Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002637.1 Hibiscus syriacus cultivar Beakdansim tig00005377_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: 3156206
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 14
Found at i:3013489 original size:2 final size:2
Alignment explanation
Indices: 3013426--3013471 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
3013416 ATACATAAAC
**
3013426 TA TA TA -A TA TA TA TA TA TA TA CC TA TA TA TA TA TA TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
3013468 TA TA
1 TA TA
3013472 AAGTAAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3013612 original size:17 final size:17
Alignment explanation
Indices: 3013523--3013613 Score: 51
Period size: 15 Copynumber: 5.9 Consensus size: 17
3013513 TAATGCATAC
3013523 ATATATATACTATAT-T
1 ATATATATACTATATAT
*
3013539 A-ATATA-AAT-TATA-
1 ATATATATACTATATAT
* *
3013552 ACATATAAACTATATAGT
1 ATATATATACTATATA-T
3013570 -T-TATATAC-ATATAT
1 ATATATATACTATATAT
*
3013584 AGT-T-TTTA-TATATAT
1 A-TATATATACTATATAT
3013599 ATATATATACTATAT
1 ATATATATACTATAT
3013614 TAATATAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 23
0.66 0.07 0.27
Matches are distributed among these distances:
13 4 0.07
14 9 0.16
15 23 0.40
16 16 0.28
17 5 0.09
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (17 bp):
ATATATATACTATATAT
Found at i:3013619 original size:17 final size:16
Alignment explanation
Indices: 3013523--3013620 Score: 64
Period size: 17 Copynumber: 6.3 Consensus size: 16
3013513 TAATGCATAC
3013523 ATATATATACTATATTA
1 ATATATATACTATA-TA
3013540 ATATA-A-A-T-TATA
1 ATATATATACTATATA
* *
3013552 ACATATAAACTATATA
1 ATATATATACTATATA
* *
3013568 GTTTATATACATATATA
1 ATATATATAC-TATATA
* * *
3013585 GTTTTTATA-TATAT-
1 ATATATATACTATATA
3013599 ATATATATACTATATTA
1 ATATATATACTATA-TA
3013616 ATATA
1 ATATA
3013621 AATAATATTT
Statistics
Matches: 64, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
12 6 0.09
13 3 0.05
14 8 0.12
15 11 0.17
16 12 0.19
17 24 0.38
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (16 bp):
ATATATATACTATATA
Found at i:3013651 original size:18 final size:18
Alignment explanation
Indices: 3013628--3013666 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3013618 ATAAATAATA
3013628 TTTTATAAACTATATACT
1 TTTTATAAACTATATACT
***
3013646 TTTTATAGTTTATATACT
1 TTTTATAAACTATATACT
3013664 TTT
1 TTT
3013667 AATAGTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTATAAACTATATACT
Found at i:3013667 original size:76 final size:78
Alignment explanation
Indices: 3013523--3013685 Score: 197
Period size: 76 Copynumber: 2.1 Consensus size: 78
3013513 TAATGCATAC
* *
3013523 ATATATATACTATATTAATATAAATTATAACATATAAACTATATAGTTTATATACATATATAG-T
1 ATATATATACTATATTAATATAAATAATAACATATAAACTATATACTTTATATACATATATAGCT
*
3013587 TTTTATA-TATAT
66 TTTAATAGTATAT
*** * **
3013599 ATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTTTATAGTTTATATA-C
1 ATATATATACTATATTAATATAAATAATAACATATAAACTATATACTTTATATA-CATATATAGC
*
3013663 TTTTAATAGTTTAT
65 TTTTAATAGTATAT
*
3013677 AAATATATA
1 ATATATATA
3013686 GTTTATATAT
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
76 48 0.66
77 13 0.18
78 12 0.16
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (78 bp):
ATATATATACTATATTAATATAAATAATAACATATAAACTATATACTTTATATACATATATAGCT
TTTAATAGTATAT
Found at i:3013677 original size:16 final size:18
Alignment explanation
Indices: 3013638--3013677 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3013628 TTTTATAAAC
*
3013638 TATATACTTTTTATAGTT
1 TATATACTTTTAATAGTT
3013656 TATATACTTTTAATAGTT
1 TATATACTTTTAATAGTT
3013674 TATA
1 TATA
3013678 AATATATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (18 bp):
TATATACTTTTAATAGTT
Found at i:3013693 original size:11 final size:11
Alignment explanation
Indices: 3013679--3013707 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
3013669 TAGTTTATAA
3013679 ATATATAGTTT
1 ATATATAGTTT
3013690 ATATATAGTTT
1 ATATATAGTTT
3013701 ATATATA
1 ATATATA
3013708 TAATTCGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (11 bp):
ATATATAGTTT
Found at i:3013697 original size:26 final size:24
Alignment explanation
Indices: 3013656--3013709 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 24
3013646 TTTTATAGTT
3013656 TATATACTTTTAATAGTTTATAAA
1 TATATACTTTTAATAGTTTATAAA
* *
3013680 TATATAGTTTATATATAGTTTATATA
1 TATATACTTT-TA-ATAGTTTATAAA
3013706 TATA
1 TATA
3013710 ATTCGCATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 9 0.35
25 2 0.08
26 15 0.58
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (24 bp):
TATATACTTTTAATAGTTTATAAA
Found at i:3013772 original size:18 final size:18
Alignment explanation
Indices: 3013728--3013872 Score: 94
Period size: 18 Copynumber: 8.3 Consensus size: 18
3013718 AAACATAATT
* *
3013728 TATATATATAGCTTATAA
1 TATAAATATAGTTTATAA
*
3013746 TA-ATTATATAGTTTATAA
1 TATA-AATATAGTTTATAA
3013764 TATAAATATAGTTTATAA
1 TATAAATATAGTTTATAA
* * *
3013782 TTTTATATACATAGTTTA-CA
1 ---TATAAATATAGTTTATAA
*
3013802 CATAAATATCA--TT-T-A
1 TATAAATAT-AGTTTATAA
3013817 TAT--ATATAGTTTATAA
1 TATAAATATAGTTTATAA
*
3013833 TA-ATTATATAGTTTATAA
1 TATA-AATATAGTTTATAA
3013851 TATAAATATAGTTTAT-A
1 TATAAATATAGTTTATAA
3013868 TATAA
1 TATAA
3013873 TTTTATATTA
Statistics
Matches: 102, Mismatches: 10, Indels: 31
0.71 0.07 0.22
Matches are distributed among these distances:
12 1 0.01
13 4 0.04
14 2 0.02
15 4 0.04
16 5 0.05
17 13 0.13
18 57 0.56
19 2 0.02
20 1 0.01
21 13 0.13
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (18 bp):
TATAAATATAGTTTATAA
Found at i:3013833 original size:87 final size:87
Alignment explanation
Indices: 3013649--3013880 Score: 296
Period size: 87 Copynumber: 2.7 Consensus size: 87
3013639 ATATACTTTT
* * *
3013649 TATAGTTTAT-ATACTTTTAATAGTTTATAA-AT--ATATAGTTTATATATAGTTTATATATATA
1 TATAGTTTATAATAATTAT-ATAGTTTATAATATAAATATAGTTTATATATA-TTTATATACATA
*
3013710 ATTCGCATAAACATAATTTATATA
64 ATTCACATAAACATAATTTATATA
* *
3013734 TATAGCTTATAATAATTATATAGTTTATAATATAAATATAGTTTATA-AT-TTTATATACATAGT
1 TATAGTTTATAATAATTATATAGTTTATAATATAAATATAGTTTATATATATTTATATACATA-A
* *
3013797 TTACACATAAATATCATTTATATA
65 TT-CACATAAACATAATTTATATA
3013821 TATAGTTTATAATAATTATATAGTTTATAATATAAATATAGTTTATATATAATTTTATAT
1 TATAGTTTATAATAATTATATAGTTTATAATATAAATATAGTTTATATAT-A-TTTATAT
3013881 TATATATATA
Statistics
Matches: 128, Mismatches: 9, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
85 31 0.24
86 10 0.08
87 66 0.52
88 14 0.11
91 7 0.05
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (87 bp):
TATAGTTTATAATAATTATATAGTTTATAATATAAATATAGTTTATATATATTTATATACATAAT
TCACATAAACATAATTTATATA
Found at i:3013883 original size:17 final size:18
Alignment explanation
Indices: 3013863--3013896 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3013853 TAAATATAGT
3013863 TTATATATA-ATTTTATA
1 TTATATATATATTTTATA
3013880 TTATATATATATTTTAT
1 TTATATATATATTTTAT
3013897 TTTTTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATATATATTTTATA
Found at i:3014548 original size:15 final size:15
Alignment explanation
Indices: 3014528--3014562 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
3014518 CTGCTTCAGG
3014528 CCTGAACTGTTTTTA
1 CCTGAACTGTTTTTA
3014543 CCTGAACTGTTTTTA
1 CCTGAACTGTTTTTA
3014558 CCTGA
1 CCTGA
3014563 TGACATCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (15 bp):
CCTGAACTGTTTTTA
Found at i:3015678 original size:17 final size:18
Alignment explanation
Indices: 3015638--3015679 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
3015628 GGTGTTTTTA
3015638 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
* *
3015656 AGATAAAAGA-AATAATT
1 AAATAAAAGATAAGAATT
3015673 AAATAAA
1 AAATAAA
3015680 TAATCTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:3016349 original size:72 final size:73
Alignment explanation
Indices: 3016269--3016494 Score: 278
Period size: 76 Copynumber: 3.1 Consensus size: 73
3016259 TAAAACATAT
*
3016269 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAA-AAAATAATATTTAAA
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAACAAAATAATATTTAAA
*
3016332 ATAATATTC
65 ATAATATCC
* * *
3016341 TAAATCCTAATTAAAATACTAAAACCTATTTAAGCTAAAATACCTAAAACAAATATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT-AAACAAA-ATAATAT-TTA
3016406 AAATAATATCC
63 AAATAATATCC
* * * * *
3016417 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATA-CAAAGATAAAATAAATGTTTAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAA-ACAAAAT-AATATTTAA
*
3016481 AATATTATCC
64 AATAATATCC
3016491 TAAA
1 TAAA
3016495 CTTGAGTTTA
Statistics
Matches: 133, Mismatches: 14, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
71 5 0.04
72 37 0.28
73 3 0.02
74 23 0.17
75 14 0.11
76 51 0.38
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.30
Consensus pattern (73 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAACAAAATAATATTTAAAA
TAATATCC
Found at i:3016368 original size:19 final size:19
Alignment explanation
Indices: 3016340--3016450 Score: 52
Period size: 19 Copynumber: 5.8 Consensus size: 19
3016330 AAATAATATT
*
3016340 CTAAATCCTAATTAAAATA
1 CTAAAACCTAATTAAAATA
* **
3016359 CTAAAACCTATTTAAGCTA
1 CTAAAACCTAATTAAAATA
*
3016378 --AAATACCTAA-AACAAATA
1 CTAAA-ACCTAATTA-AAATA
** *
3016396 -TAAAATATAA-AAATAATA
1 CTAAAACCTAATTAA-AATA
*
3016414 TCCTAAAACTTAATTAAAATA
1 -C-TAAAACCTAATTAAAATA
*
3016435 CTAAAACCTATTTAAA
1 CTAAAACCTAATTAAA
3016451 CTAAAATACA
Statistics
Matches: 69, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
17 5 0.07
18 18 0.26
19 31 0.45
20 1 0.01
21 12 0.17
22 2 0.03
ACGTcount: A:0.56, C:0.14, G:0.01, T:0.29
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:3016420 original size:32 final size:32
Alignment explanation
Indices: 3016379--3016440 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
3016369 TTTAAGCTAA
3016379 AATACCTAAAAC-AAATATAAAATA-TAAAAAT
1 AATACCTAAAACTAAAT-TAAAATACTAAAAAT
*
3016410 AATATCCTAAAACTTAATTAAAATACTAAAA
1 AATA-CCTAAAACTAAATTAAAATACTAAAA
3016441 CCTATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (32 bp):
AATACCTAAAACTAAATTAAAATACTAAAAAT
Found at i:3021384 original size:17 final size:18
Alignment explanation
Indices: 3021348--3021389 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
3021338 GTTGTTTTTA
3021348 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
*
3021366 AAATAAAAGA-AATAATT
1 AAATAAAAGATAAGAATT
3021383 AAATAAA
1 AAATAAA
3021390 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:3022138 original size:76 final size:71
Alignment explanation
Indices: 3021964--3022157 Score: 228
Period size: 76 Copynumber: 2.7 Consensus size: 71
3021954 AACAAGCTAA
* * * * *
3021964 AACATCTTAAATCCTAATTAAAACACTTAAAA-CTATTTAAATTAAAATACCTAAAAAATAATAT
1 AACATCCTAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAACACCTAAAAAATAAAAT
3022028 ATAAAAT
65 ATAAAAT
* * *
3022035 AATATTCTAAATCCCAATTAAAATACTAAAACCTATTTAAACTAAAACACCTAAAACAAAGATAA
1 AACATCCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAACACCT--AA-AAA-ATAA
3022100 AATATAAAAAT
62 AATAT-AAAAT
* * *
3022111 AACATCCTAAAACTTAATTAAAGTACTAAAACCTATTTAAACTAAAA
1 AACATCCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAA
3022158 TACAAAGATA
Statistics
Matches: 103, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
70 5 0.05
71 39 0.38
73 2 0.02
74 3 0.03
75 8 0.08
76 46 0.45
ACGTcount: A:0.56, C:0.15, G:0.01, T:0.28
Consensus pattern (71 bp):
AACATCCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAACACCTAAAAAATAAAATA
TAAAAT
Found at i:3022184 original size:76 final size:77
Alignment explanation
Indices: 3021964--3022184 Score: 203
Period size: 76 Copynumber: 3.0 Consensus size: 77
3021954 AACAAGCTAA
* * * * * *
3021964 AACATCTTAAATCCTAATTAAAACACTTAAAA-CTATTTAAATTAAAATACCT---A-AAAA-AT
1 AACATCCTAAAACCCAATTAAAATAC-TAAAACCTATTTAAACTAAAACACCTAAAATAAAATAT
3022023 AATATAT-AAAAT
65 AATATATAAAAAT
* * * *
3022035 AATATTCTAAATCCCAATTAAAATACTAAAACCTATTTAAACTAAAACACCTAAAACAAAGATA-
1 AACATCCTAAAACCCAATTAAAATACTAAAACCTATTTAAACTAAAACACCTAAAATAAA-ATAT
3022099 AA-ATATAAAAAT
65 AATATATAAAAAT
** * *
3022111 AACATCCTAAAACTTAATTAAAGTACTAAAACCTATTTAAACTAAAATA-C-AAAGATAAAATAT
1 AACATCCTAAAACCCAATTAAAATACTAAAACCTATTTAAACTAAAACACCTAAA-ATAAAATAT
*
3022174 AATATTTAAAA
65 AATATATAAAA
3022185 TATTATCCTA
Statistics
Matches: 123, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
70 5 0.04
71 39 0.32
74 7 0.06
75 14 0.11
76 57 0.46
77 1 0.01
ACGTcount: A:0.57, C:0.14, G:0.01, T:0.28
Consensus pattern (77 bp):
AACATCCTAAAACCCAATTAAAATACTAAAACCTATTTAAACTAAAACACCTAAAATAAAATATA
ATATATAAAAAT
Found at i:3026149 original size:3 final size:3
Alignment explanation
Indices: 3026141--3026198 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
3026131 GCAACAATTG
* **
3026141 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3026185 TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA
3026199 CGGGAAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 5 0.11
3 37 0.82
4 3 0.07
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:3028182 original size:21 final size:21
Alignment explanation
Indices: 3028157--3028196 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3028147 TAACCCCCAC
3028157 TTTTATGTCTTCGACTATAAT
1 TTTTATGTCTTCGACTATAAT
* *
3028178 TTTTATTTCTTGGACTATA
1 TTTTATGTCTTCGACTATA
3028197 TCAGAGCAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.10, T:0.55
Consensus pattern (21 bp):
TTTTATGTCTTCGACTATAAT
Found at i:3035907 original size:20 final size:20
Alignment explanation
Indices: 3035884--3035926 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
3035874 TTTTTGACTT
* * *
3035884 AAAGGATCAATTTCTTAGTA
1 AAAGAATCAATTCCTTAATA
*
3035904 AAAGAATCGATTCCTTAATA
1 AAAGAATCAATTCCTTAATA
3035924 AAA
1 AAA
3035927 AGATTGATCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (20 bp):
AAAGAATCAATTCCTTAATA
Found at i:3040638 original size:21 final size:21
Alignment explanation
Indices: 3040612--3040664 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
3040602 GTTTCCAGAT
3040612 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
* *
3040633 TCGCAACGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
3040654 TCGCAATGCGA
1 TCGCAATGCGA
3040665 TTTACATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:3040703 original size:21 final size:21
Alignment explanation
Indices: 3040673--3040870 Score: 192
Period size: 21 Copynumber: 9.6 Consensus size: 21
3040663 GATTTACATA
*
3040673 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
3040694 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
3040715 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
3040736 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
3040757 TT--CGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
3040776 TTCACGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
3040799 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* **
3040818 TTCGCGTTGTGATTTTCCAA-
1 TTCGCGTTGCGATAGTCCAAG
* *
3040838 TT-TCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
3040858 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
3040871 TTATTTCAAA
Statistics
Matches: 143, Mismatches: 26, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
19 35 0.24
20 4 0.03
21 96 0.67
23 8 0.06
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:3040725 original size:42 final size:40
Alignment explanation
Indices: 3040679--3040895 Score: 281
Period size: 42 Copynumber: 5.3 Consensus size: 40
3040669 CATATTCGCA
* * * *
3040679 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATATTCCAAATT--CG
*
3040721 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATATTCCAAATTCG
* *
3040761 TTGCGATAGTCAAAGTTCACGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGA--TATTCCAAATTCG
* * *
3040803 TTGCGATAGTCGAAGTTCGCGTTGTGATTTTCCAATTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATATTCCAAATTCG
*
3040843 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTTCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGA--TATTCCAAATTCG
3040885 TTGCGATAGTC
1 TTGCGATAGTC
3040896 CAAAATCGCA
Statistics
Matches: 154, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
40 64 0.42
42 90 0.58
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (40 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATATTCCAAATTCG
Found at i:3040784 original size:82 final size:80
Alignment explanation
Indices: 3040679--3040895 Score: 290
Period size: 82 Copynumber: 2.6 Consensus size: 80
3040669 CATATTCGCA
* * *
3040679 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTT
1 TTGCGATAGTCAAAGTTCGCGTTGCGATAGTCCAAATT--CGTTGCGATAGTCGAAGTTCGCGTT
3040744 GCGATTTTCCAAATTCG
64 GCGATTTTCCAAATTCG
* *
3040761 TTGCGATAGTCAAAGTTCACGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1 TTGCGATAGTCAAAGTTCGCGTTGCGA--TAGTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
* *
3040826 GTGATTTTCCAATTTCG
64 GCGATTTTCCAAATTCG
* * *
3040843 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTTCAAATTCGTTGCGATAGTC
1 TTGCGATAGTCAAAGTTCGCGTTGCGA--TAGTCCAAATTCGTTGCGATAGTC
3040896 CAAAATCGCA
Statistics
Matches: 123, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
82 115 0.93
84 8 0.07
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (80 bp):
TTGCGATAGTCAAAGTTCGCGTTGCGATAGTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGC
GATTTTCCAAATTCG
Found at i:3041002 original size:6 final size:6
Alignment explanation
Indices: 3040991--3041037 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
3040981 ACGTATTACC
* * *
3040991 ACGACA ACGACA ACGACA ACGACA ACGACC ACGACC ACGACC ACGAC
1 ACGACA ACGACA ACGACA ACGACA ACGACA ACGACA ACGACA ACGAC
3041038 CCGAGACGGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.43, C:0.40, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACA
Found at i:3041038 original size:18 final size:18
Alignment explanation
Indices: 3040988--3041038 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
3040978 GACACGTATT
*
3040988 ACCACGACAACGACAACG
1 ACCACGACAACGACCACG
*
3041006 ACAACGACAACGACCACG
1 ACCACGACAACGACCACG
*
3041024 ACCACGACCACGACC
1 ACCACGACAACGACC
3041039 CGAGACGGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.41, C:0.43, G:0.16, T:0.00
Consensus pattern (18 bp):
ACCACGACAACGACCACG
Found at i:3041569 original size:6 final size:6
Alignment explanation
Indices: 3041549--3041603 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
3041539 TCTCGTCTCG
*
3041549 GGTCG- GGTCG- GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
3041595 GGTCGT GGT
1 GGTCGT GGT
3041604 AATACGTGTC
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
5 10 0.21
6 38 0.79
ACGTcount: A:0.00, C:0.16, G:0.55, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:3041761 original size:42 final size:42
Alignment explanation
Indices: 3041698--3041834 Score: 226
Period size: 42 Copynumber: 3.3 Consensus size: 42
3041688 TGCGATTTTG
3041698 GACTATCGCAACGAA-CTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATC-TGGAATAAATCGCAACGCGAACTTC
3041740 GACTATCGCAACGAATCTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATCTGGAATAAATCGCAACGCGAACTTC
* *
3041782 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATCTGGAATAAATCGCAACGCGAACTTC
3041822 GACTATCGCAACG
1 GACTATCGCAACG
3041835 CGAACTTGGA
Statistics
Matches: 92, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
40 31 0.34
41 1 0.01
42 59 0.64
43 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (42 bp):
GACTATCGCAACGAATCTGGAATAAATCGCAACGCGAACTTC
Found at i:3041858 original size:21 final size:21
Alignment explanation
Indices: 3041695--3041858 Score: 162
Period size: 21 Copynumber: 7.9 Consensus size: 21
3041685 CGTTGCGATT
3041695 TTGGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
3041714 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
3041737 TTCGACTATCGCAA--CGAA-
1 TTGGACTATCGCAACGCGAAC
*
3041755 TCTGGAATAAATCGCAACGCGAAC
1 T-TGGACT--ATCGCAACGCGAAC
* *
3041779 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
**
3041798 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
3041819 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
3041840 TTGGACTATCGCAATGCGA
1 TTGGACTATCGCAACGCGA
3041859 TATCGCAATG
Statistics
Matches: 118, Mismatches: 15, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
18 1 0.01
19 29 0.25
21 69 0.58
23 18 0.15
24 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:3041864 original size:13 final size:13
Alignment explanation
Indices: 3041846--3041873 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3041836 GAACTTGGAC
3041846 TATCGCAATGCGA
1 TATCGCAATGCGA
3041859 TATCGCAATGCGA
1 TATCGCAATGCGA
3041872 TA
1 TA
3041874 GTCGAAGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (13 bp):
TATCGCAATGCGA
Found at i:3042397 original size:6 final size:6
Alignment explanation
Indices: 3042386--3042412 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3042376 TAAAACATAG
3042386 TAATTA TAATTA TAATTA TAATTA TAA
1 TAATTA TAATTA TAATTA TAATTA TAA
3042413 GGAGTCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TAATTA
Found at i:3044348 original size:17 final size:17
Alignment explanation
Indices: 3044315--3044346 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3044305 CAACTAAACA
3044315 TCTTTTAATATTTAAAT
1 TCTTTTAATATTTAAAT
3044332 TCTTTTAA-ATTTAAA
1 TCTTTTAATATTTAAA
3044347 ATAATAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TCTTTTAATATTTAAAT
Found at i:3045904 original size:3 final size:3
Alignment explanation
Indices: 3045896--3045937 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
3045886 TCCTTTTTAA
*
3045896 TAT TAT TAT CAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3045938 TTACAAATCC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3048118 original size:131 final size:130
Alignment explanation
Indices: 3047792--3048156 Score: 396
Period size: 131 Copynumber: 2.8 Consensus size: 130
3047782 TCGATATTGC
* * * *
3047792 AAATAGTAATATATTTTCATTTC-AGTTGGGGTAATAAATGACTGCTCTAAGGCATGAAAGGTCA
1 AAATAGTAATATCTCTTCATTTCGA-TTGGAGTAATAAATGACTGCTTTAAGGCATGAAAGGTCA
* * * * *
3047856 TTTATTCTCGATTGGAAATAATTC-GATATTATCATTATCTCTCAAATTAATATTGATTTTTAGG
65 TTTATTCTCGATTGGAAATAA-TCAGATATTATTATTTTCACTCAAATTAATATTGAATTTTAAG
3047920 AT
129 AT
* * * ** *
3047922 ATAATAGTGATATCTCTTCAGTTT-GATTGGAGCAATAAATGACTGCTTCAAGGTGTGAGAGGTC
1 A-AATAGTAATATCTCTTCA-TTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAAAGGTC
* * * * * * * *
3047986 ATATATTCTCAATTGAAAATCATCATATATTATTGTTTTCACT-AGAATTGATATTTAATTTTAA
64 ATTTATTCTCGATTGGAAATAATCAGATATTATTATTTTCACTCA-AATTAATATTGAATTTTAA
3048050 GAT
128 GAT
* * * *
3048053 GAAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATAACCGTTTTAAGGCATGAAAAGTCA
1 -AAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAAAGGTCA
*
3048118 TTTATTCTCGATTGGAAATAATTAGATATTATTATTTTC
65 TTTATTCTCGATTGGAAATAATCAGATATTATTATTTTC
3048157 TCCCTTAAAA
Statistics
Matches: 188, Mismatches: 40, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
130 7 0.04
131 176 0.94
132 5 0.03
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (130 bp):
AAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAAAGGTCAT
TTATTCTCGATTGGAAATAATCAGATATTATTATTTTCACTCAAATTAATATTGAATTTTAAGAT
Found at i:3056359 original size:134 final size:134
Alignment explanation
Indices: 3056084--3056666 Score: 615
Period size: 134 Copynumber: 4.4 Consensus size: 134
3056074 ACAAGAGAAG
* * * * ** * *
3056084 CAAGTCTGCCTTGATTCAATCTTCCTTAAAGAACAATGGAAT-AACTCAACATCCCCATACCTGA
1 CAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAA-TCAATGTCCCCAGATCTGA
* * * *
3056148 TTTTCCCTCAAGAAAAA--A-AATAGATCCCTCTATTTCAAGATTAGATATTCCCTGAGTAACA-
65 TTTTCCCTCAAGAAAAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAG
3056209 TTGGAA
130 TT-GAA
* * ** *
3056215 CAAGTATGCCTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAGTTGATGTCCCCAGATCTTAT
1 CAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATGTCCCCAGATCTGAT
* * *
3056280 TTTCCCTCAATAAAAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGT
66 TTTCCCTCAAGAAAAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAGT
3056345 TGAA
131 TGAA
* * * *
3056349 CAAGTCTGCCTCGATTCAATCTTCCAT-AATTAACAGTGGAATGAATCAATGTCCCTAGATATGA
1 CAAGTCTGCCTCGATTCAATCTTCCCTGAA-GAACAGTGGAATGAATCAATGTCCCCAGATCTGA
* * * * *
3056413 TTTTCCCTCAAGAAGAAGCAGAATAGATCACTCTCTTCCAAGATTTGATATTTCCTAAGTAACAG
65 TTTTCCCTCAAGAAAAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAG
*
3056478 TTAAA
130 TTGAA
* * ** * *
3056483 CATGTCTACCTCGATTCAATCTT-CCTTCAGTAACAGTGAAATGAATCAAAGTCCCCAAGATCTG
1 CAAGTCTGCCTCGATTCAATCTTCCCTGAAG-AACAGTGGAATGAATCAATGTCCCC-AGATCTG
* * ** * * * *
3056547 ATATTT-CCTCAATAAGAAGTGGAACATATCCATCTCTTTCAAGATTTGACATTCCCTAAGTGAC
64 AT-TTTCCCTCAAGAAAAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAAC
* *
3056611 AATGGAA
128 AGTTGAA
* * *
3056618 CAAGTCTACCTCGATTCAGTCTTCCCTGAAGAACAGTGGAATGAGTCAA
1 CAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAA
3056667 CGTTTCTCGA
Statistics
Matches: 376, Mismatches: 65, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
131 65 0.17
132 1 0.00
133 5 0.01
134 199 0.53
135 98 0.26
136 8 0.02
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29
Consensus pattern (134 bp):
CAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATGTCCCCAGATCTGAT
TTTCCCTCAAGAAAAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAGT
TGAA
Found at i:3056635 original size:269 final size:265
Alignment explanation
Indices: 3056084--3056666 Score: 645
Period size: 269 Copynumber: 2.2 Consensus size: 265
3056074 ACAAGAGAAG
* * * * * ** * * **
3056084 CAAGTCTGCCTTGATTCAATCTTCCTTAAAGAACAATGGAAT-AACTCAACATCCCCATACCTGA
1 CAAGTCTACCTCGATTCAATCTTCCATGAAGAACAGTGGAATGAA-TCAATGTCCCTAGATATGA
* * * *
3056148 TTTTCCCTCAAGAAAAAAAATAGATCCCTCTATTTCAAGATTAGATATTCCCTGAGTAACATTGG
65 TTTTCCCTCAAGAAAAAAAATAGATCACTCTATTCCAAGATTAGATATTCCCTAAGTAACATTGA
* * * ** * *
3056213 AACAAGTATGCCTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAGTTGATGTCCCCAGATCTT
130 AACAAGTATACCTCGATTCAATCTTCCCTGAAGAACAGTGAAATGAATCAAAGTCCCCAGATCTG
* * *
3056278 ATTTTCCCTCAATAAAAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACA
195 ATTTTCCCTCAATAAAAAGCAGAACAAATCCATCTCTTTCAAGATTTGACATTCCCTAAGTAACA
* *
3056343 GTTGAA
260 ATGGAA
* *
3056349 CAAGTCTGCCTCGATTCAATCTTCCAT-AATTAACAGTGGAATGAATCAATGTCCCTAGATATGA
1 CAAGTCTACCTCGATTCAATCTTCCATGAA-GAACAGTGGAATGAATCAATGTCCCTAGATATGA
* * * *
3056413 TTTTCCCTCAAGAAGAAGCAGAATAGATCACTCTCTTCCAAGATTTGATATTTCCTAAGTAACAG
65 TTTTCCCTCAAGAA-AA--AAAATAGATCACTCTATTCCAAGATTAGATATTCCCTAAGTAACA-
* * **
3056478 TT-AAACATGTCTACCTCGATTCAATCTT-CCTTCAGTAACAGTGAAATGAATCAAAGTCCCCAA
126 TTGAAACAAGTATACCTCGATTCAATCTTCCCTGAAG-AACAGTGAAATGAATCAAAGTCCCC-A
* ** *
3056541 GATCTGATATTT-CCTCAATAAGAAGTGGAACATATCCATCTCTTTCAAGATTTGACATTCCCTA
189 GATCTGAT-TTTCCCTCAATAAAAAGCAGAACAAATCCATCTCTTTCAAGATTTGACATTCCCTA
*
3056605 AGTGACAATGGAA
253 AGTAACAATGGAA
* * *
3056618 CAAGTCTACCTCGATTCAGTCTTCCCTGAAGAACAGTGGAATGAGTCAA
1 CAAGTCTACCTCGATTCAATCTTCCATGAAGAACAGTGGAATGAATCAA
3056667 CGTTTCTCGA
Statistics
Matches: 264, Mismatches: 44, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
264 2 0.01
265 62 0.23
266 4 0.02
267 5 0.02
268 80 0.30
269 106 0.40
270 5 0.02
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29
Consensus pattern (265 bp):
CAAGTCTACCTCGATTCAATCTTCCATGAAGAACAGTGGAATGAATCAATGTCCCTAGATATGAT
TTTCCCTCAAGAAAAAAAATAGATCACTCTATTCCAAGATTAGATATTCCCTAAGTAACATTGAA
ACAAGTATACCTCGATTCAATCTTCCCTGAAGAACAGTGAAATGAATCAAAGTCCCCAGATCTGA
TTTTCCCTCAATAAAAAGCAGAACAAATCCATCTCTTTCAAGATTTGACATTCCCTAAGTAACAA
TGGAA
Found at i:3060982 original size:23 final size:23
Alignment explanation
Indices: 3060952--3060998 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
3060942 GAAAGGTTCG
3060952 AGTGATGAACCTAATCTCTTCTC
1 AGTGATGAACCTAATCTCTTCTC
3060975 AGTGATGAACCTAATCTCTTCTC
1 AGTGATGAACCTAATCTCTTCTC
3060998 A
1 A
3060999 TGGATAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.34
Consensus pattern (23 bp):
AGTGATGAACCTAATCTCTTCTC
Found at i:3064269 original size:20 final size:20
Alignment explanation
Indices: 3064241--3064278 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3064231 ATACTTGACC
* *
3064241 CTAGGGTATTGATACTACAT
1 CTAGAGTATCGATACTACAT
3064261 CTAGAGTATCGATACTAC
1 CTAGAGTATCGATACTAC
3064279 CCACTTTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (20 bp):
CTAGAGTATCGATACTACAT
Found at i:3065595 original size:20 final size:20
Alignment explanation
Indices: 3065567--3065604 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3065557 ATACTTGACC
* *
3065567 CTAGGGTATTGATACTACAT
1 CTAGAGTATCGATACTACAT
3065587 CTAGAGTATCGATACTAC
1 CTAGAGTATCGATACTAC
3065605 CCACTTTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (20 bp):
CTAGAGTATCGATACTACAT
Found at i:3076593 original size:31 final size:30
Alignment explanation
Indices: 3076546--3076618 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 30
3076536 GTATGAGTCA
* *
3076546 CAACAGAGTTAATATTGCATTCAGATAATG
1 CAACAGAGTTAATATTGCAATCAAATAATG
* *
3076576 CACATAGAGTTAGTATTGCAATCAAATAATG
1 CA-ACAGAGTTAATATTGCAATCAAATAATG
3076607 CAACAGAGTTAA
1 CAACAGAGTTAA
3076619 CATGACATTC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 10 0.28
31 26 0.72
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (30 bp):
CAACAGAGTTAATATTGCAATCAAATAATG
Found at i:3078688 original size:49 final size:50
Alignment explanation
Indices: 3078616--3078716 Score: 125
Period size: 49 Copynumber: 2.0 Consensus size: 50
3078606 ATTTTAATAA
*
3078616 AAAAATTATATTTTATTCAAACTCGTCACATC-AGCGTGAAGAGTTTGAAT
1 AAAAATTATATTTTATTCAAACTCGTCACATCGA-CGTGAAGAGTTTCAAT
* ** * *
3078666 AAAAA-TATTTTTTATTGGAACTCGTCATATCGACGTGACGAGTTTCAAT
1 AAAAATTATATTTTATTCAAACTCGTCACATCGACGTGAAGAGTTTCAAT
3078715 AA
1 AA
3078717 CATTATAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
49 38 0.86
50 6 0.14
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.35
Consensus pattern (50 bp):
AAAAATTATATTTTATTCAAACTCGTCACATCGACGTGAAGAGTTTCAAT
Found at i:3080961 original size:21 final size:20
Alignment explanation
Indices: 3080918--3080961 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3080908 GTTTTGGGAA
*
3080918 AAAAGTATCGACACATATTT
1 AAAAGTATCGACACATATGT
* *
3080938 AAAAGTGTCGATACATAATGT
1 AAAAGTATCGACACAT-ATGT
3080959 AAA
1 AAA
3080962 TCTATTTGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (20 bp):
AAAAGTATCGACACATATGT
Found at i:3081719 original size:182 final size:182
Alignment explanation
Indices: 3081404--3082235 Score: 1001
Period size: 182 Copynumber: 4.5 Consensus size: 182
3081394 TTTACTACGT
* * * *
3081404 GTTTTATCATTTCGAGACTGATTTTTTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
1 GTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
* * *
3081469 TTTTATAAAGTATCGACACTTTATTGGTGCTATAACTTATTTTCTTTTAAATTCCAAAAGTGTCG
66 TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCG
*
3081534 ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCTCTTTACCG
131 ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCG
3081586 GTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
1 GTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
* *
3081651 TTTTATAAAGTATCGACAGTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTTTCG
66 TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCG
* *
3081716 ATACTTATAATAAAGTATCGACACTTTCAACATATTCGGTAGCTCTTTACCG
131 ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCG
* * **
3081768 GTTTTGTCATTTCGAGACTGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATTAATACAT
1 GTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
* * *
3081833 TTTTATAAAGTATCGACACTTTATTAGCGATATAA---CTTCTCTTTTAAATTTCAAAAGTGTCG
66 TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCG
* * * *
3081895 ATACTTATAATAAAGTATCGACACTATAAACATATCTGGTAGCGCTTTACCT
131 ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCG
** * *
3081947 GTTTTGTCATTTATAGACCGGTTTTGTTATTTTTTTACCTGTTAT-TTGTTATGGATCGATACAT
1 GTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
* * * * *
3082011 TTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTTTTTAC
66 TTTTATAAAGTATCGACAC-TT---TAT-T---G--GCGCTATAAC--TTCT-TC--TCTTTTAA
* ** * * * * *
3082076 ATGT-TATATTGTTATAAATCGATATATTTTTATAAAGTATCGACACTTTCAATATATCC-GTAG
116 AT-TCCA-AAAG---T--GTCGATA-CTTATAATAAAGTATCGACACTTTCAACATATCCGGTAG
*
3082139 CGCTTTACCT
173 CGCTTTACCG
** * *
3082149 GTTTTGTCATTTATAGACCGGTTTTTTCATTTTTTTACCTGTTATATTGTTATGGATCGATACAT
1 GTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
*
3082214 TTTTATAAAGTATTGACACTTT
66 TTTTATAAAGTATCGACACTTT
3082236 CAATATATAC
Statistics
Matches: 569, Mismatches: 54, Indels: 37
0.86 0.08 0.06
Matches are distributed among these distances:
178 36 0.06
179 112 0.20
182 268 0.47
183 1 0.00
188 6 0.01
193 1 0.00
194 2 0.00
196 9 0.02
197 3 0.01
199 1 0.00
200 1 0.00
202 65 0.11
203 64 0.11
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (182 bp):
GTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCG
ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCG
Found at i:3082071 original size:91 final size:91
Alignment explanation
Indices: 3081967--3082160 Score: 327
Period size: 91 Copynumber: 2.1 Consensus size: 91
3081957 TTATAGACCG
* * **
3081967 GTTTTGTTATTTTTTTACCTGTTAT-TTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
1 GTTTTGTCATTTTTTTACATGTTATATTGTTATAAATCGATACATTTTTATAAAGTATCGACACT
3082031 TTCAATATATCCGGTAGCGCTTTACCT
66 TTCAATATATCC-GTAGCGCTTTACCT
*
3082058 GTTTTGTCATTTTTTTACATGTTATATTGTTATAAATCGATATATTTTTATAAAGTATCGACACT
1 GTTTTGTCATTTTTTTACATGTTATATTGTTATAAATCGATACATTTTTATAAAGTATCGACACT
3082123 TTCAATATATCCGTAGCGCTTTACCT
66 TTCAATATATCCGTAGCGCTTTACCT
3082149 GTTTTGTCATTT
1 GTTTTGTCATTT
3082161 ATAGACCGGT
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
91 49 0.51
92 48 0.49
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.48
Consensus pattern (91 bp):
GTTTTGTCATTTTTTTACATGTTATATTGTTATAAATCGATACATTTTTATAAAGTATCGACACT
TTCAATATATCCGTAGCGCTTTACCT
Found at i:3082253 original size:203 final size:207
Alignment explanation
Indices: 3081904--3082457 Score: 742
Period size: 203 Copynumber: 2.6 Consensus size: 207
3081894 GATACTTATA
* * * *
3081904 ATAAAGTATCGACACTATAAACATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATC-CGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
3081969 TTTGTT-ATTTTTTTACCTGTTAT-TTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
65 TTT-TTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
*
3082032 TCAATATATCCGGTAGCGCTTTA-C-C-T-GTTTTGTCATTTTTTTACATGTTATATTGTTATAA
129 TCAATATATACGGTAGCGCTTTACCTCTTAGTTTTGTCATTTTTTTACATGTTATATTGTTATAA
* *
3082093 ATCGATATATTTTT
194 ATCAACATATTTTT
3082107 ATAAAGTATCGACACTTTCAATATATCCGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTT
1 ATAAAGTATCGACACTTTCAATATATCCGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTT
*
3082172 TTTTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATTGACACTTTC
66 TTTTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTC
*
3082237 AATATATACGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTG
131 AATATATACGGTAGCGCTTTACC-------TC---T-T--A---GTTTTGTCATTTTTTTACATG
**
3082302 TTATATTGTTATGGATCAACATATTTTT
180 TTATATTGTTATAAATCAACATATTTTT
*
3082330 ATAAAGTGTCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCC-GTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* ** *
3082395 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATTAATATATTTTTATAAAGTATCGACAC
65 TTTTTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
3082458 AAACCGACAA
Statistics
Matches: 310, Mismatches: 17, Indels: 26
0.88 0.05 0.07
Matches are distributed among these distances:
201 2 0.01
202 56 0.18
203 85 0.27
204 1 0.00
212 1 0.00
217 1 0.00
223 71 0.23
224 42 0.14
225 51 0.16
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (207 bp):
ATAAAGTATCGACACTTTCAATATATCCGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTT
TTTTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTC
AATATATACGGTAGCGCTTTACCTCTTAGTTTTGTCATTTTTTTACATGTTATATTGTTATAAAT
CAACATATTTTT
Found at i:3082285 original size:112 final size:111
Alignment explanation
Indices: 3082058--3082457 Score: 665
Period size: 112 Copynumber: 3.6 Consensus size: 111
3082048 CGCTTTACCT
* ** *
3082058 GTTTTGTCATTTTTTTACATGTTATATTGTTATAAATCGATATATTTTTATAAAGTATCGACACT
1 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTTATAAAGTATCGACACT
*
3082123 TTCAATATATCCGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
66 TTCAATATATCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
* * * *
3082169 GTTTTTTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATTGACACT
1 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTTATAAAGTATCGACACT
3082234 TTCAATATATACGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
66 TTCAATATAT-CGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
* *
3082281 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAACATATTTTTATAAAGTGTCGACACT
1 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTTATAAAGTATCGACACT
3082346 TTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
66 TTCAATATAT-CGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
*
3082393 GTTTTGTCATTTTTTTTACCTGTTATATTGTTATGGATTAATATATTTTTATAAAGTATCGACAC
1 GTTTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTTATAAAGTATCGACAC
3082458 AAACCGACAA
Statistics
Matches: 270, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
111 69 0.26
112 149 0.55
113 52 0.19
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (111 bp):
GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTTATAAAGTATCGACACT
TTCAATATATCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
Found at i:3083473 original size:22 final size:22
Alignment explanation
Indices: 3083445--3083491 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
3083435 TGGGTTAGGG
3083445 TTGGGTCAAGCCCTTTACCCGA
1 TTGGGTCAAGCCCTTTACCCGA
* *
3083467 TTGGGTCAGGCCTTTTACCCGA
1 TTGGGTCAAGCCCTTTACCCGA
3083489 TTG
1 TTG
3083492 AGTTTCTGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.15, C:0.28, G:0.26, T:0.32
Consensus pattern (22 bp):
TTGGGTCAAGCCCTTTACCCGA
Found at i:3083680 original size:42 final size:43
Alignment explanation
Indices: 3083600--3083706 Score: 121
Period size: 42 Copynumber: 2.5 Consensus size: 43
3083590 GATATATAAT
** **
3083600 AAAAATTATATAACAT-TATATTTCAAAAATAATATGTTTTTA
1 AAAAATTATATATTATATATATTTCAAAAATAATATGTTTCAA
* *
3083642 TAAAATTATATATTATATATGTTTCCAAAAA-AAT-TGTTTCAA
1 AAAAATTATATATTATATATATTT-CAAAAATAATATGTTTCAA
3083684 AAAAATTATATATATATATATAT
1 AAAAATTATATAT-TATATATAT
3083707 ATATGTTTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
42 31 0.57
43 17 0.31
44 6 0.11
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.43
Consensus pattern (43 bp):
AAAAATTATATATTATATATATTTCAAAAATAATATGTTTCAA
Found at i:3083686 original size:14 final size:15
Alignment explanation
Indices: 3083661--3083690 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3083651 ATATTATATA
3083661 TGTTTCCAAAAAAAT
1 TGTTTCCAAAAAAAT
3083676 TGTTT-CAAAAAAAT
1 TGTTTCCAAAAAAAT
3083690 T
1 T
3083691 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (15 bp):
TGTTTCCAAAAAAAT
Found at i:3084615 original size:8 final size:8
Alignment explanation
Indices: 3084602--3084662 Score: 122
Period size: 8 Copynumber: 7.6 Consensus size: 8
3084592 ATTGTAAATT
3084602 AAAAATAA
1 AAAAATAA
3084610 AAAAATAA
1 AAAAATAA
3084618 AAAAATAA
1 AAAAATAA
3084626 AAAAATAA
1 AAAAATAA
3084634 AAAAATAA
1 AAAAATAA
3084642 AAAAATAA
1 AAAAATAA
3084650 AAAAATAA
1 AAAAATAA
3084658 AAAAA
1 AAAAA
3084663 GATTTTTAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 53 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAATAA
Found at i:3084676 original size:1 final size:1
Alignment explanation
Indices: 3084602--3084662 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
3084592 ATTGTAAATT
* * * * * * *
3084602 AAAAATAAAAAAATAAAAAAATAAAAAAATAAAAAAATAAAAAAATAAAAAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3084663 GATTTTTAAA
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (1 bp):
A
Found at i:3085528 original size:3 final size:3
Alignment explanation
Indices: 3085514--3085563 Score: 57
Period size: 3 Copynumber: 15.7 Consensus size: 3
3085504 AAATTAAATA
3085514 AAT AAGT AAT AAT AAT AA- AAT AAT AAAT AAT CAAT AAT AAT ATAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT -AAT AAT -AAT AAT AAT A-AT AAT
3085562 AA
1 AA
3085564 AAATTATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
2 2 0.05
3 28 0.67
4 12 0.29
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3085537 original size:14 final size:14
Alignment explanation
Indices: 3085520--3085565 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 14
3085510 AATAAATAAG
3085520 TAATAATAATAAAA
1 TAATAATAATAAAA
3085534 TAATAAATAATCAATAA
1 TAAT-AATAAT-AA-AA
3085551 TAATATATAATAAAA
1 TAATA-ATAATAAAA
3085566 ATTATATAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 4 0.14
15 8 0.29
16 5 0.18
17 11 0.39
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:3085540 original size:25 final size:24
Alignment explanation
Indices: 3085510--3085564 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
3085500 AAAAAAATTA
3085510 AATAAATAAGT-AATAATAATAAAAT
1 AATAAATAA-TCAATAATAAT-AAAT
*
3085535 AATAAATAATCAATAATAATATAT
1 AATAAATAATCAATAATAATAAAT
3085559 AATAAA
1 AATAAA
3085565 AATTATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (24 bp):
AATAAATAATCAATAATAATAAAT
Found at i:3085560 original size:7 final size:6
Alignment explanation
Indices: 3085514--3085563 Score: 57
Period size: 7 Copynumber: 7.8 Consensus size: 6
3085504 AAATTAAATA
3085514 AATAAGT AATAAT AATAA- AATAAT AAATAAT CAATAAT AATATAT AATAA
1 AATAA-T AATAAT AATAAT AATAAT -AATAAT -AATAAT AATA-AT AATAA
3085564 AAATTATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 5 0.13
6 11 0.28
7 23 0.59
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (6 bp):
AATAAT
Found at i:3085719 original size:37 final size:36
Alignment explanation
Indices: 3085688--3086037 Score: 191
Period size: 36 Copynumber: 9.5 Consensus size: 36
3085678 AAAATATGCA
3085688 TAAAAACTATATATTATATGTTTTCAAAAAAT-TTT
1 TAAAAACTATATATTATATGTTTTCAAAAAATATTT
* * *
3085723 TCAAAA-TTTATA-TATACGTTTT--AAAAATATTT
1 TAAAAACTATATATTATATGTTTTCAAAAAATATTT
* *
3085755 TAAAATA-TATATATTTTATGTTTACAAAAACAT-TTT
1 TAAAA-ACTATATATTATATGTTTTCAAAAA-ATATTT
* * *
3085791 CAAAAATTATATTATATATATGTTTTTAAAAAATATTT
1 TAAAAACTATA-TAT-TATATGTTTTCAAAAAATATTT
* ***
3085829 T-AAAACTATATATTATATGGTTTTTAAAACCGATTT
1 TAAAAACTATATATTATAT-GTTTTCAAAAAATATTT
* * *
3085865 TAAAAACTATATATTATATACATTTTCAAAAACTGTTTT
1 TAAAAACTATATATTATAT--GTTTTCAAAAAAT-ATTT
* ** * * *
3085904 TCAAAACTATATAAAACACGTTTT-AAAAAATGTGTTT
1 TAAAAACTATATATTATATGTTTTCAAAAAA--TATTT
* * * * ***
3085941 TCAAAATTATATAATATATGTTTTTAAATCGTATTT
1 TAAAAACTATATATTATATGTTTTCAAAAAATATTT
* *
3085977 TCAAAA-TCATAT-TATATATATTTTCAAAAATCGATATTTT
1 TAAAAACT-ATATAT-TATATGTTTTCAAAAA---ATA-TTT
3086017 TAAAAAAACTATATATTATAT
1 T--AAAAACTATATATTATAT
3086038 ATATTTTGAA
Statistics
Matches: 242, Mismatches: 46, Indels: 47
0.72 0.14 0.14
Matches are distributed among these distances:
31 6 0.02
32 7 0.03
33 15 0.06
34 12 0.05
35 12 0.05
36 64 0.26
37 59 0.24
38 29 0.12
39 19 0.08
40 4 0.02
42 13 0.05
43 2 0.01
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
TAAAAACTATATATTATATGTTTTCAAAAAATATTT
Found at i:3085825 original size:74 final size:71
Alignment explanation
Indices: 3085688--3085884 Score: 210
Period size: 67 Copynumber: 2.7 Consensus size: 71
3085678 AAAATATGCA
3085688 TAAAAACTATATATTATATGTTTTCAAAAA-ATTTTTC--AAA--AT-TTATATATACGTTTTAA
1 TAAAAA-TATATATTATATGTTTTCAAAAACA-TTTTCAAAAATTATATTATATATACGTTTTAA
3085747 AAATATTT
64 AAATATTT
* * *
3085755 TAAAATATATATATTTTATGTTTACAAAAACATTTTCAAAAATTATATTATATATATGTTTTTAA
1 TAAAA-ATATATATTATATGTTTTCAAAAACATTTTCAAAAATTATATTATATATACG-TTTT-A
3085820 AAAATATTT
63 AAAATATTT
* * *
3085829 TAAAACTATATATTATATGGTTTTTAAAACCGATTTT-AAAAACTATATATTATATA
1 TAAAAATATATATTATAT-GTTTTCAAAAAC-ATTTTCAAAAA-T-TATATTATATA
3085885 CATTTTCAAA
Statistics
Matches: 109, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
67 31 0.28
68 2 0.02
69 3 0.03
71 2 0.02
72 10 0.09
73 15 0.14
74 29 0.27
75 6 0.06
76 11 0.10
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (71 bp):
TAAAAATATATATTATATGTTTTCAAAAACATTTTCAAAAATTATATTATATATACGTTTTAAAA
ATATTT
Found at i:3085896 original size:74 final size:68
Alignment explanation
Indices: 3085690--3085916 Score: 208
Period size: 74 Copynumber: 3.2 Consensus size: 68
3085680 AATATGCATA
* * *
3085690 AAAACTATATATTATATGTTTTCAAAAAATTTTTCAAAATT-TA-TATATACGTTTT-AAAAATA
1 AAAACTATATATTATATGTTTTCAAAACA-TTTTAAAAATTATATTATATACATTTTAAAAAATA
3085752 TTTT
65 TTTT
* * * *
3085756 AAAATATATATATTTTATGTTTACAAAAACATTTTCAAAAATTATATTATATATATGTTTTTAAA
1 AAAA-CTATATATTATATGTTTTC-AAAACATTTT-AAAAATTATATTATATACA---TTTTAAA
3085821 AAATATTTT
60 AAATATTTT
*
3085830 AAAACTATATATTATATGGTTTTTAAAACCGATTTTAAAAACTATATATTATATACATTTTCAAA
1 AAAACTATATATTATAT-GTTTTCAAAA-C-ATTTTAAAAA-T-TATATTATATACATTTT-AAA
* *
3085895 AACTGTTTTT
60 AAAT-ATTTT
3085905 CAAAACTATATA
1 -AAAACTATATA
3085917 AAACACGTTT
Statistics
Matches: 130, Mismatches: 14, Indels: 24
0.77 0.08 0.14
Matches are distributed among these distances:
66 4 0.03
67 20 0.15
68 11 0.08
69 2 0.02
70 6 0.05
73 23 0.18
74 31 0.24
75 10 0.08
76 23 0.18
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (68 bp):
AAAACTATATATTATATGTTTTCAAAACATTTTAAAAATTATATTATATACATTTTAAAAAATAT
TTT
Found at i:3085897 original size:39 final size:36
Alignment explanation
Indices: 3085825--3085916 Score: 103
Period size: 39 Copynumber: 2.4 Consensus size: 36
3085815 TTTAAAAAAT
** *
3085825 ATTTTAAAACTATATATTATATGGTTTTTAAAACCG
1 ATTTTAAAACTATATATTATATCATTTTAAAAACCG
*
3085861 ATTTTAAAAACTATATATTATATACATTTTCAAAAACTG
1 ATTTT-AAAACTATATATTATAT-CATTTT-AAAAACCG
*
3085900 TTTTTCAAAACTATATA
1 ATTTT-AAAACTATATA
3085917 AAACACGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
36 5 0.11
37 17 0.36
38 4 0.09
39 21 0.45
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.43
Consensus pattern (36 bp):
ATTTTAAAACTATATATTATATCATTTTAAAAACCG
Found at i:3086030 original size:17 final size:18
Alignment explanation
Indices: 3085991--3086033 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3085981 AATCATATTA
* *
3085991 TATATATTTTCAAAAATC
1 TATATATTTTAAAAAAAC
*
3086009 GATAT-TTTTAAAAAAAC
1 TATATATTTTAAAAAAAC
3086026 TATATATT
1 TATATATT
3086034 ATATATATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (18 bp):
TATATATTTTAAAAAAAC
Found at i:3090176 original size:29 final size:30
Alignment explanation
Indices: 3090143--3090206 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
3090133 TTTTAGATCT
*
3090143 TTTAAATTTCTATTTTTGTT-TTTTGGTCC
1 TTTAAATTTCTATATTTGTTATTTTGGTCC
* *
3090172 TTTAAGTTTCTGTATTTGTTATTTTGGTCC
1 TTTAAATTTCTATATTTGTTATTTTGGTCC
3090202 TTTAA
1 TTTAA
3090207 CTTTATGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 17 0.55
30 14 0.45
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.62
Consensus pattern (30 bp):
TTTAAATTTCTATATTTGTTATTTTGGTCC
Found at i:3090199 original size:30 final size:29
Alignment explanation
Indices: 3090143--3090218 Score: 98
Period size: 30 Copynumber: 2.6 Consensus size: 29
3090133 TTTTAGATCT
* *
3090143 TTTAAATTTCTATTTTTGTTTTTTGGTCC
1 TTTAAATTTCTGTATTTGTTTTTTGGTCC
*
3090172 TTTAAGTTTCTGTATTTGTTATTTTGGTCC
1 TTTAAATTTCTGTATTTGTT-TTTTGGTCC
* *
3090202 TTTAACTTTATGTATTT
1 TTTAAATTTCTGTATTT
3090219 ACTATTTAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 17 0.41
30 24 0.59
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (29 bp):
TTTAAATTTCTGTATTTGTTTTTTGGTCC
Found at i:3090225 original size:30 final size:30
Alignment explanation
Indices: 3090163--3090225 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
3090153 TATTTTTGTT
* * **
3090163 TTTTGGTCCTTTAAGTTTCTGTATTTGTTA
1 TTTTGGTCCTTTAACTTTATGTATTTACTA
3090193 TTTTGGTCCTTTAACTTTATGTATTTACTA
1 TTTTGGTCCTTTAACTTTATGTATTTACTA
3090223 TTT
1 TTT
3090226 AACCCTCTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.16, C:0.11, G:0.13, T:0.60
Consensus pattern (30 bp):
TTTTGGTCCTTTAACTTTATGTATTTACTA
Found at i:3095521 original size:32 final size:32
Alignment explanation
Indices: 3095479--3095542 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
3095469 AAGAAACGAT
*
3095479 GAATGATGGGGTATCATTGGAGATTCAACATC
1 GAATGATGGGGCATCATTGGAGATTCAACATC
* * *
3095511 GAATGTTGGGGCATCTTTGGGGATTCAACATC
1 GAATGATGGGGCATCATTGGAGATTCAACATC
3095543 TTGATGTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.30
Consensus pattern (32 bp):
GAATGATGGGGCATCATTGGAGATTCAACATC
Found at i:3095924 original size:30 final size:32
Alignment explanation
Indices: 3095870--3095928 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 32
3095860 GAAACGCAAA
*
3095870 ATCTTTGAGTTTGTTTCTCTTGAAACAAAACC
1 ATCTTTGAGTTCGTTTCTCTTGAAACAAAACC
3095902 ATCTTTGAG-TCGTTTC-CTTGAAACAAA
1 ATCTTTGAGTTCGTTTCTCTTGAAACAAA
3095929 TTTTGTCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 11 0.42
31 6 0.23
32 9 0.35
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.39
Consensus pattern (32 bp):
ATCTTTGAGTTCGTTTCTCTTGAAACAAAACC
Found at i:3096331 original size:135 final size:130
Alignment explanation
Indices: 3096027--3096334 Score: 363
Period size: 130 Copynumber: 2.3 Consensus size: 130
3096017 CCTCATCGTA
* *
3096027 TAGGAACCA-TGTCATCCCCTGACTAGACCTCCTCATCACGTAGGAGCTGTGTCACCCCTAATAA
1 TAGGAA-CAGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCTGTGTCACCCCTAATAA
* * * *
3096091 CCAGCCGTCCTCATCATGTAGGAATCGTGTTATCATCCCTAAAGATGGCATATCATCCTCATCAC
65 CCAGCCGTCCTCATCACGTAGGAATCGTGTTATCACCCCTAAAGATGGCAGAACATCCTCATCAC
3096156 G
130 G
* * *
3096157 TAGGAACCGTGTCATCCACCGACCAGACCTCATCATCACGTAGGAGAC-GTGTCACCCCTAGATA
1 TAGGAACAGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAG-CTGTGTCACCCCTA-ATA
* * *
3096221 ACCAGCCGTCCTCTTCGCGTAGGAA-CTGTGTTATCACCCTCTTTAAAGATGGCCAAGAAC-TCT
64 ACCAGCCGTCCTCATCACGTAGGAATC-GTGTTATCACCC-C--TAAAGATGG-C-AGAACATCC
3096284 TCATCACG
123 TCATCACG
* * * *
3096292 TATGAGCAGTGTCATCCCCCGACGAGATCTCCTCATCACGTAG
1 TAGGAACAGTGTCATCCCCCGACCAGACCTCCTCATCACGTAG
3096335 AAGTCGTATC
Statistics
Matches: 150, Mismatches: 19, Indels: 13
0.82 0.10 0.07
Matches are distributed among these distances:
129 1 0.01
130 52 0.35
131 37 0.25
132 1 0.01
134 9 0.06
135 47 0.31
136 3 0.02
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.24
Consensus pattern (130 bp):
TAGGAACAGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCTGTGTCACCCCTAATAAC
CAGCCGTCCTCATCACGTAGGAATCGTGTTATCACCCCTAAAGATGGCAGAACATCCTCATCACG
Found at i:3096558 original size:3 final size:3
Alignment explanation
Indices: 3096544--3096611 Score: 120
Period size: 3 Copynumber: 23.0 Consensus size: 3
3096534 TCTACAAAAA
*
3096544 ATT ATT -TT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3096591 ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
3096612 TACATACTTA
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 60 0.97
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3097564 original size:29 final size:30
Alignment explanation
Indices: 3097532--3097595 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
3097522 TTTTAGACCT
* *
3097532 TTTAAATTTTTATTTTTGTT-TTTTGGTCC
1 TTTAAATTTCTATATTTGTTATTTTGGTCC
* *
3097561 TTTAAGTTTCTGTATTTGTTATTTTGGTCC
1 TTTAAATTTCTATATTTGTTATTTTGGTCC
3097591 TTTAA
1 TTTAA
3097596 CTTTATGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.16, C:0.08, G:0.12, T:0.64
Consensus pattern (30 bp):
TTTAAATTTCTATATTTGTTATTTTGGTCC
Found at i:3097586 original size:30 final size:29
Alignment explanation
Indices: 3097546--3097607 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
3097536 AATTTTTATT
* *
3097546 TTTGTTTTTTGGTCCTTTAAGTTTCTGTA
1 TTTGTTTTTTGGTCCTTTAACTTTATGTA
3097575 TTTGTTATTTTGGTCCTTTAACTTTATGTA
1 TTTGTT-TTTTGGTCCTTTAACTTTATGTA
3097605 TTT
1 TTT
3097608 ACTGTTCAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.13, C:0.10, G:0.15, T:0.63
Consensus pattern (29 bp):
TTTGTTTTTTGGTCCTTTAACTTTATGTA
Found at i:3100537 original size:6 final size:6
Alignment explanation
Indices: 3100526--3100566 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
3100516 TCCTTTCAAA
* *
3100526 TATATG TATATG TATATG TATATG TATATA TATATA TATAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TATAT
3100567 CCCTTATTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:3100856 original size:43 final size:43
Alignment explanation
Indices: 3100809--3100906 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 43
3100799 ACACAGAGAG
* *
3100809 AAAGAAGAAAAGATATAAAAAAATGAAAC-AT-AAAAAAGATAGA
1 AAAGAAGAAAA-AAATAAAAAAATGAAACAATGAAAAAA-AAAGA
*
3100852 AAAGAAAGAAAAAAATAGAAAAATGAAACAAATGAAAAAAAAAGA
1 AAAG-AAGAAAAAAATAAAAAAATGAAAC-AATGAAAAAAAAAGA
3100897 AAAGAA-AAAA
1 AAAGAAGAAAA
3100907 TGAGAGAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
43 23 0.48
44 9 0.19
45 10 0.21
46 6 0.12
ACGTcount: A:0.77, C:0.02, G:0.13, T:0.08
Consensus pattern (43 bp):
AAAGAAGAAAAAAATAAAAAAATGAAACAATGAAAAAAAAAGA
Found at i:3100884 original size:17 final size:16
Alignment explanation
Indices: 3100825--3100890 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 16
3100815 GAAAAGATAT
*
3100825 AAAAAAATGAAACAT-
1 AAAAAAATGAAAAATG
*
3100840 AAAAAAGATAGAAAAGAAAG
1 AAAAAA-AT-G-AAA-AATG
3100860 AAAAAAATAGAAAAATG
1 AAAAAAAT-GAAAAATG
*
3100877 AAACAAATGAAAAA
1 AAAAAAATGAAAAA
3100891 AAAAGAAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
15 6 0.14
16 8 0.19
17 11 0.26
18 6 0.14
19 5 0.12
20 6 0.14
ACGTcount: A:0.76, C:0.03, G:0.12, T:0.09
Consensus pattern (16 bp):
AAAAAAATGAAAAATG
Found at i:3100918 original size:29 final size:29
Alignment explanation
Indices: 3100886--3100980 Score: 70
Period size: 31 Copynumber: 3.1 Consensus size: 29
3100876 GAAACAAATG
3100886 AAAAAAAAAGAAAAGAAAAAATGAGAGAA
1 AAAAAAAAAGAAAAGAAAAAATGAGAGAA
***
3100915 AAAAGGGGAA-AAAAGAAAAAAATTGAGAGAA
1 AAAA-AAAAAGAAAAG-AAAAAA-TGAGAGAA
*
3100946 AATGAGAAAAATGAAAAGAAATAAA-GA-AGAA
1 AA--A-AAAAAAGAAAAGAAA-AAATGAGAGAA
3100977 AAAA
1 AAAA
3100981 TCGATCAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 17
0.68 0.09 0.23
Matches are distributed among these distances:
28 1 0.02
29 10 0.20
30 8 0.16
31 16 0.31
32 2 0.04
33 5 0.10
34 9 0.18
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (29 bp):
AAAAAAAAAGAAAAGAAAAAATGAGAGAA
Found at i:3101625 original size:28 final size:28
Alignment explanation
Indices: 3101585--3101693 Score: 155
Period size: 28 Copynumber: 3.9 Consensus size: 28
3101575 GCAAGAATCC
*
3101585 AACCTGTAACACATTACCTCCCCAAATT
1 AACCTGAAACACATTACCTCCCCAAATT
*
3101613 AACCTGAAACACATTACCTCACCAAATT
1 AACCTGAAACACATTACCTCCCCAAATT
* *
3101641 AACCTGAAACACATTACCACCCCAAAAT
1 AACCTGAAACACATTACCTCCCCAAATT
* * *
3101669 AACATGAAGCACATTACCTTCCCAA
1 AACCTGAAACACATTACCTCCCCAA
3101694 GACAGCCTAA
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 72 1.00
ACGTcount: A:0.41, C:0.34, G:0.05, T:0.20
Consensus pattern (28 bp):
AACCTGAAACACATTACCTCCCCAAATT
Found at i:3103492 original size:278 final size:278
Alignment explanation
Indices: 3102966--3103794 Score: 1161
Period size: 278 Copynumber: 3.0 Consensus size: 278
3102956 AGCTAAACAA
* * * *
3102966 CATGAT-ATTTTCAAAAGAATTTTTAAAGAAACTAAGTCTGATTTTCAGGGGTTTCTTGATGATG
1 CATGATGA-TTTCAAATGAGTTTTT-AA-AAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATT
* * * ** *
3103030 ATTTTCAATGAGTTTTTAAAAAGGAAGCTAATTCAAATTTTTAGGGGTTCCTTGATGACAACTAA
63 ATATCCAAAGAGTTTTT-AAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGATGACAACTAA
* * *
3103095 GAAACTAAGCTTGATTTTTATGGGTTTCTTGATGCGTAAGTCCTTCGGGCCATCAGTAAGTCTTT
127 GAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTT
* * * * *
3103160 CGAGGATAATGCTTAAATCCTTTGGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGT-CTTCC
192 CGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTT-A
*
3103224 GGGCCATCAATAAGACCTTCTG-G
256 GGGCCATCCATAAGACCTTC-GAG
3103247 C-TGGATGATTTCAAATGAGTTTTTAAAAACTAAGCCTGATTTAT-AGGGGTTTTCTTGATGATT
1 CAT-GATGATTTCAAATGAGTTTTTAAAAACTAAGCCTGATTT-TCAGGGG-TTTCTTGATGATT
* * *
3103310 ATATCCAAAGAGTTTTTAAAAGGAAACTAAGCCTAATTTTTAGGGGTTCATTGATGAAAACTAAG
63 ATATCCAAAGAGTTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGATGACAACTAAG
* *
3103375 AAACT-AGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGTGTCATCAGTAAGTCTTTC
128 AAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTC
*
3103439 GACCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTAGG
193 GAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTAGG
3103504 GCCATCCATAAGACCTTCGAG
258 GCCATCCATAAGACCTTCGAG
* * *
3103525 CATGATGATTTCAAATAAGTTTTTAGAAACTAAGCCTTATTTTCA-GGGTTTCTTGATGATTATA
1 CATGATGATTTCAAATGAGTTTTTAAAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATA
* * * *
3103589 TCCAAAGAGTTTTTAAAAGGAAGTTAAGCCTAACTTTTAGGGGTTCCTTAATGACAACTAAGAAG
66 TCCAAAGAGTTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGATGACAACTAAGAAA
*
3103654 CTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAG
131 CTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAG
* * * * * *
3103719 CATGATG-TGTAAGTCTTTCGGGCCATCTATAAGTATTTCGAACAAGATGATAAGTCCTTTGGGC
196 CATGATGCT-TAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGC
3103783 CATCCATAAGAC
260 CATCCATAAGAC
3103795 ATCTGGGTAG
Statistics
Matches: 493, Mismatches: 45, Indels: 24
0.88 0.08 0.04
Matches are distributed among these distances:
276 77 0.16
277 131 0.27
278 165 0.33
279 71 0.14
280 30 0.06
281 18 0.04
282 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (278 bp):
CATGATGATTTCAAATGAGTTTTTAAAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATA
TCCAAAGAGTTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGATGACAACTAAGAAA
CTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAG
CATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCC
ATCCATAAGACCTTCGAG
Found at i:3103515 original size:41 final size:41
Alignment explanation
Indices: 3103402--3103533 Score: 140
Period size: 42 Copynumber: 3.2 Consensus size: 41
3103392 AAGGGTTTCT
* *
3103402 TGATGAGTAAGTCCTTCGTGTCAT-CAGTAAGTCTTTCGACCA
1 TGATGA-TAAGTCCTTCGGGTCATCCA-TAAGTCTTTCGAGCA
* * *
3103444 TGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCA
1 TGATG-ATAAGTCCTTCGGGTCATCCATAAGTCTTTCGAGCA
* * * * *
3103486 AGATGATAAGTCCTTAGGGCCATCCATAAGACCTTCGAGCA
1 TGATGATAAGTCCTTCGGGTCATCCATAAGTCTTTCGAGCA
3103527 TGATGAT
1 TGATGAT
3103534 TTCAAATAAG
Statistics
Matches: 74, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
41 35 0.47
42 38 0.51
43 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (41 bp):
TGATGATAAGTCCTTCGGGTCATCCATAAGTCTTTCGAGCA
Found at i:3103739 original size:42 final size:41
Alignment explanation
Indices: 3103679--3103792 Score: 117
Period size: 42 Copynumber: 2.7 Consensus size: 41
3103669 AAGGGTTTCT
* *
3103679 TGATGAGTAAGTCCTTCGGGCCATC-AGTAAGTCTTTC-AAGCA
1 TGATG-GTAAGTCTTTCGGGCCATCTA-TAAGTATTTCGAA-CA
3103721 TGATGTGTAAGTCTTTCGGGCCATCTATAAGTATTTCGAACA
1 TGATG-GTAAGTCTTTCGGGCCATCTATAAGTATTTCGAACA
* * *
3103763 AGATGATAAGTCCTTT-GGGCCATCCATAAG
1 TGATGGTAAGT-CTTTCGGGCCATCTATAAG
3103793 ACATCTGGGT
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
41 18 0.29
42 42 0.67
43 3 0.05
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (41 bp):
TGATGGTAAGTCTTTCGGGCCATCTATAAGTATTTCGAACA
Found at i:3105497 original size:31 final size:28
Alignment explanation
Indices: 3105430--3105502 Score: 69
Period size: 31 Copynumber: 2.5 Consensus size: 28
3105420 TCACTAGTAG
3105430 TTTGT-TTTTATTTATTTTGAATTCGCC
1 TTTGTATTTTATTTATTTTGAATTCGCC
**
3105457 TTTAAATTTTAATTTATTTT-AATTTAGCGCC
1 TTTGTATTTT-ATTTATTTTGAA-TT--CGCC
3105488 TTTGTATTTTTATTT
1 TTTGTA-TTTTATTT
3105503 TAACTTTAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
27 3 0.08
28 6 0.17
29 11 0.31
31 12 0.33
32 4 0.11
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.63
Consensus pattern (28 bp):
TTTGTATTTTATTTATTTTGAATTCGCC
Found at i:3112283 original size:9 final size:9
Alignment explanation
Indices: 3112269--3112294 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3112259 AATGATGAGA
3112269 AAATAAAGT
1 AAATAAAGT
3112278 AAATAAAGT
1 AAATAAAGT
3112287 AAATAAAG
1 AAATAAAG
3112295 AAGAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (9 bp):
AAATAAAGT
Found at i:3113649 original size:13 final size:14
Alignment explanation
Indices: 3113620--3113652 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3113610 ACATCACACC
*
3113620 ATCATAGTAACAAT
1 ATCATAGCAACAAT
3113634 ATCATAGCAA-AAT
1 ATCATAGCAACAAT
3113647 ATCATA
1 ATCATA
3113653 ATTAGTCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (14 bp):
ATCATAGCAACAAT
Found at i:3115968 original size:22 final size:23
Alignment explanation
Indices: 3115923--3115996 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 23
3115913 TTTATTTATT
* *
3115923 TATATTTATATGTTAGTATTATA
1 TATATTTATATGTTACTATAATA
3115946 T-TATTTATATG-TACTCATAATA
1 TATATTTATATGTTACT-ATAATA
* *
3115968 TATATATATATATATA-TATATATA
1 TATATTTATATGT-TACTATA-ATA
3115992 TATAT
1 TATAT
3115997 ATACTACTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
21 3 0.07
22 16 0.38
23 12 0.29
24 9 0.21
25 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (23 bp):
TATATTTATATGTTACTATAATA
Found at i:3115972 original size:2 final size:2
Alignment explanation
Indices: 3115965--3115999 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3115955 TGTACTCATA
3115965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3116000 CTACTATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3125822 original size:21 final size:21
Alignment explanation
Indices: 3125789--3125842 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
3125779 ACTTTGGTTC
* *
3125789 AAAA-TCAACATTTCA-ACTT
1 AAAAGTCAGCATTTCATAATT
*
3125808 AAAATTTCAGCATTTCATAATT
1 AAAA-GTCAGCATTTCATAATT
3125830 AAAAGTCAGCATT
1 AAAAGTCAGCATT
3125843 GAATACCCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 4 0.14
21 18 0.62
22 7 0.24
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (21 bp):
AAAAGTCAGCATTTCATAATT
Found at i:3142147 original size:19 final size:19
Alignment explanation
Indices: 3142123--3142195 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 19
3142113 ATCTAATGTT
3142123 GGTATCGATACCGATAAGG
1 GGTATCGATACCGATAAGG
*
3142142 GGTATCGATACCCTAGTAAGG
1 GGTATCGATA-CCGA-TAAGG
* *
3142163 TAGTATCGATACCATGGTAA-G
1 -GGTATCGATACC--GATAAGG
3142184 GGTATCGATACC
1 GGTATCGATACC
3142196 AGGCAACATC
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
19 10 0.23
20 14 0.32
21 8 0.18
22 12 0.27
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (19 bp):
GGTATCGATACCGATAAGG
Found at i:3142171 original size:22 final size:20
Alignment explanation
Indices: 3142123--3142196 Score: 80
Period size: 22 Copynumber: 3.6 Consensus size: 20
3142113 ATCTAATGTT
*
3142123 GGTATCGATACCGATA--AGG
1 GGTATCGATACC-ATAGTAAG
*
3142142 GGTATCGATACCCTAGTAAG
1 GGTATCGATACCATAGTAAG
*
3142162 GTAGTATCGATACCATGGTAAG
1 G--GTATCGATACCATAGTAAG
3142184 GGTATCGATACCA
1 GGTATCGATACCA
3142197 GGCAACATCG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
18 2 0.04
19 12 0.26
20 15 0.32
22 18 0.38
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (20 bp):
GGTATCGATACCATAGTAAG
Found at i:3142284 original size:95 final size:96
Alignment explanation
Indices: 3142088--3142289 Score: 225
Period size: 95 Copynumber: 2.1 Consensus size: 96
3142078 AAAGGAATGT
* *
3142088 TAGTATCAATACCAAGAAACATCGAATCTAATGTTGGTATCGATACCGATAAGGGGTATCGATAC
1 TAGTATCGATACCAAGAAACATCGAACCTAATGTTGGTATCGATACCGATAAGGGGTATCGATAC
* * *
3142153 CCTAGTAAGGTAGTATCGATACCATGGTAAG
66 CATAGTAAGGAAGTATCGATACCAGGGTAAG
* * * * * *
3142184 -GGTATCGATACCAGGCAACATCGAACCTATTTTTGGTATCGATACC-CTAAGGGGGTATC-AGT
1 TAGTATCGATACCAAGAAACATCGAACCTAATGTTGGTATCGATACCGATAA-GGGGTATCGA-T
* *
3142246 ACCATAGTATA-GAAGTATCGGTACTAGGGT-AG
64 ACCATAGTA-AGGAAGTATCGATACCAGGGTAAG
3142278 TAGTATCGATAC
1 TAGTATCGATAC
3142290 TATGGAACCA
Statistics
Matches: 88, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
94 6 0.07
95 81 0.92
96 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (96 bp):
TAGTATCGATACCAAGAAACATCGAACCTAATGTTGGTATCGATACCGATAAGGGGTATCGATAC
CATAGTAAGGAAGTATCGATACCAGGGTAAG
Found at i:3143056 original size:30 final size:30
Alignment explanation
Indices: 3143020--3143094 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
3143010 AAGATGCCCC
3143020 AAGTGTCCTTACACACTACAGAGTTGCACT
1 AAGTGTCCTTACACACTACAGAGTTGCACT
* * *
3143050 AAGTGTCCTTATACACTATAGTGTTGCACT
1 AAGTGTCCTTACACACTACAGAGTTGCACT
* *
3143080 AAATATCCTTACACA
1 AAGTGTCCTTACACA
3143095 TTAGTGCTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (30 bp):
AAGTGTCCTTACACACTACAGAGTTGCACT
Found at i:3143458 original size:2 final size:2
Alignment explanation
Indices: 3143451--3143483 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3143441 ATTGACACTT
*
3143451 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3143484 CAAAATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3148557 original size:39 final size:39
Alignment explanation
Indices: 3148503--3148608 Score: 144
Period size: 39 Copynumber: 2.7 Consensus size: 39
3148493 TGAAAATCTA
3148503 CGATTCCTTCTATAAAGGATTGATCATTGAGGAATCGAT
1 CGATTCCTTCTATAAAGGATTGATCATTGAGGAATCGAT
* * *
3148542 CGATTCCTTCTATAAAGGATCGTTCATTGAGGAATGGAT
1 CGATTCCTTCTATAAAGGATTGATCATTGAGGAATCGAT
*
3148581 TGA-TCCTTTCTATAAAGGATAT-ATCATT
1 CGATTCC-TTCTATAAAGGAT-TGATCATT
3148609 TTCTTACTGA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
38 3 0.05
39 56 0.95
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (39 bp):
CGATTCCTTCTATAAAGGATTGATCATTGAGGAATCGAT
Found at i:3152436 original size:30 final size:30
Alignment explanation
Indices: 3152396--3152470 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
3152386 AAGATGCCCC
3152396 AAGTGTCCTTACACACTATAGAGTTGCACT
1 AAGTGTCCTTACACACTATAGAGTTGCACT
* * *
3152426 AAGTGCCCTTATACACTATAGTGTTGCACT
1 AAGTGTCCTTACACACTATAGAGTTGCACT
*
3152456 AAATGTCCTTACACA
1 AAGTGTCCTTACACA
3152471 TTAGTGCTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (30 bp):
AAGTGTCCTTACACACTATAGAGTTGCACT
Found at i:3152834 original size:2 final size:2
Alignment explanation
Indices: 3152827--3152861 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3152817 ATTGACACTT
*
3152827 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3152862 TAGCCTCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.