Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 11 of 235
Found at i:2954135 original size:18 final size:18
Alignment explanation
Indices: 2954092--2954147 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
2954082 GTTAGCAGTA
*
2954092 AAGGTGGTGAGGGTGGTG
1 AAGGTGGTAAGGGTGGTG
2954110 -AGGT--TAAGGGTGGTG
1 AAGGTGGTAAGGGTGGTG
*
2954125 AAGGTGGTAAGGGTGTTG
1 AAGGTGGTAAGGGTGGTG
2954143 AAGGT
1 AAGGT
2954148 TTAAATAGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 10 0.30
16 4 0.12
17 4 0.12
18 15 0.45
ACGTcount: A:0.21, C:0.00, G:0.54, T:0.25
Consensus pattern (18 bp):
AAGGTGGTAAGGGTGGTG
Found at i:2954161 original size:57 final size:57
Alignment explanation
Indices: 2954100--2954261 Score: 135
Period size: 57 Copynumber: 2.8 Consensus size: 57
2954090 TAAAGGTGGT
* ** *
2954100 GAGGGTGGTGAGGTTAAGGGTGGTGAAGGTGGTAAGGGTGTTGAAGGTTTAAATAGA
1 GAGGGTGCTGAGGTTAAGGGCAGTAAAGGTGGTAAGGGTGTTGAAGGTTTAAATAGA
* *** * ** * *
2954157 GAGGGTGCTGATGTTGCTGGCAGTAAAGGTGGTGAGGGTGTTGAAGGTTTAGGTGGG
1 GAGGGTGCTGAGGTTAAGGGCAGTAAAGGTGGTAAGGGTGTTGAAGGTTTAAATAGA
* ** ** * * *
2954214 GAGGGTGTTGATATTACTGGCAATGAAGGTGGTAAGGGTGGTGAAGGT
1 GAGGGTGCTGAGGTTAAGGGCAGTAAAGGTGGTAAGGGTGTTGAAGGT
2954262 GGTGAGGGTG
Statistics
Matches: 85, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
57 85 1.00
ACGTcount: A:0.23, C:0.03, G:0.47, T:0.27
Consensus pattern (57 bp):
GAGGGTGCTGAGGTTAAGGGCAGTAAAGGTGGTAAGGGTGTTGAAGGTTTAAATAGA
Found at i:2954260 original size:18 final size:18
Alignment explanation
Indices: 2954237--2954279 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2954227 TTACTGGCAA
2954237 TGAAGGTGGTAAGGGTGG
1 TGAAGGTGGTAAGGGTGG
* *
2954255 TGAAGGTGGTGAGGGTGT
1 TGAAGGTGGTAAGGGTGG
2954273 TGAAGGT
1 TGAAGGT
2954280 TTAGATTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.53, T:0.26
Consensus pattern (18 bp):
TGAAGGTGGTAAGGGTGG
Found at i:2968980 original size:34 final size:34
Alignment explanation
Indices: 2968937--2969001 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
2968927 TAATATTTTA
2968937 ATTAATAATTTATGTTATAAAAAATCACGAGCTG
1 ATTAATAATTTATGTTATAAAAAATCACGAGCTG
2968971 ATTAATAATTTATGTTATAAAAAATCACGAG
1 ATTAATAATTTATGTTATAAAAAATCACGAG
2969002 TTTATGTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (34 bp):
ATTAATAATTTATGTTATAAAAAATCACGAGCTG
Found at i:2971417 original size:12 final size:13
Alignment explanation
Indices: 2971400--2971446 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 13
2971390 AATGAATACA
2971400 AAATATAT-TATT
1 AAATATATATATT
*
2971412 AAATAT-TAAATT
1 AAATATATATATT
2971424 AAA-ATA-ATA-T
1 AAATATATATATT
2971434 AAATATATATATT
1 AAATATATATATT
2971447 TAAAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
10 4 0.14
11 8 0.29
12 15 0.54
13 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATATATATATT
Found at i:2971449 original size:24 final size:24
Alignment explanation
Indices: 2971422--2971467 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2971412 AAATATTAAA
* *
2971422 TTAAAATAATATAAATATATATAT
1 TTAAAAAAATATAAAAATATATAT
*
2971446 TTAAAAAAATTTAAAAATATAT
1 TTAAAAAAATATAAAAATATAT
2971468 GAGTGGGTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TTAAAAAAATATAAAAATATATAT
Found at i:2976998 original size:45 final size:45
Alignment explanation
Indices: 2976934--2977021 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
2976924 GGTGGAACAA
2976934 TCCTAGTACTACAAAAAGGTAACAAGGTGGCAGAGTTCTCATGAG
1 TCCTAGTACTACAAAAAGGTAACAAGGTGGCAGAGTTCTCATGAG
*
2976979 TCCTAGTACTACGAAAAGGTAACAAGGTGGCAGAGTTCTCATG
1 TCCTAGTACTACAAAAAGGTAACAAGGTGGCAGAGTTCTCATG
2977022 TGTAGCAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (45 bp):
TCCTAGTACTACAAAAAGGTAACAAGGTGGCAGAGTTCTCATGAG
Found at i:2977238 original size:12 final size:12
Alignment explanation
Indices: 2977221--2977245 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2977211 AATCATTCTT
2977221 AAAAAATTTTAA
1 AAAAAATTTTAA
2977233 AAAAAATTTTAA
1 AAAAAATTTTAA
2977245 A
1 A
2977246 TTCTAAAATT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAAAATTTTAA
Found at i:2977570 original size:18 final size:18
Alignment explanation
Indices: 2977544--2977579 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2977534 TCAAACGGTT
*
2977544 AAATTTTTTTAATGTTTA
1 AAATATTTTTAATGTTTA
*
2977562 AAATATTTTTAATTTTTA
1 AAATATTTTTAATGTTTA
2977580 TATTTTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
AAATATTTTTAATGTTTA
Found at i:2977730 original size:33 final size:35
Alignment explanation
Indices: 2977675--2977739 Score: 82
Period size: 33 Copynumber: 1.9 Consensus size: 35
2977665 TTTTAAAATT
*
2977675 CTTTTAAATTAATATATATTCTT-T-TTTTTTGAA
1 CTTTTAAATTAATAGATATTCTTATATTTTTTGAA
*
2977708 CTTTTATAATTTATAGAT-TTCTTATATTTTTT
1 CTTTTA-AATTAATAGATATTCTTATATTTTTT
2977740 AACAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 11 0.41
34 10 0.37
35 6 0.22
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (35 bp):
CTTTTAAATTAATAGATATTCTTATATTTTTTGAA
Found at i:2986680 original size:47 final size:47
Alignment explanation
Indices: 2986602--2987014 Score: 727
Period size: 47 Copynumber: 8.7 Consensus size: 47
2986592 CCCTTCGGGA
* * * * * *
2986602 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
2986649 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2986696 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2986743 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2986790 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2986837 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
2986884 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2986931 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2986980 CTTATCACATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
2987015 AGAATCCTAA
Statistics
Matches: 352, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
47 306 0.87
49 46 0.13
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:2988223 original size:13 final size:13
Alignment explanation
Indices: 2988205--2988229 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2988195 TACTAAATTT
2988205 TCATGGATTCAAA
1 TCATGGATTCAAA
2988218 TCATGGATTCAA
1 TCATGGATTCAA
2988230 TATACCATTA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAA
Found at i:2992636 original size:10 final size:9
Alignment explanation
Indices: 2992610--2992661 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 9
2992600 TAGTTGCTTA
2992610 TTTATTATTT
1 TTTATT-TTT
2992620 CTTTATTTTT
1 -TTTATTTTT
2992630 GTTTATTTTT
1 -TTTATTTTT
2992640 TTTATTTTT
1 TTTATTTTT
2992649 ATTT-TGTTTT
1 -TTTAT-TTTT
2992659 TTT
1 TTT
2992662 TCGGGCATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
9 13 0.34
10 19 0.50
11 6 0.16
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.83
Consensus pattern (9 bp):
TTTATTTTT
Found at i:2992645 original size:19 final size:19
Alignment explanation
Indices: 2992607--2992661 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
2992597 ATTTAGTTGC
2992607 TTATTTATTATTTCTTTATTT
1 TTATTTATT-TTT-TTTATTT
*
2992628 TTGTTTATTTTTTTTATTT
1 TTATTTATTTTTTTTATTT
2992647 TTATTT-TGTTTTTTT
1 TTATTTAT-TTTTTTT
2992662 TCGGGCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 1 0.03
19 19 0.61
20 3 0.10
21 8 0.26
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.82
Consensus pattern (19 bp):
TTATTTATTTTTTTTATTT
Found at i:2992651 original size:15 final size:15
Alignment explanation
Indices: 2992607--2992662 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
2992597 ATTTAGTTGC
2992607 TTATTTATTATTTCTTT
1 TTATTT-TTATTT-TTT
*
2992624 ATTTTTGTTTATTTTTT
1 -TTATT-TTTATTTTTT
2992641 TTATTTTTATTTTGTT
1 TTATTTTTATTTT-TT
2992657 TT-TTTT
1 TTATTTT
2992663 CGGGCATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
15 12 0.35
16 8 0.24
17 3 0.09
18 10 0.29
19 1 0.03
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.82
Consensus pattern (15 bp):
TTATTTTTATTTTTT
Found at i:2992694 original size:3 final size:3
Alignment explanation
Indices: 2992686--2992732 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2992676 ATTTATTTCA
2992686 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2992733 AACCATTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2992832 original size:12 final size:12
Alignment explanation
Indices: 2992807--2992867 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
2992797 CTTTTACTTG
2992807 TATTT-ATTTAT
1 TATTTCATTTAT
*
2992818 TATTTCATTTGT
1 TATTTCATTTAT
*
2992830 TATTTCATTCAT
1 TATTTCATTTAT
* *
2992842 TATTCCTTTTTAT
1 TATTTC-ATTTAT
*
2992855 TATTTTATTTAT
1 TATTTCATTTAT
2992867 T
1 T
2992868 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
11 5 0.13
12 26 0.67
13 8 0.21
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.69
Consensus pattern (12 bp):
TATTTCATTTAT
Found at i:2992878 original size:11 final size:10
Alignment explanation
Indices: 2992807--2992881 Score: 55
Period size: 12 Copynumber: 7.1 Consensus size: 10
2992797 CTTTTACTTG
2992807 TATTTATTTAT
1 TATTTATTT-T
2992818 TATTTCATTTGT
1 TATTT-ATTT-T
*
2992830 TATTTCATTCAT
1 TATTT-ATT-TT
**
2992842 TATTCCTTTT
1 TATTTATTTT
2992852 TA-TTA-TTT
1 TATTTATTTT
2992860 TATTTATTTT
1 TATTTATTTT
2992870 TATTTTATTTT
1 TA-TTTATTTT
2992881 T
1 T
2992882 GTCCTCATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
8 5 0.10
9 4 0.08
10 8 0.15
11 16 0.31
12 19 0.37
ACGTcount: A:0.20, C:0.07, G:0.01, T:0.72
Consensus pattern (10 bp):
TATTTATTTT
Found at i:2994679 original size:33 final size:33
Alignment explanation
Indices: 2994525--2994669 Score: 141
Period size: 33 Copynumber: 4.4 Consensus size: 33
2994515 AAAATGGGTA
* ** * *
2994525 ACAACTTGAAAAGGATATATGTAC-TTAAATGGT
1 ACAACTTGAAAAGGATATGTACACTTTGAGT-GT
* * * *
2994558 AC-ACTTGACAAGGTTATGTACACTTTGTGTAT
1 ACAACTTGAAAAGGATATGTACACTTTGAGTGT
* * * *
2994590 ACAATTTGAAAAGGCTAAGTACACTTTGTGTGT
1 ACAACTTGAAAAGGATATGTACACTTTGAGTGT
2994623 ACAACTTGAAAAGGATATGTACACTTTGAGTGT
1 ACAACTTGAAAAGGATATGTACACTTTGAGTGT
*
2994656 ACCACTTGAAAAGG
1 ACAACTTGAAAAGG
2994670 GAATTTACAC
Statistics
Matches: 91, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
32 19 0.21
33 72 0.79
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (33 bp):
ACAACTTGAAAAGGATATGTACACTTTGAGTGT
Found at i:2994687 original size:33 final size:33
Alignment explanation
Indices: 2994556--2994690 Score: 103
Period size: 33 Copynumber: 4.1 Consensus size: 33
2994546 TACTTAAATG
* * * * *
2994556 GTAC-ACTTGACAAGGTTATGTACACTTTGTGT
1 GTACAACTTGAAAAGGATATGTACACCTCGAGT
* * * * * * *
2994588 ATACAATTTGAAAAGGCTAAGTACACTTTGTGT
1 GTACAACTTGAAAAGGATATGTACACCTCGAGT
* *
2994621 GTACAACTTGAAAAGGATATGTACACTTTGAGT
1 GTACAACTTGAAAAGGATATGTACACCTCGAGT
* *
2994654 GTACCACTTGAAAAGGGA-ATTTACACCTCGAGT
1 GTACAACTTGAAAA-GGATATGTACACCTCGAGT
2994687 GTAC
1 GTAC
2994691 GATTGGAAAA
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
32 3 0.03
33 81 0.93
34 3 0.03
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (33 bp):
GTACAACTTGAAAAGGATATGTACACCTCGAGT
Found at i:2994689 original size:66 final size:65
Alignment explanation
Indices: 2994556--2994690 Score: 146
Period size: 66 Copynumber: 2.1 Consensus size: 65
2994546 TACTTAAATG
* * * * * * * *
2994556 GTACACTTGACAAGGTTATGTACACTTTGTGTATACAATTTGAAAAGGCTAAGTACACTTTGTGT
1 GTACACTTGAAAAGGATATGTACACTTTGAGTATACAACTTGAAAAGGCGAAGTACACCTCGAGT
* * *
2994621 GTACAACTTGAAAAGGATATGTACACTTTGAGTGTACCACTTGAAAAGG-GAATTTACACCTCGA
1 GTAC-ACTTGAAAAGGATATGTACACTTTGAGTATACAACTTGAAAAGGCGAA-GTACACCTCGA
2994685 GT
64 GT
2994687 GTAC
1 GTAC
2994691 GATTGGAAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
65 6 0.11
66 51 0.89
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (65 bp):
GTACACTTGAAAAGGATATGTACACTTTGAGTATACAACTTGAAAAGGCGAAGTACACCTCGAGT
Found at i:3002163 original size:33 final size:33
Alignment explanation
Indices: 3002102--3002215 Score: 140
Period size: 33 Copynumber: 3.5 Consensus size: 33
3002092 TACTTAAATG
* * *
3002102 GTAC-ACTTGACAAGGTTATGTACACTTTGTGT
1 GTACAACTTGAAAAGGATAAGTACACTTTGTGT
* * *
3002134 ATACAATTTGAAAAGGCTAAGTACACTTTGTGT
1 GTACAACTTGAAAAGGATAAGTACACTTTGTGT
* *
3002167 GTACAACTTGAAAAGGATATGTACACTTTGAGT
1 GTACAACTTGAAAAGGATAAGTACACTTTGTGT
*
3002200 GTACCACTTGAAAAGG
1 GTACAACTTGAAAAGG
3002216 GAATTTACAC
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
32 3 0.04
33 67 0.96
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (33 bp):
GTACAACTTGAAAAGGATAAGTACACTTTGTGT
Found at i:3002225 original size:33 final size:34
Alignment explanation
Indices: 3002102--3002248 Score: 124
Period size: 33 Copynumber: 4.5 Consensus size: 34
3002092 TACTTAAATG
* * *
3002102 GTAC-ACTTGACAA-GGTTATGTACACTTTGTGT
1 GTACAACTTGAAAAGGGATATGTACACTTTGAGT
* * * * *
3002134 ATACAATTTGAAAA-GGCTAAGTACACTTTGTGT
1 GTACAACTTGAAAAGGGATATGTACACTTTGAGT
3002167 GTACAACTTGAAAA-GGATATGTACACTTTGAGT
1 GTACAACTTGAAAAGGGATATGTACACTTTGAGT
* * * *
3002200 GTACCACTTGAAAAGGGA-ATTTACACCTCGAGT
1 GTACAACTTGAAAAGGGATATGTACACTTTGAGT
* * *
3002233 ATACGACTGGAAAAGG
1 GTACAACTTGAAAAGG
3002249 TTACATCCAT
Statistics
Matches: 96, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
32 3 0.03
33 90 0.94
34 3 0.03
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (34 bp):
GTACAACTTGAAAAGGGATATGTACACTTTGAGT
Found at i:3004739 original size:16 final size:16
Alignment explanation
Indices: 3004718--3004750 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3004708 GCCAAAACCA
3004718 AAGAAATGGACCAAAG
1 AAGAAATGGACCAAAG
3004734 AAGAAATGGACCAAAG
1 AAGAAATGGACCAAAG
3004750 A
1 A
3004751 TTGGAACAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.12, G:0.24, T:0.06
Consensus pattern (16 bp):
AAGAAATGGACCAAAG
Found at i:3006655 original size:19 final size:19
Alignment explanation
Indices: 3006631--3006670 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3006621 GACGCCTCCT
*
3006631 TTGCATT-CATGCATTTGCA
1 TTGCATTACAT-CATATGCA
3006650 TTGCATTACATCATATGCA
1 TTGCATTACATCATATGCA
3006669 TT
1 TT
3006671 AAAGGCTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.42
Consensus pattern (19 bp):
TTGCATTACATCATATGCA
Found at i:3008128 original size:35 final size:35
Alignment explanation
Indices: 3008084--3008250 Score: 174
Period size: 35 Copynumber: 4.6 Consensus size: 35
3008074 TCCTCATTGA
** *
3008084 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* * ** *
3008119 AATGCCATACTTACATTTCTTAACTCAGAATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAG--T--A-TGGAT
*
3008159 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
3008194 AATACCATACCTATATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
3008229 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
3008251 CTTTGCCATG
Statistics
Matches: 110, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
35 80 0.73
36 1 0.01
37 1 0.01
38 1 0.01
39 3 0.03
40 24 0.22
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:3008190 original size:75 final size:73
Alignment explanation
Indices: 3008079--3008250 Score: 199
Period size: 75 Copynumber: 2.4 Consensus size: 73
3008069 GGTTTTCCTC
** * * * **
3008079 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACTTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
3008143 TCAGAATGG
65 TCAGAATGG
* *
3008152 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTATATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
*
3008217 CTCAGTATGG
64 CTCAGAATGG
3008227 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
3008251 CTTTGCCATG
Statistics
Matches: 86, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 55 0.64
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGAATGG
Found at i:3016338 original size:53 final size:51
Alignment explanation
Indices: 3016213--3016362 Score: 210
Period size: 53 Copynumber: 2.9 Consensus size: 51
3016203 AAGGAAGGAA
* * **
3016213 GCCAATGTGAAAACCCGCAAAGGGCGTTTTGAGACTTTCTAAAAAAAAAGG
1 GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGACTTAATAAAAAAAAAGG
* *
3016264 GCCAAAGTGAAAACTCGCAAAGGGCGCTTTGAGACTAAATAAAAATGAAAAGG
1 GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGACTTAATAAAAA--AAAAGG
* *
3016317 GCCAAAGTGAAAACCCACAAAGGGCACTTTGAGACTTAATAAAAAA
1 GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGACTTAATAAAAAA
3016363 GAGAGAGAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 40 0.46
53 47 0.54
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (51 bp):
GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGACTTAATAAAAAAAAAGG
Found at i:3018067 original size:176 final size:176
Alignment explanation
Indices: 3017525--3018362 Score: 1057
Period size: 176 Copynumber: 4.7 Consensus size: 176
3017515 GCGACATTGG
* * * ** * * ***
3017525 TGAAAATTGGAGATCTTATCTCCCTGAAGTTGTAGTAGAGCAGATCAAAAATATTTAATCTTATC
1 TGAAGATTGAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCGAAGATAGCGAATCTTATC
*
3017590 TCCATGTATCGGCAATGGAGTAGATTTTACCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCA
66 TCCATGTATCGGCAATGGAGCAGATTTTACCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCA
**
3017655 GGTTGAAGAGCGAGTCTTATCTTTCTGAGGTAACAAGAAAGCAGAC
131 GGTTGAAGAATGAGTCTTATCTTTCTGAGGTAACAAGAAAGCAGAC
* * *
3017701 TGAAGATTAAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCGCAA-ATGGCTAATCT
1 TGAAGATTGAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGA---TCG-AAGATAGCGAATCT
* * * * * *
3017765 TATCTCCATGTATCGGTAATGGGGCAGATTTAAGCCACCATCCTTATCTCTCTGAGGTAACAAGC
62 TATCTCCATGTATCGGCAATGGAGCAGATTTTA-CCACCAGCCTTATCTCTCTGAGGTAGCAAGA
* * **
3017830 GAGCAGGTTGTAGAATGAGTCTTATCTTTCTGAGGTAGCAAGAAAGTGGAC
126 GAGCAGGTTGAAGAATGAGTCTTATCTTTCTGAGGTAACAAGAAAGCAGAC
* * * * * *
3017881 TGAGGATTGAAGATTTTATCTCCCTGAAGTTGCAGCAGAGTAGATCGAAGATGGCGAATCTTCTC
1 TGAAGATTGAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCGAAGATAGCGAATCTTATC
* * *
3017946 TCTATGTATCAGCAATGGAGCAGATTTTACCACCAGCCTTATCTCTCTGAGATAGCAAGAGAGCA
66 TCCATGTATCGGCAATGGAGCAGATTTTACCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCA
* * * * *
3018011 GGTTAAAGAATGAGTCTTATCTTTCTGAGGAAATAAGGAAGCAAAC
131 GGTTGAAGAATGAGTCTTATCTTTCTGAGGTAACAAGAAAGCAGAC
* * *
3018057 TGAAGATTGAAGATCTTATCTTCCTGAAGTTGCAGTGGAGGAGATCGAAGATAGCGAATCTTATC
1 TGAAGATTGAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCGAAGATAGCGAATCTTATC
** * * * *
3018122 TCCATACACTCGACAATGGAGTAGATTTAAGCCACCGGCCTTATCTCTCTGAGGTAGCAAGAGAG
66 TCCATGTA-TCGGCAATGGAGCAGATTTTA-CCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAG
* * *
3018187 CAGGTTGAAGAATGAATCTTATCTTTCTAAGGTAGCAAGAAAGCAGAC
129 CAGGTTGAAGAATGAGTCTTATCTTTCTGAGGTAACAAGAAAGCAGAC
* * **
3018235 TGAAGATTGAAAATCTTATCGCCCTGAAGTTGCAGCGGAGCAGATCGAAGATAATGAATCTTATC
1 TGAAGATTGAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCGAAGATAGCGAATCTTATC
* * * * *
3018300 TCCATGTATTGGCAATGAAGCAGATTTTACCACCAGCCTTATCTTTTTGAGATAGCAAGAGAG
66 TCCATGTATCGGCAATGGAGCAGATTTTACCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAG
3018363 TAGTTGCAGC
Statistics
Matches: 563, Mismatches: 91, Indels: 16
0.84 0.14 0.02
Matches are distributed among these distances:
176 201 0.36
177 73 0.13
178 136 0.24
179 39 0.07
180 114 0.20
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (176 bp):
TGAAGATTGAAGATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATCGAAGATAGCGAATCTTATC
TCCATGTATCGGCAATGGAGCAGATTTTACCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCA
GGTTGAAGAATGAGTCTTATCTTTCTGAGGTAACAAGAAAGCAGAC
Found at i:3018239 original size:43 final size:44
Alignment explanation
Indices: 3018161--3018254 Score: 118
Period size: 43 Copynumber: 2.1 Consensus size: 44
3018151 AGCCACCGGC
* * **
3018161 CTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGAATG-AAT
1 CTTATCTCTCTAAGGTAGCAAGAAAGCAGACTGAAGAATGAAAT
* *
3018204 CTTATCTTTCTAAGGTAGCAAGAAAGCAGACTGAAGATTGAAAAT
1 CTTATCTCTCTAAGGTAGCAAGAAAGCAGACTGAAGAATG-AAAT
3018249 CTTATC
1 CTTATC
3018255 GCCCTGAAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 34 0.79
45 9 0.21
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (44 bp):
CTTATCTCTCTAAGGTAGCAAGAAAGCAGACTGAAGAATGAAAT
Found at i:3018324 original size:354 final size:354
Alignment explanation
Indices: 3017537--3018362 Score: 1134
Period size: 354 Copynumber: 2.3 Consensus size: 354
3017527 AAAATTGGAG
* * * * * *
3017537 ATCTTATCTCCCTGAAGTTGTAGTAGAGCAGATCAAAAATATTTAATCTTATCTCCATGTATCGG
1 ATCTTATCTCCCTGAAGTTGCAGCAGAGCAGATCGAAGATAATGAATCTTATCTCCATGTATCGG
* * * *
3017602 CAATGGAGTAGATTTTACCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGAGCG
66 CAATGGAGCAGATTTTACCACCAGCCTTATCTCTCTGAGATAGCAAGAGAGCAGGTTAAAGAACG
* *
3017667 AGTCTTATCTTTCTGAGGTAACAAGAAAGCAGACTGAAGATTAAAGATCTTATCTCCCTGAAGTT
131 AGTCTTATCTTTCTGAGGAAACAAGAAAGCAAACTGAAGATTAAAGATCTTATCTCCCTGAAGTT
* * ** ** *
3017732 GCAGCGGAGCAGATCTTCGCAAATGGCTAATCTTATCTCCATGTATCGGTAATGGGGCAGATTTA
196 GCAGCGGAGCAGA--TTCGCAAATAGCGAATCTTATCTCCATACATCGACAATGGAGCAGATTTA
* * * * *
3017797 AGCCACCATCCTTATCTCTCTGAGGTAACAAGCGAGCAGGTTGTAGAATGAGTCTTATCTTTCTG
259 AGCCACCAGCCTTATCTCTCTGAGGTAACAAGAGAGCAGGTTGAAGAATGAATCTTATCTTTCTA
** * *
3017862 AGGTAGCAAGAAAGTGGACTGAGGATTGAAG
324 AGGTAGCAAGAAAGCAGACTGAAGATTGAAA
* * *** * * *
3017893 ATTTTATCTCCCTGAAGTTGCAGCAGAGTAGATCGAAGATGGCGAATCTTCTCTCTATGTATCAG
1 ATCTTATCTCCCTGAAGTTGCAGCAGAGCAGATCGAAGATAATGAATCTTATCTCCATGTATCGG
*
3017958 CAATGGAGCAGATTTTACCACCAGCCTTATCTCTCTGAGATAGCAAGAGAGCAGGTTAAAGAATG
66 CAATGGAGCAGATTTTACCACCAGCCTTATCTCTCTGAGATAGCAAGAGAGCAGGTTAAAGAACG
* * * *
3018023 AGTCTTATCTTTCTGAGGAAATAAGGAAGCAAACTGAAGATTGAAGATCTTATCTTCCTGAAGTT
131 AGTCTTATCTTTCTGAGGAAACAAGAAAGCAAACTGAAGATTAAAGATCTTATCTCCCTGAAGTT
* * *
3018088 GCAGTGGAGGAGA-TCG-AAGATAGCGAATCTTATCTCCATACACTCGACAATGGAGTAGATTTA
196 GCAGCGGAGCAGATTCGCAA-ATAGCGAATCTTATCTCCATACA-TCGACAATGGAGCAGATTTA
* *
3018151 AGCCACCGGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGAATGAATCTTATCTTTCTA
259 AGCCACCAGCCTTATCTCTCTGAGGTAACAAGAGAGCAGGTTGAAGAATGAATCTTATCTTTCTA
3018216 AGGTAGCAAGAAAGCAGACTGAAGATTGAAA
324 AGGTAGCAAGAAAGCAGACTGAAGATTGAAA
* * *
3018247 ATCTTATCGCCCTGAAGTTGCAGCGGAGCAGATCGAAGATAATGAATCTTATCTCCATGTATTGG
1 ATCTTATCTCCCTGAAGTTGCAGCAGAGCAGATCGAAGATAATGAATCTTATCTCCATGTATCGG
* * *
3018312 CAATGAAGCAGATTTTACCACCAGCCTTATCTTTTTGAGATAGCAAGAGAG
66 CAATGGAGCAGATTTTACCACCAGCCTTATCTCTCTGAGATAGCAAGAGAG
3018363 TAGTTGCAGC
Statistics
Matches: 409, Mismatches: 59, Indels: 6
0.86 0.12 0.01
Matches are distributed among these distances:
352 2 0.00
353 22 0.05
354 203 0.50
356 182 0.44
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (354 bp):
ATCTTATCTCCCTGAAGTTGCAGCAGAGCAGATCGAAGATAATGAATCTTATCTCCATGTATCGG
CAATGGAGCAGATTTTACCACCAGCCTTATCTCTCTGAGATAGCAAGAGAGCAGGTTAAAGAACG
AGTCTTATCTTTCTGAGGAAACAAGAAAGCAAACTGAAGATTAAAGATCTTATCTCCCTGAAGTT
GCAGCGGAGCAGATTCGCAAATAGCGAATCTTATCTCCATACATCGACAATGGAGCAGATTTAAG
CCACCAGCCTTATCTCTCTGAGGTAACAAGAGAGCAGGTTGAAGAATGAATCTTATCTTTCTAAG
GTAGCAAGAAAGCAGACTGAAGATTGAAA
Found at i:3023616 original size:20 final size:20
Alignment explanation
Indices: 3023593--3023630 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3023583 CTAAAAAAAT
3023593 AAAAAA-AAAACAAAAAGAAG
1 AAAAAAGAAAA-AAAAAGAAG
3023613 AAAAAAGAAAAAAAAAGA
1 AAAAAAGAAAAAAAAAGA
3023631 GGTCAAGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.87, C:0.03, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAAAAAAAGAAG
Found at i:3023629 original size:10 final size:10
Alignment explanation
Indices: 3023593--3023630 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
3023583 CTAAAAAAAT
3023593 AAAAAAA-AA
1 AAAAAAAGAA
*
3023602 ACAAAAAGAA
1 AAAAAAAGAA
*
3023612 GAAAAAAGAA
1 AAAAAAAGAA
3023622 AAAAAAAGA
1 AAAAAAAGA
3023631 GGTCAAGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 6 0.25
10 18 0.75
ACGTcount: A:0.87, C:0.03, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:3024611 original size:44 final size:45
Alignment explanation
Indices: 3024518--3024826 Score: 180
Period size: 45 Copynumber: 6.8 Consensus size: 45
3024508 TCATGGCAAC
* * * * ** *
3024518 TCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGAAGCCA-CTAA
1 TCTTATTTCCCTGAAGTTGCAGTGGAGTAGATTAAAGATAGCGAA
* * * * * *
3024562 CCTTATTTCCTTGAAGTTACAGTGGAGTAGGTTAAAGTTA-CGAG
1 TCTTATTTCCCTGAAGTTGCAGTGGAGTAGATTAAAGATAGCGAA
* * * **
3024606 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGTAGATAGCGAA
1 TCTTATTTCCCTGAAGTTGCAGTGGAGTAGATTAAAGATAGCGAA
* * *
3024651 TCTTATTTCCCTGAAGTTGTAGTGGAATAGATTAAAGCTACAAATTA-CAAA
1 TCTTATTTCCCTGAAGTTGCAGTGGAGTAGATTAAAG------A-TAGCGAA
* * ***
3024702 TCTTATCTCCCTGAAGTTGCAGTGAAGTAGATTGAATTTTA---AA
1 TCTTATTTCCCTGAAGTTGCAGTGGAGTAGATT-AAAGATAGCGAA
* * * * * *
3024745 TCTTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAAAATAGTGAA
1 TCTTATTTCCCTGAAGTTGCAGTGGAGTAGATTAAAGATAGCGAA
* * * *
3024790 TCTTAGTTCCCTGAAGTTGCAGTAGAATATATTAAAG
1 TCTTATTTCCCTGAAGTTGCAGTGGAGTAGATTAAAG
3024827 CTACAAGTTA
Statistics
Matches: 201, Mismatches: 52, Indels: 23
0.73 0.19 0.08
Matches are distributed among these distances:
42 4 0.02
43 31 0.15
44 62 0.31
45 67 0.33
51 33 0.16
52 4 0.02
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (45 bp):
TCTTATTTCCCTGAAGTTGCAGTGGAGTAGATTAAAGATAGCGAA
Found at i:3024770 original size:139 final size:139
Alignment explanation
Indices: 3024606--3024859 Score: 384
Period size: 139 Copynumber: 1.8 Consensus size: 139
3024596 AAGTTACGAG
** * * *
3024606 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGTAGATAGCGAATCTTATTTCCCTGAAGTTGT
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAAATAGCGAATCTTAGTTCCCTGAAGTTGC
* *
3024671 AGTGGAATAGATTAAAGCTACAAATTACAAATCTTAT-CTCCCTGAAGTTGCAGTGAAGTAGATT
66 AGTAGAATAGATTAAAGCTACAAATTACAAATCCTATAC-CCCTGAAGTTGCAGTGAAGTAGATT
3024735 GAATTTTAAA
130 GAATTTTAAA
* *
3024745 TCTTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAAAATAGTGAATCTTAGTTCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAAATAGCGAATCTTAGTTCCCTGAAGTTGC
* * *
3024810 AGTAGAATATATTAAAGCTACAAGTTACAAATCCTATACCTCTGAAGTTG
66 AGTAGAATAGATTAAAGCTACAAATTACAAATCCTATACCCCTGAAGTTG
3024860 TAGTAGGTCG
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
139 101 0.99
140 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (139 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAAATAGCGAATCTTAGTTCCCTGAAGTTGC
AGTAGAATAGATTAAAGCTACAAATTACAAATCCTATACCCCTGAAGTTGCAGTGAAGTAGATTG
AATTTTAAA
Found at i:3024777 original size:94 final size:96
Alignment explanation
Indices: 3024606--3024780 Score: 239
Period size: 94 Copynumber: 1.8 Consensus size: 96
3024596 AAGTTACGAG
* *
3024606 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGTAGATAGCGAATCTTATTTCCCTGAAGTTGT
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGTAGATAGCAAATCTTATCTCCCTGAAGTTGT
* *
3024671 AGTGGAATAGATTAAAGCTACAAATTACAAA
66 AGTAGAACAGATTAAAGCTACAAATTACAAA
* ***
3024702 TCTTATCTCCCTGAAGTTGCAGT-GAAGTAGATTG-A-ATTTTAAATCTTATCTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTAG-AGCAGATTGTAGATAGCAAATCTTATCTCCCTGAAGTTG
*
3024764 TAGTAGAGCAGATTAAA
65 TAGTAGAACAGATTAAA
3024781 AATAGTGAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
94 36 0.52
95 2 0.03
96 31 0.45
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.33
Consensus pattern (96 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGTAGATAGCAAATCTTATCTCCCTGAAGTTGT
AGTAGAACAGATTAAAGCTACAAATTACAAA
Found at i:3025232 original size:45 final size:45
Alignment explanation
Indices: 3025163--3025324 Score: 150
Period size: 45 Copynumber: 3.6 Consensus size: 45
3025153 ATTAAAGTTA
* * *
3025163 CAAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATCGAAGATAG
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGAGTAGATCGAAGATAG
* * * * *
3025208 CAAACCTTATCCCCCTAAAGTTGCAGTGGGGTAGGTTGAAGTTATG
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGAGTAGATCGAAGATA-G
* * * *
3025254 -AAACC-TATCTCCTTGAAGTTGCAGTGGAGCAGA-CTAAAGATAG
1 CAAACCTTATCTCCCTAAAGTTGCAGTGGAGTAGATC-GAAGATAG
* * *
3025297 CAAATCTTATTTCCCTAAAGTTTCAGTG
1 CAAACCTTATCTCCCTAAAGTTGCAGTG
3025325 AAATAGATTA
Statistics
Matches: 91, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
43 1 0.01
44 31 0.34
45 58 0.64
46 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (45 bp):
CAAACCTTATCTCCCTAAAGTTGCAGTGGAGTAGATCGAAGATAG
Found at i:3027945 original size:3 final size:3
Alignment explanation
Indices: 3027939--3028102 Score: 65
Period size: 3 Copynumber: 54.7 Consensus size: 3
3027929 TTTTTTTACA
* *
3027939 TAT TAT TAA TAT TAT TAC TAT TAT T-T TAT T-T CTAT TAT TAT CT-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT
* * * * * *
3027983 TAT TAT TAC TGT TAG TAT TAT T-T TCAT TAC TAT TAT TTT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
* * * * *
3028028 CA- TAT TAAT TAT T-T TCT AACG TAT TAT TAT TACT AAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT
* *
3028074 T-T CTAGT T-T TTT TAT TAT TAT TAA TAT TA
1 TAT -TA-T TAT TAT TAT TAT TAT TAT TAT TA
3028103 GTGTATGTAT
Statistics
Matches: 118, Mismatches: 27, Indels: 32
0.67 0.15 0.18
Matches are distributed among these distances:
2 12 0.10
3 94 0.80
4 11 0.09
5 1 0.01
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:3027967 original size:23 final size:23
Alignment explanation
Indices: 3027941--3027986 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3027931 TTTTTACATA
3027941 TTATTAATATTATTA-CTATTATT
1 TTATTAATATTATTATCT-TTATT
**
3027964 TTATTTCTATTATTATCTTTATT
1 TTATTAATATTATTATCTTTATT
3027987 ATTACTGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (23 bp):
TTATTAATATTATTATCTTTATT
Found at i:3028126 original size:17 final size:16
Alignment explanation
Indices: 3028104--3028135 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3028094 TTAATATTAG
3028104 TGTATGTATATTATATA
1 TGTATGTATA-TATATA
3028121 TGTATGTATATATAT
1 TGTATGTATATATAT
3028136 TTATATATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (16 bp):
TGTATGTATATATATA
Found at i:3028360 original size:21 final size:22
Alignment explanation
Indices: 3028331--3028447 Score: 102
Period size: 22 Copynumber: 5.5 Consensus size: 22
3028321 ATGTGTTCAA
3028331 TATTATAT-TTTTT-ATA-TAT
1 TATTATATATTTTTAATACTAT
*
3028350 TATTATATA-TTTTAATATTAT
1 TATTATATATTTTTAATACTAT
*
3028371 TAGTTATAT-TTTTTTATACTAT
1 TA-TTATATATTTTTAATACTAT
* * *
3028393 TATATGTATATTTATAATATTA-
1 TAT-TATATATTTTTAATACTAT
* *
3028415 TATTGTATATTTCTAATACTAT
1 TATTATATATTTTTAATACTAT
3028437 TATTTATATAT
1 TA-TTATATAT
3028448 GTATATATGT
Statistics
Matches: 80, Mismatches: 9, Indels: 14
0.78 0.09 0.14
Matches are distributed among these distances:
19 12 0.15
20 3 0.04
21 22 0.28
22 27 0.34
23 16 0.20
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (22 bp):
TATTATATATTTTTAATACTAT
Found at i:3028447 original size:44 final size:44
Alignment explanation
Indices: 3028333--3028452 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 44
3028323 GTGTTCAATA
3028333 TTATATTTTTTATA-TATTA-TTATATATTT-TAATATTATTAG
1 TTATATTTTTTATACTATTATTTATATATTTATAATATTATTAG
* * *
3028374 TTATATTTTTTTATACTATTATATGTATATTTATAATATTA-TAT
1 TTATA-TTTTTTATACTATTATTTATATATTTATAATATTATTAG
* * *
3028418 TGTATATTTCTAATACTATTATTTATATATGTATA
1 T-TATATTTTTTATACTATTATTTATATATTTATA
3028453 TATGTGTGTA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
41 5 0.08
42 9 0.14
43 5 0.08
44 35 0.53
45 12 0.18
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (44 bp):
TTATATTTTTTATACTATTATTTATATATTTATAATATTATTAG
Found at i:3028675 original size:27 final size:28
Alignment explanation
Indices: 3028625--3028684 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
3028615 CCATCTTATG
* *
3028625 TATATATTTTTAAATACTATATTGTATA
1 TATATATTCTTAAATACCATATTGTATA
*
3028653 TATATATTCTT-AATACCATATTGTGTA
1 TATATATTCTTAAATACCATATTGTATA
3028680 TATAT
1 TATAT
3028685 CATTATTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.52
Consensus pattern (28 bp):
TATATATTCTTAAATACCATATTGTATA
Found at i:3031890 original size:122 final size:119
Alignment explanation
Indices: 3031690--3031912 Score: 270
Period size: 122 Copynumber: 1.8 Consensus size: 119
3031680 TAAAACGACC
* * * *
3031690 AGAAACACACTCAAAGTAATTATATTACTTTGTAAACAAGGTATCTTAGTATTATCCAACTGAGT
1 AGAAACACACTCAAAATAATTATATTACTTTGTAAACAAGGTATCTTAATATTACCCAACTGAAT
**
3031755 TGGTGCTCGGTTGACTCATGGCATCAACTCAATTAAGTAATTAATATAAAGTAT
66 TGGTGCTCGGTTGACTCATAACATCAACTCAATTAAGTAATTAATATAAAGTAT
* * * *
3031809 AGAAACACCCTCAAAATAA-TATAATTTACTTTGTAAAGCGATGTTATTTTAATCATTACCCAA-
1 AGAAACACACTCAAAATAATTAT-A-TTACTTTGTAAA-C-AAGGTATCTTAAT-ATTACCCAAC
* * *
3031872 TGAATTGGTGCTTGGTTGACTCGTAATATCAACTCAATTAA
61 TGAATTGGTGCTCGGTTGACTCATAACATCAACTCAATTAA
3031913 AAACGTTTGA
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 18 0.21
120 12 0.14
121 1 0.01
122 44 0.51
123 8 0.09
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (119 bp):
AGAAACACACTCAAAATAATTATATTACTTTGTAAACAAGGTATCTTAATATTACCCAACTGAAT
TGGTGCTCGGTTGACTCATAACATCAACTCAATTAAGTAATTAATATAAAGTAT
Found at i:3035917 original size:19 final size:18
Alignment explanation
Indices: 3035888--3035942 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 18
3035878 TAAGAATTAT
*
3035888 TTTAGTTTTATTTTTTTA
1 TTTATTTTTATTTTTTTA
**
3035906 TTTATTTCTTATTTTAATA
1 TTTATTT-TTATTTTTTTA
*
3035925 TTTATTTTTATGTTTTTA
1 TTTATTTTTATTTTTTTA
3035943 AATGTATTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 14 0.47
19 16 0.53
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.75
Consensus pattern (18 bp):
TTTATTTTTATTTTTTTA
Found at i:3044783 original size:5 final size:6
Alignment explanation
Indices: 3044765--3044790 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3044755 TTATACCCGA
3044765 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
3044791 TGATAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:3047480 original size:16 final size:17
Alignment explanation
Indices: 3047443--3047482 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
3047433 AGTTTATAAT
3047443 ATTT-TATATTATGTTA
1 ATTTATATATTATGTTA
3047459 ATTTTATATATTATG-TA
1 A-TTTATATATTATGTTA
3047476 ATTTATA
1 ATTTATA
3047483 ACACATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.32
17 6 0.27
18 9 0.41
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (17 bp):
ATTTATATATTATGTTA
Found at i:3053164 original size:118 final size:118
Alignment explanation
Indices: 3052953--3053166 Score: 329
Period size: 118 Copynumber: 1.8 Consensus size: 118
3052943 TTTAATCTGG
* * **
3052953 TCTACTGCAACTTCAGATAGATAAGATTTGCTATCTTCGGTCTGCTCCACTGTAACTTCAAGGAA
1 TCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTACAACTTCAAGGAA
* * * *
3053018 ATAAGACTTGCGGCTTTAACCTGTTCCACTATAATTTCAAAGAGATAATCTAC
66 ATAAGACTTGCGACTTCAACATGCTCCACTATAATTTCAAAGAGATAATCTAC
* *
3053071 TCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTACAACTTCAGGGAG
1 TCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTACAACTTCAAGGAA
*
3053136 ATAAGACTTGTGACTTCAACATGCTCCACTA
66 ATAAGACTTGCGACTTCAACATGCTCCACTA
3053167 CAACTTCAGG
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
118 85 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (118 bp):
TCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTACAACTTCAAGGAA
ATAAGACTTGCGACTTCAACATGCTCCACTATAATTTCAAAGAGATAATCTAC
Found at i:3053168 original size:44 final size:43
Alignment explanation
Indices: 3053074--3053318 Score: 237
Period size: 44 Copynumber: 5.5 Consensus size: 43
3053064 AATCTACTCT
* * *
3053074 ACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGACTTG-TATCTTCA-ACTGCTCC
*
3053119 ACTACAACTTCAGGGAGATAAGACTTGTGA-CTTCAACATGCTCC
1 ACTGCAACTTCAGGGAGATAAGACTTGT-ATCTTCAAC-TGCTCC
* * * * *
3053163 ACTACAACTTCAGGGAGATAAG-CTT-TAAAGCTTTAATCTACTCT
1 ACTGCAACTTCAGGGAGATAAGACTTGT--ATCTTCAA-CTGCTCC
* * ** *
3053207 ACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCGGTCTGTTCC
1 ACTGCAACTTCAGGGAGATAAGACTTG-TATCTTC-AACTGCTCC
3053252 ACTGCAACTTCAGGGAGATAAGACTTGTGA-CTTCAACCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGACTTGT-ATCTTCAA-CTGCTCC
3053296 ACTGCAACTTCAGGGAGATAAGA
1 ACTGCAACTTCAGGGAGATAAGA
3053319 TTATTCTCAA
Statistics
Matches: 166, Mismatches: 23, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
42 1 0.01
43 5 0.03
44 97 0.58
45 62 0.37
47 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (43 bp):
ACTGCAACTTCAGGGAGATAAGACTTGTATCTTCAACTGCTCC
Found at i:3053304 original size:133 final size:133
Alignment explanation
Indices: 3053063--3053317 Score: 465
Period size: 133 Copynumber: 1.9 Consensus size: 133
3053053 TTCAAAGAGA
3053063 TAATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTACAACT
1 TAATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTACAACT
3053128 TCAGGGAGATAAGACTTGTGACTTCAACATGCTCCACTACAACTTCAGGGAGATAAGCTTTAAAG
66 TCAGGGAGATAAGACTTGTGACTTCAACATGCTCCACTACAACTTCAGGGAGATAAGCTTTAAAG
3053193 CTT
131 CTT
* * *
3053196 TAATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCGGTCTGTTCCACTGCAACT
1 TAATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTACAACT
* *
3053261 TCAGGGAGATAAGACTTGTGACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAG
66 TCAGGGAGATAAGACTTGTGACTTCAACATGCTCCACTACAACTTCAGGGAGATAAG
3053318 ATTATTCTCA
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
133 117 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (133 bp):
TAATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTACAACT
TCAGGGAGATAAGACTTGTGACTTCAACATGCTCCACTACAACTTCAGGGAGATAAGCTTTAAAG
CTT
Found at i:3065206 original size:3 final size:3
Alignment explanation
Indices: 3065198--3065297 Score: 94
Period size: 3 Copynumber: 33.7 Consensus size: 3
3065188 GAAAGAAAAT
* * * *
3065198 ATA ATA ATA ATA ATA ATA GTA ATA GTA ATA AT- ACA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
3065245 ATA ACA AAA ATA GTA ATA ATA GTA ATA AAA ATA ATA GTA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3065293 ATA AT
1 ATA AT
3065298 GGTAATTGTT
Statistics
Matches: 75, Mismatches: 21, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
2 1 0.01
3 74 0.99
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:3066655 original size:15 final size:15
Alignment explanation
Indices: 3066637--3066666 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3066627 TACATGATAG
*
3066637 TTCTTTTTTGTTTGT
1 TTCTTTTCTGTTTGT
3066652 TTCTTTTCTGTTTGT
1 TTCTTTTCTGTTTGT
3066667 CTTTGCGTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.10, G:0.13, T:0.77
Consensus pattern (15 bp):
TTCTTTTCTGTTTGT
Found at i:3066990 original size:18 final size:19
Alignment explanation
Indices: 3066967--3067005 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
3066957 GGACTTTTGA
3066967 TTTATTATTTTT-TTTGGT
1 TTTATTATTTTTATTTGGT
3066985 TTTATTATTTTTATTTGGT
1 TTTATTATTTTTATTTGGT
3067004 TT
1 TT
3067006 CTGTTTCAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (19 bp):
TTTATTATTTTTATTTGGT
Found at i:3084396 original size:22 final size:22
Alignment explanation
Indices: 3084369--3084453 Score: 127
Period size: 22 Copynumber: 3.9 Consensus size: 22
3084359 AACTAAAATG
*
3084369 GTAAGCACTATCGAGCTGAACA
1 GTAAGCTCTATCGAGCTGAACA
*
3084391 GTAAGCTCTATTGAGCTGAACA
1 GTAAGCTCTATCGAGCTGAACA
*
3084413 GTAAGCTCTATTGAGCTGAACA
1 GTAAGCTCTATCGAGCTGAACA
3084435 GTAAGCTC-ATACGAGCTGA
1 GTAAGCTCTAT-CGAGCTGA
3084454 TATATCGGTA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
21 2 0.03
22 57 0.97
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (22 bp):
GTAAGCTCTATCGAGCTGAACA
Found at i:3084432 original size:44 final size:44
Alignment explanation
Indices: 3084340--3084442 Score: 136
Period size: 44 Copynumber: 2.3 Consensus size: 44
3084330 CTTGAGCTAA
3084340 TGAACAGTAAGCTCTAATGAACTAAAATGGTAAGCACTATCGAGC
1 TGAACAGTAAGCTCTAATGAACTAAAA-GGTAAGCACTATCGAGC
* * * * *
3084385 TGAACAGTAAGCTCTATTGAGCTGAACA-GTAAGCTCTATTGAGC
1 TGAACAGTAAGCTCTAATGAACT-AAAAGGTAAGCACTATCGAGC
3084429 TGAACAGTAAGCTC
1 TGAACAGTAAGCTC
3084443 ATACGAGCTG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
44 28 0.54
45 21 0.40
46 3 0.06
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24
Consensus pattern (44 bp):
TGAACAGTAAGCTCTAATGAACTAAAAGGTAAGCACTATCGAGC
Found at i:3088776 original size:57 final size:57
Alignment explanation
Indices: 3088688--3088801 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
3088678 AAATTAGGGA
3088688 ACAATAATGGAATTGAGTGCTTCACAATCACATTGCCATGGTAAAACCACGGACTTG
1 ACAATAATGGAATTGAGTGCTTCACAATCACATTGCCATGGTAAAACCACGGACTTG
*
3088745 ACAATAATGGAATTGAGTGCTTCACAATCACATTGCCATGGTAAAACCATGGACTTG
1 ACAATAATGGAATTGAGTGCTTCACAATCACATTGCCATGGTAAAACCACGGACTTG
3088802 CACATAGTCA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (57 bp):
ACAATAATGGAATTGAGTGCTTCACAATCACATTGCCATGGTAAAACCACGGACTTG
Found at i:3089018 original size:52 final size:52
Alignment explanation
Indices: 3088868--3089022 Score: 177
Period size: 52 Copynumber: 3.0 Consensus size: 52
3088858 CACATATAAT
* *
3088868 ACCGATGCCATATCCCAGATATGGTCTTATAT-GGAATCACATTATCACATCAC
1 ACCGATGCCATAGCCCAGCTATGGTCTTATATGGGAA-CACA-TATCACATCAC
* * * * **
3088921 ATCGACGCCATAGCCCAGCTATGGTCTTATATAGGAACACGTATCACATTGC
1 ACCGATGCCATAGCCCAGCTATGGTCTTATATGGGAACACATATCACATCAC
* * **
3088973 ACCGATGCCATAGCCCAGCTATAGTCTTATACGGGCGCACATATCACATC
1 ACCGATGCCATAGCCCAGCTATGGTCTTATATGGGAACACATATCACATC
3089023 TTTTTCGTCA
Statistics
Matches: 85, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
52 50 0.59
53 31 0.36
54 4 0.05
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (52 bp):
ACCGATGCCATAGCCCAGCTATGGTCTTATATGGGAACACATATCACATCAC
Found at i:3089918 original size:3 final size:3
Alignment explanation
Indices: 3089912--3090036 Score: 74
Period size: 3 Copynumber: 41.0 Consensus size: 3
3089902 TCATTCCTAA
* * * *
3089912 TAT TAT TAA TAC TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* ** * * * * *
3089960 TAT TCT GGT TAT TAA CA- TAT AAT TAT TTT TAAT GTAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT -TAT TAT TAT TAT
* *
3090006 TAGT TAT TAC TAT T-T CTAG TAT TAT TAT TAT
1 TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TAT
3090037 ATATAATATT
Statistics
Matches: 91, Mismatches: 25, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
2 2 0.02
3 83 0.91
4 5 0.05
5 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:3090493 original size:28 final size:27
Alignment explanation
Indices: 3090453--3090539 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 27
3090443 TTTTTAATAC
*
3090453 TATATTTTTAAATACCATATATATTG-TG
1 TATATTCTTAAATA--ATATATATTGATG
*
3090481 TATATTCTTAAATATTATATATTGTATG
1 TATATTCTTAAATAATATATATTG-ATG
* *
3090509 TATTTTCTT-AATAAT-TATATTATATG
1 TATATTCTTAAATAATATATATT-GATG
3090535 TATAT
1 TATAT
3090540 ATAGTACGTC
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
26 22 0.44
27 5 0.10
28 23 0.46
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.54
Consensus pattern (27 bp):
TATATTCTTAAATAATATATATTGATG
Found at i:3090512 original size:26 final size:25
Alignment explanation
Indices: 3090469--3090537 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
3090459 TTTAAATACC
* *
3090469 ATATATATTGTGTATATTCTTAAATA
1 ATATATATTGTATGTATTCTT-AATA
*
3090495 TTATATATTGTATGTATTTTCTTAATA
1 ATATATATTGTATGTA--TTCTTAATA
*
3090522 AT-TATATTATATGTAT
1 ATATATATTGTATGTAT
3090538 ATATAGTACG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
24 1 0.03
26 25 0.69
27 5 0.14
28 5 0.14
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (25 bp):
ATATATATTGTATGTATTCTTAATA
Found at i:3102320 original size:12 final size:12
Alignment explanation
Indices: 3102303--3102328 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3102293 ACCATAAAAA
3102303 AACAATAATAAT
1 AACAATAATAAT
3102315 AACAATAATAAT
1 AACAATAATAAT
3102327 AA
1 AA
3102329 TAAGAATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AACAATAATAAT
Found at i:3102338 original size:6 final size:6
Alignment explanation
Indices: 3102330--3102373 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
3102320 TAATAATAAT
*
3102330 AAGAAT AAGAAA AAGAAA AAGAAA AAGAAGA AA-AGAA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAA-A AAGA-AA AAGAAA A
3102374 GGAGAGGCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (6 bp):
AAGAAA
Found at i:3103537 original size:64 final size:64
Alignment explanation
Indices: 3103459--3103582 Score: 178
Period size: 64 Copynumber: 1.9 Consensus size: 64
3103449 TCATTCGTAA
* * * *
3103459 CACATCTAGTTAGGAGCATTTGATTCACT-TCGATCATAGCCTTCTAATTATTTGACATAAACAT
1 CACATCTAGTTAGGAACAATTGATTCA-TGTCGATCATAGCATCCTAATTATTTGACATAAACAT
* *
3103523 CACATCTAGTTAGGAACAATTGATTCATGTTGATCATAGCATCCTAATTATTTGGCATAA
1 CACATCTAGTTAGGAACAATTGATTCATGTCGATCATAGCATCCTAATTATTTGACATAA
3103583 GCATAAGCCT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 1 0.02
64 52 0.98
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (64 bp):
CACATCTAGTTAGGAACAATTGATTCATGTCGATCATAGCATCCTAATTATTTGACATAAACAT
Found at i:3103673 original size:45 final size:45
Alignment explanation
Indices: 3103609--3103814 Score: 115
Period size: 45 Copynumber: 4.7 Consensus size: 45
3103599 CAGAATGTAG
* * *
3103609 ATCTTGTCTCCCTGAAGTTGTAGTGGGGCAAATCGAAGATGACGA
1 ATCTTGGCTTCCTGAAGTTGTAGTGGAGCAAATCGAAGATGACGA
* * * **
3103654 ATCTTGGCTTCCTGAAGTTGCAGTGAAGCAGAT-TTA-A-G-C-A
1 ATCTTGGCTTCCTGAAGTTGTAGTGGAGCAAATCGAAGATGACGA
* * * ** * * *
3103694 AGTCCTT-GCTCCCTAAAGTTGTAGTGGAG-TAGGCTGAATATTA-TA
1 A-T-CTTGGCTTCCTGAAGTTGTAGTGGAGCAAATC-GAAGATGACGA
* * *
3103739 TATCTT-GCGTCCATGAAGTTGTAGTGGGGCAAATCGAAGACGACGA
1 -ATCTTGGCTTCC-TGAAGTTGTAGTGGAGCAAATCGAAGATGACGA
* *
3103785 ATCTTGGCTTCCTGAAGTTGCAGTGAAGCA
1 ATCTTGGCTTCCTGAAGTTGTAGTGGAGCA
3103815 GATTTAAGGA
Statistics
Matches: 114, Mismatches: 34, Indels: 26
0.66 0.20 0.15
Matches are distributed among these distances:
40 2 0.02
41 20 0.18
42 5 0.04
43 2 0.02
44 8 0.07
45 68 0.60
46 9 0.08
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (45 bp):
ATCTTGGCTTCCTGAAGTTGTAGTGGAGCAAATCGAAGATGACGA
Found at i:3103843 original size:131 final size:131
Alignment explanation
Indices: 3103606--3104443 Score: 1227
Period size: 131 Copynumber: 6.4 Consensus size: 131
3103596 AAACAGAATG
* *
3103606 TAGATCTTGTCTCCCTGAAGTTGTAGTGGGGCAAATCGAAGATGACGAATCTTGGCTTCCTGAAG
1 TAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCGAAGACGACGAATCTTGGCTTCCTGAAG
*
3103671 TTGCAGTGAAGCAGATTTAAGCAAGTCCTTGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAATATT
66 TTGCAGTGAAGCAGATTTAAGCAAGTCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAATATT
3103736 A
131 A
* * *
3103737 TATATCTTG-CGTCCATGAAGTTGTAGTGGGGCAAATCGAAGACGACGAATCTTGGCTTCCTGAA
1 TAGATCTTGTC-TCCCTGAAGTTGCAGTGGGGCAAATCGAAGACGACGAATCTTGGCTTCCTGAA
* * * *
3103801 GTTGCAGTGAAGCAGATTTAAGGAAGTTCTATCTCCCTAAAGTTGTAGTGGAGTAGGCTAAATAT
65 GTTGCAGTGAAGCAGATTTAAGCAAGTCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAATAT
3103866 TA
130 TA
* * *
3103868 TAGATCTTGTCTCCCTGAAGTTGCAGTGGGACAAATCGAAGACGATGAATCTTGGCTTCTTGAAG
1 TAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCGAAGACGACGAATCTTGGCTTCCTGAAG
*
3103933 TTGCAGTGAAGCAGATTTAAGCAAGTCCTAGCTCTCTAAAGTTGTAGTGGAGTAGGCTGAATATT
66 TTGCAGTGAAGCAGATTTAAGCAAGTCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAATATT
*
3103998 G
131 A
* * *
3103999 TAGATCTTGTCTCTCTGAAGTTGCAGTGGAGCAAATCGAAGACGACGAATCTTGGCTTCTTGAAG
1 TAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCGAAGACGACGAATCTTGGCTTCCTGAAG
* * **
3104064 TTGTAGTGAAGCAGATTTAAGCAAATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGACGA-T
66 TTGCAGTGAAGCAGATTTAAGCAAGTCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAATATT
3104128 A
131 A
3104129 GTAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCGAAGACGACGAATCTTGGCTTCCTGAA
1 -TAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCGAAGACGACGAATCTTGGCTTCCTGAA
* * * *
3104194 TTTGTAGTGAAGCAGATTTAAGCAAGTACTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAGAT
65 GTTGCAGTGAAGCAGATTTAAGCAAGTCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAATAT
*
3104259 TG
130 TA
* *
3104261 TAGATCTTGTCTCCCTGAAGTTGCAGTGGAGCAAATCGAAGACAACGAATCTTGGCTTCCTGAAG
1 TAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCGAAGACGACGAATCTTGGCTTCCTGAAG
* * ** ** *
3104326 TTACAGTGAAGCAGATTTAAGCAAG-CCTTAACTCCCT-AAGCCGTAG-GGTAACAGGCTGAAGA
66 TTGCAGTGAAGCAGATTTAAGCAAGTCC-TAGCTCCCTAAAGTTGTAGTGG-AGTAGGCTGAATA
*
3104388 TTG
129 TTA
* * * * *
3104391 TAGATCTTGTCTCCCCGAAGTTGCAGTGGAGCAGATCGAAGATGATGAATCTT
1 TAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCGAAGACGACGAATCTT
3104444 ATATCTCTAG
Statistics
Matches: 647, Mismatches: 54, Indels: 13
0.91 0.08 0.02
Matches are distributed among these distances:
129 2 0.00
130 72 0.11
131 571 0.88
132 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (131 bp):
TAGATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCGAAGACGACGAATCTTGGCTTCCTGAAG
TTGCAGTGAAGCAGATTTAAGCAAGTCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAATATT
A
Found at i:3104051 original size:45 final size:45
Alignment explanation
Indices: 3104002--3104338 Score: 153
Period size: 45 Copynumber: 7.7 Consensus size: 45
3103992 AATATTGTAG
* *
3104002 ATCTTGTCTCTCTGAAGTTGCAGTGGAGCAAATCGAAGACGACGA
1 ATCTTGGCTCCCTGAAGTTGCAGTGGAGCAAATCGAAGACGACGA
* * * * * **
3104047 ATCTTGGCTTCTTGAAGTTGTAGTGAAGCAGATTTAAG-C-A--A
1 ATCTTGGCTCCCTGAAGTTGCAGTGGAGCAAATCGAAGACGACGA
* * * * * * ** *
3104088 ATCCTAGCTCCCTAAAGTTGTAGTGGAG--TA-GGCTGACGATAGTA
1 ATCTTGGCTCCCTGAAGTTGCAGTGGAGCAAATCGAAGACGA-CG-A
* *
3104132 GATCTTGTCTCCCTGAAGTTGCAGTGGGGCAAATCGAAGACGACGA
1 -ATCTTGGCTCCCTGAAGTTGCAGTGGAGCAAATCGAAGACGACGA
* * * * * ** * *
3104178 ATCTTGGCTTCCTGAATTTGTAGTGAAGCAGATTTAAG-C-AAGT
1 ATCTTGGCTCCCTGAAGTTGCAGTGGAGCAAATCGAAGACGACGA
* * * * ** *
3104221 A-C-TAGCTCCCTAAAGTTGTAGTGGAG-TAGGCTGAAGATTGTA-G-
1 ATCTTGGCTCCCTGAAGTTGCAGTGGAGCAAATC-GAAGA-CG-ACGA
* *
3104264 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAAATCGAAGACAACGA
1 ATCTTGGCTCCCTGAAGTTGCAGTGGAGCAAATCGAAGACGACGA
* * *
3104309 ATCTTGGCTTCCTGAAGTTACAGTGAAGCA
1 ATCTTGGCTCCCTGAAGTTGCAGTGGAGCA
3104339 GATTTAAGCA
Statistics
Matches: 205, Mismatches: 67, Indels: 40
0.66 0.21 0.13
Matches are distributed among these distances:
38 1 0.00
39 2 0.01
40 1 0.00
41 45 0.22
42 1 0.00
43 6 0.03
44 6 0.03
45 132 0.64
46 3 0.01
47 2 0.01
48 6 0.03
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (45 bp):
ATCTTGGCTCCCTGAAGTTGCAGTGGAGCAAATCGAAGACGACGA
Found at i:3107557 original size:132 final size:132
Alignment explanation
Indices: 3107315--3107794 Score: 642
Period size: 132 Copynumber: 3.7 Consensus size: 132
3107305 ATTATTCATT
* *
3107315 TAAAAATTCTTTAAAACGAAGACGAGATTTGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
1 TAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
* ***
3107380 GCTGGGTTGCAATTTCACGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACCCATGTCT
66 GCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCGTTCATGTCT
3107445 TC
131 TC
* * * * * *
3107447 TAAAGATTCTTTAAAACGAAGGCGAGGTTTGGTATTTGGCAATTCACGGAATCGTGCCCTAATGT
1 TAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
* *
3107512 GTTGGGTTGCAATTTCTCGTTTGCTCAAAATGATCGAATATCCCTTCAAAATTTCGTTCATGTCT
66 GCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCGTTCATGTCT
3107577 TC
131 TC
* * *
3107579 TAAAAATCCTTTAAAACGAAGGCGATG-TTCGATATTTGACAATTCGTGGAATCGTGCCCTAACG
1 TAAAAATTCTTTAAAACGAAGGCGA-GATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACG
* * * *
3107643 TGCTGGGTTGCAATTTCTCGTTTGCTCAAAGTAATCGAATGTCCCTTTAGAATTTCGTTCATGTC
65 TGCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCGTTCATGTC
3107708 TTC
130 TTC
* * * ** * * * * *
3107711 T-AAAACTCTTTAAAACAAATGTAATACTCGGTGTTTGGCAATTCG-GGAATCGTGCCCTATCGT
1 TAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
*
3107774 GCTGGGTTGCAATTTCCCGTT
66 GCTGGGTTGCAATTTCTCGTT
3107795 CGTTCAATGA
Statistics
Matches: 307, Mismatches: 39, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
130 37 0.12
131 32 0.10
132 237 0.77
133 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (132 bp):
TAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
GCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCGTTCATGTCT
TC
Found at i:3123694 original size:13 final size:13
Alignment explanation
Indices: 3123678--3123710 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3123668 TGTAATTAAA
*
3123678 TTAGTTAATTAGT
1 TTAGATAATTAGT
3123691 TTAGATAATTAGT
1 TTAGATAATTAGT
3123704 TTA-ATAA
1 TTAGATAA
3123711 ACAAAACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:3127044 original size:22 final size:23
Alignment explanation
Indices: 3127013--3127055 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3127003 GGGTGAACTT
3127013 GATAGGAAAAACACGGGTGTGGG
1 GATAGGAAAAACACGGGTGTGGG
*
3127036 GATA-GAAAACCACGGGTGTG
1 GATAGGAAAAACACGGGTGTG
3127056 CTAGGGACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.35, C:0.12, G:0.40, T:0.14
Consensus pattern (23 bp):
GATAGGAAAAACACGGGTGTGGG
Found at i:3131838 original size:5 final size:5
Alignment explanation
Indices: 3131828--3131904 Score: 61
Period size: 5 Copynumber: 14.8 Consensus size: 5
3131818 TCATTCTCAT
*
3131828 TTTTA TTTTA TTTTA -TTTA TTTTA TTTTTA TTTTTC TTTTGA TTTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA -TTTTA TTTT-A -TTTTA
*
3131876 TTTTCA TTTCAA TTTTA --TTA TTTTA TTTT
1 TTTT-A TTT-TA TTTTA TTTTA TTTTA TTTT
3131905 GAAATACATA
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
3 3 0.05
4 4 0.07
5 30 0.50
6 19 0.32
7 4 0.07
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:3131848 original size:14 final size:15
Alignment explanation
Indices: 3131829--3131904 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 15
3131819 CATTCTCATT
3131829 TTTATTTTA-TTTTA
1 TTTATTTTATTTTTA
3131843 TTTATTTTATTTTTA
1 TTTATTTTATTTTTA
*
3131858 TTTTTCTTTTGATTTTTA
1 --TTTATTTT-ATTTTTA
* *
3131876 TTTTCATTTCAATTTTA
1 -TTT-ATTTTATTTTTA
3131893 -TTATTTTATTTT
1 TTTATTTTATTTT
3131905 GAAATACATA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 17 0.33
15 7 0.14
17 17 0.33
18 10 0.20
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (15 bp):
TTTATTTTATTTTTA
Found at i:3131874 original size:7 final size:6
Alignment explanation
Indices: 3131826--3131884 Score: 57
Period size: 6 Copynumber: 9.7 Consensus size: 6
3131816 TCTCATTCTC
* * *
3131826 ATTTTT A-TTTT ATTTTAT TTATTTT ATTTTT ATTTTT CTTTTG ATTTTT
1 ATTTTT ATTTTT ATTTT-T AT-TTTT ATTTTT ATTTTT ATTTTT ATTTTT
*
3131875 ATTTTC ATTT
1 ATTTTT ATTT
3131885 CAATTTTATT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
5 5 0.12
6 31 0.72
7 4 0.09
8 3 0.07
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (6 bp):
ATTTTT
Found at i:3134806 original size:13 final size:13
Alignment explanation
Indices: 3134790--3134822 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3134780 TTTAATTAAA
*
3134790 TTAGTTAATTAGT
1 TTAGATAATTAGT
3134803 TTAGATAATTAGT
1 TTAGATAATTAGT
3134816 TTA-ATAA
1 TTAGATAA
3134823 ACAAATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:3135675 original size:18 final size:19
Alignment explanation
Indices: 3135641--3135681 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
3135631 TAATTAATAG
3135641 TTAATATAATATATTATAA
1 TTAATATAATATATTATAA
* *
3135660 TTAATA-AATATCTTATAC
1 TTAATATAATATATTATAA
3135678 TTAA
1 TTAA
3135682 AGTATAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAATATAATATATTATAA
Found at i:3142151 original size:27 final size:27
Alignment explanation
Indices: 3142103--3142261 Score: 132
Period size: 27 Copynumber: 5.9 Consensus size: 27
3142093 GCGAGGCTGC
* * *
3142103 CAGATATTGTGA-TGAAGTCACCAAATA
1 CAGATATTGTGACAG-AGCCACCAGATA
3142130 CAGATATTGTGACAGAGCCACCAGA-A
1 CAGATATTGTGACAGAGCCACCAGATA
**
3142156 CAGATATATGTGGTAGAGCCACCAGAT-
1 CAGATAT-TGTGACAGAGCCACCAGATA
* *
3142183 CAGATAATCGTGGC-GTAGCCACCAGA-A
1 CAGAT-ATTGTGACAG-AGCCACCAGATA
* *
3142210 CAGATATATGTGGCAGAGCCACTAGAT-
1 CAGATAT-TGTGACAGAGCCACCAGATA
*
3142237 CAGATAATTGTGACATAGCCACCAG
1 CAGAT-ATTGTGACAGAGCCACCAG
3142262 GACGCTTCCT
Statistics
Matches: 110, Mismatches: 12, Indels: 20
0.77 0.08 0.14
Matches are distributed among these distances:
26 11 0.10
27 93 0.85
28 6 0.05
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (27 bp):
CAGATATTGTGACAGAGCCACCAGATA
Found at i:3142206 original size:54 final size:54
Alignment explanation
Indices: 3142121--3142261 Score: 194
Period size: 54 Copynumber: 2.6 Consensus size: 54
3142111 GTGATGAAGT
* * * *
3142121 CACCAAATACAGAT-ATTGTGACAGAGCCACCAGAACAGATATATGTGGTAGAGC
1 CACCAGAT-CAGATAATCGTGACATAGCCACCAGAACAGATATATGTGGCAGAGC
* *
3142175 CACCAGATCAGATAATCGTGGCGTAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATCGTGACATAGCCACCAGAACAGATATATGTGGCAGAGC
* *
3142229 CACTAGATCAGATAATTGTGACATAGCCACCAG
1 CACCAGATCAGATAATCGTGACATAGCCACCAG
3142262 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
53 5 0.07
54 71 0.93
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATCGTGACATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:3143906 original size:26 final size:26
Alignment explanation
Indices: 3143875--3143982 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
3143865 TGAAATGCCC
*
3143875 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
3143901 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
3143927 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
3143953 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
3143979 ATCA
1 ATCA
3143983 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:3148304 original size:39 final size:40
Alignment explanation
Indices: 3148209--3148470 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
3148199 TTGAATGATG
*
3148209 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
3148247 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
3148288 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
3148327 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
3148366 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
3148405 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
3148444 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
3148471 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:3157620 original size:40 final size:40
Alignment explanation
Indices: 3157436--3157738 Score: 404
Period size: 40 Copynumber: 7.7 Consensus size: 40
3157426 TTGAATGATG
* *
3157436 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * * *
3157475 TTCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
3157515 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
3157554 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
3157593 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
3157633 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
3157673 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
3157714 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
3157739 AACGAGGAGC
Statistics
Matches: 243, Mismatches: 14, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
39 91 0.37
40 142 0.58
41 10 0.04
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:3157756 original size:120 final size:119
Alignment explanation
Indices: 3157436--3157771 Score: 357
Period size: 119 Copynumber: 2.8 Consensus size: 119
3157426 TTGAATGATG
* * * *
3157436 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATTCGGACTAAGAT-CCGAAGGCA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAA-TTACTAA-ATCCGGGCTAAG-TCCCGAAGGCA
** * * *
3157497 TTTGTGCGAGAT-ACTAATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
62 TTTGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
3157554 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAATTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
** * *
3157619 TGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
66 AACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
3157673 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAATTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
* * *
3157737 TGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
64 TGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
3157772 TACGTGATTT
Statistics
Matches: 189, Mismatches: 20, Indels: 17
0.84 0.09 0.08
Matches are distributed among these distances:
117 11 0.06
118 57 0.30
119 60 0.32
120 59 0.31
121 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (119 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAATTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
AACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:3161436 original size:13 final size:13
Alignment explanation
Indices: 3161418--3161443 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3161408 TATATATATT
3161418 TATCCCAAAACAA
1 TATCCCAAAACAA
3161431 TATCCCAAAACAA
1 TATCCCAAAACAA
3161444 CATACAATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
TATCCCAAAACAA
Found at i:3162505 original size:9 final size:9
Alignment explanation
Indices: 3162491--3162516 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3162481 AACCATTGCA
3162491 AAAAAAATG
1 AAAAAAATG
3162500 AAAAAAATG
1 AAAAAAATG
3162509 AAAAAAAT
1 AAAAAAAT
3162517 CAACGATATC
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:0.81, C:0.00, G:0.08, T:0.12
Consensus pattern (9 bp):
AAAAAAATG
Found at i:3164534 original size:26 final size:26
Alignment explanation
Indices: 3164498--3164605 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
3164488 TGATACAAAT
*
3164498 TGATAGTGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
3164524 TGATAATGGGTTAGATAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3164550 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3164576 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3164602 TGAT
1 TGAT
3164606 GGGAATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:3166144 original size:26 final size:25
Alignment explanation
Indices: 3166092--3166144 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
3166082 TTTACAGTTT
3166092 TACCCCTAGTAGGTAAATTACCGAAA
1 TACCCCTAG-AGGTAAATTACCGAAA
*
3166118 TACCCCTAG-GGTTAAATTGACCTAAA
1 TACCCCTAGAGG-TAAATT-ACCGAAA
3166144 T
1 T
3166145 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 2 0.08
25 6 0.25
26 16 0.67
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (25 bp):
TACCCCTAGAGGTAAATTACCGAAA
Found at i:3168099 original size:18 final size:19
Alignment explanation
Indices: 3168076--3168112 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3168066 TTTTAAAAAA
3168076 TATAAA-ATTTAGAATTTT
1 TATAAATATTTAGAATTTT
*
3168094 TATAAATATTTTGAATTTT
1 TATAAATATTTAGAATTTT
3168113 GTTTATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:3173327 original size:33 final size:32
Alignment explanation
Indices: 3173290--3173360 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
3173280 ACTATTTAGT
*
3173290 TATTACTT-ATTTTAAGTTCTCTTTTATATATTA
1 TATTA-TTCATTTTAAATTCT-TTTTATATATTA
* *
3173323 TATTATTCATTTTAAATTGTTTTTATATAGTA
1 TATTATTCATTTTAAATTCTTTTTATATATTA
3173355 T-TTATT
1 TATTATT
3173361 TTGAACTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 5 0.15
32 14 0.41
33 15 0.44
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (32 bp):
TATTATTCATTTTAAATTCTTTTTATATATTA
Found at i:3173356 original size:27 final size:26
Alignment explanation
Indices: 3173321--3173490 Score: 118
Period size: 25 Copynumber: 6.6 Consensus size: 26
3173311 TTTTATATAT
3173321 TATATTATTCATTTTAAATTGTTTTTA
1 TATATTATTCATTTTAAATTG-TTTTA
* * * * *
3173348 TATAGTATTTATTTTGAACTGTTATA
1 TATATTATTCATTTTAAATTGTTTTA
* *
3173374 T-TA-TATACTATTTTAAATTGTTTCA
1 TATATTATTC-ATTTTAAATTGTTTTA
* *
3173399 TATATTATT-ATTTTAAGTTG--CTA
1 TATATTATTCATTTTAAATTGTTTTA
*
3173422 TATATTATTCATCTTTAAACTAT-TTTTT
1 TATATTATTCAT-TTTAAA-T-TGTTTTA
* * * *
3173450 TATATTTTTTATTTCAAATTGCTTTA
1 TATATTATTCATTTTAAATTGTTTTA
*
3173476 TATATTATTTATTTT
1 TATATTATTCATTTT
3173491 GTTTTTCTTT
Statistics
Matches: 108, Mismatches: 25, Indels: 21
0.70 0.16 0.14
Matches are distributed among these distances:
23 10 0.09
24 5 0.05
25 31 0.29
26 25 0.23
27 26 0.24
28 11 0.10
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.60
Consensus pattern (26 bp):
TATATTATTCATTTTAAATTGTTTTA
Found at i:3173426 original size:52 final size:55
Alignment explanation
Indices: 3173314--3173429 Score: 136
Period size: 52 Copynumber: 2.2 Consensus size: 55
3173304 AGTTCTCTTT
* *
3173314 TATATATTATATTATTCATTTTAAATTGTTTTTATATAGTATTTATTTTGAACTG
1 TATATATTATATTACTCATTTTAAATTGTTTTCATATAGTATTTATTTTGAACTG
* *
3173369 T-TATATTATA-TACT-ATTTTAAATTG-TTTCATATATTA-TTATTTT-AAGTTG
1 TATATATTATATTACTCATTTTAAATTGTTTTCATATAGTATTTATTTTGAA-CTG
3173419 CTATATATTAT
1 -TATATATTAT
3173430 TCATCTTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
49 2 0.04
50 9 0.17
51 11 0.20
52 19 0.35
53 3 0.06
54 9 0.17
55 1 0.02
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (55 bp):
TATATATTATATTACTCATTTTAAATTGTTTTCATATAGTATTTATTTTGAACTG
Found at i:3178278 original size:26 final size:26
Alignment explanation
Indices: 3178242--3178295 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
3178232 TACTGTAAAG
3178242 TACAACTAAGAGTTTCTCAGACATAA
1 TACAACTAAGAGTTTCTCAGACATAA
*
3178268 TACAACTAAGAGTTTCTCGGACATAA
1 TACAACTAAGAGTTTCTCAGACATAA
3178294 TA
1 TA
3178296 ATGTCTGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.28
Consensus pattern (26 bp):
TACAACTAAGAGTTTCTCAGACATAA
Found at i:3184442 original size:44 final size:44
Alignment explanation
Indices: 3184329--3184649 Score: 246
Period size: 44 Copynumber: 7.0 Consensus size: 44
3184319 CTAAAAATAA
* *
3184329 ACAAATTTTATCTCCCTGAAGTTACAGTGGAGCAGATTGATGACAGGCT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-A--A-A-GCT
** *
3184378 ACAAATCTTATCTCTTTGAAGTTGCAGTGGAGCAGATTAAAGCC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT
* * * ** *
3184422 ACAAATCTTATCTCCCTGAAGTTGTAATGGAGTAGACCAAAGAT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT
* * * * *
3184466 AGTAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAGAT
1 A-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT
* * * * ** *
3184511 AATAAACCTTATCTCCTTAAAGTTATAGTGGAGCAGATTGAAGCTACAAGAT
1 -ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-----TA-AAGCT
* * *
3184563 AGCAAATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTGAAGCT
1 A-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT
* * *
3184608 ACTAATCTTATCTCCCTGAAATTGCAGTGGAGCAAATTAAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
3184650 TGAACTAATC
Statistics
Matches: 223, Mismatches: 39, Indels: 25
0.78 0.14 0.09
Matches are distributed among these distances:
44 73 0.33
45 73 0.33
46 3 0.01
48 1 0.00
49 34 0.15
51 3 0.01
52 36 0.16
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (44 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT
Found at i:3184527 original size:45 final size:45
Alignment explanation
Indices: 3184331--3184641 Score: 230
Period size: 45 Copynumber: 6.7 Consensus size: 45
3184321 AAAAATAAAC
* * * * *
3184331 AAATTTTATCTCCCTGAAGTTACAGTGGAGCAGATTGATGACAGGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA----AT
** * ** *
3184380 AAATCTTATCTCTTTGAAGTTGCAGTGGAGCAGATTAAAG-CCAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAAT
* * * *** *
3184424 AAATCTTATCTCCCTGAAGTTGTAATGGAGTAGACCAAAGATAGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAAT
* *
3184469 AAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAGATAAT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAAT
* * * ** *
3184514 AAACCTTATCTCCTTAAAGTTATAGTGGAGCAGATTGAAGCTACAAGAT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--A-TA-AT
* * * *
3184563 AGCAAATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTGAAGCTACT
1 ---AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAAT
*
3184611 -AATCTTATCTCCCTGAAATTGCAGTGGAGCA
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
3184642 AATTAAAGTG
Statistics
Matches: 214, Mismatches: 40, Indels: 21
0.78 0.15 0.08
Matches are distributed among these distances:
44 63 0.29
45 73 0.34
47 1 0.00
48 3 0.01
49 37 0.17
52 37 0.17
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (45 bp):
AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAAT
Found at i:3184675 original size:186 final size:183
Alignment explanation
Indices: 3184336--3184680 Score: 399
Period size: 186 Copynumber: 1.9 Consensus size: 183
3184326 TAAACAAATT
* * * * ** *
3184336 TTATCTCCCTGAAGTTACAGTGGAGCAGATTGATGACAGGCTACAAATCTTATCTCTTTGAAGTT
1 TTATCTCCCTAAAGTTACAGTGGAGCAGATTGAAGACAAGATACAAATCTTATCTCCCTAAAGTT
* * * * *
3184401 GCAGTGGAGCAGATTAAAGCCACAAATCTTATCTCCCTGAAGTTGTAATGGAGTAGACCAAAGAT
66 ACAGTGGAGCAGATTAAAGCCACAAATCTTATCTCCCTGAAATTGCAATGGAGCAAACCAAAGAT
* ** *
3184466 AGTAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAGATAATAAACC
131 ACTAAATCCAATCACCTTGAAGTTGCAGTGGAGCAGACTGAAGATAATAAACC
* *
3184519 TTATCTCCTTAAAGTTATAGTGGAGCAGATTGAAGCTACAAGATAGCAAATCTTATCTCCCTAAA
1 TTATCTCCCTAAAGTTACAGTGGAGCAGATTGAAG--ACAAGATA-CAAATCTTATCTCCCTAAA
* * * * **
3184584 GTTACAGTGGAGCAGATTGAAGCTACTAATCTTATCTCCCTGAAATTGCAGTGGAGCAAATTAAA
63 GTTACAGTGGAGCAGATTAAAGCCACAAATCTTATCTCCCTGAAATTGCAATGGAGCAAACCAAA
3184649 G-TGAACT-AATCCAAT-ACCTCTGAAGTTGCAGT
128 GAT--ACTAAATCCAATCACCT-TGAAGTTGCAGT
3184681 AGGTCGGATT
Statistics
Matches: 132, Mismatches: 24, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
183 31 0.23
185 10 0.08
186 89 0.67
187 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (183 bp):
TTATCTCCCTAAAGTTACAGTGGAGCAGATTGAAGACAAGATACAAATCTTATCTCCCTAAAGTT
ACAGTGGAGCAGATTAAAGCCACAAATCTTATCTCCCTGAAATTGCAATGGAGCAAACCAAAGAT
ACTAAATCCAATCACCTTGAAGTTGCAGTGGAGCAGACTGAAGATAATAAACC
Found at i:3192010 original size:33 final size:32
Alignment explanation
Indices: 3191973--3192043 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
3191963 ACTGTTTAGT
*
3191973 TATTACTT-ATTTTAAGTTCTCTTTTATATATTA
1 TATTA-TTCATTTTAAATTCT-TTTTATATATTA
* *
3192006 TATTATTCATTTTAAATTGTTTTTATATAGTA
1 TATTATTCATTTTAAATTCTTTTTATATATTA
3192038 T-TTATT
1 TATTATT
3192044 TTGAACTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 5 0.15
32 14 0.41
33 15 0.44
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (32 bp):
TATTATTCATTTTAAATTCTTTTTATATATTA
Found at i:3192039 original size:27 final size:26
Alignment explanation
Indices: 3192004--3192177 Score: 149
Period size: 27 Copynumber: 6.5 Consensus size: 26
3191994 TTTTATATAT
3192004 TATATTATTCATTTTAAATTGTTTTTA
1 TATATTATTCATTTTAAATTG-TTTTA
* * * *
3192031 TATAGTATTTATTTTGAACTGTTTTA
1 TATATTATTCATTTTAAATTGTTTTA
* *
3192057 T-TA-TATACTATTTTAAATTGTTTCA
1 TATATTATTC-ATTTTAAATTGTTTTA
* *
3192082 TATATTATT-ATTTTAAGTTGTTATA
1 TATATTATTCATTTTAAATTGTTTTA
*
3192107 TATATTATTCATCTTTAAACTGTTTTA
1 TATATTATTCAT-TTTAAATTGTTTTA
3192134 TATATATATT-ATTTATTTCAAATTGTTTTA
1 TATAT-TATTCA--T-TTT-AAATTGTTTTA
* *
3192164 TATGTTATTTATTT
1 TATATTATTCATTT
3192178 CGTTTTTCTT
Statistics
Matches: 118, Mismatches: 19, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
24 3 0.03
25 38 0.32
26 10 0.08
27 39 0.33
28 5 0.04
29 8 0.07
30 15 0.13
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.60
Consensus pattern (26 bp):
TATATTATTCATTTTAAATTGTTTTA
Found at i:3192124 original size:52 final size:52
Alignment explanation
Indices: 3191999--3192147 Score: 164
Period size: 52 Copynumber: 2.8 Consensus size: 52
3191989 TTCTCTTTTA
*
3191999 TATATTATATTATTCATTTTAAATTGTTTTTATATAGTATTTATTTTGAACTGTTT
1 TATA-TATATTATTCATTTTAAATTG-TTTTATATATTA-TTATTTTGAAC-GTTT
* *
3192055 TAT-TATA-TACT-ATTTTAAATTGTTTCATATATTATTATTTT-AA-GTTGT
1 TATATATATTATTCATTTTAAATTGTTTTATATATTATTATTTTGAACGTT-T
*
3192103 TATATATATTATTCATCTTTAAACTGTTTTATATATATATTATTT
1 TATATATATTATTCAT-TTTAAATTGTTTTATATAT-TATTATTT
3192148 ATTTCAAATT
Statistics
Matches: 81, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
47 3 0.04
48 4 0.05
49 6 0.07
50 10 0.12
51 12 0.15
52 28 0.35
53 11 0.14
54 4 0.05
56 3 0.04
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (52 bp):
TATATATATTATTCATTTTAAATTGTTTTATATATTATTATTTTGAACGTTT
Found at i:3192141 original size:31 final size:30
Alignment explanation
Indices: 3192103--3192166 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
3192093 TTTAAGTTGT
*
3192103 TATATATATTATTCATCTTTAAACTGTTTTA
1 TATATATATTATTCAT-TTCAAACTGTTTTA
* *
3192134 TATATATATTATTTATTTCAAATTGTTTTA
1 TATATATATTATTCATTTCAAACTGTTTTA
3192164 TAT
1 TAT
3192167 GTTATTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (30 bp):
TATATATATTATTCATTTCAAACTGTTTTA
Found at i:3192148 original size:25 final size:26
Alignment explanation
Indices: 3192004--3192147 Score: 136
Period size: 25 Copynumber: 5.5 Consensus size: 26
3191994 TTTTATATAT
*
3192004 TATAT-TATTCATTTTAAATTGTTTT-
1 TATATATATT-ATTTTAAACTGTTTTA
*
3192029 TATATAGTATTTATTTTGAACTGTTTTA
1 TATATA-TA-TTATTTTAAACTGTTTTA
* * *
3192057 T-TATATACTATTTTAAATTGTTTCA
1 TATATATATTATTTTAAACTGTTTTA
** *
3192082 TATAT-TATTATTTTAAGTTGTTATA
1 TATATATATTATTTTAAACTGTTTTA
3192107 TATAT-TATTCATCTTTAAACTGTTTTA
1 TATATATATT-AT-TTTAAACTGTTTTA
3192134 TATATATATTATTT
1 TATATATATTATTT
3192148 ATTTCAAATT
Statistics
Matches: 98, Mismatches: 13, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
25 45 0.46
26 9 0.09
27 37 0.38
28 7 0.07
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.59
Consensus pattern (26 bp):
TATATATATTATTTTAAACTGTTTTA
Found at i:3192780 original size:140 final size:140
Alignment explanation
Indices: 3192243--3193194 Score: 1023
Period size: 140 Copynumber: 7.0 Consensus size: 140
3192233 TACAACAAAA
* * * *
3192243 TAGTCCTAAGACGACACTTTTGTGGCGACACTTTCCTAAGTGTCGGGATAGACTGGCCAATATAC
1 TAGTCCTAAGACGACACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
* * * * * * *
3192308 GGTTTAGCCAACTATTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGT
66 GCTTTGGCCAACTCTTTGCATAAGGGTTGCGATATGTATGCCTAAGACAACGCTTAAATAAGAGT
3192373 TGGCTTTGTC
131 TGGCTTTGTC
* * * *
3192383 TAGTCCTAAGGCGACACTTTTGGGGTGACA-TTTCGTAGGTGTTGGGATAGACTTGCCAACATAC
1 TAGTCCTAAGACGACACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
* ** * * *
3192447 GCTTTCGCCAACTCTTTAAATAAGGGTTGGGATATGTATGCCTAAGGCAACGCTTGAATAAGAGT
66 GCTTTGGCCAACTCTTTGCATAAGGGTTGCGATATGTATGCCTAAGACAACGCTTAAATAAGAGT
*
3192512 TGGCTTTTGTG
131 TGGC-TTTGTC
*
3192523 TAGTCCTAAGACGACACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAT
1 TAGTCCTAAGACGACACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
*
3192588 GCTTTGGCCAGCTCTTTGCATAAGGGTTGCGATATGTATGCCTAAGACAACGCTTAAATAAGAGT
66 GCTTTGGCCAACTCTTTGCATAAGGGTTGCGATATGTATGCCTAAGACAACGCTTAAATAAGAGT
3192653 TGGCTTTTGTC
131 TGGC-TTTGTC
* *
3192664 TAGTCCTAAGACGACATTTTTGGGGCGACACTTTCCTAAGTGTT-GGATAGACTTGCCAACATAT
1 TAGTCCTAAGACGACACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
3192728 GCTTTGGCCAACTCTTTGCATAAGGGTTGCGATATGTATGCCTAAGACAACGCTTAAATAAGAGT
66 GCTTTGGCCAACTCTTTGCATAAGGGTTGCGATATGTATGCCTAAGACAACGCTTAAATAAGAGT
3192793 TGGCTTTGTC
131 TGGCTTTGTC
* * *
3192803 CAGTCCTAAGACGACA----T----------TTTCCTAAGTGTTGGGATAGACTTGTCGACATAC
1 TAGTCCTAAGACGACACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
** * * * * * * * *
3192854 TTTTTGGTCAACTTTTTGTACAAGGGTTGGGATATGCATGCTTAAGGCAACGCTTAAATAAGAGT
66 GCTTTGGCCAACTCTTTGCATAAGGGTTGCGATATGTATGCCTAAGACAACGCTTAAATAAGAGT
*
3192919 CGGCTTTGTC
131 TGGCTTTGTC
* * * * * * * * *
3192929 GA-ACACTATGCCTACACATTTGGGTCAACACTTTCCTAAGTGTTGGAATAGACTTGCCAACATA
1 TAGTC-CTAAGACGACACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATA
* * * * * **
3192993 CACTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACTTTTAAATAAGAG
65 CGCTTTGGCCAACTCTTTGCATAAGGGTTGCGATATGTATGCCTAAGACAACGCTTAAATAAGAG
*
3193058 TCGG--TT-T-
130 TTGGCTTTGTC
* * * * *
3193065 T-GTCC--A-A-G--AC-TAT--GCCAACACTTTCCTAAGTGTTGGGATAGACTTGTCAACATAT
1 TAGTCCTAAGACGACACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
* * * * * *
3193120 GCTTTGGCCAACTCTTTGTATAAGAGATG-GTATATGCATGCCTAAGGCAACACTTAAATAAGAG
66 GCTTTGGCCAACTCTTTGCATAAGGGTTGCG-ATATGTATGCCTAAGACAACGCTTAAATAAGAG
*
3193184 TTAGCTTTGTC
130 TTGGCTTTGTC
3193195 CAATAGTATG
Statistics
Matches: 709, Mismatches: 79, Indels: 58
0.84 0.09 0.07
Matches are distributed among these distances:
125 15 0.02
126 187 0.26
128 4 0.01
129 3 0.00
130 1 0.00
135 2 0.00
136 1 0.00
137 1 0.00
138 2 0.00
139 112 0.16
140 239 0.34
141 142 0.20
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (140 bp):
TAGTCCTAAGACGACACTTTTGGGGCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATAC
GCTTTGGCCAACTCTTTGCATAAGGGTTGCGATATGTATGCCTAAGACAACGCTTAAATAAGAGT
TGGCTTTGTC
Found at i:3192913 original size:126 final size:126
Alignment explanation
Indices: 3192691--3193196 Score: 559
Period size: 126 Copynumber: 3.9 Consensus size: 126
3192681 TTTTGGGGCG
*
3192691 ACACTTTCCTAAGTGTT-GGATAGACTTGCCAACATATGCTTTGGCCAACTCTTTGCATAAGGGT
1 ACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATATGCTTTGGCCAACTCTTTGTATAAGGGT
* * * * *
3192755 TGCGATATGTATGCCTAAGACAACGCTTAAATAAGAGTTGGCTTTGTCCAGTCCTAAGACG
66 TGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCAGTCCTAAGACA
* * * * * * *
3192816 ACATTTTCCTAAGTGTTGGGATAGACTTGTCGACATACT-TTTTGGTCAACTTTTTGTACAAGGG
1 ACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATA-TGCTTTGGCCAACTCTTTGTATAAGGG
* *
3192880 TTGGGATATGCATGCTTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCGAACACTATGCCTACA
65 TTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTC---CA--GT-CCT--A
*
3192945 CATTTGGGTCA
122 -A-----GACA
* **
3192956 ACACTTTCCTAAGTGTTGGAATAGACTTGCCAACATACACTTTGGCCAACTCTTTGTATAAGGGT
1 ACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATATGCTTTGGCCAACTCTTTGTATAAGGGT
** * * * *
3193021 TGGGATATGCATGCCTAAGGCAACTTTTAAATAAGAGTCGGTTTTGTCCAAG-ACTATGCCA
66 TGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCC-AGTCCTAAGACA
* * *
3193082 ACACTTTCCTAAGTGTTGGGATAGACTTGTCAACATATGCTTTGGCCAACTCTTTGTATAAGAGA
1 ACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATATGCTTTGGCCAACTCTTTGTATAAGGGT
* * **
3193147 TGGTATATGCATGCCTAAGGCAACACTTAAATAAGAGTTAGCTTTGTCCA
66 TGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCA
3193197 ATAGTATGTC
Statistics
Matches: 318, Mismatches: 45, Indels: 36
0.80 0.11 0.09
Matches are distributed among these distances:
125 17 0.05
126 186 0.58
127 1 0.00
129 2 0.01
131 1 0.00
132 4 0.01
134 3 0.01
135 1 0.00
137 1 0.00
138 1 0.00
140 101 0.32
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (126 bp):
ACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATATGCTTTGGCCAACTCTTTGTATAAGGGT
TGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCAGTCCTAAGACA
Found at i:3193037 original size:266 final size:265
Alignment explanation
Indices: 3192268--3193194 Score: 1016
Period size: 266 Copynumber: 3.4 Consensus size: 265
3192258 ACTTTTGTGG
* * * * * * * *
3192268 CGACACTTTCCTAAGTGTCGGGATAGACTGGCCAATATACGGTTTAGCCAACTATTTGTATAAGG
1 CGACACTTTCCTAAGTGTTGGGATAGACTTGTCAACATATGCTTTGGCCAACTCTTTGTATAAGG
* * *
3192333 GTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTTTGTCTAGTCCTAAGGCGAC
66 GTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTTTGTCGAGACCTAAGACGAC
* ** * * * *
3192398 ACTTTTGGGGTGACA-TTTCGTAGGTGTTGGGATAGACTTGCCAACATACGCTTTCGCCAACTCT
131 ACATTTGGGGCAACACTTTCCTAAGTGTT-GGATAGACTTGCCAACATACACTTTGGCCAACTCT
** * * * * *
3192462 TTAAATAAGGGTTGGGATATGTATGCCTAAGGCAACGCTTGAATAAGAGTTGGCTTTTGTGTAGT
195 TTGCATAAGGGTTGCGATATGCATGCCTAAGACAACGCTTAAATAAGAGTCGGC---T-T-T-GT
* *
3192527 CCTAAGACGACACTTTTGGGG
254 CC-AAGACTA-A-------GA
* * *
3192548 CGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATATGCTTTGGCCAGCTCTTTGCATAAGG
1 CGACACTTTCCTAAGTGTTGGGATAGACTTGTCAACATATGCTTTGGCCAACTCTTTGTATAAGG
* * * * *
3192613 GTTGCGATATGTATGCCTAAGACAACGCTTAAATAAGAGTTGGCTTTTGTCTAGTCCTAAGACGA
66 GTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGC-TTTGTCGAGACCTAAGACGA
** * **
3192678 CATTTTTGGGGCGACACTTTCCTAAGTGTTGGATAGACTTGCCAACATATGCTTTGGCCAACTCT
130 CACATTTGGGGCAACACTTTCCTAAGTGTTGGATAGACTTGCCAACATACACTTTGGCCAACTCT
* *
3192743 TTGCATAAGGGTTGCGATATGTATGCCTAAGACAACGCTTAAATAAGAGTTGGCTTTGTCC-AGT
195 TTGCATAAGGGTTGCGATATGCATGCCTAAGACAACGCTTAAATAAGAGTCGGCTTTGTCCAAG-
*
3192807 CCTAAGA
259 ACTAAGA
* * * * * *
3192814 CGACATTTTCCTAAGTGTTGGGATAGACTTGTCGACATACT-TTTTGGTCAACTTTTTGTACAAG
1 CGACACTTTCCTAAGTGTTGGGATAGACTTGTCAACATA-TGCTTTGGCCAACTCTTTGTATAAG
* * * * *
3192878 GGTTGGGATATGCATGCTTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCGA-ACACTATGCCT
65 GGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTTTGTCGAGAC-CTAAGACG
*
3192942 ACACATTTGGGTCAACACTTTCCTAAGTGTTGGAATAGACTTGCCAACATACACTTTGGCCAACT
129 ACACATTTGGGGCAACACTTTCCTAAGTGTTGG-ATAGACTTGCCAACATACACTTTGGCCAACT
* * * ** *
3193007 CTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACTTTTAAATAAGAGTCGGTTTTGTCCAA
193 CTTTGCATAAGGGTTGCGATATGCATGCCTAAGACAACGCTTAAATAAGAGTCGGCTTTGTCCAA
* *
3193072 GACTATGC
258 GACTAAGA
* *
3193080 CAACACTTTCCTAAGTGTTGGGATAGACTTGTCAACATATGCTTTGGCCAACTCTTTGTATAAGA
1 CGACACTTTCCTAAGTGTTGGGATAGACTTGTCAACATATGCTTTGGCCAACTCTTTGTATAAGG
* * * *
3193145 GATGGTATATGCATGCCTAAGGCAACACTTAAATAAGAGTTAGCTTTGTC
66 GTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTTTGTC
3193195 CAATAGTATG
Statistics
Matches: 562, Mismatches: 77, Indels: 30
0.84 0.12 0.04
Matches are distributed among these distances:
264 1 0.00
265 42 0.07
266 281 0.50
267 3 0.01
273 3 0.01
274 2 0.00
275 4 0.01
276 1 0.00
277 1 0.00
278 1 0.00
280 97 0.17
281 115 0.20
282 11 0.02
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (265 bp):
CGACACTTTCCTAAGTGTTGGGATAGACTTGTCAACATATGCTTTGGCCAACTCTTTGTATAAGG
GTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTTTGTCGAGACCTAAGACGAC
ACATTTGGGGCAACACTTTCCTAAGTGTTGGATAGACTTGCCAACATACACTTTGGCCAACTCTT
TGCATAAGGGTTGCGATATGCATGCCTAAGACAACGCTTAAATAAGAGTCGGCTTTGTCCAAGAC
TAAGA
Found at i:3193503 original size:7 final size:7
Alignment explanation
Indices: 3193475--3193556 Score: 60
Period size: 7 Copynumber: 11.9 Consensus size: 7
3193465 TTTCTTTGGT
3193475 TTTAGGG
1 TTTAGGG
* *
3193482 TTTAAGA
1 TTTAGGG
*
3193489 TTTGGGG
1 TTTAGGG
3193496 TTTAGGG
1 TTTAGGG
3193503 TTTAGGG
1 TTTAGGG
3193510 TTT-GCGG
1 TTTAG-GG
**
3193517 TTTAAAG
1 TTTAGGG
* *
3193524 -TCATGG
1 TTTAGGG
*
3193530 TTTATGG
1 TTTAGGG
*
3193537 TTTAAGG
1 TTTAGGG
3193544 TTTAGGG
1 TTTAGGG
3193551 TTTAGG
1 TTTAGG
3193557 TTTTTGTAAA
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
6 4 0.07
7 54 0.93
ACGTcount: A:0.18, C:0.02, G:0.35, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:3194756 original size:35 final size:35
Alignment explanation
Indices: 3194710--3194792 Score: 157
Period size: 35 Copynumber: 2.4 Consensus size: 35
3194700 TCTGCCCTAT
*
3194710 TCCAGCCACTGGTGCATCTGCCGTCGACCACCTGC
1 TCCAGCCACTGGTGCATCTGCCGTCCACCACCTGC
3194745 TCCAGCCACTGGTGCATCTGCCGTCCACCACCTGC
1 TCCAGCCACTGGTGCATCTGCCGTCCACCACCTGC
3194780 TCCAGCCACTGGT
1 TCCAGCCACTGGT
3194793 ATGTCACGGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.14, C:0.43, G:0.22, T:0.20
Consensus pattern (35 bp):
TCCAGCCACTGGTGCATCTGCCGTCCACCACCTGC
Found at i:3206443 original size:35 final size:35
Alignment explanation
Indices: 3206404--3206489 Score: 138
Period size: 35 Copynumber: 2.4 Consensus size: 35
3206394 TATCCCGACC
*
3206404 TTTTTAAGTTTGCCTTAGACGGGTTTATCCTAACT-
1 TTTTTAAG-TTGCCTTAGACGGGTTTATCCCAACTG
3206439 TTTTTAAGGTTGCCTTAGACGGGTTTATCCCAACTG
1 TTTTTAA-GTTGCCTTAGACGGGTTTATCCCAACTG
3206475 TTTTTAAGTTGCCTT
1 TTTTTAAGTTGCCTT
3206490 GGAAAAGGTC
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
35 40 0.83
36 8 0.17
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (35 bp):
TTTTTAAGTTGCCTTAGACGGGTTTATCCCAACTG
Found at i:3206645 original size:108 final size:105
Alignment explanation
Indices: 3206533--3207063 Score: 300
Period size: 111 Copynumber: 4.8 Consensus size: 105
3206523 TGTAAATGGG
* *
3206533 TCTATCCCAACATTTTTAACGTTGTCTTAGATAGGTCAATCCCAACCTTTTCTAAAAGTTGCTTT
1 TCTATCCCAACATTTTTAACGTTG-CTTAGA-AGGTCTATCCCAACCTTTT-TAAAAGTTGCCTT
* * *
3206598 AGACAAGATCTATTCCAACCTTTTGGAGGTTACCTTAGACGA-A
63 AGACAAG-TCTATTCCAACCTTTTGAAGGTTACCTTAAACAAGA
* * * ** * *
3206641 TCTATCCCAACCTTTTTAAGGTTGCTTTAGACAAGTCTATCGTAACCTTTTTTTAAGGTTGCCTT
1 TCTATCCCAACATTTTTAACGTTGC-TTAGA-AGGTCTATCCCAACC-TTTTTAAAAGTTGCCTT
* * *
3206706 AAACAAGTCTA-TCTCAACCCTTTTTTAAGGTTGCCTTAAACAAGA
63 AGACAAGTCTATTC-CAA-CC-TTTTGAAGGTTACCTTAAACAAGA
* * *
3206751 TCTATCCCAACCTTTTTTAAATGTTGCCTTAGGCAAGGTCTATCCCAACATTTTTAAAAGGTTGC
1 TCTATCCCAA-CATTTTT-AACGTTG-CTTA-G-AAGGTCTATCCCAACCTTTTTAAAA-GTTGC
* * * * * * *
3206816 CTTAGATAAGGTCTATCCCAACCTTTTTTAAAGGTTGCCCTAGACAAGG
60 CTTAGACAA-GTCTATTCCAACC--TTTTGAAGGTTACCTTAAACAAGA
* * * * * * *
3206865 TCTA-CACCAACCTATTTAAGGTTGCTTTAGACGATTCTATCCCAATCTTTTTTAAAGGTTGCCT
1 TCTATC-CCAACATTTTTAACGTTGC-TTAGAAG-GTCTATCCCAA-CCTTTTTAAAAGTTGCCT
* * * * * * * * *
3206929 TAGACAAGGTTTA-TCGCAACTTTTTTTAAATGTTTCCTTAGATATGG
62 TAGACAA-GTCTATTC-CAAC--CTTTTGAAGGTTACCTTAAACAAGA
* * * * *
3206976 TCTATCCCAACTTTTTTTAAAGGTTATCTTAGACTGGTCTATCCCAACCTTTTT-AAGGTTGCCT
1 TCTATCCCAAC-ATTTTT-AACGTT-GCTTAGA-AGGTCTATCCCAACCTTTTTAAAAGTTGCCT
* *
3207040 TAAACAGGTCTA-TCACAACCTTTT
62 TAGACAAGTCTATTC-CAACCTTTT
3207064 TCAAAGGTTG
Statistics
Matches: 338, Mismatches: 58, Indels: 54
0.75 0.13 0.12
Matches are distributed among these distances:
106 2 0.01
107 8 0.02
108 60 0.18
109 21 0.06
110 24 0.07
111 83 0.25
112 45 0.13
113 54 0.16
114 40 0.12
115 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (105 bp):
TCTATCCCAACATTTTTAACGTTGCTTAGAAGGTCTATCCCAACCTTTTTAAAAGTTGCCTTAGA
CAAGTCTATTCCAACCTTTTGAAGGTTACCTTAAACAAGA
Found at i:3206863 original size:259 final size:257
Alignment explanation
Indices: 3206391--3207109 Score: 672
Period size: 259 Copynumber: 2.8 Consensus size: 257
3206381 TGAGACAAAT
* * * *
3206391 ATCTATCCCGA-CCTTTTT-AAGTTTGCCTTAGAC-GGGTTTATC-CTAAC-TTTTTT-AAGGTT
1 ATCTATCCCAATCCTTTTTAAAGGTTGCCTTAGACAAGGTCTATCGC-AACTTTTTTTAAAGGTT
* ** * * * *
3206450 GCCTTAGAC-GGGTTTATCCCAA-CTGTTTTT-AA-GTTGCCTTGGAAA-AGGTCTATCTCAA-C
65 GCCTTAAACATAGTCTATCCCAACCT-TTTTTAAAGGTTACCTT--AAACAGATCTATCCCAACC
* ** * * *
3206509 TTATTTAAGGTTG-TTGTAAATGGGTCTATCCCAACATTTTT-AACGTTGTCTTAGATAGGTCAA
127 TT-TTTAAGGTTGCCT-TAAACAGGTCTATCCCAACATTTTTAAAGGTTGCCTTAGATAGGTCTA
* * ** ** *
3206572 TCCCAACCTTTTCTAAAAGTTGCTTTAGACAAGATCTATTCCAACCT-TTTGGAGGTTACCTTAG
190 TCCCAACCTTTTTTAAAGGTTGCCCTAGACAAGATCTACACCAACCTATTT-AAGGTTACCTTAG
3206636 ACGA
254 ACGA
* *
3206640 ATCTATCCCAA-CCTTTTT-AAGGTTGCTTTAGACAA-GTCTATCGTAACCTTTTTTT-AAGGTT
1 ATCTATCCCAATCCTTTTTAAAGGTTGCCTTAGACAAGGTCTATCGCAA-CTTTTTTTAAAGGTT
* *
3206701 GCCTTAAACA-AGTCTATCTCAACCCTTTTTT-AAGGTTGCCTTAAACAAGATCTATCCCAACCT
65 GCCTTAAACATAGTCTATCCCAA-CCTTTTTTAAAGGTTACCTTAAAC-AGATCTATCCCAACC-
* **
3206764 TTTTTAAATGTTGCCTTAGGCAAGGTCTATCCCAACATTTTTAAAAGGTTGCCTTAGATAAGGTC
127 TTTTT-AAGGTTGCCTTAAAC-AGGTCTATCCCAACATTTTT-AAAGGTTGCCTTAGAT-AGGTC
* * *
3206829 TATCCCAACCTTTTTTAAAGGTTGCCCTAGACAAGGTCTACACCAACCTATTTAAGGTTGCTTTA
188 TATCCCAACCTTTTTTAAAGGTTGCCCTAGACAAGATCTACACCAACCTATTTAAGGTTACCTTA
3206894 GACGA
253 GACGA
* * * * *
3206899 TTCTATCCCAATCTTTTTTAAAGGTTGCCTTAGACAAGGTTTATCGCAACTTTTTTTAAATGTTT
1 ATCTATCCCAATCCTTTTTAAAGGTTGCCTTAGACAAGGTCTATCGCAACTTTTTTTAAAGGTTG
* * * * * * * *
3206964 CCTTAGATATGGTCTATCCCAACTTTTTTTAAAGGTTATCTTAGACTGGTCTATCCCAACCTTTT
66 CCTTAAACATAGTCTATCCCAACCTTTTTTAAAGGTTACCTTAAACAGATCTATCCCAACCTTTT
* * *
3207029 TAAGGTTGCCTTAAACAGGTCTATCACAACCTTTTTCAAAGGTTGGCCTT-GACTAGGTCTATCG
131 TAAGGTTGCCTTAAACAGGTCTATCCCAACATTTTT-AAAGGTT-GCCTTAGA-TAGGTCTATCC
3207093 CAACCTTTTTTAAAGGT
193 CAACCTTTTTTAAAGGT
3207110 CGGCATTGAC
Statistics
Matches: 388, Mismatches: 55, Indels: 44
0.80 0.11 0.09
Matches are distributed among these distances:
249 38 0.10
250 1 0.00
251 32 0.08
252 7 0.02
253 21 0.05
254 4 0.01
255 10 0.03
256 20 0.05
258 13 0.03
259 123 0.32
260 27 0.07
261 29 0.07
262 41 0.11
263 22 0.06
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (257 bp):
ATCTATCCCAATCCTTTTTAAAGGTTGCCTTAGACAAGGTCTATCGCAACTTTTTTTAAAGGTTG
CCTTAAACATAGTCTATCCCAACCTTTTTTAAAGGTTACCTTAAACAGATCTATCCCAACCTTTT
TAAGGTTGCCTTAAACAGGTCTATCCCAACATTTTTAAAGGTTGCCTTAGATAGGTCTATCCCAA
CCTTTTTTAAAGGTTGCCCTAGACAAGATCTACACCAACCTATTTAAGGTTACCTTAGACGA
Found at i:3207064 original size:35 final size:35
Alignment explanation
Indices: 3206392--3207102 Score: 509
Period size: 38 Copynumber: 19.5 Consensus size: 35
3206382 GAGACAAATA
* * *
3206392 TCTATCCCGACCTTTTTAAGTTTGCCTTAGACGGG
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAGG
* * * *
3206427 TTTATCCTAACTTTTTTAAGGTTGCCTTAGACGGG
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAGG
* * * *
3206462 TTTATCCCAACTGTTTTTAA-GTTGCCTTGGAAAAGG
1 TCTATCCCAAC-CTTTTTAAGGTTGCCTTAG-ACAGG
* * * **
3206498 TCTATCTCAA-CTTATTTAAGGTTG-TTGTAAATGGG
1 TCTATCCCAACCTT-TTTAAGGTTGCCT-TAGACAGG
* * * *
3206533 TCTATCCCAACATTTTTAACGTTGTCTTAGATAGG
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAGG
* * * *
3206568 TCAATCCCAACCTTTTCTAAAAGTTGCTTTAGACAAGA
1 TCTATCCCAACCTTTT-T-AAGGTTGCCTTAGAC-AGG
* ** * *
3206606 TCTATTCCAACCTTTTGGAGGTTACCTTAGAC-GAA
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAG-G
* *
3206641 TCTATCCCAACCTTTTTAAGGTTGCTTTAGACAAG
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAGG
** * *
3206676 TCTATCGTAACCTTTTTTTAAGGTTGCCTTAAACAAG
1 TCTATCCCAACC--TTTTTAAGGTTGCCTTAGACAGG
* * *
3206713 TCTATCTCAACCCTTTTTTAAGGTTGCCTTAAACAAGA
1 TCTATCCCAA-CC-TTTTTAAGGTTGCCTTAGAC-AGG
* *
3206751 TCTATCCCAACCTTTTTTAAATGTTGCCTTAGGCAAGG
1 TCTATCCCAACC-TTTTT-AAGGTTGCCTTAGAC-AGG
* *
3206789 TCTATCCCAACATTTTTAAAAGGTTGCCTTAGATAAGG
1 TCTATCCCAACCTTTTT--AAGGTTGCCTTAGA-CAGG
*
3206827 TCTATCCCAACCTTTTTTAAAGGTTGCCCTAGACAAGG
1 TCTATCCCAACC-TTTTT-AAGGTTGCCTTAGAC-AGG
* * *
3206865 TCTA-CACCAACCTATTTAAGGTTGCTTTAGAC-GAT
1 TCTATC-CCAACCTTTTTAAGGTTGCCTTAGACAG-G
*
3206900 TCTATCCCAATCTTTTTTAAAGGTTGCCTTAGACAAGG
1 TCTATCCCAA-CCTTTTT-AAGGTTGCCTTAGAC-AGG
* * * * * *
3206938 TTTATCGCAACTTTTTTTAAATGTTTCCTTAGATATGG
1 TCTATCCCAAC-CTTTTT-AAGGTTGCCTTAGACA-GG
* ** *
3206976 TCTATCCCAACTTTTTTTAAAGGTTATCTTAGACTGG
1 TCTATCCCAAC-CTTTTT-AAGGTTGCCTTAGACAGG
*
3207013 TCTATCCCAACCTTTTTAAGGTTGCCTTAAACAGG
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAGG
*
3207048 TCTATCACAACCTTTTTCAAAGGTTGGCCTT-GACTAGG
1 TCTATCCCAACCTTTTT--AAGGTT-GCCTTAGAC-AGG
*
3207086 TCTATCGCAACCTTTTT
1 TCTATCCCAACCTTTTT
3207103 TAAAGGTCGG
Statistics
Matches: 549, Mismatches: 93, Indels: 65
0.78 0.13 0.09
Matches are distributed among these distances:
34 4 0.01
35 172 0.31
36 62 0.11
37 116 0.21
38 189 0.34
39 6 0.01
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (35 bp):
TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAGG
Found at i:3207139 original size:39 final size:38
Alignment explanation
Indices: 3207049--3207152 Score: 118
Period size: 38 Copynumber: 2.7 Consensus size: 38
3207039 TTAAACAGGT
* * * * * *
3207049 CTATCACAACCTTTTTCAAAGGTTGGCCTTGACTAGGT
1 CTATCGCAACCTTTTTTAAAGGTCGGCATTGACTAAGC
3207087 CTATCGCAACCTTTTTTAAAGGTCGGCATTGACTAAGC
1 CTATCGCAACCTTTTTTAAAGGTCGGCATTGACTAAGC
* **
3207125 CTTTCGCAACCCTTTAATAAAGGTCGGC
1 CTATCGCAA-CCTTTTTTAAAGGTCGGC
3207153 TTATGTTGAC
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
38 40 0.71
39 16 0.29
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (38 bp):
CTATCGCAACCTTTTTTAAAGGTCGGCATTGACTAAGC
Found at i:3211986 original size:148 final size:145
Alignment explanation
Indices: 3211714--3212142 Score: 587
Period size: 146 Copynumber: 2.9 Consensus size: 145
3211704 TTAAATAAAT
* * * * * * * *
3211714 TGATAATTGTGCATAATAAAACTCGAATATGAGCCCCAAATTTTATTTGTTGAGGAAAGGTATAG
1 TGATAATTGTGTATAATAAAACTCGAATTTGGGTCTCAAATTTTAATTGTTAAGGAAAGCTATAG
* * *
3211779 TTTTGATTTGAACAATGTAACCTTTCACAT-CTTTAACATTTTATCTTGTTTTCAGAGGATGAGT
66 TTTTTATTTGAACAATGTAA-CTTTC-CATGCTATAACATTTTATCTTGTTTTCAAAGGATGAGT
3211843 CACATTAGAGACTCACATA
129 CACATTAGAGACT--CATA
3211862 TGATAATTGTGTATAATAAAACTCGAATTTGGGTCTCAAATTTTAATTGCTT-AGGAAAGCTATA
1 TGATAATTGTGTATAATAAAACTCGAATTTGGGTCTCAAATTTTAATTG-TTAAGGAAAGCTATA
* * *
3211926 GTTTTTATTTGAACAATGTAACTTTCTATGCCTCTAATATTTTATCTTGTTTTCAAAGGATGAGT
65 GTTTTTATTTGAACAATGTAACTTTCCATG-CTATAACATTTTATCTTGTTTTCAAAGGATGAGT
3211991 CACATTAGAGACTCATA
129 CACATTAGAGACTCATA
* *
3212008 TGAAAATTGTGTATAATAAAACTCGAATTTGGGTCTCAAATTTTAATTGTTAAGGAGAGCTATAG
1 TGATAATTGTGTATAATAAAACTCGAATTTGGGTCTCAAATTTTAATTGTTAAGGAAAGCTATAG
* *
3212073 TTTTTATTTGAACAATGTAAAC-CTCCATGTCTATAACATTTTATCTTGTTCTCAAATGG-TGAG
66 TTTTTATTTGAACAATGT-AACTTTCCATG-CTATAACATTTTATCTTGTTTTCAAA-GGATGAG
3212136 TCACATT
128 TCACATT
3212143 GGATATTCAC
Statistics
Matches: 255, Mismatches: 20, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
145 2 0.01
146 123 0.48
147 10 0.04
148 118 0.46
149 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.39
Consensus pattern (145 bp):
TGATAATTGTGTATAATAAAACTCGAATTTGGGTCTCAAATTTTAATTGTTAAGGAAAGCTATAG
TTTTTATTTGAACAATGTAACTTTCCATGCTATAACATTTTATCTTGTTTTCAAAGGATGAGTCA
CATTAGAGACTCATA
Found at i:3213668 original size:40 final size:40
Alignment explanation
Indices: 3213624--3213743 Score: 116
Period size: 41 Copynumber: 3.0 Consensus size: 40
3213614 TGTAAAACAT
*
3213624 AGAGCAATAGTGGCG-TTTTACCAAAAACGCCGCTAAAAAC
1 AGAGCAATAGCGGCGCTTTT-CCAAAAACGCCGCTAAAAAC
* *** *
3213664 AGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAATA
1 AGAGCAATAGCGGCGCTTTTCCAAAAACGCCGCTAAAAA-C
* *** *
3213705 AGAGCATTAGCGGCGCTTTTGGTAAAACACCGCTAAAAA
1 AGAGCAATAGCGGCGCTTTTCCAAAAACGCCGCTAAAAA
3213744 GTTTAGGGTT
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
40 29 0.41
41 42 0.59
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.20
Consensus pattern (40 bp):
AGAGCAATAGCGGCGCTTTTCCAAAAACGCCGCTAAAAAC
Found at i:3213720 original size:41 final size:40
Alignment explanation
Indices: 3213647--3213743 Score: 167
Period size: 41 Copynumber: 2.4 Consensus size: 40
3213637 CGTTTTACCA
*
3213647 AAAACGCCGCTAAAAACAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAAAAGAGCATTAGCGGCGCTTTTGGT
3213687 AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAA-AAGAGCATTAGCGGCGCTTTTGGT
*
3213728 AAAACACCGCTAAAAA
1 AAAACGCCGCTAAAAA
3213744 GTTTAGGGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
40 16 0.30
41 38 0.70
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.19
Consensus pattern (40 bp):
AAAACGCCGCTAAAAAAAGAGCATTAGCGGCGCTTTTGGT
Found at i:3213841 original size:21 final size:22
Alignment explanation
Indices: 3213817--3213860 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
3213807 GGTTTATGTA
*
3213817 TTATGGTTTAAGGGTT-GGGGT
1 TTATGATTTAAGGGTTAGGGGT
3213838 TTATGATTTAAGGGTTAGGGGT
1 TTATGATTTAAGGGTTAGGGGT
3213860 T
1 T
3213861 AGGGGTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.18, C:0.00, G:0.39, T:0.43
Consensus pattern (22 bp):
TTATGATTTAAGGGTTAGGGGT
Found at i:3213859 original size:28 final size:28
Alignment explanation
Indices: 3213828--3213881 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
3213818 TATGGTTTAA
* *
3213828 GGGTT-GGGGTTTATGATTTAAGGGTTAG
1 GGGTTAGGGGTTAAT-ACTTAAGGGTTAG
3213856 GGGTTAGGGGTTAATACTTAAGGGTT
1 GGGTTAGGGGTTAATACTTAAGGGTT
3213882 TTTATTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.20, C:0.02, G:0.41, T:0.37
Consensus pattern (28 bp):
GGGTTAGGGGTTAATACTTAAGGGTTAG
Found at i:3214116 original size:21 final size:21
Alignment explanation
Indices: 3214090--3214133 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3214080 TTATGGTTAG
* *
3214090 GGGATATAGTTTAGGGTTTAA
1 GGGATATACTTTAGGGATTAA
3214111 GGGATATACTTTAGGGATTAA
1 GGGATATACTTTAGGGATTAA
3214132 GG
1 GG
3214134 TTATAGGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.02, G:0.34, T:0.34
Consensus pattern (21 bp):
GGGATATACTTTAGGGATTAA
Found at i:3214467 original size:15 final size:15
Alignment explanation
Indices: 3214447--3214495 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
3214437 TTCCCCGATT
3214447 TCCCCCAACTTCTTC
1 TCCCCCAACTTCTTC
*
3214462 TCCCCCAA---ATT-
1 TCCCCCAACTTCTTC
3214473 TCCCCCAACTTCTTC
1 TCCCCCAACTTCTTC
*
3214488 TCCTCCAA
1 TCCCCCAA
3214496 AATTTTTACC
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
11 8 0.30
12 2 0.07
14 2 0.07
15 15 0.56
ACGTcount: A:0.18, C:0.51, G:0.00, T:0.31
Consensus pattern (15 bp):
TCCCCCAACTTCTTC
Found at i:3214479 original size:26 final size:26
Alignment explanation
Indices: 3214444--3214496 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
3214434 AATTTCCCCG
3214444 ATTTCCCCCAACTTCTTCTCCCCCAA
1 ATTTCCCCCAACTTCTTCTCCCCCAA
*
3214470 ATTTCCCCCAACTTCTTCTCCTCCAA
1 ATTTCCCCCAACTTCTTCTCCCCCAA
3214496 A
1 A
3214497 ATTTTTACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.21, C:0.47, G:0.00, T:0.32
Consensus pattern (26 bp):
ATTTCCCCCAACTTCTTCTCCCCCAA
Found at i:3217341 original size:14 final size:13
Alignment explanation
Indices: 3217318--3217347 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
3217308 ATTACTATAA
3217318 TAATTATATGAAG
1 TAATTATATGAAG
3217331 TAATATATATGAAG
1 TAAT-TATATGAAG
3217345 TAA
1 TAA
3217348 AATTATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (13 bp):
TAATTATATGAAG
Found at i:3217726 original size:183 final size:183
Alignment explanation
Indices: 3217418--3217969 Score: 1068
Period size: 183 Copynumber: 3.0 Consensus size: 183
3217408 GATATAGTTC
* * * *
3217418 CATGTGTCTATATTAGTGAATTAATGTTGTATATGTTTCAGTTACTGCTTCCTGCTCCTCCTGCA
1 CATGTGTCTGTATTAGTGAATTAATGTTGTATGTATTTCAGTTACTGATTCCTGCTCCTCCTGCA
3217483 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACCGATATAGATAAA
66 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACCGATATAGATAAA
3217548 GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
131 GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
3217601 CATGTGTCTGTATTAGTGAATTAATGTTGTATGTATTTCAGTTACTGATTCCTGCTCCTCCTGCA
1 CATGTGTCTGTATTAGTGAATTAATGTTGTATGTATTTCAGTTACTGATTCCTGCTCCTCCTGCA
3217666 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACCGATATAGATAAA
66 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACCGATATAGATAAA
3217731 GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
131 GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
3217784 CATGTGTCTGTATTAGTGAATTAATGTTGTATGTATTTCAGTTACTGATTCCTGCTCCTCCTGCA
1 CATGTGTCTGTATTAGTGAATTAATGTTGTATGTATTTCAGTTACTGATTCCTGCTCCTCCTGCA
3217849 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACCGATATAGATAAA
66 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACCGATATAGATAAA
3217914 GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
131 GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
3217967 CAT
1 CAT
3217970 CTGTTCTAGG
Statistics
Matches: 365, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 365 1.00
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (183 bp):
CATGTGTCTGTATTAGTGAATTAATGTTGTATGTATTTCAGTTACTGATTCCTGCTCCTCCTGCA
ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACCGATATAGATAAA
GTTTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
Found at i:3218190 original size:15 final size:15
Alignment explanation
Indices: 3218170--3218198 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3218160 GGAGTAGACC
3218170 AGGTACGTTTTATTA
1 AGGTACGTTTTATTA
3218185 AGGTACGTTTTATT
1 AGGTACGTTTTATT
3218199 TCAAAATTCT
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:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (15 bp):
AGGTACGTTTTATTA
Found at i:3219060 original size:30 final size:30
Alignment explanation
Indices: 3219024--3219138 Score: 95
Period size: 30 Copynumber: 3.4 Consensus size: 30
3219014 TTTACGATTC
3219024 TTTTTTTATATTATTATATTCAAATTACTA
1 TTTTTTTATATTATTATATTCAAATTACTA
* * *
3219054 TTTTTTTATATTAATAATGTTTGATTTTAATATTTACGATTC
1 TTTTTTTATA-T--T-AT-TAT-A-TTCAA-A-TTAC---TA
3219096 TTTTTTTATATTATTATATTCAAATTACTA
1 TTTTTTTATATTATTATATTCAAATTACTA
3219126 TTTTTTTATATTA
1 TTTTTTTATATTA
3219139 ATAATGTTTG
Statistics
Matches: 67, Mismatches: 6, Indels: 24
0.69 0.06 0.25
Matches are distributed among these distances:
30 24 0.36
31 1 0.01
33 5 0.07
34 3 0.04
35 6 0.09
36 2 0.03
37 6 0.09
38 3 0.04
39 5 0.07
41 1 0.01
42 11 0.16
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTTTTTATATTATTATATTCAAATTACTA
Found at i:3219074 original size:72 final size:72
Alignment explanation
Indices: 3218946--3219178 Score: 429
Period size: 72 Copynumber: 3.3 Consensus size: 72
3218936 AAAATTAAAC
3218946 TACGATTC-TTTTTTATATTATTATATTCAAATTACTA-TTTTTTATATTAATAATGTTTGATTT
1 TACGATTCTTTTTTTATATTATTATATTCAAATTACTATTTTTTTATATTAATAATGTTTGATTT
3219009 TAATATT
66 TAATATT
3219016 TACGATTCTTTTTTTATATTATTATATTCAAATTACTATTTTTTTATATTAATAATGTTTGATTT
1 TACGATTCTTTTTTTATATTATTATATTCAAATTACTATTTTTTTATATTAATAATGTTTGATTT
3219081 TAATATT
66 TAATATT
3219088 TACGATTCTTTTTTTATATTATTATATTCAAATTACTATTTTTTTATATTAATAATGTTTGATTT
1 TACGATTCTTTTTTTATATTATTATATTCAAATTACTATTTTTTTATATTAATAATGTTTGATTT
*
3219153 T-TTA-T
66 TAATATT
3219158 TACGATTCTTTTTTTATATTA
1 TACGATTCTTTTTTTATATTA
3219179 ATATGTACTT
Statistics
Matches: 160, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
70 30 0.19
71 31 0.19
72 99 0.62
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (72 bp):
TACGATTCTTTTTTTATATTATTATATTCAAATTACTATTTTTTTATATTAATAATGTTTGATTT
TAATATT
Done.