Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009608.1 Hibiscus syriacus cultivar Beakdansim tig00116994_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: 1053610
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:654071 original size:21 final size:21
Alignment explanation
Indices: 654053--654332 Score: 95
Period size: 21 Copynumber: 13.3 Consensus size: 21
654043 CATATTCGTA
*
654053 TTGCGATAGTCTAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
654074 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
* * *
654095 TTGCGATTTATTCTAAATT--CG
1 TTGCGA--TAGTCGAAGTTCGCG
* * *
654116 TTACGATTTATTTC-AAATT--CG
1 TTGCGA--TA-GTCGAAGTTCGCG
* *
654137 TTGCGATAGTCCAAATTCGCG
1 TTGCGATAGTCGAAGTTCGCG
* *
654158 TTGCGATTTATTCCAAGTT--CG
1 TTGCGA--TAGTCGAAGTTCGCG
*
654179 TTGTGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
* * * *
654200 TTGTGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCGAAGTTCGCG
* * *
654221 TTGCGATTTATTCAAAATT--CG
1 TTGCGA--TAGTCGAAGTTCGCG
654242 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
* *
654263 TTGCGATTTATTCCAAGTT--CG
1 TTGCGA--TAGTCGAAGTTCGCG
* * *
654284 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCGAAGTTCGCG
*
654305 TTGTGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
654326 TTGCGAT
1 TTGCGAT
654333 TTATTCCAAA
Statistics
Matches: 213, Mismatches: 28, Indels: 36
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.01
19 32 0.15
21 142 0.67
22 3 0.01
23 34 0.16
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.39
Consensus pattern (21 bp):
TTGCGATAGTCGAAGTTCGCG
Found at i:654139 original size:42 final size:42
Alignment explanation
Indices: 654093--654361 Score: 232
Period size: 42 Copynumber: 6.4 Consensus size: 42
654083 TCGAAGTTCG
* * * *
654093 CGTTGCGATTTATTCTAAATT-CGTTACGATTTATTTCAAATT
1 CGTTGCGA-TTAGTCCAAATTCCGTTGCGATTTATTCCAAATT
*
654135 CGTTGCGA-TAGTCCAAATTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATTAGTCCAAATTC-CGTTGCGATTTATTCCAAATT
* * * *
654177 CGTTGTGA-TAGTCGAAGTTCGCGTTGTGATTTATTCCAAATT
1 CGTTGCGATTAGTCCAAATTC-CGTTGCGATTTATTCCAAATT
* * * * *
654219 CGTTGCGATTTATTCAAAATT-CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGA-TTAGTCCAAATTCCGTTGCGATTTATTCCAAATT
* *
654259 CGCGTTGCGATTTATTCCAAGTT-CGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TTAGTCCAAATTCCGTTGCGATTTATTCCAAATT
* * *
654303 CGTTGTGA-TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTAGTCCAAATTC-CGTTGCGATTTATTCCAAATT
654345 CGTTGCGA-TAGTCCAAA
1 CGTTGCGATTAGTCCAAA
654362 ATCGCAACGA
Statistics
Matches: 188, Mismatches: 29, Indels: 20
0.79 0.12 0.08
Matches are distributed among these distances:
40 26 0.14
42 146 0.78
44 16 0.09
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.39
Consensus pattern (42 bp):
CGTTGCGATTAGTCCAAATTCCGTTGCGATTTATTCCAAATT
Found at i:654202 original size:63 final size:62
Alignment explanation
Indices: 654053--654353 Score: 342
Period size: 63 Copynumber: 4.8 Consensus size: 62
654043 CATATTCGTA
* * * * *
654053 TTGCGATAGTCTAAGTTCGCGTTGCGA-TAGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAATT--CGTTGCGATTTATTCCAAATTCG
* * * * *
654116 TTACGATTTATTTC-AAATT--CGTTGCGA-TAGTCCAAATTCGCGTTGCGATTTATTCCAAGTT
1 TTGCGA--TA-GTCGAAGTTCGCGTTGCGATTATTCCAAATT--CGTTGCGATTTATTCCAAATT
654177 CG
61 CG
* * *
654179 TTGTGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGATTTATTCAAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATTCGTTGCGATTTATTCCAAATTCG
*
654242 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATTCGTTGCGATTTATTCCAAATTCG
*
654305 TTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGAT
1 TTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATTCGTTGCGAT
654354 AGTCCAAAAT
Statistics
Matches: 209, Mismatches: 21, Indels: 16
0.85 0.09 0.07
Matches are distributed among these distances:
60 2 0.01
61 6 0.03
63 183 0.88
65 16 0.08
66 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (62 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAATTCGTTGCGATTTATTCCAAATTCG
Found at i:654228 original size:105 final size:105
Alignment explanation
Indices: 654072--654366 Score: 384
Period size: 105 Copynumber: 2.8 Consensus size: 105
654062 TCTAAGTTCG
* * *
654072 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCGTTACGATTTATTTCAAATTCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGATTTATTTCAAATTCG
654137 TTGCGATAGTCCAAATTCGCGTTGCGATTTATTCCAAGTT
66 TTGCGATAGTCCAAATTCGCGTTGCGATTTATTCCAAGTT
*
654177 CGTTGTGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGATTTA-TTCAAAATTC
1 CGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGATTTATTTC-AAATTC
* *
654241 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
65 GTTGCGATAGTCCAAATTCGCGTTGCGATTTATTCCAAGTT
* * * * * * *
654282 CGTTGCGATTTATTCCAAATT--CGTTGTGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAA
1 CGTTGCGA--TAGTCGAAGTTCGCGTTGTGATTTATTCCAAATT--CGTTGCGATTTATTTCAAA
*
654343 TTCGTTGCGATAGTCCAAAATCGC
62 TTCGTTGCGATAGTCCAAATTCGC
654367 AACGACGGTA
Statistics
Matches: 167, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
103 8 0.05
104 3 0.02
105 146 0.87
106 2 0.01
107 8 0.05
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (105 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGATTTATTTCAAATTCG
TTGCGATAGTCCAAATTCGCGTTGCGATTTATTCCAAGTT
Found at i:654976 original size:6 final size:6
Alignment explanation
Indices: 654946--655009 Score: 98
Period size: 6 Copynumber: 11.2 Consensus size: 6
654936 TCTCGTCTTG
*
654946 GGTCG- GGTCG- GGTCG- GGTTGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
654991 GGTCGT GGTCGT GGTCGT G
1 GGTCGT GGTCGT GGTCGT G
655010 ATAATGGTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
5 14 0.25
6 42 0.75
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:655017 original size:18 final size:18
Alignment explanation
Indices: 654978--655017 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
654968 GTCGTGGTCG
* **
654978 TGGTCGTGGTCGTGGTCG
1 TGGTCGTGGTCGTGATAA
654996 TGGTCGTGGTCGTGATAA
1 TGGTCGTGGTCGTGATAA
655014 TGGT
1 TGGT
655018 AATGGTAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.07, C:0.12, G:0.45, T:0.35
Consensus pattern (18 bp):
TGGTCGTGGTCGTGATAA
Found at i:655204 original size:61 final size:61
Alignment explanation
Indices: 655109--655246 Score: 242
Period size: 61 Copynumber: 2.3 Consensus size: 61
655099 CGTTGCGATT
*
655109 TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
*
655170 TTGGACTATCGCAGCGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
655231 TTGGA-TAATCGCAACG
1 TTGGACT-ATCGCAACG
655247 CGAACTTGGA
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
60 1 0.01
61 72 0.99
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.22
Consensus pattern (61 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
Found at i:655263 original size:61 final size:62
Alignment explanation
Indices: 655137--655459 Score: 274
Period size: 65 Copynumber: 5.2 Consensus size: 62
655127 TTTGGAATAA
* * * *
655137 ATCGCAATGCGAACTTCGACTATCGCAACGAACTTGGACT--ATCGC-A-GCGAATTTGGAAT
1 ATCGCAA-GCGAACTTCGAATATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
*
655196 AAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG-AT-AATCGCAACGCGAACTTGGACT
1 --ATCGCAA-GCGAACTTCGAATATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
* * ***
655259 ATCGC-A-CGAATTTGGAATAAATCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAAGCGAACTTCGAATATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
* *
655319 ATCGCAA-CGAATTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTGGAC
1 ATCGCAAGCGAACTTCGAAT--ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTGGAC
655383 T
62 T
* * * * * *
655384 ATCGCAA-CGAATTTGGAATAAATCGCAACGTGAATTTCGACT--ATTGCAACGCGAACTTGGAC
1 ATCGCAAGCGAACTTCGAAT--ATCGCAAC--GAACTTGGAATAAATCGCAACGCGAACTTGGAC
655446 T
62 T
*
655447 ATCACAATGCGAA
1 ATCGCAA-GCGAA
655460 TATGTAAATC
Statistics
Matches: 230, Mismatches: 18, Indels: 24
0.85 0.07 0.09
Matches are distributed among these distances:
58 22 0.10
59 2 0.01
60 29 0.13
61 59 0.26
62 1 0.00
63 42 0.18
65 75 0.33
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (62 bp):
ATCGCAAGCGAACTTCGAATATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
Found at i:655458 original size:21 final size:20
Alignment explanation
Indices: 655109--655459 Score: 236
Period size: 21 Copynumber: 16.9 Consensus size: 20
655099 CGTTGCGATT
*
655109 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
*
655128 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
655151 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
*
655170 TTGGACTATCGC-AGCGAAT
1 TTGGACTATCGCAAGCGAAC
*
655189 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
655212 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
655231 TTGGA-TAATCGCAACGCGAAC
1 TTGGACT-ATCGCAA-GCGAAC
*
655252 TTGGACTATCGC-A-CGAAT
1 TTGGACTATCGCAAGCGAAC
* ***
655270 TTGGAATAAATCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
*
655289 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
655312 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
*
655331 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
655354 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
655377 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
* * *
655396 TTGGAATAAATCGCAACGTGAAT
1 TTGGACT--ATCGCAA-GCGAAC
* *
655419 TTCGACTATTGCAACGCGAAC
1 TTGGACTATCGCAA-GCGAAC
*
655440 TTGGACTATCACAATGCGAA
1 TTGGACTATCGCAA-GCGAA
655460 TATGTAAATC
Statistics
Matches: 269, Mismatches: 37, Indels: 50
0.76 0.10 0.14
Matches are distributed among these distances:
18 14 0.05
19 80 0.30
20 1 0.00
21 100 0.37
22 2 0.01
23 72 0.27
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:655460 original size:65 final size:63
Alignment explanation
Indices: 655219--655449 Score: 341
Period size: 65 Copynumber: 3.7 Consensus size: 63
655209 AACTTCGACT
655219 ATCGCAAC-GAACTTGG-ATAATCGCAACGCGAACTTGGACTATCGC-ACGAATTTGGAATAA
1 ATCGCAACGGAACTTGGAATAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
655279 AT--CAAC-GAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGGAACTTGGAAT-AATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
655340 ATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACG-GAACTTGGAAT-AATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
* * * *
655405 ATCGCAACGTGAATTTCGACT-ATTGCAACGCGAACTTGGACTATC
1 ATCGCAACG-GAACTTGGAATAATCGCAACGCGAACTTGGACTATC
655450 ACAATGCGAA
Statistics
Matches: 159, Mismatches: 5, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
58 12 0.08
59 2 0.01
60 29 0.18
61 17 0.11
63 27 0.17
65 72 0.45
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (63 bp):
ATCGCAACGGAACTTGGAATAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
Found at i:657924 original size:3 final size:3
Alignment explanation
Indices: 657916--657994 Score: 133
Period size: 3 Copynumber: 26.0 Consensus size: 3
657906 TGGGCCATAC
657916 ATA ATA ATA ATTA ATA A-A ATA ATA ATA ATA ATA AGTA ATA ATA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
657962 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
657995 GGAAAATAGA
Statistics
Matches: 73, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.03
3 65 0.89
4 6 0.08
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:658863 original size:22 final size:20
Alignment explanation
Indices: 658829--658871 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
658819 TTGTTTTTAG
658829 AAAAATGTCTTAAGAGAGAAA
1 AAAAATGTCTTAAGAGA-AAA
*
658850 AAAAATTGTTTTAAGAGAAAA
1 AAAAA-TGTCTTAAGAGAAAA
658871 A
1 A
658872 GACTCAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.58, C:0.02, G:0.16, T:0.23
Consensus pattern (20 bp):
AAAAATGTCTTAAGAGAAAA
Found at i:659114 original size:37 final size:35
Alignment explanation
Indices: 659026--659114 Score: 108
Period size: 37 Copynumber: 2.5 Consensus size: 35
659016 TCAGAAAAAA
*
659026 TGTCTCAAGCAAAAC-GAATTTTTTTTAGAGAAAT
1 TGTCTCAAGCAAAACAAAATTTTTTTTAGAGAAAT
* * *
659060 AGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAGT
1 TGTCTCAAGCAAAACAAAATTT-TTTTTAGAGAAA-T
*
659097 TGTCTCAAGCAATACAAA
1 TGTCTCAAGCAAAACAAA
659115 GAGAAAGTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
34 12 0.27
35 5 0.11
36 12 0.27
37 16 0.36
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (35 bp):
TGTCTCAAGCAAAACAAAATTTTTTTTAGAGAAAT
Found at i:659124 original size:26 final size:26
Alignment explanation
Indices: 659088--659140 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
659078 ATTTGTTTTT
659088 AGAGAAAGTTGTCTCAAGCAATACAA
1 AGAGAAAGTTGTCTCAAGCAATACAA
659114 AGAGAAAGTTGTCTCAAGCAATACAA
1 AGAGAAAGTTGTCTCAAGCAATACAA
659140 A
1 A
659141 TTTATTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (26 bp):
AGAGAAAGTTGTCTCAAGCAATACAA
Found at i:659528 original size:16 final size:16
Alignment explanation
Indices: 659507--659546 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
659497 GTCATATATC
* *
659507 ATGTATGTATGTGTTG
1 ATGTATGTATATATTG
*
659523 ATGTATGTTTATATTG
1 ATGTATGTATATATTG
659539 ATGTATGT
1 ATGTATGT
659547 TTCTTGATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.53
Consensus pattern (16 bp):
ATGTATGTATATATTG
Found at i:665531 original size:23 final size:23
Alignment explanation
Indices: 665497--665556 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
665487 CATTTTATAT
*
665497 GGCACTTTGGTGCAATTCTACGC
1 GGCACTTAGGTGCAATTCTACGC
* *
665520 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTAGGTGCAATTCTACGC
*
665543 GGTACTTAGGTGCA
1 GGCACTTAGGTGCA
665557 TTTATATGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.30
Consensus pattern (23 bp):
GGCACTTAGGTGCAATTCTACGC
Found at i:668969 original size:24 final size:24
Alignment explanation
Indices: 668942--668988 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
668932 TACTATGCAT
668942 TTCTACGCGACACTTCGGTGCAAA
1 TTCTACGCGACACTTCGGTGCAAA
* * *
668966 TTCTACGTGGCACTTTGGTGCAA
1 TTCTACGCGACACTTCGGTGCAA
668989 TTTATACGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (24 bp):
TTCTACGCGACACTTCGGTGCAAA
Found at i:670232 original size:30 final size:30
Alignment explanation
Indices: 670169--670233 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
670159 TTCCTGGAGG
* * *
670169 GGACCACGCGCTACTGCAGGTGATCCTGTT
1 GGACCACGCCCTACTGCAGCTGATCCTGCT
* **
670199 GGACCACGCCCTGCTGCAGCTGATTTTGCT
1 GGACCACGCCCTACTGCAGCTGATCCTGCT
670229 GGACC
1 GGACC
670234 TCAACCTGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.15, C:0.32, G:0.29, T:0.23
Consensus pattern (30 bp):
GGACCACGCCCTACTGCAGCTGATCCTGCT
Found at i:674110 original size:5 final size:5
Alignment explanation
Indices: 674100--674130 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
674090 TTTTGCAAAG
*
674100 ATAAA ATAAA ATAAA ATAAA ACAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
674131 GTGAAAAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (5 bp):
ATAAA
Found at i:675966 original size:3 final size:3
Alignment explanation
Indices: 675958--676040 Score: 134
Period size: 3 Copynumber: 27.7 Consensus size: 3
675948 TAACATGTAT
675958 TAA TAA TAA TTAA TAA TAA -AA GTAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
676004 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
676041 TGAAAATAGT
Statistics
Matches: 76, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.05
3 67 0.88
4 5 0.07
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:683353 original size:27 final size:27
Alignment explanation
Indices: 683311--683363 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
683301 ACCTGATAAT
*
683311 GTCTCAATAGTAAGGCCCATGCCTAAC
1 GTCTCAATAGTAAGGCCCACGCCTAAC
* *
683338 GTCTTAATAGTGAGGCCCACGCCTAA
1 GTCTCAATAGTAAGGCCCACGCCTAA
683364 ACTACCCAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (27 bp):
GTCTCAATAGTAAGGCCCACGCCTAAC
Found at i:683791 original size:31 final size:27
Alignment explanation
Indices: 683756--683836 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
683746 AAAAAGTTGA
*
683756 GTCGGGTGGAGGGTATATATTTTTCGATCGG
1 GTCGGGTGGAGGATATATATTTTT---T-GG
* * * *
683787 GTCGGGTGAAGGATGTAAAATTTTTGG
1 GTCGGGTGGAGGATATATATTTTTTGG
683814 GTCGGGTGGAGGATATATATTTT
1 GTCGGGTGGAGGATATATATTTT
683837 CGGCCAACCT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
27 21 0.51
28 1 0.02
31 19 0.46
ACGTcount: A:0.21, C:0.06, G:0.37, T:0.36
Consensus pattern (27 bp):
GTCGGGTGGAGGATATATATTTTTTGG
Found at i:686927 original size:17 final size:17
Alignment explanation
Indices: 686905--686947 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
686895 TAATTTGATT
*
686905 AATGAACTAGT-TAAATG
1 AATGAACTAGTGT-AATC
686922 AATGAACTAGTGTAATC
1 AATGAACTAGTGTAATC
686939 AATGAACTA
1 AATGAACTA
686948 ATTTTATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 23 0.96
18 1 0.04
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (17 bp):
AATGAACTAGTGTAATC
Found at i:687683 original size:20 final size:20
Alignment explanation
Indices: 687660--687697 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
687650 AATCATCCTA
*
687660 ATTCTTCCAGTATCAATACT
1 ATTCATCCAGTATCAATACT
*
687680 ATTCATCTAGTATCAATA
1 ATTCATCCAGTATCAATA
687698 ATCAAACCCA
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:0.34, C:0.21, G:0.05, T:0.39
Consensus pattern (20 bp):
ATTCATCCAGTATCAATACT
Found at i:689692 original size:39 final size:39
Alignment explanation
Indices: 689649--689726 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
689639 ATTAGATTAG
*
689649 TTAAATCTTAATTTTGTCCTAGCCCCATAGATAAAATTT
1 TTAAATCTTAATTTTGTCCTAGCCCAATAGATAAAATTT
689688 TTAAATCTTAATTTTGTCCTAGCCCAATAGATAAAATTT
1 TTAAATCTTAATTTTGTCCTAGCCCAATAGATAAAATTT
689727 CCCAGCAAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.41
Consensus pattern (39 bp):
TTAAATCTTAATTTTGTCCTAGCCCAATAGATAAAATTT
Found at i:692188 original size:21 final size:19
Alignment explanation
Indices: 692156--692213 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
692146 GTTAATATCG
692156 GAAATAATCATTTTCGGTAA
1 GAAATAA-CATTTTCGGTAA
*
692176 CGAAATTAACATTTCCGGTAA
1 -GAAA-TAACATTTTCGGTAA
*
692197 -AAATAACATTTTAGGTA
1 GAAATAACATTTTCGGTA
692214 GAGTTCTACC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 12 0.36
19 3 0.09
21 15 0.45
22 3 0.09
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (19 bp):
GAAATAACATTTTCGGTAA
Found at i:692622 original size:31 final size:32
Alignment explanation
Indices: 692553--692613 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
692543 ATATTCAAAG
692553 ATTTTAAAATAAATATCATATATTAATATTAA
1 ATTTTAAAATAAATATCATATATTAATATTAA
*
692585 ATTTTAAAAT-AATGTCATATATTAATATT
1 ATTTTAAAATAAATATCATATATTAATATT
692614 TATCTTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 18 0.64
32 10 0.36
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (32 bp):
ATTTTAAAATAAATATCATATATTAATATTAA
Found at i:693710 original size:41 final size:39
Alignment explanation
Indices: 693665--693775 Score: 114
Period size: 41 Copynumber: 3.0 Consensus size: 39
693655 GAGACAACGT
693665 TCGTGTTCGTTTATTTATTTTTAAAGGTGTTCATGTTCGGG
1 TCGTGTTCGTTTATTTATTTTTAAAGGTGTTCATGTTC--G
* *
693706 TCGTGTTCGTTTA---ATTTTTTAA--T-ATCATGTT--
1 TCGTGTTCGTTTATTTATTTTTAAAGGTGTTCATGTTCG
*
693737 T-GTGTTCGTTTATTTATTTTTAAAGGTGTTCGTGTTCG
1 TCGTGTTCGTTTATTTATTTTTAAAGGTGTTCATGTTCG
693775 T
1 T
693776 TCATTTAACG
Statistics
Matches: 57, Mismatches: 5, Indels: 19
0.70 0.06 0.23
Matches are distributed among these distances:
30 11 0.19
31 1 0.02
33 8 0.14
35 8 0.14
36 7 0.12
38 9 0.16
41 13 0.23
ACGTcount: A:0.15, C:0.09, G:0.21, T:0.55
Consensus pattern (39 bp):
TCGTGTTCGTTTATTTATTTTTAAAGGTGTTCATGTTCG
Found at i:694557 original size:20 final size:20
Alignment explanation
Indices: 694532--694570 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
694522 TCTGGTTTCA
694532 AGTATCGATATTGGATGAAC
1 AGTATCGATATTGGATGAAC
*
694552 AGTATCGATATTGGTTGAA
1 AGTATCGATATTGGATGAA
694571 TTGGGACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (20 bp):
AGTATCGATATTGGATGAAC
Found at i:696468 original size:23 final size:23
Alignment explanation
Indices: 696440--696531 Score: 103
Period size: 23 Copynumber: 4.0 Consensus size: 23
696430 GGATGTTATA
* *
696440 CGTTTAACATTCGTGAATATGTT
1 CGTTTAACGTTCGTGAACATGTT
* *
696463 TGTTTAACGTTTGTGAACATGTT
1 CGTTTAACGTTCGTGAACATGTT
* *
696486 CATTTAACGTTCGTAAACATGTT
1 CGTTTAACGTTCGTGAACATGTT
* * *
696509 CGTTTAGCGTTTGTGAAAATGTT
1 CGTTTAACGTTCGTGAACATGTT
696532 AAAAAATGTT
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (23 bp):
CGTTTAACGTTCGTGAACATGTT
Found at i:696508 original size:46 final size:46
Alignment explanation
Indices: 696442--696531 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 46
696432 ATGTTATACG
* * * *
696442 TTTAACATTCGTGAATATGTTTGTTTAACGTTTGTGAACATGTTCA
1 TTTAACATTCGTAAACATGTTCGTTTAACGTTTGTGAAAATGTTCA
* *
696488 TTTAACGTTCGTAAACATGTTCGTTTAGCGTTTGTGAAAATGTT
1 TTTAACATTCGTAAACATGTTCGTTTAACGTTTGTGAAAATGTT
696532 AAAAAATGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (46 bp):
TTTAACATTCGTAAACATGTTCGTTTAACGTTTGTGAAAATGTTCA
Found at i:696806 original size:16 final size:17
Alignment explanation
Indices: 696770--696810 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
696760 GGGTCAATCC
696770 CAACAAAATCAAGAAAA
1 CAACAAAATCAAGAAAA
* *
696787 CAACAAAATC-ATACAA
1 CAACAAAATCAAGAAAA
696803 CAACAAAA
1 CAACAAAA
696811 AACCCAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.68, C:0.22, G:0.02, T:0.07
Consensus pattern (17 bp):
CAACAAAATCAAGAAAA
Found at i:698614 original size:24 final size:24
Alignment explanation
Indices: 698553--698658 Score: 151
Period size: 24 Copynumber: 4.4 Consensus size: 24
698543 CTTGATACCA
* **
698553 AGTCAACTCGAAACTGAGTTGATCG
1 AGTCAACTC-AGACTGAGTCAATCG
**
698578 AGTC-ACTCAGACTGAGTCGGTCG
1 AGTCAACTCAGACTGAGTCAATCG
698601 AGTCAACTCAGACTGAGTCAATCG
1 AGTCAACTCAGACTGAGTCAATCG
698625 AGTCAACTCAGACTGAGTCAATCG
1 AGTCAACTCAGACTGAGTCAATCG
698649 AGTCAACTCA
1 AGTCAACTCA
698659 ATCGAACTGA
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
23 16 0.21
24 55 0.73
25 4 0.05
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.22
Consensus pattern (24 bp):
AGTCAACTCAGACTGAGTCAATCG
Found at i:698620 original size:15 final size:15
Alignment explanation
Indices: 698600--698645 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
698590 TGAGTCGGTC
698600 GAGTCAACTCAGACT
1 GAGTCAACTCAGACT
698615 GAGTCAA-T----C-
1 GAGTCAACTCAGACT
698624 GAGTCAACTCAGACT
1 GAGTCAACTCAGACT
698639 GAGTCAA
1 GAGTCAA
698646 TCGAGTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
9 7 0.28
10 2 0.08
14 2 0.08
15 14 0.56
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (15 bp):
GAGTCAACTCAGACT
Found at i:700483 original size:24 final size:24
Alignment explanation
Indices: 700451--700505 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
700441 AGCACTAGAT
700451 GAGGTCGTCGACCTAGTCGTTGGC
1 GAGGTCGTCGACCTAGTCGTTGGC
700475 GAGGTCGTCGACCTAGTCGTTGGC
1 GAGGTCGTCGACCTAGTCGTTGGC
700499 GAGGTCG
1 GAGGTCG
700506 AGCGGCTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.13, C:0.24, G:0.40, T:0.24
Consensus pattern (24 bp):
GAGGTCGTCGACCTAGTCGTTGGC
Found at i:707587 original size:60 final size:60
Alignment explanation
Indices: 707508--707636 Score: 170
Period size: 60 Copynumber: 2.1 Consensus size: 60
707498 TGGAAGACCT
* * * *
707508 AAAGTTTAGGGACCAATTTAGAATGTGA-TTCATAGTTTGAGGATGAAATTTAAATGTTCA
1 AAAGTTTAAGGACCAATTTAGAATGAGAGTT-ATAGTTTAAGGATGAAATTGAAATGTTCA
* * *
707568 AAAGTTTAAGGACTAATTTAGAATGAGAGTTATAGTTTAAGGATGAAATTGGAATGTTTA
1 AAAGTTTAAGGACCAATTTAGAATGAGAGTTATAGTTTAAGGATGAAATTGAAATGTTCA
*
707628 AAAGCTTAA
1 AAAGTTTAA
707637 AGCTTAATAA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 58 0.97
61 2 0.03
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.34
Consensus pattern (60 bp):
AAAGTTTAAGGACCAATTTAGAATGAGAGTTATAGTTTAAGGATGAAATTGAAATGTTCA
Found at i:708758 original size:30 final size:30
Alignment explanation
Indices: 708710--708775 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
708700 GATATTAGTT
* * * *
708710 GGGCGGGCGGATGTGGGGCGGGTGGATGCG
1 GGGCGGACAGATGCGGGGCGGGTGGATACG
708740 GGGCGGACAGATGCGGGGCGGGTGGATACG
1 GGGCGGACAGATGCGGGGCGGGTGGATACG
708770 GGGCGG
1 GGGCGG
708776 GTAAGGTCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.11, C:0.15, G:0.64, T:0.11
Consensus pattern (30 bp):
GGGCGGACAGATGCGGGGCGGGTGGATACG
Found at i:708777 original size:15 final size:15
Alignment explanation
Indices: 708710--708777 Score: 82
Period size: 15 Copynumber: 4.5 Consensus size: 15
708700 GATATTAGTT
* *
708710 GGGCGGGCGGATGTG
1 GGGCGGGTGGATGCG
708725 GGGCGGGTGGATGCG
1 GGGCGGGTGGATGCG
***
708740 GGGCGGACAGATGCG
1 GGGCGGGTGGATGCG
*
708755 GGGCGGGTGGATACG
1 GGGCGGGTGGATGCG
708770 GGGCGGGT
1 GGGCGGGT
708778 AAGGTCTCAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.10, C:0.15, G:0.63, T:0.12
Consensus pattern (15 bp):
GGGCGGGTGGATGCG
Found at i:710189 original size:20 final size:20
Alignment explanation
Indices: 710161--710232 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
710151 CTGCACCGTG
*
710161 GTTTCGAAACCAATAGAGGA
1 GTTTAGAAACCAATAGAGGA
*
710181 GTTTAGAAACCAA-ATGGGGA
1 GTTTAGAAACCAATA-GAGGA
*
710201 -TTTAGAAACCATATA-AGGG
1 GTTTAGAAACCA-ATAGAGGA
710220 GTTTCA-AAACCAA
1 GTTT-AGAAACCAA
710233 ACGAGTAAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
19 15 0.35
20 26 0.60
21 2 0.05
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (20 bp):
GTTTAGAAACCAATAGAGGA
Found at i:719622 original size:13 final size:13
Alignment explanation
Indices: 719585--719624 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
719575 TCGATATTGA
719585 AAAATAAATA-TT
1 AAAATAAATATTT
*
719597 AAAATAATTTATTT
1 AAAATAA-ATATTT
719611 AAAATAAATATTT
1 AAAATAAATATTT
719624 A
1 A
719625 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:721021 original size:3 final size:3
Alignment explanation
Indices: 721013--721049 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
721003 ATATATATAT
* *
721013 TAA TAA TAA TAA TAA TTA TAA TTA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
721050 TATTATATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:721063 original size:15 final size:15
Alignment explanation
Indices: 720994--721052 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
720984 TTGGGTTTTG
* *
720994 TAATATTAAATATATA
1 TAATAATAATTATA-A
* *
721010 TATTAATAATAATAA
1 TAATAATAATTATAA
*
721025 TAATTATAATTATAA
1 TAATAATAATTATAA
721040 TAATAATAATTAT
1 TAATAATAATTAT
721053 TATATAAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
15 25 0.71
16 10 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATAATAATTATAA
Found at i:721459 original size:113 final size:113
Alignment explanation
Indices: 721300--721574 Score: 511
Period size: 113 Copynumber: 2.5 Consensus size: 113
721290 GTTGAATAAG
*
721300 CTTCTTATTATGAAC-T-TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
1 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
721363 AAAGCTAATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAATT
66 AAAGCTAATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAATT
721411 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
1 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
721476 AAAGCTAATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAATT
66 AAAGCTAATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAATT
*
721524 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-TTCTTCTTATTATG
1 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
721575 GACTTCTTCT
Statistics
Matches: 160, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
111 14 0.09
112 14 0.09
113 132 0.82
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
AAAGCTAATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAATT
Found at i:721580 original size:39 final size:39
Alignment explanation
Indices: 721521--721597 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
721511 GGTTGAACAA
721521 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
1 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* *
721560 ATTCTTCTTATTATGGACTTCTTCTTCCTTCTTCAGAT
1 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
721598 AAATTCTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.17, C:0.25, G:0.08, T:0.51
Consensus pattern (39 bp):
ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:721608 original size:36 final size:38
Alignment explanation
Indices: 721525--721615 Score: 123
Period size: 39 Copynumber: 2.4 Consensus size: 38
721515 GAACAAATTC
**
721525 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATTC
1 TTCT-ATTATGAACTTCTTCTTCCTTCTTCAGATGATAA
*
721564 TTCTTATTATGGACTTCTTCTTCCTTCTTCAGAT-A-AA
1 TTC-TATTATGAACTTCTTCTTCCTTCTTCAGATGATAA
721601 TTCTATTATGAACTT
1 TTCTATTATGAACTT
721616 TCTCTGGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
36 11 0.23
37 3 0.06
38 1 0.02
39 31 0.66
40 1 0.02
ACGTcount: A:0.21, C:0.22, G:0.08, T:0.49
Consensus pattern (38 bp):
TTCTATTATGAACTTCTTCTTCCTTCTTCAGATGATAA
Found at i:721895 original size:112 final size:112
Alignment explanation
Indices: 721650--721975 Score: 566
Period size: 112 Copynumber: 2.9 Consensus size: 112
721640 AACTAAAGTC
721650 GAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 GAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC-T
**
721715 C-TTCT-GAAAAGCTAATCCATCAAGTGATGGATTTAAGCAAAAGGTT
65 CGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTAAGCAAAAGGTT
721761 GAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 GAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
721826 GAACTGGAAAAGCTAATCCATCAAGTGATGGATTTAAGCAAAAGGTT
66 GAACTGGAAAAGCTAATCCATCAAGTGATGGATTTAAGCAAAAGGTT
721873 GAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACT
* * * *
721938 CGAACTGGAAAAGTTGATCTATCAAATGATGGATTTAA
65 CGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTAA
721976 ATCTTTGCTA
Statistics
Matches: 206, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
110 2 0.01
111 65 0.32
112 73 0.35
113 66 0.32
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (112 bp):
GAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
GAACTGGAAAAGCTAATCCATCAAGTGATGGATTTAAGCAAAAGGTT
Found at i:722950 original size:83 final size:83
Alignment explanation
Indices: 722811--723199 Score: 652
Period size: 83 Copynumber: 4.7 Consensus size: 83
722801 TTGGGGTTCA
722811 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
722876 AAATTCAATGACTGGTTT
66 AAATTCAATGACTGGTTT
722894 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
* * *
722959 CAATTCAATGATTGGCTT
66 AAATTCAATGACTGGTTT
722977 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
*
723042 AAATTCAATAACTGGTTT
66 AAATTCAATGACTGGTTT
* * *
723060 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCCTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
* * *
723125 AATTTCAATGATTGGTTC
66 AAATTCAATGACTGGTTT
* * * *
723143 TGCCAAACCTGATCAGATAACTCAAAGAACACTTCCAGAAGATGCCATGAGTACATT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
723200 GTATTTGTTC
Statistics
Matches: 287, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 287 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (83 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
AAATTCAATGACTGGTTT
Found at i:724352 original size:1 final size:1
Alignment explanation
Indices: 724348--724424 Score: 55
Period size: 1 Copynumber: 77.0 Consensus size: 1
724338 TTGACCCCCC
* * * * * * ** *
724348 TTTTTCTTTTTTCTTTTTTTTTCTTTTTTTTCTTTTTTCTCTTTTCCTTTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
724413 TTCTTCTTTTTT
1 TTTTTTTTTTTT
724425 CTTCAAGCAT
Statistics
Matches: 56, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:724360 original size:7 final size:7
Alignment explanation
Indices: 724348--724427 Score: 82
Period size: 7 Copynumber: 12.1 Consensus size: 7
724338 TTGACCCCCC
724348 TTTTTCT
1 TTTTTCT
724355 TTTTTCT
1 TTTTTCT
724362 TTTTT-T
1 TTTTTCT
*
724368 TTCTT-T
1 TTTTTCT
724374 TTTTTCT
1 TTTTTCT
724381 TTTTTCT
1 TTTTTCT
*
724388 CTTTTC-
1 TTTTTCT
*
724394 -CTTT-T
1 TTTTTCT
724399 TTTTTCT
1 TTTTTCT
724406 TTTTT-T
1 TTTTTCT
724412 TTTCTTCT
1 TTT-TTCT
724420 TTTTTCT
1 TTTTTCT
724427 T
1 T
724428 CAAGCATAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
5 3 0.05
6 17 0.27
7 38 0.61
8 4 0.06
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:724369 original size:10 final size:10
Alignment explanation
Indices: 724354--724427 Score: 85
Period size: 10 Copynumber: 6.9 Consensus size: 10
724344 CCCCTTTTTC
724354 TTTTTTCTTT
1 TTTTTTCTTT
724364 TTTTTTCTTT
1 TTTTTTCTTT
*
724374 TTTTTCTTTTT
1 TTTTT-TCTTT
724385 TCTCTTTTCCTTT
1 T-T-TTTT-CTTT
724398 TTTTTTCTTTT
1 TTTTTTC-TTT
*
724409 TTTTTTCTTC
1 TTTTTTCTTT
724419 TTTTTTCTT
1 TTTTTTCTT
724428 CAAGCATAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
10 27 0.48
11 19 0.34
12 3 0.05
13 7 0.12
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:724403 original size:34 final size:33
Alignment explanation
Indices: 724348--724412 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 33
724338 TTGACCCCCC
*
724348 TTTTTCTTTTTTCTTTTTTTTTCTTTTTTTTCT
1 TTTTTCTTTTTCCTTTTTTTTTCTTTTTTTTCT
724381 TTTTTCTCTTTTCCTTTTTTTTTCTTTTTTTT
1 TTTTTCT-TTTTCCTTTTTTTTTCTTTTTTTT
724413 TTCTTCTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 7 0.23
34 23 0.77
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (33 bp):
TTTTTCTTTTTCCTTTTTTTTTCTTTTTTTTCT
Found at i:724425 original size:39 final size:41
Alignment explanation
Indices: 724347--724426 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 41
724337 CTTGACCCCC
* * *
724347 CTTTTTCTTTTTTCTTTTTTTTTCTTTTTTTTCTTTTTTCT
1 CTTTTCCTTTTTTCTTTCTTTTTCTTTTTCTTCTTTTTTCT
724388 CTTTTCCTTTTTT-TTTCTTTTT-TTTTTCTTCTTTTTTCT
1 CTTTTCCTTTTTTCTTTCTTTTTCTTTTTCTTCTTTTTTCT
724427 TCAAGCATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 16 0.44
40 8 0.22
41 12 0.33
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (41 bp):
CTTTTCCTTTTTTCTTTCTTTTTCTTTTTCTTCTTTTTTCT
Found at i:724428 original size:10 final size:10
Alignment explanation
Indices: 724351--724428 Score: 78
Period size: 9 Copynumber: 8.3 Consensus size: 10
724341 ACCCCCCTTT
724351 TTCTTTTTTC
1 TTCTTTTTTC
724361 -T-TTTTTT-
1 TTCTTTTTTC
724368 TTCTTTTTT-
1 TTCTTTTTTC
724377 TTCTTTTTTC
1 TTCTTTTTTC
*
724387 -TC-TTTTCC
1 TTCTTTTTTC
*
724395 TTTTTTTTTC
1 TTCTTTTTTC
*
724405 TTTTTTTTTTC
1 -TTCTTTTTTC
724416 TTCTTTTTTC
1 TTCTTTTTTC
724426 TTC
1 TTC
724429 AAGCATAATA
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
8 12 0.21
9 19 0.33
10 17 0.29
11 10 0.17
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:731762 original size:15 final size:15
Alignment explanation
Indices: 731739--731770 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
731729 TGAAATGAAT
731739 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
731754 AATGCATGTATGCAA
1 AATGAATGTATGCAA
731769 AA
1 AA
731771 AGGTATTGAT
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:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:735801 original size:13 final size:13
Alignment explanation
Indices: 735764--735803 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
735754 TCGATATTGA
735764 AAAATAAATA-TT
1 AAAATAAATATTT
*
735776 AAAATAATTTATTT
1 AAAATAA-ATATTT
735790 AAAATAAATATTT
1 AAAATAAATATTT
735803 A
1 A
735804 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:735804 original size:17 final size:17
Alignment explanation
Indices: 735777--735821 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
735767 ATAAATATTA
735777 AAATAATTTATTTAAAAT
1 AAAT-ATTTATTTAAAAT
**
735795 AAATATTTATTTATTAT
1 AAATATTTATTTAAAAT
*
735812 ATATATTTAT
1 AAATATTTAT
735822 GACTACATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATATTTATTTAAAAT
Found at i:737239 original size:15 final size:15
Alignment explanation
Indices: 737170--737228 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
737160 TTGGGTTTTG
* *
737170 TAATATTAAATATATA
1 TAATAATAATTATA-A
* *
737186 TATTAATAATAATAA
1 TAATAATAATTATAA
* *
737201 TTATTATAATTATAA
1 TAATAATAATTATAA
737216 TAATAATAATTAT
1 TAATAATAATTAT
737229 TATATAAATA
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
15 23 0.70
16 10 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TAATAATAATTATAA
Found at i:737239 original size:24 final size:25
Alignment explanation
Indices: 737180--737239 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 25
737170 TAATATTAAA
*
737180 TATATATATTAATAATAATAATTAT
1 TATATATAATAATAATAATAATTAT
*
737205 TATA-ATTATAATAATAATAATTAT
1 TATATATAATAATAATAATAATTAT
737229 TATATA-AATAA
1 TATATATAATAA
737240 CATTAAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TATATATAATAATAATAATAATTAT
Found at i:739072 original size:29 final size:28
Alignment explanation
Indices: 739004--739072 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
738994 GTTATTTATT
*
739004 TCTAACTATTAACTTTTATTTTATTGCA
1 TCTAACTATTGACTTTTATTTTATTGCA
* *
739032 TATTAGCTATTGACTTTTATTTTATTGCA
1 T-CTAACTATTGACTTTTATTTTATTGCA
*
739061 CTCTAACCATTG
1 -TCTAACTATTG
739073 TTTATTTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 1 0.03
29 31 0.94
30 1 0.03
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (28 bp):
TCTAACTATTGACTTTTATTTTATTGCA
Found at i:739815 original size:17 final size:17
Alignment explanation
Indices: 739793--739825 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
739783 AGTTTTGGCA
739793 ACTTTTTAATAATTTTC
1 ACTTTTTAATAATTTTC
739810 ACTTTTTAATAATTTT
1 ACTTTTTAATAATTTT
739826 GGCAACTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (17 bp):
ACTTTTTAATAATTTTC
Found at i:743075 original size:43 final size:42
Alignment explanation
Indices: 743020--743325 Score: 292
Period size: 43 Copynumber: 7.1 Consensus size: 42
743010 AACCAAAAAT
*
743020 GCCGCAATAGGTCAGGATCTATAGCGGCGTTTTTGGAACAAAC
1 GCCGCAAAAGGTCA-GATCTATAGCGGCGTTTTTGGAACAAAC
* *
743063 GCCGCAAAAGGTC-GATATTAATAGCGGCG-TTTTAGAACAAAC
1 GCCGCAAAAGGTCAGAT-CT-ATAGCGGCGTTTTTGGAACAAAC
* * * * * *
743105 GCCGTAACAGGTTGATATTTATAGTGGCGTTTTTGGAACAAAC
1 GCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAACAAAC
** * * * * *
743148 GCCTTAAAAGGATGATATCTATAGCGCCATATTTGGAACAAAC
1 GCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAACAAAC
* *
743191 GCCGTAATAGGTCAGATCTATAGCGGCGTTTTTTTGGAACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCG--TTTTTGGAACAAAC
* **
743235 GCCGCAAAAGGTCTGATCTATAGCGGTATTTTTTGGAACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGG-CGTTTTTGGAACAAAC
* * * *
743278 GCTGCAAAAGATCATATCTATAGCGGCGTTTTTGGATACAAAT
1 GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-ACAAAC
743321 GCCGC
1 GCCGC
743326 TAATTTCCTT
Statistics
Matches: 217, Mismatches: 37, Indels: 18
0.80 0.14 0.07
Matches are distributed among these distances:
41 3 0.01
42 51 0.24
43 125 0.58
44 38 0.18
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (42 bp):
GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAAC
Found at i:743272 original size:87 final size:83
Alignment explanation
Indices: 743020--743325 Score: 301
Period size: 85 Copynumber: 3.6 Consensus size: 83
743010 AACCAAAAAT
*
743020 GCCGCAATAGGTCAGGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC-GATATTAA
1 GCCGCAATAGGTCA-GATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCTGAT-CT-A
** *
743084 TAGCGGCGTTTTAGAACAAAC
63 TAGCGGATTTTTGGAACAAAC
* * * * * * ** *
743105 GCCGTAACAGGTTGATATTTATAGTGGCGTTTTTGGAACAAACGCCTTAAAAGG-ATGATATCTA
1 GCCGCAATAGG-TCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCTG--ATCTA
* *
743169 TAGCGCCATATTTGGAACAAAC
63 TAGCG-GATTTTTGGAACAAAC
*
743191 GCCGTAATAGGTCAGATCTATAGCGGCGTTTTTTTGGAACAAACGCCGCAAAAGGTCTGATCTAT
1 GCCGCAATAGGTCAGATCTATAGCGGCG--TTTTTGGAACAAACGCCGCAAAAGGTCTGATCTAT
743256 AGCGGTATTTTTTGGAACAAAC
64 AGCGG-A-TTTTTGGAACAAAC
* * * * *
743278 GCTGCAAAAGATCATATCTATAGCGGCGTTTTTGGATACAAATGCCGC
1 GCCGCAATAGGTCAGATCTATAGCGGCGTTTTTGGA-ACAAACGCCGC
743326 TAATTTCCTT
Statistics
Matches: 179, Mismatches: 31, Indels: 21
0.77 0.13 0.09
Matches are distributed among these distances:
85 71 0.40
86 45 0.25
87 61 0.34
88 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (83 bp):
GCCGCAATAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCTGATCTATAG
CGGATTTTTGGAACAAAC
Found at i:747674 original size:15 final size:16
Alignment explanation
Indices: 747656--747711 Score: 66
Period size: 15 Copynumber: 3.7 Consensus size: 16
747646 TTATGTAATT
747656 AATTAA-AATACCAAA
1 AATTAATAATACCAAA
*
747671 AATTAATAATA--ATAT
1 AATTAATAATACCA-AA
747686 AATTAA-AATACCAAA
1 AATTAATAATACCAAA
747701 AATTAATAATA
1 AATTAATAATA
747712 ATATAATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 5 0.15
15 20 0.59
16 9 0.26
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (16 bp):
AATTAATAATACCAAA
Found at i:747689 original size:30 final size:30
Alignment explanation
Indices: 747651--747725 Score: 143
Period size: 30 Copynumber: 2.5 Consensus size: 30
747641 AATTTTTATG
747651 TAAT-TAATTAAAATACCAAAAATTAATAA
1 TAATATAATTAAAATACCAAAAATTAATAA
747680 TAATATAATTAAAATACCAAAAATTAATAA
1 TAATATAATTAAAATACCAAAAATTAATAA
747710 TAATATAATTAAAATA
1 TAATATAATTAAAATA
747726 ATTAAATTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 4 0.09
30 41 0.91
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATTAAAATACCAAAAATTAATAA
Found at i:748383 original size:31 final size:31
Alignment explanation
Indices: 748340--748410 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
748330 AAATCTAAAC
*
748340 TTTGTGAAGAAACATGTGGACCCGTCAGAAA
1 TTTGTGACGAAACATGTGGACCCGTCAGAAA
*
748371 TTTGTGACGAAACATGTGGACCTGTCAGAAA
1 TTTGTGACGAAACATGTGGACCCGTCAGAAA
748402 TTTGTGACG
1 TTTGTGACG
748411 GAATAGGTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (31 bp):
TTTGTGACGAAACATGTGGACCCGTCAGAAA
Found at i:748428 original size:31 final size:31
Alignment explanation
Indices: 748363--748443 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
748353 ATGTGGACCC
* * * *
748363 GTCAGAAATTTGTGACGAAACATGTGGACCT
1 GTCAGAAATTTGTGACGGAACAGGTGAACAT
*
748394 GTCAGAAATTTGTGACGGAATAGGTGAACAT
1 GTCAGAAATTTGTGACGGAACAGGTGAACAT
*
748425 GTCAGAAATATGTGACGGA
1 GTCAGAAATTTGTGACGGA
748444 TCCACATATT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (31 bp):
GTCAGAAATTTGTGACGGAACAGGTGAACAT
Found at i:748459 original size:31 final size:31
Alignment explanation
Indices: 748424--748484 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
748414 TAGGTGAACA
* *
748424 TGTCAGAAATATGTGACGGATCCACATATTT
1 TGTCACAAATATGTGACGGACCCACATATTT
* * *
748455 TGTCACAAATTTGTGATGGGCCCACATATT
1 TGTCACAAATATGTGACGGACCCACATATT
748485 CCATCACAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (31 bp):
TGTCACAAATATGTGACGGACCCACATATTT
Found at i:748546 original size:21 final size:20
Alignment explanation
Indices: 748510--748550 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
748500 AAAACTTTTT
748510 TTTTTTATAAAAATCATATA
1 TTTTTTATAAAAATCATATA
748530 TTTTTTA-AAAATTATCATATA
1 TTTTTTATAAAA--ATCATATA
748551 AAAAAGAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
21 8 0.42
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTTTATAAAAATCATATA
Found at i:757271 original size:113 final size:113
Alignment explanation
Indices: 757070--757613 Score: 713
Period size: 113 Copynumber: 4.8 Consensus size: 113
757060 TTCCGCTTCT
* * * * *
757070 TCTGAAGGGAATATCAGATC--AGGAAGAAGAGACACCTATTCTGCTTACTTCTGAATGGAATAT
1 TCTGAAGGGAATATCAAATCTTA-GAA-AAGAGAAACCTGTTCCGCTTAC-TCTGAAGGGAATAT
*
757133 CAGATCTGAGGG-AGTTGATCCATTGAATC-GAAGCAAACTTGTTCCACTTAC
63 CAGATCTG-GGGAAGTTGATCCATTGAATCAG-GGCAAACTTGTTCCACTTAC
* * * * ** *
757184 TTTGAAGGTAATATCCAATCTT-GTAAAAGAGAGACCTGTTCTACTTACTCTAAAGGGAATATCA
1 TCTGAAGGGAATATCAAATCTTAG-AAAAGAGAAACCTGTTCCGCTTACTCTGAAGGGAATATCA
* * * *
757248 TATCTGAGGG-AGTTGATCCATTGAATCAGGGTAGACTTTTTCCACTTAC
65 GATCTG-GGGAAGTTGATCCATTGAATCAGGGCAAACTTGTTCCACTTAC
* *
757297 TCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACCTGTTCCGCTTACTCTGAAGGGAATATCAG
1 TCTGAAGGGAATATCAAATCTTAGAAAAGAGAAACCTGTTCCGCTTACTCTGAAGGGAATATCAG
* *
757362 ATCTGGGGAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCACTTAC
66 ATCTGGGGAAGTTGATCCATTGAATCAGGGCAAACTTGTTCCACTTAC
* *
757410 TCTGAAGGGAATATCAAATCTTAGAAAAGGAAAAACTTGTTCCGCTTACTCTGAAGGGAATATCA
1 TCTGAAGGGAATATCAAATCTTAGAAAA-GAGAAACCTGTTCCGCTTACTCTGAAGGGAATATCA
757475 GATCTGGGGAAGTTGATCCATTGAATCAGGGCAAACTTGTTCCACTTAC
65 GATCTGGGGAAGTTGATCCATTGAATCAGGGCAAACTTGTTCCACTTAC
* * * *
757524 TCTGAAGGGAATATCAAATCTTAGAAAAGAAAAACCTGTTCCACTTACTCTGAAGAGAATATCTG
1 TCTGAAGGGAATATCAAATCTTAGAAAAGAGAAACCTGTTCCGCTTACTCTGAAGGGAATATCAG
* *
757589 ATATGGGGAAGTTGATCTATTGAAT
66 ATCTGGGGAAGTTGATCCATTGAAT
757614 TGGGATCGAA
Statistics
Matches: 389, Mismatches: 34, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
112 3 0.01
113 238 0.61
114 146 0.38
115 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (113 bp):
TCTGAAGGGAATATCAAATCTTAGAAAAGAGAAACCTGTTCCGCTTACTCTGAAGGGAATATCAG
ATCTGGGGAAGTTGATCCATTGAATCAGGGCAAACTTGTTCCACTTAC
Found at i:757491 original size:227 final size:226
Alignment explanation
Indices: 757070--757613 Score: 720
Period size: 227 Copynumber: 2.4 Consensus size: 226
757060 TTCCGCTTCT
* * * * * *
757070 TCTGAAGGGAATATCAGATC-AGGAAGAAGAGACACCTATTCTGCTTACTTCTGAATGGAATATC
1 TCTGAAGGGAATATCAAATCTTGGAA-AAGAGAAACCTGTTCCGCTTAC-TCTGAAGGGAATATC
* *
757134 AGATCTGAGGG-AGTTGATCCATTGAATCGAAGCAAACTTGTTCCACTTACTTTGAAGGTAATAT
64 AGATCTG-GGGAAGTTGATCCATTGAATCGAAGCAAACTTGTTCCACTTACTCTGAAGGGAATAT
* * * * *
757198 CCAATCTTGTAAAAGAGAGACCTGTTCTACTTACTCTAAAGGGAATATCATATCTGAGGGAGTTG
128 CAAATCTTGTAAAAGAAAAACCTGTTCCACTTACTCTAAAGGGAATATCAGATCTGAGGGAGTTG
* * *
757263 ATCCATTGAATCAGGGTAGACTTTTTCCACTTAC
193 ATCCATTGAATCAGGGCAAACTTGTTCCACTTAC
*
757297 TCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACCTGTTCCGCTTACTCTGAAGGGAATATCAG
1 TCTGAAGGGAATATCAAATCTTGGAAAAGAGAAACCTGTTCCGCTTACTCTGAAGGGAATATCAG
* * *
757362 ATCTGGGGAAGTTGATCCATTGAATC-AGGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCA
66 ATCTGGGGAAGTTGATCCATTGAATCGA-AGCAAACTTGTTCCACTTACTCTGAAGGGAATATCA
* * *
757426 AATCTTAG-AAAAGGAAAAACTTGTTCCGCTTACTCTGAAGGGAATATCAGATCTG-GGGAAGTT
130 AATCTT-GTAAAA-GAAAAACCTGTTCCACTTACTCTAAAGGGAATATCAGATCTGAGGG-AGTT
757489 GATCCATTGAATCAGGGCAAACTTGTTCCACTTAC
192 GATCCATTGAATCAGGGCAAACTTGTTCCACTTAC
* * * * *
757524 TCTGAAGGGAATATCAAATCTTAGAAAAGAAAAACCTGTTCCACTTACTCTGAAGAGAATATCTG
1 TCTGAAGGGAATATCAAATCTTGGAAAAGAGAAACCTGTTCCGCTTACTCTGAAGGGAATATCAG
* *
757589 ATATGGGGAAGTTGATCTATTGAAT
66 ATCTGGGGAAGTTGATCCATTGAAT
757614 TGGGATCGAA
Statistics
Matches: 281, Mismatches: 30, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
225 4 0.01
226 81 0.29
227 192 0.68
228 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (226 bp):
TCTGAAGGGAATATCAAATCTTGGAAAAGAGAAACCTGTTCCGCTTACTCTGAAGGGAATATCAG
ATCTGGGGAAGTTGATCCATTGAATCGAAGCAAACTTGTTCCACTTACTCTGAAGGGAATATCAA
ATCTTGTAAAAGAAAAACCTGTTCCACTTACTCTAAAGGGAATATCAGATCTGAGGGAGTTGATC
CATTGAATCAGGGCAAACTTGTTCCACTTAC
Found at i:777393 original size:3 final size:3
Alignment explanation
Indices: 777387--777422 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
777377 ATTATATTAT
*
777387 TAA TAA TAA TAA TGA TATA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA
777423 TTATTATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:777411 original size:19 final size:19
Alignment explanation
Indices: 777387--777423 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
777377 ATTATATTAT
*
777387 TAATAATAATAATGATATA
1 TAATAATAATAATAATATA
777406 TAATAATAATAATAATAT
1 TAATAATAATAATAATAT
777424 TATTATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TAATAATAATAATAATATA
Found at i:778191 original size:41 final size:41
Alignment explanation
Indices: 778145--778229 Score: 125
Period size: 41 Copynumber: 2.1 Consensus size: 41
778135 AGATTCTAGT
*
778145 GTGGCTTTGATGGTGTGGTCCCGCATAGAAGATTTAGAAGA
1 GTGGCTTTGATGGTGTGGTCCCGCAGAGAAGATTTAGAAGA
* * * *
778186 GTGGCTTTGTTGGTGTGGTCCTGTAGAGAAGATTTGGAAGA
1 GTGGCTTTGATGGTGTGGTCCCGCAGAGAAGATTTAGAAGA
778227 GTG
1 GTG
778230 AATTTCTGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.21, C:0.09, G:0.38, T:0.32
Consensus pattern (41 bp):
GTGGCTTTGATGGTGTGGTCCCGCAGAGAAGATTTAGAAGA
Found at i:778550 original size:48 final size:48
Alignment explanation
Indices: 778496--778592 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 48
778486 GTTGAACAAA
* * * *
778496 ATTTCTGACGGAATCATTGTCCCATCATAAATTAAATTGCTATTTTTT
1 ATTTCTGACAGAATCATTATCCCATCAAAAATTAAATTGCTATATTTT
* *
778544 ATTTCTGACAGAATGATTATTCCATCAAAAATTAAATTGCTATATTTT
1 ATTTCTGACAGAATCATTATCCCATCAAAAATTAAATTGCTATATTTT
778592 A
1 A
778593 ATTAAAGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.42
Consensus pattern (48 bp):
ATTTCTGACAGAATCATTATCCCATCAAAAATTAAATTGCTATATTTT
Found at i:778565 original size:113 final size:113
Alignment explanation
Indices: 778423--778660 Score: 379
Period size: 113 Copynumber: 2.1 Consensus size: 113
778413 TAAATGTAGT
* * *
778423 TATTTTTTATTTCCGACGGAATCACTATTCCATCACAAATTAAATTGGTATATTTTAATTAAAGT
1 TATTTTTTATTTCCGACAGAATCACTATTCCATCAAAAATTAAATTGCTATATTTTAATTAAAGT
*
778488 TGAACAAAA-TTTCTGACGGAATCATTGTCCCATCATAAATTAAATTGC
66 TGAACAAAATTTTC-GACGGAATCATTGTCCCATCATAAATTAAATTGA
* * *
778536 TATTTTTTATTTCTGACAGAATGATTATTCCATCAAAAATTAAATTGCTATATTTTAATTAAAGT
1 TATTTTTTATTTCCGACAGAATCACTATTCCATCAAAAATTAAATTGCTATATTTTAATTAAAGT
*
778601 TGAACAAAATTTTCGACGGAATCATTGTCCCGTCATAAATTAAATTGA
66 TGAACAAAATTTTCGACGGAATCATTGTCCCATCATAAATTAAATTGA
778649 TATTTTGTTATT
1 TATTTT-TTATT
778661 GAAATGAATA
Statistics
Matches: 115, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
113 106 0.92
114 9 0.08
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (113 bp):
TATTTTTTATTTCCGACAGAATCACTATTCCATCAAAAATTAAATTGCTATATTTTAATTAAAGT
TGAACAAAATTTTCGACGGAATCATTGTCCCATCATAAATTAAATTGA
Found at i:781886 original size:55 final size:55
Alignment explanation
Indices: 781806--781954 Score: 228
Period size: 55 Copynumber: 2.7 Consensus size: 55
781796 TGGAAGAAGA
* * *
781806 GTCTGCTCTACTATT-TTTTAGGGGAGATCAGACTTGAGAAATCTTTGGAAAACGG
1 GTCTGCTCCACTATTCTTTTA-GGGAGATAAGACTCGAGAAATCTTTGGAAAACGG
* *
781861 GTCTGCTCCACTATTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGGAAAATGG
1 GTCTGCTCCACTATTCTTTTAGGGAGATAAGACTCGAGAAATCTTTGGAAAACGG
*
781916 GTCTGCTCCACTATTCTTTTAGAGAGATAAGACTCGAGA
1 GTCTGCTCCACTATTCTTTTAGGGAGATAAGACTCGAGA
781955 TTGATTTTAT
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
55 82 0.95
56 4 0.05
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (55 bp):
GTCTGCTCCACTATTCTTTTAGGGAGATAAGACTCGAGAAATCTTTGGAAAACGG
Found at i:782032 original size:89 final size:88
Alignment explanation
Indices: 781973--783502 Score: 1779
Period size: 89 Copynumber: 17.2 Consensus size: 88
781963 ATTCATTGTT
* * * * *
781973 TCTTCAGGAAGACCAAATCTTAAGTAAGAAGAATCTGCTCCACTACTCTTCCGGGGAGATCATAC
1 TCTTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTCTACTCTTCCGGGGAGATCAGAC
* *
782038 TCAAGATTGATTCGCTTCGCTAC
66 TCGAGATTGATTTGCTTCGCTAC
* * * **
782061 TCTTTCCGGAAGACCAAATTTGAAATAAGAAAAATCTGCTCCTCTACTCTTCTTGGGAGATCAGA
1 TC-TTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTCTACTCTTCCGGGGAGATCAGA
* * * *
782126 CTCCAGATTGATTTTCTTCGCAAA
65 CTCGAGATTGATTTGCTTCGCTAC
* * * ***
782150 TATTTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCCCCTCTACTTTTCAAAGGAGATCAGA
1 T-CTTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTCTACTCTTCCGGGGAGATCAGA
782215 CTCGAGATTGATTTGCTTCGCTAC
65 CTCGAGATTGATTTGCTTCGCTAC
* * * *
782239 TCTTTCGGGAAGACCAAATCTTAAATAAGAAGAATCTGCTCCTCTATTATTCCGGGGATATCAGA
1 TC-TTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTCTACTCTTCCGGGGAGATCAGA
* * * *
782304 CTCAAAATTGATTTGATTCACTAC
65 CTCGAGATTGATTTGCTTCGCTAC
* * * *
782328 TCTTTCGGGAAGACCAAATCTAAAATAAGAATAATCTACTCCTCTACTCTTCCGAGGAGATCAGA
1 TC-TTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTCTACTCTTCCGGGGAGATCAGA
*
782393 CTCGAGATTGATTTGCTTCACTAC
65 CTCGAGATTGATTTGCTTCGCTAC
* * * *
782417 TCTTTTGGGAAGACCAAATCTGAAATAAAAAGAATATGCTCCTCTACTCTTCCAGGGAGATCAGA
1 TC-TTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTCTACTCTTCCGGGGAGATCAGA
782482 CTCGAGATTGATTTGCTTCGCTAC
65 CTCGAGATTGATTTGCTTCGCTAC
* * * * * * *
782506 TCTTTCGGGAATACCAAATATAAAATAAGAAGAATCTACTCCACTACTTTTCCAGGGAGATCAGA
1 TC-TTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTCTACTCTTCCGGGGAGATCAGA
* *
782571 CTCAAGATTGATTTACTTCGCTAC
65 CTCGAGATTGATTTGCTTCGCTAC
* * * *
782595 TCTTACAGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTTTACTCTTCTGGGGAGATCAGT
1 TCTT-CGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTCTACTCTTCCGGGGAGATCAGA
* *
782660 CTCGAGAATGATTTTCTTCGCTAC
65 CTCGAGATTGATTTGCTTCGCTAC
* * * *
782684 TCTTTCGGGAAGACCAAATCTAAAATAAGAAGAATATGTTCCTCTACTCTTCTGGGGAGATCAGA
1 TC-TTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTCTACTCTTCCGGGGAGATCAGA
* *
782749 CTCAAGATTGATTTGCTTTGCTAC
65 CTCGAGATTGATTTGCTTCGCTAC
* * ** * * * **
782773 TTTTTTGGGAAGACTGAATCTGAAATAAGAAGAATCTACTCCACTACTCTTCTGATGAGATCAGA
1 -TCTTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTCTACTCTTCCGGGGAGATCAGA
*
782838 CTCAAGATTGATTTGCTTCGCTAC
65 CTCGAGATTGATTTGCTTCGCTAC
* * * * * *
782862 TCTTTTGAGAAAACCAAATCTGAAATAAGAAGAATATGCTCCTCTACTATTTCGGGGAGATCAGA
1 TC-TTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTCTACTCTTCCGGGGAGATCAGA
* *
782927 CTCGAAATTGATTTGATTCGCTAC
65 CTCGAGATTGATTTGCTTCGCTAC
* * * * * * * * *
782951 TCCTTTGGGAACATCAAATCTAAAATAAGAAGAATATGTTCCTATACTCTTTCGGGGAGATCATA
1 T-CTTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTCTACTCTTCCGGGGAGATCAGA
* * *
783016 TTCAAAATTGATTTGCTTCGCTAC
65 CTCGAGATTGATTTGCTTCGCTAC
* * * * * **
783040 TCTTTTGGGAATACCAAATTTGAAATAAGAATAATCTGCTCCTCTA-TATTTTGGGGAGATCAGA
1 TC-TTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTCTACTCTTCCGGGGAGATCAGA
* *
783104 CTTGAGATTGATTTGCTTCACTAC
65 CTCGAGATTGATTTGCTTCGCTAC
* *
783128 TGCTTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTTTACTCTTCCGGGGAGATCAAA
1 T-CTTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTCTACTCTTCCGGGGAGATCAGA
783193 CTCGAGATTGATTTGCTTCGCTAC
65 CTCGAGATTGATTTGCTTCGCTAC
* * *
783217 TCTTTCGGGAAGACCAAATATGAAATAAGAAGAATCTACTCCTCTACTCTTTCGGGGAGATCAGA
1 TC-TTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTCTACTCTTCCGGGGAGATCAGA
* *
783282 CTCGAGATTAATATGCTTCGCTAC
65 CTCGAGATTGATTTGCTTCGCTAC
* * * * * * *
783306 TCTTTCAGGAAGATCAAATATGAAACAAGAAGAATATGCTCCTCTACTCTTCTGGGGAGATTAGA
1 TC-TTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTCTACTCTTCCGGGGAGATCAGA
*
783371 ATCGAGATTGATTTGCTTCGCTAC
65 CTCGAGATTGATTTGCTTCGCTAC
* * * **
783395 TCTTTTC-GAAAGACCAAATCTGAAGTAAGAAGAATCTG-TACCACTACTCTTCTAGGGAGATCA
1 TC--TTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCT-CCTCTACTCTTCCGGGGAGATCA
*
783458 GACTCGAGATTGATTTGCTTCGCTAT
63 GACTCGAGATTGATTTGCTTCGCTAC
*
783484 TCTTTCGAGAAGACCAAAT
1 TC-TTCGGGAAGACCAAAT
783503 AAAACTTGAT
Statistics
Matches: 1236, Mismatches: 191, Indels: 29
0.85 0.13 0.02
Matches are distributed among these distances:
88 85 0.07
89 1143 0.92
90 8 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (88 bp):
TCTTCGGGAAGACCAAATCTGAAATAAGAAGAATCTGCTCCTCTACTCTTCCGGGGAGATCAGAC
TCGAGATTGATTTGCTTCGCTAC
Found at i:783344 original size:47 final size:47
Alignment explanation
Indices: 783206--783356 Score: 132
Period size: 47 Copynumber: 3.3 Consensus size: 47
783196 GAGATTGATT
* * * *
783206 TGCTTCGCTACTCTTTCGGGAAGACCAAATATGAAATAAGAAGAATC
1 TGCTCCGCTACTCTTTCGGGAAGATCAAATATGAAACAAGAAGAATA
* * * ** * **
783253 TACTCCTCTACTCTTTCGGGGAGATC----A-GACTCGAGATTAATA
1 TGCTCCGCTACTCTTTCGGGAAGATCAAATATGAAACAAGAAGAATA
* *
783295 TGCTTCGCTACTCTTTCAGGAAGATCAAATATGAAACAAGAAGAATA
1 TGCTCCGCTACTCTTTCGGGAAGATCAAATATGAAACAAGAAGAATA
*
783342 TGCTCCTCTACTCTT
1 TGCTCCGCTACTCTT
783357 CTGGGGAGAT
Statistics
Matches: 75, Mismatches: 24, Indels: 10
0.69 0.22 0.09
Matches are distributed among these distances:
42 29 0.39
43 1 0.01
46 1 0.01
47 44 0.59
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (47 bp):
TGCTCCGCTACTCTTTCGGGAAGATCAAATATGAAACAAGAAGAATA
Found at i:783637 original size:62 final size:62
Alignment explanation
Indices: 783551--784352 Score: 424
Period size: 62 Copynumber: 12.5 Consensus size: 62
783541 ATCAGATAAA
*
783551 ATTGACTTCTCTTT-ACGAGGAAGTCAAGGATTGACTCTGCTAGGGAGTCAGAGATAACAAAG
1 ATTGACTTCT-TTTCACGAGAAAGTCAAGGATTGACTCTGCTAGGGAGTCAGAGATAACAAAG
* * ** * *
783613 ATTAACTTCTTTTTATAAGAAAGTCAAGGATTGACTCTGATGGGGAGTCA-AGAATAACAAAG
1 ATTGACTTCTTTTCACGAGAAAGTCAAGGATTGACTCTGCTAGGGAGTCAGAG-ATAACAAAG
* * * * *
783675 ATTGACTT-TTCTTTACGAGGAAGTCAAGGATTGGTTCCTCT-TTACGAGGTAGTC-GGGAATAA
1 ATTGACTTCTT-TTCACGAGAAAGTCAAGGATT-G--ACTCTGCTA-G-GG-AGTCAGAG-ATAA
*
783737 AAAAG
58 CAAAG
* * * * * * * *
783742 ATTGACTTCTCTTCAC-AAAGAAGTCAAGAATTAACTCTACTAGGGAGTCAGGGATAAAAAAT
1 ATTGACTTCTTTTCACGAGA-AAGTCAAGGATTGACTCTGCTAGGGAGTCAGAGATAACAAAG
* * * *
783804 ATTGACTTCTTTTTACGAGGAAGTCAAGGATTGACTCTGATGGGGAGTCATGA-ATAACAAAG
1 ATTGACTTCTTTTCACGAGAAAGTCAAGGATTGACTCTGCTAGGGAGTCA-GAGATAACAAAG
* * *
783866 GTTGACTTCTTTTCACGAGGAAGTCAAGGATTGACTCCTCTTCATGAGGGAGTCA-AGAATAACA
1 ATTGACTTCTTTTCACGAGAAAGTCAAGGATTGA---CTCTGC-T-AGGGAGTCAGAG-ATAACA
783930 AAG
60 AAG
* ** * * * * *
783933 GTTGACTTCACTTCACGATG-AAGTTAA-GAGTTGAATTCTCTTCGCGAGGGAGTCAGGGATTAT
1 ATTGACTTCTTTTCACGA-GAAAGTCAAGGA-TTG-A--CTC-T-GCTAGGGAGTCAGAGATAAC
*
783996 AAAA
59 AAAG
* * * *
784000 ATTGACTTCTCTTCACGAGGAAGTCAA-GAGTTGACTCCT-CTTTGTGGGAGTCAG-GAATAAAA
1 ATTGACTTCTTTTCACGAGAAAGTCAAGGA-TTGACT-CTGC--T-AGGGAGTCAGAG-ATAACA
784062 AAG
60 AAG
* * *
784065 ATTTACTTCTTTTCA-GA-AGAAGCCAAGGATTGACTCCCCTTTG-TGAGGGAGTCAGGGATAAC
1 ATTGACTTCTTTTCACGAGA-AAGTCAAGGATTGACT---C--TGCT-AGGGAGTCAGAGATAAC
784127 AAAG
59 AAAG
* * * *
784131 GTTGACTT-TTCTTTACGAGAAAGTCAAGGATTGACTCTGCTGGGGAGTAAG-GAATAACAAAG
1 ATTGACTTCTT-TTCACGAGAAAGTCAAGGATTGACTCTGCTAGGGAGTCAGAG-ATAACAAAG
* * * * * * *
784193 ATTGAATT-TTCTTAATGAGAAATTCAAGGATCGACTCTTCTTAATAAGGGAGTCAGGGATAACA
1 ATTGACTTCTT-TTCACGAGAAAGTCAAGGATTGACTCTGC----T-AGGGAGTCAGAGATAACA
784257 AA-
60 AAG
* * * * * * *
784259 ATTTAACTTATCTTT-ATGAGAAAGTCAAGGATTGACTCTACTGGGGAGTTATGA-ATAATAAAG
1 A-TTGACTTCT-TTTCACGAGAAAGTCAAGGATTGACTCTGCTAGGGAGTCA-GAGATAACAAAG
* * *
784322 GTTGACTTCTCTTCATGAGAAAGTCAAGGAT
1 ATTGACTTCTTTTCACGAGAAAGTCAAGGAT
784353 AACGAAGGTT
Statistics
Matches: 587, Mismatches: 93, Indels: 120
0.73 0.12 0.15
Matches are distributed among these distances:
61 10 0.02
62 255 0.43
63 11 0.02
64 25 0.04
65 45 0.08
66 40 0.07
67 188 0.32
68 11 0.02
69 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.29
Consensus pattern (62 bp):
ATTGACTTCTTTTCACGAGAAAGTCAAGGATTGACTCTGCTAGGGAGTCAGAGATAACAAAG
Found at i:783744 original size:67 final size:67
Alignment explanation
Indices: 783655--784296 Score: 361
Period size: 67 Copynumber: 9.9 Consensus size: 67
783645 GACTCTGATG
** * * **
783655 GGGAGTCAAGAATAACAAAGATTGACTTTTCTTTACGAGGAAGTCAAGGATTGGTTCCTCTTTAC
1 GGGAGTCGGGAATAAAAAAGATTGACTTTTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTTAC
783720 GA
66 GA
* * * * * *
783722 GGTAGTCGGGAATAAAAAAGATTGACTTCTCTTCACAAAGAAGTCAAGAATT-A--ACTC--TAC
1 GGGAGTCGGGAATAAAAAAGATTGACTTTTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTTAC
*
783782 TA
66 GA
* * *
783784 GGGAGTCAGGG-ATAAAAAATATTGACTTCTT-TTTACGAGGAAGTCAAGGATTGA---CTC-TG
1 GGGAGTC-GGGAATAAAAAAGATTGACTT-TTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTT
*
783843 ATG-
64 ACGA
** * * *
783846 GGGAGTCATGAATAACAAAGGTTGACTTCTT-TTCACGAGGAAGTCAAGGATTGACTCCTCTTCA
1 GGGAGTCGGGAATAAAAAAGATTGACTT-TTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTTA
*
783910 TGA
65 CGA
** * * ** * * * * **
783913 GGGAGTCAAGAATAACAAAGGTTGACTTCACTTCACGATGAAGTTAA-GAGTTGAATTCTCTTCG
1 GGGAGTCGGGAATAAAAAAGATTGACTTTTCTTCACGAGGAAGTCAAGGA-TTGACTCCTCTTTA
783977 CGA
65 CGA
* * *
783980 GGGAGTCAGGGATTATAAAA-ATTGACTTCTCTTCACGAGGAAGTCAA-GAGTTGACTCCTCTTT
1 GGGAGTC-GGGAATAAAAAAGATTGACTTTTCTTCACGAGGAAGTCAAGGA-TTGACTCCTCTTT
*
784043 --GT
64 ACGA
* * * * * *
784045 GGGAGTCAGGAATAAAAAAGATTTACTTCTT-TTCA-GAAGAAGCCAAGGATTGACTCCCCTTTG
1 GGGAGTCGGGAATAAAAAAGATTGACTT-TTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTTA
*
784108 TGA
65 CGA
* * * *
784111 GGGAGTCAGGG-ATAACAAAGGTTGACTTTTCTTTACGAGAAAGTCAAGGATTGACT-CTGC--T
1 GGGAGTC-GGGAATAAAAAAGATTGACTTTTCTTCACGAGGAAGTCAAGGATTGACTCCT-CTTT
784172 --G-
64 ACGA
** * * * * * * * * * *
784173 GGGAGTAAGGAATAACAAAGATTGAATTTTCTTAATGAGAAATTCAAGGATCGACTCTTCTTAAT
1 GGGAGTCGGGAATAAAAAAGATTGACTTTTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTTAC
*
784238 AA
66 GA
* * * * * *
784240 GGGAGTCAGGG-ATAACAAAA-TTTAACTTATCTTTATGAGAAAGTCAAGGATTGACTC
1 GGGAGTC-GGGAATAA-AAAAGATTGACTTTTCTTCACGAGGAAGTCAAGGATTGACTC
784297 TACTGGGGAG
Statistics
Matches: 454, Mismatches: 90, Indels: 62
0.75 0.15 0.10
Matches are distributed among these distances:
61 3 0.01
62 138 0.30
63 8 0.02
64 33 0.07
65 27 0.06
66 33 0.07
67 200 0.44
68 12 0.03
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (67 bp):
GGGAGTCGGGAATAAAAAAGATTGACTTTTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTTAC
GA
Found at i:783886 original size:191 final size:190
Alignment explanation
Indices: 783551--784197 Score: 636
Period size: 191 Copynumber: 3.3 Consensus size: 190
783541 ATCAGATAAA
* * * * * *
783551 ATTGACTTCTCTTTACGAGGAAGTCAAGGATTGACTCTGCTAGGGAGTCAGAGATAACAAAGATT
1 ATTGACTTCTCTTCACGAAGAAGTCAAGAATTAACTCTGCTAGGGAGTCAGGGATAA-AAAAATT
* ** *
783616 AACTTCTTTTTATAAGAAAGTCAAGGATTGACTCTGATGGGGAGTCAAGAATAACAAAGATTGAC
65 GACTTCTTTTTACGAGGAAGTCAAGGATTGACTCTGATGGGGAGTCAAGAATAACAAAGATTGAC
* ** * * **
783681 TT-TTCTTTACGAGGAAGTCAAGGATTGGTTCCTCTTTACGAGGTAGTCGGGAATAAAAAAG
130 TTCTT-TTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAATAAAAAAG
* *
783742 ATTGACTTCTCTTCACAAAGAAGTCAAGAATTAACTCTACTAGGGAGTCAGGGATAAAAAATATT
1 ATTGACTTCTCTTCACGAAGAAGTCAAGAATTAACTCTGCTAGGGAGTCAGGGATAAAAAA-ATT
* *
783807 GACTTCTTTTTACGAGGAAGTCAAGGATTGACTCTGATGGGGAGTCATGAATAACAAAGGTTGAC
65 GACTTCTTTTTACGAGGAAGTCAAGGATTGACTCTGATGGGGAGTCAAGAATAACAAAGATTGAC
* *
783872 TTCTTTTCACGAGGAAGTCAAGGATTGACTCCTCTTCATGAGGGAGTCAAGAATAACAAAG
130 TTCTTTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAATAAAAAAG
* * * * * * *
783933 GTTGACTTCACTTCACGATGAAGTTAAGAGTTGAATTCTCTTCGCGAGGGAGTCAGGGATTATAA
1 ATTGACTTCTCTTCACGAAGAAGTCAAGAATT-AA--CTC-T-GCTAGGGAGTCAGGGA-TAAAA
* * ** * *
783998 AAATTGACTTCTCTTCACGAGGAAGTCAA-GAGTTGACTCCTCTTTGTGGGAGTCAGGAATAAAA
60 AAATTGACTTCTTTTTACGAGGAAGTCAAGGA-TTGACT-CT-GATG-GGGAGTCAAGAATAACA
* * * * *** * *
784062 AAGATTTACTTCTTTTCA-GAAGAAGCCAAGGATTGACTCCCCTTTGTGAGGGAGTCAGGGATAA
121 AAGATTGACTTCTTTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAATAA
*
784126 CAAAG
186 AAAAG
* * * * * * * * *
784131 GTTGACTTTTCTTTACG-AGAAAGTCAAGGATTGACTCTGCTGGGGAGTAAGGAATAACAAAGAT
1 ATTGACTTCTCTTCACGAAG-AAGTCAAGAATTAACTCTGCTAGGGAGTCAGGGATAA-AAAAAT
784195 TGA
64 TGA
784198 ATTTTCTTAA
Statistics
Matches: 381, Mismatches: 61, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
190 3 0.01
191 187 0.49
192 6 0.02
193 20 0.05
194 4 0.01
195 6 0.02
196 45 0.12
197 10 0.03
198 69 0.18
199 31 0.08
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (190 bp):
ATTGACTTCTCTTCACGAAGAAGTCAAGAATTAACTCTGCTAGGGAGTCAGGGATAAAAAAATTG
ACTTCTTTTTACGAGGAAGTCAAGGATTGACTCTGATGGGGAGTCAAGAATAACAAAGATTGACT
TCTTTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAATAAAAAAG
Found at i:783909 original size:29 final size:28
Alignment explanation
Indices: 783863--783922 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
783853 ATGAATAACA
* *
783863 AAGGTTGACTTCTTTTCACGAGGAAGTC
1 AAGGTTGACTCCTCTTCACGAGGAAGTC
* *
783891 AAGGATTGACTCCTCTTCATGAGGGAGTC
1 AAGG-TTGACTCCTCTTCACGAGGAAGTC
783920 AAG
1 AAG
783923 AATAACAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (28 bp):
AAGGTTGACTCCTCTTCACGAGGAAGTC
Found at i:784254 original size:129 final size:129
Alignment explanation
Indices: 783592--784352 Score: 374
Period size: 129 Copynumber: 5.9 Consensus size: 129
783582 TGACTCTGCT
* * * **
783592 AGGGAGTCAGAGATAAC-AAAGATTAACTTCTTTTTATAAGAAAGTCAAGGATTGACTCTGA-TG
1 AGGGAGTCAGGGATAACAAAAG-TTAACTTATCTTTACGAGAAAGTCAAGGATTGACTCT-ACTG
* * * * * * ** * *
783655 GGGAGTCAA-GAATAACAAAGATTGACTTTTCTTTACGAGGAAGTCAAGGATTGGTTCCTCTTTA
64 GGGAGT-AAGGAATAACAAAGATTGAATTCTCTTAATGAGAAAGTCAAGGATCGACTCTTCTTAA
**
783719 CG
128 TA
* * * * * * *
783721 AGGTAGTC-GGGAATAA-AAAAGATTGACTTCTCTTCAC-AAAGAAGTCAAGAATTAACTCTACT
1 AGGGAGTCAGGG-ATAACAAAAG-TTAACTTATCTTTACGAGA-AAGTCAAGGATTGACTCTACT
* * * * * * * * * * * *
783783 AGGGAGTCAGGGATAAAAAATATTGACTTCTTTTTACGAGGAAGTCAAGGATTGA--C-TC-TGA
63 GGGGAGTAAGGAATAACAAAGATTGAATTCTCTTAATGAGAAAGTCAAGGATCGACTCTTCTTAA
783844 T-
128 TA
* * * * * * * *
783845 GGGGAGTCATGAATAACAAAGGTTGACTTCT-TTTCACGAGGAAGTCAAGGATTGACTCCTCTTC
1 AGGGAGTCAGGGATAACAAAAGTTAACTTATCTTT-ACGAGAAAGTCAAGGATTGA---CTCTAC
* * * * * * * *
783909 ATGAGGGAGTCAA-GAATAACAAAGGTTGACTTCACTTCACGATG-AAGTTAA-GAGTTGAAT-T
62 -TG-GGGAGT-AAGGAATAACAAAGATTGAATTCTCTTAATGA-GAAAGTCAAGGA-TCGACTCT
****
783970 CTCTTCGCG
122 -TCTTAATA
* * * * * * *
783979 AGGGAGTCAGGGATTATAAAAATTGACTTCTCTTCACGAGGAAGTCAA-GAGTTGACTCCT-CTT
1 AGGGAGTCAGGGATAACAAAAGTTAACTTATCTTTACGAGAAAGTCAAGGA-TTGACT-CTAC--
* * * * * * * * **
784042 TGTGGGAGTCAGGAATAAAAAAGATTTACTTCTTTTCA-GA-AGAAGCCAAGGATTGACTCCCCT
62 TG-GGGAGTAAGGAATAACAAAGATTGAATTCTCTTAATGAGA-AAGTCAAGGATCGACTCTTCT
** *
784105 TTGTG
125 TAATA
* * * *
784110 AGGGAGTCAGGGATAACAAAGGTTGACTTTTCTTTACGAGAAAGTCAAGGATTGACTCTGCTGGG
1 AGGGAGTCAGGGATAACAAAAGTTAACTTATCTTTACGAGAAAGTCAAGGATTGACTCTACTGGG
* *
784175 GAGTAAGGAATAACAAAGATTGAATTTTCTTAATGAGAAATTCAAGGATCGACTCTTCTTAATA
66 GAGTAAGGAATAACAAAGATTGAATTCTCTTAATGAGAAAGTCAAGGATCGACTCTTCTTAATA
* *
784239 AGGGAGTCAGGGATAACAAAATTTAACTTATCTTTATGAGAAAGTCAAGGATTGACTCTACTGGG
1 AGGGAGTCAGGGATAACAAAAGTTAACTTATCTTTACGAGAAAGTCAAGGATTGACTCTACTGGG
* * * * * *
784304 GAGTTATGAATAATAAAGGTTGACTTCTCTTCATGAGAAAGTCAAGGAT
66 GAGTAAGGAATAACAAAGATTGAATTCTCTTAATGAGAAAGTCAAGGAT
784353 AACGAAGGTT
Statistics
Matches: 494, Mismatches: 102, Indels: 72
0.74 0.15 0.11
Matches are distributed among these distances:
123 2 0.00
124 33 0.07
125 8 0.02
126 2 0.00
127 6 0.01
128 37 0.07
129 249 0.50
130 5 0.01
131 69 0.14
132 37 0.07
133 3 0.01
134 41 0.08
135 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.29
Consensus pattern (129 bp):
AGGGAGTCAGGGATAACAAAAGTTAACTTATCTTTACGAGAAAGTCAAGGATTGACTCTACTGGG
GAGTAAGGAATAACAAAGATTGAATTCTCTTAATGAGAAAGTCAAGGATCGACTCTTCTTAATA
Found at i:785582 original size:44 final size:43
Alignment explanation
Indices: 785534--785619 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 43
785524 CCTAATATTT
** *
785534 ATACTTATGGATGATACGGACCTTCAAAAAAGTGTCCCACATTA
1 ATACTTATAAATGATACGGACCTTC-AAAAAGTGCCCCACATTA
* *
785578 ATACTTCTAAATGATATGGACCTTCAAAAAGTGCCCCACATT
1 ATACTTATAAATGATACGGACCTTCAAAAAGTGCCCCACATT
785620 CATCATTTCT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 16 0.43
44 21 0.57
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (43 bp):
ATACTTATAAATGATACGGACCTTCAAAAAGTGCCCCACATTA
Found at i:789113 original size:14 final size:14
Alignment explanation
Indices: 789094--789120 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
789084 TGAGTACTGG
789094 TCCATGTGATATAA
1 TCCATGTGATATAA
789108 TCCATGTGATATA
1 TCCATGTGATATA
789121 GAATTATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (14 bp):
TCCATGTGATATAA
Found at i:789161 original size:16 final size:15
Alignment explanation
Indices: 789140--789205 Score: 50
Period size: 16 Copynumber: 4.5 Consensus size: 15
789130 GAATATGATA
789140 TATGTGAAAACATGTC
1 TATGTG-AAACATGTC
*
789156 TATGTG--ACAAGT-
1 TATGTGAAACATGTC
* *
789168 TATGTG-AATATGATA
1 TATGTGAAACATG-TC
789183 TATGTGAAAACATGTC
1 TATGTG-AAACATGTC
789199 TATGTGA
1 TATGTGA
789206 CAAGTTATGT
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
12 6 0.15
13 8 0.20
14 1 0.03
15 7 0.17
16 13 0.32
17 5 0.12
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35
Consensus pattern (15 bp):
TATGTGAAACATGTC
Found at i:789173 original size:43 final size:43
Alignment explanation
Indices: 789124--789218 Score: 190
Period size: 43 Copynumber: 2.2 Consensus size: 43
789114 TGATATAGAA
789124 TTATGTGAATATGATATATGTGAAAACATGTCTATGTGACAAG
1 TTATGTGAATATGATATATGTGAAAACATGTCTATGTGACAAG
789167 TTATGTGAATATGATATATGTGAAAACATGTCTATGTGACAAG
1 TTATGTGAATATGATATATGTGAAAACATGTCTATGTGACAAG
789210 TTATGTGAA
1 TTATGTGAA
789219 ACTGAACTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.36
Consensus pattern (43 bp):
TTATGTGAATATGATATATGTGAAAACATGTCTATGTGACAAG
Found at i:789641 original size:21 final size:22
Alignment explanation
Indices: 789617--789726 Score: 134
Period size: 23 Copynumber: 5.0 Consensus size: 22
789607 GGTTCTACGC
789617 GGTCCTTCGGGACA-TCTATGT
1 GGTCCTTCGGGACATTCTATGT
**
789638 GGTCCTTCGGGACAATTCTGCGT
1 GGTCCTTCGGGAC-ATTCTATGT
* * *
789661 GATCTTTCGGGACAATTCTACGT
1 GGTCCTTCGGGAC-ATTCTATGT
789684 GGTCCTTCGGGACA-TCTATGT
1 GGTCCTTCGGGACATTCTATGT
*
789705 GGTCCTTAGGGACATTCTATGT
1 GGTCCTTCGGGACATTCTATGT
789727 TGCACATCGG
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
21 32 0.42
22 9 0.12
23 36 0.47
ACGTcount: A:0.16, C:0.23, G:0.27, T:0.34
Consensus pattern (22 bp):
GGTCCTTCGGGACATTCTATGT
Found at i:789673 original size:23 final size:23
Alignment explanation
Indices: 789609--789723 Score: 105
Period size: 21 Copynumber: 5.2 Consensus size: 23
789599 GAGTCGAGGG
* *
789609 TTCTACGCGGTCCTTCGGGAC-A
1 TTCTACGTGATCCTTCGGGACAA
* *
789631 -TCTATGTGGTCCTTCGGGACAA
1 TTCTACGTGATCCTTCGGGACAA
* *
789653 TTCTGCGTGATCTTTCGGGACAA
1 TTCTACGTGATCCTTCGGGACAA
*
789676 TTCTACGTGGTCCTTCGGGAC-A
1 TTCTACGTGATCCTTCGGGACAA
* * *
789698 -TCTATGTGGTCCTTAGGGAC-A
1 TTCTACGTGATCCTTCGGGACAA
789719 TTCTA
1 TTCTA
789724 TGTTGCACAT
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
21 37 0.47
22 6 0.08
23 36 0.46
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (23 bp):
TTCTACGTGATCCTTCGGGACAA
Found at i:789984 original size:18 final size:18
Alignment explanation
Indices: 789938--789985 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
789928 AAAGGGATTA
* *
789938 ATGATAATAATATTGATG
1 ATGATAATGATGTTGATG
*
789956 ATGATAGTGATGTTGATG
1 ATGATAATGATGTTGATG
789974 ATGATAATGATG
1 ATGATAATGATG
789986 GTATATGTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (18 bp):
ATGATAATGATGTTGATG
Found at i:793253 original size:37 final size:37
Alignment explanation
Indices: 793212--793295 Score: 168
Period size: 37 Copynumber: 2.3 Consensus size: 37
793202 TGCATAAGTT
793212 TATATGTTATATGCAATGTTATACATAAGCTATGCGC
1 TATATGTTATATGCAATGTTATACATAAGCTATGCGC
793249 TATATGTTATATGCAATGTTATACATAAGCTATGCGC
1 TATATGTTATATGCAATGTTATACATAAGCTATGCGC
793286 TATATGTTAT
1 TATATGTTAT
793296 TTTATGTGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.40
Consensus pattern (37 bp):
TATATGTTATATGCAATGTTATACATAAGCTATGCGC
Found at i:793554 original size:21 final size:21
Alignment explanation
Indices: 793528--793590 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
793518 ACGCGGTCGA
793528 TCCTTCGGGACATCTATGTGG
1 TCCTTCGGGACATCTATGTGG
* *
793549 TCCTTCCGGACAATTCTACGTGG
1 TCCTTCGGGAC-A-TCTATGTGG
*
793572 TGCTTCGGGACATCTATGT
1 TCCTTCGGGACATCTATGT
793591 TGTATTTTGG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 16 0.46
22 2 0.06
23 17 0.49
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.33
Consensus pattern (21 bp):
TCCTTCGGGACATCTATGTGG
Found at i:793838 original size:15 final size:15
Alignment explanation
Indices: 793818--793846 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
793808 GATTAAAGGG
793818 ATTAATGATAATAAT
1 ATTAATGATAATAAT
793833 ATTAATGATAATAA
1 ATTAATGATAATAA
793847 ACCGTGTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (15 bp):
ATTAATGATAATAAT
Found at i:799714 original size:29 final size:29
Alignment explanation
Indices: 799667--799749 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
799657 CTCACCTAAC
*
799667 TAAATTGATGTAAGGAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
799697 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
799726 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
799750 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:804334 original size:29 final size:29
Alignment explanation
Indices: 804291--804373 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
804281 CTCACCTAAC
804291 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
804321 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
804350 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
804374 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:805584 original size:11 final size:10
Alignment explanation
Indices: 805570--805628 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 10
805560 TATATGTGAC
805570 TAATATGAAAA
1 TAATAT-AAAA
805581 TAATAATAAAA
1 TAAT-ATAAAA
805592 TAATATAAAA
1 TAATATAAAA
*
805602 GTAATAACAAAA
1 -TAAT-ATAAAA
*
805614 TAATAAATAAA
1 TAATATA-AAA
805625 TAAT
1 TAAT
805629 GATTAAAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 8 0.19
11 27 0.64
12 7 0.17
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (10 bp):
TAATATAAAA
Found at i:805628 original size:22 final size:22
Alignment explanation
Indices: 805570--805628 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
805560 TATATGTGAC
* *
805570 TAATATGAAAATAATAATAAAA
1 TAATATAAAAATAATAACAAAA
*
805592 TAATATAAAAGTAATAACAAAA
1 TAATATAAAAATAATAACAAAA
805614 TAATA-AATAAATAAT
1 TAATATAA-AAATAAT
805629 GATTAAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 2 0.06
22 30 0.94
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (22 bp):
TAATATAAAAATAATAACAAAA
Found at i:806859 original size:3 final size:3
Alignment explanation
Indices: 806845--806903 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
806835 TTTGTATCTG
* *
806845 TAA TAA -AA TAA TAA TAA TTA TAA TAA TAG TAA TAA TAA TAA TAA -ATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
806892 TAA TAA TAA TAA
1 TAA TAA TAA TAA
806904 AAAAAAACCA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 3 0.06
3 45 0.92
4 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:807384 original size:112 final size:112
Alignment explanation
Indices: 807251--807673 Score: 572
Period size: 112 Copynumber: 3.8 Consensus size: 112
807241 TAGAGTTATG
807251 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
*
807316 TATGAACTTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
66 TATGAACTTTCTCTGGAAATGTTGATCCATCGAATGATGAATTCAAA
* ** * * **
807363 CAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTTTCAGACGAGTTCTTCTCAT
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
* *
807428 TATGAACTCTAC-CT-GACAATGTTGAT-CA---AATGATGAATTTAAA
66 TATGAACT-TTCTCTGGA-AATGTTGATCCATCGAATGATGAATTCAAA
*
807471 CAAAAGGTTGAACAAGCTCTTCTCATCATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCA
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGTTCTTCTCA
* * * * *
807536 TTATGAACTTTCTCTGGTAATGCTGATCCATCGAGTGATGAATTCGAG
65 TTATGAACTTTCTCTGGAAATGTTGATCCATCGAATGATGAATTCAAA
* * * *
807584 CAAAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTTTCTTCAGATGAGTTCTTCTCAT
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
* *
807649 TATGAACTCT-TCTGGAAATGCTGAT
66 TATGAACTTTCTCTGGAAATGTTGAT
807674 GACCCAAAGG
Statistics
Matches: 270, Mismatches: 32, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
108 52 0.19
109 39 0.14
110 3 0.01
111 18 0.07
112 107 0.40
113 51 0.19
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (112 bp):
CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
TATGAACTTTCTCTGGAAATGTTGATCCATCGAATGATGAATTCAAA
Found at i:807566 original size:221 final size:220
Alignment explanation
Indices: 807251--807658 Score: 692
Period size: 221 Copynumber: 1.9 Consensus size: 220
807241 TAGAGTTATG
*
807251 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
1 CAAAAGGTTGAACAAGCTCTTCTCATCATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
*
807316 TATGAACTTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATT
*
807381 CTTCTCATTATGAATTTCTTCTTCTTT-TTCAGACGAGTTCTTCTCATTATGAACTCTACCTGAC
131 CTTCTCATTATGAACTTCTTCTT-TTTCTTCAGACGAGTTCTTCTCATTATGAACTCTACCTGAC
807445 AATGTTGATCAAATGATGAATTTAAA
195 AATGTTGATCAAATGATGAATTTAAA
807471 CAAAAGGTTGAACAAGCTCTTCTCATCATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCA
1 CAAAAGGTTGAACAAGCTCTTCTCATCATGAACTTCTTCTT-CTTCTTCAGATAAGTTCTTCTCA
* * * * * * *
807536 TTATGAACTTTCTCTGGTAATGCTGATCCATCGAGTGATGAATTCGAGCAAAATGTTGAACAAGT
65 TTATGAACTTTCTCTGGAAAAGCTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAAT
*
807601 TCTTCTCATTATGAACTTCTTCTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTCT
130 TCTTCTCATTATGAACTTCTTCTTTTTCTTCAGACGAGTTCTTCTCATTATGAACTCT
807659 TCTGGAAATG
Statistics
Matches: 175, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
220 43 0.25
221 132 0.75
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (220 bp):
CAAAAGGTTGAACAAGCTCTTCTCATCATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGCTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATT
CTTCTCATTATGAACTTCTTCTTTTTCTTCAGACGAGTTCTTCTCATTATGAACTCTACCTGACA
ATGTTGATCAAATGATGAATTTAAA
Found at i:807928 original size:75 final size:76
Alignment explanation
Indices: 807671--808052 Score: 705
Period size: 76 Copynumber: 5.1 Consensus size: 76
807661 TGGAAATGCT
* *
807671 GATGACCCAAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
807736 TAGGACTTACA
66 TAGGACTTACA
807747 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
807812 TAGGACTTACA
66 TAGGACTTACA
807823 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATC-TGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
807887 TAGGACTTACA
66 TAGGACTTACA
807898 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
* *
807963 CAGGACTTATA
66 TAGGACTTACA
*
807974 GATGACCCTAAGG-TTTGAAAACATTAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
808038 TAGGACTTACA
66 TAGGACTTACA
808049 GATG
1 GATG
808053 TGTGAAATAG
Statistics
Matches: 298, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
75 138 0.46
76 160 0.54
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (76 bp):
GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
TAGGACTTACA
Found at i:807946 original size:151 final size:151
Alignment explanation
Indices: 807671--808052 Score: 703
Period size: 151 Copynumber: 2.5 Consensus size: 151
807661 TGGAAATGCT
*
807671 GATGACCCAAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCTAAGG-TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
807736 TAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
65 TAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
*
807801 ATCATGCACTGTAGGACTTACA
130 ATCATGCACTGCAGGACTTACA
807823 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATC-TGCACTG
1 GATGACCCTAAGG-TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
807887 TAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
65 TAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
*
807952 ATCATGCACTGCAGGACTTATA
130 ATCATGCACTGCAGGACTTACA
*
807974 GATGACCCTAAGGTTTGAAAACATTAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGT
1 GATGACCCTAAGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGT
808039 AGGACTTACAGATG
66 AGGACTTACAGATG
808053 TGTGAAATAG
Statistics
Matches: 224, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
150 42 0.19
151 127 0.57
152 55 0.25
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (151 bp):
GATGACCCTAAGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGT
AGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACA
TCATGCACTGCAGGACTTACA
Found at i:808761 original size:21 final size:22
Alignment explanation
Indices: 808720--808779 Score: 104
Period size: 21 Copynumber: 2.8 Consensus size: 22
808710 AAATCCGATA
*
808720 AATCTTTCATCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAAGAG
808742 AATCTATCATCTTT-AAAAGAG
1 AATCTATCATCTTTGAAAAGAG
808763 AATCTATCATCTTTGAA
1 AATCTATCATCTTTGAA
808780 GAATGTAGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 21 0.58
22 15 0.42
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (22 bp):
AATCTATCATCTTTGAAAAGAG
Found at i:815416 original size:20 final size:20
Alignment explanation
Indices: 815393--815431 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
815383 CGAACATAAA
*
815393 AATGCAAATATAAAAATGTG
1 AATGCAAACATAAAAATGTG
* *
815413 AATGTAACCATAAAAATGT
1 AATGCAAACATAAAAATGT
815432 AAATTGTGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.26
Consensus pattern (20 bp):
AATGCAAACATAAAAATGTG
Found at i:817041 original size:26 final size:23
Alignment explanation
Indices: 816990--817045 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
816980 TTAATACCTG
* *
816990 AATAAAATAAATAAATAAATATT
1 AATAAAATAAATAAAAAAATAGT
817013 AATAAAATAATATAAAAATAATAAGT
1 AATAAAATAA-ATAAAAA-AAT-AGT
817039 AATAAAA
1 AATAAAA
817046 AATTTGAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 10 0.36
24 6 0.21
25 3 0.11
26 9 0.32
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (23 bp):
AATAAAATAAATAAAAAAATAGT
Found at i:817812 original size:11 final size:10
Alignment explanation
Indices: 817798--817856 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 10
817788 TATATGTGAC
817798 TAATATGAAAA
1 TAATAT-AAAA
817809 TAATAATAAAA
1 TAAT-ATAAAA
817820 TAATATAAAA
1 TAATATAAAA
*
817830 GTAATAACAAAA
1 -TAAT-ATAAAA
*
817842 TAATAAATAAA
1 TAATATA-AAA
817853 TAAT
1 TAAT
817857 GATTAAAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 8 0.19
11 27 0.64
12 7 0.17
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (10 bp):
TAATATAAAA
Found at i:817856 original size:22 final size:22
Alignment explanation
Indices: 817798--817856 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
817788 TATATGTGAC
* *
817798 TAATATGAAAATAATAATAAAA
1 TAATATAAAAATAATAACAAAA
*
817820 TAATATAAAAGTAATAACAAAA
1 TAATATAAAAATAATAACAAAA
817842 TAATA-AATAAATAAT
1 TAATATAA-AAATAAT
817857 GATTAAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 2 0.06
22 30 0.94
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (22 bp):
TAATATAAAAATAATAACAAAA
Found at i:819114 original size:14 final size:15
Alignment explanation
Indices: 819086--819119 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
819076 ACTTAAATAT
*
819086 TTTTTATTTATTTAA
1 TTTTTATATATTTAA
819101 TTTTTATATA-TTAA
1 TTTTTATATATTTAA
819115 TTTTT
1 TTTTT
819120 GGCACATTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTATATATTTAA
Found at i:826566 original size:17 final size:17
Alignment explanation
Indices: 826544--826590 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 17
826534 AAAAGTTGAC
*
826544 CGTTGACCATTGACCGT
1 CGTTGACCATTGACCAT
826561 CGTTGACCACTATTGACCAT
1 CGTTGA-C-C-ATTGACCAT
826581 CGTTGACCAT
1 CGTTGACCAT
826591 AACTTTGACC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 8 0.31
18 2 0.08
19 2 0.08
20 14 0.54
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.30
Consensus pattern (17 bp):
CGTTGACCATTGACCAT
Found at i:826577 original size:20 final size:20
Alignment explanation
Indices: 826552--826589 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
826542 ACCGTTGACC
*
826552 ATTGACCGTCGTTGACCACT
1 ATTGACCATCGTTGACCACT
826572 ATTGACCATCGTTGACCA
1 ATTGACCATCGTTGACCA
826590 TAACTTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (20 bp):
ATTGACCATCGTTGACCACT
Found at i:827592 original size:25 final size:25
Alignment explanation
Indices: 827544--827593 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
827534 AGGTTAACTC
* *
827544 TTTTATGAGATTTATTGCAGTATGA
1 TTTTATGAGATTTACTGCACTATGA
*
827569 TTTTATGAGATTTACTGGACTATGA
1 TTTTATGAGATTTACTGCACTATGA
827594 CTTGTTTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.28, C:0.06, G:0.20, T:0.46
Consensus pattern (25 bp):
TTTTATGAGATTTACTGCACTATGA
Found at i:833329 original size:12 final size:12
Alignment explanation
Indices: 833312--833348 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
833302 TAGAGTTGAT
833312 AAGTTGAATTTG
1 AAGTTGAATTTG
833324 AAGTTGAATTTG
1 AAGTTGAATTTG
*
833336 AAGTTAAATTTG
1 AAGTTGAATTTG
833348 A
1 A
833349 CTTGTCATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.41
Consensus pattern (12 bp):
AAGTTGAATTTG
Found at i:834739 original size:31 final size:31
Alignment explanation
Indices: 834701--834887 Score: 243
Period size: 31 Copynumber: 6.0 Consensus size: 31
834691 AGAGTCGAGG
834701 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
* *
834732 GTTTACCTATGTTC-TCCGAGACATATGGATT
1 GTTTACCTATGTTCTTCAG-GACATATGGACT
** *
834763 GTTTACCTATGTTCTTTGGGATATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
* *
834794 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
834825 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
* * * *
834856 GTTTACATAGGTTATTC-GGAATATATGGACT
1 GTTTACCTATGTTCTTCAGG-ACATATGGACT
834887 G
1 G
834888 GTCATTCAGG
Statistics
Matches: 140, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
30 5 0.04
31 133 0.95
32 2 0.01
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCAGGACATATGGACT
Found at i:834860 original size:93 final size:93
Alignment explanation
Indices: 834701--834887 Score: 277
Period size: 93 Copynumber: 2.0 Consensus size: 93
834691 AGAGTCGAGG
* *
834701 GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTCTCCGAGACATATGGATTGTT
1 GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTCTCAGAGACATATGGACTGTT
* * * * *
834766 TACCTATGTTCTTTGGGATATATGGACT
66 TACATAGGTTATTCGGAATATATGGACT
* *
834794 GTTTACCTATGTTCTTCGGGATATATGGACTGTTTACCTATGTTCTTCAG-GACATATGGACTGT
1 GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTC-TCAGAGACATATGGACTGT
834858 TTACATAGGTTATTCGGAATATATGGACT
65 TTACATAGGTTATTCGGAATATATGGACT
834887 G
1 G
834888 GTCATTCAGG
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
93 81 0.96
94 3 0.04
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.40
Consensus pattern (93 bp):
GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTCTCAGAGACATATGGACTGTT
TACATAGGTTATTCGGAATATATGGACT
Found at i:834874 original size:62 final size:62
Alignment explanation
Indices: 834701--834887 Score: 275
Period size: 62 Copynumber: 3.0 Consensus size: 62
834691 AGAGTCGAGG
* * * *
834701 GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTCTCCGAGACATATGGATT
1 GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTCTTCGGGATATATGGACT
** *
834763 GTTTACCTATGTTCTTTGGGATATATGGACTGTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTCTTCGGGATATATGGACT
* * * *
834825 GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACATAGGTTATTCGGAATATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTCTTCGGGATATATGGACT
834887 G
1 G
834888 GTCATTCAGG
Statistics
Matches: 111, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 111 1.00
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.40
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTCTTCGGGATATATGGACT
Found at i:836940 original size:31 final size:31
Alignment explanation
Indices: 836900--837021 Score: 79
Period size: 31 Copynumber: 3.9 Consensus size: 31
836890 CTAATGTGAC
* *
836900 TCTTAGGTAGGCTCTACGGCCTTGAGATCAT
1 TCTTAGGTAGGCTCTACGGCCCTAAGATCAT
* * * **
836931 TCTTGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCTCTACGGCCCTAAGAT-CAT
* * *
836963 TCTTAGGTAGGC-CTCATGGCCCCGAA-ATCTT
1 TCTTAGGTAGGCTCT-ACGG-CCCTAAGATCAT
* *
836994 TCTTGGGTAGGCTCT-CAGGCCTTAAGAT
1 TCTTAGGTAGGCTCTAC-GGCCCTAAGAT
837022 GTTCCCTTAG
Statistics
Matches: 68, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
30 4 0.06
31 41 0.60
32 18 0.26
33 5 0.07
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30
Consensus pattern (31 bp):
TCTTAGGTAGGCTCTACGGCCCTAAGATCAT
Found at i:836968 original size:63 final size:63
Alignment explanation
Indices: 836900--837023 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
836890 CTAATGTGAC
** *
836900 TCTTAGGTAGG-CTCTACGGCCTTGAGATCATTCTTGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCTC-ACGGCCCCGAAATCATTCTTGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* * * *
836963 TCTTAGGTAGGCCTCATGGCCCCGAAATCTTTCTTGGGTAGGCTCTCAGGCCTTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCATTCTTGGGTAGGCCCTCAGGCCCTAAGATGT
837024 TCCCTTAGGT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.17, C:0.24, G:0.28, T:0.31
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCATTCTTGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:837088 original size:25 final size:25
Alignment explanation
Indices: 837040--837089 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
837030 AGGTTAACTC
*
837040 TTTTATGAGATTTACTACAGTATGA
1 TTTTATGAGATTTACTACACTATGA
**
837065 TTTTATGAGATTTACTGGACTATGA
1 TTTTATGAGATTTACTACACTATGA
837090 CTTGTTTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (25 bp):
TTTTATGAGATTTACTACACTATGA
Found at i:839647 original size:19 final size:19
Alignment explanation
Indices: 839604--839647 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
839594 AAATGACCAA
*
839604 CAAATTCGCAACACGATCT
1 CAAATTCGCAACACGAACT
**
839623 CAAATTCGCAATGCGAACT
1 CAAATTCGCAACACGAACT
*
839642 CCAATT
1 CAAATT
839648 TTGCAACACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.30, G:0.11, T:0.23
Consensus pattern (19 bp):
CAAATTCGCAACACGAACT
Found at i:839733 original size:20 final size:19
Alignment explanation
Indices: 839705--839753 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
839695 GCGAATTTGT
839705 AAATTGCAACACAGAAGTC
1 AAATTGCAACACAGAAGTC
*
839724 AAATTCGCAACACATAAGTC
1 AAATT-GCAACACAGAAGTC
839744 AAATTTGCAA
1 AAA-TTGCAA
839754 AGCGCGTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 20 0.74
21 2 0.07
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.20
Consensus pattern (19 bp):
AAATTGCAACACAGAAGTC
Done.