Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007819.1 Hibiscus syriacus cultivar Beakdansim tig00110156_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: 3855360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2745 characters in sequence are not A, C, G, or T
File 2 of 17
Found at i:206796 original size:42 final size:42
Alignment explanation
Indices: 206608--206786 Score: 295
Period size: 42 Copynumber: 4.3 Consensus size: 42
206598 GGAAACTGAT
* *
206608 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCG
1 TTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCG
* *
206650 TTGCTATAGTCAAAGTTCGCATTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCG
* * *
206692 TTACGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCG
206734 TTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCG
206776 TTGCGATAGTC
1 TTGCGATAGTC
206787 CAAAATCGCA
Statistics
Matches: 125, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 125 1.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCG
Found at i:207711 original size:42 final size:42
Alignment explanation
Indices: 207652--207798 Score: 276
Period size: 42 Copynumber: 3.5 Consensus size: 42
207642 TGCGATTTTG
207652 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
207694 GACTATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
207736 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
207778 GACTATCGCAAAGAACTTGGA
1 GACTATCGCAACGAACTTGGA
207799 CTATCGCAAT
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 102 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:207765 original size:63 final size:60
Alignment explanation
Indices: 207677--207832 Score: 156
Period size: 63 Copynumber: 2.5 Consensus size: 60
207667 CTTGGAATAA
* * * *
207677 ATCGCAACGCGAACTTCGACT--ATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTCGACT
1 ATCGCAA-GCGAACTTGGAATAAATCGCAACGAACTTCGAAT--ATCGCAA--AGAACTTCGACT
* *
207740 ATCGCAA-CGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAAGAACTTGGACT
1 ATCGCAAGCGAACTTGGAATAAATCGCAA--CGAACTTCGAATATCGCAAAGAACTTCGACT
*
207801 ATCGCAATGCGAATTTGGAATAAATCGCAACG
1 ATCGCAA-GCGAACTTGGAATAAATCGCAACG
207833 CGAACTTAGA
Statistics
Matches: 80, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
61 29 0.36
63 41 0.51
65 10 0.12
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (60 bp):
ATCGCAAGCGAACTTGGAATAAATCGCAACGAACTTCGAATATCGCAAAGAACTTCGACT
Found at i:207828 original size:42 final size:41
Alignment explanation
Indices: 207655--207832 Score: 223
Period size: 42 Copynumber: 4.2 Consensus size: 41
207645 GATTTTGGAC
* *
207655 TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGAC
1 TATCGCAACGAACTTGGAAT-AATCGCAATGCGAACTTCGAA
*
207697 TATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTCGAC
1 TATCGCAACGAACTTGGAAT-AATCGCAATGCGAACTTCGAA
* *
207739 TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGAC
1 TATCGCAACGAACTTGGAAT-AATCGCAATGCGAACTTCGAA
* * * *
207781 TATCGCAAAGAACTTGGACT-ATCGCAATGCGAATTTGGAA
1 TATCGCAACGAACTTGGAATAATCGCAATGCGAACTTCGAA
207821 TAAATCGCAACG
1 T--ATCGCAACG
207833 CGAACTTAGA
Statistics
Matches: 125, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
40 17 0.14
42 108 0.86
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.21
Consensus pattern (41 bp):
TATCGCAACGAACTTGGAATAATCGCAATGCGAACTTCGAA
Found at i:207828 original size:84 final size:83
Alignment explanation
Indices: 207655--207832 Score: 277
Period size: 84 Copynumber: 2.1 Consensus size: 83
207645 GATTTTGGAC
*
207655 TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
1 TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAAGAACTTGGAAT-AA
*
207720 TCGCAATGCGAACTTCGAC
65 TCGCAATGCGAACTTCGAA
*
207739 TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAAGAACTTGGACT-AT
1 TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAAGAACTTGGAATAAT
* *
207803 CGCAATGCGAATTTGGAA
66 CGCAATGCGAACTTCGAA
207821 TAAATCGCAACG
1 T--ATCGCAACG
207833 CGAACTTAGA
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
82 18 0.21
84 69 0.79
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.21
Consensus pattern (83 bp):
TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAAGAACTTGGAATAAT
CGCAATGCGAACTTCGAA
Found at i:207833 original size:63 final size:61
Alignment explanation
Indices: 207729--207848 Score: 195
Period size: 63 Copynumber: 1.9 Consensus size: 61
207719 ATCGCAATGC
*
207729 GAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAA
1 GAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTAGACTATCGCAAA
* *
207790 GAACTTGGACTATCGCAATGCGAATTTGGAATAAATCGCAACGCGAACTTAGACTATCG
1 GAACTTCGACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTAGACTATCG
207849 TAACGAATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 17 0.31
63 37 0.69
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (61 bp):
GAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTAGACTATCGCAAA
Found at i:207846 original size:44 final size:40
Alignment explanation
Indices: 207790--207869 Score: 106
Period size: 44 Copynumber: 1.9 Consensus size: 40
207780 CTATCGCAAA
*
207790 GAACTTGGACTATCGCAATGCGAATTTGGAATAAATCGCAACGC
1 GAACTTAGACTATCGCAA--CGAATTT-GAA-AAATCGCAACGC
*
207834 GAACTTAGACTATCGTAACGAATTTGAAAAATCGCA
1 GAACTTAGACTATCGCAACGAATTTGAAAAATCGCA
207870 TTGCGATAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 8 0.24
41 3 0.09
42 7 0.21
44 16 0.47
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.24
Consensus pattern (40 bp):
GAACTTAGACTATCGCAACGAATTTGAAAAATCGCAACGC
Found at i:207868 original size:63 final size:63
Alignment explanation
Indices: 207740--207875 Score: 177
Period size: 63 Copynumber: 2.2 Consensus size: 63
207730 AACTTCGACT
* * **
207740 ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAAGAACTTGGACT
1 ATCGCAATGCGAACTTGGAATAAATCGCAACGCGAACTTAGACTATCGCAAAGAACTTGAAAA
* * * *
207801 ATCGCAATGCGAATTTGGAATAAATCGCAACGCGAACTTAGACTATCGTAACGAATTTGAAAA
1 ATCGCAATGCGAACTTGGAATAAATCGCAACGCGAACTTAGACTATCGCAAAGAACTTGAAAA
*
207864 ATCGCATTGCGA
1 ATCGCAATGCGA
207876 TAGTCGATGT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
61 7 0.11
63 57 0.89
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (63 bp):
ATCGCAATGCGAACTTGGAATAAATCGCAACGCGAACTTAGACTATCGCAAAGAACTTGAAAA
Found at i:209263 original size:3 final size:3
Alignment explanation
Indices: 209255--209302 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
209245 GGGCCTGCAA
209255 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
209303 CCGGACAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:213455 original size:21 final size:21
Alignment explanation
Indices: 213416--213455 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
213406 ATACAGATGT
**
213416 GAAATGCAAAGATGTAAATAC
1 GAAATGCAAAGATACAAATAC
213437 GAAATGCAAAGATACAAAT
1 GAAATGCAAAGATACAAAT
213456 GCAAAATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.10, G:0.17, T:0.17
Consensus pattern (21 bp):
GAAATGCAAAGATACAAATAC
Found at i:213462 original size:21 final size:21
Alignment explanation
Indices: 213417--213463 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
213407 TACAGATGTG
** *
213417 AAATGCAAAGATGTAAATACG
1 AAATGCAAAGATACAAATACA
*
213438 AAATGCAAAGATACAAATGCA
1 AAATGCAAAGATACAAATACA
213459 AAATG
1 AAATG
213464 TGTTGATCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (21 bp):
AAATGCAAAGATACAAATACA
Found at i:217500 original size:3 final size:3
Alignment explanation
Indices: 217492--217542 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
217482 GGATCTGTAT
217492 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
217540 ATA
1 ATA
217543 TCTCGGACAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:218118 original size:23 final size:23
Alignment explanation
Indices: 218067--218120 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
218057 TAATATATAA
* *
218067 TATTAATAAAAATATTATTTATT
1 TATTAATAAAAATATTATTGAAT
*
218090 TCTTAA-AAATAATATTATTGAAT
1 TATTAATAAA-AATATTATTGAAT
218113 TATTAATA
1 TATTAATA
218121 GTGAATACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 3 0.12
23 21 0.84
24 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TATTAATAAAAATATTATTGAAT
Found at i:218390 original size:22 final size:23
Alignment explanation
Indices: 218365--218407 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
218355 TATTCTAATA
218365 TTTTTAAAATAA-TAATATTAAG
1 TTTTTAAAATAAGTAATATTAAG
*
218387 TTTTTATAATAAGTAATATTA
1 TTTTTAAAATAAGTAATATTA
218408 TTTATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
TTTTTAAAATAAGTAATATTAAG
Found at i:218415 original size:22 final size:20
Alignment explanation
Indices: 218363--218416 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
218353 ATTATTCTAA
*
218363 TATTTTTAAAATAATAATAT
1 TATTTTTATAATAATAATAT
218383 TAAGTTTTTATAATAAGTAATAT
1 T-A-TTTTTATAATAA-TAATAT
218406 TATTTATTATA
1 TATTT-TTATA
218417 TTTTATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 1 0.03
21 4 0.14
22 17 0.59
23 7 0.24
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
TATTTTTATAATAATAATAT
Found at i:218529 original size:14 final size:14
Alignment explanation
Indices: 218497--218527 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
218487 CAAACACTAT
218497 AAAATATTTTTCAG
1 AAAATATTTTTCAG
218511 AAAATA-TTTTCAG
1 AAAATATTTTTCAG
218524 AAAA
1 AAAA
218528 ATGTAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (14 bp):
AAAATATTTTTCAG
Found at i:222737 original size:19 final size:19
Alignment explanation
Indices: 222710--222749 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
222700 GTCCTCCTCC
*
222710 CAAGTATTCACGAAATGCA
1 CAAGCATTCACGAAATGCA
222729 CAAGCATTCACGAAATGCA
1 CAAGCATTCACGAAATGCA
222748 CA
1 CA
222750 GGGTTGAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.17
Consensus pattern (19 bp):
CAAGCATTCACGAAATGCA
Found at i:223914 original size:12 final size:12
Alignment explanation
Indices: 223899--223928 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
223889 CTCTCTATCT
223899 CTCCCTCTCCCC
1 CTCCCTCTCCCC
*
223911 CTCCCCCTCCCC
1 CTCCCTCTCCCC
223923 CTCCCT
1 CTCCCT
223929 TATAATGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.77, G:0.00, T:0.23
Consensus pattern (12 bp):
CTCCCTCTCCCC
Found at i:241224 original size:2 final size:2
Alignment explanation
Indices: 241217--241267 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
241207 CGAAGACTAT
241217 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
241259 TA TA TA TA T
1 TA TA TA TA T
241268 TATCTCATTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:243255 original size:13 final size:13
Alignment explanation
Indices: 243237--243262 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
243227 TTACAAACGC
243237 GCATATGAAGACT
1 GCATATGAAGACT
243250 GCATATGAAGACT
1 GCATATGAAGACT
243263 ATTCAACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:243642 original size:18 final size:17
Alignment explanation
Indices: 243606--243639 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
243596 TAGATAATAA
243606 AAAATACATAAAAATTT
1 AAAATACATAAAAATTT
* *
243623 AAAATATATAATAATTT
1 AAAATACATAAAAATTT
243640 TAATTTTTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATACATAAAAATTT
Found at i:246189 original size:20 final size:20
Alignment explanation
Indices: 246163--246209 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
246153 TATATATATA
*
246163 TTATTTTAATT-AT-TTTAT
1 TTATTTTTATTAATATTTAT
246181 CTTATTTTTATTAATATTTAT
1 -TTATTTTTATTAATATTTAT
246202 TTATTTTT
1 TTATTTTT
246210 TATATTAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
20 10 0.40
21 5 0.20
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATTTTTATTAATATTTAT
Found at i:250968 original size:12 final size:12
Alignment explanation
Indices: 250951--250980 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
250941 CATTCATCCG
250951 AAAAGAAGAAAA
1 AAAAGAAGAAAA
250963 AAAAG-AGAAAA
1 AAAAGAAGAAAA
250974 AAAAGAA
1 AAAAGAA
250981 AAGGAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAGAAGAAAA
Found at i:252763 original size:78 final size:78
Alignment explanation
Indices: 252634--252779 Score: 256
Period size: 78 Copynumber: 1.9 Consensus size: 78
252624 AAATAGAATG
* *
252634 TTGAGATATTTTGAAGGCCTATTTTAGACAGAAATGATCCATGTGGGGCATTTTGAAGGCTCACA
1 TTGAGATATTTTGAAGGCCCATTTCAGACAGAAATGATCCATGTGGGGCATTTTGAAGGCTCACA
252699 TTAGTATGAAGGT
66 TTAGTATGAAGGT
* *
252712 TTGAGATATTTTGAAGTCCCATTTCAGACAGAAATGATCCATGTGGGGCATTTTGAAGGCTCAGA
1 TTGAGATATTTTGAAGGCCCATTTCAGACAGAAATGATCCATGTGGGGCATTTTGAAGGCTCACA
252777 TTA
66 TTA
252780 ACAAGAAGGA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 64 1.00
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (78 bp):
TTGAGATATTTTGAAGGCCCATTTCAGACAGAAATGATCCATGTGGGGCATTTTGAAGGCTCACA
TTAGTATGAAGGT
Found at i:253784 original size:54 final size:54
Alignment explanation
Indices: 253702--253917 Score: 324
Period size: 54 Copynumber: 4.0 Consensus size: 54
253692 GATTGAAAAA
* *
253702 ATCTGGGCATAAACCACAAGAAATGATGAATGTGTTGTTAAATATTTTGCGAAC
1 ATCTGGGCAGAAACCACAAGAAATGATGAATGTGTTGTCAAATATTTTGCGAAC
* * *
253756 ATCTGGGTAGAAACCACAAGAAAAGATGAATGTGTTGTCAAATATTTTGTGAAC
1 ATCTGGGCAGAAACCACAAGAAATGATGAATGTGTTGTCAAATATTTTGCGAAC
* *
253810 ATCTGGGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATATTTTGCGAAC
1 ATCTGGGCAGAAACCACAAGAAATGATGAATGTGTTGTCAAATATTTTGCGAAC
* * * * *
253864 ATTTGGGCAGAAGCCACAAGAAATGATGAATGTATTATCAAATATTTTACGAAC
1 ATCTGGGCAGAAACCACAAGAAATGATGAATGTGTTGTCAAATATTTTGCGAAC
253918 CAGTTATGGT
Statistics
Matches: 148, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 148 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (54 bp):
ATCTGGGCAGAAACCACAAGAAATGATGAATGTGTTGTCAAATATTTTGCGAAC
Found at i:255055 original size:36 final size:36
Alignment explanation
Indices: 255015--255361 Score: 192
Period size: 37 Copynumber: 9.4 Consensus size: 36
255005 ATTTATATCA
*
255015 CTTGAGATTGTTTTTCTTAAAAC-AAATTGTGTCTCG
1 CTTGAGATAGTTTTTCTTAAAACAAAATT-TGTCTCG
* ** ** * *
255051 CTTGAGACAGTTTCACTCGAAACAACAATTTATCTCA
1 CTTGAGATAGTTTTTCTTAAAACAA-AATTTGTCTCG
* *
255088 CTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTTG
1 CTTGAGATAGTTTTTCTTAAAACAAAATTTGTCTCG
* ** * * * *
255124 CTTGAGACAGTTTCACTCAAAACAACAATTTATGTCA
1 CTTGAGATAGTTTTTCTTAAAACAA-AATTTGTCTCG
* * * *
255161 CTTGAGATTGTTTTTCTTAAAACCAGATTCGTCTCG
1 CTTGAGATAGTTTTTCTTAAAACAAAATTTGTCTCG
** ** * *
255197 CTTGAGATAGTTTCACTCGAAACAGAAATTTATCTCA
1 CTTGAGATAGTTTTTCTTAAAACA-AAATTTGTCTCG
** ** * *
255234 CTCAAGATAGTTTTTCCCAAAGCAAAGAATTGTCTCG
1 CTTGAGATAGTTTTTCTTAAAACAAA-ATTTGTCTCG
* * * * * *
255271 CATGAGACAATTGTTTCAATTGAAACAAGAAATTTTATCTCA
1 CTTGAGATAGTT-TTTC--TTAAAAC-A-AAA-TTTGTCTCG
** * *
255313 CTCAAGATAATTTTTCTTAAAACAAGATTTGTCTCG
1 CTTGAGATAGTTTTTCTTAAAACAAAATTTGTCTCG
*
255349 CTTGAGACAGTTT
1 CTTGAGATAGTTT
255362 CACTAGAAAC
Statistics
Matches: 219, Mismatches: 81, Indels: 22
0.68 0.25 0.07
Matches are distributed among these distances:
36 87 0.40
37 92 0.42
38 9 0.04
39 6 0.03
40 3 0.01
41 6 0.03
42 16 0.07
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (36 bp):
CTTGAGATAGTTTTTCTTAAAACAAAATTTGTCTCG
Found at i:255093 original size:37 final size:37
Alignment explanation
Indices: 255004--255246 Score: 165
Period size: 36 Copynumber: 6.6 Consensus size: 37
254994 TTCAAATAGT
* * ** *
255004 AATTTATATCACTTGAGATTGTTTTTCTTAAAAC-A-
1 AATTTATCTCACTTGAGATAGTTTCACTCAAAACAAC
* * * *
255039 AATTGTGTCTCGCTTGAGACAGTTTCACTCGAAACAAC
1 AATT-TATCTCACTTGAGATAGTTTCACTCAAAACAAC
* ** *
255077 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA-
1 AATTTATCTCACTTGAGATAGTTTCACTCAAAACAAC
* ** *
255113 AATTTGTCTTGCTTGAGACAGTTTCACTCAAAACAAC
1 AATTTATCTCACTTGAGATAGTTTCACTCAAAACAAC
* * ** *
255150 AATTTATGTCACTTGAGATTGTTTTTCTTAAAAC--C
1 AATTTATCTCACTTGAGATAGTTTCACTCAAAACAAC
** * *
255185 AGATTCGTCTCGCTTGAGATAGTTTCACTCGAAACAGA-
1 A-ATTTATCTCACTTGAGATAGTTTCACTCAAAACA-AC
**
255223 AATTTATCTCACTCAAGATAGTTT
1 AATTTATCTCACTTGAGATAGTTT
255247 TTCCCAAAGC
Statistics
Matches: 152, Mismatches: 48, Indels: 14
0.71 0.22 0.07
Matches are distributed among these distances:
35 6 0.04
36 73 0.48
37 68 0.45
38 5 0.03
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (37 bp):
AATTTATCTCACTTGAGATAGTTTCACTCAAAACAAC
Found at i:255127 original size:73 final size:73
Alignment explanation
Indices: 255004--255372 Score: 427
Period size: 73 Copynumber: 5.0 Consensus size: 73
254994 TTCAAATAGT
*
255004 AATTTATATCACTTGAGATTGTTTTTCTTAAAAC-AAATTGTGTCTCGCTTGAGACAGTTTCACT
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATT-TGTCTCGCTTGAGACAGTTTCACT
255068 CGAAACAAC
65 CGAAACAAC
*
255077 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTTGCTTGAGACAGTTTCACTC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
*
255142 AAAACAAC
66 GAAACAAC
* * * * *
255150 AATTTATGTCACTTGAGATTGTTTTTCTTAAAACCAGATTCGTCTCGCTTGAGATAGTTTCACTC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
255215 GAAACAGA-
66 GAAACA-AC
** * ** * * *
255223 AATTTATCTCACTCAAGATAGTTTTTCCCAAAGCAAAGAATTGTCTCGCATGAGACAATTGTTTC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-ATTTGTCTCGCTTGAGAC-A--GTTTC
* * *
255288 AATTGAAACAAGA
62 ACTCGAAACAA-C
** ** *
255301 AATTTTATCTCACTCAAGATAATTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTCACT
1 AA-TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACT
*
255366 AGAAACA
65 CGAAACA
255373 GAAATTTCCA
Statistics
Matches: 253, Mismatches: 34, Indels: 16
0.83 0.11 0.05
Matches are distributed among these distances:
73 156 0.62
74 20 0.08
75 14 0.06
76 1 0.00
77 14 0.06
78 18 0.07
79 30 0.12
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (73 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
GAAACAAC
Found at i:255315 original size:79 final size:76
Alignment explanation
Indices: 255206--255379 Score: 210
Period size: 79 Copynumber: 2.3 Consensus size: 76
255196 GCTTGAGATA
* * *
255206 GTTTCACTCGAAACAGAAATTTATCTCACTCAAGATAGTTTTTCCCAAAGCAAAGAATTGTCTCG
1 GTTTCAATCGAAACAGAAATTTATCTCACTCAAGATAATTTTTCCCAAAAC-AAGAATTGTCTCG
255271 CATGAGACAATT
65 CATGAGACAATT
* ** *
255283 GTTTCAATTGAAACAAGAAATTTTATCTCACTCAAGATAATTTTTCTTAAAACAAGATTTGTCTC
1 GTTTCAATCGAAAC-AGAAA-TTTATCTCACTCAAGATAATTTTTCCCAAAACAAGAATTGTCTC
*
255348 GCTTGAGAC-A--
64 GCATGAGACAATT
* *
255358 GTTTCACTAGAAACAGAAATTT
1 GTTTCAATCGAAACAGAAATTT
255380 CCATCACTCG
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
73 3 0.04
74 5 0.06
75 12 0.14
77 13 0.15
78 24 0.28
79 28 0.33
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (76 bp):
GTTTCAATCGAAACAGAAATTTATCTCACTCAAGATAATTTTTCCCAAAACAAGAATTGTCTCGC
ATGAGACAATT
Found at i:255958 original size:2 final size:2
Alignment explanation
Indices: 255953--255981 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
255943 TTTTTTAGAT
255953 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
255982 TATTTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:256038 original size:10 final size:9
Alignment explanation
Indices: 256018--256118 Score: 52
Period size: 9 Copynumber: 11.1 Consensus size: 9
256008 TTTATATATA
*
256018 TATATTATT
1 TATATTTTT
256027 TACTATTTTT
1 TA-TATTTTT
256037 TAT-TTTTT
1 TATATTTTT
256045 TAT-TTATTT
1 TATATT-TTT
* *
256054 TATA-TATA
1 TATATTTTT
256062 TATATTATTT
1 TATATT-TTT
*
256072 T-TACTTTT
1 TATATTTTT
256080 TATTATTTTT
1 TA-TATTTTT
256090 T-TATTTATT
1 TATATTT-TT
*
256099 TGT-TTTATT
1 TATATTT-TT
256108 TATATATTTT
1 TATAT-TTTT
256118 T
1 T
256119 TTCTTCTTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 21
0.72 0.08 0.21
Matches are distributed among these distances:
8 24 0.33
9 25 0.34
10 22 0.30
11 2 0.03
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.73
Consensus pattern (9 bp):
TATATTTTT
Found at i:256052 original size:4 final size:4
Alignment explanation
Indices: 256000--256244 Score: 71
Period size: 4 Copynumber: 60.8 Consensus size: 4
255990 TATTATTAGT
* * * * *
256000 TTTA TTAA TTTA TATA TATA TATTA TTTA -CTA TTT- TTTA TTTT TTTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * *
256047 TTTA TTTTA TATA TATA TATTA -TT- TTTA CTT- TTTA -TTA TTTT TTTA
1 TTTA -TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * * *
256093 TTTA TTTGT TTTA TTTA TATA TTTT TTTC TTCTT TTTC TTTA TTT- TTTA
1 TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA
* * * * * *
256142 TTTT TTATA TTTA TTTT TCTTA -GTA TTT- TATC TTTA CTTTC TTTA TCTTA
1 TTTA TT-TA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA -TTTA TTTA T-TTA
* * * *
256192 TCT- TTTA TTTAA TTTG TTT- TTTC TTCA TTTTAA TTTAA TTTA TTTA
1 TTTA TTTA TTT-A TTTA TTTA TTTA TTTA -TTT-A TTT-A TTTA TTTA
256238 TTTA TTT
1 TTTA TTT
256245 CTTACATTTT
Statistics
Matches: 178, Mismatches: 40, Indels: 46
0.67 0.15 0.17
Matches are distributed among these distances:
3 26 0.15
4 110 0.62
5 41 0.23
6 1 0.01
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:256063 original size:46 final size:44
Alignment explanation
Indices: 255969--256151 Score: 173
Period size: 46 Copynumber: 4.2 Consensus size: 44
255959 TATATATATA
* * *
255969 TATATATATATATTATTT--TTTTATTATTAGTTTTA-TTA-ATT
1 TATATATATATATTATTTACTTTTTTTATT-TTTTTATTTATTTT
256010 TATATATATATATTATTTACTATTTTTTATTTTTTTATTTA-TTT
1 TATATATATATATTATTTACT-TTTTTTATTTTTTTATTTATTTT
256054 TATATATATATATTATTTTTACTTTTTATTATTTTTTTATTTATTTGT
1 TATATATATATATTA--TTTACTTTTT-TTATTTTTTTATTTATTT-T
* * * * * *
256102 TTTATTTATATATTTTTTTCTTCTTTTTCTTTATTT-TTTATTTT
1 TATATATATATATTATTTACTT-TTTTTATTTTTTTATTTATTTT
256146 T-TATAT
1 TATATAT
256152 TTATTTTTCT
Statistics
Matches: 122, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
41 18 0.15
43 10 0.08
44 30 0.25
45 11 0.09
46 35 0.29
47 5 0.04
48 13 0.11
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.72
Consensus pattern (44 bp):
TATATATATATATTATTTACTTTTTTTATTTTTTTATTTATTTT
Found at i:256105 original size:50 final size:45
Alignment explanation
Indices: 255965--256151 Score: 174
Period size: 44 Copynumber: 4.2 Consensus size: 45
255955 TATATATATA
* * *
255965 TATATATATATATATATTATTT--TTTTATTATTAGTTTTA-TTAATT
1 TATATATATATAT-TATT-TTTACTTTTTTTATT-TTTTTATTTATTT
256010 TATATATATATATTA--TTTACTATTTTTTATTTTTTTATTTATTT
1 TATATATATATATTATTTTTACT-TTTTTTATTTTTTTATTTATTT
256054 TATATATATATATTATTTTTACTTTTTATTATTTTTTTATTTATTTGT
1 TATATATATATATTATTTTTACTTTTT-TTATTTTTTTATTTA-TT-T
* * * *
256102 TTTATTTATATATT-TTTTT-CTTCTTTTTCTTTATTT-TTTATTT
1 TATATATATATATTATTTTTACTT-TTTTTATTTTTTTATTTATTT
*
256145 TTTATAT
1 TATATAT
256152 TTATTTTTCT
Statistics
Matches: 124, Mismatches: 8, Indels: 22
0.81 0.05 0.14
Matches are distributed among these distances:
41 3 0.02
43 13 0.10
44 32 0.26
45 21 0.17
46 32 0.26
47 10 0.08
48 13 0.10
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (45 bp):
TATATATATATATTATTTTTACTTTTTTTATTTTTTTATTTATTT
Found at i:256106 original size:13 final size:12
Alignment explanation
Indices: 256035--256157 Score: 78
Period size: 13 Copynumber: 10.2 Consensus size: 12
256025 TTTACTATTT
256035 TTTATTTTTTTA
1 TTTATTTTTTTA
*
256047 TTTATTTTATATA
1 TTTATTTT-TTTA
* * *
256060 TATATATTATT-
1 TTTATTTTTTTA
*
256071 TTTA-CTTTTTA
1 TTTATTTTTTTA
256082 -TTATTTTTTTA
1 TTTATTTTTTTA
256093 TTTATTTGTTTTA
1 TTTATTT-TTTTA
*
256106 TTTATATATTTT-
1 TTTAT-TTTTTTA
* *
256118 TTTCTTCTTTTTC
1 TTTATT-TTTTTA
256131 TTTA-TTTTTTA
1 TTTATTTTTTTA
256142 TTT-TTTATATTTA
1 TTTATTT-T-TTTA
256155 TTT
1 TTT
256158 TTCTTAGTAT
Statistics
Matches: 86, Mismatches: 14, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
10 7 0.08
11 20 0.23
12 25 0.29
13 33 0.38
14 1 0.01
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:256140 original size:20 final size:20
Alignment explanation
Indices: 256030--256159 Score: 90
Period size: 20 Copynumber: 6.3 Consensus size: 20
256020 TATTATTTAC
256030 TATTTTTTATTTTTT-TATT
1 TATTTTTTATTTTTTATATT
* *
256049 TATTTTATATATATATATTATTTT
1 TATTTT-T-TAT-T-TTTTATATT
256073 TACTTTTTATTATTTTTT-TATT
1 TA--TTTT-TTATTTTTTATATT
* * *
256095 TATTTGTT-TTATTTATATA
1 TATTTTTTATTTTTTATATT
* *
256114 T-TTTTTTCTTCTTTT-TCTT
1 TATTTTTTATT-TTTTATATT
256133 TATTTTTTATTTTTTATATT
1 TATTTTTTATTTTTTATATT
256153 TATTTTT
1 TATTTTT
256160 CTTAGTATTT
Statistics
Matches: 86, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
18 10 0.12
19 21 0.24
20 25 0.29
21 3 0.03
22 6 0.07
23 6 0.07
24 6 0.07
25 3 0.03
26 6 0.07
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.77
Consensus pattern (20 bp):
TATTTTTTATTTTTTATATT
Found at i:256149 original size:39 final size:38
Alignment explanation
Indices: 256087--256162 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 38
256077 TTTTATTATT
256087 TTTTTATTTATTTGTTTTATTTATATATT-TTTTTCTTC
1 TTTTTATTTATTTGTTTTATTTATAT-TTATTTTTCTTC
* * *
256125 TTTTTCTTTATTTTTTATTTTTTATATTTATTTTTCTT
1 TTTTTATTTATTTGTT-TTATTTATATTTATTTTTCTT
256163 AGTATTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 16 0.48
39 17 0.52
ACGTcount: A:0.14, C:0.05, G:0.01, T:0.79
Consensus pattern (38 bp):
TTTTTATTTATTTGTTTTATTTATATTTATTTTTCTTC
Found at i:259367 original size:14 final size:12
Alignment explanation
Indices: 259346--259387 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 12
259336 TAATCAGAGC
259346 AAAAAGAGAAAA
1 AAAAAGAGAAAA
259358 AATCAAAGAG-AAA
1 AA--AAAGAGAAAA
259371 AAAAAGAGAAAA
1 AAAAAGAGAAAA
259383 AAAAA
1 AAAAA
259388 CAAAGGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.22
12 10 0.37
13 5 0.19
14 6 0.22
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (12 bp):
AAAAAGAGAAAA
Found at i:259378 original size:11 final size:11
Alignment explanation
Indices: 259346--259386 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
259336 TAATCAGAGC
259346 AAAAAGAGAAAA
1 AAAAAGAG-AAA
259358 AATCAAAGAGAAA
1 AA--AAAGAGAAA
259371 AAAAAGAGAAA
1 AAAAAGAGAAA
259382 AAAAA
1 AAAAA
259387 ACAAAGGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 14 0.52
12 2 0.07
13 5 0.19
14 6 0.22
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (11 bp):
AAAAAGAGAAA
Found at i:259588 original size:69 final size:69
Alignment explanation
Indices: 259470--259607 Score: 224
Period size: 69 Copynumber: 2.0 Consensus size: 69
259460 GATTCAAACT
*
259470 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
259535 TCAA
66 TCAA
* * *
259539 ATGAGATTGATCAAGCACAATCA-TTTCTGAATTACTGAATCACTCCACTCGAAGATCATGGAGC
1 ATGAGATTGATCAAGCACAATCATTTTC-GAATCACTGAACCACTCCACTCGAAGATCATAGAGC
259603 ATCAA
65 ATCAA
259608 GAGAGAGACA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 4 0.06
69 60 0.94
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.25
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
TCAA
Found at i:260635 original size:32 final size:32
Alignment explanation
Indices: 260545--260636 Score: 130
Period size: 32 Copynumber: 2.8 Consensus size: 32
260535 TGAGGGCATC
*
260545 TTTGAAGATTCAACATCAAATGTTGGAGCATTT
1 TTTG-AGATTCAACATCAAATGTTGGGGCATTT
* *
260578 TTTTAGATTTAACATCAAATGTTGGGGCATTT
1 TTTGAGATTCAACATCAAATGTTGGGGCATTT
* *
260610 TTTGAGATTCAACATCGAATATTGGGG
1 TTTGAGATTCAACATCAAATGTTGGGG
260637 AATCTTTGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
32 49 0.94
33 3 0.06
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATGTTGGGGCATTT
Found at i:261356 original size:106 final size:106
Alignment explanation
Indices: 261233--261555 Score: 484
Period size: 106 Copynumber: 3.0 Consensus size: 106
261223 ATATCGTGCC
*
261233 ACTCGAGACAACACAAGTTCAACTCCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
261298 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
261339 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* **
261404 AATTTCGGAGCCAATTTCAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * **
261445 ACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGCCTGGCTATCAACAAATAATTTCTT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * * * *
261510 AGTTCCAGAGCCAATTTTAACTTCACGGCGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
261551 ACTCG
1 ACTCG
261556 GAACAATACA
Statistics
Matches: 196, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 196 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:262036 original size:34 final size:32
Alignment explanation
Indices: 261983--262052 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
261973 CCTTACAAAC
*
261983 TCCCTAGTTTTTCCAGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCAGGCTAAACTAGAACCTT
*
262015 TCCCTAGCTTTTACACAGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CAGGCTAAACTAGAACCTT
262049 TCCC
1 TCCC
262053 CTTTACAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCAGGCTAAACTAGAACCTT
Found at i:262447 original size:20 final size:20
Alignment explanation
Indices: 262380--262460 Score: 101
Period size: 20 Copynumber: 4.0 Consensus size: 20
262370 ACCGTTAGAC
*
262380 AGGGGGAATCGGTACCCCCG
1 AGGGGGAATCGGTACCCCCT
** *
262400 A-GGGGAATCTATTCCCCCT
1 AGGGGGAATCGGTACCCCCT
262419 GAGGGGGGAATCGGTACCCCCT
1 -A-GGGGGAATCGGTACCCCCT
262441 AGGGGGAATCGGTACCCCCT
1 AGGGGGAATCGGTACCCCCT
262461 GAGCAATCTG
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
19 14 0.27
20 21 0.41
21 1 0.02
22 15 0.29
ACGTcount: A:0.20, C:0.30, G:0.35, T:0.16
Consensus pattern (20 bp):
AGGGGGAATCGGTACCCCCT
Found at i:262460 original size:42 final size:41
Alignment explanation
Indices: 262381--262463 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
262371 CCGTTAGACA
* *
262381 GGGGGAATCGGTACCCCCGAGGGGAATCTATTCCCCCTGAG
1 GGGGGAATCGGTACCCCCGAGGGGAATCGATACCCCCTGAG
* *
262422 GGGGGAATCGGTACCCCCTAGGGGGAATCGGTACCCCCTGAG
1 GGGGGAATCGGTACCCCCGA-GGGGAATCGATACCCCCTGAG
262464 CAATCTGATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 19 0.51
42 18 0.49
ACGTcount: A:0.19, C:0.29, G:0.36, T:0.16
Consensus pattern (41 bp):
GGGGGAATCGGTACCCCCGAGGGGAATCGATACCCCCTGAG
Found at i:265870 original size:20 final size:20
Alignment explanation
Indices: 265845--265903 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
265835 TAGACAGGGA
*
265845 GGAATCTGTTCCCCCTGGGG
1 GGAATCTGTACCCCCTGGGG
265865 GGAATCTGTACCCCCTGGGG
1 GGAATCTGTACCCCCTGGGG
265885 GGAATCTGTACCCCCTGGG
1 GGAATCTGTACCCCCTGGG
265904 CAATCTGATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.14, C:0.31, G:0.34, T:0.22
Consensus pattern (20 bp):
GGAATCTGTACCCCCTGGGG
Found at i:266486 original size:36 final size:37
Alignment explanation
Indices: 266439--266525 Score: 95
Period size: 37 Copynumber: 2.4 Consensus size: 37
266429 ATTGAAAACA
* * * * **
266439 TTTCCCATGAAA-TAAATTTTATCTCGCTTGGGGTAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGAAAG
*
266475 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAAAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGAAAG
*
266512 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
266526 TAAACATTGA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 11 0.26
37 31 0.74
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGAAAG
Found at i:266505 original size:87 final size:87
Alignment explanation
Indices: 266241--266506 Score: 388
Period size: 87 Copynumber: 3.1 Consensus size: 87
266231 GACAATTTCT
* * *
266241 CTTGAAACATAAACATTGAAAATATTTTCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTTC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
* *
266306 TTTGAAATGAAATTTTGTCTCC
66 CTTGAAACGAAATTTTGTCTCC
* *
266328 TTTAAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
* *
266393 CTTGAAACGAAATTTTATTTCC
66 CTTGAAACGAAATTTTGTCTCC
* * * * * *
266415 CTTGAAACAGAAACATTGAAAACATTTCCCATGAAATAAATTTTATCTCGCTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
*
266480 CTTGAAACAAAATTTTGTCTCC
66 CTTGAAACGAAATTTTGTCTCC
266502 CTTGA
1 CTTGA
266507 GAAAGTTTCT
Statistics
Matches: 159, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 159 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (87 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
CTTGAAACGAAATTTTGTCTCC
Found at i:266514 original size:37 final size:37
Alignment explanation
Indices: 266473--266627 Score: 107
Period size: 37 Copynumber: 4.4 Consensus size: 37
266463 CGCTTGGGGT
266473 AGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAA
1 AGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAA
* *
266510 AGTTTCTCTTGAAACATAAA---------CATTGA-AA
1 AGTTTCCCTTGAAACA-AAATTTTGTCTCCCTTGAGAA
* * ** * *
266538 ACATTTCCTTTGAAA-TTAATTTTGTCTCTCTTGAGAT
1 A-GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAA
* * *
266575 AGTTTCCCTTGAAACAAAAATTTGTCCCCCTTGAGAT
1 AGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAA
*
266612 AGTTTCTCTTGAAACA
1 AGTTTCCCTTGAAACA
266628 TAAACCTTGA
Statistics
Matches: 87, Mismatches: 18, Indels: 26
0.66 0.14 0.20
Matches are distributed among these distances:
27 2 0.02
28 3 0.03
29 15 0.17
36 15 0.17
37 49 0.56
38 3 0.03
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (37 bp):
AGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAA
Found at i:266531 original size:102 final size:102
Alignment explanation
Indices: 266410--266654 Score: 364
Period size: 102 Copynumber: 2.4 Consensus size: 102
266400 CGAAATTTTA
* * * * *
266410 TTTCCCTTGAAACAGAAACATTGAAAACATTTCCCATGAAATAAATTTTATCTCGCTTGGGGTAG
1 TTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAG
* *
266475 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAAAG
66 TTTCCCTTGAAACAAAAATTTGTCCCCCTTGAGAAAG
* * * *
266512 TTTCTCTTGAAACATAAACATTGAAAACATTTCCTTTGAAATTAATTTTGTCTCTCTTGAGATAG
1 TTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAG
*
266577 TTTCCCTTGAAACAAAAATTTGTCCCCCTTGAGATAG
66 TTTCCCTTGAAACAAAAATTTGTCCCCCTTGAGAAAG
* *
266614 TTTCTCTTGAAACATAAACCTTGAAAACGTTTCCCTTGAAA
1 TTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
266655 CACAAAATAT
Statistics
Matches: 128, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 128 1.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.36
Consensus pattern (102 bp):
TTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAG
TTTCCCTTGAAACAAAAATTTGTCCCCCTTGAGAAAG
Found at i:266742 original size:37 final size:37
Alignment explanation
Indices: 266692--266792 Score: 168
Period size: 36 Copynumber: 2.8 Consensus size: 37
266682 AAAACGAATT
*
266692 TTGAGATAGTTTCCCTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
* *
266729 TTGAGACAGTTTCCCTTTAAAC-AAATTTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
266765 TTGAGACAGTTTCCCTTGAAACAAAATC
1 TTGAGACAGTTTCCCTTGAAACAAAATC
266793 ATTAAATATC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 34 0.59
37 24 0.41
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.37
Consensus pattern (37 bp):
TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
Found at i:266869 original size:102 final size:102
Alignment explanation
Indices: 266705--266891 Score: 279
Period size: 102 Copynumber: 1.8 Consensus size: 102
266695 AGATAGTTTC
*
266705 CCTTGAAACAAAATCTTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAATTTTGTCTCTCTTGAG
1 CCTTGAAACAAAATCTTGTCTCCCTTGAGACAGTTTCCCTTTAAACAAATTTTGTCTCTCTTGAG
266770 ACAGTTTCCCTTGAAACAAAATCATTAAATATCTTTT
66 ACAGTTTCCCTTGAAACAAAATCATTAAATATCTTTT
* * *
266807 CCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTT-CTTTTAGAACTAAGTTTTGTCTCTCTTG
1 CCTTGAAACAAAATCTTGTCTCCCTTGAGACAGTTTCCCTTTA-AAC-AAATTTTGTCTCTCTTG
* **
266870 AGACATTTTCTTTTGAAACAAA
64 AGACAGTTTCCCTTGAAACAAA
266892 TTTTGTCCCT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
100 5 0.07
101 27 0.36
102 44 0.58
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (102 bp):
CCTTGAAACAAAATCTTGTCTCCCTTGAGACAGTTTCCCTTTAAACAAATTTTGTCTCTCTTGAG
ACAGTTTCCCTTGAAACAAAATCATTAAATATCTTTT
Found at i:266904 original size:36 final size:36
Alignment explanation
Indices: 266692--266925 Score: 157
Period size: 36 Copynumber: 6.6 Consensus size: 36
266682 AAAACGAATT
* ** * *
266692 TTGAGATAGTTTCCCTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCTTTTGAAAC-AAATTTTGTCCCTC
* *
266729 TTGAGACAGTTTCCCTTT-AAACAAATTTTGTCTCTC
1 TTGAGACAGTTT-CTTTTGAAACAAATTTTGTCCCTC
** * *
266765 TTGAGACAGTTTCCCTTGAAACAAA----AT-CAT-
1 TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
** * * *
266795 TAAATATC-TTTTC-CTTGAAACAAATTTTGTCTCC-C
1 TTGAGA-CAGTTTCTTTTGAAACAAATTTTGTC-CCTC
* *
266830 TTGAGACAGTTTCTTTT-AGAACTAAGTTTTGTCTCTC
1 TTGAGACAGTTTCTTTTGA-AAC-AAATTTTGTCCCTC
*
266867 TTGAGACATTTTCTTTTGAAACAAATTTTGTCCCTC
1 TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
*
266903 TTGAGACAGTTTCTCTTGAAACA
1 TTGAGACAGTTTCTTTTGAAACA
266926 CAAAAAAAAC
Statistics
Matches: 156, Mismatches: 25, Indels: 33
0.73 0.12 0.15
Matches are distributed among these distances:
29 11 0.07
30 7 0.04
31 2 0.01
32 1 0.01
33 1 0.01
34 1 0.01
35 13 0.08
36 71 0.46
37 44 0.28
38 5 0.03
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.40
Consensus pattern (36 bp):
TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
Found at i:266981 original size:39 final size:37
Alignment explanation
Indices: 266911--267004 Score: 131
Period size: 39 Copynumber: 2.6 Consensus size: 37
266901 TCTTGAGACA
*
266911 GTTTCTCTTG-AA-ACACAAAAAAAACCCTTGAAATT
1 GTTTCTCTTGAAACACACAAAAAAAACCCTTGAAAAT
*
266946 GTTTCTCTTGAAACACACACACAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACACA-A-AAAAAACCCTTGAAAAT
266985 GTTTCTCTTGAAACAC-CAAA
1 GTTTCTCTTGAAACACACAAA
267005 CCCTCGAGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
35 10 0.19
36 3 0.06
37 6 0.11
38 3 0.06
39 31 0.58
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (37 bp):
GTTTCTCTTGAAACACACAAAAAAAACCCTTGAAAAT
Found at i:267139 original size:84 final size:85
Alignment explanation
Indices: 267008--267165 Score: 219
Period size: 84 Copynumber: 1.9 Consensus size: 85
266998 CACCAAACCC
* * * *
267008 TCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGCCTAGAAGGGT
1 TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAACATAACTCAAGCCAAGAAGGGC
267073 TATCTGTCACCAAAAGACCT
66 TATCTGTCACCAAAAGACCT
** * * * *
267093 TCGAGTTCGACTATGCTCAGC-TCTAAGGCACATCATTTATAGCATAACTCAAGGCAAGAAGGGC
1 TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAACATAACTCAAGCCAAGAAGGGC
267157 TATCTGTCA
66 TATCTGTCA
267166 ATAAAATTGT
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
84 45 0.71
85 18 0.29
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (85 bp):
TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAACATAACTCAAGCCAAGAAGGGC
TATCTGTCACCAAAAGACCT
Found at i:268021 original size:19 final size:19
Alignment explanation
Indices: 267999--268042 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
267989 TTAATTATTA
267999 TTATTTTATTTATTTAACT
1 TTATTTTATTTATTTAACT
268018 TTATTTTATTTATTTAACT
1 TTATTTTATTTATTTAACT
268037 TTATTT
1 TTATTT
268043 ATACGTACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTTTATTTATTTAACT
Found at i:268022 original size:10 final size:10
Alignment explanation
Indices: 268007--268043 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
267997 TATTATTTTA
268007 TTTATTTAAC
1 TTTATTTAAC
*
268017 TTTATTTTA-
1 TTTATTTAAC
268026 TTTATTTAAC
1 TTTATTTAAC
268036 TTTATTTA
1 TTTATTTA
268044 TACGTACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTATTTAAC
Found at i:268178 original size:2 final size:2
Alignment explanation
Indices: 268173--268197 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
268163 TTTTTTAGAT
268173 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
268198 TAATTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:268294 original size:39 final size:38
Alignment explanation
Indices: 268183--268304 Score: 122
Period size: 39 Copynumber: 3.1 Consensus size: 38
268173 TATATATATA
* *
268183 TATATATATATATATTAATTTTTA-TTATCAGTTTTATTAAT
1 TATATATATATATATT-ATTTTTATTTATTA-TTTT-TT-TT
* *
268224 T-TATATATATATACTATTTTTATTAATTTATTTTTTTT
1 TATATATATATATATTATTTTTATTTA-TTATTTTTTTT
*
268262 TATATATATATATATTATTTTTACTTTATTATTATTATTT
1 TATATATATATATATTATTTTTA-TTTATTATT-TTTTTT
268302 TAT
1 TAT
268305 TTATTTGTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
38 2 0.03
39 34 0.49
40 30 0.43
41 3 0.04
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (38 bp):
TATATATATATATATTATTTTTATTTATTATTTTTTTT
Found at i:268365 original size:55 final size:54
Alignment explanation
Indices: 268238--268371 Score: 139
Period size: 53 Copynumber: 2.5 Consensus size: 54
268228 ATATATATAC
** *
268238 TATTTTTATTAATTTAT-TTTTTTTTATATATATATATATTATTTTTACTTTAT
1 TATTTTTATTTTTTTATATTTATTTTATATATATATATATTATTTTTACTTTAT
* * * * * * *
268291 TATTATTATTTTATT-TATTTGTTTTATTTATATATATTTTCTTCTTTTTCTTTA-
1 TATTTTTATTTTTTTATATTTATTTTATATATATATATATT-AT-TTTTACTTTAT
268345 TATTTTTATTTTTTTATATTTATTTTA
1 TATTTTTATTTTTTTATATTTATTTTA
268372 CTTACTATTT
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
52 1 0.02
53 31 0.48
54 14 0.22
55 19 0.29
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (54 bp):
TATTTTTATTTTTTTATATTTATTTTATATATATATATATTATTTTTACTTTAT
Found at i:269024 original size:123 final size:123
Alignment explanation
Indices: 268805--269094 Score: 499
Period size: 123 Copynumber: 2.4 Consensus size: 123
268795 GGTTACGACA
* *
268805 AAGAGGAAGAAGAAGTTCATAATGAGAATAACTTGTTCAACCTTTTGCTCTACTCTATCGCAGAA
1 AAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAA
* *
268870 TGAGATAGATCAACATCAATATTTCCAGAAGGAGTTCATAATGAAAAGAACTCATCTG
66 GGAGATAGATCAACATCAACATTTCCAGAAGGAGTTCATAATGAAAAGAACTCATCTG
*
268928 AAGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAA
1 AAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAA
* *
268993 GGAGATAGATCAGCATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTG
66 GGAGATAGATCAACATCAACATTTCCAGAAGGAGTTCATAATGAAAAGAACTCATCTG
* *
269051 AAGAAGAAGAAGAAGTTCACAATGAGAAGAACTTGTTCAACCTT
1 AAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
269095 AGTTCAATTC
Statistics
Matches: 157, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
123 157 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (123 bp):
AAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAA
GGAGATAGATCAACATCAACATTTCCAGAAGGAGTTCATAATGAAAAGAACTCATCTG
Found at i:270498 original size:19 final size:19
Alignment explanation
Indices: 270465--270501 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
270455 ATGACTAACA
**
270465 AAATCGCAATGCGATCTCT
1 AAATCGCAACACGATCTCT
270484 AAATCGCAACACGATCTC
1 AAATCGCAACACGATCTC
270502 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCGCAACACGATCTCT
Found at i:270550 original size:20 final size:20
Alignment explanation
Indices: 270527--270991 Score: 169
Period size: 20 Copynumber: 22.6 Consensus size: 20
270517 GTTTCCAGAT
*
270527 TCGCAATGCGATTTTGACTA
1 TCGCAATGCGATTATGACTA
* *
270547 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTATG-ACTA
* *
270567 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTATGACTA
* * * *
270587 TCGTAACGCGATAAT-ACAGAA
1 TCGCAATGCGATTATGAC--TA
** * **
270608 TCGCGTTGTTGCGATTTTAGAAAA
1 TCGC---AATGCGATTAT-GACTA
* *
270632 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTATG-ACTA
* * *
270652 TCGCAACGCGATAAT-ACAAAA
1 TCGCAATGCGATTATGAC--TA
* *
270673 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTATGACTA
* *
270693 TCGCAACGCGATAAT-ACATAA
1 TCGCAATGCGATTATGAC-T-A
* *
270714 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTATGACTA
* *
270734 TCGCAACGCGATAAT-ACATAA
1 TCGCAATGCGATTATGAC-T-A
* *
270755 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTATGACTA
* *
270775 TCGCAACGCGATAAT-ACATAA
1 TCGCAATGCGATTATGAC-T-A
* *
270796 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTATGACTA
* *
270816 TCGCAACGCGATAAT-ACATAA
1 TCGCAATGCGATTATGAC-T-A
* *
270837 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTATGACTA
* *
270857 TCGCAACGCGATAAT-ACATAA
1 TCGCAATGCGATTATGAC-T-A
* *
270878 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTATGACTA
* *
270898 TCGCAACGCGATAAT-ACATAA
1 TCGCAATGCGATTATGAC-T-A
* *
270919 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTATGACTA
* *
270939 TCGCAACGCGATAAT-ACATAA
1 TCGCAATGCGATTATGAC-T-A
* * * *
270960 TCGCAACGTGATTCTAACTA
1 TCGCAATGCGATTATGACTA
*
270980 TTGCAATGCGAT
1 TCGCAATGCGAT
270992 AATACAAAAG
Statistics
Matches: 350, Mismatches: 60, Indels: 70
0.73 0.12 0.15
Matches are distributed among these distances:
18 1 0.00
19 17 0.05
20 171 0.49
21 132 0.38
22 16 0.05
24 12 0.03
26 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGATTATGACTA
Found at i:270673 original size:41 final size:41
Alignment explanation
Indices: 270651--271013 Score: 654
Period size: 41 Copynumber: 8.9 Consensus size: 41
270641 GAATATGTAA
*
270651 ATCGCAACGCGATAATACAAAATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
270692 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
270733 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
270774 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
270815 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
270856 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
270897 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
* *
270938 ATCGCAACGCGATAATACATAATCGCAACGTGATTCTAACT
1 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
* * * * *
270979 ATTGCAATGCGATAATACAAAAGCGCAATGCGATT
1 ATCGCAACGCGATAATACATAATCGCAACGCGATT
271014 TTCTAAATTT
Statistics
Matches: 313, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 313 1.00
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
Found at i:271052 original size:19 final size:20
Alignment explanation
Indices: 271028--271068 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
271018 AAATTTACGT
271028 TAGTCCAAATT-CGTTGCGA
1 TAGTCCAAATTACGTTGCGA
*
271047 TAGTCCAAGTTCACGTTGCGA
1 TAGTCCAAATT-ACGTTGCGA
271068 T
1 T
271069 TTCTTAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
21 9 0.47
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (20 bp):
TAGTCCAAATTACGTTGCGA
Found at i:271463 original size:19 final size:20
Alignment explanation
Indices: 271438--271528 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
271428 CTTATTTTGT
271438 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
*
271458 -TTTTTCACTATCACAACAAC
1 ATTTTTCACTATCGCAAC-AC
271478 ACGTTTTTCAAACTATCGCAACAC
1 A--TTTTTC--ACTATCGCAACAC
*
271502 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
271521 ATTTTTCA
1 ATTTTTCA
271529 AAATCGCGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 30 0.50
20 7 0.12
21 4 0.07
23 6 0.10
24 3 0.05
25 10 0.17
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.35
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:271500 original size:44 final size:41
Alignment explanation
Indices: 271438--271530 Score: 118
Period size: 44 Copynumber: 2.2 Consensus size: 41
271428 CTTATTTTGT
* *
271438 ATTTTTC--ACTATCGCAACACTTTTTCACTATCACAACAAC
1 ATTTTTCAAACTATCGCAACACATTTTAACTATCACAAC-AC
*
271478 ACGTTTTTCAAACTATCGCAACACATTTTAACTATCGCAACAC
1 A--TTTTTCAAACTATCGCAACACATTTTAACTATCACAACAC
271521 ATTTTTCAAA
1 ATTTTTCAAA
271531 ATCGCGTTGC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
40 1 0.02
41 9 0.20
42 6 0.13
43 3 0.07
44 27 0.59
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.34
Consensus pattern (41 bp):
ATTTTTCAAACTATCGCAACACATTTTAACTATCACAACAC
Found at i:272218 original size:19 final size:20
Alignment explanation
Indices: 272194--272238 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
272184 TATATATATA
272194 TTATTTTAATT-AT-TTTAT
1 TTATTTTAATTAATATTTAT
*
272212 CTTATTTTTATTAATATTTAT
1 -TTATTTTAATTAATATTTAT
272233 TTATTT
1 TTATTT
272239 AGTTTTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 10 0.43
20 8 0.35
21 5 0.22
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATTTTAATTAATATTTAT
Found at i:273426 original size:21 final size:21
Alignment explanation
Indices: 273400--273441 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
273390 ATGGTCCTTC
273400 TCCATCATCTGACCACAGAGT
1 TCCATCATCTGACCACAGAGT
273421 TCCATCATCTGACCACAGAGT
1 TCCATCATCTGACCACAGAGT
273442 ACCGGTGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (21 bp):
TCCATCATCTGACCACAGAGT
Found at i:275208 original size:2 final size:2
Alignment explanation
Indices: 275201--275263 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
275191 TGTGCATGAA
275201 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
275243 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
275264 GAAAGCTCCA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:295831 original size:20 final size:20
Alignment explanation
Indices: 295806--295998 Score: 78
Period size: 20 Copynumber: 9.7 Consensus size: 20
295796 GATTTTCAAG
* *
295806 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
295826 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
295846 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
295866 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
295886 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
295906 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
295926 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
295946 AATCGCAACGATAATCA-GTA
1 AATCGCAACGCGAA-CACATA
* *
295966 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
295986 AATCGCAACGCGA
1 AATCGCAACGCGA
295999 TTTTTAAAGC
Statistics
Matches: 151, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
19 3 0.02
20 145 0.96
21 3 0.02
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:295853 original size:40 final size:40
Alignment explanation
Indices: 295806--295997 Score: 154
Period size: 40 Copynumber: 4.8 Consensus size: 40
295796 GATTTTCAAG
*
295806 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAAC-CATA
* * * * * *
295846 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
* * * * * *
295886 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
* * * * * *
295926 TATCGCAACGCGTATCCGTAAATCGCAACG-ATAATCAGTA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCA-TA
* * *
295966 AATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AATCGCAACGCGAATACGAAAATCGCAACGCG
295998 ATTTTTAAAG
Statistics
Matches: 132, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
39 3 0.02
40 127 0.96
41 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
Found at i:295874 original size:60 final size:60
Alignment explanation
Indices: 295806--295998 Score: 246
Period size: 60 Copynumber: 3.2 Consensus size: 60
295796 GATTTTCAAG
** * *
295806 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGAACACGTAAATCGCAACGCGTATCCGTA
* * * *
295866 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCG-AACACGTAAATCGCAACGCGTATCCGTA
* * **
295926 TATCGCAACGCGTATCCGTAAATCGCAACGATAATCA-GTAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGAA-CACGTAAATCGCAACGCGTATCCGTA
295986 AATCGCAACGCGA
1 AATCGCAACGCGA
295999 TTTTTAAAGC
Statistics
Matches: 114, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
59 1 0.01
60 111 0.97
61 2 0.02
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGAATCCGTAAATCGCAACGCGAACACGTAAATCGCAACGCGTATCCGTA
Found at i:296416 original size:33 final size:33
Alignment explanation
Indices: 296377--296447 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
296367 TTCACTTAGA
296377 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
296410 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
296443 TTTCA
1 TTTCA
296448 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:296553 original size:21 final size:20
Alignment explanation
Indices: 296527--296619 Score: 116
Period size: 21 Copynumber: 4.5 Consensus size: 20
296517 TGCAGAAGAG
296527 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
296548 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
296568 TCTGCAACGAGAGAAATGAAAA
1 TC-GCAACGAGA-AAATGAAAA
*
296590 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
296609 TCGCAACGAGA
1 TCGCAACGAGA
296620 GAATCGCAAC
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
19 18 0.30
20 9 0.15
21 25 0.41
22 9 0.15
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:296588 original size:42 final size:40
Alignment explanation
Indices: 296527--296622 Score: 138
Period size: 42 Copynumber: 2.4 Consensus size: 40
296517 TGCAGAAGAG
* * **
296527 TCGCAACGAGATAAATGAAAATCGCAACGTGAAAATGACTA
1 TCGCAACGAGAGAAATGAAAATCGCAACGCG-AAATGAAAA
296568 TCTGCAACGAGAGAAATGAAAATCGCAACGCGAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAATCGCAACGCGAAATGAAAA
296609 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
296623 TCGCAACGCG
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 12 0.24
41 11 0.22
42 27 0.54
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (40 bp):
TCGCAACGAGAGAAATGAAAATCGCAACGCGAAATGAAAA
Found at i:296604 original size:19 final size:19
Alignment explanation
Indices: 296527--296619 Score: 96
Period size: 19 Copynumber: 4.6 Consensus size: 19
296517 TGCAGAAGAG
296527 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAG--AAATGAAAA
* **
296548 TCGCAACGTGAAAATGACTA
1 TCGCAACGAG-AAATGAAAA
296568 TCTGCAACGAGAGAAATGAAAA
1 TC-GCAAC--GAGAAATGAAAA
*
296590 TCGCAACGCGAAATGAAAA
1 TCGCAACGAGAAATGAAAA
296609 TCGCAACGAGA
1 TCGCAACGAGA
296620 GAATCGCAAC
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
19 21 0.35
20 9 0.15
21 19 0.32
22 9 0.15
23 2 0.03
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
TCGCAACGAGAAATGAAAA
Found at i:296698 original size:21 final size:21
Alignment explanation
Indices: 296672--296736 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
296662 CGCGTTGCGA
296672 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
296693 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
296713 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
296734 TTC
1 TTC
296737 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:296733 original size:20 final size:20
Alignment explanation
Indices: 296671--296734 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
296661 TCGCGTTGCG
296671 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
296691 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
296712 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
296732 ATT
1 ATT
296735 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:297929 original size:14 final size:14
Alignment explanation
Indices: 297910--297945 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
297900 ATTGTTTAAT
297910 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
297924 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
297938 TGATTTGT
1 TGATTTGT
297946 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:298060 original size:19 final size:19
Alignment explanation
Indices: 298036--298123 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
298026 GCATTATGTT
298036 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
298055 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
298072 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
298088 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
298107 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
298124 CGAGAGAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 29 0.48
20 16 0.26
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:298155 original size:53 final size:53
Alignment explanation
Indices: 298036--298142 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
298026 GCATTATGTT
298036 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
298088 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
298141 GA
1 GA
298143 TTTTCATTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 19 0.35
53 35 0.65
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (53 bp):
GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:298160 original size:19 final size:19
Alignment explanation
Indices: 298132--298374 Score: 265
Period size: 19 Copynumber: 13.7 Consensus size: 19
298122 AACGAGAGAA
*
298132 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
298151 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
298170 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
298187 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
298204 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
298223 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
298239 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
298256 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
298275 TCCGCATTGCGATTCTCA--
1 T-CGCATTGCGATTTTCATT
298293 -CG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
298309 TCGCATTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
298328 TCCGCATTGCGATTTTC--T
1 T-CGCATTGCGATTTTCATT
*
298346 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
298362 TCGCATTGCGATT
1 TCGCATTGCGATT
298375 CTCTCGTTGC
Statistics
Matches: 190, Mismatches: 11, Indels: 46
0.77 0.04 0.19
Matches are distributed among these distances:
14 33 0.17
16 17 0.09
17 16 0.08
18 5 0.03
19 80 0.42
20 39 0.21
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:298201 original size:53 final size:53
Alignment explanation
Indices: 298138--298374 Score: 422
Period size: 53 Copynumber: 4.5 Consensus size: 53
298128 AGAATCGCAA
298138 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
298191 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
298243 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCACGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
* * *
298296 TGCGATTTTCATTTCGCATTGCAATTTTCATTTCCGCATTGCGATTTTCTTGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
298349 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
298375 CTCTCGTTGC
Statistics
Matches: 176, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
52 52 0.30
53 124 0.70
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:298258 original size:105 final size:106
Alignment explanation
Indices: 298138--298374 Score: 422
Period size: 105 Copynumber: 2.2 Consensus size: 106
298128 AGAATCGCAA
*
298138 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCACGTTGCGATTTTCAT
*
298203 TTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
66 TTCGCATTGCAATTTTCATTTCCGCATTGCGATTCTCTCGT
298243 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCACGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCACGTTGCGATTTTCAT
* *
298308 TTCGCATTGCAATTTTCATTTCCGCATTGCGATTTTCTTGT
66 TTCGCATTGCAATTTTCATTTCCGCATTGCGATTCTCTCGT
*
298349 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
298375 CTCTCGTTGC
Statistics
Matches: 126, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
105 84 0.67
106 42 0.33
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (106 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCACGTTGCGATTTTCAT
TTCGCATTGCAATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:298299 original size:86 final size:84
Alignment explanation
Indices: 298209--298388 Score: 224
Period size: 86 Copynumber: 2.1 Consensus size: 84
298199 TCATTTCGCA
*
298209 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-TTGCGATTTTCATTTCGCATTGCGATTT
1 TTGCGATTTTCATTTCGCATTGCAATTTCATCTCCGATTGCGATTTTC--TT-G--TTGCGATTT
298270 TCATTTCCGCATTGCGATTCTCACG
61 TCATTT-CGCATTGCGATTCTCACG
* *
298295 TTGCGATTTTCATTTCGCATTGCAATTTTCATTTCCGCATTGCGATTTTCTTGTTGGGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCAA-TTTCATCTCCG-ATTGCGATTTTCTTGTTGCGATTTTCA
*
298360 TTTCGCATTGCGATTCTCTCG
64 TTTCGCATTGCGATTCTCACG
298381 TTGCGATT
1 TTGCGATT
298389 GTAATTTCCG
Statistics
Matches: 84, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
86 49 0.58
87 14 0.17
88 3 0.04
89 3 0.04
90 4 0.05
92 11 0.13
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (84 bp):
TTGCGATTTTCATTTCGCATTGCAATTTCATCTCCGATTGCGATTTTCTTGTTGCGATTTTCATT
TCGCATTGCGATTCTCACG
Found at i:298372 original size:33 final size:33
Alignment explanation
Indices: 298138--298388 Score: 177
Period size: 33 Copynumber: 7.2 Consensus size: 33
298128 AGAATCGCAA
*
298138 TGCGATTTTCATTTCGCATTGCGATTTTCAT-T
1 TGCGATTTTCATTTCGCATTGCGATTTTCTTGT
* * * *
298170 TCCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCG-ATTTTC-ATT-TCGCATTGCGATTTTC--TT-G--T
* *
298210 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCTTGT
*
298243 TGCGATTTTCATTTCGCATTGCGATTTTCAT-T
1 TGCGATTTTCATTTCGCATTGCGATTTTCTTGT
* * * *
298275 TCCGCA-TTGCGATTCTCACGTTGCGATTTTCATTTCGCAT
1 TGCG-ATTTTC-ATT-TCGCATTGCGATTTTC--TT-G--T
*
298315 TGCAATTTTCATTTCCGCATTGCGATTTTCTTGT
1 TGCGATTTTCATTT-CGCATTGCGATTTTCTTGT
* * *
298349 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCTTGT
298382 TGCGATT
1 TGCGATT
298389 GTAATTTCCG
Statistics
Matches: 169, Mismatches: 29, Indels: 41
0.71 0.12 0.17
Matches are distributed among these distances:
32 13 0.08
33 60 0.36
34 41 0.24
35 1 0.01
36 4 0.02
37 2 0.01
38 14 0.08
39 21 0.12
40 13 0.08
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCTTGT
Found at i:300690 original size:12 final size:12
Alignment explanation
Indices: 300673--300697 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
300663 TCTTCGGGGA
300673 CTTTTTCTTCTT
1 CTTTTTCTTCTT
300685 CTTTTTCTTCTT
1 CTTTTTCTTCTT
300697 C
1 C
300698 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:300906 original size:24 final size:24
Alignment explanation
Indices: 300872--300918 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
300862 CTGAAACATC
300872 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
300896 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
300919 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:301519 original size:22 final size:21
Alignment explanation
Indices: 301471--301520 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
301461 AAAACCTGTT
*
301471 GCCGGAT-TGGGAAGGATGTC
1 GCCGGATATAGGAAGGATGTC
**
301491 GTTGGATATAGGAACGGATGTC
1 GCCGGATATAGGAA-GGATGTC
301513 GCCGGATA
1 GCCGGATA
301521 GAGTGATAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 5 0.22
21 5 0.22
22 13 0.57
ACGTcount: A:0.24, C:0.14, G:0.40, T:0.22
Consensus pattern (21 bp):
GCCGGATATAGGAAGGATGTC
Found at i:301639 original size:20 final size:20
Alignment explanation
Indices: 301611--301859 Score: 250
Period size: 20 Copynumber: 12.4 Consensus size: 20
301601 AAATTTCAGT
* * *
301611 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
301631 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
301651 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* **
301671 GTTGCGATTTACTGATTATC
1 GTTGCGATTTACGGATTCGC
*
301691 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
301711 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
301731 ATTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
301751 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
301771 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
301791 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
*
301811 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
301831 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
301851 GTTGCGATT
1 GTTGCGATT
301860 CTGTAAAATC
Statistics
Matches: 204, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 203 1.00
21 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:301877 original size:21 final size:20
Alignment explanation
Indices: 301853--301923 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 20
301843 ATATTCGCGT
301853 TGCGATTCTGTAAAATCGCAA
1 TGCGATT-TGTAAAATCGCAA
** *
301874 TGCGAATTTGTACTATCGCAT
1 TGCG-ATTTGTAAAATCGCAA
**
301895 TGCGA-TTGTCAAGAATCGCGT
1 TGCGATTTGT-AA-AATCGCAA
301916 TGCGATTT
1 TGCGATTT
301924 TGGAAACTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
19 4 0.10
20 2 0.05
21 29 0.73
22 5 0.12
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
TGCGATTTGTAAAATCGCAA
Found at i:307797 original size:29 final size:29
Alignment explanation
Indices: 307752--307821 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
307742 CAGTTGGTCG
* *
307752 TAGGTCGCCATGACATCCGGGCGACCTAC
1 TAGGTCGTCATGACATCCGGACGACCTAC
*
307781 TAGGTCGTCATGCCATCCGGACGACCTAC
1 TAGGTCGTCATGACATCCGGACGACCTAC
*
307810 TAGGTTGTCATG
1 TAGGTCGTCATG
307822 TCTTCCCGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.20, C:0.30, G:0.27, T:0.23
Consensus pattern (29 bp):
TAGGTCGTCATGACATCCGGACGACCTAC
Found at i:310842 original size:14 final size:15
Alignment explanation
Indices: 310825--310861 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
310815 TTTCGTCCCG
*
310825 TATTTTTATAAT-AT
1 TATTATTATAATAAT
310839 TATTATTATAATAAT
1 TATTATTATAATAAT
310854 TA-TATTAT
1 TATTATTAT
310862 TATTACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTATTATAATAAT
Found at i:327320 original size:16 final size:16
Alignment explanation
Indices: 327299--327329 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
327289 ATAAATAAAT
327299 GAACATAAACGAACAC
1 GAACATAAACGAACAC
327315 GAACATAAACGAACA
1 GAACATAAACGAACA
327330 AATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:328527 original size:24 final size:24
Alignment explanation
Indices: 328492--328537 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
328482 AAAATTGAGT
328492 CATAAACAAACATAACCGAACGAA
1 CATAAACAAACATAACCGAACGAA
*
328516 CATAAACGAACATAACCGAACG
1 CATAAACAAACATAACCGAACG
328538 TTCACGAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.54, C:0.26, G:0.11, T:0.09
Consensus pattern (24 bp):
CATAAACAAACATAACCGAACGAA
Found at i:329476 original size:187 final size:187
Alignment explanation
Indices: 329161--329535 Score: 723
Period size: 187 Copynumber: 2.0 Consensus size: 187
329151 GAAATAAACC
329161 ACTGCCTTCATTCCATCTTCTCGGCGAGAAAACAACGAATAAAAAACAAGGAAAATGTGAGTAAT
1 ACTGCCTTCATTCCATCTTCTCGGCGAGAAAACAACGAATAAAAAACAAGGAAAATGTGAGTAAT
*
329226 CACCTGAGGAGGAGAAGGAATCGCAGAAACGAGATAATCAACGGAAAATTTGTATAAATACCGCA
66 CACCTGAGGAAGAGAAGGAATCGCAGAAACGAGATAATCAACGGAAAATTTGTATAAATACCGCA
*
329291 TCGATTGTTAATGCATGCGAGAGAATGGAGATTAAAATGGTTTTAAAGAATGAAAGA
131 TCGATTGTTAATGCAGGCGAGAGAATGGAGATTAAAATGGTTTTAAAGAATGAAAGA
329348 ACTGCCTTCATTCCATCTTCTCGGCGAGAAAACAACGAATAAAAAACAAGGAAAATGTGAGTAAT
1 ACTGCCTTCATTCCATCTTCTCGGCGAGAAAACAACGAATAAAAAACAAGGAAAATGTGAGTAAT
*
329413 CACCTGAGGAAGAGAAGGAATCGCAGAAACGCGATAATCAACGGAAAATTTGTATAAATACCGCA
66 CACCTGAGGAAGAGAAGGAATCGCAGAAACGAGATAATCAACGGAAAATTTGTATAAATACCGCA
329478 TCGATTGTTAATGCAGGCGAGAGAATGGAGATTAAAATGGTTTTAAAGAATGAAAGA
131 TCGATTGTTAATGCAGGCGAGAGAATGGAGATTAAAATGGTTTTAAAGAATGAAAGA
329535 A
1 A
329536 TTACAGTTAG
Statistics
Matches: 185, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
187 185 1.00
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (187 bp):
ACTGCCTTCATTCCATCTTCTCGGCGAGAAAACAACGAATAAAAAACAAGGAAAATGTGAGTAAT
CACCTGAGGAAGAGAAGGAATCGCAGAAACGAGATAATCAACGGAAAATTTGTATAAATACCGCA
TCGATTGTTAATGCAGGCGAGAGAATGGAGATTAAAATGGTTTTAAAGAATGAAAGA
Found at i:340881 original size:12 final size:10
Alignment explanation
Indices: 340851--340883 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
340841 ACGAAGTATC
340851 TGTTTATATA
1 TGTTTATATA
340861 TGTTTATATA
1 TGTTTATATA
*
340871 TGTTTAAATA
1 TGTTTATATA
340881 TGT
1 TGT
340884 AAAAGTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (10 bp):
TGTTTATATA
Found at i:341460 original size:60 final size:60
Alignment explanation
Indices: 341347--341460 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
341337 CTATAGCTTA
* * *
341347 TTGCTTTGTTGAGTCATCTGACTATTAAAAGTTACAAAATGGTCCTTCGACTATAGGACG
1 TTGCTTTGTTGAGTCATCTAACTATTAAAAGTTACAAAATGGTCATTCAACTATAGGACG
* * *
341407 TTGCTTTGTTGAGTGCCTC-AACTATTAGAAGTTACAAAATGGTCATTTAACTAT
1 TTGCTTTGTTGAGT-CATCTAACTATTAAAAGTTACAAAATGGTCATTCAACTAT
341461 TCATTATATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 44 0.94
61 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (60 bp):
TTGCTTTGTTGAGTCATCTAACTATTAAAAGTTACAAAATGGTCATTCAACTATAGGACG
Found at i:342023 original size:20 final size:19
Alignment explanation
Indices: 341992--342039 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
341982 TACGGTTAAG
341992 AAGAAAGAAAGGAAGAAGA
1 AAGAAAGAAAGGAAGAAGA
*
342011 AAGAAATGAAAGGAATAAGA
1 AAGAAA-GAAAGGAAGAAGA
*
342031 AAGGAAGAA
1 AAGAAAGAA
342040 GAAGAAAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.04
Consensus pattern (19 bp):
AAGAAAGAAAGGAAGAAGA
Found at i:342056 original size:11 final size:11
Alignment explanation
Indices: 341991--342042 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
341981 GTACGGTTAA
341991 GAAGAAAGAAAG
1 GAAG-AAGAAAG
342003 GAAGAAGAAA-
1 GAAGAAGAAAG
*
342013 GAA-ATGAAAG
1 GAAGAAGAAAG
*
342023 GAATAAGAAAG
1 GAAGAAGAAAG
342034 GAAGAAGAA
1 GAAGAAGAA
342043 GAAAGGGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 5 0.14
10 6 0.17
11 20 0.57
12 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (11 bp):
GAAGAAGAAAG
Found at i:342366 original size:42 final size:42
Alignment explanation
Indices: 342307--342388 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
342297 CCCGAAATCT
* *
342307 CGTGTTTGTTTCATGTAATTCATTTTCCGGAAAATATTTTTC
1 CGTGTTTGTTTCATGTAATTCATTTTACGAAAAATATTTTTC
* *
342349 CGTGTTTGTTTCATGTAATTCGTTTTACGAAAAATGTTTT
1 CGTGTTTGTTTCATGTAATTCATTTTACGAAAAATATTTT
342389 CTAGTGTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (42 bp):
CGTGTTTGTTTCATGTAATTCATTTTACGAAAAATATTTTTC
Found at i:342396 original size:42 final size:42
Alignment explanation
Indices: 342308--342398 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
342298 CCGAAATCTC
* *
342308 GTGTTTGTTTCATGTAATTCATTTTCCGGAAAATATTTTTCC
1 GTGTTTGTTTCATGTAATTCATTTTACGGAAAATATTTTTCA
*
342350 GTGTTTGTTTCATGTAATTCGTTTTAC-GAAAA-ATGTTTTCTA
1 GTGTTTGTTTCATGTAATTCATTTTACGGAAAATAT-TTTTC-A
342392 GTGTTTG
1 GTGTTTG
342399 GTTGGAGGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 2 0.05
41 10 0.23
42 32 0.73
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.51
Consensus pattern (42 bp):
GTGTTTGTTTCATGTAATTCATTTTACGGAAAATATTTTTCA
Found at i:342657 original size:26 final size:24
Alignment explanation
Indices: 342595--342657 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
342585 CATTTTAATC
342595 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
342619 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
342642 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
342658 ATTTTTAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:342672 original size:22 final size:23
Alignment explanation
Indices: 342629--342672 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
342619 AAAATATATT
*
342629 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAACAATATAA
* *
342652 TATT-ATATTTTTAACATTATA
1 TATTAATATTTCTAACAATATA
342673 CTAAAATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTAATATTTCTAACAATATAA
Found at i:342993 original size:14 final size:15
Alignment explanation
Indices: 342972--343012 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
342962 TTCCATAAAT
342972 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
342987 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
343001 GTAATTCATTTT
1 GTAATTCATTTT
343013 TTAAAAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:343468 original size:17 final size:16
Alignment explanation
Indices: 343448--343513 Score: 78
Period size: 16 Copynumber: 3.8 Consensus size: 16
343438 TTTTTTAATT
343448 TATTATTGTTTAAAAAA
1 TATT-TTGTTTAAAAAA
343465 TATTTTGTTTAAAAATA
1 TATTTTGTTTAAAAA-A
343482 GTTATTGTTGTTTAAAAAAA
1 --TATT-TTGTTT-AAAAAA
343502 TATTTTGTTTAA
1 TATTTTGTTTAA
343514 TTTATATTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
16 13 0.30
17 11 0.25
18 4 0.09
19 4 0.09
20 7 0.16
21 5 0.11
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (16 bp):
TATTTTGTTTAAAAAA
Found at i:343494 original size:20 final size:17
Alignment explanation
Indices: 343447--343513 Score: 82
Period size: 17 Copynumber: 3.8 Consensus size: 17
343437 TTTTTTTAAT
343447 TTATTATTGTTTAAAAAA
1 TTATT-TTGTTTAAAAAA
343465 -TATTTTGTTTAAAAATA
1 TTATTTTGTTTAAAAA-A
343482 GTTATTGTTGTTTAAAAAA
1 -TTATT-TTGTTTAAAAAA
*
343501 ATATTTTGTTTAA
1 TTATTTTGTTTAA
343514 TTTATATTAG
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
16 11 0.25
17 13 0.30
18 4 0.09
19 5 0.11
20 11 0.25
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (17 bp):
TTATTTTGTTTAAAAAA
Found at i:343740 original size:16 final size:16
Alignment explanation
Indices: 343719--343749 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
343709 TTATTAGTAA
343719 TCATTACTAAATCATG
1 TCATTACTAAATCATG
*
343735 TCATTATTAAATCAT
1 TCATTACTAAATCAT
343750 TAAATATCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (16 bp):
TCATTACTAAATCATG
Found at i:346948 original size:11 final size:11
Alignment explanation
Indices: 346932--346973 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
346922 TTTAATTGAA
346932 TTATTTATATT
1 TTATTTATATT
346943 TTATTTATATT
1 TTATTTATATT
*
346954 TTATCTTAT-TA
1 TTAT-TTATATT
346965 TTATTTATA
1 TTATTTATA
346974 AATATTCGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 4 0.14
11 20 0.71
12 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTTATATT
Found at i:346969 original size:16 final size:17
Alignment explanation
Indices: 346931--346973 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
346921 TTTTAATTGA
*
346931 ATTATTTATATTTTATT
1 ATTATTTATATCTTATT
346948 -TATATTT-TATCTTATT
1 AT-TATTTATATCTTATT
346964 ATTATTTATA
1 ATTATTTATA
346974 AATATTCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTATTTATATCTTATT
Found at i:347014 original size:20 final size:20
Alignment explanation
Indices: 346979--347016 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
346969 TTATAAATAT
**
346979 TCGAATTTATTCAATTTAAA
1 TCGAATTTATAAAATTTAAA
346999 TCGAATTTATAAAATTTA
1 TCGAATTTATAAAATTTA
347017 TGTATGGACA
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:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (20 bp):
TCGAATTTATAAAATTTAAA
Found at i:347133 original size:17 final size:16
Alignment explanation
Indices: 347113--347153 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
347103 AAATAATTAT
347113 TAATGATTTAGATTTAA
1 TAATGATTT-GATTTAA
*
347130 TAATGATATGATTTAA
1 TAATGATTTGATTTAA
*
347146 TAACGATT
1 TAATGATT
347154 ATTAATAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.44
Consensus pattern (16 bp):
TAATGATTTGATTTAA
Found at i:347144 original size:16 final size:17
Alignment explanation
Indices: 347113--347148 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
347103 AAATAATTAT
*
347113 TAATGATTTAGATTTAA
1 TAATGATATAGATTTAA
347130 TAATGATAT-GATTTAA
1 TAATGATATAGATTTAA
347146 TAA
1 TAA
347149 CGATTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (17 bp):
TAATGATATAGATTTAA
Found at i:347225 original size:65 final size:60
Alignment explanation
Indices: 347072--347287 Score: 183
Period size: 59 Copynumber: 3.5 Consensus size: 60
347062 CCAAAATAAT
* * *
347072 TAATAATGATTTAGTAATGATTACTAATAATAAATAATTATTAATGA-TT--T-A-GATTTAA
1 TAATAATGATTTAATAATGATTACTAATAATTAA-AATTA-TAA-GATTTAATAATGATTTGA
* * ** * *
347130 TAATGATATGATTTAATAACGATTATTAATAATTATTTATTATAAATATTTAATGATTTGAATTT
1 TAAT-A-ATGATTTAATAATGATTACTAATAATTA-AAATTAT-AAGATTTAAT-A-ATG-ATTT
347195 GA
59 GA
* *
347197 TATTAATGATTTAGTAATGATTACTAATAA-TAAAATTATAAGATTTAATAATGATTTGA
1 TAATAATGATTTAATAATGATTACTAATAATTAAAATTATAAGATTTAATAATGATTTGA
* *
347256 TAATAATGTTTTAATAATGATTACTACTAATT
1 TAATAATGATTTAATAATGATTACTAATAATT
347288 TGATAATATT
Statistics
Matches: 124, Mismatches: 21, Indels: 24
0.73 0.12 0.14
Matches are distributed among these distances:
58 4 0.03
59 35 0.28
60 35 0.28
61 1 0.01
62 10 0.08
63 5 0.04
64 2 0.02
65 22 0.18
66 2 0.02
67 8 0.06
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (60 bp):
TAATAATGATTTAATAATGATTACTAATAATTAAAATTATAAGATTTAATAATGATTTGA
Found at i:347252 original size:11 final size:11
Alignment explanation
Indices: 347200--347277 Score: 52
Period size: 11 Copynumber: 6.7 Consensus size: 11
347190 AATTTGATAT
*
347200 TAATGATTTAG
1 TAATGATTTAA
347211 TAATGATTACTAA
1 TAATGATT--TAA
* *
347224 TAATAAAATT-A
1 TAAT-GATTTAA
347235 TAA-GATTTAA
1 TAATGATTTAA
347245 TAATGATTTGATAA
1 TAATGA-TT--TAA
*
347259 TAATGTTTTAA
1 TAATGATTTAA
347270 TAATGATT
1 TAATGATT
347278 ACTACTAATT
Statistics
Matches: 52, Mismatches: 7, Indels: 16
0.69 0.09 0.21
Matches are distributed among these distances:
9 3 0.06
10 4 0.08
11 24 0.46
12 3 0.06
13 8 0.15
14 10 0.19
ACGTcount: A:0.45, C:0.01, G:0.10, T:0.44
Consensus pattern (11 bp):
TAATGATTTAA
Found at i:347552 original size:15 final size:15
Alignment explanation
Indices: 347532--347560 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
347522 TTTATTATTA
347532 ATATTTAATGATTTG
1 ATATTTAATGATTTG
347547 ATATTTAATGATTT
1 ATATTTAATGATTT
347561 AGTAATGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (15 bp):
ATATTTAATGATTTG
Found at i:347567 original size:26 final size:27
Alignment explanation
Indices: 347537--347645 Score: 92
Period size: 21 Copynumber: 4.3 Consensus size: 27
347527 TATTAATATT
347537 TAATGATTTGATAT-TTAATGATTTAG
1 TAATGATTTGATATATTAATGATTTAG
* * *
347563 TAATGATATGATATAGTAATGATTACTAA
1 TAATGATTTGATATATTAATGATT--TAG
*
347592 TAATGATTT-AT-TATTAGT-A-TT--
1 TAATGATTTGATATATTAATGATTTAG
*
347613 TAATGATTTG--ATACTAATGATTTAG
1 TAATGATTTGATATATTAATGATTTAG
347638 TAATGATT
1 TAATGATT
347646 ATTAATAATA
Statistics
Matches: 66, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
21 14 0.21
22 1 0.02
23 3 0.05
25 9 0.14
26 14 0.21
27 13 0.20
28 2 0.03
29 10 0.15
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.47
Consensus pattern (27 bp):
TAATGATTTGATATATTAATGATTTAG
Found at i:347579 original size:16 final size:16
Alignment explanation
Indices: 347554--347585 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
347544 TTGATATTTA
*
347554 ATGATTTAGTAATGAT
1 ATGATATAGTAATGAT
347570 ATGATATAGTAATGAT
1 ATGATATAGTAATGAT
347586 TACTAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (16 bp):
ATGATATAGTAATGAT
Found at i:350012 original size:57 final size:57
Alignment explanation
Indices: 349936--350048 Score: 133
Period size: 57 Copynumber: 2.0 Consensus size: 57
349926 ATTATAACTT
* *
349936 AAACTAATAAACTATTTTTTTAT-TATAATCA-AACTT-AACTTAAACTAACAAACTAAA
1 AAACTAATAAACTAATTTTTTATATATAAT-ATAACTTCAAC--AAACAAACAAACTAAA
* * *
349993 AAACTAATTAGCTAATTTTTTTTATATAATATAACTTCAACAAACAAACAAACTAA
1 AAACTAATAAACTAATTTTTTATATATAATATAACTTCAACAAACAAACAAACTAA
350049 TATAAATTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
57 34 0.71
58 11 0.23
59 3 0.06
ACGTcount: A:0.50, C:0.14, G:0.01, T:0.35
Consensus pattern (57 bp):
AAACTAATAAACTAATTTTTTATATATAATATAACTTCAACAAACAAACAAACTAAA
Done.