATGATATACCCAAAAAAATCTACTATTGGTAATAAAACATTACCGGGAATAAGATTCTCGGC
456 AGAATGATATACCCAAAAAAATCTACTATTGGTAATAAAACATTACCGGGAATAAGATTCTCGGC
*
13678 CAACCAAACATGAGAATGTCTCACAATCCTTGAACCAAACACCCCCTTAGAGT
521 CAACCAAACATGAGAATGTCCCACAATCCTTGAACCAAACACCCCCTTAGAGT
* * * *
13731 GAATGATTGAGCAGTGGGTTGAAAATTATT-ATGCGTTTGGTTCACGGAATGTAAGATTATCAGT
1 GAATGATTGAGCAGTGGGTTGAAAATTATTCA-ACGTTTGATTCACGGAATATAAAATTATCAGT
* * * *
13795 GAGAATAAAAGATTACCAAG-GAATAAAATTACTAGGAATGTTGTATTTTGTGTTTGGTTGGTTT
65 GAGAATAAAAAATTA-CAAGAGAATAAAATTAATAGGAATATTATATTTTGTGTTTGGTTGGTTT
* * *
13859 TGCAGGAATGTAAAATTACCGTGTTTGGTTAAAGGAATAAAAGATTATTAGAATGTATATTTGAC
129 AGCAGGAATGTAAAATTACCGTGTTTGGTTAAAGAAATAAAAGATTATTAGAATGCATATTTGAC
* *
13924 CAAATTACCTTTATTATATATTTGTATAATATTACAAATTGTAAAATTTTATATATTTTCTTTAA
194 CAAACTACCTTTATTATATATTTATATAATATTACAAATTGTAAAATTTTATATATTTTCTTTAA
13989 AAAATTAAATTCATAATATTTATATAAATTTTTTACAAAATTAAAAATATAAAAAATGTTTAATG
259 AAAATTAAATTCATAATATTTATATAAATTTTTTACAAAATTAAAAATATAAAAAATGTTTAATG
*
14054 AAATGGTAAATTTTTTTTAACACCTGAACTTCATATAAAATTTTAATTATAGA-TTTTTTTTGTA
324 AAAGGGTAAA-TTTTTTTAACACCTGAACTTCATATAAAATTTTAATTATAGATTTTTTTTTGTA
* *
14118 AATCTAAAATAATTTAAGGATAAATTTGTAATTTAACATTTGTAGAATTTTTATTATTCAATGAC
388 AATCTAAAATAATTTAAGGATAAAATTGTAATTTAACATTTGTAAAATTTTTATTATTCAATGAC
*
14183 AGAAGAATGATATACCCAAAAAAATCTACTATTGGTAATAAAATATTACCGGGAATAAGATTCTC
453 AGAAGAATGATATACCCAAAAAAATCTACTATTGGTAATAAAACATTACCGGGAATAAGATTCTC
14248 GGCCAACCAAACATGAGAATGTCCCACAATCCTTGAACCAAACACCCCCTTAGAGT
518 GGCCAACCAAACATGAGAATGTCCCACAATCCTTGAACCAAACACCCCCTTAGAGT
14304 GAA
1 GAA
14307 AACATATATT
Statistics
Matches: 544, Mismatches: 29, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
572 1 0.00
573 499 0.92
574 44 0.08
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (573 bp):
GAATGATTGAGCAGTGGGTTGAAAATTATTCAACGTTTGATTCACGGAATATAAAATTATCAGTG
AGAATAAAAAATTACAAGAGAATAAAATTAATAGGAATATTATATTTTGTGTTTGGTTGGTTTAG
CAGGAATGTAAAATTACCGTGTTTGGTTAAAGAAATAAAAGATTATTAGAATGCATATTTGACCA
AACTACCTTTATTATATATTTATATAATATTACAAATTGTAAAATTTTATATATTTTCTTTAAAA
AATTAAATTCATAATATTTATATAAATTTTTTACAAAATTAAAAATATAAAAAATGTTTAATGAA
AGGGTAAATTTTTTTAACACCTGAACTTCATATAAAATTTTAATTATAGATTTTTTTTTGTAAAT
CTAAAATAATTTAAGGATAAAATTGTAATTTAACATTTGTAAAATTTTTATTATTCAATGACAGA
AGAATGATATACCCAAAAAAATCTACTATTGGTAATAAAACATTACCGGGAATAAGATTCTCGGC
CAACCAAACATGAGAATGTCCCACAATCCTTGAACCAAACACCCCCTTAGAGT
Found at i:14355 original size:22 final size:23
Alignment explanation
Indices: 14330--14373 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
14320 TAATATAGAT
14330 TTTTAT-ATAAATATAAATAAAA
1 TTTTATGATAAATATAAATAAAA
* *
14352 TTTTATGGTAAATATAAGTAAA
1 TTTTATGATAAATATAAATAAA
14374 TAAATAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (23 bp):
TTTTATGATAAATATAAATAAAA
Found at i:23838 original size:28 final size:30
Alignment explanation
Indices: 23807--23871 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
23797 TGCTAACTAC
* *
23807 AGGTGTCTAC-GTTTTCTCCATT-ACTTTT
1 AGGTGTCTACAATATTCTCCATTCACTTTT
*
23835 AGGTGTCTACAATATTCTCCGTTGCACTTTT
1 AGGTGTCTACAATATTCTCCATT-CACTTTT
23866 AGGTGT
1 AGGTGT
23872 ATACCGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 10 0.32
29 9 0.29
31 12 0.39
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (30 bp):
AGGTGTCTACAATATTCTCCATTCACTTTT
Found at i:25625 original size:2 final size:2
Alignment explanation
Indices: 25618--25676 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
25608 AACATTACTT
25618 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25660 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
25677 GATAACTTCA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30134 original size:28 final size:28
Alignment explanation
Indices: 30103--30159 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
30093 ATTCATATTC
30103 TTTTATTTAATTTAATAAACGAATGTTA
1 TTTTATTTAATTTAATAAACGAATGTTA
30131 TTTTATTTAATTTAATAAACGAATGTTA
1 TTTTATTTAATTTAATAAACGAATGTTA
30159 T
1 T
30160 ACGAGCAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.51
Consensus pattern (28 bp):
TTTTATTTAATTTAATAAACGAATGTTA
Found at i:31893 original size:15 final size:15
Alignment explanation
Indices: 31873--31901 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31863 AAGAATTACG
31873 TTATTTTAATTTAAT
1 TTATTTTAATTTAAT
31888 TTATTTTAATTTAA
1 TTATTTTAATTTAA
31902 CAAAGCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATTTTAATTTAAT
Found at i:36263 original size:147 final size:147
Alignment explanation
Indices: 36040--36330 Score: 528
Period size: 147 Copynumber: 2.0 Consensus size: 147
36030 GCGGTGACGA
36040 CGCATATTGATGACGACCGAAACGGGGTGGTTCGAGGGTAATGGCTAGGGTTATTTGATTTTGGG
1 CGCATATTGATGACGACCGAAACGGGGTGGTTCGAGGGTAATGGCTAGGGTTATTTGATTTTGGG
*
36105 GGAAAAACTTTGAGATTTGAGGTTAGTTCCCGAATAAGGGGGTTTATGGATTAACACCCAGTAAA
66 GGAAAAACTTTGAGATTTAAGGTTAGTTCCCGAATAAGGGGGTTTATGGATTAACACCCAGTAAA
36170 ATTATAATAAAACACGG
131 ATTATAATAAAACACGG
* *
36187 CGCATATTGATGACGATCGGAACGGGGTGGTTCGAGGGTAATGGCTAGGGTTATTTGATTTTGGG
1 CGCATATTGATGACGACCGAAACGGGGTGGTTCGAGGGTAATGGCTAGGGTTATTTGATTTTGGG
* * *
36252 GGGAAAACTTTGAGATTTAAGGTTAGTTTCCGAATAAGGGGGTTTATGGGTTAACACCCAGTAAA
66 GGAAAAACTTTGAGATTTAAGGTTAGTTCCCGAATAAGGGGGTTTATGGATTAACACCCAGTAAA
36317 ATTATAATAAAACA
131 ATTATAATAAAACA
36331 TATATTTAAA
Statistics
Matches: 138, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
147 138 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.29
Consensus pattern (147 bp):
CGCATATTGATGACGACCGAAACGGGGTGGTTCGAGGGTAATGGCTAGGGTTATTTGATTTTGGG
GGAAAAACTTTGAGATTTAAGGTTAGTTCCCGAATAAGGGGGTTTATGGATTAACACCCAGTAAA
ATTATAATAAAACACGG
Found at i:37024 original size:13 final size:13
Alignment explanation
Indices: 37006--37030 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36996 TAAAAATAAT
37006 TTAAAATATAAAA
1 TTAAAATATAAAA
37019 TTAAAATATAAA
1 TTAAAATATAAA
37031 GTGGTCAGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAATATAAAA
Found at i:40444 original size:16 final size:16
Alignment explanation
Indices: 40423--40453 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
40413 GTTCAAAATC
40423 GGGTACCCGAAGTACT
1 GGGTACCCGAAGTACT
40439 GGGTACCCGAAGTAC
1 GGGTACCCGAAGTAC
40454 CAGGTATCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.16
Consensus pattern (16 bp):
GGGTACCCGAAGTACT
Found at i:40459 original size:16 final size:16
Alignment explanation
Indices: 40424--40464 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
40414 TTCAAAATCG
**
40424 GGTACCCGAAGTACTG
1 GGTACCCGAAGTACCA
40440 GGTACCCGAAGTACCA
1 GGTACCCGAAGTACCA
*
40456 GGTATCCGA
1 GGTACCCGA
40465 TTCTCCGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (16 bp):
GGTACCCGAAGTACCA
Found at i:46426 original size:2 final size:2
Alignment explanation
Indices: 46421--46494 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
46411 CTATTTTTTA
46421 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46463 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46495 TACCCTTTTG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53913 original size:79 final size:79
Alignment explanation
Indices: 53824--53981 Score: 298
Period size: 79 Copynumber: 2.0 Consensus size: 79
53814 ATAAAAATGA
53824 GAAAACAACTCTCAAGAAACTCTCTAAATTCTCTCTAGTATTAGAAGAAAGCTAGAATGCTTTGA
1 GAAAACAACTCTCAAGAAACTCTCTAAATTCTCTCTAGTATTAGAAGAAAGCTAGAATGCTTTGA
53889 GATGATTTTGAAGC
66 GATGATTTTGAAGC
* *
53903 GAAAACAACTCTTAAGAAACTCTCTAAATTCTCTCTAGTATTAGAAGAAAGCTAGAATGCTTTGG
1 GAAAACAACTCTCAAGAAACTCTCTAAATTCTCTCTAGTATTAGAAGAAAGCTAGAATGCTTTGA
53968 GATGATTTTGAAGC
66 GATGATTTTGAAGC
53982 TATATGAGCT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (79 bp):
GAAAACAACTCTCAAGAAACTCTCTAAATTCTCTCTAGTATTAGAAGAAAGCTAGAATGCTTTGA
GATGATTTTGAAGC
Found at i:63450 original size:2 final size:2
Alignment explanation
Indices: 63443--63471 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
63433 ACGGCAAACA
63443 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
63472 ATTATGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65748 original size:6 final size:6
Alignment explanation
Indices: 65737--65777 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
65727 TTTGCGGATT
* * *
65737 TCCCTA TCCCTA TCCCTA TCCTTA TCCCTG TCCTTA TCCCT
1 TCCCTA TCCCTA TCCCTA TCCCTA TCCCTA TCCCTA TCCCT
65778 GTCCTTATCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.12, C:0.46, G:0.02, T:0.39
Consensus pattern (6 bp):
TCCCTA
Found at i:65754 original size:12 final size:12
Alignment explanation
Indices: 65737--65786 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
65727 TTTGCGGATT
*
65737 TCCCTATCCCTA
1 TCCCTATCCTTA
65749 TCCCTATCCTTA
1 TCCCTATCCTTA
*
65761 TCCCTGTCCTTA
1 TCCCTATCCTTA
*
65773 TCCCTGTCCTTA
1 TCCCTATCCTTA
65785 TC
1 TC
65787 TTCGTACTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.12, C:0.44, G:0.04, T:0.40
Consensus pattern (12 bp):
TCCCTATCCTTA
Found at i:68876 original size:19 final size:20
Alignment explanation
Indices: 68848--68893 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
68838 GTGCCCAACC
68848 AAATAAAAAT-AAAATGCAT
1 AAATAAAAATGAAAATGCAT
* *
68867 AAATAGAAATGAAAGTGCAT
1 AAATAAAAATGAAAATGCAT
68887 AAATAAA
1 AAATAAA
68894 TAAACATTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.65, C:0.04, G:0.11, T:0.20
Consensus pattern (20 bp):
AAATAAAAATGAAAATGCAT
Found at i:69557 original size:15 final size:15
Alignment explanation
Indices: 69537--69568 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
69527 TGACCGCCGA
69537 CCCGCTCCCCTAGGT
1 CCCGCTCCCCTAGGT
69552 CCCGCTCCCCTAGGT
1 CCCGCTCCCCTAGGT
69567 CC
1 CC
69569 AACAGTGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.56, G:0.19, T:0.19
Consensus pattern (15 bp):
CCCGCTCCCCTAGGT
Found at i:71398 original size:3 final size:3
Alignment explanation
Indices: 71390--71417 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
71380 TATATAGGGT
71390 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
71418 AAAAAATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:72214 original size:27 final size:25
Alignment explanation
Indices: 72184--72241 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 25
72174 TTAAAATGAA
* *
72184 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATATTT--ATCAAGTTAAT
72211 AATAAAATATATTTATCAAGTTAAT
1 AATAAAATATATTTATCAAGTTAAT
72236 -ATAAAA
1 AATAAAA
72242 AACATTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 6 0.21
25 10 0.34
27 13 0.45
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (25 bp):
AATAAAATATATTTATCAAGTTAAT
Found at i:72279 original size:25 final size:25
Alignment explanation
Indices: 72200--72284 Score: 86
Period size: 25 Copynumber: 3.4 Consensus size: 25
72190 ATATTTTTAA
72200 ATTAAGTTAATA-ATAAAATATATTT
1 ATTAAGTTAATATATAAAA-ATATTT
* *
72225 ATCAAGTTAATATA-AAAAACATTCT
1 ATTAAGTTAATATATAAAAATATT-T
*
72250 TTTAAGTTAATATATATAAAATA-TT
1 ATTAAGTTAATATATA-AAAATATTT
*
72275 ATTAATTTAA
1 ATTAAGTTAA
72285 GTATTTATAC
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
24 4 0.08
25 37 0.76
26 3 0.06
27 5 0.10
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (25 bp):
ATTAAGTTAATATATAAAAATATTT
Found at i:72422 original size:2 final size:2
Alignment explanation
Indices: 72415--72456 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
72405 TATTACGAAT
72415 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
72456 T
1 T
72457 TTAAGAAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:72966 original size:66 final size:66
Alignment explanation
Indices: 72860--72992 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
72850 TTTTTAAAAA
72860 TGTTTGTTAGCGGTCTTCTCGACGCATACATAAATAGCAAGCATTGGTACACAAAACACAAGCTT
1 TGTTTGTTAGCGGTCTTCTCGACGCATACATAAATAGCAAGCATTGGTACACAAAACACAAGCTT
72925 T
66 T
72926 TGTTTGTTAGCGGTCTTCTCGACGCATACATAAATAGCAAGCATTGGTACACAAAACACAAGCTT
1 TGTTTGTTAGCGGTCTTCTCGACGCATACATAAATAGCAAGCATTGGTACACAAAACACAAGCTT
72991 T
66 T
72992 T
1 T
72993 TATGGTCTTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (66 bp):
TGTTTGTTAGCGGTCTTCTCGACGCATACATAAATAGCAAGCATTGGTACACAAAACACAAGCTT
T
Found at i:73684 original size:3 final size:3
Alignment explanation
Indices: 73676--73705 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
73666 AAGGTAAACC
73676 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
73706 TGATTTAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:82739 original size:31 final size:32
Alignment explanation
Indices: 82687--82766 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 32
82677 CACATGTCGT
* **
82687 TAAATTATCAA-TTTTGGTCTGTTTTAATACC
1 TAAACTATCAATTTTTTATCTGTTTTAATACC
82718 TAAACTATC-ATTTTTTATCTGTTTTAATACC
1 TAAACTATCAATTTTTTATCTGTTTTAATACC
*
82749 TAAACTTTCAATTTTTTA
1 TAAACTATCAATTTTTTA
82767 ATCCCATCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
30 1 0.02
31 34 0.79
32 8 0.19
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.51
Consensus pattern (32 bp):
TAAACTATCAATTTTTTATCTGTTTTAATACC
Found at i:84506 original size:26 final size:29
Alignment explanation
Indices: 84470--84542 Score: 121
Period size: 29 Copynumber: 2.6 Consensus size: 29
84460 AGAAGAAAAA
* *
84470 GAAGAAGAAGAAAAAGGAGGGGTTGGGTT
1 GAAGAAGAAGAGAGAGGAGGGGTTGGGTT
84499 GAAGAAGAAGAGAGAGGAGGGGTTGGGTT
1 GAAGAAGAAGAGAGAGGAGGGGTTGGGTT
84528 GAAGAAGAAGA-AGAG
1 GAAGAAGAAGAGAGAG
84543 TCGATCAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
28 4 0.10
29 38 0.90
ACGTcount: A:0.42, C:0.00, G:0.47, T:0.11
Consensus pattern (29 bp):
GAAGAAGAAGAGAGAGGAGGGGTTGGGTT
Found at i:91565 original size:2 final size:2
Alignment explanation
Indices: 91558--91594 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
91548 AATCCAAGTT
91558 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
91595 TAACAGTGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:92266 original size:7 final size:7
Alignment explanation
Indices: 92254--92278 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
92244 CCCTTAATTA
92254 AAATATC
1 AAATATC
92261 AAATATC
1 AAATATC
92268 AAATATC
1 AAATATC
92275 AAAT
1 AAAT
92279 TGTTGTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATATC
Found at i:93363 original size:76 final size:76
Alignment explanation
Indices: 93252--93395 Score: 173
Period size: 76 Copynumber: 1.9 Consensus size: 76
93242 CGGGGTGGGT
* ** * * *
93252 ACAAATAAAATTTCAGGGTCGACATCTTTAGTAAAATAAACAACTACCATAAAGAAATTT-AGAT
1 ACAAATAAAATTTCAGGATAAACACCTTTAATAAAATAAACAACTAACATAAAGAAATTTGAG-T
93316 TCCATGGTGAAC
65 TCCATGGTGAAC
* * ** *
93328 ACAAATAAAATTTTAGGATAAACACCTTTAATAAAATGAATGACTAACATCAAGAAATTTGAGTT
1 ACAAATAAAATTTCAGGATAAACACCTTTAATAAAATAAACAACTAACATAAAGAAATTTGAGTT
93393 CCA
66 CCA
93396 GGAAGGGCAC
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
76 54 0.96
77 2 0.04
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.27
Consensus pattern (76 bp):
ACAAATAAAATTTCAGGATAAACACCTTTAATAAAATAAACAACTAACATAAAGAAATTTGAGTT
CCATGGTGAAC
Found at i:94734 original size:63 final size:63
Alignment explanation
Indices: 94634--94759 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
94624 TTTTCTCGTG
*
94634 TTGTTTTAAAGTATGGTGGTCATATGAAATCCGAAATGTCAATGACTTAAAATATTATTAGAC
1 TTGTTTTAAAGTATGGTGGTCATATGAAATCCAAAATGTCAATGACTTAAAATATTATTAGAC
*
94697 TTGTTTTAAAGTATGGTGGTCATATGAAATCCAAAATGTCAATGACTTAAAGTATTATTAGAC
1 TTGTTTTAAAGTATGGTGGTCATATGAAATCCAAAATGTCAATGACTTAAAATATTATTAGAC
94760 AAAAAATATT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (63 bp):
TTGTTTTAAAGTATGGTGGTCATATGAAATCCAAAATGTCAATGACTTAAAATATTATTAGAC
Found at i:96400 original size:20 final size:20
Alignment explanation
Indices: 96377--96446 Score: 140
Period size: 20 Copynumber: 3.5 Consensus size: 20
96367 ACTCAGTTTC
96377 CAAATTCGCATTGCGATTTA
1 CAAATTCGCATTGCGATTTA
96397 CAAATTCGCATTGCGATTTA
1 CAAATTCGCATTGCGATTTA
96417 CAAATTCGCATTGCGATTTA
1 CAAATTCGCATTGCGATTTA
96437 CAAATTCGCA
1 CAAATTCGCA
96447 ACATTTAATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
CAAATTCGCATTGCGATTTA
Found at i:96405 original size:40 final size:41
Alignment explanation
Indices: 96361--96448 Score: 128
Period size: 40 Copynumber: 2.2 Consensus size: 41
96351 GAACTCCAAT
*
96361 TTCGCAACT-C-AGTTTCCAAATTCGCATTGCGATTTACAAA
1 TTCGCAACTGCGA-TTTACAAATTCGCATTGCGATTTACAAA
*
96401 TTCGC-ATTGCGATTTACAAATTCGCATTGCGATTTACAAA
1 TTCGCAACTGCGATTTACAAATTCGCATTGCGATTTACAAA
96441 TTCGCAAC
1 TTCGCAAC
96449 ATTTAATTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 2 0.05
40 38 0.90
41 2 0.05
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.33
Consensus pattern (41 bp):
TTCGCAACTGCGATTTACAAATTCGCATTGCGATTTACAAA
Found at i:96475 original size:41 final size:42
Alignment explanation
Indices: 96377--96490 Score: 121
Period size: 40 Copynumber: 2.8 Consensus size: 42
96367 ACTCAGTTTC
* **
96377 CAAATTCGCATTGCGATTTACAAATTCG---CATTGCGATTTA
1 CAAATTCGCACTGCGATTTACAAATTCGCAACATT-TAATTTA
*
96417 CAAATTCGCATTGCGATTTACAAATTCGCAACATTTAATTT-
1 CAAATTCGCACTGCGATTTACAAATTCGCAACATTTAATTTA
* *
96458 CAAATTCGCAACT-CGATTTTCGAATTCGCAACA
1 CAAATTCGC-ACTGCGATTTACAAATTCGCAACA
96491 CGAATTTTAA
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
40 28 0.43
41 27 0.42
42 6 0.09
43 4 0.06
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.33
Consensus pattern (42 bp):
CAAATTCGCACTGCGATTTACAAATTCGCAACATTTAATTTA
Found at i:96505 original size:20 final size:19
Alignment explanation
Indices: 96462--96529 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
96452 TAATTTCAAA
*
96462 TTCGCAACTCGATTTTCGAA-
1 TTCGCAACACGATTTT--AAT
96482 TTCGCAACACGAATTTTAAT
1 TTCGCAACACG-ATTTTAAT
* *
96502 TTCGCAACA-GGTTTTATT
1 TTCGCAACACGATTTTAAT
96520 TTCGCAACAC
1 TTCGCAACAC
96530 AAATGTTTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
18 15 0.36
19 3 0.07
20 19 0.45
21 5 0.12
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (19 bp):
TTCGCAACACGATTTTAAT
Found at i:97147 original size:12 final size:12
Alignment explanation
Indices: 97130--97163 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
97120 ACCACATTTC
97130 CAATATCAAACA
1 CAATATCAAACA
97142 CAATATCAAACA
1 CAATATCAAACA
*
97154 CAATCTCAAA
1 CAATATCAAA
97164 ACCCACAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.18
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:97320 original size:24 final size:24
Alignment explanation
Indices: 97293--97342 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
97283 TCGAAATTTT
97293 ATCTTGGTCAATACCCGGACTTTG
1 ATCTTGGTCAATACCCGGACTTTG
* *
97317 ATCTTGGTCAATACTCGGATTTTG
1 ATCTTGGTCAATACCCGGACTTTG
97341 AT
1 AT
97343 GATGTTTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (24 bp):
ATCTTGGTCAATACCCGGACTTTG
Found at i:100007 original size:63 final size:64
Alignment explanation
Indices: 99939--100088 Score: 223
Period size: 63 Copynumber: 2.4 Consensus size: 64
99929 AATTTAAAAC
*
99939 AACAAATCAACTTTTACAAATCAATTAAACAATCAAAAAATAAGAATTA-TTACTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACTCATCAATTA
* *** * *
100002 AACAAATCAACTTTTACAATTCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATTAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACTCATCAATTA
100066 AACAAATCAAC-TTTACAAATCAA
1 AACAAATCAACTTTTACAAATCAA
100089 CTTTTACAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
63 55 0.71
64 23 0.29
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACTCATCAATTA
Found at i:100085 original size:13 final size:14
Alignment explanation
Indices: 100067--100099 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
100057 CATTAATTAA
100067 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
100080 ACAAATCAACTTTT
1 ACAAATCAACTTTT
100094 ACAAAT
1 ACAAAT
100100 ACATCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:100563 original size:22 final size:21
Alignment explanation
Indices: 100538--100579 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
100528 GGATTCTACC
100538 TAAAAATCAC-AAAATATATATA
1 TAAAAAT-ACTAAAATA-ATATA
100560 TAAAAATACTAAAATAATAT
1 TAAAAATACTAAAATAATAT
100580 TATTTGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAATACTAAAATAATATA
Found at i:103937 original size:19 final size:18
Alignment explanation
Indices: 103914--103960 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 18
103904 TTATGAAACT
*
103914 TAAAATCGCAACGCTAAC
1 TAAAATCGCAACGCGAAC
103932 TGAAAATCGCAACGCGATAC
1 T-AAAATCGCAACGCGA-AC
103952 TAAAATCGC
1 TAAAATCGC
103961 GTTGTGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 22 0.85
20 3 0.12
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.17
Consensus pattern (18 bp):
TAAAATCGCAACGCGAAC
Found at i:104359 original size:22 final size:22
Alignment explanation
Indices: 104333--104375 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
104323 AGATAGACAG
*
104333 ATTTCGTCGGAGATGGGGACGA
1 ATTTCGTCGGAGATAGGGACGA
104355 ATTTCGTCGGAGATAGGGACG
1 ATTTCGTCGGAGATAGGGACG
104376 GATGTCGCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.14, G:0.40, T:0.23
Consensus pattern (22 bp):
ATTTCGTCGGAGATAGGGACGA
Found at i:104558 original size:20 final size:20
Alignment explanation
Indices: 104533--104581 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
104523 TAAATGCGCT
*
104533 TTGCGAATTTGACTTCTATG
1 TTGCGAATTTAACTTCTATG
*
104553 TTGCGAATTTAACTTCTGTG
1 TTGCGAATTTAACTTCTATG
*
104573 TTGTGAATT
1 TTGCGAATT
104582 ACAGATTCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTAACTTCTATG
Found at i:109934 original size:2 final size:2
Alignment explanation
Indices: 109927--109953 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
109917 CCCTCCCGCA
109927 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
109954 ACCATGTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:112923 original size:596 final size:596
Alignment explanation
Indices: 111791--113000 Score: 2420
Period size: 596 Copynumber: 2.0 Consensus size: 596
111781 AAATTAATCA
111791 ATATATATATATATATATTGATATAATTCAATCCATATATCTTAATTAGGAAAAAGGATAATCTA
1 ATATATATATATATATATTGATATAATTCAATCCATATATCTTAATTAGGAAAAAGGATAATCTA
111856 TTTTCGAAACCAAACAAAGCACAAGCAAGCCGATGAGAATATTGGGGCAACTTGTACAATTATAC
66 TTTTCGAAACCAAACAAAGCACAAGCAAGCCGATGAGAATATTGGGGCAACTTGTACAATTATAC
111921 ATATCAATCGGACAAAAGATTTGGTGAACAACAATAAATTGGCTTAATTCCGAGCACATATTTTC
131 ATATCAATCGGACAAAAGATTTGGTGAACAACAATAAATTGGCTTAATTCCGAGCACATATTTTC
111986 CATTTTTCTTCCATAATTCATAGCTTTCAATTTGCCTTGATGTCTCCATCTCCCTTGTTTGCTTC
196 CATTTTTCTTCCATAATTCATAGCTTTCAATTTGCCTTGATGTCTCCATCTCCCTTGTTTGCTTC
112051 CAATGTCCAAACTCTTTTATATTATTCCACCCTTGAGCATATGATTTATAGAGGAACATTTGATT
261 CAATGTCCAAACTCTTTTATATTATTCCACCCTTGAGCATATGATTTATAGAGGAACATTTGATT
112116 CAAGATATTAAATATGACGTGACATGTGTTAGATATGGCTCATAAATATATTGGTAAAGCCCTCG
326 CAAGATATTAAATATGACGTGACATGTGTTAGATATGGCTCATAAATATATTGGTAAAGCCCTCG
112181 CGGTACGATACAAGGTTATTTTTGTAAATATGTACCAGAGTTTATTTATTATAAAAGGAGATGTA
391 CGGTACGATACAAGGTTATTTTTGTAAATATGTACCAGAGTTTATTTATTATAAAAGGAGATGTA
112246 ACCAAAACCTATGAGACATTGAATAAAAATTCTAGCGCCACCTTGGGCACCGAGGACGTAAGCAC
456 ACCAAAACCTATGAGACATTGAATAAAAATTCTAGCGCCACCTTGGGCACCGAGGACGTAAGCAC
112311 ATTGCTGAACCTCGTTAAAATTATTGTGTTCTTTCCGTTTTCTTTACCCGATTATTCAACACGTG
521 ATTGCTGAACCTCGTTAAAATTATTGTGTTCTTTCCGTTTTCTTTACCCGATTATTCAACACGTG
112376 ACATGTTTAAT
586 ACATGTTTAAT
112387 ATATATATATATATATATTGATATAATTCAATCCATATATCTTAATTAGGAAAAAGGATAATCTA
1 ATATATATATATATATATTGATATAATTCAATCCATATATCTTAATTAGGAAAAAGGATAATCTA
112452 TTTTCGAAACCAAACAAAGCACAAGCAAGCCGATGAGAATATTGGGGCAACTTGTACAATTATAC
66 TTTTCGAAACCAAACAAAGCACAAGCAAGCCGATGAGAATATTGGGGCAACTTGTACAATTATAC
112517 ATATCAATCGGACAAAAGATTTGGTGAACAACAATAAATTGGCTTAATTCCGAGCACATATTTTC
131 ATATCAATCGGACAAAAGATTTGGTGAACAACAATAAATTGGCTTAATTCCGAGCACATATTTTC
112582 CATTTTTCTTCCATAATTCATAGCTTTCAATTTGCCTTGATGTCTCCATCTCCCTTGTTTGCTTC
196 CATTTTTCTTCCATAATTCATAGCTTTCAATTTGCCTTGATGTCTCCATCTCCCTTGTTTGCTTC
112647 CAATGTCCAAACTCTTTTATATTATTCCACCCTTGAGCATATGATTTATAGAGGAACATTTGATT
261 CAATGTCCAAACTCTTTTATATTATTCCACCCTTGAGCATATGATTTATAGAGGAACATTTGATT
112712 CAAGATATTAAATATGACGTGACATGTGTTAGATATGGCTCATAAATATATTGGTAAAGCCCTCG
326 CAAGATATTAAATATGACGTGACATGTGTTAGATATGGCTCATAAATATATTGGTAAAGCCCTCG
112777 CGGTACGATACAAGGTTATTTTTGTAAATATGTACCAGAGTTTATTTATTATAAAAGGAGATGTA
391 CGGTACGATACAAGGTTATTTTTGTAAATATGTACCAGAGTTTATTTATTATAAAAGGAGATGTA
112842 ACCAAAACCTATGAGACATTGAATAAAAATTCTAGCGCCACCTTGGGCACCGAGGACGTAAGCAC
456 ACCAAAACCTATGAGACATTGAATAAAAATTCTAGCGCCACCTTGGGCACCGAGGACGTAAGCAC
112907 ATTGCTGAACCTCGTTAAAATTATTGTGTTCTTTCCGTTTTCTTTACCCGATTATTCAACACGTG
521 ATTGCTGAACCTCGTTAAAATTATTGTGTTCTTTCCGTTTTCTTTACCCGATTATTCAACACGTG
112972 ACATGTTTAAT
586 ACATGTTTAAT
112983 ATATATATATATATATAT
1 ATATATATATATATATAT
113001 ATATATATAT
Statistics
Matches: 614, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
596 614 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (596 bp):
ATATATATATATATATATTGATATAATTCAATCCATATATCTTAATTAGGAAAAAGGATAATCTA
TTTTCGAAACCAAACAAAGCACAAGCAAGCCGATGAGAATATTGGGGCAACTTGTACAATTATAC
ATATCAATCGGACAAAAGATTTGGTGAACAACAATAAATTGGCTTAATTCCGAGCACATATTTTC
CATTTTTCTTCCATAATTCATAGCTTTCAATTTGCCTTGATGTCTCCATCTCCCTTGTTTGCTTC
CAATGTCCAAACTCTTTTATATTATTCCACCCTTGAGCATATGATTTATAGAGGAACATTTGATT
CAAGATATTAAATATGACGTGACATGTGTTAGATATGGCTCATAAATATATTGGTAAAGCCCTCG
CGGTACGATACAAGGTTATTTTTGTAAATATGTACCAGAGTTTATTTATTATAAAAGGAGATGTA
ACCAAAACCTATGAGACATTGAATAAAAATTCTAGCGCCACCTTGGGCACCGAGGACGTAAGCAC
ATTGCTGAACCTCGTTAAAATTATTGTGTTCTTTCCGTTTTCTTTACCCGATTATTCAACACGTG
ACATGTTTAAT
Found at i:112988 original size:2 final size:2
Alignment explanation
Indices: 112981--113012 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
112971 GACATGTTTA
112981 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
113013 TATTTTGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:114092 original size:60 final size:59
Alignment explanation
Indices: 114024--114189 Score: 174
Period size: 60 Copynumber: 2.8 Consensus size: 59
114014 ATTCTAATAT
* *
114024 TAAATTAGTCTTTAATCTTTTGAATATTCCAATTTCATACCCAAATTATGA-ATCTCATTC
1 TAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCAT-CCCAAATTAT-ATATCTCATTC
* * * * * *
114084 TAAATTAGTCCTTAAACTTTTGAACATTCTAATTTTATCCCTAAACTATATCTCTCTTTC
1 TAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATCCC-AAATTATATATCTCATTC
** * *
114144 T-AATTAGTCCCCAAACATTTGAATATCCCAATTTCATCCCCAAATT
1 TAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCAT-CCCAAATT
114190 CATCCTAATA
Statistics
Matches: 87, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
59 37 0.43
60 50 0.57
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (59 bp):
TAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATCCCAAATTATATATCTCATTC
Found at i:114177 original size:59 final size:59
Alignment explanation
Indices: 114042--114183 Score: 153
Period size: 59 Copynumber: 2.4 Consensus size: 59
114032 TCTTTAATCT
* ** *
114042 TTTGAATATTCCAATTTCATACCCAAATTATGAATCTCATTCTAAATTAGTCCTTAAACT
1 TTTGAATATTCCAATTTCAT-CCCAAACTATGAATCTCATTCTAAATTAGTCCCCAAACA
* * * * *
114102 TTTGAACATTCTAATTTTATCCCTAAACTAT-ATCTCTCTTTCT-AATTAGTCCCCAAACA
1 TTTGAATATTCCAATTTCATCCC-AAACTATGA-ATCTCATTCTAAATTAGTCCCCAAACA
*
114161 TTTGAATATCCCAATTTCATCCC
1 TTTGAATATTCCAATTTCATCCC
114184 CAAATTCATC
Statistics
Matches: 67, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
59 36 0.54
60 31 0.46
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (59 bp):
TTTGAATATTCCAATTTCATCCCAAACTATGAATCTCATTCTAAATTAGTCCCCAAACA
Found at i:114759 original size:23 final size:23
Alignment explanation
Indices: 114715--114762 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
114705 GTGTTCGTTT
* *
114715 ATTTATTGTTCACTAACATGTTC
1 ATTTAATGTTCACAAACATGTTC
**
114738 ATTTAATGTTCACAAATGTGTTC
1 ATTTAATGTTCACAAACATGTTC
114761 AT
1 AT
114763 GAACATGTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (23 bp):
ATTTAATGTTCACAAACATGTTC
Found at i:114760 original size:35 final size:35
Alignment explanation
Indices: 114721--114795 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
114711 GTTTATTTAT
*
114721 TGTTCACT-AACATGTTCATTTAATGTTCACAAATG
1 TGTTCA-TGAACATGTTCATTTAATGTTCACAAACG
* *
114756 TGTTCATGAACATGTTCGTTTAATGTTCGCAAACG
1 TGTTCATGAACATGTTCATTTAATGTTCACAAACG
114791 TGTTC
1 TGTTC
114796 GTTTATATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 1 0.03
35 35 0.97
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (35 bp):
TGTTCATGAACATGTTCATTTAATGTTCACAAACG
Found at i:114782 original size:23 final size:24
Alignment explanation
Indices: 114756--114819 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
114746 TTCACAAATG
*
114756 TGTTCATGAACATGTTCGTTTA-A
1 TGTTCACGAACATGTTCGTTTATA
* * *
114779 TGTTCGCAAACGTGTTCGTTTATA
1 TGTTCACGAACATGTTCGTTTATA
*
114803 TATTCACGAACATGTTC
1 TGTTCACGAACATGTTC
114820 ATAAACATGT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (24 bp):
TGTTCACGAACATGTTCGTTTATA
Found at i:115079 original size:27 final size:27
Alignment explanation
Indices: 115040--115092 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
115030 GAGAATAGGG
*
115040 TAAACGAGTTTGTTCATGAACATAAAA
1 TAAACGAGCTTGTTCATGAACATAAAA
* *
115067 TAAACGAGCTTGTTCGTGAATATAAA
1 TAAACGAGCTTGTTCATGAACATAAA
115093 TGAACCGAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (27 bp):
TAAACGAGCTTGTTCATGAACATAAAA
Found at i:117038 original size:16 final size:16
Alignment explanation
Indices: 117009--117051 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
116999 CATTTAATAA
117009 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
* *
117025 ATAAATGAATACGAAC
1 ATAAACGAACACGAAC
117041 ATAAACGAACA
1 ATAAACGAACA
117052 TAAAAGTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.12
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:118144 original size:14 final size:14
Alignment explanation
Indices: 118127--118205 Score: 85
Period size: 14 Copynumber: 5.9 Consensus size: 14
118117 GATTGGGTTA
* *
118127 AACATAAATGAATG
1 AACATAAACGAACG
118141 AACATAAACG----
1 AACATAAACGAACG
*
118151 AACATAACCGAACG
1 AACATAAACGAACG
* *
118165 AACATAACCGAATG
1 AACATAAACGAACG
118179 AACATAAACGAACG
1 AACATAAACGAACG
118193 AACATAAACGAAC
1 AACATAAACGAAC
118206 ATAACCGAAC
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
10 9 0.16
14 47 0.84
ACGTcount: A:0.56, C:0.20, G:0.13, T:0.11
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:118178 original size:38 final size:38
Alignment explanation
Indices: 118127--118214 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 38
118117 GATTGGGTTA
** * *
118127 AACATAAATGAATGAACATAAACGAACATAAC-CGAACG
1 AACATAACCGAATGAACATAAACGAAC-GAACACAAACG
*
118165 AACATAACCGAATGAACATAAACGAACGAACATAAACG
1 AACATAACCGAATGAACATAAACGAACGAACACAAACG
118203 AACATAACCGAA
1 AACATAACCGAA
118215 CGTTCACGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
37 3 0.07
38 41 0.93
ACGTcount: A:0.56, C:0.20, G:0.12, T:0.11
Consensus pattern (38 bp):
AACATAACCGAATGAACATAAACGAACGAACACAAACG
Found at i:118216 original size:14 final size:14
Alignment explanation
Indices: 118147--118216 Score: 94
Period size: 14 Copynumber: 5.3 Consensus size: 14
118137 AATGAACATA
118147 AACGAACATAACCG
1 AACGAACATAACCG
118161 AACGAACATAACCG
1 AACGAACATAACCG
* *
118175 AATGAACATAAACG
1 AACGAACATAACCG
118189 AACGAACAT-A---
1 AACGAACATAACCG
118199 AACGAACATAACCG
1 AACGAACATAACCG
118213 AACG
1 AACG
118217 TTCACGAGCG
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
10 9 0.18
11 1 0.02
13 1 0.02
14 38 0.78
ACGTcount: A:0.53, C:0.24, G:0.14, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:124755 original size:3 final size:3
Alignment explanation
Indices: 124747--124785 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
124737 AGCGTTGTAT
124747 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
124786 TTTTTTCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:125117 original size:23 final size:23
Alignment explanation
Indices: 125082--125126 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
125072 TTTTCAATAA
125082 ATTTATCTATATGACATATTTTT
1 ATTTATCTATATGACATATTTTT
* * * *
125105 ATTTGTCTTTATGGCATGTTTT
1 ATTTATCTATATGACATATTTT
125127 CTTCTGCCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.09, G:0.11, T:0.58
Consensus pattern (23 bp):
ATTTATCTATATGACATATTTTT
Found at i:140892 original size:17 final size:17
Alignment explanation
Indices: 140870--140903 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
140860 GTTTAGTGCT
140870 ACAAAATGGAAGTGAAA
1 ACAAAATGGAAGTGAAA
140887 ACAAAATGGAAGTGAAA
1 ACAAAATGGAAGTGAAA
140904 GTTTTCATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.24, T:0.12
Consensus pattern (17 bp):
ACAAAATGGAAGTGAAA
Found at i:142218 original size:19 final size:19
Alignment explanation
Indices: 142194--142237 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
142184 AACCGACTGA
*
142194 GAACCGGTAAAACCGG-GAT
1 GAACCGGCAAAACCGGTG-T
142213 GAACCGGCAAAACCGGTGT
1 GAACCGGCAAAACCGGTGT
142232 GAACCG
1 GAACCG
142238 CCGGTTCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.34, C:0.25, G:0.32, T:0.09
Consensus pattern (19 bp):
GAACCGGCAAAACCGGTGT
Found at i:144565 original size:43 final size:43
Alignment explanation
Indices: 144502--144584 Score: 141
Period size: 43 Copynumber: 1.9 Consensus size: 43
144492 TTTTCAAATT
*
144502 AACCCTCCCTGTTAAGCCAAACTATTGCTTTCCAGTCTCAAGC
1 AACCCTCCCTGTTAAGCCAAACTATTGCTTCCCAGTCTCAAGC
144545 AACCCTCCCTGTTATA-CCAAACTATTGCTTCCCAGTCTCA
1 AACCCTCCCTGTTA-AGCCAAACTATTGCTTCCCAGTCTCA
144585 TCTTAAATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
43 37 0.97
44 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.10, T:0.29
Consensus pattern (43 bp):
AACCCTCCCTGTTAAGCCAAACTATTGCTTCCCAGTCTCAAGC
Found at i:150491 original size:25 final size:26
Alignment explanation
Indices: 150454--150559 Score: 78
Period size: 25 Copynumber: 4.1 Consensus size: 26
150444 TATCTTAGTG
* * *
150454 TATAAATACTTAAATTCATAATATTT
1 TATATATACTTAAATTAAAAATATTT
*
150480 TATATATA-TTAACTTAAAAATATTT
1 TATATATACTTAAATTAAAAATATTT
* *
150505 T-TATATTAACTT--ATTAAATATATCT
1 TATATA-T-ACTTAAATTAAAAATATTT
*
150530 TAT-TATTAACTTAATTTAAAAATATTT
1 TATATA-T-ACTTAAATTAAAAATATTT
150557 TAT
1 TAT
150560 TTTTATTTTC
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
24 4 0.06
25 36 0.56
26 9 0.14
27 15 0.23
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (26 bp):
TATATATACTTAAATTAAAAATATTT
Found at i:150512 original size:22 final size:23
Alignment explanation
Indices: 150484--150543 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
150474 ATATTTTATA
*
150484 TATATTAACTTAAAAATAT-TTT
1 TATATTAACTTAAAAATATATCT
*
150506 TATATTAACTTATTAAATATATCT
1 TATATTAACTTA-AAAATATATCT
150530 TATTATTAACTTAA
1 TA-TATTAACTTAA
150544 TTTAAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 12 0.38
23 6 0.19
24 4 0.12
25 10 0.31
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (23 bp):
TATATTAACTTAAAAATATATCT
Found at i:150548 original size:27 final size:26
Alignment explanation
Indices: 150473--150560 Score: 89
Period size: 25 Copynumber: 3.5 Consensus size: 26
150463 TTAAATTCAT
150473 AATAT-TTTATATATATTAACTTAA--A
1 AATATATTT-TAT-TATTAACTTAATTA
150498 AATAT-TTTTA-TATTAACTT-ATTA
1 AATATATTTTATTATTAACTTAATTA
*
150521 AATATATCTTATTATTAACTTAATTTA
1 AATATATTTTATTATTAACTTAA-TTA
*
150548 AAAATATTTTATT
1 AATATATTTTATT
150561 TTTATTTTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
21 1 0.02
22 9 0.17
23 6 0.11
24 6 0.11
25 17 0.31
26 1 0.02
27 14 0.26
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (26 bp):
AATATATTTTATTATTAACTTAATTA
Found at i:152115 original size:21 final size:21
Alignment explanation
Indices: 152091--152135 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
152081 AAATGACCGG
* *
152091 ATTAACATAATATTTTAGGTA
1 ATTAACAGAAAATTTTAGGTA
* *
152112 ATTACCGGAAAATTTTAGGTA
1 ATTAACAGAAAATTTTAGGTA
152133 ATT
1 ATT
152136 TTTACCAGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (21 bp):
ATTAACAGAAAATTTTAGGTA
Found at i:153913 original size:25 final size:25
Alignment explanation
Indices: 153872--153924 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
153862 TAGAATTATG
*
153872 GAATAAGCTAAGGATGCAAATTAGT
1 GAATAAGCTAAGAATGCAAATTAGT
* *
153897 GAATAAGCTGAA-AATGCATATTGGT
1 GAATAAGCT-AAGAATGCAAATTAGT
153922 GAA
1 GAA
153925 ATCTTCCTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.43, C:0.08, G:0.25, T:0.25
Consensus pattern (25 bp):
GAATAAGCTAAGAATGCAAATTAGT
Found at i:154850 original size:59 final size:59
Alignment explanation
Indices: 154758--154889 Score: 219
Period size: 59 Copynumber: 2.2 Consensus size: 59
154748 CAACAGACTG
*
154758 CATATTCGGGTTGGCACTAAAGGATACTTAGTGCAGATGGTGAGCACGACCTTATGTGT
1 CATATTCGGGTTAGCACTAAAGGATACTTAGTGCAGATGGTGAGCACGACCTTATGTGT
* * *
154817 CATATTTGGGTTAGCACTAAAGGATACTTAGTGCAGGTGGTGGGCACGACCTTATGTGT
1 CATATTCGGGTTAGCACTAAAGGATACTTAGTGCAGATGGTGAGCACGACCTTATGTGT
*
154876 CATATTCGGTTTAG
1 CATATTCGGGTTAG
154890 TACTTCGGTG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 67 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (59 bp):
CATATTCGGGTTAGCACTAAAGGATACTTAGTGCAGATGGTGAGCACGACCTTATGTGT
Found at i:159583 original size:3 final size:3
Alignment explanation
Indices: 159575--159620 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
159565 ATGTAAATTA
* *
159575 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
159621 TACAAAAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:159876 original size:40 final size:41
Alignment explanation
Indices: 159832--160051 Score: 131
Period size: 41 Copynumber: 5.2 Consensus size: 41
159822 ACATGGTTCC
* * *
159832 TACGTGATGAGGAAATCTGGTCAAGGG-TTGACACTGCTCA
1 TACGTGATGAAGAAATCTGGTCAAGGGAATGACACGGCTCA
** **
159872 TACGTGATGAAGAGTTCTGGTCTGGGGAATGACACGGCTCA
1 TACGTGATGAAGAAATCTGGTCAAGGGAATGACACGGCTCA
** * * *
159913 TACGTGATGAAGAGTTCTGGCCATCTAAAGGTG-ATAACACGGTTCC
1 TACGTGATGAAGAAATCTGG---TC--AAGG-GAATGACACGGCTCA
* *** * * *
159959 TACGTGATGAGGACGGCTGGTTATCTATGG-TTGACACGGCTCA
1 TACGTGATGAAGAAATCTGG---TCAAGGGAATGACACGGCTCA
** **
160002 TACGTGATGAAGAGTTCTGGTCTGGGGAATGACACGGCTCA
1 TACGTGATGAAGAAATCTGGTCAAGGGAATGACACGGCTCA
160043 TACGTGATG
1 TACGTGATG
160052 GAGAGTTCTG
Statistics
Matches: 141, Mismatches: 31, Indels: 15
0.75 0.17 0.08
Matches are distributed among these distances:
40 27 0.19
41 52 0.37
43 26 0.18
44 4 0.03
46 31 0.22
47 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (41 bp):
TACGTGATGAAGAAATCTGGTCAAGGGAATGACACGGCTCA
Found at i:159985 original size:46 final size:46
Alignment explanation
Indices: 159903--160141 Score: 166
Period size: 46 Copynumber: 5.4 Consensus size: 46
159893 CTGGGGAATG
* * **
159903 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAGGAGTGCTGGTTATCTAAAGGTGATA
* * * *
159949 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT-ATGGT--TG
1 ACACGGCTCATACGTGATGAGGA-GTGCTGGTTATCTAAAGGTGATA
* * * *
159992 ACACGGCTCATACGTGATGAAGAGTTCTGG---TCT---GGGGAATG
1 ACACGGCTCATACGTGATGAGGAGTGCTGGTTATCTAAAGGTG-ATA
* **
160033 ACACGGCTCATACGTGATG-GAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAG-GAGTGCTGGTTATCTAAAGGTGATA
* * * *
160079 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT-ATGGT--TG
1 ACACGGCTCATACGTGATGAGGA-GTGCTGGTTATCTAAAGGTGATA
160122 ACACGGCTCATACGTGATGA
1 ACACGGCTCATACGTGATGA
160142 AGAGATCTGG
Statistics
Matches: 154, Mismatches: 25, Indels: 31
0.73 0.12 0.15
Matches are distributed among these distances:
38 2 0.01
40 3 0.02
41 30 0.19
42 1 0.01
43 44 0.29
44 3 0.02
45 8 0.05
46 57 0.37
47 6 0.04
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (46 bp):
ACACGGCTCATACGTGATGAGGAGTGCTGGTTATCTAAAGGTGATA
Found at i:160010 original size:43 final size:43
Alignment explanation
Indices: 159857--160141 Score: 174
Period size: 41 Copynumber: 6.6 Consensus size: 43
159847 TCTGGTCAAG
* * * **
159857 GGTTGACACTGCTCATACGTGATGAAGAGTTCTGG---TCTGG
1 GGTTGACACGGCTCATACGTGATGAGGAGTGCTGGTTATCTAT
* * * ** *
159897 GGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAA
1 GG-TTGACACGGCTCATACGTGATGAGGAGTGCTGGTTATCT-AT
* * *
159942 GGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAT
1 GGT--TGACACGGCTCATACGTGATGAGGA-GTGCTGGTTATCTAT
* * **
159987 GGTTGACACGGCTCATACGTGATGAAGAGTTCTGG---TCTGG
1 GGTTGACACGGCTCATACGTGATGAGGAGTGCTGGTTATCTAT
* * ** *
160027 GGAATGACACGGCTCATACGTGATG-GAGAGTTCTGGCCATCTAAA
1 GG-TTGACACGGCTCATACGTGATGAG-GAGTGCTGGTTATCT-AT
* * *
160072 GGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAT
1 GGT--TGACACGGCTCATACGTGATGAGGA-GTGCTGGTTATCTAT
160117 GGTTGACACGGCTCATACGTGATGA
1 GGTTGACACGGCTCATACGTGATGA
160142 AGAGATCTGG
Statistics
Matches: 191, Mismatches: 35, Indels: 35
0.73 0.13 0.13
Matches are distributed among these distances:
40 7 0.04
41 61 0.32
42 1 0.01
43 44 0.23
44 6 0.03
45 12 0.06
46 57 0.30
47 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (43 bp):
GGTTGACACGGCTCATACGTGATGAGGAGTGCTGGTTATCTAT
Found at i:160024 original size:130 final size:130
Alignment explanation
Indices: 159778--160181 Score: 606
Period size: 130 Copynumber: 3.2 Consensus size: 130
159768 TGTTGGGGAC
* * * * * *
159778 GACACTGCTCATACGTGATGAAGAGTTCGGGTCGTCT-AAGG-G-TGACATGGTTCCTACGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
*** * * *
159840 GAGGAAATCTGG---TCAAGGGTTGACACTGCTCATACGTGATGAAGAGTTCTGGTCTGGGGAAT
66 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGTTCTGGTCTGGGGAAT
159902 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
159967 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGTTCTGGTCTGGGGAAT
66 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGTTCTGGTCTGGGGAAT
*
160032 GACACGGCTCATACGTGATGGAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
*
160097 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGG-AT
66 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGTTCTGGTCTGGGGAAT
* * *
160161 GACACGGTTCCTACATGATGA
1 GACACGGCTCATACGTGATGA
160182 GGACGACTGG
Statistics
Matches: 256, Mismatches: 18, Indels: 7
0.91 0.06 0.02
Matches are distributed among these distances:
124 33 0.13
125 4 0.02
126 1 0.00
127 27 0.11
129 19 0.07
130 172 0.67
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (130 bp):
GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
GAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGTTCTGGTCTGGGGAAT
Found at i:160151 original size:89 final size:83
Alignment explanation
Indices: 160031--160191 Score: 214
Period size: 83 Copynumber: 1.9 Consensus size: 83
160021 GTCTGGGGAA
* * * *
160031 TGACACGGCTCATACGTGATGGAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG---TCT---GGGGATAACACGGTTCCTACATGA
*
160096 TGAGGACGGCTGGTTATCTATGGT
60 TGAGGACGACTGGTTATCTATGGT
*
160120 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATAACACGGTTCCTACATGATGAGGA
160185 CGACTGG
66 CGACTGG
160192 CCATCTTTAG
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
83 33 0.50
86 3 0.05
89 30 0.45
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (83 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATAACACGGTTCCTACATGATGAGGA
CGACTGGTTATCTATGGT
Found at i:160152 original size:43 final size:42
Alignment explanation
Indices: 159778--160152 Score: 246
Period size: 43 Copynumber: 8.8 Consensus size: 42
159768 TGTTGGGGAC
* * * *
159778 GACACTGCTCATACGTGATGAAGAGTTCGGGTCGTCTAAGGGT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGT-ATCTAAGGTT
* * * * **
159821 GACATGGTTCCTACGTGATGAGGAAATCTGG--TC-AAGGGTT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGTATCTAA-GGTT
* ** *
159861 GACACTGCTCATACGTGATGAAGAGTTCTGG--TCTGGGGAAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGTATCTAAGG-TT
*
159902 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGG-TATCT-AAGGT--T
* * * * * *
159948 AACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTT
1 GACACGGCTCATACGTGATGAAGA-GTTCTGG-TATCTAAGGTT
** *
159991 GACACGGCTCATACGTGATGAAGAGTTCTGG--TCTGGGGAAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGTATCTAAGG-TT
* *
160032 GACACGGCTCATACGTGATGGAGAGTTCTGGCCATCTAAAGGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGG-TATCT-AAGGT--T
* * * * * *
160078 AACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTT
1 GACACGGCTCATACGTGATGAAGA-GTTCTGG-TATCTAAGGTT
*
160121 GACACGGCTCATACGTGATGAAGAGATCTGGT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGT
160153 CTGGGGATGA
Statistics
Matches: 255, Mismatches: 57, Indels: 41
0.72 0.16 0.12
Matches are distributed among these distances:
39 2 0.01
40 38 0.15
41 62 0.24
42 3 0.01
43 73 0.29
44 6 0.02
45 12 0.05
46 57 0.22
47 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (42 bp):
GACACGGCTCATACGTGATGAAGAGTTCTGGTATCTAAGGTT
Found at i:160259 original size:28 final size:28
Alignment explanation
Indices: 160210--160263 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
160200 AGGAGTTATG
*
160210 GTTTCAAGAGAAACCAAATCAAAGATTT
1 GTTTCAAGAGAAAACAAATCAAAGATTT
*
160238 GTTTCAAGA-AAAATAAACTCAAAGAT
1 GTTTCAAGAGAAAACAAA-TCAAAGAT
160264 GATATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (28 bp):
GTTTCAAGAGAAAACAAATCAAAGATTT
Found at i:160623 original size:15 final size:15
Alignment explanation
Indices: 160599--160657 Score: 91
Period size: 15 Copynumber: 3.9 Consensus size: 15
160589 AAGATGATCT
*
160599 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
160614 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
160629 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
* *
160644 TATTTCAAGTGAAA
1 TGTTTCAAGAGAAA
160658 CGACTCAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.31
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:160710 original size:31 final size:30
Alignment explanation
Indices: 160644--160720 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 30
160634 CAAGAGAAAA
*
160644 TATTTCAAGTGAAACGACTCAAAAATGGTTT
1 TATTTCAAGTGAAACAACTCAAAAAT-GTTT
* *
160675 TATTTCAATTGAAACAAACTCAAAGAT-TTT
1 TATTTCAAGTGAAAC-AACTCAAAAATGTTT
* *
160705 GTATTTCTAGAGAAAC
1 -TATTTCAAGTGAAAC
160721 TGCCTCAAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
30 3 0.08
31 26 0.68
32 9 0.24
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (30 bp):
TATTTCAAGTGAAACAACTCAAAAATGTTT
Found at i:160885 original size:63 final size:64
Alignment explanation
Indices: 160814--160938 Score: 189
Period size: 64 Copynumber: 2.0 Consensus size: 64
160804 AAGGTTGGTA
* * *
160814 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
* * *
160877 TTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
160939 GGATCTCATC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 17 0.31
64 38 0.69
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (64 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
Found at i:160986 original size:36 final size:37
Alignment explanation
Indices: 160946--161017 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
160936 GATGGATCTC
* **
160946 ATCTTAAGTGAGACCAAA-TTTGTTT-CAAATGAAACT
1 ATCTTAAGAGAGAAAAAATTTTGTTTCCAAA-GAAACT
160982 ATCTTAAGAGAGAAAAAATTTTGTTTCCAAAGAAAC
1 ATCTTAAGAGAGAAAAAATTTTGTTTCCAAAGAAAC
161018 AAACTCAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 15 0.48
37 12 0.39
38 4 0.13
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (37 bp):
ATCTTAAGAGAGAAAAAATTTTGTTTCCAAAGAAACT
Found at i:161064 original size:27 final size:28
Alignment explanation
Indices: 160999--161062 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 28
160989 GAGAGAAAAA
*
160999 ATTTTGTTTCCAAAGAAACAAACTCAAAG
1 ATTTT-TTTCAAAAGAAACAAACTCAAAG
*
161028 ATTTTTTTCAAAAGAAACAATCTCAAAG
1 ATTTTTTTCAAAAGAAACAAACTCAAAG
161056 ATTTTTT
1 ATTTTTT
161063 CACAAAATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
28 28 0.85
29 5 0.15
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (28 bp):
ATTTTTTTCAAAAGAAACAAACTCAAAG
Found at i:161128 original size:52 final size:53
Alignment explanation
Indices: 161049--161151 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 53
161039 AAGAAACAAT
161049 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
161102 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
161152 AAATAAATAG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 41 0.84
53 8 0.16
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:161224 original size:29 final size:28
Alignment explanation
Indices: 161147--161710 Score: 310
Period size: 29 Copynumber: 19.5 Consensus size: 28
161137 CAAAACTTTG
* * *
161147 TTTCAAAATAAATAGACTCAAAG--ATT
1 TTTCAAAAGAAACAAACTCAAAGATATT
*
161173 TTTCAAAAGAAAC-GACTCAAAGATATT
1 TTTCAAAAGAAACAAACTCAAAGATATT
* * *
161200 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAACAAACTCAAAGATATT
*
161229 TATTCAAAAGGAACAAACTCAAAGAT-TT
1 T-TTCAAAAGAAACAAACTCAAAGATATT
* *** *
161257 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTT
1 TTTCAAAAGAAACAAACTC-A-A-AG---ATA--TT
* * *
161293 GTTTCAAAATAAATAGACTCAAAGAT-TT
1 -TTTCAAAAGAAACAAACTCAAAGATATT
161321 TTTCAAAAGAAAC-AACTCAAAGATATT
1 TTTCAAAAGAAACAAACTCAAAGATATT
* * *
161348 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAACAAACTCAAAGATATT
*
161377 TATTCAAAAGGAACAAACTCAAAGAT-TT
1 T-TTCAAAAGAAACAAACTCAAAGATATT
* *** *
161405 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATCGT
1 TTTCAAAAGAAACAAACTC-A-A-AG----ATAT--T
* * * *
161442 TTT-AAAATAAATAGACTCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGATATT
*
161469 TTTCAAAAGAAA-TAACTCAAAGATATT
1 TTTCAAAAGAAACAAACTCAAAGATATT
* * *
161496 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAACAAACTCAAAGATATT
*
161525 TATTCAAAAGGAACAAACTCAAAGAT-TT
1 T-TTCAAAAGAAACAAACTCAAAGATATT
* *** *
161553 TTTCAAGAGAAACTGTCTCAAGAGACAAAAATCGT
1 TTTCAAAAGAAACAAACTCAA-AG----ATAT--T
* * *
161588 TTT-AAAATAAATAGACTCAAAGAT-TT
1 TTTCAAAAGAAACAAACTCAAAGATATT
161614 TTTCAAAAGAAAC-AACTCAAAGATATT
1 TTTCAAAAGAAACAAACTCAAAGATATT
* * *
161641 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAACAAACTCAAAGATATT
*
161670 TATTCAAAAGGAACAAACTCAAAGAT-TT
1 T-TTCAAAAGAAACAAACTCAAAGATATT
*
161698 TTTCAAGAGAAAC
1 TTTCAAAAGAAAC
161711 TGTCTCAAGA
Statistics
Matches: 427, Mismatches: 69, Indels: 83
0.74 0.12 0.14
Matches are distributed among these distances:
25 9 0.02
26 35 0.08
27 96 0.22
28 69 0.16
29 152 0.36
30 4 0.01
31 1 0.00
32 1 0.00
33 6 0.01
34 16 0.04
35 7 0.02
36 13 0.03
37 18 0.04
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.27
Consensus pattern (28 bp):
TTTCAAAAGAAACAAACTCAAAGATATT
Found at i:161362 original size:148 final size:147
Alignment explanation
Indices: 161101--161739 Score: 1096
Period size: 148 Copynumber: 4.4 Consensus size: 147
161091 TTTGTTTCAG
* * * *
161101 ACTCAAAGA-TTTTTC-A-CGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
1 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-ATCGTTTCAAAATAAATAGA
*
161163 CTCAAAGA-TTTTTCAAAAGAAACGACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATT
65 CTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATT
161227 TTTATTCAAAAGGAACAA
130 TTTATTCAAAAGGAACAA
* *
161245 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
1 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-ATCGTTTCAAAATAAATAGA
161310 CTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATT
65 CTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATT
161375 TTTATTCAAAAGGAACAA
130 TTTATTCAAAAGGAACAA
*
161393 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATCGTTTTAAAATAAATAGAC
1 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATCGTTTCAAAATAAATAGAC
*
161458 TCAAAGATTTTTTTCAAAAGAAATAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATT
66 TCAAAGA-TTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATT
161523 TTTATTCAAAAGGAACAA
130 TTTATTCAAAAGGAACAA
*
161541 ACTCAAAGATTTTTTCAAGAGAAACTGTCTC-A-AGAGACAAAAATCGTTTTAAAATAAATAGAC
1 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATCGTTTCAAAATAAATAGAC
161604 TCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTT
66 TCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTT
161669 TTATTCAAAAGGAACAA
131 TTATTCAAAAGGAACAA
*
161686 ACTCAAAGATTTTTTCAAGAGAAACTGTCTC-A-AGAGACAAAAATCGTTTTAAAA
1 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATCGTTTCAAAA
161740 GATTCAAATA
Statistics
Matches: 482, Mismatches: 8, Indels: 9
0.97 0.02 0.02
Matches are distributed among these distances:
144 9 0.02
145 134 0.28
146 39 0.08
147 78 0.16
148 222 0.46
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.27
Consensus pattern (147 bp):
ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATCGTTTCAAAATAAATAGAC
TCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTT
TTATTCAAAAGGAACAA
Found at i:161677 original size:293 final size:294
Alignment explanation
Indices: 161101--161739 Score: 1105
Period size: 293 Copynumber: 2.2 Consensus size: 294
161091 TTTGTTTCAG
* * * * *
161101 ACTCAAAGA-TTTTTC-A-CGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
1 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-ATCGTTTTAAAATAAATAGA
*
161163 CTCAAAGATTTTTCAAAAGAAACGACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTT
65 CTCAAAGATTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTT
* *
161228 TTATTCAAAAGGAACAAACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTT
130 TTATTCAAAAGGAACAAACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACATC
161293 GTTTCAAAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAG
195 GTTTCAAAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAG
161358 GAACAAACTCCAAGATTTTTATTCAAAAGGAACAA
260 GAACAAACTCCAAGATTTTTATTCAAAAGGAACAA
161393 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATCGTTTTAAAATAAATAGAC
1 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATCGTTTTAAAATAAATAGAC
*
161458 TCAAAGATTTTTTTCAAAAGAAATAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATT
66 TCAAAGA--TTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATT
161523 TTTATTCAAAAGGAACAAACTCAAAGATTTTTTCAAGAGAAACTGTCTC-A-AGAGACAAAA-AT
129 TTTATTCAAAAGGAACAAACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACAT
*
161585 CGTTTTAAAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAA
194 CGTTTCAAAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAA
161650 GGAACAAACTCCAAGATTTTTATTCAAAAGGAACAA
259 GGAACAAACTCCAAGATTTTTATTCAAAAGGAACAA
161686 ACTCAAAGATTTTTTCAAGAGAAACTGTCTC-A-AGAGACAAAAATCGTTTTAAAA
1 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATCGTTTTAAAA
161740 GATTCAAATA
Statistics
Matches: 332, Mismatches: 10, Indels: 11
0.94 0.03 0.03
Matches are distributed among these distances:
291 22 0.07
292 10 0.03
293 137 0.41
294 36 0.11
295 24 0.07
296 103 0.31
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.27
Consensus pattern (294 bp):
ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATCGTTTTAAAATAAATAGAC
TCAAAGATTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTT
TATTCAAAAGGAACAAACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACATCG
TTTCAAAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGG
AACAAACTCCAAGATTTTTATTCAAAAGGAACAA
Found at i:162059 original size:36 final size:36
Alignment explanation
Indices: 161948--162066 Score: 102
Period size: 36 Copynumber: 3.4 Consensus size: 36
161938 AGAAAATGAT
** * *
161948 GTCTCAAGCGAGATGAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGA-AAAC
** **
161982 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
*
162018 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
*
162053 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
162067 TCAACTTTGT
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
34 18 0.26
35 12 0.18
36 38 0.56
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:162078 original size:36 final size:36
Alignment explanation
Indices: 161982--162066 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
161972 TTAAGATATA
* **
161982 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
162018 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
162053 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
162067 TCAACTTTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 7 0.17
36 35 0.83
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:162198 original size:105 final size:101
Alignment explanation
Indices: 162018--162250 Score: 290
Period size: 105 Copynumber: 2.3 Consensus size: 101
162008 TAGAGAAATT
* *
162018 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATG
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATG
* *
162083 TGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
65 TGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
162120 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACAAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * *
162184 TAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
60 TAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
**
162225 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
162251 AAAATTCTCA
Statistics
Matches: 114, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
101 5 0.04
102 21 0.18
103 2 0.02
104 4 0.04
105 77 0.68
106 5 0.04
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (101 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:162719 original size:4 final size:4
Alignment explanation
Indices: 162710--162899 Score: 371
Period size: 4 Copynumber: 47.5 Consensus size: 4
162700 TTTATGTATC
162710 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
162758 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
162806 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
162854 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT GTGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
162900 ATACTTTTCT
Statistics
Matches: 184, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 184 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:164104 original size:12 final size:11
Alignment explanation
Indices: 164076--164113 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
164066 TCCTCTTTTG
*
164076 TTCTTTGCTTT
1 TTCTTTGATTT
164087 TTCTTTGATTT
1 TTCTTTGATTT
164098 TTGCTTTGATTT
1 TT-CTTTGATTT
164110 TTCT
1 TTCT
164114 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:164800 original size:20 final size:20
Alignment explanation
Indices: 164772--164812 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
164762 CAAAGAGAGG
*
164772 GAATGTTTCAAGGTCTAAAA
1 GAATATTTCAAGGTCTAAAA
*
164792 GAATATTTCAAGGTCTCAAA
1 GAATATTTCAAGGTCTAAAA
164812 G
1 G
164813 TGATAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (20 bp):
GAATATTTCAAGGTCTAAAA
Found at i:164820 original size:26 final size:24
Alignment explanation
Indices: 164744--164823 Score: 78
Period size: 26 Copynumber: 3.3 Consensus size: 24
164734 TCAAGGTGGA
164744 AAGAATGTTTCAAGGTCTCAAAGAG
1 AAGAATGTTTCAAGGTCTCAAAG-G
*
164769 AGGGAATGTTTCAAGGTCT--AA--
1 A-AGAATGTTTCAAGGTCTCAAAGG
*
164790 AAGAATATTTCAAGGTCTCAAAGTG
1 AAGAATGTTTCAAGGTCTCAAAG-G
164815 ATAGAATGT
1 A-AGAATGT
164824 CAAAAATTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
20 15 0.34
21 1 0.02
22 2 0.05
24 2 0.05
25 2 0.05
26 22 0.50
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.28
Consensus pattern (24 bp):
AAGAATGTTTCAAGGTCTCAAAGG
Found at i:164822 original size:46 final size:45
Alignment explanation
Indices: 164730--164823 Score: 125
Period size: 46 Copynumber: 2.1 Consensus size: 45
164720 ATAAATGCAG
* * *
164730 TGTTTCAAGGTGGAAAGAATGTTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
* * *
164775 TGTTTCAAGGTCTAAAAGAATATTTCAAGGTCTCAAAGTGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
164821 TGT
1 TGT
164824 CAAAAATTGG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 11 0.26
46 31 0.74
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.29
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Done.