Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008243.1 Hibiscus syriacus cultivar Beakdansim tig00110893_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10265705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 49
Found at i:2492739 original size:14 final size:14
Alignment explanation
Indices: 2492720--2492756 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2492710 TTTTTCCATA
2492720 TAGATCTCCTCATC
1 TAGATCTCCTCATC
2492734 TAGATCTCCTCATC
1 TAGATCTCCTCATC
2492748 TAGATCTCC
1 TAGATCTCC
2492757 ATTCATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (14 bp):
TAGATCTCCTCATC
Found at i:2496206 original size:31 final size:31
Alignment explanation
Indices: 2496119--2496245 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
2496109 AGAGTCGAGG
2496119 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
2496150 GAATTACCTATG-TCTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
* *
2496182 GTATACATATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * *
2496213 GTTTACCTAGGTTCTTCGGAACCTATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
2496244 GT
1 GT
2496246 TGCCAAGGAT
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
31 52 0.66
32 27 0.34
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:2496287 original size:30 final size:30
Alignment explanation
Indices: 2496233--2496304 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
2496223 GTTCTTCGGA
* * *
2496233 ACCTATGGACAGTTGCCAAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
*
2496263 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
2496293 ACCTCTGGATAG
1 ACCTCTGGATAG
2496305 GTCCTTCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCAAGGATCTTTATG
Found at i:2503087 original size:30 final size:30
Alignment explanation
Indices: 2503035--2503114 Score: 115
Period size: 30 Copynumber: 2.6 Consensus size: 30
2503025 CTTTTAAAAC
*
2503035 TTGCAATATAGTCCCCTAACATTTAGTCCGT
1 TTGCAATATGGTCCCC-AACATTTAGTCCGT
* * *
2503066 TTTCAATATGGTTCCCAACATTTATTCCGT
1 TTGCAATATGGTCCCCAACATTTAGTCCGT
2503096 TTGCAATATGGTCCCCAAC
1 TTGCAATATGGTCCCCAAC
2503115 GTAACTGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 30 0.70
31 13 0.30
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.36
Consensus pattern (30 bp):
TTGCAATATGGTCCCCAACATTTAGTCCGT
Found at i:2505571 original size:23 final size:22
Alignment explanation
Indices: 2505542--2505590 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
2505532 TCATTTTTTA
2505542 AAAAAAATAAATAAAAATGCAAT
1 AAAAAAATAAATAAAAATG-AAT
* *
2505565 AAAAAAATAATTAAAAGTGAAT
1 AAAAAAATAAATAAAAATGAAT
2505587 AAAA
1 AAAA
2505591 TTCAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.18
Consensus pattern (22 bp):
AAAAAAATAAATAAAAATGAAT
Found at i:2508091 original size:17 final size:16
Alignment explanation
Indices: 2508065--2508096 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2508055 AATATGGATT
2508065 TAAAATTTTTAGAATA
1 TAAAATTTTTAGAATA
2508081 TAAATATTTTTAGAAT
1 TAAA-ATTTTTAGAAT
2508097 TGAAGGTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TAAAATTTTTAGAATA
Found at i:2511652 original size:36 final size:36
Alignment explanation
Indices: 2511605--2511685 Score: 162
Period size: 36 Copynumber: 2.2 Consensus size: 36
2511595 CTTGATTTCA
2511605 ATTCAGCCTCTGGCCCTGAAATAAAGGACAACAAGG
1 ATTCAGCCTCTGGCCCTGAAATAAAGGACAACAAGG
2511641 ATTCAGCCTCTGGCCCTGAAATAAAGGACAACAAGG
1 ATTCAGCCTCTGGCCCTGAAATAAAGGACAACAAGG
2511677 ATTCAGCCT
1 ATTCAGCCT
2511686 GTGATGCCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (36 bp):
ATTCAGCCTCTGGCCCTGAAATAAAGGACAACAAGG
Found at i:2514207 original size:120 final size:119
Alignment explanation
Indices: 2513976--2514212 Score: 386
Period size: 120 Copynumber: 2.0 Consensus size: 119
2513966 GTGAACTTTT
*
2513976 CACTACTGATTTGGTTACATTTGGATTATTTTCTGTACAGAAACCGTTACTAGAATTGGAAGCAA
1 CACTACTGATTTGGTTACATTTGGATTATTTTCTGTACAGAAACAGTTACTAGAATTGGAAGCAA
* *
2514041 AAGGGCGCGTTCTGCAACTTTTTGTTGTTTTTTGATCATGGCCGGAGGCATGTG
66 AAGGGCGCGTTCTGCAACTTTTTGTTATTTTCTGATCATGGCCGGAGGCATGTG
* * *
2514095 CACTACTGATTTGGTTGCATTTGGCTTATTTTCTGTGCAGAGAACAGTTTACTAGAATTGGAAGC
1 CACTACTGATTTGGTTACATTTGGATTATTTTCTGTACAGA-AACAG-TTACTAGAATTGGAAGC
*
2514160 AAAA-GGCGCGTTCTGCAACTTTTTGTTATTTTCTGATCATGGTCGGAGGCATG
64 AAAAGGGCGCGTTCTGCAACTTTTTGTTATTTTCTGATCATGGCCGGAGGCATG
2514213 GACACGACGA
Statistics
Matches: 109, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
119 38 0.35
120 50 0.46
121 21 0.19
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.36
Consensus pattern (119 bp):
CACTACTGATTTGGTTACATTTGGATTATTTTCTGTACAGAAACAGTTACTAGAATTGGAAGCAA
AAGGGCGCGTTCTGCAACTTTTTGTTATTTTCTGATCATGGCCGGAGGCATGTG
Found at i:2517724 original size:45 final size:47
Alignment explanation
Indices: 2517673--2517760 Score: 135
Period size: 45 Copynumber: 1.9 Consensus size: 47
2517663 CGAATAAATA
*
2517673 CATGCGAACTAGATATCATGTGGTCAGG-TTTATTTTT-TGAACAAG
1 CATGCGAACTAGATATCATGCGGTCAGGATTTATTTTTGTGAACAAG
* *
2517718 CATGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1 CATGCGAACTAGATATCATGCGGTCAGGATTTATTTTTGTGAA
2517761 TAACAAAGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 25 0.66
46 9 0.24
47 4 0.11
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (47 bp):
CATGCGAACTAGATATCATGCGGTCAGGATTTATTTTTGTGAACAAG
Found at i:2526316 original size:20 final size:20
Alignment explanation
Indices: 2526288--2526345 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
2526278 CAAAAGACCT
* * *
2526288 CATACATGTTCCAAATAATA
1 CATATATGTCCCAAAGAATA
*
2526308 CATATATGTCCCGAAGAATA
1 CATATATGTCCCAAAGAATA
2526328 CATATATGTCCCGAAAGA
1 CATATATGTCCC-AAAGA
2526346 CCACGTAGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 28 0.88
21 4 0.12
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (20 bp):
CATATATGTCCCAAAGAATA
Found at i:2530832 original size:37 final size:36
Alignment explanation
Indices: 2530737--2530842 Score: 89
Period size: 36 Copynumber: 3.0 Consensus size: 36
2530727 TCTTGGTTAA
*
2530737 TGGCCAAACTTTGAACATGGG-AATTTCATATTTGG
1 TGGCCAAACTTTGAACATGGGAAAATTCATATTTGG
* *
2530772 TGG-CTAAC-TTGTACACATTGGAAAATTC-T-TTGGTAGG
1 TGGCCAAACTTTG-A-ACATGGGAAAATTCATATT--T-GG
*
2530809 TGGCCAAACTTTGAACATGGG-AAATCCATATTTG
1 TGGCCAAACTTTGAACATGGGAAAATTCATATTTG
2530843 ATCCCTAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 20
0.68 0.07 0.25
Matches are distributed among these distances:
33 3 0.05
34 7 0.13
35 11 0.20
36 12 0.22
37 12 0.22
38 7 0.13
39 3 0.05
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (36 bp):
TGGCCAAACTTTGAACATGGGAAAATTCATATTTGG
Found at i:2535982 original size:24 final size:24
Alignment explanation
Indices: 2535937--2535982 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
2535927 TAAAATATAA
*
2535937 AAATAATATTATCTTAATAAAAAT
1 AAATAATATTATCTTAACAAAAAT
* * *
2535961 AAATAGTATTATTTTCACAAAA
1 AAATAATATTATCTTAACAAAA
2535983 TTCGAGTTCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATAATATTATCTTAACAAAAAT
Found at i:2537759 original size:29 final size:30
Alignment explanation
Indices: 2537703--2537763 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
2537693 TTCAATACAC
* * *
2537703 GAAATATAATATTCTTCGTCATTTAATTAT
1 GAAATATAATATTCTTCATCAGTCAATTAT
*
2537733 GAAA-ATAATATTCTTTATCAGTCAATTAT
1 GAAATATAATATTCTTCATCAGTCAATTAT
2537762 GA
1 GA
2537764 CTTATCATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (30 bp):
GAAATATAATATTCTTCATCAGTCAATTAT
Found at i:2537917 original size:8 final size:7
Alignment explanation
Indices: 2537903--2537947 Score: 51
Period size: 6 Copynumber: 6.7 Consensus size: 7
2537893 TTTACCCATT
2537903 TTATTTA
1 TTATTTA
2537910 TATATTTA
1 T-TATTTA
2537918 TTA-TTA
1 TTATTTA
*
2537924 TTA-TCA
1 TTATTTA
2537930 TTATTTA
1 TTATTTA
2537937 TTA-TTA
1 TTATTTA
2537943 TTATT
1 TTATT
2537948 GTTATTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 17 0.52
7 9 0.27
8 7 0.21
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (7 bp):
TTATTTA
Found at i:2537923 original size:3 final size:3
Alignment explanation
Indices: 2537915--2537963 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
2537905 ATTTATATAT
* * *
2537915 TTA TTA TTA TTA TCA TTA TTTA TTA TTA TTA TTG TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
2537961 TTA
1 TTA
2537964 AATATTACAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2539285 original size:25 final size:27
Alignment explanation
Indices: 2539256--2539320 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 27
2539246 TTCAAATTTC
*
2539256 ATTTTTGATTATT-TTT-TAATACTAT
1 ATTTTTAATTATTATTTGTAATACTAT
*
2539281 ATTTTTAATTATTATTTGTAATATTAT
1 ATTTTTAATTATTATTTGTAATACTAT
*
2539308 -TTTTTTATTATTA
1 ATTTTTAATTATTA
2539321 CTTTTTATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 12 0.34
26 15 0.43
27 8 0.23
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (27 bp):
ATTTTTAATTATTATTTGTAATACTAT
Found at i:2539296 original size:13 final size:12
Alignment explanation
Indices: 2539280--2539344 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 12
2539270 TTTAATACTA
2539280 TATTTTTAATTAT
1 TATTTTT-ATTAT
2539293 TATTTGTAATATTAT
1 TATTT-T--TATTAT
2539308 T-TTTTTATTAT
1 TATTTTTATTAT
2539319 TACTTTTTATTAT
1 TA-TTTTTATTAT
*
2539332 TATTCTTATTAT
1 TATTTTTATTAT
2539344 T
1 T
2539345 TATATAAATA
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
11 7 0.15
12 10 0.22
13 18 0.39
14 4 0.09
15 6 0.13
16 1 0.02
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (12 bp):
TATTTTTATTAT
Found at i:2539312 original size:27 final size:25
Alignment explanation
Indices: 2539257--2539344 Score: 83
Period size: 25 Copynumber: 3.5 Consensus size: 25
2539247 TCAAATTTCA
* *
2539257 TTTTTGATTATT-TTTTAATACTAT
1 TTTTTTATTATTATTTTAATATTAT
*
2539281 ATTTTTAATTATTATTTGTAATATTAT
1 -TTTTTTATTATTATTT-TAATATTAT
2539308 TTTTTTATTATTACTTTT--TATTAT
1 TTTTTTATTATTA-TTTTAATATTAT
*
2539332 TATTCTTATTATT
1 T-TTTTTATTATT
2539345 TATATAAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
24 7 0.13
25 21 0.38
26 16 0.29
27 11 0.20
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.68
Consensus pattern (25 bp):
TTTTTTATTATTATTTTAATATTAT
Found at i:2539347 original size:16 final size:17
Alignment explanation
Indices: 2539311--2539347 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2539301 ATATTATTTT
*
2539311 TTTATTATTACTTTTTA
1 TTTATTATTACTTATTA
2539328 -TTATTATT-CTTATTA
1 TTTATTATTACTTATTA
2539343 TTTAT
1 TTTAT
2539348 ATAAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATTATTACTTATTA
Found at i:2539564 original size:20 final size:19
Alignment explanation
Indices: 2539539--2539576 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2539529 TTTTTAAATC
2539539 ATATATTAACTATTTTAATT
1 ATATATTAA-TATTTTAATT
*
2539559 ATATATTAATTTTTTAAT
1 ATATATTAATATTTTAAT
2539577 ATTGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATATTAATATTTTAATT
Found at i:2539665 original size:29 final size:29
Alignment explanation
Indices: 2539632--2539688 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
2539622 ATATTTCTAA
2539632 ATAAAAAAATATTTTATTTATAAATATAT
1 ATAAAAAAATATTTTATTTATAAATATAT
** * *
2539661 ATAAATTAATATTTTTTTTATAATTATA
1 ATAAAAAAATATTTTATTTATAAATATA
2539689 ATTTTGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
ATAAAAAAATATTTTATTTATAAATATAT
Found at i:2541758 original size:8 final size:7
Alignment explanation
Indices: 2541734--2541775 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
2541724 TTTTCATACA
2541734 TGCA-TT
1 TGCATTT
2541740 TGCATTT
1 TGCATTT
2541747 TGCATCTT
1 TGCAT-TT
2541755 TGCATTT
1 TGCATTT
* *
2541762 TTCATTG
1 TGCATTT
2541769 TGCATTT
1 TGCATTT
2541776 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:2541758 original size:15 final size:14
Alignment explanation
Indices: 2541734--2541775 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
2541724 TTTTCATACA
2541734 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
2541747 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
2541762 TTCATTGTGCATTT
1 TGCATTTTGCATTT
2541776 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:2544296 original size:8 final size:7
Alignment explanation
Indices: 2544273--2544336 Score: 53
Period size: 7 Copynumber: 9.4 Consensus size: 7
2544263 TCCAGCAAAG
*
2544273 AAAGAAG
1 AAAGAAA
*
2544280 AAGGAAA
1 AAAGAAA
2544287 AAATG-AA
1 AAA-GAAA
2544294 AAAGAAA
1 AAAGAAA
2544301 AAAGAAA
1 AAAGAAA
*
2544308 AAAG-GA
1 AAAGAAA
2544314 AAA-AAA
1 AAAGAAA
*
2544320 GAAGAAA
1 AAAGAAA
*
2544327 AAGGAAA
1 AAAGAAA
2544334 AAA
1 AAA
2544337 AGGAAAATTG
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
6 8 0.18
7 35 0.80
8 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (7 bp):
AAAGAAA
Found at i:2544297 original size:21 final size:20
Alignment explanation
Indices: 2544273--2544335 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
2544263 TCCAGCAAAG
*
2544273 AAAGAAGAAGGAAAAAATGAA
1 AAAGAAGAA-GAAAAAAGGAA
*
2544294 AAAGAAAAAAGAAAAAAGGAA
1 AAAG-AAGAAGAAAAAAGGAA
2544315 AAA-AAGAAG-AAAAAGGAA
1 AAAGAAGAAGAAAAAAGGAA
2544333 AAA
1 AAA
2544336 AAGGAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
18 12 0.32
19 5 0.13
21 17 0.45
22 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.02
Consensus pattern (20 bp):
AAAGAAGAAGAAAAAAGGAA
Found at i:2544327 original size:18 final size:16
Alignment explanation
Indices: 2544280--2544343 Score: 71
Period size: 18 Copynumber: 4.0 Consensus size: 16
2544270 AAGAAAGAAG
*
2544280 AAGGAAAAAATG-AAA
1 AAGGAAAAAAAGAAAA
2544295 AA-G-AAAAAAGAAAA
1 AAGGAAAAAAAGAAAA
2544309 AAGGAAAAAAAGAAGAAA
1 AAGGAAAAAAAG-A-AAA
2544327 AAGGAAAAAAAGGAAAA
1 AAGGAAAAAAA-GAAAA
2544344 TTGAATCAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
13 6 0.14
14 6 0.14
15 3 0.07
16 7 0.17
17 4 0.10
18 15 0.36
19 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (16 bp):
AAGGAAAAAAAGAAAA
Found at i:2544343 original size:8 final size:8
Alignment explanation
Indices: 2544280--2544343 Score: 62
Period size: 9 Copynumber: 8.0 Consensus size: 8
2544270 AAGAAAGAAG
2544280 AAGGAAAA
1 AAGGAAAA
*
2544288 AATG-AAA
1 AAGGAAAA
2544295 AA-GAAAA
1 AAGGAAAA
2544302 AA-GAAAA
1 AAGGAAAA
2544309 AAGGAAAAA
1 AAGG-AAAA
*
2544318 AAGAAGAAA
1 AAGGA-AAA
2544327 AAGGAAAAA
1 AAGG-AAAA
2544336 AAGGAAAA
1 AAGGAAAA
2544344 TTGAATCAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
6 1 0.02
7 17 0.35
8 9 0.19
9 20 0.42
10 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (8 bp):
AAGGAAAA
Found at i:2546855 original size:116 final size:115
Alignment explanation
Indices: 2546597--2546923 Score: 503
Period size: 116 Copynumber: 2.8 Consensus size: 115
2546587 AAGTGCCATG
* * * *
2546597 TGCTCATAGTAGAAATAAGAAGACCCAATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
2546662 TGGTTTGGTATGAATCCCAAAAACCAATCATTGGATTTGAAAGATTAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATT
* * *
2546712 TTCTCATGGTAGAAATAAGGGGGCCCAATGGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
2546777 TGGTTTGGTATGAACCCCAAAAAACCAATCATTAGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCC-AAAAACCAATCATTAGATTTGAAAGATGAATT
2546828 TGCTCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * *
2546893 TGGTTCGATAGGAACCAC-AGAACCAATCATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATT
2546924 GGAATTAAAA
Statistics
Matches: 193, Mismatches: 18, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
114 12 0.06
115 75 0.39
116 106 0.55
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (115 bp):
TGCTCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATT
Found at i:2548084 original size:491 final size:491
Alignment explanation
Indices: 2547158--2548140 Score: 1912
Period size: 491 Copynumber: 2.0 Consensus size: 491
2547148 ACCACATCTC
2547158 TTCATGGCTATTGAAACCTCAGCCTCTGAGAATCCCATTTTCGTCAAATATAACAGTTTATTCTC
1 TTCATGGCTATTGAAACCTCAGCCTCTGAGAATCCCATTTTCGTCAAATATAACAGTTTATTCTC
2547223 CTCATCAGAATAAGAATTCAGGATTTCCTCGATATCAGAAGAACTATCAATATCTGTGAAATCAT
66 CTCATCAGAATAAGAATTCAGGATTTCCTCGATATCAGAAGAACTATCAATATCTGTGAAATCAT
2547288 CCTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAATCAACATATTGCATGGGTGTGGAT
131 CCTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAATCAACATATTGCATGGGTGTGGAT
2547353 TTTTCAAAAGCCTGTATCACTGTATATGTAGTCTTGCTATTGCATCAGATTACTGTTTGCATAAA
196 TTTTCAAAAGCCTGTATCACTGTATATGTAGTCTTGCTATTGCATCAGATTACTGTTTGCATAAA
2547418 TTGGTTTCTCTCCCACAGAAAAGTATATTTCAGAGATGGCTTTCACTAAAAGATGATAAGCCACT
261 TTGGTTTCTCTCCCACAGAAAAGTATATTTCAGAGATGGCTTTCACTAAAAGATGATAAGCCACT
*
2547483 GTGTCAGCCTGGAACGGATTACCAAGCTATTTTTACTTCATTGCCTGACTAAATCCCTCCAGATA
326 GTGTCAGCCTGGAACGGATTACCAAGCTATTTTTACTTAATTGCCTGACTAAATCCCTCCAGATA
*
2547548 CAGAAAATGGTCACCTCATTCAGAAGACACATATTTCATACGTTTCTGTCAGAATGATTGAATAC
391 CAGAAAATGGTCACCTCATTCAGAAGACACATATTTCAGACGTTTCTGTCAGAATGATTGAATAC
2547613 TTCTTAAGTTTGTGACAACATAAAGAGAATTTCAGT
456 TTCTTAAGTTTGTGACAACATAAAGAGAATTTCAGT
*
2547649 TTCATGGTTATTGAAACCTCAGCCTCTGAGAATCCCATTTTCGTCAAATATAACAGTTTATTCTC
1 TTCATGGCTATTGAAACCTCAGCCTCTGAGAATCCCATTTTCGTCAAATATAACAGTTTATTCTC
2547714 CTCATCAGAATAAGAATTCAGGATTTCCTCGATATCAGAAGAACTATCAATATCTGTGAAATCAT
66 CTCATCAGAATAAGAATTCAGGATTTCCTCGATATCAGAAGAACTATCAATATCTGTGAAATCAT
2547779 CCTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAATCAACATATTGCATGGGTGTGGAT
131 CCTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAATCAACATATTGCATGGGTGTGGAT
* *
2547844 TTTTCAAGAGCCTGTATTACTGTATATGTAGTCTTGCTATTGCATCAGATTACTGTTTGCATAAA
196 TTTTCAAAAGCCTGTATCACTGTATATGTAGTCTTGCTATTGCATCAGATTACTGTTTGCATAAA
*
2547909 TTGGTTTCTCTCCCACAGAAAAGTATATTTCAGAGATGGCTTTCACTGAAAGATGATAAGCCACT
261 TTGGTTTCTCTCCCACAGAAAAGTATATTTCAGAGATGGCTTTCACTAAAAGATGATAAGCCACT
2547974 GTGTCAGCCTGGAACGGATTACCAAGCTATTTTTACTTAATTGCCTGACTAAATCCCTCCAGATA
326 GTGTCAGCCTGGAACGGATTACCAAGCTATTTTTACTTAATTGCCTGACTAAATCCCTCCAGATA
2548039 CAGAAAATGGTCACCTCATTCAGAAGACACATATTTCAGACGTTTCTGTCAGAATGATTGAATAC
391 CAGAAAATGGTCACCTCATTCAGAAGACACATATTTCAGACGTTTCTGTCAGAATGATTGAATAC
2548104 TTCTTAAGTTTGTGACAACATAAAGAGAATTTCAGT
456 TTCTTAAGTTTGTGACAACATAAAGAGAATTTCAGT
2548140 T
1 T
2548141 ACTTGACAAT
Statistics
Matches: 486, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
491 486 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (491 bp):
TTCATGGCTATTGAAACCTCAGCCTCTGAGAATCCCATTTTCGTCAAATATAACAGTTTATTCTC
CTCATCAGAATAAGAATTCAGGATTTCCTCGATATCAGAAGAACTATCAATATCTGTGAAATCAT
CCTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAATCAACATATTGCATGGGTGTGGAT
TTTTCAAAAGCCTGTATCACTGTATATGTAGTCTTGCTATTGCATCAGATTACTGTTTGCATAAA
TTGGTTTCTCTCCCACAGAAAAGTATATTTCAGAGATGGCTTTCACTAAAAGATGATAAGCCACT
GTGTCAGCCTGGAACGGATTACCAAGCTATTTTTACTTAATTGCCTGACTAAATCCCTCCAGATA
CAGAAAATGGTCACCTCATTCAGAAGACACATATTTCAGACGTTTCTGTCAGAATGATTGAATAC
TTCTTAAGTTTGTGACAACATAAAGAGAATTTCAGT
Found at i:2550506 original size:113 final size:113
Alignment explanation
Indices: 2550308--2550812 Score: 938
Period size: 113 Copynumber: 4.5 Consensus size: 113
2550298 TAGCAAAGAT
*
2550308 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
2550373 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
2550421 TCAAATCCATCATTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
2550486 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
2550534 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTAATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * * *
2550599 AGAAGGAATAAGAAATTCATAATGATAAGAATTTGTTTAACTTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
2550647 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
2550712 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
2550760 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAA
2550813 AAACCTGTTC
Statistics
Matches: 378, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 378 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (113 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:2550999 original size:113 final size:113
Alignment explanation
Indices: 2550797--2551117 Score: 426
Period size: 113 Copynumber: 2.8 Consensus size: 113
2550787 TTTCCAGAGA
* * * * * * *
2550797 AAGTTCATAATGAGAAAAACCTGTTCAACTTTTTCCTTAAATTCATCACTCGGTGGAACAACAGT
1 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCGATGGATCAACATT
* *
2550862 ACCAGTTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAG
66 ACCAGTTAGAATTCATAATAAGAAGAACTCATCTAAAGAAGGAAGAAG
* *
2550910 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCAACATT
1 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCGATGGATCAACATT
* *
2550975 ACCAGTTCGAATTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAG
66 ACCAGTTAGAATTCATAATAAGAAGAACTCATCTAAAGAAGGAAGAAG
* * * * *
2551023 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGGTCAACATT
1 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCGATGGATCAACATT
* * * * * *
2551088 GCCAGGTAGAGTTTATAATGAGCAGAACTC
66 ACCAGTTAGAATTCATAATAAGAAGAACTC
2551118 GTCATCTGAA
Statistics
Matches: 181, Mismatches: 27, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
113 181 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (113 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCGATGGATCAACATT
ACCAGTTAGAATTCATAATAAGAAGAACTCATCTAAAGAAGGAAGAAG
Found at i:2551200 original size:92 final size:92
Alignment explanation
Indices: 2551035--2551222 Score: 222
Period size: 92 Copynumber: 2.1 Consensus size: 92
2551025 GTTCATAATG
* * * * * *
2551035 AGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGGTCAACATTGCCAGGTAGAGT
1 AGAAGAATTTGTTCAACCTTTTGCTCAAATTCATCACTCGATGGATCAACATTGCCAGGAAGAGT
* * *
2551100 TTATAATGAGCAGAACTCGTCATCTGA
66 TCACAATGAGAAGAACTCGTCATCTGA
* * * *
2551127 AGAATAATTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGCATTTCCA-GAAGGAG
1 AGAAGAATTTGTTCAACCTTTTGCTCAAATTCATCACTCGATGGATCAACATTGCCAGGAA-GAG
2551191 TTCACAATGAGAAGAA--C-TCATCTGA
65 TTCACAATGAGAAGAACTCGTCATCTGA
2551216 AGAAGAA
1 AGAAGAA
2551223 AAAGTTCACA
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
89 14 0.17
90 1 0.01
91 2 0.02
92 64 0.79
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (92 bp):
AGAAGAATTTGTTCAACCTTTTGCTCAAATTCATCACTCGATGGATCAACATTGCCAGGAAGAGT
TCACAATGAGAAGAACTCGTCATCTGA
Found at i:2551491 original size:8 final size:7
Alignment explanation
Indices: 2551477--2551521 Score: 51
Period size: 6 Copynumber: 6.7 Consensus size: 7
2551467 TTTACCCATT
2551477 TTATTTA
1 TTATTTA
2551484 TATATTTA
1 T-TATTTA
2551492 TTA-TTA
1 TTATTTA
*
2551498 TTA-TCA
1 TTATTTA
2551504 TTATTTA
1 TTATTTA
2551511 TTA-TTA
1 TTATTTA
2551517 TTATT
1 TTATT
2551522 GTTATTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 17 0.52
7 9 0.27
8 7 0.21
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (7 bp):
TTATTTA
Found at i:2551497 original size:3 final size:3
Alignment explanation
Indices: 2551489--2551537 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
2551479 ATTTATATAT
* * *
2551489 TTA TTA TTA TTA TCA TTA TTTA TTA TTA TTA TTG TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
2551535 TTA
1 TTA
2551538 AATATTACAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2552832 original size:25 final size:24
Alignment explanation
Indices: 2552803--2552869 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 24
2552793 TTCAAATTTC
*
2552803 ATTTTTGATTATTTTT-TAATACTAT
1 ATTTTTAATTATTTTTGTAATA-T-T
2552828 ATTTTTAATTATTATTTGTAATATT
1 ATTTTTAATTATT-TTTGTAATATT
*
2552853 ATTTTATTATTATTTTT
1 ATTTT-TAATTATTTTT
2552870 ATTATTCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
25 21 0.57
26 11 0.30
27 5 0.14
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.67
Consensus pattern (24 bp):
ATTTTTAATTATTTTTGTAATATT
Found at i:2552843 original size:3 final size:3
Alignment explanation
Indices: 2552835--2552884 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
2552825 TATATTTTTA
* * *
2552835 ATT ATT ATT -TGT AAT ATT ATT -TT ATT ATT ATT TTT ATT ATT CTT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2552879 ATT ATT
1 ATT ATT
2552885 TATATAAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 3 0.08
3 35 0.92
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:2552869 original size:12 final size:12
Alignment explanation
Indices: 2552827--2552875 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
2552817 TTTAATACTA
2552827 TATTTTTAATTAT
1 TATTTTT-ATTAT
* *
2552840 TATTTGTAATAT
1 TATTTTTATTAT
2552852 TA-TTTTATTAT
1 TATTTTTATTAT
2552863 TATTTTTATTAT
1 TATTTTTATTAT
2552875 T
1 T
2552876 CTTATTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
11 9 0.29
12 16 0.52
13 6 0.19
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TATTTTTATTAT
Found at i:2552883 original size:12 final size:11
Alignment explanation
Indices: 2552830--2552884 Score: 60
Period size: 12 Copynumber: 4.9 Consensus size: 11
2552820 AATACTATAT
2552830 TTTTAATTATTA
1 TTTT-ATTATTA
*
2552842 TTTGTAATATTA
1 TTT-TATTATTA
2552854 TTTTATTATTA
1 TTTTATTATTA
2552865 -TTT-TTATTA
1 TTTTATTATTA
2552874 TTCTTATTATT
1 TT-TTATTATT
2552885 TATATAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 6 0.16
10 4 0.11
11 9 0.24
12 17 0.46
13 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:2553104 original size:20 final size:19
Alignment explanation
Indices: 2553067--2553116 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
2553057 TAAATATCCT
*
2553067 ATTTTTTAAATCATATATTA
1 ATTTTTT-AATTATATATTA
*
2553087 ATTATTTTAATTATATATTT
1 ATT-TTTTAATTATATATTA
2553107 ATTTTTTAAT
1 ATTTTTTAAT
2553117 ATTGAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 7 0.26
20 16 0.59
21 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTTTAATTATATATTA
Found at i:2553118 original size:119 final size:120
Alignment explanation
Indices: 2552967--2553208 Score: 280
Period size: 120 Copynumber: 2.0 Consensus size: 120
2552957 TTAATAATCA
*
2552967 TATTTTAATATATATTTATTTATTTTTCAATATT-AAG-AAAGGGCAT-TCTTAAAACAAC-TAG
1 TATTTTAATATATA-TTATTTATTTTTCAATATTGAAGAAAAGAGC-TGTCTTAAAAC-ACTTAG
* * * * *
2553028 ATGTTCATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTTTAAATCATATATTAAT
63 AAG-TCATTTTCTGATATTTCTAAATAAAAAAATATCCTA-TTTATAAAT-ATATATAAAT
* **
2553089 TATTTTAAT-TATA-TATTTATTTTTTAATATTGAAGAAAAGAGCTGTCTTAAGGCACTTAGAAG
1 TATTTTAATATATATTATTTATTTTTCAATATTGAAGAAAAGAGCTGTCTTAAAACACTTAGAAG
* **
2553152 TCTTTTTCTGATATTTCTAAATAAAAAAATATTTTATTTATAAATATATATAAAT
66 TCATTTTCTGATATTTCTAAATAAAAAAATATCCTATTTATAAATATATATAAAT
2553207 TA
1 TA
2553209 ATATTTTTTT
Statistics
Matches: 104, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
118 11 0.11
119 25 0.24
120 37 0.36
121 22 0.21
122 9 0.09
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (120 bp):
TATTTTAATATATATTATTTATTTTTCAATATTGAAGAAAAGAGCTGTCTTAAAACACTTAGAAG
TCATTTTCTGATATTTCTAAATAAAAAAATATCCTATTTATAAATATATATAAAT
Found at i:2553204 original size:29 final size:29
Alignment explanation
Indices: 2553172--2553228 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
2553162 ATATTTCTAA
2553172 ATAAAAAAATATTTTATTTATAAATATAT
1 ATAAAAAAATATTTTATTTATAAATATAT
** * *
2553201 ATAAATTAATATTTTTTTTATAATTATA
1 ATAAAAAAATATTTTATTTATAAATATA
2553229 ATTTTGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
ATAAAAAAATATTTTATTTATAAATATAT
Found at i:2553857 original size:2 final size:2
Alignment explanation
Indices: 2553852--2553893 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2553842 TATAAAAAAG
2553852 AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2553892 AT
1 AT
2553894 TCAACTTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2559151 original size:13 final size:13
Alignment explanation
Indices: 2559133--2559161 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2559123 TGAGTTCGTG
2559133 GCTCGTCTCTGTT
1 GCTCGTCTCTGTT
2559146 GCTCGTCTCTGTT
1 GCTCGTCTCTGTT
2559159 GCT
1 GCT
2559162 TGTTTCCCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.24, T:0.45
Consensus pattern (13 bp):
GCTCGTCTCTGTT
Found at i:2559694 original size:3 final size:3
Alignment explanation
Indices: 2559686--2559752 Score: 89
Period size: 3 Copynumber: 22.0 Consensus size: 3
2559676 ATATATATAT
* *
2559686 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TATT TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
**
2559732 TAA TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
2559753 AATTTAAATG
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 54 0.96
4 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2559730 original size:34 final size:34
Alignment explanation
Indices: 2559692--2559758 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
2559682 ATATTAATAA
*
2559692 TAATAATAATAATAATAATAATAATAATATTTAG
1 TAATAATAATAATAATAATAATAATAAAATTTAG
**
2559726 TAATAATAATTTTAATAATAATAATAAAATTTA
1 TAATAATAATAATAATAATAATAATAAAATTTA
2559759 AATGAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (34 bp):
TAATAATAATAATAATAATAATAATAAAATTTAG
Found at i:2560012 original size:76 final size:76
Alignment explanation
Indices: 2559881--2560090 Score: 366
Period size: 76 Copynumber: 2.8 Consensus size: 76
2559871 GATGGAAATG
* *
2559881 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
2559946 CCCGAATGCTT
66 CCCGAAGGCTT
*
2559957 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2560022 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
2560033 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACTCGAAGGTTTTGAAAACATCA
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
2560091 TGCACTGAAG
Statistics
Matches: 127, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 127 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:2560090 original size:45 final size:45
Alignment explanation
Indices: 2560022--2560135 Score: 165
Period size: 45 Copynumber: 2.5 Consensus size: 45
2560012 TCAAAAAGCT
*
2560022 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
2560069 CTCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * *
2560114 CCCTAAGGCTTTGAAGACATCA
1 CCCGAAGGTTTTGAAAACATCA
2560136 AAAAGCTCCC
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 54 0.89
47 7 0.11
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:2560103 original size:121 final size:122
Alignment explanation
Indices: 2559946--2560462 Score: 800
Period size: 121 Copynumber: 4.4 Consensus size: 122
2559936 TCAAAAAGCT
* *
2559946 CCCGAATGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAA-GGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
*
2560011 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
65 ATCAAAAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
* *
2560069 CTCGAAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAGACA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACA
*
2560133 TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
66 TCAAAAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
2560190 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACA
*
2560255 TCAAAAAGCTACCGAAGGCTTTTTGG-AA-A-CAT---C--AA--A---A-AGCTG-
66 TCAAAAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
* * *
2560297 -CCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGG-TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
2560361 ATCAAAAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
65 ATCAAAAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
2560419 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATG
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATG
2560463 TGGGAAATAG
Statistics
Matches: 362, Mismatches: 14, Indels: 38
0.87 0.03 0.09
Matches are distributed among these distances:
106 7 0.02
107 80 0.22
108 6 0.02
109 2 0.01
110 3 0.01
112 1 0.00
113 1 0.00
114 2 0.01
115 2 0.01
116 1 0.00
117 1 0.00
119 3 0.01
120 2 0.01
121 158 0.44
122 81 0.22
123 12 0.03
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (122 bp):
CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACA
TCAAAAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:2560157 original size:76 final size:76
Alignment explanation
Indices: 2560077--2560440 Score: 375
Period size: 76 Copynumber: 4.8 Consensus size: 76
2560067 GACTCGAAGG
* * *
2560077 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAGACATCAAAAAGC
1 TTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
*
2560142 TCCCGAAGGCT
66 TACCGAAGGCT
* *
2560153 TTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATC---ATG
1 TTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAG
*
2560215 C-ACTGAAGGAC-
65 CTACCGAAGG-CT
*** * * * * ** * * ** *
2560226 TTACAGATGACCCTAAGGCTTTGAA-AACAT-CA-AAAAGCTACCGAAGGCTTTTTGGAAACATC
1 TTTTGGA--AACATCATGCACTGAAGGACTTACAGATGA-C--CCGAAGGC--TTTGAAAACATC
*
2560288 AAAAAGCTGCCGAAGGCT
59 AAAAAGCTACCGAAGGCT
*
2560306 TTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
2560371 TACCGAAGGCT
66 TACCGAAGGCT
*
2560382 TTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCA
1 TTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
2560441 TGCACTGAAG
Statistics
Matches: 228, Mismatches: 43, Indels: 34
0.75 0.14 0.11
Matches are distributed among these distances:
72 2 0.01
73 13 0.06
74 7 0.03
75 17 0.07
76 139 0.61
77 11 0.05
78 18 0.08
79 6 0.03
80 13 0.06
81 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (76 bp):
TTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
TACCGAAGGCT
Found at i:2560194 original size:47 final size:47
Alignment explanation
Indices: 2560143--2560257 Score: 191
Period size: 46 Copynumber: 2.5 Consensus size: 47
2560133 TCAAAAAGCT
*
2560143 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
2560190 CCCGAAGG-TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
2560236 CCCTAAGGC--TTTGAAAACATCA
1 CCCGAAGGCTTTTTGAAAACATCA
2560258 AAAAGCTACC
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
45 13 0.20
46 44 0.68
47 8 0.12
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (47 bp):
CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:2560288 original size:31 final size:31
Alignment explanation
Indices: 2560245--2560319 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
2560235 ACCCTAAGGC
*
2560245 TTTGAAAACATCAAAAAGCTACCGAAGGCTT
1 TTTGGAAACATCAAAAAGCTACCGAAGGCTT
*
2560276 TTTGGAAACATCAAAAAGCTGCCGAAGGCTT
1 TTTGGAAACATCAAAAAGCTACCGAAGGCTT
2560307 TTTGGAAACATCA
1 TTTGGAAACATCA
2560320 TGCACTGAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (31 bp):
TTTGGAAACATCAAAAAGCTACCGAAGGCTT
Found at i:2560384 original size:107 final size:106
Alignment explanation
Indices: 2560191--2560395 Score: 374
Period size: 107 Copynumber: 1.9 Consensus size: 106
2560181 TACAGATGAC
*
2560191 CCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACAT
1 CCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACAT
2560256 CAAAAAGCTACCGAAGGCTTTTTGGAAACATCAAAAAGCTG
66 CAAAAAGCTACCGAAGGCTTTTTGGAAACATCAAAAAGCTG
* *
2560297 CCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACA
1 CCGAAGG-TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACA
2560362 TCAAAAAGCTACCGAAGGCTTTTTGGAAACATCA
65 TCAAAAAGCTACCGAAGGCTTTTTGGAAACATCA
2560396 TGCACTGAAG
Statistics
Matches: 95, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
106 7 0.07
107 88 0.93
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.22
Consensus pattern (106 bp):
CCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACAT
CAAAAAGCTACCGAAGGCTTTTTGGAAACATCAAAAAGCTG
Found at i:2560439 original size:45 final size:46
Alignment explanation
Indices: 2560373--2560462 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 46
2560363 CAAAAAGCTA
*
2560373 CCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
1 CCGAAGGC-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGAC
2560420 CCGAAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATG
1 CCGAAGGCTTTTGAAAACATCATGCACTGAAGGACTTACAGATG
2560463 TGGGAAATAG
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
45 35 0.83
47 7 0.17
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.23
Consensus pattern (46 bp):
CCGAAGGCTTTTGAAAACATCATGCACTGAAGGACTTACAGATGAC
Found at i:2561606 original size:54 final size:54
Alignment explanation
Indices: 2561524--2561745 Score: 311
Period size: 54 Copynumber: 4.1 Consensus size: 54
2561514 TCAGAATAGC
** * * *
2561524 ATGTTCGTAAAACATTTGACGGCGCATTCATCCTTTCCTGTGGCTTCTGCTCAG
1 ATGTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTAGCTTCTGCTCAG
* *
2561578 ATGTTCGTAAAATATTTGACAACACATTCATCCTTTCATGTAGTTTCTGCTCAG
1 ATGTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTAGCTTCTGCTCAG
* *
2561632 ATGTTTGTAAAACATTTGACAACACATTCAT-CTTCTCATGTGGCTTCTGCTCAG
1 ATGTTCGTAAAACATTTGACAACACATTCATCCTT-TCATGTAGCTTCTGCTCAG
* * * *
2561686 ATGTTCGTAAAATATTTGATAACACATTCATCCTTTCCTGTAGTTTCTGCTCAG
1 ATGTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTAGCTTCTGCTCAG
2561740 ATGTTC
1 ATGTTC
2561746 AAGAAAATTC
Statistics
Matches: 149, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
53 3 0.02
54 143 0.96
55 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.38
Consensus pattern (54 bp):
ATGTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTAGCTTCTGCTCAG
Found at i:2561713 original size:108 final size:108
Alignment explanation
Indices: 2561524--2561745 Score: 365
Period size: 108 Copynumber: 2.1 Consensus size: 108
2561514 TCAGAATAGC
** * *
2561524 ATGTTCGTAAAACATTTGACGGCGCATTCATCCTTTCCTGTGGCTTCTGCTCAGATGTTCGTAAA
1 ATGTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCTCAGATGTTCGTAAA
2561589 ATATTTGACAACACATTCATCCTTTCATGTAGTTTCTGCTCAG
66 ATATTTGACAACACATTCATCCTTTCATGTAGTTTCTGCTCAG
*
2561632 ATGTTTGTAAAACATTTGACAACACATTCAT-CTTCTCATGTGGCTTCTGCTCAGATGTTCGTAA
1 ATGTTCGTAAAACATTTGACAACACATTCATCCTT-TCATGTGGCTTCTGCTCAGATGTTCGTAA
* *
2561696 AATATTTGATAACACATTCATCCTTTCCTGTAGTTTCTGCTCAG
65 AATATTTGACAACACATTCATCCTTTCATGTAGTTTCTGCTCAG
2561740 ATGTTC
1 ATGTTC
2561746 AAGAAAATTC
Statistics
Matches: 105, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
107 3 0.03
108 102 0.97
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.38
Consensus pattern (108 bp):
ATGTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCTCAGATGTTCGTAAA
ATATTTGACAACACATTCATCCTTTCATGTAGTTTCTGCTCAG
Found at i:2562864 original size:35 final size:34
Alignment explanation
Indices: 2562825--2562897 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 34
2562815 CATTACTTCT
2562825 TATTGAGATGAACCTTCAAAATGCCCAAATATTC
1 TATTGAGATGAACCTTCAAAATGCCCAAATATTC
** * *
2562859 ATATTGTTATGAGCCTTCAAAATGCCCCAATATTC
1 -TATTGAGATGAACCTTCAAAATGCCCAAATATTC
2562894 TATT
1 TATT
2562898 TCTGATTGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
34 4 0.12
35 30 0.88
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (34 bp):
TATTGAGATGAACCTTCAAAATGCCCAAATATTC
Found at i:2563869 original size:114 final size:114
Alignment explanation
Indices: 2563669--2563894 Score: 353
Period size: 114 Copynumber: 2.0 Consensus size: 114
2563659 GATCATGCAG
* * * * *
2563669 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGGTTCTGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
* *
2563734 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGAAGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* * *
2563783 TTCATCTTTTAAATCCAATGATTGGTTTTGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGGTTCTGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
*
2563848 ACACTTCCAGAAGAAGCTATTGAGTCTTCTTATTTCTACTATGAGCA
66 ACACTTCCAGAAGAAGCTATTGAGTCTCCTTATTTCTACTATGAGCA
2563895 CATGGCACTT
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATCGGTTCTGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGAAGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:2564690 original size:13 final size:13
Alignment explanation
Indices: 2564672--2564699 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2564662 TCCTGTAACC
2564672 AATGTTACCCTAT
1 AATGTTACCCTAT
2564685 AATGTTACCCTAT
1 AATGTTACCCTAT
2564698 AA
1 AA
2564700 AAAGGCCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (13 bp):
AATGTTACCCTAT
Found at i:2568735 original size:15 final size:15
Alignment explanation
Indices: 2568717--2568754 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2568707 TAAAAGTATG
2568717 AATGCAAAAATGAAA
1 AATGCAAAAATGAAA
* *
2568732 AATGCAAAGATGCAA
1 AATGCAAAAATGAAA
2568747 AATG-AAAA
1 AATGCAAAA
2568755 TGCATATATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.63, C:0.08, G:0.16, T:0.13
Consensus pattern (15 bp):
AATGCAAAAATGAAA
Found at i:2571334 original size:591 final size:593
Alignment explanation
Indices: 2570211--2571392 Score: 2350
Period size: 591 Copynumber: 2.0 Consensus size: 593
2570201 CCAACTAATT
2570211 GAAAGAAAAAATTTATTTATCATGGTATATAATAAATCCTAACCTCATGCTTTCTAGTTCCATGC
1 GAAAGAAAAAATTTATTTATCATGGTATATAATAAATCCTAACCTCATGCTTTCTAGTTCCATGC
2570276 TTTGTTTGGAAAAATTAACCTAATCGCATGATTTCTAGTTCGCATGCATTTATTCAGGGAGAAAA
66 TTTGTTTGGAAAAATTAACCTAATCGCATGATTTCTAGTTCGCATGCATTTATTCAGGGAGAAAA
2570341 AAATAATAATAAATTAAAAGCTAGAGCTTATTTCTCCTTTGTGTACACCTATGAACAAAGGTTCA
131 AAATAATAATAAATTAAAAGCTAGAGCTTATTTCTCCTTTGTGTACACCTATGAACAAAGGTTCA
2570406 GTACTGTCTTAGATTAGGTGAATTTCTAGGGTTTATAATATGCAGAGTTTCAGTTCTAGGAGTAA
196 GTACTGTCTTAGATTAGGTGAATTTCTAGGGTTTATAATATGCAGAGTTTCAGTTCTAGGAGTAA
2570471 AGGTACTCGAATTGTCCTTGTTGATGCCTCCTTGGGCTGTTAACCCTCAATCCTAGTCCATCACA
261 AGGTACTCGAATTGTCCTTGTTGATGCCTCCTTGGGCTGTTAACCCTCAATCCTAGTCCATCACA
2570536 GACTAAAGTGGATCGAGTTCAATTCGAGGGGATACATTTCTCTATGCCTGACACGGAGAATAAAT
326 GACTAAAGTGGATCGAGTTCAATTCGAGGGGATACATTTCTCTATGCCTGACACGGAGAATAAAT
2570601 TCTCACGAAGACATAGAGCATATGAACCCCGAAAGTTACTGGCTAGGTCTGACACGGAGAATAAA
391 TCTCACGAAGACATAGAGCATATGAACCCCGAAAGTTACTGGCTAGGTCTGACACGGAGAATAAA
2570666 TTCTCACGAAGACGTCGCTTTCACTCCCACTTAAAAGGGACAAACTCAATTATAGAGCTTTATGT
456 TTCTCACGAAGACGTCGCTTTCACTCCCACTTAAAAGGGACAAACTCAATTATAGAGCTTTATGT
2570731 TATGCAATGCAAGTGTTGTGTGTGAGGAGAAATGTTCAAACCTCTAACAGATAAATGAAATAATT
521 TATGCAATGCAAGTGTTGTGTGTGAGGAGAAATGTTCAAACCTCTAACAGATAAATGAAATAATT
2570796 AATACCCC
586 AATACCCC
2570804 GAAAGAAAAAATTTATTTATCATGGTATATAATAAATCCTAACCTCATGCTTTCTAGTTCCATGC
1 GAAAGAAAAAATTTATTTATCATGGTATATAATAAATCCTAACCTCATGCTTTCTAGTTCCATGC
2570869 TTTGTTTGG-AAAATTAACCTAATCGCATGATTTCTAGTTCGCATGCATTTATTCAGGGAG-AAA
66 TTTGTTTGGAAAAATTAACCTAATCGCATGATTTCTAGTTCGCATGCATTTATTCAGGGAGAAAA
2570932 AAATAATAATAAATTAAAAGCTAGAGCTTATTTCTCCTTTGTGTACACCTATGAACAAAGGTTCA
131 AAATAATAATAAATTAAAAGCTAGAGCTTATTTCTCCTTTGTGTACACCTATGAACAAAGGTTCA
2570997 GTACTGTCTTAGATTAGGTGAATTTCTAGGGTTTATAATATGCAGAGTTTCAGTTCTAGGAGTAA
196 GTACTGTCTTAGATTAGGTGAATTTCTAGGGTTTATAATATGCAGAGTTTCAGTTCTAGGAGTAA
2571062 AGGTACTCGAATTGTCCTTGTTGATGCCTCCTTGGGCTGTTAACCCTCAATCCTAGTCCATCACA
261 AGGTACTCGAATTGTCCTTGTTGATGCCTCCTTGGGCTGTTAACCCTCAATCCTAGTCCATCACA
2571127 GACTAAAGTGGATCGAGTTCAATTCGAGGGGATACATTTCTCTATGCCTGACACGGAGAATAAAT
326 GACTAAAGTGGATCGAGTTCAATTCGAGGGGATACATTTCTCTATGCCTGACACGGAGAATAAAT
2571192 TCTCACGAAGACATAGAGCATATGAACCCCGAAAGTTACTGGCTAGGTCTGACACGGAGAATAAA
391 TCTCACGAAGACATAGAGCATATGAACCCCGAAAGTTACTGGCTAGGTCTGACACGGAGAATAAA
2571257 TTCTCACGAAGACGTCGCTTTCACTCCCACTTAAAAGGGACAAACTCAATTATAGAGCTTTATGT
456 TTCTCACGAAGACGTCGCTTTCACTCCCACTTAAAAGGGACAAACTCAATTATAGAGCTTTATGT
2571322 TATGCAATGCAAGTGTTGTGTGTGAGGAGAAATGTTCAAACCTCTAACAGATAAATGAAATAATT
521 TATGCAATGCAAGTGTTGTGTGTGAGGAGAAATGTTCAAACCTCTAACAGATAAATGAAATAATT
2571387 AATACC
586 AATACC
2571393 TGAATAAAAA
Statistics
Matches: 589, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
591 464 0.79
592 51 0.09
593 74 0.13
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (593 bp):
GAAAGAAAAAATTTATTTATCATGGTATATAATAAATCCTAACCTCATGCTTTCTAGTTCCATGC
TTTGTTTGGAAAAATTAACCTAATCGCATGATTTCTAGTTCGCATGCATTTATTCAGGGAGAAAA
AAATAATAATAAATTAAAAGCTAGAGCTTATTTCTCCTTTGTGTACACCTATGAACAAAGGTTCA
GTACTGTCTTAGATTAGGTGAATTTCTAGGGTTTATAATATGCAGAGTTTCAGTTCTAGGAGTAA
AGGTACTCGAATTGTCCTTGTTGATGCCTCCTTGGGCTGTTAACCCTCAATCCTAGTCCATCACA
GACTAAAGTGGATCGAGTTCAATTCGAGGGGATACATTTCTCTATGCCTGACACGGAGAATAAAT
TCTCACGAAGACATAGAGCATATGAACCCCGAAAGTTACTGGCTAGGTCTGACACGGAGAATAAA
TTCTCACGAAGACGTCGCTTTCACTCCCACTTAAAAGGGACAAACTCAATTATAGAGCTTTATGT
TATGCAATGCAAGTGTTGTGTGTGAGGAGAAATGTTCAAACCTCTAACAGATAAATGAAATAATT
AATACCCC
Found at i:2573101 original size:13 final size:13
Alignment explanation
Indices: 2573083--2573111 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2573073 TGAGTTCGTG
2573083 GCTCGTCTCTGTT
1 GCTCGTCTCTGTT
2573096 GCTCGTCTCTGTT
1 GCTCGTCTCTGTT
2573109 GCT
1 GCT
2573112 TGTTTCCCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.24, T:0.45
Consensus pattern (13 bp):
GCTCGTCTCTGTT
Found at i:2573619 original size:2 final size:2
Alignment explanation
Indices: 2573612--2573650 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2573602 TAGGCTTGTA
2573612 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2573651 ATAATAATAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2573656 original size:3 final size:3
Alignment explanation
Indices: 2573648--2573697 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
2573638 ATATATATAT
* * * *
2573648 ATA ATA ATA ATA ATA ATA TTTA GTA ATA ATA ATT TTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
2573694 ATA A
1 ATA A
2573698 AATTTAAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 37 0.95
4 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:2578250 original size:34 final size:34
Alignment explanation
Indices: 2578207--2578271 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
2578197 TGTCCATCCG
2578207 ATCCGACCCG-AGAATA-ATGACTCCTCCACCCAAA
1 ATCCGACCCGCAGAATACAT-AC-CCTCCACCCAAA
*
2578241 ATCCGACCCGCATAATACATACCCTCCACCC
1 ATCCGACCCGCAGAATACATACCCTCCACCC
2578272 GACCGGAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 19 0.68
35 7 0.25
36 2 0.07
ACGTcount: A:0.32, C:0.43, G:0.09, T:0.15
Consensus pattern (34 bp):
ATCCGACCCGCAGAATACATACCCTCCACCCAAA
Found at i:2581783 original size:30 final size:30
Alignment explanation
Indices: 2581747--2581826 Score: 115
Period size: 30 Copynumber: 2.6 Consensus size: 30
2581737 CAACAGTTAC
2581747 GTTGGGGACTATATTGCAAATGGAATAAAT
1 GTTGGGGACTATATTGCAAATGGAATAAAT
* * *
2581777 GTTGGGGACCATATTGAAAATGGACTAAAT
1 GTTGGGGACTATATTGCAAATGGAATAAAT
*
2581807 GTTAGGGGATTATATTGCAA
1 GTT-GGGGACTATATTGCAA
2581827 GTTTTAAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 30 0.70
31 13 0.30
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (30 bp):
GTTGGGGACTATATTGCAAATGGAATAAAT
Found at i:2582908 original size:31 final size:31
Alignment explanation
Indices: 2582872--2582949 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
2582862 TTTAAAACTT
*
2582872 GGGGACCATATTGCAAACAGAATAAATGTTG
1 GGGGACCATATTGCAAACAGAATAAATATTG
* *
2582903 GGGGACCATATTGCAAACGGACTAAATATTG
1 GGGGACCATATTGCAAACAGAATAAATATTG
* **
2582934 GAGGACTGTATTGCAA
1 GGGGACCATATTGCAA
2582950 GTTTTAAAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGAATAAATATTG
Found at i:2586972 original size:13 final size:13
Alignment explanation
Indices: 2586954--2586982 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2586944 TCTTGGACTT
2586954 TTTTCCTCCAAAA
1 TTTTCCTCCAAAA
2586967 TTTTCCTCCAAAA
1 TTTTCCTCCAAAA
2586980 TTT
1 TTT
2586983 ACGTGCACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.45
Consensus pattern (13 bp):
TTTTCCTCCAAAA
Found at i:2588973 original size:18 final size:18
Alignment explanation
Indices: 2588934--2588974 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2588924 GGAAAGGCGG
* * *
2588934 CGGTATCATATATGGTTG
1 CGGTATCATAAATGGCTA
2588952 CGGTATCATAAATGGCTA
1 CGGTATCATAAATGGCTA
2588970 CGGTA
1 CGGTA
2588975 GCTGCTGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (18 bp):
CGGTATCATAAATGGCTA
Found at i:2591076 original size:29 final size:29
Alignment explanation
Indices: 2591001--2591079 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
2590991 TACTGCTACG
*
2591001 GGTGTTAGATCGGGAAATATAATCTGACC
1 GGTGTTAGATCGGAAAATATAATCTGACC
* **
2591030 GGTGTTAAATCAAAAAATATAATCTGACC
1 GGTGTTAGATCGGAAAATATAATCTGACC
*
2591059 GGTGTTAGATCGGTAAATATA
1 GGTGTTAGATCGGAAAATATA
2591080 CCGATCACCA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (29 bp):
GGTGTTAGATCGGAAAATATAATCTGACC
Found at i:2592557 original size:16 final size:16
Alignment explanation
Indices: 2592533--2592617 Score: 61
Period size: 16 Copynumber: 5.2 Consensus size: 16
2592523 ATCTATTTTA
*
2592533 ATTACTATATTTATAT
1 ATTATTATATTTATAT
2592549 ATTATTATATTT-TAATT
1 ATTATTATATTTAT-A-T
2592566 ATTTATTATATTTA-AT
1 A-TTATTATATTTATAT
* *
2592582 AATTAATAATATTAAT-T
1 -ATT-ATTATATTTATAT
2592599 ATTATTAT-TATTATAT
1 ATTATTATAT-TTATAT
2592615 ATT
1 ATT
2592618 TATTTAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
14 1 0.02
15 8 0.15
16 22 0.40
17 13 0.24
18 11 0.20
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATTATATTTATAT
Found at i:2594824 original size:6 final size:6
Alignment explanation
Indices: 2594815--2594854 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
2594805 TTCAATTGAA
*
2594815 TTATTT TTATTT TTATTT TTA-TT TTATTA TTATTAT TTAT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATT-T TTAT
2594855 AAATAATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
5 5 0.17
6 21 0.70
7 4 0.13
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (6 bp):
TTATTT
Found at i:2594832 original size:12 final size:12
Alignment explanation
Indices: 2594815--2594854 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
2594805 TTCAATTGAA
2594815 TTATTTTTATTT
1 TTATTTTTATTT
2594827 TTATTTTTA-TT
1 TTATTTTTATTT
*
2594838 TTATTATTATTAT
1 TTATTTTTATT-T
2594851 TTAT
1 TTAT
2594855 AAATAATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 10 0.40
12 10 0.40
13 5 0.20
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTATTTTTATTT
Found at i:2594841 original size:17 final size:18
Alignment explanation
Indices: 2594819--2594854 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2594809 ATTGAATTAT
*
2594819 TTTTATTTTTATT-TTTA
1 TTTTATTATTATTATTTA
2594836 TTTTATTATTATTATTTA
1 TTTTATTATTATTATTTA
2594854 T
1 T
2594855 AAATAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTATTATTATTATTTA
Found at i:2595047 original size:26 final size:25
Alignment explanation
Indices: 2595007--2595103 Score: 83
Period size: 26 Copynumber: 3.8 Consensus size: 25
2594997 ATTACTAATG
2595007 TTATTAA-TAATGATTTAATAATTA
1 TTATTAATTAATGATTTAATAATTA
* *
2595031 TTATTAATCTAATGATTTGATATTTAA
1 TTATTAAT-TAATGATTTAATAATT-A
* *
2595058 TGATTTATTAATGATTACTAATAATTA
1 TTATTAATTAATGATT--TAATAATTA
*
2595085 TTTATT-ATAAAT-ATTTAAT
1 -TTATTAATTAATGATTTAAT
2595104 GTTTTGGATT
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
24 11 0.19
26 25 0.42
27 13 0.22
28 10 0.17
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (25 bp):
TTATTAATTAATGATTTAATAATTA
Found at i:2597155 original size:20 final size:20
Alignment explanation
Indices: 2597127--2597355 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
2597117 AAATTTCAGT
* * *
2597127 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2597147 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
2597167 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2597187 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
2597207 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2597227 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2597247 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
2597267 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
2597287 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
2597307 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
2597327 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
2597347 GTTGCGATT
1 GTTGCGATT
2597356 CTTGAAAATC
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:2597408 original size:21 final size:20
Alignment explanation
Indices: 2597323--2597420 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
2597313 ATTTATGTGT
* *
2597323 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
2597343 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
2597364 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
2597385 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
2597406 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
2597421 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:2597416 original size:42 final size:43
Alignment explanation
Indices: 2597323--2597421 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
2597313 ATTTATGTGT
* *
2597323 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
2597364 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
2597406 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
2597422 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:2598364 original size:31 final size:30
Alignment explanation
Indices: 2598328--2598401 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 30
2598318 TTAAATTCTA
2598328 TTATTTTATTTATT-GTGAATATTTTATTCAT
1 TTATTTTATTTATTAGTGAATATTTTATT--T
**
2598359 TTATTTT-TTTATTAGTTTATATTTTATTT
1 TTATTTTATTTATTAGTGAATATTTTATTT
*
2598388 TTATATTATTTATT
1 TTATTTTATTTATT
2598402 TAATTAGGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 7 0.18
30 12 0.32
31 19 0.50
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.70
Consensus pattern (30 bp):
TTATTTTATTTATTAGTGAATATTTTATTT
Found at i:2598369 original size:8 final size:8
Alignment explanation
Indices: 2598326--2598398 Score: 53
Period size: 8 Copynumber: 9.0 Consensus size: 8
2598316 TTTTAAATTC
2598326 TATTATTT
1 TATTATTT
2598334 TATTTATTGT
1 TA-TTATT-T
* *
2598344 GAATATTT
1 TATTATTT
2598352 TATTCA-TT
1 TATT-ATTT
*
2598360 TATTTTTT
1 TATTATTT
*
2598368 TATTAGTT
1 TATTATTT
2598376 TA-TATTT
1 TATTATTT
2598383 TATT-TTT
1 TATTATTT
2598390 ATATTATTT
1 -TATTATTT
2598399 ATTTAATTAG
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
7 9 0.18
8 26 0.52
9 13 0.26
10 2 0.04
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.70
Consensus pattern (8 bp):
TATTATTT
Found at i:2598388 original size:23 final size:22
Alignment explanation
Indices: 2598358--2598400 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
2598348 ATTTTATTCA
*
2598358 TTTATTTTTTTATTAGTTTATAT
1 TTTATTTTTATATTA-TTTATAT
2598381 TTTATTTTTATATTATTTAT
1 TTTATTTTTATATTATTTAT
2598401 TTAATTAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTATTTTTATATTATTTATAT
Found at i:2599486 original size:20 final size:20
Alignment explanation
Indices: 2599461--2599534 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
2599451 TGTCAAAGTA
2599461 CATCCATGCACCCTGCAGTG
1 CATCCATGCACCCTGCAGTG
2599481 CATCCATGCA-CCTGCCACTAGTG
1 CATCCATGCACCCTG---C-AGTG
** * *
2599504 CATTGATGTACCATGCAGTG
1 CATCCATGCACCCTGCAGTG
2599524 CATCCATGCAC
1 CATCCATGCAC
2599535 TCAAACATCG
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 4 0.10
20 22 0.52
21 1 0.02
22 1 0.02
23 11 0.26
24 3 0.07
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23
Consensus pattern (20 bp):
CATCCATGCACCCTGCAGTG
Found at i:2599727 original size:20 final size:22
Alignment explanation
Indices: 2599689--2599728 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
2599679 TTTTAATAGA
2599689 AAAATCATCCCCAAATGGCTCC
1 AAAATCATCCCCAAATGGCTCC
2599711 AAAA-CATCCCC-AATGGCT
1 AAAATCATCCCCAAATGGCT
2599729 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAATCATCCCCAAATGGCTCC
Found at i:2599988 original size:34 final size:33
Alignment explanation
Indices: 2599943--2600013 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
2599933 TTTGTTAAAG
* * *
2599943 GGGAAATGTTCTAGCTTAGCTCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCGTG-AAAAACTA
* *
2599977 GGGAAAGGTTCTAGTTTATCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGAAAAACTA
2600010 GGGA
1 GGGA
2600014 GTTGTAAAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 11 0.34
34 21 0.66
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTTAGCCCGTGAAAAACTA
Found at i:2602398 original size:13 final size:12
Alignment explanation
Indices: 2602369--2602394 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2602359 AACCCGTAAT
2602369 AATAAGTATAAA
1 AATAAGTATAAA
2602381 AATAAGTATAAA
1 AATAAGTATAAA
2602393 AA
1 AA
2602395 ATAATTAGGA
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:0.00, G:0.08, T:0.23
Consensus pattern (12 bp):
AATAAGTATAAA
Found at i:2602810 original size:81 final size:80
Alignment explanation
Indices: 2602661--2602911 Score: 246
Period size: 81 Copynumber: 3.1 Consensus size: 80
2602651 CAATACAGAA
* * * *
2602661 GTCAAATTCGCAATACATAAGTTAAATTCGCAACGC-GATAGTCAAATTCGCAACACTGA-AGTC
1 GTCAAATTCGCAACACAAAAGTCAAATTCGCAAC-CAGATAGTCAAATTCGCAACGC-GATAGTC
*
2602724 AAATTCACAACGCGAATCT
64 AAATTCGCAACGCGAA--T
* ** *
2602743 GT-AAA-TCGCAACGCGAATTTGT-AAA-TCGCAACATAGA-AGTCAAAATTCGCAACGCGATAG
1 GTCAAATTCGCAACAC-AA-AAGTCAAATTCGCAAC-CAGATAGTC-AAATTCGCAACGCGATAG
*
2602803 TCAAATTCGCAACACTGAAT
62 TCAAATTCGCAACGC-GAAT
*
2602823 GTCAAATTCGCAACACAAAAGTCAAATTCGCAACCCGATAGTCAAATTCGCAACGCGATAGTCAA
1 GTCAAATTCGCAACACAAAAGTCAAATTCGCAACCAGATAGTCAAATTCGCAACGCGATAGTCAA
* *
2602888 ATTCGCAATGCGAAA
66 ATTCGCAACGCGAAT
*
2602903 GTGAAATTC
1 GTCAAATTC
2602912 ACAAAGCGCG
Statistics
Matches: 139, Mismatches: 19, Indels: 24
0.76 0.10 0.13
Matches are distributed among these distances:
80 36 0.26
81 77 0.55
82 26 0.19
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (80 bp):
GTCAAATTCGCAACACAAAAGTCAAATTCGCAACCAGATAGTCAAATTCGCAACGCGATAGTCAA
ATTCGCAACGCGAAT
Found at i:2602900 original size:20 final size:20
Alignment explanation
Indices: 2602660--2602911 Score: 205
Period size: 20 Copynumber: 12.5 Consensus size: 20
2602650 ACAATACAGA
**
2602660 AGTCAAATTCGCAATAC-AT
1 AGTCAAATTCGCAACGCGAT
*
2602679 AAGTTAAATTCGCAACGCGAT
1 -AGTCAAATTCGCAACGCGAT
*
2602700 AGTCAAATTCGCAACACTGA-
1 AGTCAAATTCGCAACGC-GAT
*
2602720 AGTCAAATTCACAACGCGAAT
1 AGTCAAATTCGCAACGCG-AT
*
2602741 CTGT-AAA-TCGCAACGCGAATT
1 -AGTCAAATTCGCAACGCG-A-T
* **
2602762 TGT-AAA-TCGCAACATAGA-
1 AGTCAAATTCGCAAC-GCGAT
2602780 AGTCAAAATTCGCAACGCGAT
1 AGTC-AAATTCGCAACGCGAT
*
2602801 AGTCAAATTCGCAACACTGA-
1 AGTCAAATTCGCAACGC-GAT
* * *
2602821 ATGTCAAATTCGCAACACAAA
1 A-GTCAAATTCGCAACGCGAT
*
2602842 AGTCAAATTCGCAACCCGAT
1 AGTCAAATTCGCAACGCGAT
2602862 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
* *
2602882 AGTCAAATTCGCAATGCGAA
1 AGTCAAATTCGCAACGCGAT
*
2602902 AGTGAAATTC
1 AGTCAAATTC
2602912 ACAAAGCGCG
Statistics
Matches: 195, Mismatches: 23, Indels: 28
0.79 0.09 0.11
Matches are distributed among these distances:
18 2 0.01
19 1 0.01
20 151 0.77
21 39 0.20
22 2 0.01
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:2603090 original size:20 final size:20
Alignment explanation
Indices: 2603033--2603091 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
2603023 GTAATTAGCG
*
2603033 TTGCGAATTTGAAAACCACA
1 TTGCGAATTTGAAAACCGCA
*
2603053 TTGTGAATTTGAAAACCGCA
1 TTGCGAATTTGAAAACCGCA
2603073 TTGCGAATTTGAAAACCGC
1 TTGCGAATTTGAAAACCGC
2603092 GTTACAATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (20 bp):
TTGCGAATTTGAAAACCGCA
Found at i:2603157 original size:20 final size:20
Alignment explanation
Indices: 2603128--2603165 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2603118 CGGTAATTAG
2603128 CGTTGAGAATTTGAAAATCT
1 CGTTGAGAATTTGAAAATCT
* *
2603148 CGTTGCGAATTTGTAAAT
1 CGTTGAGAATTTGAAAAT
2603166 TCGCAACGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (20 bp):
CGTTGAGAATTTGAAAATCT
Found at i:2603158 original size:97 final size:97
Alignment explanation
Indices: 2602973--2603160 Score: 286
Period size: 97 Copynumber: 1.9 Consensus size: 97
2602963 TCGGTAATTA
* * * * * *
2602973 GCATTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATGTCGGTAATTAGCGTTGCG
1 GCATTGCGAATTTGAAAACCGCGTTACAATAGTACTGTTTACCTATATCGGTAATTAGCGTTGAG
*
2603038 AATTTGAAAACCACATTGTGAATTTGAAAACC
66 AATTTGAAAACCACATTGCGAATTTGAAAACC
2603070 GCATTGCGAATTTGAAAACCGCGTTACAATAGTACTGTTTACCTATATCGGTAATTAGCGTTGAG
1 GCATTGCGAATTTGAAAACCGCGTTACAATAGTACTGTTTACCTATATCGGTAATTAGCGTTGAG
* * *
2603135 AATTTGAAAATCTCGTTGCGAATTTG
66 AATTTGAAAACCACATTGCGAATTTG
2603161 TAAATTCGCA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
97 81 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (97 bp):
GCATTGCGAATTTGAAAACCGCGTTACAATAGTACTGTTTACCTATATCGGTAATTAGCGTTGAG
AATTTGAAAACCACATTGCGAATTTGAAAACC
Found at i:2603258 original size:20 final size:20
Alignment explanation
Indices: 2603203--2603251 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
2603193 AACAGTACTA
2603203 TCGCAACGCGATTTACAAAT
1 TCGCAACGCGATTTACAAAT
*
2603223 TCGCAACGAGATTTACAAAT
1 TCGCAACGCGATTTACAAAT
2603243 TCGCAACGC
1 TCGCAACGC
2603252 TAATTACCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGATTTACAAAT
Found at i:2603288 original size:37 final size:37
Alignment explanation
Indices: 2603166--2603288 Score: 101
Period size: 37 Copynumber: 3.2 Consensus size: 37
2603156 ATTTGTAAAT
*
2603166 TCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
1 TCGCAACGCTAATTACCGATATATGTAAACAGTACTA
* * * * *
2603203 TCGCAACGCGATTTA-C-AAAT-TCG-CAACGAGATTTACAAA
1 TCGCAACGCTAATTACCGATATAT-GTAAAC-AG---TAC-TA
2603242 TTCGCAACGCTAATTACCGATATATGTAAACAGTACTA
1 -TCGCAACGCTAATTACCGATATATGTAAACAGTACTA
2603280 TCGCAACGC
1 TCGCAACGC
2603289 GATTTACAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 22
0.66 0.11 0.23
Matches are distributed among these distances:
34 3 0.05
35 6 0.09
36 1 0.02
37 22 0.34
38 4 0.06
39 4 0.06
40 13 0.20
41 1 0.02
42 6 0.09
43 4 0.06
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (37 bp):
TCGCAACGCTAATTACCGATATATGTAAACAGTACTA
Found at i:2603289 original size:77 final size:77
Alignment explanation
Indices: 2603162--2603352 Score: 330
Period size: 77 Copynumber: 2.5 Consensus size: 77
2603152 GCGAATTTGT
2603162 AAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTACAAATTCGC
1 AAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTACAAATTCGC
2603227 AACGA-GATTTAC
66 AAC-ACGATTTAC
* *
2603239 AAATTCGCAACGCTAATTACCGATATATGTAAACAGTACTATCGCAACGCGATTTACAAATTCGT
1 AAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTACAAATTCGC
2603304 AACACGATTTAC
66 AACACGATTTAC
* *
2603316 AAATTTGCAATGCTAATTACCGATATAGGTAAACAGT
1 AAATTCGCAACGCTAATTACCGATATAGGTAAACAGT
2603353 GTTGCGAATT
Statistics
Matches: 108, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
76 1 0.01
77 107 0.99
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (77 bp):
AAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGATTTACAAATTCGC
AACACGATTTAC
Found at i:2603411 original size:20 final size:20
Alignment explanation
Indices: 2603386--2603451 Score: 98
Period size: 20 Copynumber: 3.3 Consensus size: 20
2603376 TAAACGCGTT
2603386 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
*
2603406 TTGCGAATTTGACTATC-GCG
1 TTGCGAATTTGACT-TCTGTG
*
2603426 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTCTGTG
2603446 TTGCGA
1 TTGCGA
2603452 TTTACAGATT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
19 1 0.02
20 38 0.93
21 2 0.05
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.41
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:2603432 original size:40 final size:40
Alignment explanation
Indices: 2603386--2603476 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 40
2603376 TAAACGCGTT
* * *
2603386 TTGCGAATTTGACTTCTGTGTTGCGAATTTGAC-TA-TCGCG
1 TTGCGAATTTGACTTATGTGTTGCG-ATTT-ACAGATTCACG
2603426 TTGCGAATTTGACTTATGTGTTGCGATTTACAGATTCACG
1 TTGCGAATTTGACTTATGTGTTGCGATTTACAGATTCACG
2603466 TTGCGAATTTG
1 TTGCGAATTTG
2603477 GAAAATCGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
38 2 0.04
39 5 0.11
40 39 0.85
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (40 bp):
TTGCGAATTTGACTTATGTGTTGCGATTTACAGATTCACG
Found at i:2603511 original size:20 final size:20
Alignment explanation
Indices: 2603445--2603512 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
2603435 TGACTTATGT
* *
2603445 GTTGCGATTTACAGATTCAC
1 GTTGCGATTTACAAATTCGC
** *
2603465 GTTGCGAATTTGGAAAATCGC
1 GTTGCG-ATTTACAAATTCGC
** *
2603486 AATGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
2603506 GTTGCGA
1 GTTGCGA
2603513 ATTTGAAAAC
Statistics
Matches: 34, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 21 0.62
21 13 0.38
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:2617599 original size:2 final size:2
Alignment explanation
Indices: 2617592--2617634 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2617582 CAATCCAAAT
2617592 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2617634 T
1 T
2617635 TGAACTTACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2618586 original size:3 final size:3
Alignment explanation
Indices: 2618578--2618603 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2618568 GCTTTGACTA
2618578 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
2618604 ATTAATCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2619105 original size:17 final size:18
Alignment explanation
Indices: 2619079--2619112 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2619069 AGATCCAATC
*
2619079 TAAAATAAATA-TATTTA
1 TAAAAAAAATATTATTTA
2619096 TAAAAAAAATATTATTT
1 TAAAAAAAATATTATTT
2619113 TTATTCAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAAAAAAATATTATTTA
Found at i:2625329 original size:21 final size:22
Alignment explanation
Indices: 2625305--2625362 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
2625295 AAATATAATT
2625305 TTAAATACTTTAATA-AAAAAA
1 TTAAATACTTTAATAGAAAAAA
*
2625326 TTAAATA-TTTAGAAAGAAAAAA
1 TTAAATACTTTA-ATAGAAAAAA
*
2625348 ATAATATACTTTAAT
1 TTAA-ATACTTTAAT
2625363 TAGTTATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.13
21 9 0.30
22 9 0.30
23 4 0.13
24 4 0.13
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (22 bp):
TTAAATACTTTAATAGAAAAAA
Found at i:2626926 original size:2 final size:2
Alignment explanation
Indices: 2626919--2626956 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
2626909 CGGGTTTAAA
2626919 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2626957 ATAATTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2633022 original size:106 final size:106
Alignment explanation
Indices: 2632891--2634044 Score: 1822
Period size: 106 Copynumber: 10.9 Consensus size: 106
2632881 AGTGAAGAAA
* * *
2632891 ATTGGACTCCAGACAATGCATGTTCAACTTCACGACGAATGGACCGCTGGTTGTCAATAAACAAC
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
* * *
2632956 TTCTCAATTTCAGAGACAATTTCAACTTCATAACGAAGGAT
66 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* *
2632997 ATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAATAAACAAT
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
*
2633062 TTCCCAATATCAGAGCCAATTTCAACTTCACAACGAAGGAT
66 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* *
2633103 ATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
* *
2633168 TTCTCAATTTTAGAGCCAATTTCAACTTCACAACGAAGGAT
66 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* *
2633209 ATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAATAAACAAT
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
* * * *
2633274 TTCCAAATTTCAAAGTCAATTTCAACTTCACAGCGAAGGAT
66 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* * *
2633315 ATTGGACTCAAGACAACGCAAGTTCAACTTAACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
*
2633380 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
66 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
*
2633421 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAT
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
2633486 TTCCCAATTTCAAGAGCCAATTTCAACTTCACAACGAAGGAT
66 TTCCCAATTTC-AGAGCCAATTTCAACTTCACAACGAAGGAT
* * *
2633528 ATTGGACTCCAGACAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAAT
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
* *
2633593 TTCCCAATTTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
66 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* *
2633634 ATTGGACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
**
2633699 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGTGAAGGAT
66 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* *
2633740 ATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAT
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
*
2633805 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
66 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* * * *
2633846 ATTGGACTCAAGACAACGCAAGTTCAACTTCACAAACGAAGGGACGGCTGGTTGTCAACAAACAA
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCAC-GACGAAGGGACCGCTGGTTGTCAATAAACAA
* *
2633911 CTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGAT
65 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* * * * * *
2633953 ATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
1 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
* * * *
2634018 TTTCCAGTTCCAGAACCAATTTCAACT
66 TTCCCAATTTCAGAGCCAATTTCAACT
2634045 CTACGACGAA
Statistics
Matches: 975, Mismatches: 71, Indels: 4
0.93 0.07 0.00
Matches are distributed among these distances:
106 774 0.79
107 201 0.21
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
Found at i:2633721 original size:425 final size:424
Alignment explanation
Indices: 2632858--2634044 Score: 1906
Period size: 425 Copynumber: 2.8 Consensus size: 424
2632848 TCCAATTTCA
* ** * * *
2632858 TTCAGAGTCTATTTCAACTTTGCAGTGAAGAAAATTGGACTCCAGACAATGCATGTTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCA
* * *
2632923 CGACGAATGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGACAATTTCAACTTCATA
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
*
2632988 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCA
131 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
*
2633053 ATAAACAATTTCCCAATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
196 ATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
* * * *
2633118 ACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTTAGAG
261 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAG
* *
2633183 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAA
326 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAA
*
2633248 GGGACCGCTGGTTGTCAATAAACAATTTCCAAAT
391 GGGACCGCTGGTTGTCAATAAACAACTTCCAAAT
* * * * *
2633282 TTCAAAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTAA
1 TTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCA
*
2633347 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
2633412 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
131 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
2633477 ATAAACAATTTCCCAATTTCAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
196 ATAAACAATTTCCCAATTTC-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
* * *
2633542 AACGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCCAATTTCAGA
260 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGA
* * *
2633607 GTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAATGCAAGTTCAACTTCACGACGA
325 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGA
*
2633672 AGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
390 AGGGACCGCTGGTTGTCAATAAACAACTTCCAAAT
*
2633707 TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCA
* *
2633772 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
* * * *
2633837 GCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACAAACGAAGGGACGGCTGGTTGTC
131 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC-GACGAAGGGACCGCTGGTTGTC
* * * * *
2633902 AACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCGAGAC
195 AATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
* * * * * *
2633967 AACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCCAGTTCCAGA
260 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGA
*
2634032 ACCAATTTCAACT
325 GCCAATTTCAACT
2634045 CTACGACGAA
Statistics
Matches: 701, Mismatches: 60, Indels: 3
0.92 0.08 0.00
Matches are distributed among these distances:
424 198 0.28
425 465 0.66
426 38 0.05
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (424 bp):
TTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
ATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAG
CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAACTTCCAAAT
Found at i:2634482 original size:36 final size:36
Alignment explanation
Indices: 2634437--2634541 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
2634427 GAAACTAAAG
*
2634437 ATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
*
2634473 ATTTTGTCTCTCTTGAGACGGTTTCTCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
*
2634509 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
2634542 TACCAACCAA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (36 bp):
ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
Found at i:2634485 original size:21 final size:21
Alignment explanation
Indices: 2634460--2634524 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
2634450 TGAGACAATT
2634460 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* * *
2634481 TCTCTTGAGAC------GGTT
1 TCTCTTGAAACAAATTTTGTC
2634496 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
2634517 TCTCTTGA
1 TCTCTTGA
2634525 GACAGTTTCC
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 12 0.38
21 20 0.62
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:2634654 original size:33 final size:33
Alignment explanation
Indices: 2634592--2634720 Score: 181
Period size: 33 Copynumber: 3.9 Consensus size: 33
2634582 CATGGAGACA
* *
2634592 GTTTCTCTTTAAACACAAAAAAAATCTTTGAAATC
1 GTTTCTCTTGAAACAC--AAAAAACCTTTGAAATC
2634627 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
*
2634660 GTTCCTCTTGAAACACAAAAAACCTTTGAAAAT-
1 GTTTCTCTTGAAACACAAAAAACCTTTG-AAATC
*
2634693 GTTTCTCTTGAAACAC-AAAGACCTTTGA
1 GTTTCTCTTGAAACACAAAAAACCTTTGA
2634721 GTTCGACTAC
Statistics
Matches: 88, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
31 1 0.01
32 10 0.11
33 58 0.66
34 4 0.05
35 15 0.17
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
Found at i:2634848 original size:83 final size:83
Alignment explanation
Indices: 2634708--2634883 Score: 262
Period size: 83 Copynumber: 2.1 Consensus size: 83
2634698 TCTTGAAACA
2634708 CAAAGACCTTTGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAACATAGCTCAAGGCA
1 CAAAGACC-TTGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAACATAGCTCAAGGCA
* *
2634773 AGAAGGGCTATTTGCTAAC
65 AGAAGGGCTATCTGCCAAC
* * * * * * *
2634792 CAAAGACCTTGAGTTCGACTACTCTCAGCTCCGAGGCACATCATTTGCAGCATAGCTTAAGTCGA
1 CAAAGACCTTGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAA
2634857 GAAGGGCTATCTGCCAAC
66 GAAGGGCTATCTGCCAAC
2634875 CAAAGACCT
1 CAAAGACCT
2634884 AACGAGTTCG
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
83 75 0.90
84 8 0.10
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (83 bp):
CAAAGACCTTGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAA
GAAGGGCTATCTGCCAAC
Found at i:2641649 original size:2 final size:2
Alignment explanation
Indices: 2641644--2641678 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2641634 AAAAACAGGT
2641644 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2641679 ATTTCCTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2643089 original size:547 final size:551
Alignment explanation
Indices: 2642150--2643149 Score: 1679
Period size: 547 Copynumber: 1.8 Consensus size: 551
2642140 ACAATTTCTA
* ** * *
2642150 TGTTATAAGCATGTTATAAAGTTTTATTTATGATCCTTGTATTTACATAAAACTTTAACCATGTT
1 TGTTATAAGCATGGTATAAAGCCTTATTTATGATCCTTATATTCACATAAAACTTTAACCATGTT
* * *
2642215 TGAAGATCTCACTAAGGTCTTTGGGATTGAAAAATAGACTTTTTAGTACTTGTTTTATGACTTTT
66 TGAAGACCTCACTAAGGTATTTGGGATTGAAAAATAGACTTTTTAGTACTTGTTTCATGACTTTT
* *
2642280 GCAGTTAGAGTATCGATACTATAGGGATAGTATCGATATTTGTTTTTCATTTTGGGCAGATTCGT
131 GCAGTTAGAG-ATC-ATAC---A--GATAGTATCGATATCTGTTCTTCATTTTGGGCAGATTCGT
* *
2642345 GAGTTTATAGGTAAGAGTATCGAAACTTTGGGTTATAATTTCGAAACTTCCATAAAATTTCAAAA
189 GAGTTTATAGGTAAGAGCATCGAAACTTTGGGTTATAATTTCGAAACTCCCATAAAATTTCAAAA
2642410 CTAGGAAGAACAAAATGTTTAAAAGTATCGTTACTTATATAAAGTATCAAAACTTTTGCAGAAGT
254 CTAGGAAGAACAAAATGTTTAAAAGTATCGTTACTTATATAAAGTATCAAAACTTTTGCAGAAGT
2642475 CTATTTTGGTCAAAACGTTACCCGAGAGGCCCTAGACCCATAATATGACCATAAATTGGATCGAA
319 CTATTTTGGTCAAAACGTTACCCGAGAGGCCCTAGACCCATAATATGACCATAAATTGGATCGAA
2642540 TAGGTGTAAAACACTAGAATAAGTGTTATAAAAGGTGTTTAAAGTTGGGTTAAAATGGATGAACT
384 TAGGTGTAAAACACTAGAATAAGTGTTATAAAAGGTGTTTAAAGTTGGGTTAAAATGGATGAACT
2642605 TATAGCTTTTTCATACCAAGTGTAGATCATGAAAAGTTAAAATGTGTTAGAAAGTTAAGTTTAAA
449 TATAGCTTTTTCATACCAAGTGTAGATCATGAAAAGTTAAAATGTGTTAGAAAGTTAAGTTTAAA
2642670 GCTTGTTTAGCAATTTCCATGGTAGATTATTCATTTGT
514 GCTTGTTTAGCAATTTCCATGGTAGATTATTCATTTGT
* * *
2642708 TGTTATAAGCATGGTATAAAGCCTTATTTATGCTCTTTATATTCACATAAAACTTTAAGCATGTT
1 TGTTATAAGCATGGTATAAAGCCTTATTTATGATCCTTATATTCACATAAAACTTTAACCATGTT
*
2642773 TGAAGACCTCACTAAGGTATTTGTGATTGAAAAATAGACTTTTTAGTACTTGTTTCATGACTTTT
66 TGAAGACCTCACTAAGGTATTTGGGATTGAAAAATAGACTTTTTAGTACTTGTTTCATGACTTTT
*
2642838 GCA-TGTAGAG-T-AT-C-GATAGTATCGATATCTGTTCTTCGTTTTGGGCAGATTCGTGAGTTT
131 GCAGT-TAGAGATCATACAGATAGTATCGATATCTGTTCTTCATTTTGGGCAGATTCGTGAGTTT
* * *
2642898 CTAGGTAAGAGCATCGAAACTTTGGGTTATAATTTTGAAACTCCCATAAAGTTTCAAAACTAGGA
195 ATAGGTAAGAGCATCGAAACTTTGGGTTATAATTTCGAAACTCCCATAAAATTTCAAAACTAGGA
* *
2642963 AGAACATAATGTTTAAAAGTATCGTTACTTATATAAAGTATCGAAACTTTTGCAGAAGTCTATTT
260 AGAACAAAATGTTTAAAAGTATCGTTACTTATATAAAGTATCAAAACTTTTGCAGAAGTCTATTT
2643028 TGGTCAAAACGTTACCCGAGAGGCCCTAGACCCATAATATGACCATAAA-TGGAATCGAATAGGT
325 TGGTCAAAACGTTACCCGAGAGGCCCTAGACCCATAATATGACCATAAATTGG-ATCGAATAGGT
2643092 GTAAAACACTAGAATAAGTGTTATAAAAGGTGTTTAAAGTTGGGTTAAAATGGATGAA
389 GTAAAACACTAGAATAAGTGTTATAAAAGGTGTTTAAAGTTGGGTTAAAATGGATGAA
2643150 ATAGTTATAG
Statistics
Matches: 418, Mismatches: 22, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
546 3 0.01
547 284 0.68
553 1 0.00
554 2 0.00
556 1 0.00
557 1 0.00
558 126 0.30
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (551 bp):
TGTTATAAGCATGGTATAAAGCCTTATTTATGATCCTTATATTCACATAAAACTTTAACCATGTT
TGAAGACCTCACTAAGGTATTTGGGATTGAAAAATAGACTTTTTAGTACTTGTTTCATGACTTTT
GCAGTTAGAGATCATACAGATAGTATCGATATCTGTTCTTCATTTTGGGCAGATTCGTGAGTTTA
TAGGTAAGAGCATCGAAACTTTGGGTTATAATTTCGAAACTCCCATAAAATTTCAAAACTAGGAA
GAACAAAATGTTTAAAAGTATCGTTACTTATATAAAGTATCAAAACTTTTGCAGAAGTCTATTTT
GGTCAAAACGTTACCCGAGAGGCCCTAGACCCATAATATGACCATAAATTGGATCGAATAGGTGT
AAAACACTAGAATAAGTGTTATAAAAGGTGTTTAAAGTTGGGTTAAAATGGATGAACTTATAGCT
TTTTCATACCAAGTGTAGATCATGAAAAGTTAAAATGTGTTAGAAAGTTAAGTTTAAAGCTTGTT
TAGCAATTTCCATGGTAGATTATTCATTTGT
Found at i:2644785 original size:30 final size:31
Alignment explanation
Indices: 2644742--2644811 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
2644732 AACAATGAGA
*
2644742 TTAAATAATATATTTAATATAAAAATAAGTGT
1 TTAAATTATAT-TTTAATATAAAAATAAGTGT
** * *
2644774 TTAAATTATATTTTTGTTTCAAAATAAGTGT
1 TTAAATTATATTTTAATATAAAAATAAGTGT
2644805 TTAAATT
1 TTAAATT
2644812 CTTTTTCAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 23 0.70
32 10 0.30
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.47
Consensus pattern (31 bp):
TTAAATTATATTTTAATATAAAAATAAGTGT
Found at i:2660983 original size:34 final size:34
Alignment explanation
Indices: 2660945--2661025 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 34
2660935 ATGATAAACG
* *
2660945 AACATTAACGAACGTAAACGAACACAATTGAACA
1 AACATAAACGAACGTAAACGAACACAAATGAACA
* *
2660979 AACATAAACGAACGTAAATGAACACAAATGAACG
1 AACATAAACGAACGTAAACGAACACAAATGAACA
**
2661013 AATGTAAACGAAC
1 AACATAAACGAAC
2661026 ACAATAAACG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.54, C:0.19, G:0.14, T:0.14
Consensus pattern (34 bp):
AACATAAACGAACGTAAACGAACACAAATGAACA
Found at i:2661000 original size:24 final size:23
Alignment explanation
Indices: 2660959--2661047 Score: 88
Period size: 24 Copynumber: 3.8 Consensus size: 23
2660949 TTAACGAACG
* *
2660959 TAAACGAACACAATTGAACAAACA
1 TAAACGAACATAAATGAACAAA-A
*
2660983 TAAACGAACGTAAATGAACACAAA
1 TAAACGAACATAAATGAACA-AAA
* ** * *
2661007 TGAACGAATGTAAACGAACACAA
1 TAAACGAACATAAATGAACAAAA
2661030 TAAACGAACATAAATGAA
1 TAAACGAACATAAATGAA
2661048 AATATTTTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
23 16 0.30
24 35 0.66
25 2 0.04
ACGTcount: A:0.57, C:0.17, G:0.12, T:0.13
Consensus pattern (23 bp):
TAAACGAACATAAATGAACAAAA
Found at i:2662624 original size:11 final size:11
Alignment explanation
Indices: 2662608--2662636 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2662598 AACACGGTGG
2662608 AGAGACAAACC
1 AGAGACAAACC
2662619 AGAGACAAACC
1 AGAGACAAACC
2662630 AGAGACA
1 AGAGACA
2662637 GAGAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.55, C:0.24, G:0.21, T:0.00
Consensus pattern (11 bp):
AGAGACAAACC
Found at i:2666185 original size:16 final size:16
Alignment explanation
Indices: 2666164--2666197 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2666154 TTAAGCTAAT
*
2666164 AAAACTACTATAGCTG
1 AAAACTACTAAAGCTG
2666180 AAAACTACTAAAGCTG
1 AAAACTACTAAAGCTG
2666196 AA
1 AA
2666198 GAGGAACCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.21
Consensus pattern (16 bp):
AAAACTACTAAAGCTG
Found at i:2684381 original size:35 final size:36
Alignment explanation
Indices: 2684331--2684427 Score: 135
Period size: 36 Copynumber: 2.7 Consensus size: 36
2684321 AACACATTCA
*
2684331 TCAATTACATTCTAAACCCCAAATTCC-AAAATACT
1 TCAATTACATCCTAAACCCCAAATTCCAAAAATACT
* *
2684366 TCAATTAAATCCTAAACCTCAAATTCCAAAAATACT
1 TCAATTACATCCTAAACCCCAAATTCCAAAAATACT
*
2684402 TCAATTACATGCC-CAACCCCAAATTC
1 TCAATTACAT-CCTAAACCCCAAATTC
2684428 ATAATTCATT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
35 24 0.44
36 28 0.52
37 2 0.04
ACGTcount: A:0.42, C:0.30, G:0.01, T:0.27
Consensus pattern (36 bp):
TCAATTACATCCTAAACCCCAAATTCCAAAAATACT
Found at i:2685427 original size:35 final size:35
Alignment explanation
Indices: 2685388--2685462 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
2685378 ATTGGGCATG
*
2685388 TAATTGAAGTATTTTTGG-ATTTGAGGTTTAGAATA
1 TAATTGAAG-AATTTTGGAATTTGAGGTTTAGAATA
* *
2685423 TAATTGAAGAATTTTGGAATTTGGGGTTTAGAATG
1 TAATTGAAGAATTTTGGAATTTGAGGTTTAGAATA
2685458 TAATT
1 TAATT
2685463 AATGGCTATG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 7 0.19
35 29 0.81
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (35 bp):
TAATTGAAGAATTTTGGAATTTGAGGTTTAGAATA
Found at i:2685803 original size:18 final size:19
Alignment explanation
Indices: 2685780--2685817 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2685770 TAAAAGTATT
2685780 ATATCATATT-TTAAATTA
1 ATATCATATTATTAAATTA
*
2685798 ATATCATATTATTTAATTA
1 ATATCATATTATTAAATTA
2685817 A
1 A
2685818 ACATATCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATCATATTATTAAATTA
Found at i:2689346 original size:29 final size:30
Alignment explanation
Indices: 2689316--2689414 Score: 96
Period size: 30 Copynumber: 3.2 Consensus size: 30
2689306 TAAACCACAA
2689316 TTAAATATAATTAAAATAAAAGAGTAAAAT
1 TTAAATATAATTAAAATAAAAGAGTAAAAT
* *
2689346 TTAAATA-AATTTAAAGAACACAAAATGACT-AAA-
1 TTAAATATAA-TT--A-AA-ATAAAA-GAGTAAAAT
*
2689379 TTAAATATAATTAAAATAAAAGTGTAAAAT
1 TTAAATATAATTAAAATAAAAGAGTAAAAT
2689409 TTAAAT
1 TTAAAT
2689415 TGCAAAAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
28 2 0.04
29 10 0.18
30 17 0.31
31 1 0.02
32 1 0.02
33 11 0.20
34 10 0.18
35 3 0.05
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (30 bp):
TTAAATATAATTAAAATAAAAGAGTAAAAT
Found at i:2689656 original size:103 final size:100
Alignment explanation
Indices: 2689541--2689727 Score: 277
Period size: 103 Copynumber: 1.8 Consensus size: 100
2689531 ATCGCCTTTA
* * * *
2689541 AAATTATTTTTTAAAAATTATATAAAGAAATAAAAAAATTAGAGTGGGATACGACTCACCTATAA
1 AAATTATATTTTAAAAATTATATAAAGAAATAAAAAAA-TAGAGTGGGACACG-CTCACCCACAA
2689606 AACTCTTTAAACTTTT-AAGAGATAAAAAAACTTATTTT
64 AACTC-TTAAA-TTTTAAAGAGATAAAAAAACTTATTTT
* *
2689644 AAATTATATTTTAAAAATTATATAAAGAAATAAAAAAATATAGTGGGACACGTTCACCCACAAAA
1 AAATTATATTTTAAAAATTATATAAAGAAATAAAAAAATAGAGTGGGACACGCTCACCCACAAAA
2689709 CTCTTAAATTTTAAAGAGA
66 CTCTTAAATTTTAAAGAGA
2689728 AAAGAAGGCT
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
99 4 0.05
100 11 0.14
101 13 0.17
102 12 0.16
103 37 0.48
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.32
Consensus pattern (100 bp):
AAATTATATTTTAAAAATTATATAAAGAAATAAAAAAATAGAGTGGGACACGCTCACCCACAAAA
CTCTTAAATTTTAAAGAGATAAAAAAACTTATTTT
Found at i:2693436 original size:55 final size:55
Alignment explanation
Indices: 2693330--2693437 Score: 146
Period size: 55 Copynumber: 2.0 Consensus size: 55
2693320 GCATTCAAAT
** *
2693330 GATTCATGAAGAAGAACATTTGACGAATGAAGAAATTTGAACCTAACTGAAGAAC
1 GATTCATGAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTAACTGAAGAAC
* * *
2693385 GATTCATGAAGAATG-ACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGA
1 GATTCATGAAGAA-GAACATCCGACGAATGAAGAAATTTGAAACTAACTGAAGA
2693438 CTGATCCAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
55 45 0.98
56 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.23
Consensus pattern (55 bp):
GATTCATGAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTAACTGAAGAAC
Found at i:2693458 original size:55 final size:55
Alignment explanation
Indices: 2693354--2693459 Score: 126
Period size: 55 Copynumber: 1.9 Consensus size: 55
2693344 AACATTTGAC
* * **
2693354 GAATGAAGAAATTTGAACCTAACTGAAGAACGATTCATGAAGAATGACATCCGAT
1 GAATGAAGAAATTTGAAACTAACTGAAGAACGATCCAAAAAGAATGACATCCGAT
* *
2693409 GAATGAAGAAATTTGAAACTGATTGAAG-ACTGATCCAAAAAGGAA-GACATC
1 GAATGAAGAAATTTGAAACTAACTGAAGAAC-GATCCAAAAA-GAATGACATC
2693460 ATGAAGATCT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
54 2 0.05
55 38 0.88
56 3 0.07
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (55 bp):
GAATGAAGAAATTTGAAACTAACTGAAGAACGATCCAAAAAGAATGACATCCGAT
Done.