Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 51
Found at i:2282389 original size:18 final size:16
Alignment explanation
Indices: 2282353--2282398 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 16
2282343 TATGAAATTG
2282353 GATTCCAATTCCTACA
1 GATTCCAATTCCTACA
*
2282369 GATTCCAATTCATTCACA
1 GATTCCAATTC-CT-ACA
2282387 GATTCCAATTCC
1 GATTCCAATTCC
2282399 CTCATAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 11 0.42
17 1 0.04
18 14 0.54
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (16 bp):
GATTCCAATTCCTACA
Found at i:2282857 original size:18 final size:17
Alignment explanation
Indices: 2282834--2282871 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2282824 TTCTATTATC
2282834 TTTTAAT-AAATTAATATT
1 TTTTAATGAAA-TAAT-TT
2282852 TTTTAATGAAATAATTT
1 TTTTAATGAAATAATTT
2282869 TTT
1 TTT
2282872 AAGATAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 11 0.58
19 3 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTTAATGAAATAATTT
Found at i:2291917 original size:200 final size:200
Alignment explanation
Indices: 2291571--2291946 Score: 477
Period size: 200 Copynumber: 1.9 Consensus size: 200
2291561 TCAACAACAC
* * * * *
2291571 AGAACTACTTCCCAACCCAGATTTCGACATAGCTTAAGTCTAGAAGAATTATATGTCGACCAAAT
1 AGAACTACTTCCCAACCCAGATTTCGACATAGCTTAAGTCGAAAAGAACTATATATCGACCAAAG
* * * * ** *
2291636 CTTTCAAGTTTGATTCCACTCAAATGGATAACACATTAACTACATGGTAGTAATGAGAAATTACC
66 CTTTCAAGTTCGATTCCACTCAAATCGAGAACACATTAACTACATGGTAGCAACAAGAAACTACC
*
2291701 TTCCGGTCATAATTCAAACT-AAGGTCTTCAAGTCTAGAAGAAGACCAAATCGATTGCGATTTAG
131 TTCCGGTCAAAATTCAAACTGAA-GTCTTCAAGTCTAGAAGAAGACCAAATCGATTGCGATTTAG
2291765 CAATGA
195 CAATGA
* * * * *
2291771 AGAACTACTTCTCAACCTAGATTTTGACATAGCTTAAGTCGAAAAGAGCTATCTATCGACCAAAG
1 AGAACTACTTCCCAACCCAGATTTCGACATAGCTTAAGTCGAAAAGAACTATATATCGACCAAAG
* * * * * *
2291836 CTTTCAAGTTCGATTCCACTCAACTCGAGAGCACATTGA-TCATATGGTAGCAACAAGGAACTAT
66 CTTTCAAGTTCGATTCCACTCAAATCGAGAACACATTAACT-ACATGGTAGCAACAAGAAACTAC
* * *
2291900 CTTCTGGTCAAAATTCAATCTGAAGTCTTTAAGTCTAGAAGAAGACC
130 CTTCCGGTCAAAATTCAAACTGAAGTCTTCAAGTCTAGAAGAAGACC
2291947 CAAGATTGAC
Statistics
Matches: 147, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
199 1 0.01
200 144 0.98
201 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (200 bp):
AGAACTACTTCCCAACCCAGATTTCGACATAGCTTAAGTCGAAAAGAACTATATATCGACCAAAG
CTTTCAAGTTCGATTCCACTCAAATCGAGAACACATTAACTACATGGTAGCAACAAGAAACTACC
TTCCGGTCAAAATTCAAACTGAAGTCTTCAAGTCTAGAAGAAGACCAAATCGATTGCGATTTAGC
AATGA
Found at i:2293005 original size:15 final size:15
Alignment explanation
Indices: 2292982--2293013 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2292972 CTAATGAAAA
2292982 TATTCTAGGATTTTT
1 TATTCTAGGATTTTT
*
2292997 TATTTTAGGATTTTT
1 TATTCTAGGATTTTT
2293012 TA
1 TA
2293014 GAGCCTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.12, T:0.62
Consensus pattern (15 bp):
TATTCTAGGATTTTT
Found at i:2293352 original size:24 final size:24
Alignment explanation
Indices: 2293303--2293352 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2293293 TTTTCCCTTT
*
2293303 ATTTTATTTATTTATTTTGATCCA
1 ATTTTATTTATTTATTTCGATCCA
*
2293327 ATTTTATTT-TTTATATTCGATTCA
1 ATTTTATTTATTTAT-TTCGATCCA
2293351 AT
1 AT
2293353 AATCCGATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.26, C:0.08, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTTATTTATTTATTTCGATCCA
Found at i:2295338 original size:18 final size:18
Alignment explanation
Indices: 2295315--2295362 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
2295305 AAATATTTAT
*
2295315 TTAATTTTTAAAATTAAA
1 TTAATTTTTAAAATGAAA
* *
2295333 TTAATTATTTGAAATGATA
1 TTAATT-TTTAAAATGAAA
2295352 TT-ATTTTTAAA
1 TTAATTTTTAAA
2295363 TTATCTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 5 0.20
18 9 0.36
19 11 0.44
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (18 bp):
TTAATTTTTAAAATGAAA
Found at i:2295504 original size:23 final size:23
Alignment explanation
Indices: 2295473--2295550 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 23
2295463 AGATAATCTA
* * *
2295473 AAATTATATTATTTCAAATAAAT
1 AAATAATATTATTTAAAATAATT
* *
2295496 AAATAATATAATTTTAAA-AATT
1 AAATAATATTATTTAAAATAATT
2295518 AAATAA-A-TATTTAAAATAATT
1 AAATAATATTATTTAAAATAATT
*
2295539 TAATAATATTAT
1 AAATAATATTAT
2295551 AAATATACTT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 7 0.16
21 10 0.22
22 10 0.22
23 18 0.40
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATAATATTATTTAAAATAATT
Found at i:2297187 original size:18 final size:18
Alignment explanation
Indices: 2297164--2297202 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2297154 TTTCAAAATA
2297164 ATATAAT-ATATATTTAAT
1 ATATAATAAT-TATTTAAT
*
2297182 ATATAATAATTATTTCAT
1 ATATAATAATTATTTAAT
2297200 ATA
1 ATA
2297203 CAAATAGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATAATAATTATTTAAT
Found at i:2301188 original size:22 final size:23
Alignment explanation
Indices: 2301163--2301218 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
2301153 AATACGAATG
2301163 TTAAAGAAATA-ATATTA-AAAAT
1 TTAAAGAAATAGA-ATTATAAAAT
*
2301185 TTAAAGATATAGAATTATAAAAT
1 TTAAAGAAATAGAATTATAAAAT
*
2301208 TTTAAGAAATA
1 TTAAAGAAATA
2301219 TTAAATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (23 bp):
TTAAAGAAATAGAATTATAAAAT
Found at i:2301935 original size:18 final size:20
Alignment explanation
Indices: 2301898--2301935 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2301888 GTTGAGAAGT
2301898 ATTTTTGACATGATGTATAAA
1 ATTTTTGACA-GATGTATAAA
2301919 ATTTTTGAC-GA-GTATAA
1 ATTTTTGACAGATGTATAA
2301936 TATATTTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
21 9 0.53
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (20 bp):
ATTTTTGACAGATGTATAAA
Found at i:2308985 original size:22 final size:22
Alignment explanation
Indices: 2308954--2309001 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
2308944 AAATTTCAGT
* *
2308954 ATTAACCGAACTAATCGACCGA
1 ATTAAACGAACTAACCGACCGA
* *
2308976 ATTAAACGAATTAACCGACTGA
1 ATTAAACGAACTAACCGACCGA
2308998 ATTA
1 ATTA
2309002 GCCAAAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.23
Consensus pattern (22 bp):
ATTAAACGAACTAACCGACCGA
Found at i:2317641 original size:16 final size:16
Alignment explanation
Indices: 2317601--2317641 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2317591 GGAAGAATTC
*
2317601 TTTTACTTTGCATTTA
1 TTTTACTTTACATTTA
*
2317617 TTTAACTTTACATTTA
1 TTTTACTTTACATTTA
*
2317633 TTTTGCTTT
1 TTTTACTTT
2317642 TCACATTTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.63
Consensus pattern (16 bp):
TTTTACTTTACATTTA
Found at i:2320005 original size:16 final size:16
Alignment explanation
Indices: 2319984--2320014 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2319974 TAATGTTTTC
*
2319984 TTTTGCTTATTACTTG
1 TTTTGCTTATGACTTG
2320000 TTTTGCTTATGACTT
1 TTTTGCTTATGACTT
2320015 CTTAATCTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (16 bp):
TTTTGCTTATGACTTG
Found at i:2324468 original size:18 final size:18
Alignment explanation
Indices: 2324445--2324479 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2324435 ATTTTTATTG
2324445 AATAAAAATAATATTTTT
1 AATAAAAATAATATTTTT
* *
2324463 AATAAATATATTATTTT
1 AATAAAAATAATATTTT
2324480 GGGTCAGGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATAAAAATAATATTTTT
Found at i:2328920 original size:59 final size:59
Alignment explanation
Indices: 2328853--2329052 Score: 256
Period size: 59 Copynumber: 3.3 Consensus size: 59
2328843 CAGACGATCA
* * * *
2328853 TTTTGTAACTTTTAATAGTCGAGGGACTAAACAAAATAGCATCCTATAATTAAGAGATT
1 TTTTGTAACTTTTAATAGTCGAGAGACTAAACAAAATAACGTCCTATAGTTAAGAGATT
* * *
2328912 TTTTGTAACTTTTAATAGTCGAGAAACTGAACAAAATAACGTCCTTTAGTTAAGAGATT
1 TTTTGTAACTTTTAATAGTCGAGAGACTAAACAAAATAACGTCCTATAGTTAAGAGATT
* * * * * *
2328971 ATTTCGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACGTCATTTAGTTAAGAGAAAAT
1 -TTTTGTAACTTTTAATAGTCGAGAGACTAAACAAAATAACGTCCTATAGTTAAGAG--ATT
2329033 TTTTGTAACTTTTAATAGTC
1 TTTTGTAACTTTTAATAGTC
2329053 TAAGGACTTA
Statistics
Matches: 124, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
59 52 0.42
60 51 0.41
61 19 0.15
62 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (59 bp):
TTTTGTAACTTTTAATAGTCGAGAGACTAAACAAAATAACGTCCTATAGTTAAGAGATT
Found at i:2328994 original size:60 final size:60
Alignment explanation
Indices: 2328852--2329052 Score: 269
Period size: 60 Copynumber: 3.4 Consensus size: 60
2328842 CCAGACGATC
* * * * *
2328852 ATTTTGTAACTTTTAATAGTCGAGGGACTAAACAAAATAGCATCCTATAATTAAGAGATT
1 ATTTTGTAACTTTTAATAGTCGAGAGACTAAACAAAATAACGTCCTTTAGTTAAGAGATT
* *
2328912 -TTTTGTAACTTTTAATAGTCGAGAAACTGAACAAAATAACGTCCTTTAGTTAAGAGATT
1 ATTTTGTAACTTTTAATAGTCGAGAGACTAAACAAAATAACGTCCTTTAGTTAAGAGATT
* * * * **
2328971 ATTTCGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACGTCATTTAGTTAAGAGAAA
1 ATTTTGTAACTTTTAATAGTCGAGAGACTAAACAAAATAACGTCCTTTAGTTAAGAGATT
2329031 ATTTTTGTAACTTTTAATAGTC
1 A-TTTTGTAACTTTTAATAGTC
2329053 TAAGGACTTA
Statistics
Matches: 124, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
59 52 0.42
60 53 0.43
61 19 0.15
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAGTCGAGAGACTAAACAAAATAACGTCCTTTAGTTAAGAGATT
Found at i:2329082 original size:60 final size:60
Alignment explanation
Indices: 2328853--2329082 Score: 220
Period size: 60 Copynumber: 3.9 Consensus size: 60
2328843 CAGACGATCA
* * * * * *
2328853 TTTTGTAACTTTTAATAGTCGAGGGACTAAACAAAATAGCATCCTATAATTAAGAG-ATT
1 TTTTGTAACTTTTAATAGTCAAGAGACTAAACAAAATAACGTCCTATAGTTAAGAGAAAT
* * * *
2328912 TTTTGTAACTTTTAATAGTCGAGAAACTGAACAAAATAACGTCCTTTAGTTAAGAG--AT
1 TTTTGTAACTTTTAATAGTCAAGAGACTAAACAAAATAACGTCCTATAGTTAAGAGAAAT
* * * * *
2328970 TATTTCGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACGTCATTTAGTTAAGAGAAAAT
1 T-TTT-GTAACTTTTAATAGTCAAGAGACTAAACAAAATAACGTCCTATAGTTAAGAG-AAAT
* *
2329033 TTTTGTAACTTTTAATAGTCTAAG-GACTTAA-AAAATAGC-TCTCTATAGTT
1 TTTTGTAACTTTTAATAGTC-AAGAGACTAAACAAAATAACGTC-CTATAGTT
2329083 GGGGACCATT
Statistics
Matches: 146, Mismatches: 18, Indels: 13
0.82 0.10 0.07
Matches are distributed among these distances:
58 2 0.01
59 54 0.37
60 60 0.41
61 22 0.15
62 5 0.03
63 3 0.02
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (60 bp):
TTTTGTAACTTTTAATAGTCAAGAGACTAAACAAAATAACGTCCTATAGTTAAGAGAAAT
Found at i:2330244 original size:7 final size:7
Alignment explanation
Indices: 2330232--2330256 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2330222 CAATATCCCA
2330232 TGCTTCT
1 TGCTTCT
2330239 TGCTTCT
1 TGCTTCT
2330246 TGCTTCT
1 TGCTTCT
2330253 TGCT
1 TGCT
2330257 AGTTAGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.28, G:0.16, T:0.56
Consensus pattern (7 bp):
TGCTTCT
Found at i:2334528 original size:35 final size:35
Alignment explanation
Indices: 2334482--2334552 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
2334472 TTGAATGTTC
2334482 GGTTGGTTCAGTACCTAGTTTATTTATTTGTATGA
1 GGTTGGTTCAGTACCTAGTTTATTTATTTGTATGA
2334517 GGTTGGTTCAGTACCTAGTTTATTTATTTGTATGA
1 GGTTGGTTCAGTACCTAGTTTATTTATTTGTATGA
2334552 G
1 G
2334553 AACAAGTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.20, C:0.08, G:0.24, T:0.48
Consensus pattern (35 bp):
GGTTGGTTCAGTACCTAGTTTATTTATTTGTATGA
Found at i:2353617 original size:14 final size:14
Alignment explanation
Indices: 2353600--2353628 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2353590 TATTATAAAC
2353600 ATAATAACAATATA
1 ATAATAACAATATA
2353614 ATAATAACAATATA
1 ATAATAACAATATA
2353628 A
1 A
2353629 AAAAGAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAATAACAATATA
Found at i:2353746 original size:17 final size:16
Alignment explanation
Indices: 2353724--2353767 Score: 72
Period size: 17 Copynumber: 2.8 Consensus size: 16
2353714 TTATGAGGTG
2353724 AAAAATAATATTATTGT
1 AAAAATAATATTATT-T
2353741 AAAAATAATATTATTT
1 AAAAATAATATTATTT
2353757 -AAAATAATATT
1 AAAAATAATATT
2353768 TAACTTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 11 0.41
16 1 0.04
17 15 0.56
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
AAAAATAATATTATTT
Found at i:2353858 original size:17 final size:17
Alignment explanation
Indices: 2353836--2353868 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2353826 CGAGATCATA
2353836 ATATTAT-TTTTCATATT
1 ATATTATATTTT-ATATT
2353853 ATATTATATTTTATAT
1 ATATTATATTTTATAT
2353869 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:2354539 original size:25 final size:25
Alignment explanation
Indices: 2354510--2354568 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
2354500 TAACTTTATT
2354510 TTAATTTAATATATTTATTATTAAC
1 TTAATTTAATATATTTATTATTAAC
2354535 TTAATTTAATATATTTATTATTAAC
1 TTAATTTAATATATTTATTATTAAC
2354560 TTAATTTAA
1 TTAATTTAA
2354569 AAATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (25 bp):
TTAATTTAATATATTTATTATTAAC
Found at i:2354607 original size:23 final size:24
Alignment explanation
Indices: 2354560--2354605 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
2354550 TATTATTAAC
2354560 TTAATTTAAAAATATATATTTTTA
1 TTAATTTAAAAATATATATTTTTA
2354584 TTAATTTAAAAATATATATTTT
1 TTAATTTAAAAATATATATTTT
2354606 ATGTTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAATTTAAAAATATATATTTTTA
Found at i:2354875 original size:3 final size:3
Alignment explanation
Indices: 2354867--2354934 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
2354857 TAGATAAAAC
2354867 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2354915 ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
2354935 GTAGTTAACC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2357896 original size:31 final size:31
Alignment explanation
Indices: 2357858--2357925 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
2357848 TTACTTGTTT
*
2357858 AACTTTAGTTGGCCTGTCTTGGGGTAAACAG
1 AACTTTAGTTAGCCTGTCTTGGGGTAAACAG
2357889 AACTTTAGTTAGCCTGTCTTGGGGTAAACAG
1 AACTTTAGTTAGCCTGTCTTGGGGTAAACAG
2357920 AACTTT
1 AACTTT
2357926 GGTGTCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (31 bp):
AACTTTAGTTAGCCTGTCTTGGGGTAAACAG
Found at i:2364350 original size:23 final size:23
Alignment explanation
Indices: 2364317--2364368 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
2364307 ATTATTATAT
2364317 GGCACTACGGTACAATTCTACGC
1 GGCACTACGGTACAATTCTACGC
* * *
2364340 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTACAATTCTACGC
2364363 GGCACT
1 GGCACT
2364369 TCAGTGCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTACAATTCTACGC
Found at i:2364375 original size:23 final size:23
Alignment explanation
Indices: 2364329--2364384 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
2364319 CACTACGGTA
*
2364329 CAATTCTACGCGGCACTCCGGTG
1 CAATTCTACGCGGCACTCCAGTG
* *
2364352 CAATTCTACGTGGCACTTCAGTG
1 CAATTCTACGCGGCACTCCAGTG
*
2364375 CAATTATACG
1 CAATTCTACG
2364385 AGTTGTGGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (23 bp):
CAATTCTACGCGGCACTCCAGTG
Found at i:2364479 original size:14 final size:14
Alignment explanation
Indices: 2364460--2364492 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2364450 TCATAGGCTA
2364460 GTGAACTTAAT-AAT
1 GTGAACTT-ATGAAT
2364474 GTGAACTTATGAAT
1 GTGAACTTATGAAT
2364488 GTGAA
1 GTGAA
2364493 TTTGATAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (14 bp):
GTGAACTTATGAAT
Found at i:2370048 original size:3 final size:3
Alignment explanation
Indices: 2370040--2370069 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
2370030 TCCAGATTTC
2370040 TCT TCT TCT TCTT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TC-T TCT TCT TCT TCT TCT TC
2370070 ACCGCGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:2370061 original size:16 final size:15
Alignment explanation
Indices: 2370036--2370068 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
2370026 AGATTCCAGA
2370036 TTTCTCTTCTTCTTC
1 TTTCTCTTCTTCTTC
2370051 TTTCTTCTTCTTCTTC
1 TTTC-TCTTCTTCTTC
2370067 TT
1 TT
2370069 CACCGCGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTCTCTTCTTCTTC
Found at i:2371164 original size:30 final size:30
Alignment explanation
Indices: 2371130--2371198 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
2371120 TTATATGAGT
* *
2371130 TATGTGATAAAGGTATGGAAATGATATGTC
1 TATGTGATAAAGGTATGAAAATAATATGTC
2371160 TATGTGATAAAGGTATGAAAATAATATGTC
1 TATGTGATAAAGGTATGAAAATAATATGTC
*
2371190 TACGTGATA
1 TATGTGATA
2371199 CAAACTATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.33
Consensus pattern (30 bp):
TATGTGATAAAGGTATGAAAATAATATGTC
Found at i:2371443 original size:23 final size:23
Alignment explanation
Indices: 2371412--2371495 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
2371402 TATTATATGA
* * **
2371412 CACTACGGTACAATTCTACGCGG
1 CACTTCGGTGCAATTCTACATGG
*
2371435 CACTCCGGTGCAATTCTACATGG
1 CACTTCGGTGCAATTCTACATGG
2371458 CACTTCGGTGCAATTCTACATGG
1 CACTTCGGTGCAATTCTACATGG
2371481 CACTTCGGTGCAATT
1 CACTTCGGTGCAATT
2371496 ATACGAGCTA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACATGG
Found at i:2375369 original size:19 final size:19
Alignment explanation
Indices: 2375324--2375374 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
2375314 CTGTAATCTC
*
2375324 TCCTTTCCTACTTCTTAAA
1 TCCTTTCTTACTTCTTAAA
2375343 TCCTTTCTTACTTCTTAAA
1 TCCTTTCTTACTTCTTAAA
2375362 TCCTTTCTT-CTTC
1 TCCTTTCTTACTTC
2375375 GATTTTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 4 0.13
19 27 0.87
ACGTcount: A:0.16, C:0.31, G:0.00, T:0.53
Consensus pattern (19 bp):
TCCTTTCTTACTTCTTAAA
Found at i:2375385 original size:11 final size:11
Alignment explanation
Indices: 2375369--2375396 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2375359 AAATCCTTTC
2375369 TTCTTCGATTT
1 TTCTTCGATTT
2375380 TTCTTCGATTT
1 TTCTTCGATTT
2375391 TTCTTC
1 TTCTTC
2375397 TCTAATATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.21, G:0.07, T:0.64
Consensus pattern (11 bp):
TTCTTCGATTT
Found at i:2375397 original size:14 final size:12
Alignment explanation
Indices: 2375365--2375396 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2375355 TCTTAAATCC
2375365 TTTCTTCTTCGA
1 TTTCTTCTTCGA
2375377 TTT-TTCTTCGA
1 TTTCTTCTTCGA
2375388 TTT-TTCTTC
1 TTTCTTCTTC
2375397 TCTAATATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 17 0.85
12 3 0.15
ACGTcount: A:0.06, C:0.22, G:0.06, T:0.66
Consensus pattern (12 bp):
TTTCTTCTTCGA
Found at i:2380971 original size:19 final size:21
Alignment explanation
Indices: 2380947--2380998 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
2380937 ATGTCATTTT
2380947 GGTATCGGTACCTTG-AG-GA
1 GGTATCGGTACCTTGAAGAGA
*
2380966 GGTATCGATACCCTTGAAGAGA
1 GGTATCGGTA-CCTTGAAGAGA
*
2380988 AGTATCGGTAC
1 GGTATCGGTAC
2380999 TGGAGGGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 9 0.33
20 5 0.19
21 3 0.11
22 10 0.37
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (21 bp):
GGTATCGGTACCTTGAAGAGA
Found at i:2381805 original size:21 final size:21
Alignment explanation
Indices: 2381753--2381823 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
2381743 GTCGAGGGTT
*
2381753 TTATGTGGTCATCTGGGACAA
1 TTATGTGGTCCTCTGGGACAA
*
2381774 TTATGTGGTCCTCTGGGATAA
1 TTATGTGGTCCTCTGGGACAA
* *
2381795 TTTTGTGGTCCT-TCGGGAAAA
1 TTATGTGGTCCTCT-GGGACAA
*
2381816 ATATGTGG
1 TTATGTGG
2381824 CACTTCGGTG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 1 0.02
21 42 0.98
ACGTcount: A:0.21, C:0.13, G:0.30, T:0.37
Consensus pattern (21 bp):
TTATGTGGTCCTCTGGGACAA
Found at i:2395338 original size:21 final size:23
Alignment explanation
Indices: 2395314--2395359 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
2395304 CATTGCTTCT
* *
2395314 CTTTTCTTTTTTC-GTTT-TTTC
1 CTTTTCTCTTCTCAGTTTGTTTC
2395335 CTTTTCTCTTCTCAGTTTGTTTC
1 CTTTTCTCTTCTCAGTTTGTTTC
2395358 CT
1 CT
2395360 GCCAACGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 4 0.19
23 6 0.29
ACGTcount: A:0.02, C:0.24, G:0.07, T:0.67
Consensus pattern (23 bp):
CTTTTCTCTTCTCAGTTTGTTTC
Found at i:2397132 original size:16 final size:16
Alignment explanation
Indices: 2397111--2397144 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2397101 AGTTTCAAGA
*
2397111 TTGAGAGTTTGAAAGT
1 TTGAGAATTTGAAAGT
*
2397127 TTGAGAATTTGAGAGT
1 TTGAGAATTTGAAAGT
2397143 TT
1 TT
2397145 AAAAGATGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.41
Consensus pattern (16 bp):
TTGAGAATTTGAAAGT
Found at i:2397161 original size:24 final size:24
Alignment explanation
Indices: 2397111--2397162 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2397101 AGTTTCAAGA
* *
2397111 TTGAGAGTTTGAAAGTTTGAGAAT
1 TTGAGAGTTTAAAAGTGTGAGAAT
*
2397135 TTGAGAGTTTAAAAGATGT-AGAGT
1 TTGAGAGTTTAAAAG-TGTGAGAAT
2397159 TTGA
1 TTGA
2397163 TAATTTCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.37
Consensus pattern (24 bp):
TTGAGAGTTTAAAAGTGTGAGAAT
Found at i:2397594 original size:171 final size:167
Alignment explanation
Indices: 2397228--2397753 Score: 579
Period size: 171 Copynumber: 3.1 Consensus size: 167
2397218 TTCCTATCAA
* * * *
2397228 TTATGTTTGATAGGATGAAACACTATGGCATGGCAGAGATTCTCT-AAAATGGGGAAAGCTCTTT
1 TTATGTTTGATAGGATGAGACACTATGGCATGGCAAAGATTCTCTAAAAATGGGGAAAACGCTTT
* * * * *
2397292 CTGTGGAATAAACCTTTT-TTTTTGTCAGATTTTATCT-ATGTCTCAGT-AATTATGTGTAGCTA
66 TTGTGGAAT-GAGCTTTTCTTTTTGTCAGATTTTATCTGATGTCTCAGTCAATTATGTGAAGATA
* *
2397354 TGATATTGACAGTTGGGGAACTATT-T-TC-A--TTAT
130 TGATATTGGCAGTTGGGGAACTATTCTCTCAACCTCAT
* * * *
2397387 TTATGTTTGAT-GCAATGAGACACTATGACATGGCAAAGATTCTCTAAAAAAGGGGGAAACCGCT
1 TTATGTTTGATAG-GATGAGACACTATGGCATGGCAAAGATTCTCT-AAAAATGGGGAAAACGCT
*
2397451 TTTTGTGGAATGAGCATTTTCTTTTTG-CTAGATTTTATCTGCATGTCTCAATCAATTATGTGAA
64 TTTTGTGGAATGAGC-TTTTCTTTTTGTC-AGATTTTATCTG-ATGTCTCAGTCAATTATGTGAA
* * *
2397515 GATATGATTTTGGCAGTCGGGGAACTATTCTCGTCAACCACAT
126 GATATGATATTGGCAGTTGGGGAACTATTCTC-TCAACCTCAT
* * * *
2397558 TCATGTTTTATGGGATGAGACACTATGGCATGGCAAAGATTCTCTGAAAAATGAGGAAAACGCTT
1 TTATGTTTGATAGGATGAGACACTATGGCATGGCAAAGATTCTCT-AAAAATGGGGAAAACGCTT
* * * * *
2397623 TTTGTGGAATGAGCTTATCCTTTTTGTCATATTTTATCTGTATGTCTTAGTCAATCATGTAAAGA
65 TTTGTGGAATGAGCTT-TTCTTTTTGTCAGATTTTATCTG-ATGTCTCAGTCAATTATGTGAAGA
* * * *
2397688 TATGATGTTGGCAATTAGGGAACTATTCCTATCAACCTCAT
128 TATGATATTGGCAGTTGGGGAACTATT-CTCTCAACCTCAT
*
2397729 TTATGTTTGATAGGATAAGACACTA
1 TTATGTTTGATAGGATGAGACACTA
2397754 CTATGATATG
Statistics
Matches: 305, Mismatches: 43, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
158 1 0.00
159 39 0.13
160 2 0.01
161 29 0.10
162 17 0.06
164 9 0.03
165 35 0.11
166 1 0.00
168 2 0.01
169 1 0.00
170 2 0.01
171 163 0.53
172 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.37
Consensus pattern (167 bp):
TTATGTTTGATAGGATGAGACACTATGGCATGGCAAAGATTCTCTAAAAATGGGGAAAACGCTTT
TTGTGGAATGAGCTTTTCTTTTTGTCAGATTTTATCTGATGTCTCAGTCAATTATGTGAAGATAT
GATATTGGCAGTTGGGGAACTATTCTCTCAACCTCAT
Found at i:2397858 original size:168 final size:168
Alignment explanation
Indices: 2397230--2397868 Score: 461
Period size: 171 Copynumber: 3.8 Consensus size: 168
2397220 CCTATCAATT
* * * * * *
2397230 ATGTTTGATAGGATGAAACACTATGGCATGGCAGAGATTCTCT-AAAATGGGGAAA-GCTCTTTC
1 ATGTTTGATAGGATGACACACTATGACATGACAAAGATTCTCTGAAAA-GAGAAAACGCT-TTT-
* ** * * * *
2397293 TGTGGAATAAACCTTT-TTTTTTGTCAGATTTTATCT--ATGTCTCAGT-AATTATGTGTAGCTA
63 TGTGGAATGAATATTTCCTTTTTGTCAGATTTTATCTGCATGTCTCAATCAATTATGTGAAGATA
* * * ** ** *
2397354 TGATATTGACAGTTGGGGAACTATT-T--TC-A--TTATTT
128 TGATGTTGGCAATCAGGGAACTATTCTCATCAACCACATTC
* * * * * *
2397389 ATGTTTGAT-GCAATGAGACACTATGACATGGCAAAGATTCTCTAAAAAAGGGGGAAACCGCTTT
1 ATGTTTGATAG-GATGACACACTATGACATGACAAAGATTCTCT-GAAAA--GAGAAAACGCTTT
** *
2397453 TTGTGGAATGAGCATTTTCTTTTTG-CTAGATTTTATCTGCATGTCTCAATCAATTATGTGAAGA
62 TTGTGGAATGAATATTTCCTTTTTGTC-AGATTTTATCTGCATGTCTCAATCAATTATGTGAAGA
* * * *
2397517 TATGATTTTGGCAGTCGGGGAACTATTCTCGTCAACCACATTC
126 TATGATGTTGGCAATCAGGGAACTATTCTCATCAACCACATTC
* * * * *
2397560 ATGTTTTATGGGATGAGACACTATGGCATGGCAAAGATTCTCTGAAAAATGAGGAAAACGCTTTT
1 ATGTTTGATAGGATGACACACTATGACATGACAAAGATTCTCTG-AAAA-GA-GAAAACGCTTTT
* * * * * * * *
2397625 TGTGGAATGAGCT-TATCCTTTTTGTCATATTTTATCTGTATGTCTTAGTCAATCATGTAAAGAT
63 TGTGGAATGA-ATATTTCCTTTTTGTCAGATTTTATCTGCATGTCTCAATCAATTATGTGAAGAT
* * *
2397689 ATGATGTTGGCAATTAGGGAACTATTC-CTATCAACCTCATTT
127 ATGATGTTGGCAATCAGGGAACTATTCTC-ATCAACCACATTC
* * * * *
2397731 ATGTTTGATAGGATAAGACACTACTATGATATGATATATATTCTCTG-AAA-A-AAAACGCTTAT
1 ATGTTTGATAGGAT--GACAC-ACTATGACATGACAAAGATTCTCTGAAAAGAGAAAACGCTTTT
* ** *
2397793 TGTGGAACGAATATTTCCTTTTTGTCAGATTTTAAATCCATGTCTCAATCAATTATGTGAAGATA
63 TGTGGAATGAATATTTCCTTTTTGTCAGATTTTATCTGCATGTCTCAATCAATTATGTGAAGATA
*
2397858 TAATGTTGGCA
128 TGATGTTGGCA
2397869 GTCACATAAC
Statistics
Matches: 387, Mismatches: 67, Indels: 43
0.78 0.13 0.09
Matches are distributed among these distances:
158 1 0.00
159 37 0.10
161 18 0.05
162 25 0.06
163 3 0.01
164 9 0.02
165 35 0.09
166 1 0.00
167 1 0.00
168 73 0.19
169 1 0.00
170 3 0.01
171 152 0.39
172 5 0.01
173 4 0.01
174 19 0.05
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.37
Consensus pattern (168 bp):
ATGTTTGATAGGATGACACACTATGACATGACAAAGATTCTCTGAAAAGAGAAAACGCTTTTTGT
GGAATGAATATTTCCTTTTTGTCAGATTTTATCTGCATGTCTCAATCAATTATGTGAAGATATGA
TGTTGGCAATCAGGGAACTATTCTCATCAACCACATTC
Found at i:2398737 original size:26 final size:27
Alignment explanation
Indices: 2398708--2398761 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
2398698 TTGATTATAA
*
2398708 AAACAACGAAA-CAT-AAACATTACATT
1 AAACAAC-AAACCATAAAACATTAAATT
2398734 AAACAACAAACCATAAAACATTAAATT
1 AAACAACAAACCATAAAACATTAAATT
2398761 A
1 A
2398762 GGATATCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 3 0.12
26 10 0.40
27 12 0.48
ACGTcount: A:0.61, C:0.19, G:0.02, T:0.19
Consensus pattern (27 bp):
AAACAACAAACCATAAAACATTAAATT
Found at i:2399484 original size:32 final size:32
Alignment explanation
Indices: 2399426--2399486 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2399416 AAGATAATAC
* *
2399426 AAAAACTTAATATAAAGGCATAATAAAAACAA
1 AAAAACTTAACATAAAGACATAATAAAAACAA
*
2399458 AAAAACTTAACAT-AAGAACATTATAAAAA
1 AAAAACTTAACATAAAG-ACATAATAAAAA
2399487 TATTAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 3 0.12
32 22 0.88
ACGTcount: A:0.66, C:0.10, G:0.05, T:0.20
Consensus pattern (32 bp):
AAAAACTTAACATAAAGACATAATAAAAACAA
Found at i:2403659 original size:21 final size:23
Alignment explanation
Indices: 2403635--2403680 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
2403625 CATTGCTTCT
* *
2403635 CTTTTCTTTTTTC-GTTT-TTTC
1 CTTTTCTCTTCTCAGTTTGTTTC
2403656 CTTTTCTCTTCTCAGTTTGTTTC
1 CTTTTCTCTTCTCAGTTTGTTTC
2403679 CT
1 CT
2403681 GCCAACGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 4 0.19
23 6 0.29
ACGTcount: A:0.02, C:0.24, G:0.07, T:0.67
Consensus pattern (23 bp):
CTTTTCTCTTCTCAGTTTGTTTC
Found at i:2405449 original size:16 final size:16
Alignment explanation
Indices: 2405428--2405461 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2405418 AGTTTCAAGA
*
2405428 TTGAGAGTTTGAAAGT
1 TTGAGAATTTGAAAGT
*
2405444 TTGAGAATTTGAGAGT
1 TTGAGAATTTGAAAGT
2405460 TT
1 TT
2405462 AAAAGATGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.41
Consensus pattern (16 bp):
TTGAGAATTTGAAAGT
Found at i:2405478 original size:24 final size:24
Alignment explanation
Indices: 2405428--2405479 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2405418 AGTTTCAAGA
* *
2405428 TTGAGAGTTTGAAAGTTTGAGAAT
1 TTGAGAGTTTAAAAGTGTGAGAAT
*
2405452 TTGAGAGTTTAAAAGATGT-AGAGT
1 TTGAGAGTTTAAAAG-TGTGAGAAT
2405476 TTGA
1 TTGA
2405480 TAATTTCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.37
Consensus pattern (24 bp):
TTGAGAGTTTAAAAGTGTGAGAAT
Found at i:2405896 original size:32 final size:32
Alignment explanation
Indices: 2405838--2405898 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2405828 AAGATAATAC
* *
2405838 AAAAACTTAATATAAAGGCATAATAAAAACAA
1 AAAAACTTAACATAAAGACATAATAAAAACAA
*
2405870 AAAAACTTAACAT-AAGAACATTATAAAAA
1 AAAAACTTAACATAAAG-ACATAATAAAAA
2405899 TATTAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 3 0.12
32 22 0.88
ACGTcount: A:0.66, C:0.10, G:0.05, T:0.20
Consensus pattern (32 bp):
AAAAACTTAACATAAAGACATAATAAAAACAA
Found at i:2412031 original size:20 final size:21
Alignment explanation
Indices: 2412006--2412049 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
2411996 AAGACAGTGT
2412006 TGTTTCTTATTATTATATA-A
1 TGTTTCTTATTATTATATATA
2412026 TGTTTCTTATTATTATATATA
1 TGTTTCTTATTATTATATATA
2412047 TGT
1 TGT
2412050 AATAATAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (21 bp):
TGTTTCTTATTATTATATATA
Found at i:2413934 original size:29 final size:29
Alignment explanation
Indices: 2413900--2413999 Score: 101
Period size: 29 Copynumber: 3.4 Consensus size: 29
2413890 ATTTAGGTCC
*
2413900 CCCAACTTTTAAAACTTGCAATACAATCT
1 CCCAACATTTAAAACTTGCAATACAATCT
* *** ** *
2413929 CTCAACATTTAGTTCGTTTGCAATACGGTCC
1 CCCAACATTTAAAAC--TTGCAATACAATCT
*
2413960 CCCAACTTTTAAAACTTGCAATACAATCT
1 CCCAACATTTAAAACTTGCAATACAATCT
2413989 CCCAACATTTA
1 CCCAACATTTA
2414000 GTTCGTTTGC
Statistics
Matches: 52, Mismatches: 17, Indels: 4
0.71 0.23 0.05
Matches are distributed among these distances:
29 31 0.60
31 21 0.40
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.32
Consensus pattern (29 bp):
CCCAACATTTAAAACTTGCAATACAATCT
Found at i:2413953 original size:31 final size:31
Alignment explanation
Indices: 2413915--2414044 Score: 138
Period size: 31 Copynumber: 4.3 Consensus size: 31
2413905 CTTTTAAAAC
* *
2413915 TTGCAATACAATCTCTCAACATTTAGTTCGT
1 TTGCAATACAATCCCCCAACATTTAGTTCGT
** * ***
2413946 TTGCAATACGGTCCCCCAACTTTTAAAAC--
1 TTGCAATACAATCCCCCAACATTTAGTTCGT
*
2413975 TTGCAATACAATCTCCCAACATTTAGTTCGT
1 TTGCAATACAATCCCCCAACATTTAGTTCGT
* * *
2414006 TTGCAATACAGTCCCCCAACATTTAGTCCAT
1 TTGCAATACAATCCCCCAACATTTAGTTCGT
2414037 TTGCAATA
1 TTGCAATA
2414045 TGGTCCCCGA
Statistics
Matches: 78, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
29 22 0.28
31 56 0.72
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (31 bp):
TTGCAATACAATCCCCCAACATTTAGTTCGT
Found at i:2413988 original size:60 final size:60
Alignment explanation
Indices: 2413895--2414030 Score: 245
Period size: 60 Copynumber: 2.3 Consensus size: 60
2413885 TTTTCATTTA
*
2413895 GGTCCCCCAACTTTTAAAACTTGCAATACAATCTCTCAACATTTAGTTCGTTTGCAATAC
1 GGTCCCCCAACTTTTAAAACTTGCAATACAATCTCCCAACATTTAGTTCGTTTGCAATAC
2413955 GGTCCCCCAACTTTTAAAACTTGCAATACAATCTCCCAACATTTAGTTCGTTTGCAATAC
1 GGTCCCCCAACTTTTAAAACTTGCAATACAATCTCCCAACATTTAGTTCGTTTGCAATAC
* *
2414015 AGTCCCCCAACATTTA
1 GGTCCCCCAACTTTTA
2414031 GTCCATTTGC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.30, C:0.29, G:0.10, T:0.32
Consensus pattern (60 bp):
GGTCCCCCAACTTTTAAAACTTGCAATACAATCTCCCAACATTTAGTTCGTTTGCAATAC
Found at i:2423229 original size:17 final size:16
Alignment explanation
Indices: 2423209--2423243 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2423199 ATATTTATAT
2423209 TTAAATATTATTGATGA
1 TTAAATATTATT-ATGA
*
2423226 TTAAATATTGTTATGA
1 TTAAATATTATTATGA
2423242 TT
1 TT
2423244 CTATAAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (16 bp):
TTAAATATTATTATGA
Found at i:2428754 original size:64 final size:64
Alignment explanation
Indices: 2428668--2428828 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 64
2428658 TTGTTTAAGG
* * *
2428668 TGCATCGATGCACATGCG-GTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGCGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTT
2428731 A
64 A
* * *
2428732 TGCATCGATGCATAAG-GAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGCGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
* *
2428796 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAGCG-AGTGCATCGATGCAT
2428829 ACCTTCAGTA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 2 0.02
64 61 0.72
65 21 0.25
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAAGCGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:2429325 original size:2 final size:2
Alignment explanation
Indices: 2429318--2429368 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
2429308 CATGAGTTAG
*
2429318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2429360 AT AT AT AT A
1 AT AT AT AT A
2429369 GGAATTGTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2429959 original size:31 final size:30
Alignment explanation
Indices: 2429921--2430019 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 30
2429911 TCGAGGGTTT
**
2429921 TACCTATGTCTTTCGAGACATATGGACAGTA
1 TACCTATGTCTAACGA-ACATATGGACAGTA
*
2429952 TACCTATGTTCTAAGGAACATATGGACAGTA
1 TACCTATG-TCTAACGAACATATGGACAGTA
* * * *
2429983 TACCTATGTTCTAAGGAATATATGGACCGTT
1 TACCTATG-TCTAACGAACATATGGACAGTA
2430014 TACCTA
1 TACCTA
2430020 GGTTCTTCGG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 56 0.92
32 5 0.08
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (30 bp):
TACCTATGTCTAACGAACATATGGACAGTA
Found at i:2430025 original size:31 final size:31
Alignment explanation
Indices: 2429938--2430047 Score: 141
Period size: 31 Copynumber: 3.6 Consensus size: 31
2429928 GTCTTTCGAG
2429938 ACATATGGACAGTATACCTATGTTCTAAGGA
1 ACATATGGACAGTATACCTATGTTCTAAGGA
2429969 ACATATGGACAGTATACCTATGTTCTAAGGA
1 ACATATGGACAGTATACCTATGTTCTAAGGA
* * * * ** *
2430000 ATATATGGACCGTTTACCTAGGTTCTTCGGG
1 ACATATGGACAGTATACCTATGTTCTAAGGA
*
2430031 ACCTATGGACAGT-TACC
1 ACATATGGACAGTATACC
2430048 GAGGATCTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
30 4 0.06
31 65 0.94
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (31 bp):
ACATATGGACAGTATACCTATGTTCTAAGGA
Found at i:2430100 original size:30 final size:30
Alignment explanation
Indices: 2430030--2430102 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
2430020 GGTTCTTCGG
* *
2430030 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
2430060 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
2430090 GACCTCTGGATAG
1 GACCTCTGGATAG
2430103 GTCCTTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:2433398 original size:64 final size:64
Alignment explanation
Indices: 2433323--2433465 Score: 184
Period size: 64 Copynumber: 2.2 Consensus size: 64
2433313 ATTGTTTAAG
*
2433323 GTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTATGCATCGATGCATAAG-G
1 GTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTATGCATCGATGCAT-AGTG
2433386 -A
63 TA
* * * *
2433387 GTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTATGCATCGATGCATGGTGTA
1 GTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTATGCATCGATGCATAGTGTA
2433452 GTGCATCGATGCAT
1 GTGCATCGATGCAT
2433466 ACCTTCATTA
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 47 0.67
65 21 0.30
66 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (64 bp):
GTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTATGCATCGATGCATAGTGTA
Found at i:2433961 original size:2 final size:2
Alignment explanation
Indices: 2433954--2433984 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2433944 CATGAGTTAG
*
2433954 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2433985 GGAATTGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2434680 original size:31 final size:30
Alignment explanation
Indices: 2434642--2434740 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 30
2434632 TCGAGGGTTT
** *
2434642 TACCTATGTCTTTCGAGATATATGGACAGTA
1 TACCTATGTCTAACGA-ACATATGGACAGTA
*
2434673 TACCTATGTTCTAAGGAACATATGGACAGTA
1 TACCTATG-TCTAACGAACATATGGACAGTA
* * * *
2434704 TACCTATGTTCTAAGGAATATATGGACCGTT
1 TACCTATG-TCTAACGAACATATGGACAGTA
2434735 TACCTA
1 TACCTA
2434741 GGTTCTTCGG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 55 0.92
32 5 0.08
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (30 bp):
TACCTATGTCTAACGAACATATGGACAGTA
Found at i:2434746 original size:31 final size:31
Alignment explanation
Indices: 2434659--2434746 Score: 140
Period size: 31 Copynumber: 2.8 Consensus size: 31
2434649 GTCTTTCGAG
2434659 ATATATGGACAGTATACCTATGTTCTAAGGA
1 ATATATGGACAGTATACCTATGTTCTAAGGA
*
2434690 ACATATGGACAGTATACCTATGTTCTAAGGA
1 ATATATGGACAGTATACCTATGTTCTAAGGA
* * *
2434721 ATATATGGACCGTTTACCTAGGTTCT
1 ATATATGGACAGTATACCTATGTTCT
2434747 TCGGGACCTA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (31 bp):
ATATATGGACAGTATACCTATGTTCTAAGGA
Found at i:2434821 original size:30 final size:30
Alignment explanation
Indices: 2434751--2434823 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
2434741 GGTTCTTCGG
* *
2434751 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
2434781 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
2434811 GACCTCTGGATAG
1 GACCTCTGGATAG
2434824 GTCCTTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:2437670 original size:2 final size:2
Alignment explanation
Indices: 2437663--2437687 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2437653 AGATATACAA
2437663 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 A
2437688 ATTGTGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2452438 original size:60 final size:59
Alignment explanation
Indices: 2452314--2452448 Score: 141
Period size: 60 Copynumber: 2.3 Consensus size: 59
2452304 TATGACCCTT
* * * *
2452314 ATTTTAAATTAGTCCATAAATTTTTAAATATTTTAACTTCATTCTTAAATTACATATATC
1 ATTTTAAATTAGTCCATAAACTTTTAAATATTTCAACTTCATCCTCAAATTACATATA-C
* *
2452374 ATTTTAAATTAGTTC-TCAAACTTTTAAATATTTCAATTTCATCCTCAAACTATGACA-ATA-
1 ATTTTAAATTAGTCCAT-AAACTTTTAAATATTTCAACTTCATCCTCAAA-T-T-ACATATAC
*
2452434 ATTTTAAATTGGTCC
1 ATTTTAAATTAGTCC
2452449 CCTAAAATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
59 1 0.02
60 54 0.86
61 1 0.02
62 4 0.06
63 3 0.05
ACGTcount: A:0.37, C:0.14, G:0.04, T:0.45
Consensus pattern (59 bp):
ATTTTAAATTAGTCCATAAACTTTTAAATATTTCAACTTCATCCTCAAATTACATATAC
Found at i:2469151 original size:32 final size:31
Alignment explanation
Indices: 2469085--2469175 Score: 94
Period size: 32 Copynumber: 2.9 Consensus size: 31
2469075 ATCGGAACTC
* * *
2469085 GGAAGGGGAAGATCGGCTGTAGAAGTCACTAG
1 GGAAGGGGAAGATCGGCCGT-GAAGTGACGAG
*
2469117 GGAAGGGGAAGATCGGCCGTCGAAGTGTCGAG
1 GGAAGGGGAAGATCGGCCGT-GAAGTGACGAG
**
2469149 GGAA-AAGAAGATCGGCCTGTGAAGTGA
1 GGAAGGGGAAGATCGGCC-GTGAAGTGA
2469176 AGTCACCATC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
31 17 0.34
32 33 0.66
ACGTcount: A:0.31, C:0.13, G:0.42, T:0.14
Consensus pattern (31 bp):
GGAAGGGGAAGATCGGCCGTGAAGTGACGAG
Found at i:2469544 original size:27 final size:27
Alignment explanation
Indices: 2469504--2469569 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 27
2469494 ACCCGAACCG
* * *
2469504 AACCGAATCAAAAAAATGAAGCC-TTTA
1 AACCGAACCGAAAAAACGAA-CCGTTTA
*
2469531 AACCGAACCG-AAAACCGAACCGTTTA
1 AACCGAACCGAAAAAACGAACCGTTTA
2469557 AAGCCGAACCGAA
1 AA-CCGAACCGAA
2469570 CCATTTTACT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
25 2 0.06
26 13 0.41
27 16 0.50
28 1 0.03
ACGTcount: A:0.47, C:0.26, G:0.15, T:0.12
Consensus pattern (27 bp):
AACCGAACCGAAAAAACGAACCGTTTA
Found at i:2470013 original size:17 final size:18
Alignment explanation
Indices: 2469982--2470015 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2469972 ACGTGTTTTG
*
2469982 TTTATATTTTCTAAAAAT
1 TTTATATTTTATAAAAAT
2470000 TTTAT-TTTTATAAAAA
1 TTTATATTTTATAAAAA
2470016 CTTAAGTTAA
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:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTATATTTTATAAAAAT
Found at i:2473609 original size:124 final size:123
Alignment explanation
Indices: 2473428--2473675 Score: 446
Period size: 124 Copynumber: 2.0 Consensus size: 123
2473418 AGGTGTTCTA
2473428 ATTCACGGTGGTTCGTAAGAATTGTCAGAAATAATCAAACAAAGTCAGATTCGAGTGGGAGCGAT
1 ATTCACGGTGGTTCGTAAGAATTGTCAGAAATAATCAAACAAAGTCAGATTCGAGTGGGAGCGAT
2473493 GGCTGCAGACG-AAGGAAGTGAAAATTGAAAAGTTCGATGTTGCAGACTTTGGCTTTTGG
66 -GCTGCAGACGAAAGGAAGTGAAAA-TGAAAAGTTCGATGTTGCAGACTTTGGCTTTTGG
2473552 ATTCACGGTGGTTCGTAAGAATTGTCAGAAATAATCCAAACAAAGTC-GATTCGAGTGGGAGCGA
1 ATTCACGGTGGTTCGTAAGAATTGTCAGAAATAAT-CAAACAAAGTCAGATTCGAGTGGGAGCGA
*
2473616 TGCTGCAGACGAAAGGAAGTGAAAATGAAAAGTTTGATGTTGCAGACTTTGGCTTTTGG
65 TGCTGCAGACGAAAGGAAGTGAAAATGAAAAGTTCGATGTTGCAGACTTTGGCTTTTGG
2473675 A
1 A
2473676 AGATGTAGAT
Statistics
Matches: 121, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
123 44 0.36
124 66 0.55
125 11 0.09
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.26
Consensus pattern (123 bp):
ATTCACGGTGGTTCGTAAGAATTGTCAGAAATAATCAAACAAAGTCAGATTCGAGTGGGAGCGAT
GCTGCAGACGAAAGGAAGTGAAAATGAAAAGTTCGATGTTGCAGACTTTGGCTTTTGG
Found at i:2484047 original size:16 final size:16
Alignment explanation
Indices: 2484026--2484064 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
2484016 CATAGAGCCA
*
2484026 AACCATGCATATAGTG
1 AACCATACATATAGTG
2484042 AACCATACATATAGTG
1 AACCATACATATAGTG
2484058 AACCATA
1 AACCATA
2484065 GAACGATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.21, G:0.13, T:0.23
Consensus pattern (16 bp):
AACCATACATATAGTG
Found at i:2486590 original size:24 final size:24
Alignment explanation
Indices: 2486563--2486620 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
2486553 TAGTTAATGC
* *
2486563 ATCGATGCACATATTACTGAGTGT
1 ATCGATGCACATACTACAGAGTGT
2486587 ATCGATGCACATACTACAGAGTGT
1 ATCGATGCACATACTACAGAGTGT
*
2486611 ACCGATGCAC
1 ATCGATGCAC
2486621 TTCAAAGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (24 bp):
ATCGATGCACATACTACAGAGTGT
Found at i:2488691 original size:11 final size:12
Alignment explanation
Indices: 2488676--2488720 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 12
2488666 GCAAAGATCC
2488676 AAAGAAAAAGCA
1 AAAGAAAAAGCA
*
2488688 AAGAGAAAAAATCA
1 AA-AG-AAAAAGCA
2488702 AAAGAAAAAGC-
1 AAAGAAAAAGCA
2488713 AAAGAAAA
1 AAAGAAAA
2488721 CGGGAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 8 0.28
12 8 0.28
13 4 0.14
14 9 0.31
ACGTcount: A:0.76, C:0.07, G:0.16, T:0.02
Consensus pattern (12 bp):
AAAGAAAAAGCA
Found at i:2488696 original size:13 final size:13
Alignment explanation
Indices: 2488678--2488717 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
2488668 AAAGATCCAA
2488678 AGAAAAAGCAAAG
1 AGAAAAAGCAAAG
*
2488691 AGAAAAAATCAAA-
1 AG-AAAAAGCAAAG
2488704 AGAAAAAGCAAAG
1 AGAAAAAGCAAAG
2488717 A
1 A
2488718 AAACGGGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 9 0.39
13 5 0.22
14 9 0.39
ACGTcount: A:0.72, C:0.07, G:0.17, T:0.03
Consensus pattern (13 bp):
AGAAAAAGCAAAG
Found at i:2489589 original size:3 final size:3
Alignment explanation
Indices: 2489581--2489612 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2489571 TTTACAAAAA
2489581 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2489613 ATTTAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2490603 original size:10 final size:10
Alignment explanation
Indices: 2490590--2490614 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2490580 TCCTCTGGCA
2490590 CTCTCTATCT
1 CTCTCTATCT
2490600 CTCTCTATCT
1 CTCTCTATCT
2490610 CTCTC
1 CTCTC
2490615 GTTTGAGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (10 bp):
CTCTCTATCT
Found at i:2490684 original size:2 final size:2
Alignment explanation
Indices: 2490677--2490705 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2490667 CGTTGGTTTC
2490677 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2490706 ATACACGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2506752 original size:20 final size:20
Alignment explanation
Indices: 2506692--2506753 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
2506682 CATGGGTACA
*
2506692 CGATACTAAGTCCCTC-AATAT
1 CGATACTAA--CCCTCGAGTAT
* *
2506713 CGGTACTAACCCTCGGGTAT
1 CGATACTAACCCTCGAGTAT
2506733 CGATACTAA-CCTCCGAGTAT
1 CGATACTAACCCT-CGAGTAT
2506753 C
1 C
2506754 AATATTACTG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
19 8 0.24
20 18 0.53
21 8 0.24
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (20 bp):
CGATACTAACCCTCGAGTAT
Found at i:2506841 original size:22 final size:22
Alignment explanation
Indices: 2506792--2506846 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
2506782 ACAAGGGGAT
* * *
2506792 GGTATCAATAC-TCTAGTTTGA
1 GGTATCGATACTTATAGTATGA
2506813 -GTATCGATACTTATAGTATGA
1 GGTATCGATACTTATAGTATGA
2506834 GGTATCGATACTT
1 GGTATCGATACTT
2506847 TCTTAAGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.31
21 8 0.28
22 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (22 bp):
GGTATCGATACTTATAGTATGA
Found at i:2508163 original size:55 final size:55
Alignment explanation
Indices: 2508072--2508837 Score: 1273
Period size: 55 Copynumber: 13.9 Consensus size: 55
2508062 TGGCACTATA
2508072 TGTGTGCAAAACTAAGAAA-TCATAATAAGTTTATGAATTTCCGTATGGGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* *
2508126 TATGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACCG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* *
2508181 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATATCCGTATAGGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* * * *
2508236 TGTGTGCAAAACAAAGAAATTCATAATAAGTTTATGAATTTCAGTATGGGAATTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* * **
2508291 TATGTGCAAAACTAAGAAATTCATAATAAGTTAATGAATTTTTGTATGGGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
*
2508346 TATGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
2508401 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* **
2508456 TGTGTGCAAAACTAAGAAATTAATAATAAGTTTATGAATTTTTGTATGGGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* *
2508511 TGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* * *
2508566 TGTGTGCAAAACTAAGAAAATCATAATAAGTTAATGAATTTCCGTGTGGGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
*
2508621 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* *
2508676 TGTGTGCAAAACTAAGAAATTCATAGTAAGTTTATGAATTTTCGTATGGGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
*
2508731 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* * *
2508786 TGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCA
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCA
2508838 TTAGGTATGC
Statistics
Matches: 665, Mismatches: 46, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
54 18 0.03
55 647 0.97
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (55 bp):
TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
Found at i:2508903 original size:110 final size:110
Alignment explanation
Indices: 2508076--2508923 Score: 814
Period size: 110 Copynumber: 7.7 Consensus size: 110
2508066 ACTATATGTG
* * * * ****
2508076 TGCAAAACTAAGAAA-TCATAATAAGTTTATGAATTTCCGTATGGGCACTGTATGTGCAAAACTA
1 TGCAAAACCAAGAAATTCATAATAAGTGTATGAATTTTCGTATGGGCAATACGGGTGCAAAACTA
* * *
2508140 AGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACCGTGTG
66 AGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTA
* * * * * * ** * *
2508185 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATATCCGTATAGGCACTGTGTGTGCAAAACAA
1 TGCAAAACCAAGAAATTCATAATAAGTGTATGAATTTTCGTATGGGCAATACGGGTGCAAAACTA
* * * *
2508250 AGAAATTCATAATAAGTTTATGAA-TTTCAGTATGGGAATTGTATG
66 AGAAATTCATAATAAGTTTATGAATTTTC-GTATGGGCACTGTGTA
* * * ****
2508295 TGCAAAACTAAGAAATTCATAATAAGT-TAATGAATTTTTGTATGGGCACTGTATGTGCAAAACT
1 TGCAAAACCAAGAAATTCATAATAAGTGT-ATGAATTTTCGTATGGGCAATACGGGTGCAAAACT
* *
2508359 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTG
65 AAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTA
* * * * ** *
2508405 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGCAAAACTA
1 TGCAAAACCAAGAAATTCATAATAAGTGTATGAATTTTCGTATGGGCAATACGGGTGCAAAACTA
* * *
2508470 AGAAATTAATAATAAGTTTATGAATTTTTGTATGGGCACTGTGTG
66 AGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTA
* * * * * * ** *
2508515 TGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTGTGTGTGCAAAACTA
1 TGCAAAACCAAGAAATTCATAATAAGTGTATGAATTTTCGTATGGGCAATACGGGTGCAAAACTA
* * * * *
2508580 AGAAAATCATAATAAGTTAATGAATTTCCGTGTGGGCACTGTGTG
66 AGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTA
* * * ** *
2508625 TGCAAAACTAAGAAATTCATAATAAGTTTATGAA-TTTCTGTATGGGCACTGTGTGTGCAAAACT
1 TGCAAAACCAAGAAATTCATAATAAGTGTATGAATTTTC-GTATGGGCAATACGGGTGCAAAACT
* *
2508689 AAGAAATTCATAGTAAGTTTATGAATTTTCGTATGGGCACTGTGTG
65 AAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTA
* * * ** *
2508735 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTGCAAAACTA
1 TGCAAAACCAAGAAATTCATAATAAGTGTATGAATTTTCGTATGGGCAATACGGGTGCAAAACTA
* * *
2508800 AGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCATTAG-GTA
66 AGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACT-GTGTA
*** * * * * *
2508845 TGCATCCCCACGTAATTCTTAATTA-TGTAGTGAATTATT-GTATTGGCAATACGGGTGC-AAAC
1 TGCAAAACCAAGAAATTCATAATAAGTGTA-TGAATT-TTCGTATGGGCAATACGGGTGCAAAAC
*
2508907 TAA-AGAATTTATAATAA
64 TAAGA-AATTCATAATAA
2508924 AATTAAATAG
Statistics
Matches: 666, Mismatches: 62, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
108 1 0.00
109 42 0.06
110 612 0.92
111 11 0.02
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (110 bp):
TGCAAAACCAAGAAATTCATAATAAGTGTATGAATTTTCGTATGGGCAATACGGGTGCAAAACTA
AGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTA
Found at i:2523105 original size:17 final size:19
Alignment explanation
Indices: 2523085--2523119 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2523075 AAATTAATGG
2523085 AGTAAAA-AAA-TAAAAAA
1 AGTAAAAGAAATTAAAAAA
2523102 AGTAAAAGAAATTAAAAA
1 AGTAAAAGAAATTAAAAA
2523120 TGAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (19 bp):
AGTAAAAGAAATTAAAAAA
Found at i:2523327 original size:37 final size:36
Alignment explanation
Indices: 2523240--2523495 Score: 140
Period size: 37 Copynumber: 7.0 Consensus size: 36
2523230 AGAAAAAAAT
*
2523240 AAAGTA-AAAATATAATA-TATA-TAAATA-A-ATAA
1 AAAGTATAAAATATAATATTA-AGAAAATATATATAA
*
2523272 AAA-TA-AAAATAGAATATTAAGAAAATATATATAA
1 AAAGTATAAAATATAATATTAAGAAAATATATATAA
* *
2523306 AAACGTATAAAATATAATATTAAGAAAAAATATATAC
1 AAA-GTATAAAATATAATATTAAGAAAATATATATAA
* * * * *
2523343 ATAGTAAATGGAGAAAAATTAATACATCTATA-CATATATATATAT
1 AAAGT--AT--A-AAATA-TAAT--AT-TA-AGAAAATATATATAA
* *
2523388 AATGATATAAGATAT-ATA-TAATGAAAATA-ATATAA
1 AAAG-TATAAAATATAATATTAA-GAAAATATATATAA
* * *
2523423 TATAAATA-AAAATAGAAAATTAAGAAAATATATATAA
1 -A-AAGTATAAAATATAATATTAAGAAAATATATATAA
*
2523460 AAACGTATAAAATATAATATTAAGAAAAAATATATA
1 AAA-GTATAAAATATAATATTAAGAAAATATATATA
2523496 CATAGTAAAT
Statistics
Matches: 170, Mismatches: 27, Indels: 49
0.69 0.11 0.20
Matches are distributed among these distances:
31 13 0.08
32 10 0.06
33 1 0.01
34 8 0.05
35 14 0.08
36 23 0.14
37 64 0.38
38 2 0.01
39 2 0.01
40 2 0.01
41 7 0.04
42 5 0.03
44 4 0.02
45 13 0.08
46 2 0.01
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (36 bp):
AAAGTATAAAATATAATATTAAGAAAATATATATAA
Found at i:2523420 original size:25 final size:23
Alignment explanation
Indices: 2523376--2523422 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
2523366 ACATCTATAC
* *
2523376 ATATATATATATAATGATATAAG
1 ATATATATATAAAATAATATAAG
2523399 ATATATATAATGAAAATAATATAA
1 ATATATAT-AT-AAAATAATATAA
2523423 TATAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.36
Consensus pattern (23 bp):
ATATATATATAAAATAATATAAG
Found at i:2523434 original size:154 final size:158
Alignment explanation
Indices: 2523263--2523593 Score: 573
Period size: 154 Copynumber: 2.1 Consensus size: 158
2523253 AATATATATA
* *
2523263 AATA-AATAAAAATAAAAATAGAATATTAAGAAAATATATATAAAAACGTATAAAATATAATATT
1 AATATAATATAAATAAAAATAGAAAATTAAGAAAATATATATAAAAACGTATAAAATATAATATT
*
2523327 AAGAAAAAATATATACATAGTAAATGGAGAAAAA-T-TA-ATACATCTATACATATATATATATA
66 AAGAAAAAATATATACATAGTAAATGGAGAAAAATTATATATACATATATACATATATATATATA
2523389 -ATGATATAAGATATATATAATGAAAAT
131 TATGATATAAGATATATATAATGAAAAT
2523416 AATATAATATAAATAAAAATAGAAAATTAAGAAAATATATATAAAAACGTATAAAATATAATATT
1 AATATAATATAAATAAAAATAGAAAATTAAGAAAATATATATAAAAACGTATAAAATATAATATT
* *
2523481 AAGAAAAAATATATACATAGTAAATGGAGAAAAATTAATATATATATATATATATATATATATAT
66 AAGAAAAAATATATACATAGTAAATGGAGAAAAATT-ATATATACATATATACATATATATATAT
2523546 ATATGATATAAGATATATATAATGAAAAT
130 ATATGATATAAGATATATATAATGAAAAT
2523575 AATATAATATAAATAAAAA
1 AATATAATATAAATAAAAA
2523594 AAGAGGAATA
Statistics
Matches: 167, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
153 4 0.02
154 92 0.55
155 1 0.01
157 2 0.01
158 22 0.13
159 46 0.28
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.31
Consensus pattern (158 bp):
AATATAATATAAATAAAAATAGAAAATTAAGAAAATATATATAAAAACGTATAAAATATAATATT
AAGAAAAAATATATACATAGTAAATGGAGAAAAATTATATATACATATATACATATATATATATA
TATGATATAAGATATATATAATGAAAAT
Found at i:2523525 original size:2 final size:2
Alignment explanation
Indices: 2523518--2523566 Score: 73
Period size: 2 Copynumber: 24.5 Consensus size: 2
2523508 AGAAAAATTA
*
2523518 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A- AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
2523560 AT AT AT A
1 AT AT AT A
2523567 ATGAAAATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
1 1 0.02
2 41 0.93
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2523576 original size:20 final size:19
Alignment explanation
Indices: 2523538--2523586 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
2523528 ATATATATAT
*
2523538 ATATATATATATGATATAAG
1 ATATATATA-ATGAAATAAG
*
2523558 ATATATATAATGAAAATAAT
1 ATATATATAATG-AAATAAG
2523578 ATA-ATATAA
1 ATATATATAA
2523587 ATAAAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (19 bp):
ATATATATAATGAAATAAG
Found at i:2523588 original size:14 final size:14
Alignment explanation
Indices: 2523516--2523590 Score: 57
Period size: 14 Copynumber: 5.2 Consensus size: 14
2523506 GGAGAAAAAT
*
2523516 TAATAT-ATATATA
1 TAATATAATATAAA
*
2523529 T-ATATATATATATA
1 TAATATA-ATATAAA
*
2523543 TATATATGATATAAGA
1 TA-ATATAATATAA-A
2523559 TATATATAATGA-AAA
1 TA-ATATAAT-ATAAA
2523574 TAATATAATATAAA
1 TAATATAATATAAA
2523588 TAA
1 TAA
2523591 AAAAAGAGGA
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
12 4 0.08
13 2 0.04
14 21 0.40
15 8 0.15
16 16 0.31
17 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (14 bp):
TAATATAATATAAA
Found at i:2525113 original size:110 final size:110
Alignment explanation
Indices: 2524911--2525175 Score: 323
Period size: 110 Copynumber: 2.4 Consensus size: 110
2524901 GTGGGTAGTA
* *
2524911 TTGTTTCGAGTCCAATA-TCCTC-CGTCGTGAAGTTGAAATTGGA-TCTG---G-AACTGGGAAA
1 TTGTCTCGAGTCCAATATTCCTCGC-T-GTGAAGTTGAAATT-GACTCTGAATGAAACT-GAAAA
* *
2524969 -TTATTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTG
62 GTTATTTGTTGACAATCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTG
* *
2525017 TTGTCTCGAGTTCAATA-TCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTT
1 TTGTCTCGAGTCCAATATTC-CTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTT
* *
2525081 ATTTGTTGACAATCAGTCGCCCCTTCATTGTGAAGTTGAGCTTGTG
65 ATTTGTTGACAATCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTG
* * *
2525127 TTGTCTTGAGTCCAATATTCCTCGCTGTGAATTTGAAATTGGCTCTGAA
1 TTGTCTCGAGTCCAATATTCCTCGCTGTGAAGTTGAAATTGACTCTGAA
2525176 ACTGGAAAGC
Statistics
Matches: 137, Mismatches: 13, Indels: 14
0.84 0.08 0.09
Matches are distributed among these distances:
105 2 0.01
106 35 0.26
107 3 0.02
108 1 0.01
109 5 0.04
110 89 0.65
111 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (110 bp):
TTGTCTCGAGTCCAATATTCCTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTA
TTTGTTGACAATCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTG
Found at i:2526068 original size:36 final size:36
Alignment explanation
Indices: 2526023--2526211 Score: 178
Period size: 36 Copynumber: 5.4 Consensus size: 36
2526013 ATTCAAAGAT
* *
2526023 TTTGTTTCAAAGGAAACTGTCTCGAGAGAGATGAAT
1 TTTGTTTCAAAGGAAACTGTCTCAAGAGAGATGAAA
* *
2526059 TTTGTTTCAAAAGAAACTGTCTCAAGGGAGATGAAA
1 TTTGTTTCAAAGGAAACTGTCTCAAGAGAGATGAAA
** *
2526095 TTTGTTTCAAATAAAACATAT-TC---A-A-AT--AA
1 TTTGTTTCAAAGGAAAC-TGTCTCAAGAGAGATGAAA
* **
2526124 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAAGGAAACTGTCTCAAGAGAGATGAAA
* * *
2526160 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAA
1 TTTGTTTCAAAGGAAACTGTCTCAAGAGAGATGAAA
* *
2526196 TTTATTTCAAGGGAAA
1 TTTGTTTCAAAGGAAA
2526212 TGTTTTCAAT
Statistics
Matches: 128, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
28 2 0.02
29 18 0.14
31 2 0.02
32 2 0.02
33 1 0.01
34 1 0.01
36 100 0.78
37 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.30
Consensus pattern (36 bp):
TTTGTTTCAAAGGAAACTGTCTCAAGAGAGATGAAA
Found at i:2526080 original size:101 final size:101
Alignment explanation
Indices: 2525960--2526298 Score: 369
Period size: 101 Copynumber: 3.3 Consensus size: 101
2525950 GAAGATTTTG
* * * *
2525960 TGTTTCAAGAGAAAATGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATATATTCAAAGATTT
* **
2526025 TGTTTCAAAGGAAACTGTCTCGAGAGAGATGAATTT
66 TGTTTCAAAGGAAACTGTCTCAAGAGAGAAAAATTT
* ** *** * * *
2526061 TGTTTCAAAAGAAACTGTCTCAAGGGAGATGAAATTTGTTTCAAATAAAACATATTCAAATAATT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATATATTCAAAGATTT
*
2526126 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
66 TGTTTCAAAGGAAACTGTCTCAAGAGAGA-AAAATTT
* * * * * *
2526162 TGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATATATTCAAAGATTT
*
2526226 ATGTTTC-AAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 -TGTTTCAAAG-GAAACTGTCTCAAGAGAGA-AAAATTT
* * * *
2526264 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
2526299 CTTCTTTTTA
Statistics
Matches: 198, Mismatches: 36, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
100 4 0.02
101 159 0.80
102 35 0.18
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (101 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATATATTCAAAGATTT
TGTTTCAAAGGAAACTGTCTCAAGAGAGAAAAATTT
Found at i:2526278 original size:37 final size:37
Alignment explanation
Indices: 2526227--2526298 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
2526217 TCAATGTTTA
* *
2526227 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTT
* *
2526264 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAAT
2526299 CTTCTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTT
Found at i:2527880 original size:69 final size:69
Alignment explanation
Indices: 2527764--2527901 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
2527754 TCTCTCTCTC
* *
2527764 TTGATGCTCTATGATCTTCGAGTTAAGTGATTCAGTGATTCGGAAATGATTGTGCTTCATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAAAATGATTGTGCTTCATCAATC
2527829 TCAT
66 TCAT
*
2527833 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAAAATGATTGTGCTTCATCAATC
2527898 TCAT
66 TCAT
2527902 AGTTTAAATC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.38
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAAAATGATTGTGCTTCATCAATC
TCAT
Found at i:2528020 original size:14 final size:13
Alignment explanation
Indices: 2527984--2528028 Score: 65
Period size: 13 Copynumber: 3.4 Consensus size: 13
2527974 TTTTCCTTTG
2527984 TTTTTATTTTCTC
1 TTTTTATTTTCTC
2527997 TTTTTATTTTCTC
1 TTTTTATTTTCTC
2528010 TTTGCTT-TTTTCTC
1 TTT--TTATTTTCTC
2528024 TTTTT
1 TTTTT
2528029 CTCTTTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.07
13 16 0.53
14 10 0.33
15 2 0.07
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTTATTTTCTC
Found at i:2531140 original size:26 final size:26
Alignment explanation
Indices: 2531109--2531183 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
2531099 AATAATAAAT
2531109 AAAACAAGAAAAAATGAAAAAATAAC
1 AAAACAAGAAAAAATGAAAAAATAAC
* * * * *
2531135 AAAACACGTAAAAATAAAAAAAAAAT
1 AAAACAAGAAAAAATGAAAAAATAAC
2531161 AAAA-AA-AACAAAATGAATAAAAT
1 AAAACAAGAA-AAAATGAA-AAAAT
2531184 GTTAAAAAAC
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
24 1 0.03
25 8 0.21
26 29 0.76
ACGTcount: A:0.77, C:0.07, G:0.05, T:0.11
Consensus pattern (26 bp):
AAAACAAGAAAAAATGAAAAAATAAC
Found at i:2531160 original size:11 final size:11
Alignment explanation
Indices: 2531144--2531168 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2531134 CAAAACACGT
2531144 AAAAATAAAAA
1 AAAAATAAAAA
2531155 AAAAATAAAAA
1 AAAAATAAAAA
2531166 AAA
1 AAA
2531169 CAAAATGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:2531273 original size:17 final size:17
Alignment explanation
Indices: 2531232--2531273 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2531222 GGAGTAAAAA
*
2531232 AATAAAAA-TAAAAAGT
1 AATAAAAATTAAAAAGG
2531248 AA-AAGAAATTAAAAAGG
1 AATAA-AAATTAAAAAGG
2531265 AATAAAAAT
1 AATAAAAAT
2531274 AATGTGTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 2 0.09
16 5 0.23
17 13 0.59
18 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.17
Consensus pattern (17 bp):
AATAAAAATTAAAAAGG
Found at i:2531342 original size:36 final size:36
Alignment explanation
Indices: 2531301--2531393 Score: 104
Period size: 36 Copynumber: 2.6 Consensus size: 36
2531291 TAGTATTTAC
*
2531301 TAAAACAAATAAAAATAATAAATATATAATACTAAG
1 TAAAACAAATAAAAATAATAAATACATAATACTAAG
* *
2531337 TAAAACAAATAAAAAATAA-AGATATACATGATATTAAG
1 TAAAACAAAT-AAAAATAATA-A-ATACATAATACTAAG
2531375 -AAAA-AAATAAAAA-AATAAA
1 TAAAACAAATAAAAATAATAAA
2531394 AAAAGTAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
33 1 0.02
34 3 0.06
35 6 0.12
36 15 0.30
37 13 0.26
38 12 0.24
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (36 bp):
TAAAACAAATAAAAATAATAAATACATAATACTAAG
Found at i:2531388 original size:8 final size:8
Alignment explanation
Indices: 2531375--2531429 Score: 56
Period size: 8 Copynumber: 6.6 Consensus size: 8
2531365 TGATATTAAG
2531375 AAAAAAAT
1 AAAAAAAT
2531383 AAAAAAAT
1 AAAAAAAT
2531391 AAAAAAAGT
1 AAAAAAA-T
*
2531400 AAAAATAT
1 AAAAAAAT
* *
2531408 AATATATAT
1 AA-AAAAAT
*
2531417 AAATAAAT
1 AAAAAAAT
2531425 AAAAA
1 AAAAA
2531430 CAAAAATAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
8 27 0.66
9 14 0.34
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (8 bp):
AAAAAAAT
Found at i:2531435 original size:46 final size:46
Alignment explanation
Indices: 2531301--2531437 Score: 114
Period size: 45 Copynumber: 3.0 Consensus size: 46
2531291 TAGTATTTAC
* *
2531301 TAAAACAAATAAAAATAATAA-ATATATAATACTAAGT-AAAAC--AAA
1 TAAAA-AAATAAAAAT-ATAATATATATAAGA-TAAATAAAAACAAAAA
*
2531346 T-AAAAAATAAAGATATACATGATAT-TAAGA-AAA-AAATAA-AAAAA
1 TAAAAAAATAAAAATATA-AT-ATATATAAGATAAATAAA-AACAAAAA
2531390 TAAAAAAAGTAAAAATATAATATATATAA-ATAAATAAAAACAAAAA
1 TAAAAAAA-TAAAAATATAATATATATAAGATAAATAAAAACAAAAA
2531436 TA
1 TA
2531438 GAATATTAAG
Statistics
Matches: 75, Mismatches: 4, Indels: 25
0.72 0.04 0.24
Matches are distributed among these distances:
42 7 0.09
43 12 0.16
44 16 0.21
45 21 0.28
46 19 0.25
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.22
Consensus pattern (46 bp):
TAAAAAAATAAAAATATAATATATATAAGATAAATAAAAACAAAAA
Found at i:2531453 original size:32 final size:35
Alignment explanation
Indices: 2531417--2531488 Score: 87
Period size: 37 Copynumber: 2.1 Consensus size: 35
2531407 TAATATATAT
2531417 AAATA-AATAAAAAC-A-AAAATAGAATATTAAGA
1 AAATACAATAAAAACGATAAAATAGAATATTAAGA
* *
2531449 AAATATCTATAAAAACGTATAAAATATAATATTAAGA
1 AAATA-CAATAAAAACG-ATAAAATAGAATATTAAGA
2531486 AAA
1 AAA
2531489 AATATATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
32 5 0.15
34 8 0.24
36 1 0.03
37 19 0.58
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.24
Consensus pattern (35 bp):
AAATACAATAAAAACGATAAAATAGAATATTAAGA
Found at i:2531531 original size:2 final size:2
Alignment explanation
Indices: 2531519--2531551 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2531509 AGAAAAATTA
*
2531519 AT AT AT CT 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 A
2531552 ATGAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2531614 original size:21 final size:20
Alignment explanation
Indices: 2531555--2531614 Score: 50
Period size: 21 Copynumber: 2.8 Consensus size: 20
2531545 ATATATAATG
2531555 AAAATAATATAATATAAATAAA
1 AAAAT-ATATAAT-TAAATAAA
* *
2531577 AAAAGGA-ATATAGTAAATAAA
1 AAAA-TATATA-ATTAAATAAA
2531598 TAAAATATATAATTAAA
1 -AAAATATATAATTAAA
2531615 AATATATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (20 bp):
AAAATATATAATTAAATAAA
Found at i:2531623 original size:18 final size:18
Alignment explanation
Indices: 2531526--2531626 Score: 64
Period size: 18 Copynumber: 5.4 Consensus size: 18
2531516 TTAATATATC
* * *
2531526 TATATATATATATATATA
1 TATATATAAATAAAAATA
*
2531544 TATATAT-AATGAAAATAA
1 TATATATAAATAAAAAT-A
*
2531562 TATAATATAAATAAAAAAA
1 TAT-ATATAAATAAAAATA
*
2531581 GGAATATAGTAAATAAATAA-A
1 --TATATA-TAAATAAA-AATA
*
2531602 -ATATATAATTAAAAATA
1 TATATATAAATAAAAATA
2531619 TATATATA
1 TATATATA
2531627 TAGGGGACGA
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
16 2 0.03
17 13 0.20
18 23 0.35
19 5 0.08
20 10 0.15
21 11 0.17
22 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
TATATATAAATAAAAATA
Found at i:2532485 original size:20 final size:20
Alignment explanation
Indices: 2532460--2532573 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
2532450 AATTGGGAAA
*
2532460 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
2532480 ATCGCAATGCGATATTTACT
1 ATCGCAACGCGATACTGACT
* * *
2532500 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
2532521 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2532541 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
2532561 TTCGCAACGCGAT
1 ATCGCAACGCGAT
2532574 TTACATAGCG
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2532566 original size:61 final size:61
Alignment explanation
Indices: 2532457--2532573 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 61
2532447 GCGAATTGGG
* * * * *
2532457 AAAATCGCAATGCGATACTGACTATCGCAATGCGATATTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATATTGACTATCGCAACGCGATAATAC
* *
2532518 AAAATCGCAACGAGATACTGACTTTCGCAACGCGAT-TCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAT-TGACTATCGCAACGCGAT
2532574 TTACATAGCG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 1 0.02
61 47 0.98
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATATTGACTATCGCAACGCGATAATAC
Found at i:2533141 original size:19 final size:19
Alignment explanation
Indices: 2533119--2533160 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2533109 AAATAACTAT
*
2533119 CGCAACGAGAAATAAAAAA
1 CGCAACGAGAAACAAAAAA
* *
2533138 CGCAACGCGAAACAAAAAT
1 CGCAACGAGAAACAAAAAA
2533157 CGCA
1 CGCA
2533161 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.24, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGAGAAACAAAAAA
Found at i:2533159 original size:38 final size:38
Alignment explanation
Indices: 2533086--2533160 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 38
2533076 AGAATAGTTT
* * * **
2533086 CGAGAATGAAAATCGCAACGCGGAAATAACTATCGCAA
1 CGAGAATAAAAAACGCAACGCGGAAACAAAAATCGCAA
2533124 CGAGAAATAAAAAACGCAACGC-GAAACAAAAATCGCA
1 CGAG-AATAAAAAACGCAACGCGGAAACAAAAATCGCA
2533161 TTGCGATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 16 0.52
39 15 0.48
ACGTcount: A:0.51, C:0.21, G:0.19, T:0.09
Consensus pattern (38 bp):
CGAGAATAAAAAACGCAACGCGGAAACAAAAATCGCAA
Found at i:2533178 original size:19 final size:19
Alignment explanation
Indices: 2533156--2533222 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
2533146 GAAACAAAAA
2533156 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
2533175 TCGCGTTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
*
2533194 TCGCGGTTGCGATTTTCATT
1 TCGC-ATTGCGATTTTCATT
2533214 TCGCATTGC
1 TCGCATTGC
2533223 AATTGTCTGG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 25 0.58
20 18 0.42
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2533202 original size:20 final size:19
Alignment explanation
Indices: 2533156--2533335 Score: 102
Period size: 20 Copynumber: 10.1 Consensus size: 19
2533146 GAAACAAAAA
*
2533156 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2533175 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
2533194 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* * *
2533214 TCGCATTGCAATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
2533230 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
2533247 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
2533261 TCTCGTTGCGA--TTC-TA
1 TCGCGTTGCGATTTTCATT
**
2533277 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
2533294 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
2533314 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2533334 TC
1 TC
2533336 AACCAAAAGA
Statistics
Matches: 127, Mismatches: 19, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
14 29 0.23
15 1 0.01
16 4 0.03
17 5 0.04
18 1 0.01
19 38 0.30
20 48 0.38
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2533237 original size:39 final size:39
Alignment explanation
Indices: 2533161--2533237 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
2533151 AAAAATCGCA
* * * **
2533161 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCATTGCAATTTCTAGGTCGCGG
2533200 TTGCGATTTTCATTTCGCATTGCAATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCATTGCAATT-TCTAGGTCGCG
2533238 ATAGTCATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 30 0.94
40 2 0.06
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCATTGCAATTTCTAGGTCGCGG
Found at i:2533267 original size:14 final size:14
Alignment explanation
Indices: 2533250--2533286 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2533240 AGTCATTTCG
*
2533250 CGTTGCGATTCTCT
1 CGTTGCGATTCTAT
2533264 CGTTGCGATTCTAT
1 CGTTGCGATTCTAT
2533278 CGTTGCGAT
1 CGTTGCGAT
2533287 AGTCATTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTAT
Found at i:2533272 original size:33 final size:33
Alignment explanation
Indices: 2533199--2533272 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
2533189 TTATTTCGCG
** * *
2533199 GTTGCGATTTTCATTTCGCATTGCAATTGTCTG
1 GTTGCGATAGTCATTTCGCATTGCAATTCTCTC
* * *
2533232 GTCGCGATAGTCATTTCGCGTTGCGATTCTCTC
1 GTTGCGATAGTCATTTCGCATTGCAATTCTCTC
2533265 GTTGCGAT
1 GTTGCGAT
2533273 TCTATCGTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.41
Consensus pattern (33 bp):
GTTGCGATAGTCATTTCGCATTGCAATTCTCTC
Found at i:2535453 original size:21 final size:21
Alignment explanation
Indices: 2535429--2535495 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2535419 TCATTCCTCG
2535429 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2535450 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2535471 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2535492 AGAG
1 AGAG
2535496 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2535453 original size:42 final size:42
Alignment explanation
Indices: 2535377--2535495 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
2535367 GACTCGCCTG
* * * * * * *
2535377 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
2535419 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
2535461 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
2535496 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:2536873 original size:14 final size:14
Alignment explanation
Indices: 2536854--2536889 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2536844 ATTGTTTAAT
2536854 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2536868 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2536882 TGATTTGT
1 TGATTTGT
2536890 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2537070 original size:18 final size:18
Alignment explanation
Indices: 2537044--2537088 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2537034 AACGCGAAAA
*
2537044 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
2537062 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
2537080 TGATGGCTC
1 TGATGGCTC
2537089 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:2538717 original size:22 final size:22
Alignment explanation
Indices: 2538690--2538733 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2538680 GATGGAGATA
*
2538690 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
*
2538712 GACGGATTTCATCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
2538734 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:2538947 original size:20 final size:20
Alignment explanation
Indices: 2538921--2538993 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
2538911 GATTATGTAT
2538921 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
2538941 AATCGCGTTACGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2538961 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
2538981 TATCTCGTTGCGA
1 TATCGCGTTGCGA
2538994 TTTTGTATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:2539030 original size:20 final size:20
Alignment explanation
Indices: 2538921--2539027 Score: 99
Period size: 20 Copynumber: 5.3 Consensus size: 20
2538911 GATTATGTAT
*
2538921 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
2538941 AATCGCGTTACGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
2538961 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
* * *
2538981 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
*
2539002 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
2539022 TATCGC
1 TATCGC
2539028 ATTACGATTT
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.04
20 54 0.76
21 12 0.17
22 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Done.