Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004846.1 Hibiscus syriacus cultivar Beakdansim tig00010927_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: 1467214
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:633101 original size:22 final size:22
Alignment explanation
Indices: 633049--633102 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
633039 GGCCTACAAA
633049 AATAATAA-AATAAAAAATATT
1 AATAATAATAATAAAAAATATT
* *
633070 AATAACAATAATAAGAAATATAT
1 AATAATAATAATAAAAAATAT-T
633093 AAT-ATAATAA
1 AATAATAATAA
633103 AATGTTTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.25
22 17 0.61
23 4 0.14
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (22 bp):
AATAATAATAATAAAAAATATT
Found at i:633576 original size:84 final size:83
Alignment explanation
Indices: 633451--633676 Score: 260
Period size: 84 Copynumber: 2.7 Consensus size: 83
633441 CTGAATGAAA
* *
633451 TCGAACTCGAAGGTC--T-TTGACAGATAGCCCTTCTTGCCTTGAGCTGTGCTACAAATGATGGT
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGAT-GT
* *
633513 GCCTTTGAGCTGAGTGGAG
65 GCCTTGGAGCTGAGCGGAG
* * * **
633532 TCGAGCTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGATGTG
* *
633597 TCTTGGAGCTGAGCGTAG
66 CCTTGGAGCTGAGCGGAG
* * * * * *
633615 TCGAACTCAAAGGTCTTTTGTTAACAAATAACCCTTTTTGCCTTGAGCTATGTTGCAAATGA
1 TCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGA
633677 ACACGATATC
Statistics
Matches: 121, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
81 14 0.12
83 31 0.26
84 76 0.63
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (83 bp):
TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGATGTG
CCTTGGAGCTGAGCGGAG
Found at i:634237 original size:240 final size:246
Alignment explanation
Indices: 633845--634329 Score: 622
Period size: 240 Copynumber: 2.0 Consensus size: 246
633835 ATGACCCCCC
* * * *
633845 TTCGTTGTGAAGTTGAGTCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATATAAAGA
1 TTCGTTGTGAAGTTGAGCCTTGAATTGAATATCCTTCATCGTGAAGTTGAAATCCAAGAT----A
* * * * *
633910 TGAATGTTGCTTCGAGTTCAATATCCTTCGTATTGAAGTTAAAATTGACTCTTAATGAAACTGGG
62 TG-ATATTGCTTCGAGTCCAATATCCTTCGCAGTGAAGTTAAAATTGACTCTGAATGAAACTGGG
* * **
633975 AAGCCCCTTCGCCATAAAGTTGATCTTTGAATTGGATATCGTTTGTCGTGAAGTTGAAATCCAAT
126 AAGCCCCTTCGCCATAAAGTTGAGCTTTGAATTGGATATCATTCATCGTGAAGTTGAAATCCAAT
* *
634040 -CTA-G-AG-TTGGCACGATATCCTTCATCGTGAAGTTAAAATCGTGGATGACCCA
191 ACTATGTAGATGGGCACGATATCCTTCACCGTGAAGTTAAAATCGTGGATGACCCA
* *
634092 TTCGTTGTGAAGTTGAGCCTTGACTTGAATATCCTTCATCGTGAAGTTGAAATCCAAGCT-TG-T
1 TTCGTTGTGAAGTTGAGCCTTGAATTGAATATCCTTCATCGTGAAGTTGAAATCCAAGATATGAT
* * ** * *
634155 ATTGTTTCGAGTCCAATATCCTTCGCCGTGAAGTTGCAATTGCCTCTGAATTAAACTGGGAAGCC
66 ATTGCTTCGAGTCCAATATCCTTCGCAGTGAAGTTAAAATTGACTCTGAATGAAACTGGGAAGCC
* * * *
634220 CCTTCGTCGTGAAGTTGAGCTTTGAATTGGATATCATTCATCGTGAAGTTGAAATCCAATATTAT
131 CCTTCGCCATAAAGTTGAGCTTTGAATTGGATATCATTCATCGTGAAGTTGAAATCCAATACTAT
* *
634285 GTAGATGGGCACGATATCCTTCGCCGTGAAGTTGAAATCGTGGAT
196 GTAGATGGGCACGATATCCTTCACCGTGAAGTTAAAATCGTGGAT
634330 TTGTGGGCAC
Statistics
Matches: 205, Mismatches: 29, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
240 108 0.53
241 2 0.01
242 3 0.01
243 2 0.01
244 36 0.18
247 54 0.26
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.33
Consensus pattern (246 bp):
TTCGTTGTGAAGTTGAGCCTTGAATTGAATATCCTTCATCGTGAAGTTGAAATCCAAGATATGAT
ATTGCTTCGAGTCCAATATCCTTCGCAGTGAAGTTAAAATTGACTCTGAATGAAACTGGGAAGCC
CCTTCGCCATAAAGTTGAGCTTTGAATTGGATATCATTCATCGTGAAGTTGAAATCCAATACTAT
GTAGATGGGCACGATATCCTTCACCGTGAAGTTAAAATCGTGGATGACCCA
Found at i:634361 original size:43 final size:43
Alignment explanation
Indices: 634290--634372 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
634280 ATTATGTAGA
*
634290 TGGGCACGATATCCTTCGCCGTGAAGTTGAAATCGTGGATTTG
1 TGGGCACGATATCCTCCGCCGTGAAGTTGAAATCGTGGATTTG
** *
634333 TGGGCACGATATCCTCCGTTGTGGAGTTGAAATCGTGGAT
1 TGGGCACGATATCCTCCGCCGTGAAGTTGAAATCGTGGAT
634373 GGCCCCTTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.30
Consensus pattern (43 bp):
TGGGCACGATATCCTCCGCCGTGAAGTTGAAATCGTGGATTTG
Found at i:634541 original size:59 final size:55
Alignment explanation
Indices: 634406--634545 Score: 131
Period size: 55 Copynumber: 2.5 Consensus size: 55
634396 CCTTGAATTG
* * * * * *
634406 AATATCCTCCGTTGTGAAGTTGAAATCCAATCTTGAGAAAGTTGGTTTTGAGTTG
1 AATATCCTTCGATGTGAAGTTGAAATCCAATCTTCAAAAAATTGGTTTTGAGTTC
* * *
634461 GATATCC-TCCATCGTGGAGTTGAAATCCAAT-TTCAAACAAATTGTGTCATTTCGAGTTC
1 AATATCCTTCGAT-GTGAAGTTGAAATCCAATCTTCAAA-AAATTG-GT--TTT-GAGTTC
634520 AATATCCTTCGATGTGAAGTTGAAAT
1 AATATCCTTCGATGTGAAGTTGAAAT
634546 TGACTCTGAA
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
54 6 0.09
55 28 0.42
56 2 0.03
58 3 0.05
59 23 0.35
60 4 0.06
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (55 bp):
AATATCCTTCGATGTGAAGTTGAAATCCAATCTTCAAAAAATTGGTTTTGAGTTC
Found at i:636204 original size:18 final size:19
Alignment explanation
Indices: 636168--636206 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
636158 TATTAAATTT
*
636168 TATATTATTTTTATTATAAA
1 TATAATATTTTTA-TATAAA
636188 TATAATATTTTTA-ATAAA
1 TATAATATTTTTATATAAA
636206 T
1 T
636207 TATCAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATAATATTTTTATATAAA
Found at i:637437 original size:21 final size:21
Alignment explanation
Indices: 637386--637438 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
637376 ATTATGACTA
637386 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
637407 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
637428 TCGCAATGCGA
1 TCGCAATGCGA
637439 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:637453 original size:20 final size:21
Alignment explanation
Indices: 637428--637479 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
637418 TTTTCCCAAT
*
637428 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
637448 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
637469 TCGCAATGCGA
1 TCGCAATGCGA
637480 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:637458 original size:41 final size:41
Alignment explanation
Indices: 637413--637583 Score: 132
Period size: 41 Copynumber: 4.2 Consensus size: 41
637403 AATTTCGCGT
*
637413 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
637454 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * **
637495 TGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATAAGTAAATCGCAA
* *
637536 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
*
637577 CGCGATT
1 TGCGATT
637584 AAGTAAATCG
Statistics
Matches: 95, Mismatches: 29, Indels: 12
0.70 0.21 0.09
Matches are distributed among these distances:
39 2 0.02
40 8 0.08
41 83 0.87
43 1 0.01
44 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:637523 original size:21 final size:21
Alignment explanation
Indices: 637489--637561 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
637479 ATACTGACTA
* *
637489 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
637510 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
637530 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
637551 TCGCAATGCGA
1 TCGCAATGCGA
637562 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:637576 original size:20 final size:20
Alignment explanation
Indices: 637551--637662 Score: 118
Period size: 20 Copynumber: 5.5 Consensus size: 20
637541 TTTTCATAAT
637551 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
637571 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
637591 TCGTAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
637612 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
637632 TAGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
637652 TCGCAATGCGA
1 TCGCAATGCGA
637663 TTTACATAGC
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
19 3 0.04
20 55 0.73
21 17 0.23
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:637613 original size:41 final size:41
Alignment explanation
Indices: 637553--637644 Score: 114
Period size: 41 Copynumber: 2.3 Consensus size: 41
637543 TTCATAATTC
* * *
637553 GCAATGCGAA-TACGTAAATCGCAACGCGATTAAGTAAATC
1 GCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAATA
* * * *
637593 GTAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAATA
1 GCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAATA
637634 GCAATGCGAAT
1 GCAATGCGAAT
637645 CTTACTATCG
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 9 0.21
41 34 0.79
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (41 bp):
GCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAATA
Found at i:637929 original size:27 final size:27
Alignment explanation
Indices: 637872--637924 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
637862 CATCGCCGGC
* *
637872 GAAATCCCTCACAACCATTCACAGTCA
1 GAAATCCCTCACAACCATTCAAAATCA
*
637899 GAAATCCCTCACAATCATTCAGAAAT
1 GAAATCCCTCACAACCATTCA-AAAT
637925 GGAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.40, C:0.32, G:0.08, T:0.21
Consensus pattern (27 bp):
GAAATCCCTCACAACCATTCAAAATCA
Found at i:638289 original size:20 final size:20
Alignment explanation
Indices: 638237--638295 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
638227 GTTGCGATTC
** *
638237 TCTCGTTGCGATAGTCATTT
1 TCTCGTTGCGATTCTCATTA
*
638257 TCGCGTTGCGATTCTCATTA
1 TCTCGTTGCGATTCTCATTA
*
638277 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTCTCATT
638296 TCAACCAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (20 bp):
TCTCGTTGCGATTCTCATTA
Found at i:640453 original size:21 final size:21
Alignment explanation
Indices: 640429--640495 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
640419 TCATTCCTCG
640429 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
640450 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
640471 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
640492 AGAG
1 AGAG
640496 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:640453 original size:42 final size:42
Alignment explanation
Indices: 640377--640495 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
640367 GACTCGCCTG
* * * *
640377 TCATCCCTC-AAGA-GTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCAT-CCTCGAAGAGGTCC-CTCCCACCATTCAAGAGGCCACTA
* *
640419 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTCGAAGAGGT-CCCTCCCACCATTCAAGAGGCCACTA
* *
640461 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAG
640496 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
41 4 0.06
42 54 0.86
43 5 0.08
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAGGCCACTA
Found at i:641871 original size:14 final size:14
Alignment explanation
Indices: 641852--641887 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
641842 ATTGTTTAAT
641852 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
641866 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
641880 TGATTTGT
1 TGATTTGT
641888 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:642036 original size:33 final size:32
Alignment explanation
Indices: 641994--642125 Score: 149
Period size: 33 Copynumber: 4.0 Consensus size: 32
641984 AAAAAGTACT
*
641994 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGA-A
*
642027 ATCGCAATGCGAAATGAAAATCGCAACGCGAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAA
* * * *
642059 TTTTGCAATACGAAATGAAAATTGCAACGAGAAA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAG-AA
* *
642093 ATCGCAACGCGAAACT-AAAATCGCAACGCGAA
1 ATCGCAATGCGAAA-TGAAAATCGCAACGAGAA
642125 A
1 A
642126 CTAAATTCGC
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
32 4 0.05
33 76 0.92
34 3 0.04
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.15
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:642050 original size:19 final size:19
Alignment explanation
Indices: 641994--642058 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
641984 AAAAAGTACT
641994 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
642013 ATTGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
642027 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
642046 ATCGCAACGCGAA
1 ATCGCAATGCGAA
642059 TTTTGCAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 9 0.25
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:642105 original size:66 final size:66
Alignment explanation
Indices: 641997--642124 Score: 213
Period size: 66 Copynumber: 1.9 Consensus size: 66
641987 AAGTACTATC
* * *
641997 GCAATGCGAAATGAAAATTGCAACGAGAGAATCGCAATGCGAAA-TGAAAATCGCAACGCGAATT
1 GCAATACGAAATGAAAATTGCAACGAGAAAATCGCAACGCGAAACT-AAAATCGCAACGCGAATT
642061 TT
65 TT
642063 GCAATACGAAATGAAAATTGCAACGAGAAAATCGCAACGCGAAACTAAAATCGCAACGCGAA
1 GCAATACGAAATGAAAATTGCAACGAGAAAATCGCAACGCGAAACTAAAATCGCAACGCGAA
642125 ACTAAATTCG
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 57 0.98
67 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (66 bp):
GCAATACGAAATGAAAATTGCAACGAGAAAATCGCAACGCGAAACTAAAATCGCAACGCGAATTT
T
Found at i:642142 original size:19 final size:19
Alignment explanation
Indices: 642090--642135 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
642080 TTGCAACGAG
642090 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
642109 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
*
642128 AAATTCGC
1 AAAATCGC
642136 TTTGCGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACT
Found at i:642179 original size:33 final size:31
Alignment explanation
Indices: 642130--642294 Score: 222
Period size: 33 Copynumber: 5.1 Consensus size: 31
642120 GCGAAACTAA
*
642130 ATTCGCTTTGCGATTTTCATTTCGCATTGCG
1 ATTCGCGTTGCGATTTTCATTTCGCATTGCG
*
642161 ATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
1 ATT--CGCGTTGCGATTTTCATTTCGCATTGCG
642194 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
1 --ATTCGCGTTGCGATTTTCATTTCGCATTGCG
*
642227 AAATTCGCGTTGCAATTTTCATTTCGCATTGCG
1 --ATTCGCGTTGCGATTTTCATTTCGCATTGCG
*
642260 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCG
1 A-T-TCGCGTTGCGATTTTCATTTCGCATTGCG
642293 AT
1 AT
642295 AGTAATTTCC
Statistics
Matches: 122, Mismatches: 6, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
31 4 0.03
32 2 0.02
33 113 0.93
35 3 0.02
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (31 bp):
ATTCGCGTTGCGATTTTCATTTCGCATTGCG
Found at i:644603 original size:12 final size:12
Alignment explanation
Indices: 644586--644622 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
644576 TCTTCGGGGA
644586 CTTTTTCTTCTT
1 CTTTTTCTTCTT
644598 CTTTTTCTTCTT
1 CTTTTTCTTCTT
644610 CTTTTTCTTCTT
1 CTTTTTCTTCTT
644622 C
1 C
644623 AGGATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:645660 original size:20 final size:21
Alignment explanation
Indices: 645635--645686 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
645625 TTTTCCTAAT
*
645635 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
645655 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
645676 TCGCAATGCGA
1 TCGCAATGCGA
645687 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:645760 original size:20 final size:20
Alignment explanation
Indices: 645671--645762 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
645661 TGCGAATTTG
* *
645671 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
645691 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
645711 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
645732 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
645752 GAAAATCGCAA
1 GAAAATCGCAA
645763 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:646059 original size:20 final size:20
Alignment explanation
Indices: 645976--646063 Score: 79
Period size: 20 Copynumber: 4.4 Consensus size: 20
645966 CAACGGGGAA
645976 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* *
645996 ATTGCAACGCAAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ** ***
646016 ATCAAAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
646036 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
646056 ATCGCAAC
1 ATCGCAAC
646064 TAGAAAATCG
Statistics
Matches: 48, Mismatches: 18, Indels: 4
0.69 0.26 0.06
Matches are distributed among these distances:
19 5 0.10
20 38 0.79
21 5 0.10
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:646131 original size:19 final size:19
Alignment explanation
Indices: 646090--646157 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
646080 GAAAAGAAAA
646090 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
646106 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
646123 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
646142 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
646158 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.22
16 3 0.07
17 3 0.07
19 29 0.64
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:647773 original size:20 final size:20
Alignment explanation
Indices: 647684--647775 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
647674 TGCGAATTTG
* *
647684 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
647704 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
647724 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
647745 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
647765 GAAAATCGCAA
1 GAAAATCGCAA
647776 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:648072 original size:20 final size:20
Alignment explanation
Indices: 647989--648076 Score: 79
Period size: 20 Copynumber: 4.4 Consensus size: 20
647979 CAACGGGGAA
647989 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* *
648009 ATTGCAACGCAAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ** ***
648029 ATCAAAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
648049 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
648069 ATCGCAAC
1 ATCGCAAC
648077 TAGAAAATCG
Statistics
Matches: 48, Mismatches: 18, Indels: 4
0.69 0.26 0.06
Matches are distributed among these distances:
19 5 0.10
20 38 0.79
21 5 0.10
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:648144 original size:19 final size:19
Alignment explanation
Indices: 648103--648170 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
648093 GAAAAGAAAA
648103 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
648119 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
648136 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
648155 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
648171 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.22
16 3 0.07
17 3 0.07
19 29 0.64
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:649785 original size:20 final size:20
Alignment explanation
Indices: 649696--649787 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
649686 TGCGAATTTG
* *
649696 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
649716 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
649736 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
649757 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
649777 GAAAATCGCAA
1 GAAAATCGCAA
649788 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:650026 original size:20 final size:20
Alignment explanation
Indices: 650001--650096 Score: 115
Period size: 20 Copynumber: 4.8 Consensus size: 20
649991 CAACGGGGAA
*
650001 ATCGCAAGGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
650021 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** *
650041 ATCGCAATTCG-AAATGAAG-A
1 ATCGCAACGCGAAAATG--GCT
650061 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
650081 ATCGCAACTCGAAAAT
1 ATCGCAACGCGAAAAT
650097 CGCAATGCGA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
19 6 0.09
20 52 0.81
21 6 0.09
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:650156 original size:19 final size:19
Alignment explanation
Indices: 650115--650182 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
650105 GAAATGAAAA
650115 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
650131 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
650148 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
650167 TCGCATTGCAATTTTC
1 TCGCATTGCGATTTTC
650183 TCGTTGCGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
14 10 0.23
16 3 0.07
17 3 0.07
19 28 0.64
ACGTcount: A:0.15, C:0.21, G:0.16, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:651799 original size:20 final size:20
Alignment explanation
Indices: 651710--651801 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
651700 TGCGAATTTG
* *
651710 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
651730 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
651750 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
651771 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
651791 GAAAATCGCAA
1 GAAAATCGCAA
651802 TCATCTTTAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:652110 original size:20 final size:20
Alignment explanation
Indices: 652015--652102 Score: 117
Period size: 20 Copynumber: 4.4 Consensus size: 20
652005 CAACGGGGAA
652015 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
652035 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** *
652055 ATCGCAATTCG-AAATGAAG-A
1 ATCGCAACGCGAAAATG--GCT
652075 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
652095 ATCGCAAC
1 ATCGCAAC
652103 TAGAAAATCG
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
19 6 0.10
20 46 0.79
21 6 0.10
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:652170 original size:19 final size:19
Alignment explanation
Indices: 652129--652196 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
652119 GAAATGAAAA
652129 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
652145 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
652162 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
652181 TCGCATTGCAATTTTC
1 TCGCATTGCGATTTTC
652197 TCGTTGCGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
14 10 0.23
16 3 0.07
17 3 0.07
19 28 0.64
ACGTcount: A:0.15, C:0.21, G:0.16, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:653813 original size:20 final size:20
Alignment explanation
Indices: 653724--653815 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
653714 TGCGAATTTG
* *
653724 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
653744 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
653764 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
653785 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
653805 GAAAATCGCAA
1 GAAAATCGCAA
653816 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:654123 original size:20 final size:20
Alignment explanation
Indices: 654028--654115 Score: 117
Period size: 20 Copynumber: 4.4 Consensus size: 20
654018 CAACGGGGAA
654028 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
654048 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** *
654068 ATCGCAATTCG-AAATGAAG-A
1 ATCGCAACGCGAAAATG--GCT
654088 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
654108 ATCGCAAC
1 ATCGCAAC
654116 TAGAAAATCG
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
19 6 0.10
20 46 0.79
21 6 0.10
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:654183 original size:19 final size:19
Alignment explanation
Indices: 654142--654209 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
654132 GAAATGAAAA
654142 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
654158 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
654175 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
654194 TCGCATTGCAATTTTC
1 TCGCATTGCGATTTTC
654210 TCGTTGCGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
14 10 0.23
16 3 0.07
17 3 0.07
19 28 0.64
ACGTcount: A:0.15, C:0.21, G:0.16, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:655743 original size:21 final size:21
Alignment explanation
Indices: 655717--655770 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
655707 GCGAATAAGT
655717 AAATCGCAATGCAAATTTGGA
1 AAATCGCAATGCAAATTTGGA
655738 AAATCGCAATGCAAATTTGGA
1 AAATCGCAATGCAAATTTGGA
655759 AAATCGCAATGC
1 AAATCGCAATGC
655771 GATACTGACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.22
Consensus pattern (21 bp):
AAATCGCAATGCAAATTTGGA
Found at i:655846 original size:20 final size:20
Alignment explanation
Indices: 655757--655848 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
655747 TGCAAATTTG
* *
655757 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
655777 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
655797 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
655818 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
655838 GAAAATCGCAA
1 GAAAATCGCAA
655849 TCATCTTTAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:656125 original size:20 final size:20
Alignment explanation
Indices: 656062--656129 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
656052 CAACGGGGAA
656062 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* ** ***
656082 ATCACAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
656102 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
656122 ATCGCAAC
1 ATCGCAAC
656130 TAGAAAATCG
Statistics
Matches: 34, Mismatches: 12, Indels: 4
0.68 0.24 0.08
Matches are distributed among these distances:
19 5 0.15
20 24 0.71
21 5 0.15
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:656197 original size:19 final size:19
Alignment explanation
Indices: 656175--656223 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
656165 AATTTTCTCG
*
656175 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
656194 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
656213 TTGCGATTTTC
1 TTGCGATTTTC
656224 TCATTGCGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.14, C:0.18, G:0.16, T:0.51
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:657755 original size:20 final size:20
Alignment explanation
Indices: 657732--657800 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
657722 ATTGCAATGC
657732 GATACTGACTATCGCAACGA
1 GATACTGACTATCGCAACGA
* *
657752 GATAAT-ACAAAATCGCAACGA
1 GATACTGAC--TATCGCAACGA
* *
657773 GATTCTGACTTTCGCAACGA
1 GATACTGACTATCGCAACGA
*
657793 GATTCTGA
1 GATACTGA
657801 AAATCGCAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 22 0.55
21 14 0.35
22 2 0.05
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (20 bp):
GATACTGACTATCGCAACGA
Found at i:657807 original size:20 final size:20
Alignment explanation
Indices: 657760--657809 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
657750 GAGATAATAC
657760 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
657780 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
657800 AAAATCGCAA
1 AAAATCGCAA
657810 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:658158 original size:19 final size:19
Alignment explanation
Indices: 658136--658184 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
658126 GATTTTCTCG
*
658136 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
658155 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
658174 TTGCGATTTTC
1 TTGCGATTTTC
658185 TCGTTGCGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.14, C:0.18, G:0.16, T:0.51
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:659747 original size:20 final size:20
Alignment explanation
Indices: 659724--659792 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
659714 ATTGCAATGC
659724 GATACTGACTATCGCAACGA
1 GATACTGACTATCGCAACGA
* *
659744 GATAAT-ACAAAATCGCAACGA
1 GATACTGAC--TATCGCAACGA
* *
659765 GATTCTGACTTTCGCAACGA
1 GATACTGACTATCGCAACGA
*
659785 GATTCTGA
1 GATACTGA
659793 AAATCGCAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 22 0.55
21 14 0.35
22 2 0.05
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (20 bp):
GATACTGACTATCGCAACGA
Found at i:659799 original size:20 final size:20
Alignment explanation
Indices: 659752--659801 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
659742 GAGATAATAC
659752 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
659772 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
659792 AAAATCGCAA
1 AAAATCGCAA
659802 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:660040 original size:20 final size:20
Alignment explanation
Indices: 660015--660102 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 20
660005 CAACGGGGAA
*
660015 ATCGCAACACGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
660035 ATCGCAACGCAAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
660055 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
*
660075 ATCGCAACGTGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
660095 ATCGCAAC
1 ATCGCAAC
660103 TAGAAAATCG
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
19 5 0.10
20 42 0.81
21 5 0.10
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:660059 original size:40 final size:41
Alignment explanation
Indices: 660015--660110 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 41
660005 CAACGGGGAA
***
660015 ATCGCAACACGAAAATG-GCTATCGCAACGCAAAAATGGCT
1 ATCGCAACACGAAAATGAAAAATCGCAACGCAAAAATGGCT
** **
660055 ATCGCAATTCG-AAATGAAAAATCGCAACGTGAAAATGGCT
1 ATCGCAACACGAAAATGAAAAATCGCAACGCAAAAATGGCT
660095 ATCGCAACTA-GAAAAT
1 ATCGCAAC-ACGAAAAT
660111 CGCAATGCGA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
39 5 0.11
40 35 0.80
41 4 0.09
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.18
Consensus pattern (41 bp):
ATCGCAACACGAAAATGAAAAATCGCAACGCAAAAATGGCT
Found at i:660170 original size:19 final size:19
Alignment explanation
Indices: 660129--660194 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
660119 GAAATGAAAA
660129 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
660145 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
660162 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
660181 TCGCATTGCGATTT
1 TCGCATTGCGATTT
660195 CTCGTTGCGA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.23
16 3 0.07
17 3 0.07
19 27 0.63
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:660351 original size:14 final size:14
Alignment explanation
Indices: 660332--660369 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
660322 CACCAAATAA
660332 ACAAATCAATATTT
1 ACAAATCAATATTT
* *
660346 ACAAATCATTTTTT
1 ACAAATCAATATTT
660360 ACAAATCAAT
1 ACAAATCAAT
660370 TAAACAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (14 bp):
ACAAATCAATATTT
Found at i:661603 original size:19 final size:19
Alignment explanation
Indices: 661570--661704 Score: 104
Period size: 19 Copynumber: 7.3 Consensus size: 19
661560 AAAAATCAAC
*
661570 TGCGGTTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
661589 TGCGATTTGT-GTTTCGCGT
1 TGCGATTT-TCATTTCGCGT
*
661608 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCGT
*
661627 TGCGA-TTT--TGT--CGT
1 TGCGATTTTCATTTCGCGT
*
661641 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCGT
**
661660 TGCGA-TAGCTATTTCCGCGT
1 TGCGATTTTC-ATTT-CGCGT
**
661680 TGCGATAGTCATTTTCGCGT
1 TGCGATTTTCA-TTTCGCGT
661700 TGCGA
1 TGCGA
661705 AAGTAAGTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
14 7 0.08
15 3 0.03
16 2 0.02
17 2 0.02
18 6 0.07
19 46 0.51
20 21 0.23
21 4 0.04
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.44
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:661647 original size:33 final size:36
Alignment explanation
Indices: 661570--661665 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 36
661560 AAAAATCAAC
* *
661570 TGCGGTTTTCATTTCGCGTTGCGATTTGTGTTTCGCGT
1 TGCGATTTTCATTTCGCATTGCGATTTGTG-TTC-CGT
661608 TGCGATTTTCATTTCGCATTGCGATTT-TG-T-CGT
1 TGCGATTTTCATTTCGCATTGCGATTTGTGTTCCGT
661641 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGAT
661666 AGCTATTTCC
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
33 28 0.50
35 1 0.02
37 2 0.04
38 25 0.45
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (36 bp):
TGCGATTTTCATTTCGCATTGCGATTTGTGTTCCGT
Found at i:661684 original size:20 final size:20
Alignment explanation
Indices: 661638--661704 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
661628 GCGATTTTGT
**
661638 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
661657 CATTGCGATAG-CTATTTCCG
1 CGTTGCGATAGTC-ATTTCCG
*
661677 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
661697 CGTTGCGA
1 CGTTGCGA
661705 AAGTAAGTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.03
19 12 0.30
20 26 0.65
21 1 0.03
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:661715 original size:20 final size:20
Alignment explanation
Indices: 661675--661730 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
661665 TAGCTATTTC
* * *
661675 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
661695 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
661715 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
661731 ACTATTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:662037 original size:19 final size:20
Alignment explanation
Indices: 662015--662058 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
662005 TTGCGATTTT
*
662015 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCAATAGC
* *
662034 CATTTCCGCGTTGCAATAGT
1 CATTTCCGCATTGCAATAGC
662054 CATTT
1 CATTT
662059 TCACGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCAATAGC
Found at i:662609 original size:18 final size:18
Alignment explanation
Indices: 662586--662633 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
662576 CGGGTCGATC
662586 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
662604 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
662622 AGGTGATGGCTC
1 AGGTGATGGCTC
662634 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:663998 original size:20 final size:20
Alignment explanation
Indices: 663950--664008 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
663940 AATAGTTTCT
* *
663950 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
663970 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
663990 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
664009 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:664289 original size:20 final size:21
Alignment explanation
Indices: 664264--664313 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
664254 CTCTGAGAGA
664264 TGGAGAT-AGACGGATTTCGC
1 TGGAGATGAGACGGATTTCGC
*
664284 TGGAGATGGGGACGGATTTCG-
1 TGGAGAT-GAGACGGATTTCGC
664305 TCGGAGATG
1 T-GGAGATG
664314 GGTGAGAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 7 0.27
21 2 0.08
22 17 0.65
ACGTcount: A:0.22, C:0.12, G:0.42, T:0.24
Consensus pattern (21 bp):
TGGAGATGAGACGGATTTCGC
Found at i:664300 original size:22 final size:22
Alignment explanation
Indices: 664272--664315 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
664262 GATGGAGATA
664272 GACGGATTTCG-CTGGAGATGGG
1 GACGGATTTCGTC-GGAGATGGG
664294 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
664316 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:664533 original size:20 final size:20
Alignment explanation
Indices: 664508--664574 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
664498 GTATTATCTC
*
664508 GTTGCGAAAGTCAGTATTGA
1 GTTGCGAAAGTCAGTATCGA
* *
664528 GTTGCGAAATTAAGTATCGA
1 GTTGCGAAAGTCAGTATCGA
*
664548 GTTGCGAAAGTCAGTATCGC
1 GTTGCGAAAGTCAGTATCGA
664568 GTTGCGA
1 GTTGCGA
664575 TTTTGTATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.28
Consensus pattern (20 bp):
GTTGCGAAAGTCAGTATCGA
Found at i:664601 original size:41 final size:41
Alignment explanation
Indices: 664482--664619 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
664472 CGCTTTGAAA
* *
664482 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** * * *
664523 ATTG-AGTTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGT
1 ATCGCA-TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* *
664563 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
664604 ACCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
664620 CCAAATTCGC
Statistics
Matches: 76, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
40 32 0.42
41 44 0.58
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:664630 original size:41 final size:41
Alignment explanation
Indices: 664542--664637 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
664532 CGAAATTAAG
* * * * ** *
664542 TATCGAGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTACCGCATTGCGATTTTCAAA
664583 TATCGCGTTGCGATAGTCAGTACCGCATTGCGATTTTCCAAA
1 TATCGCGTTGCGATAGTCAGTACCGCATTGCGATTTT-CAAA
664625 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
664638 TTTCTTATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTACCGCATTGCGATTTTCAAA
Found at i:664649 original size:20 final size:21
Alignment explanation
Indices: 664606--664656 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
664596 TAGTCAGTAC
664606 CGCATTGCGATTTTCCAAATT
1 CGCATTGCGATTTTCCAAATT
* **
664627 CGCGTTGCGATTTT-CTTATT
1 CGCATTGCGATTTTCCAAATT
664647 CGCATTGCGA
1 CGCATTGCGA
664657 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.39
Consensus pattern (21 bp):
CGCATTGCGATTTTCCAAATT
Found at i:664698 original size:21 final size:22
Alignment explanation
Indices: 664646--664698 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
664636 ATTTTCTTAT
664646 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
664667 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
664688 TCGCATTGCGA
1 TCGCATTGCGA
664699 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:665140 original size:22 final size:24
Alignment explanation
Indices: 665092--665145 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
665082 ATAATTTTTT
*
665092 ATATTTT-TATTATAATTTAAATCA
1 ATATTTTATATTAT-ATTTAAATAA
665116 ATATTTTATATTAT-TTT-AATAA
1 ATATTTTATATTATATTTAAATAA
*
665138 ATAATTTA
1 ATATTTTA
665146 AAGATCATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 11 0.41
23 3 0.11
24 7 0.26
25 6 0.22
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
ATATTTTATATTATATTTAAATAA
Found at i:680681 original size:23 final size:24
Alignment explanation
Indices: 680655--680699 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
680645 CAACTCGACT
* *
680655 GAGTTAACTCGTTAACT-TTGATC
1 GAGTCAACCCGTTAACTGTTGATC
*
680678 GAGTCAACCCGTTGACTGTTGA
1 GAGTCAACCCGTTAACTGTTGA
680700 CTTTGACCGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (24 bp):
GAGTCAACCCGTTAACTGTTGATC
Found at i:682030 original size:23 final size:23
Alignment explanation
Indices: 681985--682060 Score: 111
Period size: 23 Copynumber: 3.4 Consensus size: 23
681975 GTATCGAACA
*
681985 ACCACATAGGTATGTCACGAAGG
1 ACCACATAGGTATGTCCCGAAGG
* *
682008 ACCACATAGGTATATCCCAAAGG
1 ACCACATAGGTATGTCCCGAAGG
682031 ACCACATA--TATGTCCCGAAGG
1 ACCACATAGGTATGTCCCGAAGG
682052 ACCACATAG
1 ACCACATAG
682061 AAATCTTCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
21 19 0.40
23 28 0.60
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (23 bp):
ACCACATAGGTATGTCCCGAAGG
Found at i:682051 original size:21 final size:21
Alignment explanation
Indices: 681985--682164 Score: 121
Period size: 21 Copynumber: 8.4 Consensus size: 21
681975 GTATCGAACA
* *
681985 ACCACATAGGTATGTCACGAAGG
1 ACCACATA--TATGTCCCAAAGG
*
682008 ACCACATAGGTATATCCCAAAGG
1 ACCACATA--TATGTCCCAAAGG
*
682031 ACCACATATATGTCCCGAAGG
1 ACCACATATATGTCCCAAAGG
* * * **
682052 ACCACATAGAAATCTTCTTAAGG
1 ACCACAT--ATATGTCCCAAAGG
*
682075 ACCATATATAT-T-CCAAAGG
1 ACCACATATATGTCCCAAAGG
* * * *
682094 ACCAAATATGTGTCTCAAAGA
1 ACCACATATATGTCCCAAAGG
*
682115 ACCACATATATGTTCCAAAGG
1 ACCACATATATGTCCCAAAGG
** **
682136 ATTACATATATGTCCTGAAGG
1 ACCACATATATGTCCCAAAGG
682157 ACCACATA
1 ACCACATA
682165 GAACCCTCAA
Statistics
Matches: 123, Mismatches: 30, Indels: 10
0.75 0.18 0.06
Matches are distributed among these distances:
19 14 0.11
20 2 0.02
21 64 0.52
23 43 0.35
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (21 bp):
ACCACATATATGTCCCAAAGG
Found at i:682574 original size:16 final size:18
Alignment explanation
Indices: 682548--682580 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
682538 CATATTTCAT
682548 ATATGCATATAA-TTATC
1 ATATGCATATAACTTATC
682565 ATAT-CATATAACTTAT
1 ATATGCATATAACTTAT
682581 GTTTTATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (18 bp):
ATATGCATATAACTTATC
Found at i:685916 original size:23 final size:23
Alignment explanation
Indices: 685886--685929 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
685876 TCAACATAGA
* *
685886 ATGTCCCGAATGACCATATAGGT
1 ATGTCCCGAAGGACCACATAGGT
685909 ATGTCCCGAAGGACCACATAG
1 ATGTCCCGAAGGACCACATAG
685930 AAATATCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (23 bp):
ATGTCCCGAAGGACCACATAGGT
Found at i:689260 original size:84 final size:84
Alignment explanation
Indices: 688986--689623 Score: 510
Period size: 84 Copynumber: 7.6 Consensus size: 84
688976 TATTGGGTAG
* * * * **
688986 GCTCCAATGCATATCATTTGCAGCATAACTTAAGTCGAGAATGGTTATCTACCAACC-AAAGACC
1 GCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGTC-ACCAAAAGACC
*
689050 TTCGAGTTCGACTAGGCTCA
65 TTCGAGTTCGACTACGCTCA
* * * *
689070 GCTCTAAGGCATATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATC--T-ACC-AAAGAACC
1 GCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGTCACCAAAAG-ACC
* * * *
689131 -TCAAGTTTGATTACACTCA
65 TTCGAGTTCGACTACGCTCA
* * * * *** * *
689150 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGATAGAAGGGTTATCTGTCACCAAAATACC
1 GC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGTCACCAAAAGACC
*
689215 TTCGAGTTCGACTACGCTAA
65 TTCGAGTTCGACTACGCTCA
* * * *
689235 GCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATATGCTAACC-AAAGACC
1 GCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-TCACCAAAAGACC
* *
689299 TCCGAGCTCGACTACGCTCA
65 TTCGAGTTCGACTACGCTCA
* * ** * *
689319 GATCCAAGGCACATTATTTGCATTATAGCTTAAGTCGAGAAGGGCTATCTG----CAAAAGACCC
1 GCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGTCACCAAAAGACCT
* * **
689380 TCGAGTTCAATTATACTCA
66 TCGAGTTCGACTACGCTCA
* * * * * * * *
689399 GCTTCGAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACC
1 GC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGTCACCAAAAGACC
** *
689464 TTTTAGTTCGACTATGCTCA
65 TTCGAGTTCGACTACGCTCA
* * * * *
689484 GCTCCAAGACACATCATTTGTAGCATAACTTAAGTCGAGAAGGGCTATATGCTAACC-GAAGACC
1 GCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-TCACCAAAAGACC
**
689548 TTCGAGTTCGACTATACTCA
65 TTCGAGTTCGACTACGCTCA
* * * * * * *
689568 GCT-CAGAGGCAAATCAAATTTACAGAATAGCTCAAGGCAAGAAGGGCTATCTGTCA
1 GCTCCA-AGGCACATC--ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGTCA
689624 ATAAATTGGT
Statistics
Matches: 434, Mismatches: 102, Indels: 35
0.76 0.18 0.06
Matches are distributed among these distances:
79 1 0.00
80 44 0.10
81 78 0.18
83 3 0.01
84 226 0.52
85 54 0.12
86 28 0.06
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (84 bp):
GCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGTCACCAAAAGACCT
TCGAGTTCGACTACGCTCA
Found at i:689418 original size:165 final size:167
Alignment explanation
Indices: 689242--689613 Score: 403
Period size: 165 Copynumber: 2.2 Consensus size: 167
689232 TAAGCTCCAA
* * * *
689242 GGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATATGCTAACC-AAAGACCTCCGAGC
1 GGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATATG-TAACCAAAAGACCTCCGAGC
* * ** * *
689306 TCGACTACGCTCAGATCCAAGGCACATTATTTGCATTATAGCTTAAGTCGAGAAGGGCTATCTGC
65 TCGACTACGCTCAGATCCAAGACACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATATGC
*
689371 -AA-AAGACCCTCGAGTTCAATTATACTCAGCTTCGAG
130 TAACAAGACCCTCGAGTTCAACTATACTCAGCTTCGAG
* * * * *** *
689407 GGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTTAGTT
1 GGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATATGTAACCAAAAGACCTCCGAGCT
* * *
689472 CGACTATGCTCAGCTCCAAGACACATCATTTGTAGCATAACTTAAGTCGAGAAGGGCTATATGCT
66 CGACTACGCTCAGATCCAAGACACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATATGCT
* *
689537 AACCGAAGACCTTCGAGTTCGACTATACTCAGC-TC-AG
131 AA-C-AAGACCCTCGAGTTCAACTATACTCAGCTTCGAG
* * * *
689574 AGGCAAATCAAATTTACAGAATAGCTCAAGGCAAGAAGGG
1 -GGCACATC--ATTTACAGCATAACTCAAGGCGAGAAGGG
689614 CTATCTGTCA
Statistics
Matches: 171, Mismatches: 28, Indels: 11
0.81 0.13 0.05
Matches are distributed among these distances:
164 4 0.02
165 103 0.60
166 2 0.01
167 2 0.01
168 9 0.05
169 25 0.15
170 26 0.15
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (167 bp):
GGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATATGTAACCAAAAGACCTCCGAGCT
CGACTACGCTCAGATCCAAGACACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATATGCT
AACAAGACCCTCGAGTTCAACTATACTCAGCTTCGAG
Found at i:689430 original size:249 final size:249
Alignment explanation
Indices: 688986--689619 Score: 847
Period size: 249 Copynumber: 2.5 Consensus size: 249
688976 TATTGGGTAG
* * * * *
688986 GCTCCAATGCATATCATTTGCAGCATAACTTAAGTCGAGAATGGTTATCTACCAACCAAAGACCT
1 GCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATATGCTAACCAAAGACCT
* * * * *
689051 TCGAGTTCGACTAGGCTCAGCTCTAAGGCATATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCT
66 TCGAGTTCGACTACGCTCAGATCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
* **
689116 ATCTACCAAAGAACCTCAAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACT
131 ATCTACAAAAGAACCTCAAGTTCAATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACT
*
689181 CAAGGATAGAAGGGTTATCTGTCACCAAAATACCTTCGAGTTCGACTACGCTAA
196 CAAGGATAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTAA
689235 GCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATATGCTAACCAAAGACCT
1 GCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATATGCTAACCAAAGACCT
* * * **
689300 CCGAGCTCGACTACGCTCAGATCCAAGGCACATTATTTGCATTATAGCTTAAGTCGAGAAGGGCT
66 TCGAGTTCGACTACGCTCAGATCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
* * * * *
689365 ATCTGCAAAAGACCCTCGAGTTCAATTATACTCAGCTTCGAGGGCACATCATTTACAGTATAACT
131 ATCTACAAAAGAACCTCAAGTTCAATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACT
* ** * *
689430 CAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTTAGTTCGACTATGCTCA
196 CAAGGATAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTAA
* * * * *
689484 GCTCCAAGACACATCATTTGTAGCATAACTTAAGTCGAGAAGGGCTATATGCTAACCGAAGACCT
1 GCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATATGCTAACCAAAGACCT
** * * * * * * *
689549 TCGAGTTCGACTATACTCAGCT-CAGAGGCAAATCAAATTTACAGAATAGCTCAAGGCAAGAAGG
66 TCGAGTTCGACTACGCTCAGATCCA-AGGCACATC--ATTTGCAGCATAGCTTAAGTCGAGAAGG
689613 GCTATCT
128 GCTATCT
689620 GTCAATAAAT
Statistics
Matches: 335, Mismatches: 47, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
248 2 0.01
249 304 0.91
251 29 0.09
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (249 bp):
GCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATATGCTAACCAAAGACCT
TCGAGTTCGACTACGCTCAGATCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
ATCTACAAAAGAACCTCAAGTTCAATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACT
CAAGGATAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTAA
Found at i:690077 original size:9 final size:10
Alignment explanation
Indices: 690062--690103 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
690052 GTTAAGATCT
690062 TTTATTTTTA
1 TTTATTTTTA
690072 -TTATTTTTA
1 TTTATTTTTA
*
690081 TTTATTTCATA
1 TTTATTT-TTA
690092 TTTATTTATTA
1 TTTATTT-TTA
690103 T
1 T
690104 ATCGTATCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 9 0.33
10 6 0.22
11 12 0.44
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:692288 original size:24 final size:24
Alignment explanation
Indices: 692238--692282 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
692228 TTTTCGAGGT
* *
692238 AAAACAATTA-AATATTATTTTAA
1 AAAACAATTATGATTTTATTTTAA
692261 AAAACAATTATGATTTTATTTT
1 AAAACAATTATGATTTTATTTT
692283 GGAAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (24 bp):
AAAACAATTATGATTTTATTTTAA
Found at i:696654 original size:23 final size:23
Alignment explanation
Indices: 696626--696684 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
696616 ACCCTCATGG
*
696626 GGGTATCGATACCCATTTAAAGA
1 GGGTATCGATACCCATTCAAAGA
** *
696649 GGGTATCGGCACCCATTCAAAGG
1 GGGTATCGATACCCATTCAAAGA
696672 GGGTATCGATACC
1 GGGTATCGATACC
696685 TAGCTACATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (23 bp):
GGGTATCGATACCCATTCAAAGA
Found at i:704264 original size:3 final size:3
Alignment explanation
Indices: 704256--704281 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
704246 ATGTAAATTC
704256 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
704282 TTTGGTAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:704692 original size:134 final size:131
Alignment explanation
Indices: 704472--704936 Score: 425
Period size: 129 Copynumber: 3.5 Consensus size: 131
704462 CTGGTCGTCT
* * * **
704472 AAGGGTGACACAACTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACGACTCATATGTGAT
1 AAGGGTGACACAACTCCTACATGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCATATGTGAT
* * * *
704537 GAAGAGTTATTGTCATCTTTAGGAAGGGTGATAACATGGTTCCTACGCGATGAGGACGACTGGTT
66 GAGGAG-AAATGCCATCTTTA-GAAGGGTGATAACATGGTTCCTACGCGATGAGGACGACTGGTT
704602 ATC
129 ATC
* ** * * *
704605 TAAGGGTGACACAACTCCTACATGATGACGAGGTCTGGTTAGTGGATGATAAGGTTCTTATGTGA
1 -AAGGGTGACACAACTCCTACATGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCATATGTGA
* * * * * * *
704670 TGAGGATGAAATACCATTTTTAG--GGATGATAA-ACGATTCCTACGTGATAAGGACGACTGGTT
65 TGAGGA-GAAATGCCATCTTTAGAAGGGTGATAACATGGTTCCTACGCGATGAGGACGACTGGTT
704732 ATC
129 ATC
*** * * * * *
704735 AAGGGTGACATGGCTTCTACATGATGAGGAGGTCTGGTCGGGGGATAACACGGTTCCTACGTGAT
1 AAGGGTGACACAACTCCTACATGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCATATGTGAT
** * *
704800 GAGGACGGTATGCCATCTTTAGAGATGGTGATAACATGGTTCCTACGCGTTGAGGACGACTGGTT
66 GAGGA-GAAATGCCATCTTTAGA-AGGGTGATAACATGGTTCCTACGCGATGAGGACGACTGGTT
704865 ATC
129 ATC
* ** * * * * * * * * * *
704868 AGGGGTGACACGGCTCTTACGTGATGTGGTGATATGGTCGG-GGATGATAGGGTTCCTACGTGAT
1 AAGGGTGACACAACTCCTACATGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCATATGTGAT
704932 GAGGA
66 GAGGA
704937 TGACAGGACA
Statistics
Matches: 267, Mismatches: 59, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
129 69 0.26
130 29 0.11
131 8 0.03
132 32 0.12
133 61 0.23
134 67 0.25
135 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.27
Consensus pattern (131 bp):
AAGGGTGACACAACTCCTACATGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCATATGTGAT
GAGGAGAAATGCCATCTTTAGAAGGGTGATAACATGGTTCCTACGCGATGAGGACGACTGGTTAT
C
Found at i:704998 original size:29 final size:30
Alignment explanation
Indices: 704955--705061 Score: 146
Period size: 29 Copynumber: 3.6 Consensus size: 30
704945 CATCTTTAAG
* * *
704955 GATAATGGTTTCAAGAGAAACCAACTCATT
1 GATAATGGCTTCAAGAGAAACCGACTCATA
*
704985 GATAAT-GTTTCAAGAGAAACCGACTCATA
1 GATAATGGCTTCAAGAGAAACCGACTCATA
* *
705014 GATAATGGCTTCAAGAGAAATCGACTCGTA
1 GATAATGGCTTCAAGAGAAACCGACTCATA
705044 GATAAT-GCTTCAAGAGAA
1 GATAATGGCTTCAAGAGAA
705062 GTTGTTTCAA
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
29 39 0.55
30 32 0.45
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (30 bp):
GATAATGGCTTCAAGAGAAACCGACTCATA
Found at i:705286 original size:63 final size:62
Alignment explanation
Indices: 705142--705358 Score: 256
Period size: 63 Copynumber: 3.4 Consensus size: 62
705132 CTAAAAGACT
* * * * *
705142 TTTGTCTCAAGAGAAACATACTCAAATATTTTCCTTCAAAAGAAATTGTCTCAAAAAAGACAAAA
1 TTTGTTTCCAGAGAAACATACTCAAAGATTTTTC-TCAAAAGAAATTGTCTC--AAGAGACAAAA
* *
705207 TTTTGTTTCCAAAGAAATATACTCAAAGATTTTTCTCAAAAGAAATTGTCTCAAGAGACAAAA
1 -TTTGTTTCCAGAGAAACATACTCAAAGATTTTTCTCAAAAGAAATTGTCTCAAGAGACAAAA
* * * * *
705270 CTTTGTTGCCAGAGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTCGAGAGACAAAA
1 -TTTGTTTCCAGAGAAACATACTCAAAGATTTTTCTCAAAAGAAATTGTCTCAAGAGACAAAA
* *
705333 TTTGTTTCAAGAGAAACA-ATTCAAAG
1 TTTGTTTCCAGAGAAACATACTCAAAG
705359 GATACTGATA
Statistics
Matches: 133, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
61 7 0.05
62 16 0.12
63 65 0.49
65 17 0.13
66 28 0.21
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (62 bp):
TTTGTTTCCAGAGAAACATACTCAAAGATTTTTCTCAAAAGAAATTGTCTCAAGAGACAAAA
Found at i:705493 original size:33 final size:33
Alignment explanation
Indices: 705444--705541 Score: 169
Period size: 33 Copynumber: 3.0 Consensus size: 33
705434 GAATCCCCAG
*
705444 AGATGCCCCAACATTCGATGTTGATTGCTTCAA
1 AGATGCCCCAATATTCGATGTTGATTGCTTCAA
*
705477 AGATTCCCCAATATTCGATGTTGATTGCTTCAA
1 AGATGCCCCAATATTCGATGTTGATTGCTTCAA
*
705510 AGATGCCCTAATATTCGATGTTGATTGCTTCA
1 AGATGCCCCAATATTCGATGTTGATTGCTTCA
705542 GTACTGATTC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (33 bp):
AGATGCCCCAATATTCGATGTTGATTGCTTCAA
Found at i:706605 original size:12 final size:14
Alignment explanation
Indices: 706572--706646 Score: 93
Period size: 15 Copynumber: 5.4 Consensus size: 14
706562 TCTTGTTTTC
*
706572 TTTTTTGCTCTTTG
1 TTTTTTTCTCTTTG
706586 CTTTTTTTC-CTTTG
1 -TTTTTTTCTCTTTG
706600 TTTTTTTTCTCTTTG
1 -TTTTTTTCTCTTTG
706615 TTTTTTTTCTCTTTG
1 -TTTTTTTCTCTTTG
706630 --TTTTTCTCTTTG
1 TTTTTTTCTCTTTG
706642 TTTTT
1 TTTTT
706647 ATTTTTTCCT
Statistics
Matches: 55, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
12 12 0.22
14 16 0.29
15 27 0.49
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (14 bp):
TTTTTTTCTCTTTG
Found at i:706611 original size:29 final size:30
Alignment explanation
Indices: 706572--706634 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
706562 TCTTGTTTTC
706572 TTTTTTGCTCTTTGCTTTTTTTC-CTTTGT
1 TTTTTTGCTCTTTGCTTTTTTTCTCTTTGT
* *
706601 TTTTTTTCTCTTTGTTTTTTTTCTCTTTGT
1 TTTTTTGCTCTTTGCTTTTTTTCTCTTTGT
706631 TTTT
1 TTTT
706635 CTCTTTGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (30 bp):
TTTTTTGCTCTTTGCTTTTTTTCTCTTTGT
Found at i:706618 original size:11 final size:12
Alignment explanation
Indices: 706603--706646 Score: 61
Period size: 12 Copynumber: 3.4 Consensus size: 12
706593 TCCTTTGTTT
706603 TTTTTCTCTTTG
1 TTTTTCTCTTTG
706615 TTTTTTTTCTCTTTG
1 ---TTTTTCTCTTTG
706630 TTTTTCTCTTTG
1 TTTTTCTCTTTG
706642 TTTTT
1 TTTTT
706647 ATTTTTTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 17 0.59
15 12 0.41
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.80
Consensus pattern (12 bp):
TTTTTCTCTTTG
Found at i:706618 original size:27 final size:26
Alignment explanation
Indices: 706572--706646 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 26
706562 TCTTGTTTTC
* * *
706572 TTTTTTGCTCTTTGCTTTTTTTCCTTTGT
1 TTTTTTTCTCTTTG-TTTTTTT--TCTCT
706601 TTTTTTTCTCTTTGTTTTTTTTCTCT
1 TTTTTTTCTCTTTGTTTTTTTTCTCT
706627 TTGTTTTTCTCTTTGTTTTT
1 TT-TTTTTCTCTTTGTTTTT
706647 ATTTTTTCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 5 0.12
27 17 0.40
28 7 0.17
29 13 0.31
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (26 bp):
TTTTTTTCTCTTTGTTTTTTTTCTCT
Found at i:711820 original size:24 final size:24
Alignment explanation
Indices: 711793--711838 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
711783 ACAGAAACAT
* *
711793 AAATGACCAAACTATGATTAAACC
1 AAATGACCAAACAATGACTAAACC
*
711817 AAATGCCCAAACAATGACTAAA
1 AAATGACCAAACAATGACTAAA
711839 AAAAAGGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.22, G:0.09, T:0.17
Consensus pattern (24 bp):
AAATGACCAAACAATGACTAAACC
Found at i:713251 original size:28 final size:28
Alignment explanation
Indices: 713219--713277 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
713209 AAATTTGTAA
*
713219 AATGTATATTAATAATAATAAATAATAT
1 AATGTAAATTAATAATAATAAATAATAT
713247 AATGTAAATTAATAATAATAAATAATAT
1 AATGTAAATTAATAATAATAAATAATAT
713275 AAT
1 AAT
713278 ATTTTTGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (28 bp):
AATGTAAATTAATAATAATAAATAATAT
Found at i:714443 original size:11 final size:12
Alignment explanation
Indices: 714407--714445 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
714397 AAATTTTTTC
714407 ATTAATTAAATA
1 ATTAATTAAATA
714419 ACTTAATATAAATA
1 A-TTAAT-TAAATA
714433 ATT-ATTAAATA
1 ATTAATTAAATA
714444 AT
1 AT
714446 ATTTAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 8 0.32
12 3 0.12
13 7 0.28
14 7 0.28
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (12 bp):
ATTAATTAAATA
Found at i:715903 original size:3 final size:3
Alignment explanation
Indices: 715890--715939 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
715880 CTGTAAAATT
*
715890 ATA ATTA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATT ATA AT- ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
715934 ATA ATA
1 ATA ATA
715940 TTTATTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.83
4 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:716273 original size:42 final size:40
Alignment explanation
Indices: 716130--716359 Score: 125
Period size: 42 Copynumber: 5.5 Consensus size: 40
716120 TCGATCTGAT
*
716130 CTTGCTT-CACTACTCTTTTTGTGAAGGCTTGATTGCATTG
1 CTTGCTTCCACTACTCTTTTTGTGAAGGCTTGATTG-ATTA
* * * * **
716170 CTTGTTTCCACTACTCTTCCATGGAGACCAAACTTTCGATCTGA-T-
1 CTTGCTTCCACTACTCTT--TTTGTGA--AGGC-TT-GAT-TGATTA
716215 CTTGCTT-CACTACTCTTTTTGTGAAGGCTTGATTGTATTAA
1 CTTGCTTCCACTACTCTTTTTGTGAAGGCTTGATTG-ATT-A
* * *
716256 CTTGTTTCCACTACTCTTTCATGT-ATACCGAACTTTCGATCTGA-T-
1 CTTGCTTCCACTACTCTTT-TTGTGA-A--G-GC-TT-GAT-TGATTA
716301 CTTGCTT-CACTACTCTTTTTGTGAAGGCTTGATTGCATTGA
1 CTTGCTTCCACTACTCTTTTTGTGAAGGCTTGATTG-ATT-A
*
716342 CTTGGTTCCACTACTCTT
1 CTTGCTTCCACTACTCTT
716360 CCGTGGAAAC
Statistics
Matches: 144, Mismatches: 19, Indels: 52
0.67 0.09 0.24
Matches are distributed among these distances:
37 4 0.03
38 8 0.06
39 6 0.04
40 9 0.06
41 23 0.16
42 26 0.18
43 12 0.08
44 22 0.15
45 15 0.10
46 4 0.03
47 7 0.05
48 6 0.04
49 2 0.01
ACGTcount: A:0.18, C:0.23, G:0.16, T:0.43
Consensus pattern (40 bp):
CTTGCTTCCACTACTCTTTTTGTGAAGGCTTGATTGATTA
Found at i:716315 original size:86 final size:85
Alignment explanation
Indices: 716090--716366 Score: 446
Period size: 86 Copynumber: 3.2 Consensus size: 85
716080 TAAAAAATCG
* *
716090 TTCCACTACTCTTCCGTGGAGATCGAACTTTCGATCTGATCTTGCTTCACTACTCTTTTTGTGAA
1 TTCCACTACTCTTCCATGGAGACCGAACTTTCGATCTGATCTTGCTTCACTACTCTTTTTGTGAA
*
716155 GGCTTGATTGCATTGCTTGT
66 GGCTTGATTGCATTACTTGT
*
716175 TTCCACTACTCTTCCATGGAGACCAAACTTTCGATCTGATCTTGCTTCACTACTCTTTTTGTGAA
1 TTCCACTACTCTTCCATGGAGACCGAACTTTCGATCTGATCTTGCTTCACTACTCTTTTTGTGAA
*
716240 GGCTTGATTGTATTAACTTGT
66 GGCTTGATTGCATT-ACTTGT
* * *
716261 TTCCACTACTCTTTCATGTATACCGAACTTTCGATCTGATCTTGCTTCACTACTCTTTTTGTGAA
1 TTCCACTACTCTTCCATGGAGACCGAACTTTCGATCTGATCTTGCTTCACTACTCTTTTTGTGAA
*
716326 GGCTTGATTGCATTGACTTGG
66 GGCTTGATTGCATT-ACTTGT
*
716347 TTCCACTACTCTTCCGTGGA
1 TTCCACTACTCTTCCATGGA
716367 AACCAAATTT
Statistics
Matches: 176, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
85 75 0.43
86 101 0.57
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.41
Consensus pattern (85 bp):
TTCCACTACTCTTCCATGGAGACCGAACTTTCGATCTGATCTTGCTTCACTACTCTTTTTGTGAA
GGCTTGATTGCATTACTTGT
Found at i:749385 original size:31 final size:30
Alignment explanation
Indices: 749347--749406 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
749337 AATTATCCTG
*
749347 AATATTTAATTTAATTT-AAATTAATTAAATA
1 AATATTTAA-TTAATTTGAAA-TAATAAAATA
749378 AATATTTAATTAATTTGAAATAATAAAAT
1 AATATTTAATTAATTTGAAATAATAAAAT
749407 CCTTAACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 15 0.56
31 12 0.44
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (30 bp):
AATATTTAATTAATTTGAAATAATAAAATA
Found at i:756099 original size:12 final size:12
Alignment explanation
Indices: 756082--756109 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
756072 TGAGCAAAGA
756082 TGTACAGTTTGT
1 TGTACAGTTTGT
756094 TGTACAGTTTGT
1 TGTACAGTTTGT
756106 TGTA
1 TGTA
756110 TATTACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.07, G:0.25, T:0.50
Consensus pattern (12 bp):
TGTACAGTTTGT
Found at i:762202 original size:21 final size:19
Alignment explanation
Indices: 762170--762209 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
762160 CCTAAAAGAT
*
762170 GAGCTATGGCTTTGTAATA
1 GAGCTATGGCTTTGCAATA
762189 GAGCTGATAGGCTTTGCAATA
1 GAGCT-AT-GGCTTTGCAATA
762210 AATTACTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 2 0.11
21 11 0.61
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.33
Consensus pattern (19 bp):
GAGCTATGGCTTTGCAATA
Found at i:777938 original size:60 final size:60
Alignment explanation
Indices: 777845--778078 Score: 303
Period size: 60 Copynumber: 3.9 Consensus size: 60
777835 CAAAACAGGA
* * *
777845 ATCCATAAGGACTTACCATAGACCACTAAGATCTAGGAGTCCATTATTGAAGATACATGC
1 ATCCATAAGGACTTAACGTAGACCACTAAGATCTAGGAGTCCAATATTGAAGATACATGC
* * * * * *
777905 ATCCATAAGAACTTAACGTACACCACTAAGATCTAAGAGTCCAATATCGATGATACATAC
1 ATCCATAAGGACTTAACGTAGACCACTAAGATCTAGGAGTCCAATATTGAAGATACATGC
* * *
777965 ATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATAT-AAGATAAAGGC
1 ATCCATAAGGACTTAACGTAGACCACTAAGATCTAGGAGTCCAATAT-TGAAGATACATGC
*
778025 ATCCATAAGGACTT-ACTGTAGACCACTAAGAT-TCAGGAGTCCAATATGGAAGAT
1 ATCCATAAGGACTTAAC-GTAGACCACTAAGATCT-AGGAGTCCAATATTGAAGAT
778079 TAAATAGGTA
Statistics
Matches: 150, Mismatches: 20, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
59 2 0.01
60 148 0.99
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.24
Consensus pattern (60 bp):
ATCCATAAGGACTTAACGTAGACCACTAAGATCTAGGAGTCCAATATTGAAGATACATGC
Found at i:778065 original size:120 final size:120
Alignment explanation
Indices: 777845--778071 Score: 343
Period size: 120 Copynumber: 1.9 Consensus size: 120
777835 CAAAACAGGA
* * *
777845 ATCCATAAGGACTTACCATAGACCACTAAGATCTAGGAGTCCATTATTGAAGATACATGCATCCA
1 ATCCATAAGGACTTACCATAGACCACTAAGATCTAGGAGTCCAATATTGAAGATAAAGGCATCCA
777910 TAAGAACTTAACGTACACCACTAAGATCTAAGAGTCCAATATCGATGATACATAC
66 TAAGAACTTAACGTACACCACTAAGATCTAAGAGTCCAATATCGATGATACATAC
*
777965 ATCCATAAGGACTTACCGTAGACCACTAAGATCTAGGAGTCCAATATAT-AAGATAAAGGCATCC
1 ATCCATAAGGACTTACCATAGACCACTAAGATCTAGGAGTCCAATAT-TGAAGATAAAGGCATCC
* * *
778029 ATAAGGACTT-ACTGTAGACCACTAAGAT-TCAGGAGTCCAATAT
65 ATAAGAACTTAAC-GTACACCACTAAGATCT-AAGAGTCCAATAT
778072 GGAAGATTAA
Statistics
Matches: 97, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
119 3 0.03
120 93 0.96
121 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.24
Consensus pattern (120 bp):
ATCCATAAGGACTTACCATAGACCACTAAGATCTAGGAGTCCAATATTGAAGATAAAGGCATCCA
TAAGAACTTAACGTACACCACTAAGATCTAAGAGTCCAATATCGATGATACATAC
Found at i:785368 original size:17 final size:16
Alignment explanation
Indices: 785346--785399 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
785336 ATGAATAAAT
*
785346 AATATAAATAATAATTA
1 AATATAAATAA-AATAA
*
785363 AATATATATAAAATAA
1 AATATAAATAAAATAA
785379 ACATATAAAAGTAAAATAA
1 A-ATAT-AAA-TAAAATAA
785398 AA
1 AA
785400 CTAAACAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 5 0.16
17 14 0.45
18 3 0.10
19 9 0.29
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (16 bp):
AATATAAATAAAATAA
Found at i:786765 original size:24 final size:23
Alignment explanation
Indices: 786738--786804 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 23
786728 ATTATTTATT
786738 TATTATTTTAATTAATAATAATAA
1 TATTATTTTAA-TAATAATAATAA
786762 TA-T-TTTTAATAATAATAATAA
1 TATTATTTTAATAATAATAATAA
* *
786783 TAGTAATTTTAAAAATAATAAT
1 TA-TTATTTTAATAATAATAAT
786805 TTAAGTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 14 0.37
22 6 0.16
23 1 0.03
24 17 0.45
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (23 bp):
TATTATTTTAATAATAATAATAA
Found at i:787143 original size:45 final size:45
Alignment explanation
Indices: 787094--787506 Score: 533
Period size: 45 Copynumber: 9.1 Consensus size: 45
787084 AGGTCTTATG
*
787094 GATGACCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACA
1 GATGACCCGAAGGTTTTGAAAACATCAAGCACTGAAGGACTTACA
*
787139 GATGACCCGAA-G----G-----ATCAAGCACTGAAGGGCTTACA
1 GATGACCCGAAGGTTTTGAAAACATCAAGCACTGAAGGACTTACA
*
787174 GATGACCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACA
1 GATGACCCGAAGGTTTTGAAAACATCAAGCACTGAAGGACTTACA
*
787219 GATCACCCGAAGGTTTTGAAAACATCAAGCACTGAA-GAGCTTACA
1 GATGACCCGAAGGTTTTGAAAACATCAAGCACTGAAGGA-CTTACA
* *
787264 GATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTATA
1 GATGACCCGAAGG-TTTTGAAAACATCAAGCACTGAAGGACTTACA
*
787310 GATGACCCGAAGGTTTTTTTTGAAAACATCATGCACTGAAGGACTTACA
1 GATGACCCGAAGG----TTTTGAAAACATCAAGCACTGAAGGACTTACA
*
787359 GATGACCCGAAGGTTTTTTTTTGGAAAACATCATGCACTGAAGGACTTACA
1 GATGACCCGAAGG-----TTTT-GAAAACATCAAGCACTGAAGGACTTACA
787410 GATGACCCGAAGGTTTTGAAAACATCAAGCACTGAAGGACTTACA
1 GATGACCCGAAGGTTTTGAAAACATCAAGCACTGAAGGACTTACA
*
787455 GATGACCCGAAGGTTTTTTTGAAAACATCATGCACTGAAGGACTTACA
1 GATGACCCGAAGG---TTTTGAAAACATCAAGCACTGAAGGACTTACA
787503 GATG
1 GATG
787507 TGGGAAATAA
Statistics
Matches: 339, Mismatches: 8, Indels: 39
0.88 0.02 0.10
Matches are distributed among these distances:
35 33 0.10
36 1 0.00
40 2 0.01
44 2 0.01
45 126 0.37
46 44 0.13
47 2 0.01
48 35 0.10
49 45 0.13
50 8 0.02
51 41 0.12
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (45 bp):
GATGACCCGAAGGTTTTGAAAACATCAAGCACTGAAGGACTTACA
Found at i:787163 original size:35 final size:35
Alignment explanation
Indices: 787117--787186 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
787107 TTTTGAAAAC
787117 ATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG
1 ATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG
787152 ATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG
1 ATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG
787187 TTTTGAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.23, G:0.29, T:0.14
Consensus pattern (35 bp):
ATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG
Found at i:787227 original size:80 final size:81
Alignment explanation
Indices: 787094--787322 Score: 316
Period size: 80 Copynumber: 2.7 Consensus size: 81
787084 AGGTCTTATG
787094 GATGACCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-ATCAAG
1 GATGACCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGAATCAAG
*
787158 CACTGAAGGGCTTACA
66 CACTGAAGAGCTTACA
*
787174 GATGACCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATCACCCGAAGGTTTTGAA
1 GATGACCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAA-G----G--
787239 AACATCAAGCACTGAAGAGCTTACA
59 -A-ATCAAGCACTGAAGAGCTTACA
* * *
787264 GATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTATAGATGACCCGAAGG
1 GATGACCCGAAGG-TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG
787323 TTTTTTTTGA
Statistics
Matches: 132, Mismatches: 6, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
80 55 0.42
81 1 0.01
85 1 0.01
86 1 0.01
90 35 0.27
91 39 0.30
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (81 bp):
GATGACCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGAATCAAG
CACTGAAGAGCTTACA
Found at i:787255 original size:25 final size:25
Alignment explanation
Indices: 787182--787255 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 25
787172 CAGATGACCC
787182 GAAGGTTTTGAAAACATCAAGCACT
1 GAAGGTTTTGAAAACATCAAGCACT
** * * *
787207 GAAGGGCTT--ACAGATC-A-C-CC
1 GAAGGTTTTGAAAACATCAAGCACT
787227 GAAGGTTTTGAAAACATCAAGCACT
1 GAAGGTTTTGAAAACATCAAGCACT
787252 GAAG
1 GAAG
787256 AGCTTACAGA
Statistics
Matches: 34, Mismatches: 10, Indels: 10
0.63 0.19 0.19
Matches are distributed among these distances:
20 8 0.24
21 1 0.03
22 6 0.18
23 6 0.18
24 1 0.03
25 12 0.35
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (25 bp):
GAAGGTTTTGAAAACATCAAGCACT
Found at i:787553 original size:145 final size:146
Alignment explanation
Indices: 787152--787506 Score: 466
Period size: 145 Copynumber: 2.5 Consensus size: 146
787142 GACCCGAAGG
* * *
787152 ATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG----TTTTGAAAACATCAAGCACTGAAGGG
1 ATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTTGAAAACATCATGCACTGAAGGA
* * * *
787213 CTTACAGATCACCCGAAG-GTTT--T--G-AAAACATCAAGCACTGAA-GAGCTTACAGATGACC
66 CTTACAGATGACCCGAAGATTTTACTAAGAAAAACATCATGAACTGAAGGA-CTTACAGATGACC
787271 CGAAGGTTTTTGAAAAC
130 CGAAGGTTTTTGAAAAC
* *
787288 ATCATGCACTGAAGGACTTATAGATGACCCGAAGGTTTTTTTTGAAAACATCATGCACTGAAGGA
1 ATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTTGAAAACATCATGCACTGAAGGA
* ** ** * *
787353 CTTACAGATGACCCGAAGGTTTTTTTTTGGAAAACATCATGCACTGAAGGACTTACAGATGACCC
66 CTTACAGATGACCCGAAGATTTTACTAAGAAAAACATCATGAACTGAAGGACTTACAGATGACCC
787418 GAAGG-TTTTGAAAAC
131 GAAGGTTTTTGAAAAC
787433 ATCAAGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTTTTGAAAACATCATGCACTGAAGGA
1 ATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTTGAAAACATCATGCACTGAAGGA
787497 CTTACAGATG
66 CTTACAGATG
787507 TGGGAAATAA
Statistics
Matches: 198, Mismatches: 10, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
136 32 0.16
140 41 0.21
141 3 0.02
143 1 0.01
144 39 0.20
145 44 0.22
146 36 0.18
147 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (146 bp):
ATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTTGAAAACATCATGCACTGAAGGA
CTTACAGATGACCCGAAGATTTTACTAAGAAAAACATCATGAACTGAAGGACTTACAGATGACCC
GAAGGTTTTTGAAAAC
Found at i:789572 original size:78 final size:78
Alignment explanation
Indices: 789477--789622 Score: 247
Period size: 78 Copynumber: 1.9 Consensus size: 78
789467 GTTTATTCCA
*
789477 ATTTCTGATTGAAATGGGCTTTCAAGATATTCCGCATGGATCTGTCTGAATTGGGCTTTCAAAAT
1 ATTTCTGATTGAAATGGGCTTTCAAGATATTCCGCATGGATCTGTCTGAATTGGGCCTTCAAAAT
789542 GCCTTATCATTCT
66 GCCTTATCATTCT
* * * *
789555 ATTTCTGGTTGATATGGGCTTTCAAGATGTTCCGCATGGATCTGTCTGAGTTGGGCCTTCAAAAT
1 ATTTCTGATTGAAATGGGCTTTCAAGATATTCCGCATGGATCTGTCTGAATTGGGCCTTCAAAAT
789620 GCC
66 GCC
789623 CCCAACCTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 63 1.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (78 bp):
ATTTCTGATTGAAATGGGCTTTCAAGATATTCCGCATGGATCTGTCTGAATTGGGCCTTCAAAAT
GCCTTATCATTCT
Found at i:793138 original size:15 final size:15
Alignment explanation
Indices: 793118--793162 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
793108 GTAATATTCA
793118 CCAGACTCTTTGTAT
1 CCAGACTCTTTGTAT
*
793133 CCAGACTCTATGTAT
1 CCAGACTCTTTGTAT
793148 CCAGACTCTTTGTAT
1 CCAGACTCTTTGTAT
793163 TGCCCACTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.38
Consensus pattern (15 bp):
CCAGACTCTTTGTAT
Found at i:794651 original size:12 final size:12
Alignment explanation
Indices: 794634--794660 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
794624 GCCAAGATGC
794634 AAATACAAATGT
1 AAATACAAATGT
794646 AAATACAAATGT
1 AAATACAAATGT
794658 AAA
1 AAA
794661 AATGCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (12 bp):
AAATACAAATGT
Found at i:794656 original size:40 final size:41
Alignment explanation
Indices: 794607--794691 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 41
794597 AAATAGTTTG
** * *
794607 AAATAAAATGTAATTATGCCAAGATGC-AAATAC-AAATGT
1 AAATAAAATGTAAAAATGCAAAAATGCAAAATACAAAATGT
*
794646 AAATACAAATGTAAAAATGCAAAAATGCAAAATGCAAAATGT
1 AAATA-AAATGTAAAAATGCAAAAATGCAAAATACAAAATGT
794688 AAAT
1 AAAT
794692 GTAAATATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
39 5 0.13
40 18 0.47
41 5 0.13
42 10 0.26
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.22
Consensus pattern (41 bp):
AAATAAAATGTAAAAATGCAAAAATGCAAAATACAAAATGT
Found at i:794669 original size:8 final size:8
Alignment explanation
Indices: 794652--794684 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
794642 ATGTAAATAC
*
794652 AAATGTAA
1 AAATGCAA
794660 AAATGCAA
1 AAATGCAA
794668 AAATGC-A
1 AAATGCAA
794675 AAATGCAA
1 AAATGCAA
794683 AA
1 AA
794685 TGTAAATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.64, C:0.09, G:0.12, T:0.15
Consensus pattern (8 bp):
AAATGCAA
Found at i:794926 original size:43 final size:44
Alignment explanation
Indices: 794864--794950 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 44
794854 CTGTGCATCA
*
794864 AACAAAACTTTTACATATAGGGGAC-AACTTTCAGTCCTAACTTC
1 AACAAAACTTTTACATATAGGGG-CTAACTTTCACTCCTAACTTC
*
794908 AACAAAAC-TTTACATATAGGGGCTAACTTTCCCTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGCTAACTTTCACTCCTAACTTC
794951 TCTAAAGCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
42 1 0.03
43 31 0.77
44 8 0.20
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.30
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGGGCTAACTTTCACTCCTAACTTC
Found at i:798666 original size:3 final size:3
Alignment explanation
Indices: 798660--798733 Score: 67
Period size: 3 Copynumber: 24.3 Consensus size: 3
798650 TTATTTTAAT
* * * *
798660 TAA TAA TAA TAA TAA TAT TTA TAA TAG TAA TAA TATT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
* ** *
798706 TAA TAA TAG TAA TTT TAA AAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
798734 TTAAGTAAAA
Statistics
Matches: 54, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
3 52 0.96
4 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:798729 original size:37 final size:41
Alignment explanation
Indices: 798654--798737 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 41
798644 TATTTATTAT
798654 TTTAATTAATAATAATAATAATATTTATAATAGTAATAAT-A
1 TTTAATTAATAATAATAATAATATTTATAATAG-AATAATAA
*
798695 TTTAA-TAATAATAATAATAGTAATTT-TAA-A-AATAATAA
1 TTTAATTAATAATAATAATAAT-ATTTATAATAGAATAATAA
798733 TTTAA
1 TTTAA
798738 GTAAAATGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
37 6 0.15
38 6 0.15
39 1 0.03
40 18 0.45
41 9 0.22
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (41 bp):
TTTAATTAATAATAATAATAATATTTATAATAGAATAATAA
Found at i:798741 original size:24 final size:25
Alignment explanation
Indices: 798680--798733 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
798670 AATAATATTT
* * *
798680 ATAATAGTAATAATATTTAATAATA
1 ATAATAATAGTAATATTTAAAAATA
798705 ATAATAATAGTAAT-TTTAAAAATA
1 ATAATAATAGTAATATTTAAAAATA
798729 ATAAT
1 ATAAT
798734 TTAAGTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
ATAATAATAGTAATATTTAAAAATA
Found at i:806595 original size:17 final size:17
Alignment explanation
Indices: 806554--806625 Score: 83
Period size: 17 Copynumber: 4.2 Consensus size: 17
806544 CTTCACGCAT
806554 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
806571 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
806589 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
*
806606 CTAGTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
806623 CTA
1 CTA
806626 ACTATTAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
17 34 0.72
18 13 0.28
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:807868 original size:17 final size:17
Alignment explanation
Indices: 807846--807917 Score: 90
Period size: 17 Copynumber: 4.2 Consensus size: 17
807836 AATTAAGAGT
807846 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
*
807863 TAGTTTGATAAATGAAC
1 TAGTTTAATAAATGAAC
*
807880 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* * *
807897 TAACTTTATTCAATGAAC
1 T-AGTTTAATAAATGAAC
807915 TAG
1 TAG
807918 ATGCATGAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
17 33 0.70
18 14 0.30
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:812366 original size:12 final size:12
Alignment explanation
Indices: 812322--812372 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
812312 CAAAGCATTT
812322 TTATTTTACTTG
1 TTATTTTACTTG
*
812334 TTCATTTT-TTTG
1 TT-ATTTTACTTG
812346 TATAGTTTTACTTG
1 T-TA-TTTTACTTG
*
812360 TTATTTTCCTTG
1 TTATTTTACTTG
812372 T
1 T
812373 CTTTTTCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 16 0.50
13 12 0.38
14 4 0.12
ACGTcount: A:0.14, C:0.10, G:0.10, T:0.67
Consensus pattern (12 bp):
TTATTTTACTTG
Found at i:818238 original size:17 final size:17
Alignment explanation
Indices: 818216--818276 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
818206 AATAAAGTTT
818216 GTTCATTAATTAAACTA
1 GTTCATTAATTAAACTA
* *
818233 GTTCATTCATCAAACTA
1 GTTCATTAATTAAACTA
818250 GTTCA-TATATTAAACTA
1 GTTCATTA-ATTAAACTA
*
818267 ATTC-TTAATT
1 GTTCATTAATT
818277 GTTTCATGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.11
17 33 0.89
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.43
Consensus pattern (17 bp):
GTTCATTAATTAAACTA
Found at i:823328 original size:22 final size:23
Alignment explanation
Indices: 823301--823360 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
823291 CCTAATTAAG
*
823301 AAATAAAATTACAAAA-TAAATT
1 AAATAAAATTACAAAATTAAATA
*
823323 AAAT-AAA-TACTAAAATTGAATA
1 AAATAAAATTAC-AAAATTAAATA
823345 AAATAAAAATTACAAA
1 AAAT-AAAATTACAAA
823361 TAATAAACGA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
20 3 0.10
21 7 0.23
22 12 0.39
24 6 0.19
25 3 0.10
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (23 bp):
AAATAAAATTACAAAATTAAATA
Found at i:824479 original size:16 final size:17
Alignment explanation
Indices: 824458--824490 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
824448 GTTGTGGCTT
824458 CGGTGG-GTGGAGAAAA
1 CGGTGGAGTGGAGAAAA
824474 CGGTGGAAGTGGAGAAA
1 CGGTGG-AGTGGAGAAA
824491 TCAGTGGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.33, C:0.06, G:0.48, T:0.12
Consensus pattern (17 bp):
CGGTGGAGTGGAGAAAA
Done.