Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 8 of 79
Found at i:2809490 original size:24 final size:23
Alignment explanation
Indices: 2809463--2809531 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
2809453 AGACTGAGCC
*
2809463 TGAAGCTGAAGATGAAGATGAAGA
1 TGAAG-TGAAGATGAGGATGAAGA
*
2809487 TGAAAGTGAAGATGAGGATGGAGA
1 TG-AAGTGAAGATGAGGATGAAGA
**
2809511 TGGGGATGAAGATGAGGATGA
1 TGAAG-TGAAGATGAGGATGA
2809532 CGAAGAAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 34 0.89
25 3 0.08
ACGTcount: A:0.41, C:0.01, G:0.41, T:0.17
Consensus pattern (23 bp):
TGAAGTGAAGATGAGGATGAAGA
Found at i:2809542 original size:6 final size:6
Alignment explanation
Indices: 2809530--2809560 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2809520 AGATGAGGAT
*
2809530 GACGAA GAAGAA GACGAA GACGAA GACGAA G
1 GACGAA GACGAA GACGAA GACGAA GACGAA G
2809561 CCGACGCCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.13, G:0.35, T:0.00
Consensus pattern (6 bp):
GACGAA
Found at i:2811940 original size:31 final size:31
Alignment explanation
Indices: 2811905--2811984 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
2811895 TATTTTTCAT
* *
2811905 TTGCTTCAATTTCTATGCTTATTCC-CCGTTA
1 TTGCTTCAATTTCCATGCTTATACCTCC-TTA
*
2811936 TTGCTTCAATTTCCATGATTATACCTCCTTA
1 TTGCTTCAATTTCCATGCTTATACCTCCTTA
2811967 TTGCTTCAATTTCCATGC
1 TTGCTTCAATTTCCATGC
2811985 CTTACAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 42 0.95
32 2 0.05
ACGTcount: A:0.19, C:0.26, G:0.09, T:0.46
Consensus pattern (31 bp):
TTGCTTCAATTTCCATGCTTATACCTCCTTA
Found at i:2819066 original size:20 final size:21
Alignment explanation
Indices: 2819023--2819066 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2819013 TATTTTTTCG
2819023 ATTGAGAAAAATCCTCTGACT
1 ATTGAGAAAAATCCTCTGACT
* *
2819044 ATTGAGAAGAATCTTCT-ACT
1 ATTGAGAAAAATCCTCTGACT
2819064 ATT
1 ATT
2819067 TTTAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (21 bp):
ATTGAGAAAAATCCTCTGACT
Found at i:2820109 original size:26 final size:26
Alignment explanation
Indices: 2820066--2820117 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
2820056 CCCTAGCGAG
*
2820066 CTTGAGTTTAAGTGGGTC-GAAGGACC
1 CTTGAATTTAAGTGGGTCAG-AGGACC
* *
2820092 CTTGAATTTGAGTTGGTCAGAGGACC
1 CTTGAATTTAAGTGGGTCAGAGGACC
2820118 ATGAACGGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.29
Consensus pattern (26 bp):
CTTGAATTTAAGTGGGTCAGAGGACC
Found at i:2821733 original size:194 final size:194
Alignment explanation
Indices: 2821363--2821740 Score: 465
Period size: 194 Copynumber: 1.9 Consensus size: 194
2821353 ATGGAGTATG
* * * * ***
2821363 TCATAGCCAACACCCAGCCTGGTAAAATATTGTCCGCTTTGGGTGCACATGGCCTCATGGTTTTG
1 TCATAGCCAACACCCAGCCCGGTAAAATATTGTCCGCCTTGAGCGCACATGGCCTCATAACTTTG
* ** * * *
2821428 TTCTTGGGAGCGCCCATACACCCCCAAAAGGCCTATTTCCATTAAAGTGTTGCTACTCCTTTATA
66 TTCTTGGAAAAGCCCATACACCCCCAAAAGGCCTATTTCCATTAAAGTGTTACTACCCCTGTATA
* * *
2821493 TAGCCCAGGTCCCTCCCGTGTTTTACCGATGTGAGATTTGCCTAGGGTGTTACATTGATAAATT
131 TAGCCCAGGTCCCTCCCATGCTTTACCAATGTGAGATTTGCCTAGGGTGTTACATTGATAAATT
* *
2821557 TCATAGCCAACACCCATCCCGGTAAGATATTGTCCGCCTTGAGCGCACATGGCCCTCATAACTTT
1 TCATAGCCAACACCCAGCCCGGTAAAATATTGTCCGCCTTGAGCGCACATGG-CCTCATAACTTT
** * * *
2821622 GTTCTTGGAAAAGGTCATAGACCCTCAAAAGGCCTCTTTCCACTT-AAGTGTTACTACCCCTGTA
65 GTTCTTGGAAAAGCCCATACACCCCCAAAAGGCCTATTTCCA-TTAAAGTGTTACTACCCCTGTA
* * * *
2821686 TATA-CGCAGGTCTCTCCCATGCTTTGCCAATGTG-GAATTTTCCTAGGGTGTTACA
129 TATAGCCCAGGTCCCTCCCATGCTTTACCAATGTGAG-ATTTGCCTAGGGTGTTACA
2821741 GAGTACGTAA
Statistics
Matches: 154, Mismatches: 27, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
193 1 0.01
194 88 0.57
195 63 0.41
196 2 0.01
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (194 bp):
TCATAGCCAACACCCAGCCCGGTAAAATATTGTCCGCCTTGAGCGCACATGGCCTCATAACTTTG
TTCTTGGAAAAGCCCATACACCCCCAAAAGGCCTATTTCCATTAAAGTGTTACTACCCCTGTATA
TAGCCCAGGTCCCTCCCATGCTTTACCAATGTGAGATTTGCCTAGGGTGTTACATTGATAAATT
Found at i:2822998 original size:17 final size:17
Alignment explanation
Indices: 2822976--2823022 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
2822966 AAAAAGTATT
*
2822976 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
*
2822993 TTAAAAAAATTTAAAAA
1 TTAAAAATATTTAAAAA
* *
2823010 ATAAATATATTTA
1 TTAAAAATATTTA
2823023 TTATATCGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:2828518 original size:15 final size:15
Alignment explanation
Indices: 2828498--2828528 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2828488 GAACCCATTT
2828498 GCGAACCTCAGGTTG
1 GCGAACCTCAGGTTG
*
2828513 GCGAACCTTAGGTTG
1 GCGAACCTCAGGTTG
2828528 G
1 G
2828529 ATATCTGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.23, G:0.35, T:0.23
Consensus pattern (15 bp):
GCGAACCTCAGGTTG
Found at i:2832963 original size:5 final size:5
Alignment explanation
Indices: 2832947--2832976 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
2832937 TATTTGTATT
2832947 CTTCC C-TCC CTTCC CTTCC CTTCC CTTCC C
1 CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC C
2832977 GTGAACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (5 bp):
CTTCC
Found at i:2834690 original size:16 final size:16
Alignment explanation
Indices: 2834669--2834700 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2834659 AGTAATATGA
*
2834669 TTATTTAAATAGGTAT
1 TTATTTAAATAAGTAT
2834685 TTATTTAAATAAGTAT
1 TTATTTAAATAAGTAT
2834701 ATCTATTCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (16 bp):
TTATTTAAATAAGTAT
Found at i:2835973 original size:21 final size:21
Alignment explanation
Indices: 2835947--2835986 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2835937 ACAATCGAGT
2835947 GGTATCGCGATAT-CCACTTTG
1 GGTATCGCGAT-TCCCACTTTG
2835968 GGTATCGCGATTCCCACTT
1 GGTATCGCGATTCCCACTT
2835987 GCCAAGGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.33
Consensus pattern (21 bp):
GGTATCGCGATTCCCACTTTG
Found at i:2844709 original size:12 final size:12
Alignment explanation
Indices: 2844692--2844716 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2844682 ATGACTGTTC
2844692 TTCAAACAGATA
1 TTCAAACAGATA
2844704 TTCAAACAGATA
1 TTCAAACAGATA
2844716 T
1 T
2844717 GGGGTGGCAA
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:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (12 bp):
TTCAAACAGATA
Found at i:2846910 original size:10 final size:10
Alignment explanation
Indices: 2846895--2846932 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
2846885 GTATTATTTA
2846895 TTTTTTTCAT
1 TTTTTTTCAT
*
2846905 TTTTTTCTCGT
1 TTTTTT-TCAT
2846916 TTTTTTTCAT
1 TTTTTTTCAT
2846926 TTTTTTT
1 TTTTTTT
2846933 TGTAAAAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.05, C:0.11, G:0.03, T:0.82
Consensus pattern (10 bp):
TTTTTTTCAT
Found at i:2846932 original size:11 final size:11
Alignment explanation
Indices: 2846895--2846933 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2846885 GTATTATTTA
2846895 TTTTTTTCATT
1 TTTTTTTCATT
* *
2846906 TTTTTCTC-GT
1 TTTTTTTCATT
2846916 TTTTTTTCATT
1 TTTTTTTCATT
2846927 TTTTTTT
1 TTTTTTT
2846934 GTAAAAGCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.05, C:0.10, G:0.03, T:0.82
Consensus pattern (11 bp):
TTTTTTTCATT
Found at i:2847296 original size:5 final size:5
Alignment explanation
Indices: 2847286--2847333 Score: 53
Period size: 5 Copynumber: 9.0 Consensus size: 5
2847276 GTCTACCTGC
2847286 AAAAT AAAAT AAAAT AAAAT AGAAGGA- AAAAT AAAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT A-AA--AT AAAAT -AAAAT AAAAT AAAAT
2847334 GTGCAAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
4 1 0.03
5 26 0.68
6 9 0.24
7 1 0.03
8 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:2850050 original size:17 final size:17
Alignment explanation
Indices: 2850028--2850060 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2850018 AGCCTAACAC
2850028 AAATA-CCAACCAAGCCT
1 AAATACCCAA-CAAGCCT
2850045 AAATACCCAACAAGCC
1 AAATACCCAACAAGCC
2850061 CAAAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.48, C:0.36, G:0.06, T:0.09
Consensus pattern (17 bp):
AAATACCCAACAAGCCT
Found at i:2851181 original size:31 final size:29
Alignment explanation
Indices: 2851110--2851181 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 29
2851100 TTTGTTTATA
*
2851110 CTTAT-TATGTAAATTTTATATATATATG
1 CTTATATATGTATATTTTATATATATATG
*
2851138 CTT-CATAT-TATATTATTAT-TATATAATTG
1 CTTATATATGTATATT-TTATATATAT-A-TG
2851167 CTTATATATGTATAT
1 CTTATATATGTATAT
2851182 ACGTATATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
27 10 0.29
28 11 0.31
29 5 0.14
30 4 0.11
31 5 0.14
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.54
Consensus pattern (29 bp):
CTTATATATGTATATTTTATATATATATG
Found at i:2854857 original size:15 final size:15
Alignment explanation
Indices: 2854837--2854865 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2854827 TGCTAAATTA
2854837 AGAGCCACTAGCCAT
1 AGAGCCACTAGCCAT
2854852 AGAGCCACTAGCCA
1 AGAGCCACTAGCCA
2854866 CTAGCCACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.34, G:0.21, T:0.10
Consensus pattern (15 bp):
AGAGCCACTAGCCAT
Found at i:2859975 original size:9 final size:9
Alignment explanation
Indices: 2859961--2859986 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2859951 TTTCTTTTCT
2859961 TTTTTTATG
1 TTTTTTATG
2859970 TTTTTTATG
1 TTTTTTATG
2859979 TTTTTTAT
1 TTTTTTAT
2859987 TAGTAGATGA
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:0.12, C:0.00, G:0.08, T:0.81
Consensus pattern (9 bp):
TTTTTTATG
Found at i:2861377 original size:20 final size:20
Alignment explanation
Indices: 2861348--2861385 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2861338 ATACATAATA
2861348 TATTAATTATCATTATACAT
1 TATTAATTATCATTATACAT
* *
2861368 TATTATTTATTATTATAC
1 TATTAATTATCATTATAC
2861386 TGGTTGAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTAATTATCATTATACAT
Found at i:2861977 original size:16 final size:16
Alignment explanation
Indices: 2861920--2861983 Score: 69
Period size: 16 Copynumber: 4.0 Consensus size: 16
2861910 GTCATTATAT
*
2861920 ATTTTATATTATTATTAA
1 ATTTTA-ATAATTATT-A
*
2861938 ATTTTAAT-ATTAAT-
1 ATTTTAATAATTATTA
*
2861952 ATTGTAATAATTATTA
1 ATTTTAATAATTATTA
2861968 ATTTTAATAATTATTA
1 ATTTTAATAATTATTA
2861984 TATACATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
14 7 0.17
15 5 0.12
16 20 0.50
17 2 0.05
18 6 0.15
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
ATTTTAATAATTATTA
Found at i:2866385 original size:23 final size:23
Alignment explanation
Indices: 2866359--2866402 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
2866349 TGGAAACTTA
2866359 ATTTGGTATAATAGTTTCATCTC
1 ATTTGGTATAATAGTTTCATCTC
2866382 ATTTGGTATAATAGTTTCATC
1 ATTTGGTATAATAGTTTCATC
2866403 AGGATTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (23 bp):
ATTTGGTATAATAGTTTCATCTC
Found at i:2869941 original size:7 final size:7
Alignment explanation
Indices: 2869896--2869926 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
2869886 TTTTAGATTT
2869896 ATTTAAGA
1 ATTTAA-A
2869904 ATTTAAA
1 ATTTAAA
2869911 ATTTAAA
1 ATTTAAA
2869918 ATTTAAA
1 ATTTAAA
2869925 AT
1 AT
2869927 ATTTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.74
8 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (7 bp):
ATTTAAA
Found at i:2878448 original size:3 final size:3
Alignment explanation
Indices: 2878435--2878467 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2878425 TCTCCAAGGT
*
2878435 TTC TAC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2878468 CCCCGCTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:2881498 original size:24 final size:24
Alignment explanation
Indices: 2881470--2881533 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
2881460 CTGTTGCTGA
2881470 TGCAGCTGCTGCTGTTCCTCATAT
1 TGCAGCTGCTGCTGTTCCTCATAT
*
2881494 TGCAGCTGCTGCAGTTCCTCATAT
1 TGCAGCTGCTGCTGTTCCTCATAT
*
2881518 TGCAGCTCCTGCTGTT
1 TGCAGCTGCTGCTGTT
2881534 GTTGATCACC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.12, C:0.30, G:0.22, T:0.36
Consensus pattern (24 bp):
TGCAGCTGCTGCTGTTCCTCATAT
Found at i:2884166 original size:20 final size:19
Alignment explanation
Indices: 2884141--2884209 Score: 84
Period size: 19 Copynumber: 3.5 Consensus size: 19
2884131 ATTATAATAT
*
2884141 AATTCAAATTAATTTTAAAA
1 AATTCAAAAT-ATTTTAAAA
**
2884161 AATTCAAAATATTTTTTAA
1 AATTCAAAATATTTTAAAA
2884180 AATTCAAAATATTTATAAAA
1 AATTCAAAATATTT-TAAAA
*
2884200 ATTTCAAAAT
1 AATTCAAAAT
2884210 TTATATTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 21 0.50
20 21 0.50
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTCAAAATATTTTAAAA
Found at i:2884181 original size:19 final size:19
Alignment explanation
Indices: 2884159--2884223 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 19
2884149 TTAATTTTAA
2884159 AAAATTCAAAATATTTTTT
1 AAAATTCAAAATATTTTTT
* *
2884178 AAAATTCAAAATATTTATA
1 AAAATTCAAAATATTTTTT
2884197 AAAATTTCAAAATTTATATTTTT
1 AAAA-TTCAAAA--TAT-TTTTT
2884220 AAAA
1 AAAA
2884224 AAATTATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 21 0.55
20 7 0.18
22 3 0.08
23 7 0.18
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATTCAAAATATTTTTT
Found at i:2884184 original size:39 final size:41
Alignment explanation
Indices: 2884141--2884223 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 41
2884131 ATTATAATAT
*
2884141 AATTCAAATTAATTT-TAAAAAATTCAAAA-TAT-TTTTTAA
1 AATTCAAAAT-ATTTATAAAAAATTCAAAATTATATTTTTAA
*
2884180 AATTCAAAATATTTATAAAAATTTCAAAATTTATATTTTTAA
1 AATTCAAAATATTTATAAAAAATTCAAAA-TTATATTTTTAA
2884222 AA
1 AA
2884224 AAATTATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
38 4 0.11
39 22 0.58
41 3 0.08
42 9 0.24
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (41 bp):
AATTCAAAATATTTATAAAAAATTCAAAATTATATTTTTAA
Found at i:2884245 original size:19 final size:19
Alignment explanation
Indices: 2884127--2884251 Score: 62
Period size: 19 Copynumber: 6.5 Consensus size: 19
2884117 CACTCTCAAC
2884127 AAAAATTATAATATAA-TTCA
1 AAAAATTATAA-A-AATTTCA
* * *
2884147 AATTAATTTTAAAAAATTCA
1 AA-AAATTATAAAAATTTCA
* * *
2884167 AAATATTTTTTAAAA-TTCA
1 AAA-AATTATAAAAATTTCA
*
2884186 AAATATTTATAAAAATTTC-
1 AAA-AATTATAAAAATTTCA
* ** *
2884205 -AAAATT-TATATTTTTAA
1 AAAAATTATAAAAATTTCA
2884222 AAAAATTATAAAAATTTCA
1 AAAAATTATAAAAATTTCA
2884241 AAAAATATATA
1 AAAAAT-TATA
2884252 TATAAAGAAA
Statistics
Matches: 81, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
16 6 0.07
17 3 0.04
18 8 0.10
19 32 0.40
20 25 0.31
21 7 0.09
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATTATAAAAATTTCA
Found at i:2884245 original size:20 final size:20
Alignment explanation
Indices: 2884122--2884245 Score: 55
Period size: 20 Copynumber: 6.4 Consensus size: 20
2884112 TTGGTCACTC
2884122 TCAACAAAAATTATAATATAA-T
1 TCAA-AAAAATTATAA-A-AATT
** * *
2884144 TCAAATTAATTTTAAAAAAT
1 TCAAAAAAATTATAAAAATT
* * * *
2884164 TCAAAATATTTTTTAAAA-T
1 TCAAAAAAATTATAAAAATT
* *
2884183 TCAAAATATTTATAAAAATT
1 TCAAAAAAATTATAAAAATT
* *
2884203 TC---AAAATT-T-ATATTT
1 TCAAAAAAATTATAAAAATT
*
2884218 TTAAAAAAATTATAAAAATT
1 TCAAAAAAATTATAAAAATT
2884238 TCAAAAAA
1 TCAAAAAA
2884246 TATATATATA
Statistics
Matches: 79, Mismatches: 16, Indels: 16
0.71 0.14 0.14
Matches are distributed among these distances:
15 5 0.06
16 1 0.01
17 4 0.05
18 6 0.08
19 20 0.25
20 31 0.39
21 8 0.10
22 4 0.05
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (20 bp):
TCAAAAAAATTATAAAAATT
Found at i:2884250 original size:35 final size:36
Alignment explanation
Indices: 2884192--2884272 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 36
2884182 TTCAAAATAT
** * *
2884192 TTATAAAAATTTCAAAATTTATATTTTTAAA-AAAA
1 TTATAAAAATTTCAAAAAATATATATATAAAGAAAA
*
2884227 TTATAAAAATTTCAAAAAATATATATATAAAGAAAG
1 TTATAAAAATTTCAAAAAATATATATATAAAGAAAA
2884263 TTA-AAAAATT
1 TTATAAAAATT
2884273 AATTTTTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 34 0.85
36 6 0.15
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (36 bp):
TTATAAAAATTTCAAAAAATATATATATAAAGAAAA
Found at i:2885056 original size:27 final size:27
Alignment explanation
Indices: 2885021--2885078 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
2885011 TTCATTTTAC
* *
2885021 TTTATTTACTAATTTTGAT-TTTTGTAT
1 TTTAATTACT-ATTTTAATCTTTTGTAT
*
2885048 TTTAATTACTATTTTAATCTTTTTTAT
1 TTTAATTACTATTTTAATCTTTTGTAT
2885075 TTTA
1 TTTA
2885079 TTTTTAGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.67
Consensus pattern (27 bp):
TTTAATTACTATTTTAATCTTTTGTAT
Found at i:2886304 original size:18 final size:19
Alignment explanation
Indices: 2886282--2886324 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2886272 TATATATAAC
2886282 ATATAATT-TATCAATAAAT
1 ATATAATTATAT-AATAAAT
2886301 -TATAAATTATATAATAAAT
1 ATAT-AATTATATAATAAAT
2886320 ATATA
1 ATATA
2886325 TGTCAAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
18 3 0.14
19 12 0.57
20 6 0.29
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATAATTATATAATAAAT
Found at i:2890740 original size:46 final size:46
Alignment explanation
Indices: 2890673--2890802 Score: 161
Period size: 46 Copynumber: 2.8 Consensus size: 46
2890663 TTAATATTCC
*
2890673 TGTATTCTCGAGTCCACAACATATGTAGGAGCTCGGAACCTAAACA
1 TGTATTCTCGAGTCCACAACATATGCAGGAGCTCGGAACCTAAACA
* * * * ** *
2890719 TGTATTCCCGAGTCCGCAACATATGCAGGAGTTTGGAACCTATTCT
1 TGTATTCTCGAGTCCACAACATATGCAGGAGCTCGGAACCTAAACA
* **
2890765 TGCATTCTCGAGTCCACAACATATGCAAAAGCTCGGAA
1 TGTATTCTCGAGTCCACAACATATGCAGGAGCTCGGAA
2890803 GCTAGGAAGC
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (46 bp):
TGTATTCTCGAGTCCACAACATATGCAGGAGCTCGGAACCTAAACA
Found at i:2893771 original size:23 final size:23
Alignment explanation
Indices: 2893745--2893797 Score: 74
Period size: 21 Copynumber: 2.4 Consensus size: 23
2893735 TTTTTTCTTT
*
2893745 TCTCTTTCACTATTATTGATTTC
1 TCTCTTTCACTATTATTGACTTC
*
2893768 TCTC-TT-ACTGTTATTGACTTC
1 TCTCTTTCACTATTATTGACTTC
2893789 TCTCTTTCA
1 TCTCTTTCA
2893798 AAATTCCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 17 0.65
22 4 0.15
23 5 0.19
ACGTcount: A:0.15, C:0.25, G:0.06, T:0.55
Consensus pattern (23 bp):
TCTCTTTCACTATTATTGACTTC
Found at i:2896897 original size:16 final size:16
Alignment explanation
Indices: 2896873--2896903 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2896863 TAAAAAAGTA
2896873 AATACATCAATCTATC
1 AATACATCAATCTATC
*
2896889 AATATATCAATCTAT
1 AATACATCAATCTAT
2896904 ACAAGTCTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.35
Consensus pattern (16 bp):
AATACATCAATCTATC
Found at i:2901244 original size:3 final size:3
Alignment explanation
Indices: 2901236--2901268 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2901226 TCTTCCTCCA
2901236 CGG CGG CGG CGG CGG CGG CGG CGG CGG CGG CGG
1 CGG CGG CGG CGG CGG CGG CGG CGG CGG CGG CGG
2901269 TAGTGTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.67, T:0.00
Consensus pattern (3 bp):
CGG
Found at i:2902888 original size:9 final size:9
Alignment explanation
Indices: 2902871--2902907 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2902861 TGAGTTTTCG
2902871 AATTCGAAT
1 AATTCGAAT
*
2902880 AACTCGAAT
1 AATTCGAAT
*
2902889 AATTTGAAT
1 AATTCGAAT
2902898 AATTCGAAT
1 AATTCGAAT
2902907 A
1 A
2902908 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:2902957 original size:20 final size:22
Alignment explanation
Indices: 2902927--2902967 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2902917 AATATTTTAC
*
2902927 ATTTTTACCCT-AAACTTTTTT
1 ATTTTTACCCTCAAAATTTTTT
2902948 ATTTTT-CCCTCAAAATTTTT
1 ATTTTTACCCTCAAAATTTTT
2902968 ACTCCTTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTTTACCCTCAAAATTTTTT
Found at i:2906085 original size:31 final size:33
Alignment explanation
Indices: 2906039--2906099 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 33
2906029 TTCTAGTACT
* * *
2906039 CAAAATATTATTTAA-T-AATTAATTTAATGAC
1 CAAAAAATTAGTTAATTAAATTAAATTAATGAC
2906070 CAAAAAATTAGTTAATTAAATTAAATTAAT
1 CAAAAAATTAGTTAATTAAATTAAATTAAT
2906100 TAAATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 13 0.52
32 1 0.04
33 11 0.44
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.39
Consensus pattern (33 bp):
CAAAAAATTAGTTAATTAAATTAAATTAATGAC
Found at i:2908431 original size:15 final size:15
Alignment explanation
Indices: 2908413--2908446 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2908403 GAAATTGTTT
* *
2908413 AAAATATAAAACATA
1 AAAATAAAAAAAATA
2908428 AAAATAAAAAAAATA
1 AAAATAAAAAAAATA
2908443 AAAA
1 AAAA
2908447 GAATCATCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAATAAAAAAAATA
Found at i:2910091 original size:23 final size:23
Alignment explanation
Indices: 2910060--2910163 Score: 106
Period size: 23 Copynumber: 4.5 Consensus size: 23
2910050 ACACCAAAAA
2910060 TTGGACAGCATAAATACAACAAT
1 TTGGACAGCATAAATACAACAAT
*
2910083 TTGGGCAGCATTTAAGCATA-AA-AA-
1 TTGGACAGCA--TAA--ATACAACAAT
* *
2910107 TTGGACAGCATATATGCAACAAT
1 TTGGACAGCATAAATACAACAAT
* *
2910130 TTGGGCAGCATAAATACAACAAA
1 TTGGACAGCATAAATACAACAAT
2910153 TTGGACAGCAT
1 TTGGACAGCAT
2910164 TTTAGCATAA
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
20 2 0.03
21 2 0.03
22 4 0.06
23 38 0.58
24 9 0.14
25 5 0.08
26 2 0.03
27 3 0.05
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.23
Consensus pattern (23 bp):
TTGGACAGCATAAATACAACAAT
Found at i:2921276 original size:106 final size:106
Alignment explanation
Indices: 2921095--2921397 Score: 417
Period size: 106 Copynumber: 2.9 Consensus size: 106
2921085 GGATATTTGG
* * * *
2921095 CTATTTAGTCGAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTCTCTCGAATTTCCAAACG
1 CTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGAATTTCCAAATG
* * ** * **
2921160 CAAAACATTGCCTCGTTTTGAAATTTTGAAAGGATATTCAA
66 CGAAATATTGCCTTATTTTGAAAGTTAAAAAGGATATTCAA
* * * * *
2921201 CTATTTGGTCAAACGAGTAATCGAAACCCAACACGTTAGGGCATGTTTTCTCGAATTTTCAAATG
1 CTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGAATTTCCAAATG
* **
2921266 CGAAATATTGCTTTATTTTGAAAGTTAAAAAGGATATTTGA
66 CGAAATATTGCCTTATTTTGAAAGTTAAAAAGGATATTCAA
* *
2921307 CTATTTGGTTGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGAGTTTCCAAATG
1 CTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGAATTTCCAAATG
2921372 CGAAATATTGCCTTATTTTGAAAGTT
66 CGAAATATTGCCTTATTTTGAAAGTT
2921398 TCTTTTTGAT
Statistics
Matches: 170, Mismatches: 27, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
106 170 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (106 bp):
CTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGAATTTCCAAATG
CGAAATATTGCCTTATTTTGAAAGTTAAAAAGGATATTCAA
Found at i:2923483 original size:9 final size:9
Alignment explanation
Indices: 2923469--2923529 Score: 95
Period size: 9 Copynumber: 6.8 Consensus size: 9
2923459 TTTGGTTAAA
2923469 AATTACCCG
1 AATTACCCG
2923478 AATTACCCG
1 AATTACCCG
2923487 AATTACCCG
1 AATTACCCG
*
2923496 AATTAACCG
1 AATTACCCG
*
2923505 AATTAACCG
1 AATTACCCG
*
2923514 AATTAACCG
1 AATTACCCG
2923523 AATTACC
1 AATTACC
2923530 GAAAAATACC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.39, C:0.28, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:2923547 original size:27 final size:27
Alignment explanation
Indices: 2923469--2923554 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
2923459 TTTGGTTAAA
* * *
2923469 AATTACCCGAATTACCCGAATTACCCG
1 AATTAACCGAAATACCCGAATTAACCG
* *
2923496 AATTAACCGAATTAACCGAATTAACCG
1 AATTAACCGAAATACCCGAATTAACCG
2923523 AATT-ACCGAAAAATACCCGAA-TAACCGG
1 AATTAACCG-AA-ATACCCGAATTAACC-G
2923551 AATT
1 AATT
2923555 TTTTATTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
26 4 0.08
27 35 0.69
28 12 0.24
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.21
Consensus pattern (27 bp):
AATTAACCGAAATACCCGAATTAACCG
Found at i:2924483 original size:178 final size:174
Alignment explanation
Indices: 2924186--2924533 Score: 570
Period size: 178 Copynumber: 2.0 Consensus size: 174
2924176 TGGGTCCTAC
* * *
2924186 AGTTACTATAAAAAAAACCCATGTGTATATAAAAATAATATTATACAAAAATTGCTATCATATTA
1 AGTTACTATAAAAAAAACCCATGTGTATATAAAAATAATATCATACAAAAAATGCTATCATATAA
*
2924251 ATCCTTTACAGCATAAGAAAGAAGTGTATTTATGAAAAATAAAAATCATTAAAAGTATTATATTA
66 ATCCTTTACAGCATAAGAAACAAGTGTATTTATGAAAAATAAAAATCATTAAAAGTATTATATTA
*
2924316 GATTTTTTTTTAAAAAGGATCAAATAAAATAAAATAAAAATATTAT
131 GA--TTTTTTTAAAAAGGATAAAATAAAATAAAATAAAAATATTAT
*
2924362 AGTTACTATAAAAAAAAAACCCATGTGTATATAAAAATCATATCATACAAAAAATGCTATCATAT
1 AGTTACTAT--AAAAAAAACCCATGTGTATATAAAAATAATATCATACAAAAAATGCTATCATAT
*
2924427 AAATCCTTTGCAGCATAAGAAACAAGTGTATTTATGAAAAATAAAAATCATTAAAAGTATTATAT
64 AAATCCTTTACAGCATAAGAAACAAGTGTATTTATGAAAAATAAAAATCATTAAAAGTATTATAT
* * *
2924492 TAGATTTTTTTAAAAAGGATAAAATAATATTAAATAATAATA
129 TAGATTTTTTTAAAAAGGATAAAATAAAATAAAATAAAAATA
2924534 CTTGATAAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
176 43 0.27
178 117 0.73
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.32
Consensus pattern (174 bp):
AGTTACTATAAAAAAAACCCATGTGTATATAAAAATAATATCATACAAAAAATGCTATCATATAA
ATCCTTTACAGCATAAGAAACAAGTGTATTTATGAAAAATAAAAATCATTAAAAGTATTATATTA
GATTTTTTTAAAAAGGATAAAATAAAATAAAATAAAAATATTAT
Found at i:2926148 original size:45 final size:45
Alignment explanation
Indices: 2926098--2926835 Score: 723
Period size: 45 Copynumber: 17.3 Consensus size: 45
2926088 ATAAGACTTG
* * * * * *
2926098 TATCTTCAATCTATTTCACTGCCGATATAGGAAGACAAGGTCTGC
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
* *
2926143 TATCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
*
2926188 TATCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
*
2926233 TATC-T--A-CTA---CGCTGCCAATACAGGAAGACAAGATCTGT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
* * *
2926271 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAATATCTGC
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
* * *
2926316 TACCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGTTCTGC
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
* * *
2926361 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAATATCTGC
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
* * *
2926406 TACCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
* *
2926451 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGA-----
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
* *
2926491 TA--TTCGATCTACTTCGCTACCAATATAGGAAGAC-A-A---G-
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
* *
2926528 -ATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGA-----
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
* *
2926567 TA--TTCGATCTACTTCGCTACCAATATAGGAAGACAAGA-----
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
* *
2926605 TA--TTCGATCTACTTCGCTACCAATATAGGAAGACAAGA-----
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
* * *
2926643 TA--TTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
* * * * *
2926686 TATCTTTGATCTACTTCGCTACCAACATAGGAAGACAAGATCTAC
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
* * *
2926731 TATCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATTTGT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
* * * * * *
2926776 TATCTTCGATCTGCTTTGCTACCAACATAGGAAGAAAAGATCTGC
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
* *
2926821 TATCTTTGACCTACT
1 TATCTTCGATCTACT
2926836 CCACTATTGC
Statistics
Matches: 615, Mismatches: 58, Indels: 40
0.86 0.08 0.06
Matches are distributed among these distances:
36 2 0.00
37 1 0.00
38 208 0.34
39 2 0.00
40 4 0.01
41 4 0.01
42 4 0.01
43 2 0.00
44 1 0.00
45 387 0.63
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (45 bp):
TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC
Found at i:2926247 original size:38 final size:38
Alignment explanation
Indices: 2926196--2926735 Score: 450
Period size: 38 Copynumber: 13.1 Consensus size: 38
2926186 GTTATCTTTG
* *
2926196 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCT
1 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCT
* * *
2926234 ATCTACTACGCTGCCAATACAGGAAGACAAGATCTGTTATCTT
1 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTG----C-T
*
2926277 CGATCTACTTCGCTACCAATATAGGAAGACAATATCTGCTACCTTT
1 --ATCTACTTCGCTACCAATATAGGAAGACAAGATCTG----C--T
* * *
2926323 GATCTACTTCGCTGCCAATACAGGAAGACAAGTTCTGCTATCTT
1 -ATCTACTTCGCTACCAATATAGGAAGACAAGATCTG----C-T
*
2926367 CGATCTACTTCGCTACCAATATAGGAAGACAATATCTGCTACCTTT
1 --ATCTACTTCGCTACCAATATAGGAAGACAAGATCTG----C--T
* *
2926413 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTT
1 -ATCTACTTCGCTACCAATATAGGAAGACAAGATCTG----C-T
* * *
2926457 CGATCTACTTCGCTACCAATATAGGAAGACAAGATATTCG
1 --ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCT
* *
2926497 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTTCG
1 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCT
* * *
2926535 ATCTACTTCGCTACCAATATAGGAAGACAAGATATTCG
1 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCT
* * *
2926573 ATCTACTTCGCTACCAATATAGGAAGACAAGATATTCG
1 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCT
* * *
2926611 ATCTACTTCGCTACCAATATAGGAAGACAAGATATTCG
1 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCT
2926649 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGTTATCTTT
1 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTG----C--T
* *
2926693 GATCTACTTCGCTACCAACATAGGAAGACAAGATCTACT
1 -ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCT
2926732 ATCT
1 ATCT
2926736 TTGATCTACT
Statistics
Matches: 450, Mismatches: 34, Indels: 36
0.87 0.07 0.07
Matches are distributed among these distances:
38 223 0.50
39 1 0.00
41 2 0.00
42 2 0.00
43 1 0.00
44 4 0.01
45 213 0.47
46 4 0.01
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.28
Consensus pattern (38 bp):
ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCT
Found at i:2926387 original size:90 final size:88
Alignment explanation
Indices: 2926098--2926835 Score: 835
Period size: 90 Copynumber: 8.7 Consensus size: 88
2926088 ATAAGACTTG
* * * * * *
2926098 TATCTTCAATCTATTTCACTGCCGATATAGGAAGACAAGGTCTGCTATCTTTGATCTACTTCGCT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAA-ATCTGCTA-CTTTGATCTACTTCGCT
2926163 GCCAATACAGGAAGACAAGATCTGT
64 GCCAATACAGGAAGACAAGATCTGT
* * * *
2926188 TATCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTG---C--T-ATCTACTACGCTG
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAA-ATCTGCTACTTTGATCTACTTCGCTG
2926247 CCAATACAGGAAGACAAGATCTGT
65 CCAATACAGGAAGACAAGATCTGT
2926271 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAATATCTGCTACCTTTGATCTACTTCGCT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAA-ATCTGCTA-CTTTGATCTACTTCGCT
* *
2926336 GCCAATACAGGAAGACAAGTTCTGC
64 GCCAATACAGGAAGACAAGATCTGT
2926361 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAATATCTGCTACCTTTGATCTACTTCGCT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAA-ATCTGCTA-CTTTGATCTACTTCGCT
2926426 GCCAATACAGGAAGACAAGATCTGT
64 GCCAATACAGGAAGACAAGATCTGT
* * *
2926451 TATCTTCGATCTACTTCGCTACCAATATAGGAAGAC-AA---GATA-TTCGATCTACTTCGCTAC
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAATCTGCTACTTTGATCTACTTCGCTGC
*
2926511 CAATATAGGAAGAC-A-A---G-
66 CAATACAGGAAGACAAGATCTGT
* * *
2926528 -ATCTTCGATCTACTTCGCTACCAATATAGGAAGAC-AA---GATA-TTCGATCTACTTCGCTAC
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAATCTGCTACTTTGATCTACTTCGCTGC
*
2926587 CAATATAGGAAGACAAGA-----
66 CAATACAGGAAGACAAGATCTGT
* * *
2926605 TA--TTCGATCTACTTCGCTACCAATATAGGAAGAC-AA---GATA-TTCGATCTACTTCGCTAC
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAATCTGCTACTTTGATCTACTTCGCTGC
*
2926663 CAATATAGGAAGACAAGATCTGT
66 CAATACAGGAAGACAAGATCTGT
* * *
2926686 TATCTTTGATCTACTTCGCTACCAACATAGGAAGACAAGATCTACTATCTTTGATCTACTTCGCT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAA-ATCTGCTA-CTTTGATCTACTTCGCT
*
2926751 GCCAATACAGGAAGACAAGATTTGT
64 GCCAATACAGGAAGACAAGATCTGT
* * * * *
2926776 TATCTTCGATCTGCTTTGCTACCAACATAGGAAGAAAAGATCTGCTATCTTTGACCTACT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAA-ATCTGCTA-CTTTGATCTACT
2926836 CCACTATTGC
Statistics
Matches: 589, Mismatches: 35, Indels: 48
0.88 0.05 0.07
Matches are distributed among these distances:
76 147 0.25
77 1 0.00
78 3 0.01
81 3 0.01
82 1 0.00
83 135 0.23
84 2 0.00
85 4 0.01
86 1 0.00
87 1 0.00
88 3 0.01
89 2 0.00
90 286 0.49
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (88 bp):
TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAATCTGCTACTTTGATCTACTTCGCTGC
CAATACAGGAAGACAAGATCTGT
Found at i:2926578 original size:76 final size:76
Alignment explanation
Indices: 2926452--2926771 Score: 478
Period size: 76 Copynumber: 4.0 Consensus size: 76
2926442 AAGATCTGTT
2926452 ATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATATTCGATCTACTTCGCTACCAATAT
1 ATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATATTCGATCTACTTCGCTACCAATAT
2926517 AGGAAGACAAG
66 AGGAAGACAAG
2926528 ATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATATTCGATCTACTTCGCTACCAATAT
1 ATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATATTCGATCTACTTCGCTACCAATAT
2926593 AGGAAGACAAG
66 AGGAAGACAAG
*
2926604 ATATTCGATCTACTTCGCTACCAATATAGGAAGACAAGATATTCGATCTACTTCGCTACCAATAT
1 ATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATATTCGATCTACTTCGCTACCAATAT
2926669 AGGAAGACAAG
66 AGGAAGACAAG
*
2926680 ATCTGTTATCTTTGATCTACTTCGCTACCAACATAGGAAGACAAGATCTACTATCTTTGATCTAC
1 ATC---T-TC---GATCTACTTCGCTACCAATATAGGAAGACAAGA--TA-T-TC---GATCTAC
* *
2926745 TTCGCTGCCAATACAGGAAGACAAG
52 TTCGCTACCAATATAGGAAGACAAG
2926770 AT
1 AT
2926772 TTGTTATCTT
Statistics
Matches: 225, Mismatches: 5, Indels: 14
0.92 0.02 0.06
Matches are distributed among these distances:
76 153 0.68
79 1 0.00
80 2 0.01
83 32 0.14
85 2 0.01
86 1 0.00
87 2 0.01
90 32 0.14
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.28
Consensus pattern (76 bp):
ATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATATTCGATCTACTTCGCTACCAATAT
AGGAAGACAAG
Found at i:2927363 original size:23 final size:21
Alignment explanation
Indices: 2927337--2927380 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
2927327 ATTAAAGATG
*
2927337 AAATTATATTTTGTATTTACATT
1 AAATTATACTTT-TA-TTACATT
2927360 AAATTATACTTTTATTACATT
1 AAATTATACTTTTATTACATT
2927381 TTAAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 2 0.10
23 11 0.55
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (21 bp):
AAATTATACTTTTATTACATT
Found at i:2927384 original size:23 final size:24
Alignment explanation
Indices: 2927337--2927390 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
2927327 ATTAAAGATG
*
2927337 AAATTATATTTTGTATTTACATT-
1 AAATTATACTTTGTATTTACATTA
2927360 AAATTATACTTT-TA-TTACATTTTA
1 AAATTATACTTTGTATTTACA--TTA
2927384 AAATTAT
1 AAATTAT
2927391 TCAATTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.19
22 2 0.07
23 13 0.48
24 7 0.26
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.54
Consensus pattern (24 bp):
AAATTATACTTTGTATTTACATTA
Found at i:2928789 original size:26 final size:26
Alignment explanation
Indices: 2928760--2928810 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
2928750 TATTTTAGAT
*
2928760 ATATACTATTTTAATTAATAATTAAA
1 ATATACTATATTAATTAATAATTAAA
* **
2928786 ATATATTATATTAATTTTTAATTAA
1 ATATACTATATTAATTAATAATTAA
2928811 TTAAGAGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
ATATACTATATTAATTAATAATTAAA
Found at i:2929409 original size:22 final size:22
Alignment explanation
Indices: 2929382--2929424 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2929372 AAAATTGAGA
* *
2929382 ATATAATGAGATTTTTTTTGTT
1 ATATAAGGAGATTTTTATTGTT
*
2929404 ATATAAGGGGATTTTTATTGT
1 ATATAAGGAGATTTTTATTGT
2929425 ATAAAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (22 bp):
ATATAAGGAGATTTTTATTGTT
Found at i:2932328 original size:19 final size:19
Alignment explanation
Indices: 2932301--2932411 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
2932291 AATCATATCT
2932301 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* ** *
2932320 TCAAAGATTATACATCATA
1 TCTAAGATTGCATATCATA
2932339 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
2932358 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
2932377 TCTACGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
2932396 TATAAGATTGCATATC
1 TCTAAGATTGCATATC
2932412 CTCAAAAATT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 81 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:2935679 original size:16 final size:14
Alignment explanation
Indices: 2935649--2935675 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2935639 AATTTTTTTT
2935649 ATTTAAAAAAATAA
1 ATTTAAAAAAATAA
2935663 ATTTAAAAAAATA
1 ATTTAAAAAAATA
2935676 TAAAATTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATTTAAAAAAATAA
Found at i:2937884 original size:16 final size:16
Alignment explanation
Indices: 2937863--2937894 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2937853 AATCGTGTGG
2937863 TGAAATTAATATTATT
1 TGAAATTAATATTATT
2937879 TGAAATTAATATTATT
1 TGAAATTAATATTATT
2937895 AGATACCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
TGAAATTAATATTATT
Found at i:2940975 original size:45 final size:45
Alignment explanation
Indices: 2940923--2941424 Score: 580
Period size: 45 Copynumber: 11.2 Consensus size: 45
2940913 TGTATATTTA
* * *
2940923 ATCTACTTCGCTGCCGATATAGGGAGACAAGGTCTTCTATCTTTG
1 ATCTACTTCGCTGCCAATATAGGAAGACAAGATCTTCTATCTTTG
* *
2940968 ATCTACTTTGCTGCCAATACAGGAAGACAAGATCTGT-TATCTTTG
1 ATCTACTTCGCTGCCAATATAGGAAGACAAGATCT-TCTATCTTTG
* * ** **
2941013 ATTTACTTCGCTGCCAATATAGGAAGACAAAATCCGCTATCTTCA
1 ATCTACTTCGCTGCCAATATAGGAAGACAAGATCTTCTATCTTTG
* * *
2941058 ATCTACTTCGTTGCCAATATAGGAAGACAAGGTCTGCTATCTTTG
1 ATCTACTTCGCTGCCAATATAGGAAGACAAGATCTTCTATCTTTG
* * * *
2941103 ATCTACTTCGCTACCAATACAGTAAGACAAGATCTGT-TATCTTTT
1 ATCTACTTCGCTGCCAATATAGGAAGACAAGATCT-TCTATCTTTG
* * * * *
2941148 ATCTACTTCACTGCCAATACACGAAGACAAGATCTGCTATCTTCG
1 ATCTACTTCGCTGCCAATATAGGAAGACAAGATCTTCTATCTTTG
* *
2941193 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTTG
1 ATCTACTTCGCTGCCAATATAGGAAGACAAGATCTTCTATCTTTG
* * * *
2941238 ATCTACTTCGCTACCGATATAAGAAGACAATATCTGT-TATCTTTG
1 ATCTACTTCGCTGCCAATATAGGAAGACAAGATCT-TCTATCTTTG
* * *
2941283 ATCTACTTCGCTACCAACATAGGAAGACAAGATCTACTATCTTTG
1 ATCTACTTCGCTGCCAATATAGGAAGACAAGATCTTCTATCTTTG
* * * *
2941328 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCAGT-TATATTCG
1 ATCTACTTCGCTGCCAATATAGGAAGACAAGATC-TTCTATCTTTG
* * *
2941373 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTACTATATTTG
1 ATCTACTTCGCTGCCAATATAGGAAGACAAGATCTTCTATCTTTG
*
2941418 ACCTACT
1 ATCTACT
2941425 CCACTATTGC
Statistics
Matches: 388, Mismatches: 61, Indels: 16
0.83 0.13 0.03
Matches are distributed among these distances:
45 387 1.00
46 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (45 bp):
ATCTACTTCGCTGCCAATATAGGAAGACAAGATCTTCTATCTTTG
Found at i:2941082 original size:90 final size:90
Alignment explanation
Indices: 2940923--2941424 Score: 671
Period size: 90 Copynumber: 5.6 Consensus size: 90
2940913 TGTATATTTA
* * * * * *
2940923 ATCTACTTCGCTGCCGATATAGGGAGACAAGGTCTTCTATCTTTGATCTACTTTGCTGCCAATAC
1 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAATAC
2940988 AGGAAGACAAGATCTGTTATCTTTG
66 AGGAAGACAAGATCTGTTATCTTTG
* * * * ** * *
2941013 ATTTACTTCGCTGCCAATATAGGAAGACAAAATCCGCTATCTTCAATCTACTTCGTTGCCAATAT
1 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAATAC
* *
2941078 AGGAAGACAAGGTCTGCTATCTTTG
66 AGGAAGACAAGATCTGTTATCTTTG
* * * * *
2941103 ATCTACTTCGCTACCAATACAGTAAGACAAGATCTGTTATCTTTTATCTACTTCACTGCCAATAC
1 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAATAC
* * *
2941168 ACGAAGACAAGATCTGCTATCTTCG
66 AGGAAGACAAGATCTGTTATCTTTG
* * *
2941193 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTACCGATAT
1 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAATAC
* *
2941258 AAGAAGACAATATCTGTTATCTTTG
66 AGGAAGACAAGATCTGTTATCTTTG
* *
2941283 ATCTACTTCGCTACCAACATAGGAAGACAAGATCTACTATCTTTGATCTACTTCGCTGCCAATAC
1 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAATAC
* * *
2941348 AGGAAGACAAGATCAGTTATATTCG
66 AGGAAGACAAGATCTGTTATCTTTG
* * *
2941373 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTACTATATTTGACCTACT
1 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACT
2941425 CCACTATTGC
Statistics
Matches: 358, Mismatches: 54, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 358 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (90 bp):
ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAATAC
AGGAAGACAAGATCTGTTATCTTTG
Found at i:2941424 original size:135 final size:135
Alignment explanation
Indices: 2940923--2941407 Score: 682
Period size: 135 Copynumber: 3.6 Consensus size: 135
2940913 TGTATATTTA
* * * * * *
2940923 ATCTACTTCGCTGCCGATATAGGGAGACAAGGTCTTCTATCTTTGATCTACTTTGCTGCCAATAC
1 ATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTACCAATAC
* * *
2940988 AGGAAGACAAGATCTGTTATCTTTGATTTACTTCGCTGCCAATATAGGAAGACAAAATCCGCTAT
66 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTAT
*
2941053 CTTCA
131 CTTCG
* *
2941058 ATCTACTTCGTTGCCAATATAGGAAGACAAGGTCTGCTATCTTTGATCTACTTCGCTACCAATAC
1 ATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTACCAATAC
* * * * *
2941123 AGTAAGACAAGATCTGTTATCTTTTATCTACTTCACTGCCAATACACGAAGACAAGATCTGCTAT
66 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTAT
2941188 CTTCG
131 CTTCG
* * *
2941193 ATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTACCGATAT
1 ATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTACCAATAC
* * * * *
2941258 AAGAAGACAATATCTGTTATCTTTGATCTACTTCGCTACCAACATAGGAAGACAAGATCTACTAT
66 AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTAT
*
2941323 CTTTG
131 CTTCG
* * * * * *
2941328 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCAGTTATATTCGATCTACTTCGCTACCAATAT
1 ATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTACCAATAC
2941393 AGGAAGACAAGATCT
66 AGGAAGACAAGATCT
2941408 ACTATATTTG
Statistics
Matches: 310, Mismatches: 40, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
135 310 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (135 bp):
ATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTACCAATAC
AGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTAT
CTTCG
Found at i:2941959 original size:23 final size:21
Alignment explanation
Indices: 2941933--2941976 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
2941923 ATTAAAGATG
*
2941933 AAATTATATTTTGTATTTACATT
1 AAATTATACTTT-TA-TTACATT
2941956 AAATTATACTTTTATTACATT
1 AAATTATACTTTTATTACATT
2941977 TTAAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 2 0.10
23 11 0.55
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (21 bp):
AAATTATACTTTTATTACATT
Found at i:2941980 original size:23 final size:24
Alignment explanation
Indices: 2941933--2941986 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
2941923 ATTAAAGATG
*
2941933 AAATTATATTTTGTATTTACATT-
1 AAATTATACTTTGTATTTACATTA
2941956 AAATTATACTTT-TA-TTACATTTTA
1 AAATTATACTTTGTATTTACA--TTA
2941980 AAATTAT
1 AAATTAT
2941987 TCAATTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.19
22 2 0.07
23 13 0.48
24 7 0.26
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.54
Consensus pattern (24 bp):
AAATTATACTTTGTATTTACATTA
Found at i:2942215 original size:24 final size:24
Alignment explanation
Indices: 2942170--2942215 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2942160 TAATGTTTTA
*
2942170 ATTATGTTCAATAATTAGAATAAT
1 ATTATGTTCAATAAATAGAATAAT
*
2942194 ATTATTTTACAATAAATA-AATA
1 ATTATGTT-CAATAAATAGAATA
2942216 TGTAAAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (24 bp):
ATTATGTTCAATAAATAGAATAAT
Found at i:2945445 original size:19 final size:19
Alignment explanation
Indices: 2945404--2945446 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2945394 TTTCAATAAT
* *
2945404 TTATATTTATTTTTAAGAT
1 TTATTTTTATTTTTAAGAA
*
2945423 TTATTTTTATTTTTTAGAA
1 TTATTTTTATTTTTAAGAA
2945442 TTATT
1 TTATT
2945447 GTTAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (19 bp):
TTATTTTTATTTTTAAGAA
Found at i:2948855 original size:3 final size:3
Alignment explanation
Indices: 2948847--2948877 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2948837 AACGGAAAAG
2948847 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2948878 GAAAGCAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2949549 original size:9 final size:9
Alignment explanation
Indices: 2949531--2949588 Score: 80
Period size: 9 Copynumber: 6.4 Consensus size: 9
2949521 TTTGGTTAAA
2949531 AATTAACCG
1 AATTAACCG
*
2949540 AATTACCCG
1 AATTAACCG
2949549 AATTAACCG
1 AATTAACCG
*
2949558 AATTACCCG
1 AATTAACCG
*
2949567 AATTATCCG
1 AATTAACCG
*
2949576 AATTAACCA
1 AATTAACCG
2949585 AATT
1 AATT
2949589 GAATCACTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:2949554 original size:18 final size:18
Alignment explanation
Indices: 2949531--2949580 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
2949521 TTTGGTTAAA
2949531 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
2949549 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
2949567 AATTATCCGAATTA
1 AATTAACCGAATTA
2949581 ACCAAATTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:2949567 original size:27 final size:27
Alignment explanation
Indices: 2949530--2949588 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
2949520 TTTTGGTTAA
2949530 AAATTAACCGAATTACCCGAATTAACC
1 AAATTAACCGAATTACCCGAATTAACC
* * *
2949557 GAATTACCCGAATTATCCGAATTAACC
1 AAATTAACCGAATTACCCGAATTAACC
2949584 AAATT
1 AAATT
2949589 GAATCACTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.25
Consensus pattern (27 bp):
AAATTAACCGAATTACCCGAATTAACC
Found at i:2949668 original size:16 final size:16
Alignment explanation
Indices: 2949647--2949679 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2949637 TTCGCTGTAT
2949647 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
2949663 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
2949679 T
1 T
2949680 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.36, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:2950337 original size:14 final size:15
Alignment explanation
Indices: 2950288--2950339 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
2950278 NTAAAATATA
2950288 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
2950303 TATTAAATATATTAT
1 AATTAAATATATTAT
2950318 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
2950331 AATTTAATA
1 AATTAAATA
2950340 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:2950550 original size:41 final size:41
Alignment explanation
Indices: 2950503--2950590 Score: 158
Period size: 41 Copynumber: 2.1 Consensus size: 41
2950493 TAAGTGAGTA
2950503 AGAATTGAACTCTAAAAATAAAAAAAAAAACATAACCATAT
1 AGAATTGAACTCTAAAAATAAAAAAAAAAACATAACCATAT
*
2950544 AGAATTGAACTCTAAAAATAAAATAAAAAACATAACCATAT
1 AGAATTGAACTCTAAAAATAAAAAAAAAAACATAACCATAT
*
2950585 CGAATT
1 AGAATT
2950591 ATCATCAAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.60, C:0.12, G:0.06, T:0.22
Consensus pattern (41 bp):
AGAATTGAACTCTAAAAATAAAAAAAAAAACATAACCATAT
Found at i:2952698 original size:18 final size:18
Alignment explanation
Indices: 2952662--2952701 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2952652 TTTATGATTC
**
2952662 GGTTGGGTTGGGTAATTG
1 GGTTGGGTTGAATAATTG
*
2952680 GGTTGGGTTGAATACTTG
1 GGTTGGGTTGAATAATTG
2952698 GGTT
1 GGTT
2952702 TAGATTGGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.12, C:0.03, G:0.45, T:0.40
Consensus pattern (18 bp):
GGTTGGGTTGAATAATTG
Found at i:2954402 original size:99 final size:100
Alignment explanation
Indices: 2954236--2954499 Score: 329
Period size: 99 Copynumber: 2.7 Consensus size: 100
2954226 GAACTAGCCA
* * *
2954236 TCACCAACATCACCACTCTCTCCTC-CATATCTCCCCTCTTTTTGATACCCAACATCAATAATTG
1 TCACCAACACCACCACTCCCTCCACTCATATCTCCCCTCTTTTTGATACCCAACATCAATAATTG
* * *
2954300 GTGCGACTCTCCGCCCAAACTGGGTGAATCGGCCT
66 GTGCGACTCTCCGCCCAAACTGGATGAACCGACCT
* * * * * * *
2954335 TCACTAGCACCATCACTCCCT-CATTCATATCTCCCCTCTTTTTGATACCCTACATCAACAATCG
1 TCACCAACACCACCACTCCCTCCACTCATATCTCCCCTCTTTTTGATACCCAACATCAATAATTG
* *
2954399 GTGCGACTCTCTGCCCAAATTGGATGAACCGACCT
66 GTGCGACTCTCCGCCCAAACTGGATGAACCGACCT
* * * *
2954434 TCACCAACACCGCCACTCCCTCCACT-GTGTCTCCCC-CTTGTTGATACCCAACATCAATAATTG
1 TCACCAACACCACCACTCCCTCCACTCATATCTCCCCTCTTTTTGATACCCAACATCAATAATTG
2954497 GTG
66 GTG
2954500 AAGTGAGCAT
Statistics
Matches: 137, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
98 27 0.20
99 107 0.78
100 3 0.02
ACGTcount: A:0.23, C:0.38, G:0.12, T:0.27
Consensus pattern (100 bp):
TCACCAACACCACCACTCCCTCCACTCATATCTCCCCTCTTTTTGATACCCAACATCAATAATTG
GTGCGACTCTCCGCCCAAACTGGATGAACCGACCT
Found at i:2957127 original size:25 final size:25
Alignment explanation
Indices: 2957099--2957185 Score: 113
Period size: 25 Copynumber: 3.5 Consensus size: 25
2957089 CACAACTCTT
2957099 ATGAGCTTCCCGATATTTAGCTCAC
1 ATGAGCTTCCCGATATTTAGCTCAC
2957124 ATGAGCTTCTCC-ATATTTAGCTCAC
1 ATGAGCTTC-CCGATATTTAGCTCAC
* * * **
2957149 GTGAGCTTCCAGATACTTAGCTTGC
1 ATGAGCTTCCCGATATTTAGCTCAC
2957174 ATGAGCTTCCCG
1 ATGAGCTTCCCG
2957186 TTTACAACTC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
24 1 0.02
25 50 0.94
26 2 0.04
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (25 bp):
ATGAGCTTCCCGATATTTAGCTCAC
Found at i:2962120 original size:2 final size:2
Alignment explanation
Indices: 2962115--2962149 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2962105 ACACACACGC
*
2962115 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2962150 CATCAACCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2964983 original size:27 final size:25
Alignment explanation
Indices: 2964940--2964995 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 25
2964930 CGAATATAAT
2964940 AAATATTTTTTATTTTTTAT-TTTA
1 AAATATTTTTTATTTTTTATATTTA
2964964 AAATACTTTTTTATTTTTTTATATTTA
1 AAATA-TTTTTTA-TTTTTTATATTTA
2964991 AAATA
1 AAATA
2964996 AATTTTTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 5 0.17
25 7 0.24
26 8 0.28
27 9 0.31
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
AAATATTTTTTATTTTTTATATTTA
Found at i:2965001 original size:26 final size:25
Alignment explanation
Indices: 2964947--2965001 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
2964937 AATAAATATT
**
2964947 TTTTATTTTTTATTTTAAAATACTT
1 TTTTATTTTTTATTTTAAAATACAA
2964972 TTTTATTTTTTTATATTTAAAATA-AA
1 TTTTA-TTTTTTAT-TTTAAAATACAA
2964998 TTTT
1 TTTT
2965002 TGGTGTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 5 0.19
26 12 0.46
27 9 0.35
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTATTTTTTATTTTAAAATACAA
Found at i:2965001 original size:27 final size:25
Alignment explanation
Indices: 2964946--2965002 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 25
2964936 TAATAAATAT
**
2964946 TTTTTATTTTTTATTTTAAAATACT
1 TTTTTATTTTTTATTTTAAAATAAA
2964971 TTTTTATTTTTTTATATTTAAAATAAA
1 TTTTTA-TTTTTTAT-TTTAAAATAAA
2964998 TTTTT
1 TTTTT
2965003 GGTGTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 6 0.21
26 8 0.29
27 14 0.50
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTTTATTTTTTATTTTAAAATAAA
Found at i:2968859 original size:22 final size:22
Alignment explanation
Indices: 2968829--2968897 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
2968819 TTATAAACTG
* *
2968829 AAATATATGAATCAATTTATTA
1 AAATATATGAATAAAATTATTA
* *
2968851 AAATCTATGTATAAAATTATT-
1 AAATATATGAATAAAATTATTA
* *
2968872 -AATATGTCAA-AAAATTATT-
1 AAATATATGAATAAAATTATTA
2968891 AAATATA
1 AAATATA
2968898 ATATATATTG
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
19 9 0.24
20 11 0.30
22 17 0.46
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (22 bp):
AAATATATGAATAAAATTATTA
Found at i:2973283 original size:31 final size:33
Alignment explanation
Indices: 2973245--2973309 Score: 89
Period size: 31 Copynumber: 2.0 Consensus size: 33
2973235 ATTTTTGTAC
* * *
2973245 GTAAAATTGTCTTA-TAAA-AATATAATTTTAT
1 GTAAAATTATCTTATTAAACAACATAATATTAT
2973276 GTAAAATTATCTTATTAAACAACATAATATTAT
1 GTAAAATTATCTTATTAAACAACATAATATTAT
2973309 G
1 G
2973310 AAAGGATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 13 0.45
32 4 0.14
33 12 0.41
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (33 bp):
GTAAAATTATCTTATTAAACAACATAATATTAT
Found at i:2983751 original size:43 final size:43
Alignment explanation
Indices: 2983703--2983789 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
2983693 GATTTAGCCT
2983703 TTAAAGTTAATTTTGATTACATGTTTCTTTTACCC-TCTGACTA
1 TTAAAGTTAATTTTGATTACATGTTTCTTTTACCCAT-TGACTA
2983746 TTAAAGTTAATTTTGATTACATGTTTCTTTTACCCATTGACTA
1 TTAAAGTTAATTTTGATTACATGTTTCTTTTACCCATTGACTA
2983789 T
1 T
2983790 GTGACTCACC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.49
Consensus pattern (43 bp):
TTAAAGTTAATTTTGATTACATGTTTCTTTTACCCATTGACTA
Found at i:2986300 original size:45 final size:46
Alignment explanation
Indices: 2986251--2986338 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 46
2986241 TTTCCATTTT
* *
2986251 GAGAAAACCACATTTATTTCCAAATG-ATTCCATTTCTCTATTCCA
1 GAGAAAACCACAATCATTTCCAAATGTATTCCATTTCTCTATTCCA
* ** *
2986296 GAGAAAACCATAATCATTTCTGAATGTTTTCCATTTCTCTATT
1 GAGAAAACCACAATCATTTCCAAATGTATTCCATTTCTCTATT
2986339 TCTATTCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 21 0.58
46 15 0.42
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.39
Consensus pattern (46 bp):
GAGAAAACCACAATCATTTCCAAATGTATTCCATTTCTCTATTCCA
Found at i:2987862 original size:52 final size:52
Alignment explanation
Indices: 2987789--2987893 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
2987779 CCAATTAACT
2987789 TACTTTGACTGATTTTATGATAGCCTTATTTTGCTATTATTGTTCATAATTA
1 TACTTTGACTGATTTTATGATAGCCTTATTTTGCTATTATTGTTCATAATTA
2987841 TACTTTGACTGATTTTATGATAGCCTTATTTTGCTATTATTGTTCATAATTA
1 TACTTTGACTGATTTTATGATAGCCTTATTTTGCTATTATTGTTCATAATTA
2987893 T
1 T
2987894 TTGTTGGATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.52
Consensus pattern (52 bp):
TACTTTGACTGATTTTATGATAGCCTTATTTTGCTATTATTGTTCATAATTA
Found at i:2990833 original size:17 final size:18
Alignment explanation
Indices: 2990808--2990851 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
2990798 ACGGAATTAG
* *
2990808 AATTGAATTGGGA-AAAT
1 AATTAAATTGAGAGAAAT
*
2990825 AATTTAATTGAGAGAAAT
1 AATTAAATTGAGAGAAAT
2990843 AATTAAATT
1 AATTAAATT
2990852 AAATTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (18 bp):
AATTAAATTGAGAGAAAT
Found at i:2991749 original size:16 final size:16
Alignment explanation
Indices: 2991728--2991783 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
2991718 TGAATTACTT
2991728 ATTACAGTTCTATTCC
1 ATTACAGTTCTATTCC
* *
2991744 ATTACAGCTCTATTCA
1 ATTACAGTTCTATTCC
**
2991760 ATTACA-ACCATATTCC
1 ATTACAGTTC-TATTCC
2991776 ATTACAGT
1 ATTACAGT
2991784 GAACCAAACG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
15 1 0.03
16 31 0.97
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACAGTTCTATTCC
Found at i:2991914 original size:43 final size:43
Alignment explanation
Indices: 2991866--2991953 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
2991856 TTGTTTAAGT
2991866 AGAATTCTTGTGAATTTTCCCTTTAAATAGGGACTATAAGCTA
1 AGAATTCTTGTGAATTTTCCCTTTAAATAGGGACTATAAGCTA
2991909 AGAATTCTTGTGAATTTTCCCTTTAAATAGGGACTATAAGCTA
1 AGAATTCTTGTGAATTTTCCCTTTAAATAGGGACTATAAGCTA
2991952 AG
1 AG
2991954 TAAAAAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (43 bp):
AGAATTCTTGTGAATTTTCCCTTTAAATAGGGACTATAAGCTA
Found at i:2995644 original size:23 final size:22
Alignment explanation
Indices: 2995594--2995645 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
2995584 GGTCCAAAAA
*
2995594 ATATGAATATTATATTAATTTT
1 ATATTAATATTATATTAATTTT
*
2995616 ATATTAATATTCATATT-TTTTT
1 ATATTAATATT-ATATTAATTTT
2995638 ATCATTAA
1 AT-ATTAA
2995646 ATTTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATTAATATTATATTAATTTT
Found at i:2995655 original size:22 final size:22
Alignment explanation
Indices: 2995612--2995655 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2995602 ATTATATTAA
*
2995612 TTTTATATTAATATTCATATTT
1 TTTTATATTAATATTCAAATTT
*
2995634 TTTTATCATTAA-ATTTAAATTT
1 TTTTAT-ATTAATATTCAAATTT
2995656 GTGCTATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTATATTAATATTCAAATTT
Found at i:2996613 original size:76 final size:77
Alignment explanation
Indices: 2996515--2996667 Score: 299
Period size: 76 Copynumber: 2.0 Consensus size: 77
2996505 AAAAGTTTAA
2996515 TTTATTATTACATTAATTAATATTATGTATGGTAAAATATTAATTCTCTTTACTTGTTCATTTTC
1 TTTATTATTACATTAATTAATATTATGTATGGTAAAATATTAATTCTCTTTACTTGTTCATTTTC
2996580 AAAATTTACATG
66 AAAATTTACATG
2996592 TTTATTATTA-ATTAATTAATATTATGTATGGTAAAATATTAATTCTCTTTACTTGTTCATTTTC
1 TTTATTATTACATTAATTAATATTATGTATGGTAAAATATTAATTCTCTTTACTTGTTCATTTTC
2996656 AAAATTTACATG
66 AAAATTTACATG
2996668 ATTTCATTCA
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 66 0.87
77 10 0.13
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (77 bp):
TTTATTATTACATTAATTAATATTATGTATGGTAAAATATTAATTCTCTTTACTTGTTCATTTTC
AAAATTTACATG
Found at i:3000986 original size:20 final size:17
Alignment explanation
Indices: 3000961--3000999 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 17
3000951 AAAACATTAT
3000961 AAAGGAAGAAGAAAGAAAAA
1 AAAGGAA-AA-AAA-AAAAA
3000981 AAAGGAAAAAAAAAAAA
1 AAAGGAAAAAAAAAAAA
3000998 AA
1 AA
3001000 GAGAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 3 0.16
19 2 0.11
20 7 0.37
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAGGAAAAAAAAAAAA
Found at i:3006249 original size:2 final size:2
Alignment explanation
Indices: 3006242--3006280 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3006232 AGAAATAATC
3006242 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3006281 ACACATACGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3009524 original size:11 final size:11
Alignment explanation
Indices: 3009496--3009528 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3009486 CTTATATTTT
3009496 TATCATAAAAA
1 TATCATAAAAA
*
3009507 -ATTATAAAAA
1 TATCATAAAAA
3009517 TATCATAAAAA
1 TATCATAAAAA
3009528 T
1 T
3009529 TAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (11 bp):
TATCATAAAAA
Found at i:3009548 original size:38 final size:39
Alignment explanation
Indices: 3009503--3009603 Score: 115
Period size: 38 Copynumber: 2.6 Consensus size: 39
3009493 TTTTATCATA
3009503 AAAAATTATAAAAATATCATAAAAATTA-AATA-T-TTAT
1 AAAAATTATAAAAAT-TCATAAAAATTAGAATAGTATTAT
3009540 ATAAAATTATAAAAATT-ATAGACAAATTAGAATAGTACTTAT
1 A-AAAATTATAAAAATTCATA-A-AAATTAGAATAGTA-TTAT
3009582 AAAAA-TATAAAAATTCA-AAAAA
1 AAAAATTATAAAAATTCATAAAAA
3009604 GCTTATAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 15
0.79 0.00 0.21
Matches are distributed among these distances:
36 3 0.05
37 3 0.05
38 23 0.41
39 5 0.09
40 12 0.21
41 5 0.09
42 5 0.09
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (39 bp):
AAAAATTATAAAAATTCATAAAAATTAGAATAGTATTAT
Found at i:3009566 original size:20 final size:18
Alignment explanation
Indices: 3009503--3009680 Score: 87
Period size: 19 Copynumber: 9.3 Consensus size: 18
3009493 TTTTATCATA
3009503 AAAAATTATAAAAATATCAT
1 AAAAATTATAAAAAT-T-AT
* *
3009523 AAAAATTA-AATATTTAT
1 AAAAATTATAAAAATTAT
3009540 ATAAAATTATAAAAATTAT
1 A-AAAATTATAAAAATTAT
* *
3009559 AGACAAATTAGAATAGTACTTAT
1 A-A-AAATTATAA-A--AATTAT
3009582 AAAAA-TATAAAAATTCA-
1 AAAAATTATAAAAATT-AT
* *
3009599 AAAAAGCTTATAAATATTGT
1 AAAAA--TTATAAAAATTAT
** * *
3009619 AATATTTTATAGAAATTCT
1 AA-AAATTATAAAAATTAT
3009638 AATAAATTATAAAAAATTAT
1 AA-AAATTAT-AAAAATTAT
3009658 -AAAATTAATAAAACA-TAT
1 AAAAATT-ATAAAA-ATTAT
3009676 AAAAA
1 AAAAA
3009681 CATATTCAAA
Statistics
Matches: 122, Mismatches: 20, Indels: 33
0.70 0.11 0.19
Matches are distributed among these distances:
17 11 0.09
18 21 0.17
19 40 0.33
20 38 0.31
21 5 0.04
22 1 0.01
23 6 0.05
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAAATTATAAAAATTAT
Found at i:3009568 original size:11 final size:9
Alignment explanation
Indices: 3009503--3009680 Score: 87
Period size: 9 Copynumber: 18.6 Consensus size: 9
3009493 TTTTATCATA
3009503 AAAAATTAT
1 AAAAATTAT
3009512 AAAAATATCAT
1 AAAAAT-T-AT
3009523 AAAAATTA-
1 AAAAATTAT
* *
3009531 AATATTTAT
1 AAAAATTAT
3009540 ATAAAATTAT
1 A-AAAATTAT
3009550 AAAAATTAT
1 AAAAATTAT
*
3009559 AGACAAATTAG
1 A-A-AAATTAT
*
3009570 AATAGTACTTAT
1 AA-A--AATTAT
3009582 AAAAA-TAT
1 AAAAATTAT
3009590 AAAAATTCA-
1 AAAAATT-AT
3009599 AAAAAGCTTAT
1 AAAAA--TTAT
* *
3009610 AAATATTGT
1 AAAAATTAT
**
3009619 AATATTTTAT
1 AA-AAATTAT
* *
3009629 AGAAATTCT
1 AAAAATTAT
3009638 AATAAATTAT
1 AA-AAATTAT
3009648 AAAAAATTAT
1 -AAAAATTAT
3009658 -AAAATTAAT
1 AAAAATT-AT
3009667 AAAACA-TAT
1 AAAA-ATTAT
3009676 AAAAA
1 AAAAA
3009681 CATATTCAAA
Statistics
Matches: 131, Mismatches: 19, Indels: 39
0.69 0.10 0.21
Matches are distributed among these distances:
8 21 0.16
9 42 0.32
10 37 0.28
11 25 0.19
12 6 0.05
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:3011646 original size:22 final size:21
Alignment explanation
Indices: 3011590--3011648 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
3011580 TCATAATAGT
* *
3011590 TCAAATAAGATGCAAAACAAA
1 TCAAATCAGATGCAGAACAAA
* *
3011611 TCAGATACATATGCAGAACAAA
1 TCAAAT-CAGATGCAGAACAAA
3011633 TCAAAATCAGATGCAG
1 TC-AAATCAGATGCAG
3011649 TTTCCTACCC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 5 0.17
22 22 0.73
23 3 0.10
ACGTcount: A:0.53, C:0.17, G:0.14, T:0.17
Consensus pattern (21 bp):
TCAAATCAGATGCAGAACAAA
Found at i:3014908 original size:26 final size:26
Alignment explanation
Indices: 3014857--3014911 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
3014847 GTCGTTAATA
*
3014857 GGAAGCTCACAAAGAGCCTTTAATCG
1 GGAAGCTCACAAAGAGCCTATAATCG
*
3014883 GGAAGCTCACGAAGAGCC-ATATATCG
1 GGAAGCTCACAAAGAGCCTATA-ATCG
3014909 GGA
1 GGA
3014912 CGCTTATAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.35, C:0.22, G:0.27, T:0.16
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCTATAATCG
Found at i:3017747 original size:21 final size:22
Alignment explanation
Indices: 3017709--3017750 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3017699 TTCATAACAC
3017709 TTTTTATAAATAAGATAAGTTT
1 TTTTTATAAATAAGATAAGTTT
* *
3017731 TTTTTTTATATAA-ATAAGTT
1 TTTTTATAAATAAGATAAGTT
3017751 ATGATAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
TTTTTATAAATAAGATAAGTTT
Found at i:3019448 original size:18 final size:18
Alignment explanation
Indices: 3019425--3019459 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3019415 GTTTCCATAC
3019425 ATTTTTCATA-ATTAATTA
1 ATTTTT-ATATATTAATTA
3019443 ATTTTTATATATTAATT
1 ATTTTTATATATTAATT
3019460 GAGTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTATATATTAATTA
Found at i:3024297 original size:124 final size:124
Alignment explanation
Indices: 3024077--3024302 Score: 373
Period size: 124 Copynumber: 1.8 Consensus size: 124
3024067 TTATTTCGAG
*
3024077 TTGACGTTTCTAAGCAAATAGTATAAAATCGCCTTCTCCAGGATGCTATTTGAGAAAAAATTGTG
1 TTGACGTTTCTAAGCAAATAGTATAAAATCGACTTCTCCAGGATGCTATTTGAGAAAAAATTGTG
**
3024142 AAATCGCACCCTTGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
66 AAATCGCACCCTCATGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
* *
3024201 TTGACGTTTCTGAGCAAATAGTATAAAATC-ACTTCTACCAGGATGTTATTTGAGAAAAAATTGT
1 TTGACGTTTCTAAGCAAATAGTATAAAATCGACTTCT-CCAGGATGCTATTTGAGAAAAAATTGT
**
3024265 GAAATCGTGCCCTCATGGACGCGATTTTGCTACAGTAG
65 GAAATCGCACCCTCATGGACGCGATTTTGCTACAGTAG
3024303 CAAGCTTGGG
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
123 5 0.05
124 89 0.95
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (124 bp):
TTGACGTTTCTAAGCAAATAGTATAAAATCGACTTCTCCAGGATGCTATTTGAGAAAAAATTGTG
AAATCGCACCCTCATGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
Found at i:3025889 original size:29 final size:29
Alignment explanation
Indices: 3025847--3025982 Score: 272
Period size: 29 Copynumber: 4.7 Consensus size: 29
3025837 ATATGGCAAT
3025847 GGGTTTTTAATTAAATTAGGTTAGGGTTA
1 GGGTTTTTAATTAAATTAGGTTAGGGTTA
3025876 GGGTTTTTAATTAAATTAGGTTAGGGTTA
1 GGGTTTTTAATTAAATTAGGTTAGGGTTA
3025905 GGGTTTTTAATTAAATTAGGTTAGGGTTA
1 GGGTTTTTAATTAAATTAGGTTAGGGTTA
3025934 GGGTTTTTAATTAAATTAGGTTAGGGTTA
1 GGGTTTTTAATTAAATTAGGTTAGGGTTA
3025963 GGGTTTTTAATTAAATTAGG
1 GGGTTTTTAATTAAATTAGG
3025983 GTTTTTATTA
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 107 1.00
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (29 bp):
GGGTTTTTAATTAAATTAGGTTAGGGTTA
Found at i:3026095 original size:71 final size:71
Alignment explanation
Indices: 3025988--3026176 Score: 306
Period size: 71 Copynumber: 2.6 Consensus size: 71
3025978 TTAGGGTTTT
*
3025988 TATTACATCAAATAAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTT
1 TATTACATCAAAT-AAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTT
3026053 CTATGCC
65 CTATGCC
* * ** *
3026060 TATTATATCAAATAAACTTTTATTTTATTACATCAAATAATATCAAAATAACTCGAAAATTTTTT
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
*
3026125 TATGCG
66 TATGCC
3026131 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAA
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAA
3026177 TGTCTATGCC
Statistics
Matches: 108, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
71 96 0.89
72 12 0.11
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (71 bp):
TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
TATGCC
Found at i:3026103 original size:35 final size:35
Alignment explanation
Indices: 3026064--3026176 Score: 88
Period size: 35 Copynumber: 3.2 Consensus size: 35
3026054 TATGCCTATT
*
3026064 ATATCAAATAAACTTTTATTTTATTACATCAAATA
1 ATATCAAATAAACTTATATTTTATTACATCAAATA
* * * ** *
3026099 ATATCAAA-ATAACTCGAAAATTTT-TT-TATGCGTATT
1 ATATCAAATA-AACT--TATATTTTATTACAT-CAAATA
* *
3026135 ACATCAAATAAACTTCTATTTTATTACATCAAATA
1 ATATCAAATAAACTTATATTTTATTACATCAAATA
3026170 ATATCAA
1 ATATCAA
3026177 TGTCTATGCC
Statistics
Matches: 55, Mismatches: 16, Indels: 14
0.65 0.19 0.16
Matches are distributed among these distances:
34 6 0.11
35 25 0.45
36 18 0.33
37 6 0.11
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.40
Consensus pattern (35 bp):
ATATCAAATAAACTTATATTTTATTACATCAAATA
Found at i:3026585 original size:18 final size:18
Alignment explanation
Indices: 3026558--3026592 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3026548 CGGAAAAGGA
* *
3026558 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
3026576 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
3026593 AAACACACTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:3027252 original size:7 final size:7
Alignment explanation
Indices: 3027242--3027266 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3027232 TTATATACAT
3027242 AATACTA
1 AATACTA
3027249 AATACTA
1 AATACTA
3027256 AATACTA
1 AATACTA
3027263 AATA
1 AATA
3027267 TCATTCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:3028447 original size:51 final size:51
Alignment explanation
Indices: 3028382--3028503 Score: 183
Period size: 51 Copynumber: 2.4 Consensus size: 51
3028372 TTTAAAAAAT
* *
3028382 GAAATTGAGGGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAAATTTGGAAG
* *
3028433 GAAATTGAGAGGAAATTTAAATTAAATATGGGTTTGAGAGAAATTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAAATTTGGAAG
3028484 GAAATTTG-GAAGGAAATTGA
1 GAAA-TTGAG-AGGAAATTGA
3028504 GAGGATTAGA
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
51 52 0.81
52 12 0.19
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAAATTTGGAAG
Found at i:3028489 original size:12 final size:12
Alignment explanation
Indices: 3028472--3028501 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
3028462 GGGTTTGAGA
3028472 GAAATTTGGAAG
1 GAAATTTGGAAG
3028484 GAAATTTGGAAG
1 GAAATTTGGAAG
3028496 GAAATT
1 GAAATT
3028502 GAGAGGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (12 bp):
GAAATTTGGAAG
Found at i:3028773 original size:29 final size:28
Alignment explanation
Indices: 3028715--3028775 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
3028705 GATTTCCCGG
3028715 AAAATGGACCATTCCGGTAAATAATCAAA
1 AAAATGGACCATTCCGGTAAATAAT-AAA
* * * **
3028744 AAATTGGCCCATTTCGGTAAATTTTAAA
1 AAAATGGACCATTCCGGTAAATAATAAA
3028772 AAAA
1 AAAA
3028776 ACGGCTTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (28 bp):
AAAATGGACCATTCCGGTAAATAATAAA
Found at i:3030132 original size:19 final size:18
Alignment explanation
Indices: 3030108--3030143 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3030098 ACTAACAGCT
3030108 ACTAACTGCATACTAACAA
1 ACTAACTG-ATACTAACAA
*
3030127 ACTAACTGATATTAACA
1 ACTAACTGATACTAACA
3030144 GCTTGTGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (18 bp):
ACTAACTGATACTAACAA
Found at i:3035156 original size:3 final size:3
Alignment explanation
Indices: 3035148--3035201 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
3035138 AAATTTTTGC
3035148 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
3035196 TGT TAT
1 TAT TAT
3035202 AGATAAGTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3056583 original size:64 final size:64
Alignment explanation
Indices: 3056504--3056635 Score: 246
Period size: 64 Copynumber: 2.1 Consensus size: 64
3056494 CGAAGGTTTT
*
3056504 AACTTGACCATAATCTGTTTTATGTTCTCTCATGCAGGTTTGAAGTCCATCTCGAGATGTTCAA
1 AACTTGACCATAATCTGTTTTATGTTCTCTCATGCAGGCTTGAAGTCCATCTCGAGATGTTCAA
*
3056568 AACTTGACCATAATCTGTTTTATGTTCTCTCATGTAGGCTTGAAGTCCATCTCGAGATGTTCAA
1 AACTTGACCATAATCTGTTTTATGTTCTCTCATGCAGGCTTGAAGTCCATCTCGAGATGTTCAA
3056632 AACT
1 AACT
3056636 ATCTATTTTG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (64 bp):
AACTTGACCATAATCTGTTTTATGTTCTCTCATGCAGGCTTGAAGTCCATCTCGAGATGTTCAA
Found at i:3059487 original size:34 final size:35
Alignment explanation
Indices: 3059430--3059496 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3059420 CAAACACTAG
*
3059430 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAAAATTTTCCAGTAAATCATTTTACAGAAAAGT
*
3059465 AAAAAATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAAAATTTTCCAGTAAATCATTTTACAGAAAA
3059497 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAAAATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:3070157 original size:30 final size:30
Alignment explanation
Indices: 3070121--3070180 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3070111 GACTAACAAT
* *
3070121 AATTAAATAAAT-TTTTAAAATTTCATAAAA
1 AATTAAA-AAATGTATTAAAAATTCATAAAA
*
3070151 AATTAAAATATGTATTAAAAATTCATAAAA
1 AATTAAAAAATGTATTAAAAATTCATAAAA
3070181 CTGGTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (30 bp):
AATTAAAAAATGTATTAAAAATTCATAAAA
Found at i:3071133 original size:24 final size:25
Alignment explanation
Indices: 3071106--3071169 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 25
3071096 CAAACACTTT
3071106 TTTATATTAAAATATATTT-TTTAA
1 TTTATATTAAAATATATTTATTTAA
* * * *
3071130 TTTA-AATAAAATGTTTTTATTTTA
1 TTTATATTAAAATATATTTATTTAA
*
3071154 TTTTTATTCAAAATAT
1 TTTATATT-AAAATAT
3071170 TTAAATATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
23 11 0.37
24 11 0.37
25 2 0.07
26 6 0.20
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTATATTAAAATATATTTATTTAA
Found at i:3072613 original size:62 final size:62
Alignment explanation
Indices: 3072529--3072651 Score: 203
Period size: 62 Copynumber: 2.0 Consensus size: 62
3072519 TTTGTTAATA
* *
3072529 ATTTATGGGATTATGTTACAAATTGTT-AGTGTTTAGTATAGGGTTTTGTGATTTTTTAGTAG
1 ATTTATGGGATTAGGTTACAAATTGTTGA-TGTTTAGTATAGAGTTTTGTGATTTTTTAGTAG
*
3072591 ATTTATGGGATTAGGTTCCAAATTGTTGATGTTTAGTATAGAGTTTTGTGATTTTTTAGTA
1 ATTTATGGGATTAGGTTACAAATTGTTGATGTTTAGTATAGAGTTTTGTGATTTTTTAGTA
3072652 ATATAATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 56 0.98
63 1 0.02
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.50
Consensus pattern (62 bp):
ATTTATGGGATTAGGTTACAAATTGTTGATGTTTAGTATAGAGTTTTGTGATTTTTTAGTAG
Found at i:3072805 original size:103 final size:105
Alignment explanation
Indices: 3072610--3072854 Score: 374
Period size: 103 Copynumber: 2.4 Consensus size: 105
3072600 ATTAGGTTCC
* *
3072610 AAATTGTT-GATGTTTAGTATAGAGTTTTGTGA-TTTTTTAGTAATATAATTTTTTTAAAAATAA
1 AAATTGTTAG-TGTTTAGTTTAGTGTTTTGTGATTTTTTTAGTAATATAATTTTTTTAAAAATAA
* *
3072673 TTTTATAGTTATTTTGTTATTAATTTATGATTAGGTTTTAT
65 TTTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAT
* * *
3072714 AAATTGTTAGTGTTTA-TTTATGTGTTTAGTGATTTTTTTAGTAATGTATTTTTTTTAAAAA-AA
1 AAATTGTTAGTGTTTAGTTTA-GTGTTTTGTGATTTTTTTAGTAATATAATTTTTTTAAAAATAA
3072777 -TTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAT
65 TTTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAT
3072817 AAATTGTTAGTGTTTAGTTTAGTGTTTTGTGATTTTTT
1 AAATTGTTAGTGTTTAGTTTAGTGTTTTGTGATTTTTT
3072855 AATGTAATTT
Statistics
Matches: 129, Mismatches: 8, Indels: 9
0.88 0.05 0.06
Matches are distributed among these distances:
103 73 0.57
104 29 0.22
105 27 0.21
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (105 bp):
AAATTGTTAGTGTTTAGTTTAGTGTTTTGTGATTTTTTTAGTAATATAATTTTTTTAAAAATAAT
TTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAT
Found at i:3072897 original size:15 final size:16
Alignment explanation
Indices: 3072879--3072918 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
3072869 ATGATGTAAT
3072879 TTTATTTG-ATTTTTA
1 TTTATTTGAATTTTTA
3072894 TTTATTTGAACATTTTTA
1 TTTATTTG-A-ATTTTTA
3072912 TTTATTT
1 TTTATTT
3072919 ATTGAAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
18 14 0.64
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.70
Consensus pattern (16 bp):
TTTATTTGAATTTTTA
Found at i:3074773 original size:457 final size:457
Alignment explanation
Indices: 3073919--3074779 Score: 1598
Period size: 457 Copynumber: 1.9 Consensus size: 457
3073909 ATCAATGGCA
*
3073919 TTGATTTCCGCTTTAGTCGAGCGATGGCGTCCAGAGACCCACACATTTCATTTGTCGTGCGGAGA
1 TTGATTTCCGCTTTAGTCGAGCGATGGCGTCCAAAGACCCACACATTTCATTTGTCGTGCGGAGA
3073984 GTGCATCATCACTCTAGAGGATGTTGCACTACAGCTCAGACTCCCCATCGACGGGAATACGGTCA
66 GTGCATCATCACTCTAGAGGATGTTGCACTACAGCTCAGACTCCCCATCGACGGGAATACGGTCA
*
3074049 CGGGCGTAAGTTTGACCTCTAGGCCGGCTGCCCTTTGCTATGACTTATTTGAACGCTCGCCAAGT
131 CGGGCGTAAGTTTGACCTCTAGGCCGGCTGCCCTTTGCTATGACTTATTTGAACGCTCACCAAGT
3074114 GAGGAGAAATTTATCAGTTTGAGGTTTTCATGGCTAAAGGCCAATTCTGAGTATTTGCCGAGTAC
196 GAGGAGAAATTTATCAGTTTGAGGTTTTCATGGCTAAAGGCCAATTCTGAGTATTTGCCGAGTAC
*
3074179 TGCCAATGGATGGGAGGTGATGCAGGTCATTCGAGCTTACATTATGCACCTTATAAGGGGTGTAC
261 TGCCAATGGATGAGAGGTGATGCAGGTCATTCGAGCTTACATTATGCACCTTATAAGGGGTGTAC
3074244 TCATGCCGAATGCAAATGGTAATAGTGTCCACTTGATGTACTTACCCCTATTATCCAATTTGCAT
326 TCATGCCGAATGCAAATGGTAATAGTGTCCACTTGATGTACTTACCCCTATTATCCAATTTGCAT
3074309 AACACTCGTTCATATAGTCGGGTTCAGATCAGTGGCATTGATCTGAACTTTTGATCTACGATAGA
391 AACACTCGTTCATATAGTCGGGTTCAGATCAGTGGCATTGATCTGAACTTTTGATCTACGATAGA
3074374 AC
456 AC
3074376 TTGATTTCCGCTTTAGTCGAGCGATGGCGTCCAAAGACCCACACATTTCATTTGTCGTGC-GAGG
1 TTGATTTCCGCTTTAGTCGAGCGATGGCGTCCAAAGACCCACACATTTCATTTGTCGTGCGGA-G
* * * *
3074440 AGTGCATCATCACTCTAGAGGATGTTGCACTACAGCTCGGGCTCCCCATCGACGGGAATGCGGTT
65 AGTGCATCATCACTCTAGAGGATGTTGCACTACAGCTCAGACTCCCCATCGACGGGAATACGGTC
*
3074505 ACGGGCGTAAGTTTGACCTCTAGGTCGGCTGCCCTTTGCTATGACTTATTTGAACGCTCACCAAG
130 ACGGGCGTAAGTTTGACCTCTAGGCCGGCTGCCCTTTGCTATGACTTATTTGAACGCTCACCAAG
* *
3074570 TGAGGGGAAATTTATCAGTTTGAGGTTTTCATGGCTAAAGTCCAATTCTGAGTATTTGCCGAGTA
195 TGAGGAGAAATTTATCAGTTTGAGGTTTTCATGGCTAAAGGCCAATTCTGAGTATTTGCCGAGTA
3074635 CTGCCAATGGATGAGAGGTGATGCAGGTCATTCGAGCTTACATTATGCACCTTATAAGGGGTGTA
260 CTGCCAATGGATGAGAGGTGATGCAGGTCATTCGAGCTTACATTATGCACCTTATAAGGGGTGTA
* *
3074700 CTCATGCCGGATGCAAATGGTAATAGTGTCCACTTGATGTACTTACCCCTATTATCCACTTTGCA
325 CTCATGCCGAATGCAAATGGTAATAGTGTCCACTTGATGTACTTACCCCTATTATCCAATTTGCA
3074765 TAACACTCGTTCATA
390 TAACACTCGTTCATA
3074780 CAGTTAGGGG
Statistics
Matches: 391, Mismatches: 12, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
456 2 0.01
457 389 0.99
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (457 bp):
TTGATTTCCGCTTTAGTCGAGCGATGGCGTCCAAAGACCCACACATTTCATTTGTCGTGCGGAGA
GTGCATCATCACTCTAGAGGATGTTGCACTACAGCTCAGACTCCCCATCGACGGGAATACGGTCA
CGGGCGTAAGTTTGACCTCTAGGCCGGCTGCCCTTTGCTATGACTTATTTGAACGCTCACCAAGT
GAGGAGAAATTTATCAGTTTGAGGTTTTCATGGCTAAAGGCCAATTCTGAGTATTTGCCGAGTAC
TGCCAATGGATGAGAGGTGATGCAGGTCATTCGAGCTTACATTATGCACCTTATAAGGGGTGTAC
TCATGCCGAATGCAAATGGTAATAGTGTCCACTTGATGTACTTACCCCTATTATCCAATTTGCAT
AACACTCGTTCATATAGTCGGGTTCAGATCAGTGGCATTGATCTGAACTTTTGATCTACGATAGA
AC
Found at i:3075648 original size:12 final size:12
Alignment explanation
Indices: 3075631--3075662 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3075621 ACATCATGCA
3075631 CCAGAGCCGGAG
1 CCAGAGCCGGAG
*
3075643 CCAGAGTCGGAG
1 CCAGAGCCGGAG
3075655 CCAGAGCC
1 CCAGAGCC
3075663 AGAGGTAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.25, C:0.34, G:0.38, T:0.03
Consensus pattern (12 bp):
CCAGAGCCGGAG
Found at i:3075673 original size:18 final size:18
Alignment explanation
Indices: 3075632--3075675 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3075622 CATCATGCAC
*
3075632 CAGAGCCGGAGCCAGAGT
1 CAGAGCCAGAGCCAGAGT
*
3075650 CGGAGCCAGAGCCAGAGGT
1 CAGAGCCAGAGCCAGA-GT
3075669 -AGAGCCA
1 CAGAGCCA
3075676 AAACTACACT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.30, C:0.27, G:0.39, T:0.05
Consensus pattern (18 bp):
CAGAGCCAGAGCCAGAGT
Done.