Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 185 of 228
Found at i:55148606 original size:18 final size:21
Alignment explanation
Indices: 55148574--55148617 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
55148564 AAAAATACAA
*
55148574 ATTTTAGAATTTTTATAAA-T
1 ATTTTAGAATTTTTAAAAATT
55148594 ATTTT-GAA-TTTTAAAAATT
1 ATTTTAGAATTTTTAAAAATT
55148613 ATTTT
1 ATTTT
55148618 CAAAATTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 9 0.41
20 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTTTAGAATTTTTAAAAATT
Found at i:55148615 original size:19 final size:20
Alignment explanation
Indices: 55148574--55148644 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
55148564 AAAAATACAA
*
55148574 ATTTTAGAATTTTTATAAA-T
1 ATTTTAGAA-TTTTAAAAATT
55148594 ATTTT-GAATTTTAAAAATT
1 ATTTTAGAATTTTAAAAATT
* *
55148613 ATTTTCA-AAATTTGAAAATT
1 ATTTT-AGAATTTTAAAAATT
*
55148633 ACTTT-GAATTTT
1 ATTTTAGAATTTT
55148645 TTGTAATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 8 0.19
19 14 0.33
20 20 0.48
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (20 bp):
ATTTTAGAATTTTAAAAATT
Found at i:55151445 original size:33 final size:29
Alignment explanation
Indices: 55151407--55151479 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 29
55151397 ACTATAAGTA
55151407 CCGAATGCACATATTCACTTATACCCACCTATG
1 CCGAATGCACATA-T-A--TATACCCACCTATG
*
55151440 CCGAATGCATACATATATATATCCACCTATG
1 CCGAATGC--ACATATATATACCCACCTATG
55151471 CCGAATGCA
1 CCGAATGCA
55151480 TTCATATACA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
29 1 0.03
31 21 0.57
33 9 0.24
34 1 0.03
35 5 0.14
ACGTcount: A:0.33, C:0.30, G:0.11, T:0.26
Consensus pattern (29 bp):
CCGAATGCACATATATATACCCACCTATG
Found at i:55151469 original size:31 final size:31
Alignment explanation
Indices: 55151426--55151487 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
55151416 CATATTCACT
55151426 TATACCCACCTATGCCGAATGCATACATATA
1 TATACCCACCTATGCCGAATGCATACATATA
* *
55151457 TATATCCACCTATGCCGAATGCATTCATATA
1 TATACCCACCTATGCCGAATGCATACATATA
55151488 CACACTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29
Consensus pattern (31 bp):
TATACCCACCTATGCCGAATGCATACATATA
Found at i:55151740 original size:41 final size:41
Alignment explanation
Indices: 55151675--55151874 Score: 251
Period size: 41 Copynumber: 4.9 Consensus size: 41
55151665 TTTAAACAAA
* * * * *
55151675 TTCACTGGCACTTCA-CCTGATAGGCTTATAGTCTAATTCTG
1 TTCACCGGCACTT-AGCCTGCTAGGCGTATAGTCTGATTCAG
* *
55151716 TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCGTATAGTCTGATTCAG
* * *
55151757 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCGTATAGTCTGATTCAG
* *
55151798 TTCACCGGCACTTAGCCTGCT-GGACGTATAGTCCGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGG-CGTATAGTCTGATTCAG
*
55151839 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGA
1 TTCACCGGCACTTAGCCTGCTAGGCGTATAGTCTGA
55151875 ACAATTTCAT
Statistics
Matches: 141, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
40 3 0.02
41 137 0.97
42 1 0.01
ACGTcount: A:0.20, C:0.28, G:0.21, T:0.29
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCGTATAGTCTGATTCAG
Found at i:55159236 original size:31 final size:31
Alignment explanation
Indices: 55159193--55159254 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
55159183 CATATTCACT
*
55159193 TATACCCACCTATGCCGAATGCATACATATA
1 TATACCCACCTATACCGAATGCATACATATA
* *
55159224 TATATCCACCTATACCGAATGCATTCATATA
1 TATACCCACCTATACCGAATGCATACATATA
55159255 CACACTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.29
Consensus pattern (31 bp):
TATACCCACCTATACCGAATGCATACATATA
Found at i:55159507 original size:41 final size:41
Alignment explanation
Indices: 55159462--55159641 Score: 220
Period size: 41 Copynumber: 4.4 Consensus size: 41
55159452 CTTCACTTGA
* * *
55159462 TAGGCTTATAGTCTAATTCCGTTCACCGGCACTTAGCCTGC
1 TAGGCGTATAGTCTGATTCAGTTCACCGGCACTTAGCCTGC
*
55159503 TAGGCCTATAG-CTTGATTCAGTTCACCGGCACTTAGCCTGC
1 TAGGCGTATAGTC-TGATTCAGTTCACCGGCACTTAGCCTGC
* * * *
55159544 TAGGCTTGTAGCCTGATTCAGTTCACCAGCACTTAGCCTGC
1 TAGGCGTATAGTCTGATTCAGTTCACCGGCACTTAGCCTGC
* * *
55159585 T-GGACGTATAGTCCGATTCAATTCACCGGCACTTAGTCTGC
1 TAGG-CGTATAGTCTGATTCAGTTCACCGGCACTTAGCCTGC
*
55159626 TAGACGTATAGTCTGA
1 TAGGCGTATAGTCTGA
55159642 ACAATTTCAC
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
40 3 0.03
41 115 0.96
42 2 0.02
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (41 bp):
TAGGCGTATAGTCTGATTCAGTTCACCGGCACTTAGCCTGC
Found at i:55177469 original size:9 final size:10
Alignment explanation
Indices: 55177443--55177471 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
55177433 ATTTTGTGAA
55177443 TTATTTAAAT
1 TTATTTAAAT
55177453 TTATTTAAAT
1 TTATTTAAAT
55177463 TTA-TTAAAT
1 TTATTTAAAT
55177472 AAATAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTATTTAAAT
Found at i:55178144 original size:29 final size:30
Alignment explanation
Indices: 55178112--55178170 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
55178102 TTTGGCCTAA
55178112 TGTGCAATTCTGTACATG-AACTTTGATTT
1 TGTGCAATTCTGTACATGAAACTTTGATTT
* * *
55178141 TGTGTAATTTTGTACATGAAATTTTGATTT
1 TGTGCAATTCTGTACATGAAACTTTGATTT
55178171 GATCAAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.49
Consensus pattern (30 bp):
TGTGCAATTCTGTACATGAAACTTTGATTT
Found at i:55178356 original size:31 final size:30
Alignment explanation
Indices: 55178316--55178394 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
55178306 AACTGAATCA
* *
55178316 AAATTAAAGTTTCATGTATATATTTGA-ACC
1 AAATAAAAGTTTCATGTATATACTT-ACACC
* *
55178346 ACAATAAAAGTTTCATATGTATACTTACACC
1 A-AATAAAAGTTTCATGTATATACTTACACC
*
55178377 AAATCAAAG-TTCATGTAT
1 AAATAAAAGTTTCATGTAT
55178395 CAAATTACAC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
29 7 0.17
30 9 0.22
31 24 0.60
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (30 bp):
AAATAAAAGTTTCATGTATATACTTACACC
Found at i:55178670 original size:3 final size:3
Alignment explanation
Indices: 55178662--55178711 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
55178652 TTGGAAGAGT
55178662 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
55178710 TT
1 TT
55178712 TTACATCAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:55183927 original size:95 final size:95
Alignment explanation
Indices: 55183800--55183987 Score: 250
Period size: 95 Copynumber: 2.0 Consensus size: 95
55183790 GAACTTGGGG
* * * * * *
55183800 TGCGATCTTATATCAACGAGTTGTTTGAAGAAGCGATATTAAATCAACTATATCAAATAAGACTG
1 TGCGATCTGAAATCAACGAGCTATTTAAAGAAGCGATATTAAATCAACCATATCAAATAAGACTG
* *
55183865 TTCATGATTTTAAATCGAACGAACATAGGT
66 ATCATGATCTTAAATCGAACGAACATAGGT
* * * *
55183895 TGCGATCTGAAATCAACGAGCTATTTAAAGAAGTGATATTAAATCAGCCATCTCAAATAAGATTG
1 TGCGATCTGAAATCAACGAGCTATTTAAAGAAGCGATATTAAATCAACCATATCAAATAAGACTG
* *
55183960 ATCATGCTCTTAAATCGAATGAACATAG
66 ATCATGATCTTAAATCGAACGAACATAG
55183988 ATTGAGATAT
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
95 79 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (95 bp):
TGCGATCTGAAATCAACGAGCTATTTAAAGAAGCGATATTAAATCAACCATATCAAATAAGACTG
ATCATGATCTTAAATCGAACGAACATAGGT
Found at i:55186304 original size:21 final size:21
Alignment explanation
Indices: 55186275--55186325 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
55186265 TGACTACGTA
*
55186275 TGTCGCGACATCGGGGTTCGT
1 TGTCGCGACATCGAGGTTCGT
* *
55186296 TGTCACGACATTGAGGTTCGT
1 TGTCGCGACATCGAGGTTCGT
55186317 TGTCGCGAC
1 TGTCGCGAC
55186326 TGTAACACCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.14, C:0.24, G:0.33, T:0.29
Consensus pattern (21 bp):
TGTCGCGACATCGAGGTTCGT
Found at i:55188144 original size:33 final size:33
Alignment explanation
Indices: 55188102--55188165 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
55188092 TTAGAGATTT
* *
55188102 GTGTATCCGATGAGTGATGGTAAAGCTCACTTC
1 GTGTATCCGATGAGTAATGATAAAGCTCACTTC
55188135 GTGTATCCGATGAGTAATGATAAAGCTCACT
1 GTGTATCCGATGAGTAATGATAAAGCTCACT
55188166 ATATGTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (33 bp):
GTGTATCCGATGAGTAATGATAAAGCTCACTTC
Found at i:55188319 original size:68 final size:68
Alignment explanation
Indices: 55188187--55188320 Score: 241
Period size: 68 Copynumber: 2.0 Consensus size: 68
55188177 AACTCAAGCG
*
55188187 CCAATCTATCATATTATATGTAACTATGTGGAACATGTTTTATGCTTAATGGAGTATGCGCTATA
1 CCAATCTATCATATTATATGTAACTATGTGGAACATGTTTTATGCTTAATGGAGTATGCACTATA
55188252 TCA
66 TCA
* *
55188255 CCAATCTATCATATTATATGTAACTGTGTGGAACATGTTTTATGCTTAATGGAGTATGTACTATA
1 CCAATCTATCATATTATATGTAACTATGTGGAACATGTTTTATGCTTAATGGAGTATGCACTATA
55188320 T
66 T
55188321 TGCAAATTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (68 bp):
CCAATCTATCATATTATATGTAACTATGTGGAACATGTTTTATGCTTAATGGAGTATGCACTATA
TCA
Found at i:55188333 original size:68 final size:68
Alignment explanation
Indices: 55188189--55188341 Score: 229
Period size: 68 Copynumber: 2.3 Consensus size: 68
55188179 CTCAAGCGCC
*
55188189 AATCTATCATATTATATGTAACTATGTGGAACATGTTTTATGCTTAATGGAGTATGCGCTATATC
1 AATCTATCATATTATATGTAACTATGTGGAACATGTTTTATGCTTAATGGAGTATGCACTATATC
*
55188254 ACC
66 ACA
* * *
55188257 AATCTATCATATTATATGTAACTGTGTGGAACATGTTTTATGCTTAATGGAGTATGTACTATATT
1 AATCTATCATATTATATGTAACTATGTGGAACATGTTTTATGCTTAATGGAGTATGCACTATATC
*
55188322 GCA
66 ACA
*
55188325 AATTTATC--ATTATATGT
1 AATCTATCATATTATATGT
55188342 GATTTAAGAG
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
66 9 0.12
68 69 0.88
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (68 bp):
AATCTATCATATTATATGTAACTATGTGGAACATGTTTTATGCTTAATGGAGTATGCACTATATC
ACA
Found at i:55197784 original size:48 final size:48
Alignment explanation
Indices: 55197709--55197808 Score: 182
Period size: 48 Copynumber: 2.1 Consensus size: 48
55197699 CCAAGGTGCT
55197709 ATCCCAAATTTAGATACTGTTTCCCCTGTGCAGCAAGAAGTTAGCACG
1 ATCCCAAATTTAGATACTGTTTCCCCTGTGCAGCAAGAAGTTAGCACG
* *
55197757 ATCCCAGATTTAGATACTGTTTTCCCTGTGCAGCAAGAAGTTAGCACG
1 ATCCCAAATTTAGATACTGTTTCCCCTGTGCAGCAAGAAGTTAGCACG
55197805 ATCC
1 ATCC
55197809 TTCCCAATAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (48 bp):
ATCCCAAATTTAGATACTGTTTCCCCTGTGCAGCAAGAAGTTAGCACG
Found at i:55208634 original size:5 final size:5
Alignment explanation
Indices: 55208624--55208651 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
55208614 CGCCATATTT
55208624 AAAAC AAAAC AAAAC AAAAC AAAAC AAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAA
55208652 TTAAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:55210438 original size:301 final size:300
Alignment explanation
Indices: 55209695--55210451 Score: 941
Period size: 302 Copynumber: 2.5 Consensus size: 300
55209685 AGGTTCTAAT
* * * * *
55209695 TTTTAATTTTAACATCGTACATATTTCACT-TGTTACTGTTAATTAGTTCTAAATAATACTTTTC
1 TTTT-ATTTTAATATCGTACATATTTCA-TATCTTACTATTAATTAGTTCCAAACAATACTTTTC
* * * * *
55209759 ATCATTTATTGTATGTTGTTTTTAAACAAACGTCCGTGTTTTAAATACGTGATTTTCATACATAT
64 ATCATTTATTGTATGTTGTTTTTAAACACACGTCTGTGTTTTAAATATGTGATTTTCACACGTAT
* * *
55209824 ACACATGTGATATGATTTCTAGTAAGAATAATGTTGTTGATCTAGTGTCACAAATTAACTCGACA
129 ACACATGTGATAAGATTTCTAGTATGAATAATGTTGTTGATCTAGTGTCACAAATTAACACGACA
* * * *
55209889 CCAATTCAGGATTAATGACAAAACAATAATAAATTGTATTCATTTAGTATTCCTAATATGATGTG
194 CCAACTCAGGATTAATGACAAAACAATAAAAAATTGTATTCATTTAGTATTCCTAATATAATGTA
* *
55209954 TTTTTGTGTTTAAATTTCATTTTACTCACAATTTAACCTATTT
259 TTTTTATGTTTAAATTTCATTTTACTCACAATTTAACCTA-TA
* *
55209997 TTTTCATTTTAATATCGTACATATTTCATATGTTACTATTAATTAGTTCCAAACCATACTTTTCA
1 TTTT-ATTTTAATATCGTACATATTTCATATCTTACTATTAATTAGTTCCAAACAATACTTTTCA
** * *
55210062 TCATTTATTGTATGTTGTTTTTAAACACACGTCTGTGTCCTAAATATGTAATTTTCACATGTATA
65 TCATTTATTGTATGTTGTTTTTAAACACACGTCTGTGTTTTAAATATGTGATTTTCACACGTATA
* * * * *
55210127 CACGTGTGATAAGATTTTTAGTATTAATAATGTTGTTGATTTAGTGTGACAAATTAACACGACAC
130 CACATGTGATAAGATTTCTAGTATGAATAATGTTGTTGATCTAGTGTCACAAATTAACACGACAC
* * *
55210192 CAACTCAGGATTGATGACAAAACAATGATAAATAATTGTATTCATTTAGTATTCTTAATCTAATG
195 CAACTCAGGATTAATGACAAAACAAT-A-AAA-AATTGTATTCATTTAGTATTCCTAATATAATG
* *
55210257 TATTTTTATGTTTAAATTT-AGTTTTACTTACAATTTAATCTA-A
257 TATTTTTATGTTTAAATTTCA-TTTTACTCACAATTTAACCTATA
* * * * *
55210300 TTTT-TTTTAATATTGTACATATTTTATGTCTTATTATTAATTAGCTCCAAACAATA-TGTTTCA
1 TTTTATTTTAATATCGTACATATTTCATATCTTACTATTAATTAGTTCCAAACAATACT-TTTCA
* * * * * * *
55210363 TTATTTATTGTATATTATTTTTAAACACACCAT-TGTGTTTTAAATATATGATTTCCACACGCAT
65 TCATTTATTGTATGTTGTTTTTAAACACA-CGTCTGTGTTTTAAATATGTGATTTTCACACGTAT
* *
55210427 ACGCATGTGATAAAATTTCTAGTAT
129 ACACATGTGATAAGATTTCTAGTAT
55210452 ACATTATAGA
Statistics
Matches: 392, Mismatches: 56, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
300 1 0.00
301 122 0.31
302 196 0.50
303 5 0.01
304 3 0.01
305 65 0.17
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.44
Consensus pattern (300 bp):
TTTTATTTTAATATCGTACATATTTCATATCTTACTATTAATTAGTTCCAAACAATACTTTTCAT
CATTTATTGTATGTTGTTTTTAAACACACGTCTGTGTTTTAAATATGTGATTTTCACACGTATAC
ACATGTGATAAGATTTCTAGTATGAATAATGTTGTTGATCTAGTGTCACAAATTAACACGACACC
AACTCAGGATTAATGACAAAACAATAAAAAATTGTATTCATTTAGTATTCCTAATATAATGTATT
TTTATGTTTAAATTTCATTTTACTCACAATTTAACCTATA
Found at i:55216061 original size:37 final size:36
Alignment explanation
Indices: 55215978--55216063 Score: 86
Period size: 37 Copynumber: 2.3 Consensus size: 36
55215968 ATTTGTGAAG
55215978 TAATAACAAACAATTTCACATGTCAATCAATTTAGAA
1 TAATAACAAACAATTTCACA-GTCAATCAATTTAGAA
* * **
55216015 CAATGACAAACAATTTTGCACA-TCAATTTATTTA-ACA
1 TAATAACAAACAA-TTT-CACAGTCAATCAATTTAGA-A
55216052 TAATAACAAACA
1 TAATAACAAACA
55216064 GTCTCGCATA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
36 1 0.03
37 32 0.80
38 3 0.08
39 4 0.10
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29
Consensus pattern (36 bp):
TAATAACAAACAATTTCACAGTCAATCAATTTAGAA
Found at i:55217456 original size:18 final size:18
Alignment explanation
Indices: 55217433--55217470 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
55217423 TCACTAGATA
55217433 AGCATATGTCTAGTCTCG
1 AGCATATGTCTAGTCTCG
55217451 AGCATATGTCTAGTCTCG
1 AGCATATGTCTAGTCTCG
55217469 AG
1 AG
55217471 TTCGAATCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (18 bp):
AGCATATGTCTAGTCTCG
Found at i:55218544 original size:42 final size:42
Alignment explanation
Indices: 55218497--55218609 Score: 172
Period size: 42 Copynumber: 2.7 Consensus size: 42
55218487 ACACCGACAT
* *
55218497 AGGACACGTGCATGTGTCTAGGTCGTGTGAATCACACAGCCA
1 AGGACACGGGCATGTGTCTAGGCCGTGTGAATCACACAGCCA
* *
55218539 AGGACACGGGCATGTGTCCAGGCCGTGTGAATCACACGGCCA
1 AGGACACGGGCATGTGTCTAGGCCGTGTGAATCACACAGCCA
* *
55218581 AGGGCACGGGCGTGTGTCTAGGCCGTGTG
1 AGGACACGGGCATGTGTCTAGGCCGTGTG
55218610 GCATATAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.21, C:0.25, G:0.35, T:0.19
Consensus pattern (42 bp):
AGGACACGGGCATGTGTCTAGGCCGTGTGAATCACACAGCCA
Found at i:55221622 original size:21 final size:21
Alignment explanation
Indices: 55221584--55221623 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
55221574 CTTTAAAATA
*
55221584 TTTTATATTTACTTTTTAATT
1 TTTTATATTTACTATTTAATT
55221605 TTTTATAATTTA-TATTTAA
1 TTTTAT-ATTTACTATTTAA
55221624 ATGTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTATATTTACTATTTAATT
Found at i:55221647 original size:30 final size:29
Alignment explanation
Indices: 55221583--55221648 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
55221573 TCTTTAAAAT
* * *
55221583 ATTTTATATTTACTTTTTAATTTTTTATA
1 ATTTTATATTTAATGTTTAAATTTTTATA
55221612 A-TTTATATTTAAATGTTTAAATTTTTA-A
1 ATTTTATATTT-AATGTTTAAATTTTTATA
55221640 GATTTTATA
1 -ATTTTATA
55221649 ATATTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 10 0.32
29 15 0.48
30 6 0.19
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (29 bp):
ATTTTATATTTAATGTTTAAATTTTTATA
Found at i:55221967 original size:13 final size:13
Alignment explanation
Indices: 55221949--55221987 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
55221939 AACCTATATT
55221949 TTAAAATTTATAA
1 TTAAAATTTATAA
55221962 TTAAAATTTGATAA
1 TTAAAATTT-ATAA
*
55221976 TAAAAATATTAT
1 TTAAAAT-TTAT
55221988 TATAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 9 0.39
14 12 0.52
15 2 0.09
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (13 bp):
TTAAAATTTATAA
Found at i:55224814 original size:64 final size:64
Alignment explanation
Indices: 55224740--55224869 Score: 233
Period size: 64 Copynumber: 2.0 Consensus size: 64
55224730 AATTCATTAG
** *
55224740 TTGATGTTGTGTTCACACAATAAAGGGAATGGAATCTTTCTTAGATATCTTGTGATTTAGGGCA
1 TTGATGTTGTGTTCACACAATAAAGGGAATAAAATCTTTCTTAGATATCTCGTGATTTAGGGCA
55224804 TTGATGTTGTGTTCACACAATAAAGGGAATAAAATCTTTCTTAGATATCTCGTGATTTAGGGCA
1 TTGATGTTGTGTTCACACAATAAAGGGAATAAAATCTTTCTTAGATATCTCGTGATTTAGGGCA
55224868 TT
1 TT
55224870 ACTTTTGATA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.38
Consensus pattern (64 bp):
TTGATGTTGTGTTCACACAATAAAGGGAATAAAATCTTTCTTAGATATCTCGTGATTTAGGGCA
Found at i:55225766 original size:20 final size:20
Alignment explanation
Indices: 55225741--55225781 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
55225731 GCTAAGGGAC
55225741 TCATGAGGCAATTAAAACAT
1 TCATGAGGCAATTAAAACAT
55225761 TCATGAGGCAATTAAAACAT
1 TCATGAGGCAATTAAAACAT
55225781 T
1 T
55225782 ATTCTAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (20 bp):
TCATGAGGCAATTAAAACAT
Found at i:55233085 original size:19 final size:20
Alignment explanation
Indices: 55233061--55233098 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55233051 AAATTAAGTT
*
55233061 TTAATTAA-TTATAATTAAC
1 TTAATTAACTAATAATTAAC
55233080 TTAATTAACTAATAATTAA
1 TTAATTAACTAATAATTAA
55233099 GTAACACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATTAACTAATAATTAAC
Found at i:55244777 original size:51 final size:51
Alignment explanation
Indices: 55244718--55244819 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
55244708 ACTAAGTGAA
55244718 GAAATTGCGTAGTTTAGATTGATAATGACAGATGAAATCTAGATGGATTCT
1 GAAATTGCGTAGTTTAGATTGATAATGACAGATGAAATCTAGATGGATTCT
55244769 GAAATTGCGTAGTTTAGATTGATAATGACAGATGAAATCTAGATGGATTCT
1 GAAATTGCGTAGTTTAGATTGATAATGACAGATGAAATCTAGATGGATTCT
55244820 TTCCTGGGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (51 bp):
GAAATTGCGTAGTTTAGATTGATAATGACAGATGAAATCTAGATGGATTCT
Found at i:55244812 original size:25 final size:25
Alignment explanation
Indices: 55244732--55244812 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
55244722 TTGCGTAGTT
55244732 TAGATTGATAATGACAGATGAAATC
1 TAGATTGATAATGACAGATGAAATC
* ** * * *
55244757 TAGATGGATTCTGA-A-ATTGCGTAGTT
1 TAGATTGATAATGACAGA-T--GAAATC
55244783 TAGATTGATAATGACAGATGAAATC
1 TAGATTGATAATGACAGATGAAATC
55244808 TAGAT
1 TAGAT
55244813 GGATTCTTTC
Statistics
Matches: 39, Mismatches: 12, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
23 1 0.03
24 2 0.05
25 19 0.49
26 14 0.36
27 2 0.05
28 1 0.03
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.32
Consensus pattern (25 bp):
TAGATTGATAATGACAGATGAAATC
Found at i:55244906 original size:13 final size:13
Alignment explanation
Indices: 55244888--55244912 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55244878 TGTCGTGTTC
55244888 TTTAGTTAATTAA
1 TTTAGTTAATTAA
55244901 TTTAGTTAATTA
1 TTTAGTTAATTA
55244913 TAGTTTTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
TTTAGTTAATTAA
Found at i:55248994 original size:43 final size:43
Alignment explanation
Indices: 55248872--55248994 Score: 201
Period size: 43 Copynumber: 2.9 Consensus size: 43
55248862 GCGCTTTCCC
* * * *
55248872 TGACCTTTAGCGGCGCTTTTTTCACAAACGCCGCTAAAGAACA
1 TGACTTTTAGCGGCTCTTTTTCCACAAACGCCGCTATAGAACA
55248915 TGACTTTTAGCGGCTCTTTTTCCACAAACGCCGCTATAGAACA
1 TGACTTTTAGCGGCTCTTTTTCCACAAACGCCGCTATAGAACA
*
55248958 TGACTTTTAGCGGCTCTTCTTCCACAAACGCCGCTAT
1 TGACTTTTAGCGGCTCTTTTTCCACAAACGCCGCTAT
55248995 TGTTTGGTGG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (43 bp):
TGACTTTTAGCGGCTCTTTTTCCACAAACGCCGCTATAGAACA
Found at i:55249197 original size:20 final size:20
Alignment explanation
Indices: 55249156--55249194 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55249146 ATTTCAAAGT
*
55249156 ATATGAATAAAATAATATTA
1 ATATGAATAAAAAAATATTA
*
55249176 ATATTAATAAATAAAATAT
1 ATATGAATAAA-AAAATAT
55249195 AATTCATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
ATATGAATAAAAAAATATTA
Found at i:55257224 original size:15 final size:15
Alignment explanation
Indices: 55257200--55257229 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55257190 TTAAATAATA
*
55257200 ATTTATATTTATATT
1 ATTTACATTTATATT
55257215 ATTTACATTTATATT
1 ATTTACATTTATATT
55257230 CTAAAATATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTACATTTATATT
Found at i:55257389 original size:21 final size:21
Alignment explanation
Indices: 55257356--55257419 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
55257346 AAGCCTTAAT
* *
55257356 CATAAATCTTAAACCCCAAAC
1 CATAAACCATAAACCCCAAAC
* * *
55257377 TATAAACCATAAATCTCAAAC
1 CATAAACCATAAACCCCAAAC
* * *
55257398 CGTAAACCTTAAACCCTAAAC
1 CATAAACCATAAACCCCAAAC
55257419 C
1 C
55257420 CGTCAATTAA
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.47, C:0.31, G:0.02, T:0.20
Consensus pattern (21 bp):
CATAAACCATAAACCCCAAAC
Found at i:55257525 original size:21 final size:22
Alignment explanation
Indices: 55257499--55257574 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 22
55257489 ATCGAAAATC
55257499 TTAAACC-CTAAACCATAAACA
1 TTAAACCACTAAACCATAAACA
* *
55257520 TTAAACCTCTAAACCACAAACA
1 TTAAACCACTAAACCATAAACA
* *
55257542 --ACAACCACCAAATCATAAAC-
1 TTA-AACCACTAAACCATAAACA
55257562 TCTAAACC-CTAAA
1 T-TAAACCACTAAA
55257575 ATTGGCCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
20 1 0.02
21 25 0.57
22 17 0.39
23 1 0.02
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.17
Consensus pattern (22 bp):
TTAAACCACTAAACCATAAACA
Found at i:55257534 original size:22 final size:21
Alignment explanation
Indices: 55257499--55257541 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
55257489 ATCGAAAATC
*
55257499 TTAAACCCTAAACCATAAACA
1 TTAAACCCTAAACCACAAACA
55257520 TTAAACCTCTAAACCACAAACA
1 TTAAACC-CTAAACCACAAACA
55257542 ACAACCACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (21 bp):
TTAAACCCTAAACCACAAACA
Found at i:55258483 original size:211 final size:213
Alignment explanation
Indices: 55258136--55258672 Score: 708
Period size: 211 Copynumber: 2.5 Consensus size: 213
55258126 GGCGTTTTCA
** * * *
55258136 GGTAAGCGCCGCTAACGACGCTATAGCTAAAGACGAAATGTTGCATTTCGGTTTAAAGTTTTTCG
1 GGTAAGCGCCGCTGTCGACGCTATAGCTCAAGACGAAACGTTGCGTTTCGGTTTAAAGTTTTTCG
* * * * *
55258201 GTGTTTTTTAGTTAAGCACCGCTAATTACGGGATATAGCGGTGTTTTATAGTAAGCGCCGCTAAT
66 GCGTTTTTTAGTTAAGCGCCGCTAATTGCGGGATATAGCGGCGTTTTATAGTAAGCGCCGCTAAC
* * **
55258266 GCCTCTATAGGTCAAGCC-AGAACGATGCATTTTGGTCAAAGTTTTTGTGGCGCTTCT-ACGGAT
131 GCCTCTATAGGTCAAGCCGA-AACGATGCATTTTGGTCAAAATTTTTGAGGCGCTTCTAAAAGAT
55258329 -ATATAGCGG-AG-TTTTTG
195 AATAT-GCGGCAGATTTTTG
**
55258346 GGTAAGTTCCGCTGTCGACGCTATAGCTCAAGACGAAACGTTGCGTTTCGGTTTTAAAGTTTTTC
1 GGTAAGCGCCGCTGTCGACGCTATAGCTCAAGACGAAACGTTGCGTTTCGG-TTTAAAGTTTTTC
* * * *
55258411 GGCATTTTCTAGTTTAGCGCCGCTAATTGCGGGATATAGCGGCGTTTTATAGTAAGCGCTGCTAA
65 GGCGTTTTTTAGTTAAGCGCCGCTAATTGCGGGATATAGCGGCGTTTTATAGTAAGCGCCGCTAA
*
55258476 CGCCTCTATAGGTCAAGCCGAAACGATGCATTTTGGTCAAAATTTTTGAGGCGCTTCTAAAAGCT
130 CGCCTCTATAGGTCAAGCCGAAACGATGCATTTTGGTCAAAATTTTTGAGGCGCTTCTAAAAGAT
*
55258541 AATATGTGGCAGCATTTTTG
195 AATATGCGGCAG-ATTTTTG
* ** *
55258561 GGTAAGCGCCGCTGTCGGCGCTATAGCTCAAGACGAAACGTTTTGTTTTGGTTTAAAG-TTTTCT
1 GGTAAGCGCCGCTGTCGACGCTATAGCTCAAGACGAAACGTTGCGTTTCGGTTTAAAGTTTTTC-
* * * * *
55258625 AGCGTTTTTTAGTTAAGCGTCGCGAATTGTGGGATATATCGGCGTTTT
65 GGCGTTTTTTAGTTAAGCGCCGCTAATTGCGGGATATAGCGGCGTTTT
55258673 CCACAACTGC
Statistics
Matches: 283, Mismatches: 36, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
210 44 0.16
211 123 0.43
212 7 0.02
213 11 0.04
214 47 0.17
215 51 0.18
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (213 bp):
GGTAAGCGCCGCTGTCGACGCTATAGCTCAAGACGAAACGTTGCGTTTCGGTTTAAAGTTTTTCG
GCGTTTTTTAGTTAAGCGCCGCTAATTGCGGGATATAGCGGCGTTTTATAGTAAGCGCCGCTAAC
GCCTCTATAGGTCAAGCCGAAACGATGCATTTTGGTCAAAATTTTTGAGGCGCTTCTAAAAGATA
ATATGCGGCAGATTTTTG
Found at i:55262014 original size:41 final size:40
Alignment explanation
Indices: 55261942--55262068 Score: 121
Period size: 41 Copynumber: 3.1 Consensus size: 40
55261932 TGAAAATAAG
* * * *
55261942 ATGTTTCAGACTTTACGTCCAAGAGGTTTGATGCTGATGAA
1 ATGTTTCAGACTTTATGT-CTAGAGGCTTGATGCCGATGAA
*
55261983 ATGTTTCAGACTTTATGTCTAGTAGGCTTGATGCCGGTGAA
1 ATGTTTCAGACTTTATGTCTAG-AGGCTTGATGCCGATGAA
* ** * *
55262024 TTACTTCAAACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAA
1 ATGTTTCAGACTTTATGTCTAG-AGGC-TTGATGCCGATGAA
55262065 ATGT
1 ATGT
55262069 ATCGGGCTTT
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
40 3 0.04
41 65 0.92
42 3 0.04
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (40 bp):
ATGTTTCAGACTTTATGTCTAGAGGCTTGATGCCGATGAA
Found at i:55263958 original size:5 final size:5
Alignment explanation
Indices: 55263948--55264001 Score: 54
Period size: 5 Copynumber: 10.0 Consensus size: 5
55263938 TACTGTTTTA
* *
55263948 AATTT AATTT AATTT AATTT AATGTT CAATTTT AAATA ATATTT AATTT
1 AATTT AATTT AATTT AATTT AAT-TT -AA-TTT AATTT A-ATTT AATTT
55263997 AATTT
1 AATTT
55264002 TGAAATTTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 29 0.71
6 7 0.17
7 4 0.10
8 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (5 bp):
AATTT
Found at i:55264010 original size:29 final size:27
Alignment explanation
Indices: 55263943--55264010 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
55263933 CATCTTACTG
* *
55263943 TTTTAAATTTAATTTAATTTAATTTAA
1 TTTTAAATTTAAATAAATTTAATTTAA
* *
55263970 TGTTCAATTTTAAATAATATTTAATTTAA
1 T-TTTAAATTTAAATAA-ATTTAATTTAA
55263999 TTTTGAAATTTA
1 TTTT-AAATTTA
55264011 GACATTGAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
27 1 0.03
28 13 0.41
29 18 0.56
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (27 bp):
TTTTAAATTTAAATAAATTTAATTTAA
Found at i:55265660 original size:27 final size:26
Alignment explanation
Indices: 55265622--55265672 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
55265612 TCATAAATAA
*
55265622 ATACGGTTAAAATAT-TGATATTATAGC
1 ATACGGATAAAA-ATGT-ATATTATAGC
55265649 ATACGGATAAAAATGTATATTATA
1 ATACGGATAAAAATGTATATTATA
55265673 TCACACATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (26 bp):
ATACGGATAAAAATGTATATTATAGC
Found at i:55270946 original size:20 final size:20
Alignment explanation
Indices: 55270921--55270963 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
55270911 ATATTTAAGA
55270921 ATTTTTTAATTAAATTACAT
1 ATTTTTTAATTAAATTACAT
*
55270941 ATTTTTTAATTAAATTATAT
1 ATTTTTTAATTAAATTACAT
55270961 ATT
1 ATT
55270964 ATCTATATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTTTAATTAAATTACAT
Found at i:55279874 original size:10 final size:10
Alignment explanation
Indices: 55279856--55279907 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
55279846 ATAAATTAAT
*
55279856 TTTTGTAAAA
1 TTTTATAAAA
55279866 TTTTATAAAAA
1 TTTTAT-AAAA
* *
55279877 TTTAAATTAAA
1 TTT-TATAAAA
55279888 TTTTATAAAA
1 TTTTATAAAA
55279898 TTTTATAAAA
1 TTTTATAAAA
55279908 ATTATTTTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 20 0.57
11 13 0.37
12 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (10 bp):
TTTTATAAAA
Found at i:55279897 original size:32 final size:32
Alignment explanation
Indices: 55279832--55279910 Score: 124
Period size: 32 Copynumber: 2.5 Consensus size: 32
55279822 TAAAAACAAT
* * *
55279832 AAATTTTATAAAAA-ATAAATTAATTTTTGTA
1 AAATTTTATAAAAATTTAAATTAAATTTTATA
55279863 AAATTTTATAAAAATTTAAATTAAATTTTATA
1 AAATTTTATAAAAATTTAAATTAAATTTTATA
55279895 AAATTTTATAAAAATT
1 AAATTTTATAAAAATT
55279911 ATTTTCCTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 14 0.32
32 30 0.68
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (32 bp):
AAATTTTATAAAAATTTAAATTAAATTTTATA
Found at i:55284477 original size:21 final size:20
Alignment explanation
Indices: 55284438--55284478 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
55284428 TGTTTCCAAG
* *
55284438 AAAAATAATAAGAATATAGA
1 AAAAAAAATAAGAACATAGA
55284458 AAAAAAAATAAGATACATAGA
1 AAAAAAAATAAGA-ACATAGA
55284479 TAACAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (20 bp):
AAAAAAAATAAGAACATAGA
Found at i:55291499 original size:21 final size:21
Alignment explanation
Indices: 55291457--55291500 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
55291447 TTGTTTGTAC
*
55291457 TTAGGTACATTTAGTAGCATT
1 TTAGGTACATTTACTAGCATT
*
55291478 TTAGG-ACATTTCACTAGTATT
1 TTAGGTACATTT-ACTAGCATT
55291499 TT
1 TT
55291501 CATCATTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.45
Consensus pattern (21 bp):
TTAGGTACATTTACTAGCATT
Found at i:55291763 original size:41 final size:41
Alignment explanation
Indices: 55291718--55291867 Score: 140
Period size: 41 Copynumber: 3.7 Consensus size: 41
55291708 GAAAGCCATA
* * *
55291718 TGACCCACATGGTTTGCCACATGGCCAACCACACGATCATG
1 TGACCCACATGGTCTGCCACACGGCCAACCACACGATCGTG
* * * * * * *
55291759 TGACCCATATAGTCTACCACACGACCTACCACATGATTGTG
1 TGACCCACATGGTCTGCCACACGGCCAACCACACGATCGTG
* ** *
55291800 TGACCCATATGGTCTGTTACACGGCCTACCACACGA-CTGTG
1 TGACCCACATGGTCTGCCACACGGCCAACCACACGATC-GTG
* *
55291841 TGACCTACATGGTCTGCCACATGGCCA
1 TGACCCACATGGTCTGCCACACGGCCA
55291868 TGTGATGTAG
Statistics
Matches: 85, Mismatches: 23, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
41 85 1.00
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (41 bp):
TGACCCACATGGTCTGCCACACGGCCAACCACACGATCGTG
Found at i:55292943 original size:14 final size:13
Alignment explanation
Indices: 55292924--55292973 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 13
55292914 TTAGGTTGTG
55292924 ACAAAAAAAAACTA
1 ACAAAAAAAAA-TA
55292938 ACAAAACAAAAATAA
1 ACAAAA-AAAAAT-A
*
55292953 ACAAATAAAAATA
1 ACAAAAAAAAATA
55292966 ACATAAAA
1 ACA-AAAA
55292974 TCAAGTACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 4 0.13
14 16 0.52
15 11 0.35
ACGTcount: A:0.78, C:0.12, G:0.00, T:0.10
Consensus pattern (13 bp):
ACAAAAAAAAATA
Found at i:55292962 original size:19 final size:19
Alignment explanation
Indices: 55292924--55292962 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
55292914 TTAGGTTGTG
*
55292924 ACAAAAAAAAACTAACAAA
1 ACAAAAAAAAACAAACAAA
* *
55292943 ACAAAAATAAACAAATAAA
1 ACAAAAAAAAACAAACAAA
55292962 A
1 A
55292963 ATAACATAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.79, C:0.13, G:0.00, T:0.08
Consensus pattern (19 bp):
ACAAAAAAAAACAAACAAA
Found at i:55297200 original size:31 final size:32
Alignment explanation
Indices: 55297144--55297206 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
55297134 AGATAATTTT
55297144 AAAGAGTTTTATTAGGATTTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTTCAATTACTCTTG
55297176 AAAGAGTTTTATTAGGA-TTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTTCAATTACTCTTG
55297207 TAATTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 14 0.45
32 17 0.55
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.43
Consensus pattern (32 bp):
AAAGAGTTTTATTAGGATTTCAATTACTCTTG
Found at i:55304281 original size:15 final size:16
Alignment explanation
Indices: 55304249--55304307 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 16
55304239 TGTAGGAACG
**
55304249 AAAAATTAAAATGTAA
1 AAAAATTAAAATACAA
55304265 AAAAATTAAAA-ACAA
1 AAAAATTAAAATACAA
* *
55304280 AAATATTAAATTA-AA
1 AAAAATTAAAATACAA
55304295 AATAAATATAAAA
1 AA-AAAT-TAAAA
55304308 ATGGCTAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 15 0.44
16 15 0.44
17 4 0.12
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (16 bp):
AAAAATTAAAATACAA
Found at i:55307129 original size:321 final size:320
Alignment explanation
Indices: 55306547--55307189 Score: 1067
Period size: 321 Copynumber: 2.0 Consensus size: 320
55306537 ACCGTTCTTT
55306547 TACTGCCTAGCTTGTAACCTCTCAAACCCGTCTGCCAAACTCCAAAACATTATGAGTATAGCTCG
1 TACTGCCTAGCTTGTAACCTCTCAAACCCGTCTGCCAAACTCCAAAACATTATGAGTATAGCTCG
* * *
55306612 ATGTGGTAAAACCACTAAATAATCAATAATGTTGAAAATCTATCGAATATCAAATAGTGCGATAC
66 ATGTGGTAAAACCACTAAATAATCAATAATGCTGAAAATCTATAGAATATCAAATAGTGCGATAA
* * *
55306677 AATCGCTAATAACATATAATATGTGATAAAATTGCCACTCCCCTCGGTACTCCAAGTGCAGTGCA
131 AATAGCTAATAACATATAATATGCGATAAAATCGCCACTCCCCTCGGTACTCCAAGTGCAGTGCA
55306742 CTGACTATGAATAATGCGGACTTAATATGCCACCGATACTCCACAGAACTCCTCCCTCAACCACA
196 CTGACTATGAATAATGCGGACTTAATATGCCACCGATACTCCACAGAACTCCTCCCTCAACCAC-
* *
55306807 AAAATCCCAACCCAATGCATATGCAATATGTCACACTATCTCGTACATAATCATATCTCAA
260 AAAATCCCAACCCAATGCATATGCAATATGTCACACAATCTCATACATAATCATATCTCAA
55306868 TACTGCCTAGCTTGTAACCT-TCCAAACCCGTCTGCCAAACTCCAAAACATTATGAGTATAGCTC
1 TACTGCCTAGCTTGTAACCTCT-CAAACCCGTCTGCCAAACTCCAAAACATTATGAGTATAGCTC
* *
55306932 GATGTGGTAAAACCACTGAATAATCAATAATGCTGAAAATCTGCTAG-ATATCAAATAGTGCGAT
65 GATGTGGTAAAACCACTAAATAATCAATAATGCTGAAAATCT-ATAGAATATCAAATAGTGCGAT
*
55306996 AAAATAGCTAATAACATATAATATGCGATAAAATCGCCACTCCCCTCGGTACTCCAGGTGCAGTG
129 AAAATAGCTAATAACATATAATATGCGATAAAATCGCCACTCCCCTCGGTACTCCAAGTGCAGTG
* ** * ** *
55307061 CACTGACTACT-AATAATGCGTACTTAATATGCCGTCGGTACTCCATGGAACTCCTCCGTCAACC
194 CACTGACTA-TGAATAATGCGGACTTAATATGCCACCGATACTCCACAGAACTCCTCCCTCAACC
55307125 ACAAAATCCCAACCCAATGCATATGCAATATGTCACACAATCTCATACATAATCATATCTCAA
258 ACAAAATCCCAACCCAATGCATATGCAATATGTCACACAATCTCATACATAATCATATCTCAA
55307188 TA
1 TA
55307190 ATTTTCACAT
Statistics
Matches: 301, Mismatches: 18, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
320 62 0.21
321 236 0.78
322 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (320 bp):
TACTGCCTAGCTTGTAACCTCTCAAACCCGTCTGCCAAACTCCAAAACATTATGAGTATAGCTCG
ATGTGGTAAAACCACTAAATAATCAATAATGCTGAAAATCTATAGAATATCAAATAGTGCGATAA
AATAGCTAATAACATATAATATGCGATAAAATCGCCACTCCCCTCGGTACTCCAAGTGCAGTGCA
CTGACTATGAATAATGCGGACTTAATATGCCACCGATACTCCACAGAACTCCTCCCTCAACCACA
AAATCCCAACCCAATGCATATGCAATATGTCACACAATCTCATACATAATCATATCTCAA
Found at i:55310087 original size:21 final size:20
Alignment explanation
Indices: 55310063--55310102 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
55310053 GCCATGACAA
* *
55310063 AATATCCTATATACCAAAATG
1 AATATACTAAATA-CAAAATG
55310084 AATATACTAAATACAAAAT
1 AATATACTAAATACAAAAT
55310103 ACAACCTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.55, C:0.15, G:0.03, T:0.28
Consensus pattern (20 bp):
AATATACTAAATACAAAATG
Found at i:55316822 original size:27 final size:27
Alignment explanation
Indices: 55316784--55316838 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
55316774 CTAAGCTTTG
55316784 AACCAACTATTCCATTTGATTAACCGA
1 AACCAACTATTCCATTTGATTAACCGA
55316811 AACCAACTATTCCATTTGATTAACCGA
1 AACCAACTATTCCATTTGATTAACCGA
55316838 A
1 A
55316839 CATATCTCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.29
Consensus pattern (27 bp):
AACCAACTATTCCATTTGATTAACCGA
Found at i:55321642 original size:32 final size:32
Alignment explanation
Indices: 55321606--55321666 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
55321596 AAATAAACAC
55321606 ATAATTATTCATTT-AATA-TTATAACTATTCAA
1 ATAA-TATT-ATTTAAATAGTTATAACTATTCAA
*
55321638 ATAATATTATTTAAATAGTTATAATTATT
1 ATAATATTATTTAAATAGTTATAACTATT
55321667 TTTTCAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
31 8 0.31
32 14 0.54
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (32 bp):
ATAATATTATTTAAATAGTTATAACTATTCAA
Found at i:55321874 original size:16 final size:15
Alignment explanation
Indices: 55321838--55321882 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
55321828 TTGTCTTGGT
*
55321838 TCTTCTATTTCTCTTAT
1 TCTT-TATTT-TCTTAA
55321855 TCTTTAATTTTCTTAA
1 TCTTT-ATTTTCTTAA
55321871 TCTTTATTTTCT
1 TCTTTATTTTCT
55321883 AACAGTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 7 0.27
16 11 0.42
17 8 0.31
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.67
Consensus pattern (15 bp):
TCTTTATTTTCTTAA
Found at i:55333238 original size:44 final size:44
Alignment explanation
Indices: 55333188--55333276 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
55333178 TTGACAATAG
*
55333188 AATATTGTGGTGAAGAAGGGACTCTGTTTTGATTTTCTATACTA
1 AATATTGTGGTGAAGAAGGGACTCTGTTCTGATTTTCTATACTA
55333232 AATATTGTGGTGAAGAAGGGACTCTGTTCTGATTTTCTATACTA
1 AATATTGTGGTGAAGAAGGGACTCTGTTCTGATTTTCTATACTA
55333276 A
1 A
55333277 CTTGAGGAGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.39
Consensus pattern (44 bp):
AATATTGTGGTGAAGAAGGGACTCTGTTCTGATTTTCTATACTA
Found at i:55337260 original size:13 final size:14
Alignment explanation
Indices: 55337242--55337283 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
55337232 TTTTAATTTC
55337242 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
55337255 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
55337270 ATTTTAAATAATAT
1 ATTTT-AATAATAT
55337284 TCTTCCCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:55337268 original size:16 final size:16
Alignment explanation
Indices: 55337246--55337282 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
55337236 AATTTCATTT
55337246 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
55337263 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
55337278 TAATA
1 TAATA
55337283 TTCTTCCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:55337332 original size:18 final size:18
Alignment explanation
Indices: 55337309--55337366 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
55337299 GAAAATACTC
*
55337309 AATATTAATATTTTAATA
1 AATATTAATATTTTAAAA
*
55337327 AATATTCAATA-TTAAAAA
1 AATATT-AATATTTTAAAA
* *
55337345 TAATATTAACATTTTAACA
1 -AATATTAATATTTTAAAA
55337364 AAT
1 AAT
55337367 TCATCCAACT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 17 0.53
19 15 0.47
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
AATATTAATATTTTAAAA
Found at i:55337693 original size:9 final size:9
Alignment explanation
Indices: 55337679--55337711 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
55337669 TATTTATGTA
55337679 TTATGTAAG
1 TTATGTAAG
55337688 TTATGTAAG
1 TTATGTAAG
*
55337697 TTATATAAG
1 TTATGTAAG
55337706 TTATGT
1 TTATGT
55337712 TATTTATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:55337716 original size:43 final size:43
Alignment explanation
Indices: 55337669--55337764 Score: 115
Period size: 43 Copynumber: 2.2 Consensus size: 43
55337659 TGATATGATA
* *
55337669 TATTTATG-TATTATGTA-AGTTATGTAAGTTATATAAGTTATGT
1 TATTTATGATATGATATATAGTTATGT-A-TTATATAAGTTATGT
*
55337712 TATTTATGATATGATATATATTTATGTATTATATAAGTTATGT
1 TATTTATGATATGATATATAGTTATGTATTATATAAGTTATGT
* *
55337755 AAATTATGAT
1 TATTTATGAT
55337765 CCAAAGTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 31 0.67
44 8 0.17
45 7 0.15
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (43 bp):
TATTTATGATATGATATATAGTTATGTATTATATAAGTTATGT
Found at i:55337718 original size:18 final size:17
Alignment explanation
Indices: 55337647--55337754 Score: 65
Period size: 16 Copynumber: 6.9 Consensus size: 17
55337637 ATCCAAAGTT
* *
55337647 TTATTTAAGTTATGATA
1 TTATATAAGTTATGTTA
* *
55337664 TGATAT-ATTTATG-TA
1 TTATATAAGTTATGTTA
* *
55337679 TTATGTAAGTTATGTAA
1 TTATATAAGTTATGTTA
55337696 GTTATATAAGTTATGTTA
1 -TTATATAAGTTATGTTA
*
55337714 TT-TAT--GATATG--A
1 TTATATAAGTTATGTTA
*
55337726 -TATAT-ATTTATG-TA
1 TTATATAAGTTATGTTA
55337740 TTATATAAGTTATGT
1 TTATATAAGTTATGT
55337755 AAATTATGAT
Statistics
Matches: 69, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
11 1 0.01
12 4 0.06
13 4 0.06
14 6 0.09
15 11 0.16
16 21 0.30
17 7 0.10
18 15 0.22
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (17 bp):
TTATATAAGTTATGTTA
Found at i:55337779 original size:61 final size:64
Alignment explanation
Indices: 55337635--55337779 Score: 169
Period size: 61 Copynumber: 2.3 Consensus size: 64
55337625 TTATATGTTT
* * * *
55337635 TGATCCAAAGTTTTATTTAAGTTATGATATGATATATTTATGTATTATGTAAGTTATGTAAGTTA
1 TGATCCAAAGTTTTATTTATGATATGA-ATGATATATTTATGTATTATATAAGTTATGTAAATTA
55337700 T-AT---AAGTTATGTTATTTATGATATG-AT-ATATATTTATGTATTATATAAGTTATGTAAAT
1 TGATCCAAAG-T-T-TTATTTATGATATGAATGATATATTTATGTATTATATAAGTTATGTAAAT
55337759 TA
63 TA
55337761 TGATCCAAAGTTTT-TTTAT
1 TGATCCAAAGTTTTATTTAT
55337780 TCTTTAAATG
Statistics
Matches: 69, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
61 41 0.59
62 7 0.10
63 2 0.03
64 15 0.22
65 4 0.06
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.50
Consensus pattern (64 bp):
TGATCCAAAGTTTTATTTATGATATGAATGATATATTTATGTATTATATAAGTTATGTAAATTA
Found at i:55337831 original size:13 final size:13
Alignment explanation
Indices: 55337813--55337839 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55337803 TAATTATCAT
55337813 CTTTAAATTTTAA
1 CTTTAAATTTTAA
55337826 CTTTAAATTTTAA
1 CTTTAAATTTTAA
55337839 C
1 C
55337840 CCTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:55340134 original size:31 final size:31
Alignment explanation
Indices: 55340099--55340157 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
55340089 GTGCACGTGC
* *
55340099 ATATATAGATTATGAAAA-TAATAATAATTAT
1 ATATATAAATTAT-AAAAGTAAAAATAATTAT
55340130 ATATATAAATTATAAAAGTAAAAATAAT
1 ATATATAAATTATAAAAGTAAAAATAAT
55340158 AATTACATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (31 bp):
ATATATAAATTATAAAAGTAAAAATAATTAT
Found at i:55341780 original size:44 final size:44
Alignment explanation
Indices: 55341732--55341842 Score: 109
Period size: 44 Copynumber: 2.5 Consensus size: 44
55341722 CTAATACACT
* * * *
55341732 CCACTACAACTTTAGGGAGATAGGATTTGTTTATTC-TGTCTACC
1 CCACTGCAACTTTAGGGAGATA-GACTTGGTTATTCGGGTCTACC
* * *
55341776 CCACTGCAA-TTTCAGGGGGATTAGACTTGGTTATTCGGGTCTGCT
1 CCACTGCAACTTT-AGGGAGA-TAGACTTGGTTATTCGGGTCTACC
*
55341821 CCACTGCAACTTTAGAGAGATA
1 CCACTGCAACTTTAGGGAGATA
55341843 ATATATGTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
43 3 0.06
44 27 0.50
45 21 0.39
46 3 0.06
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (44 bp):
CCACTGCAACTTTAGGGAGATAGACTTGGTTATTCGGGTCTACC
Found at i:55341910 original size:44 final size:43
Alignment explanation
Indices: 55341815--55342149 Score: 269
Period size: 44 Copynumber: 7.8 Consensus size: 43
55341805 GTTATTCGGG
* * * *
55341815 TCTGCTCCACTGCAACTTTAGAGAGATAATA-TA-TGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTGCTTTAA
* * *
55341856 TCCGCTCCACTGCAACTTCAGGGACATAGGATTATTGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTATT-GCTTTAA
* * *
55341900 TCTGCTCCACTGCAACTTCAAGGAGATGAGATTCGCCA-T-CTTTAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT----ATTGCTTTAA
* *
55341945 TCTGC-CTCACTGCAACTTCAGGGGGATAAGA--CTTGCTTACTCAA
1 TCTGCTC-CACTGCAACTTCAGGGAGATAAGATTATTGCTT--T-AA
** * *
55341989 TCTGCTCCACTGCAACTTCAGGGAGATAAGACAAGATGC---GA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTA-TTGCTTTAA
* * * *
55342030 TCTGCT-CTCTGCAACTTTAGAGAGATAAGATCTATTACTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATTGCTTTAA
* * *
55342073 TCCGCTCCACTGCAACTTTAGGGAGATAGGATTATTGACTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTG-CTTTAA
*
55342117 TCTGCTCCACTGCAACTTCAAGGAGATAAGATT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT
55342150 CGCCATCTTC
Statistics
Matches: 232, Mismatches: 39, Indels: 43
0.74 0.12 0.14
Matches are distributed among these distances:
40 24 0.10
41 36 0.16
42 2 0.01
43 12 0.05
44 121 0.52
45 32 0.14
47 4 0.02
48 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTGCTTTAA
Found at i:55342333 original size:50 final size:50
Alignment explanation
Indices: 55342179--55342338 Score: 137
Period size: 50 Copynumber: 3.2 Consensus size: 50
55342169 AACTGGAAAC
* *
55342179 AAGATTCGCCGTCGTAGCTTCAACCTGTTCCACTACA-CTTCCAGGGGAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACATC-GCCAGGGGAGT
* * * * ** * * ** **
55342229 AAGATTCGCCGTTGCAGCTTCAGTCTTTTTAATTGCAAT-G-TTGGGGAAAC
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTAC-ATCGCCAGGGG-AGT
*
55342279 AAGATTCCCCGTCGTAGCTTCAATCTGTTCCACTACATCGCCAGGGGAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACATCGCCAGGGGAGT
55342329 AAGATTCGCC
1 AAGATTCGCC
55342339 ATTGCAGCTT
Statistics
Matches: 77, Mismatches: 28, Indels: 10
0.67 0.24 0.09
Matches are distributed among these distances:
49 6 0.08
50 66 0.86
51 5 0.06
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (50 bp):
AAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACATCGCCAGGGGAGT
Found at i:55343528 original size:25 final size:26
Alignment explanation
Indices: 55343500--55343548 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
55343490 AGTGTCTTGA
55343500 AAAGAAAAAAGTA-TTCAAGAACAGT
1 AAAGAAAAAAGTATTTCAAGAACAGT
*
55343525 AAAGAATAAAGTATTTCAAGAACA
1 AAAGAAAAAAGTATTTCAAGAACA
55343549 AACAAATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.59, C:0.08, G:0.14, T:0.18
Consensus pattern (26 bp):
AAAGAAAAAAGTATTTCAAGAACAGT
Found at i:55345548 original size:27 final size:27
Alignment explanation
Indices: 55345501--55345740 Score: 304
Period size: 27 Copynumber: 8.9 Consensus size: 27
55345491 GGGTATACCA
*
55345501 GTCATT-TTCCCTATGGGGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
* * * *
55345527 TTCATAT-TACTCTATAGGGGTATTTTG
1 GTCAT-TCTACCCTATGGGGGTATTTCG
*
55345554 GTCATTCTACCTTATGGGGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
* *
55345581 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
* * * *
55345608 ATCATTCTACCCTATGAGGATATTTTG
1 GTCATTCTACCCTATGGGGGTATTTCG
*
55345635 GTCATTCTACCCTATGGGGGTATTTTG
1 GTCATTCTACCCTATGGGGGTATTTCG
*
55345662 ATCATTCTACCCTATGGGGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
*
55345689 GTCATTCTACCCTATGAGGGTATTTCG
1 GTCATTCTACCCTATGGGGGTATTTCG
* *
55345716 ATCATTCTACCCTATGAGGGTATTT
1 GTCATTCTACCCTATGGGGGTATTT
55345741 TAGTCATTTT
Statistics
Matches: 185, Mismatches: 27, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
26 5 0.03
27 180 0.97
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (27 bp):
GTCATTCTACCCTATGGGGGTATTTCG
Found at i:55345632 original size:81 final size:81
Alignment explanation
Indices: 55345501--55345753 Score: 350
Period size: 81 Copynumber: 3.1 Consensus size: 81
55345491 GGGTATACCA
* *
55345501 GTCATTTT-CCCTATGGGGGTATTTCGTTCATAT-TACTCTAT-AGGGGTATTTTGGTCATTCTA
1 GTCATTTTACCCTATGGGGGTATTTCGATCAT-TCTACCCTATGA-GGGTATTTTGGTCATTCTA
* *
55345563 CCTTATGGGGGTATTTCG
64 CCCTATGGGGGTATTTTG
* *
55345581 GTCATTTTACCCTATAGGGGTATTTCGATCATTCTACCCTATGAGGATATTTTGGTCATTCTACC
1 GTCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATGAGGGTATTTTGGTCATTCTACC
55345646 CTATGGGGGTATTTTG
66 CTATGGGGGTATTTTG
* * * * *
55345662 ATCATTCTACCCTATGGGGGTATTTCGGTCATTCTACCCTATGAGGGTATTTCGATCATTCTACC
1 GTCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATGAGGGTATTTTGGTCATTCTACC
* *
55345727 CTATGAGGGTATTTTA
66 CTATGGGGGTATTTTG
55345743 GTCATTTTACC
1 GTCATTTTACC
55345754 TATTTTGGTG
Statistics
Matches: 153, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
80 9 0.06
81 143 0.93
82 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (81 bp):
GTCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATGAGGGTATTTTGGTCATTCTACC
CTATGGGGGTATTTTG
Found at i:55350978 original size:16 final size:16
Alignment explanation
Indices: 55350953--55350985 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55350943 AAATTTTATA
55350953 TATTTTTTTCT-TTTT
1 TATTTTTTTCTCTTTT
55350968 TATTATTTTTCTCTTTT
1 TATT-TTTTTCTCTTTT
55350985 T
1 T
55350986 TTTAGAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 7 0.44
17 5 0.31
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (16 bp):
TATTTTTTTCTCTTTT
Found at i:55350987 original size:19 final size:19
Alignment explanation
Indices: 55350946--55350986 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
55350936 TAAATCAAAA
*
55350946 TTTTATATATTTTTTTCTT
1 TTTTATATATTTTTCTCTT
55350965 TTTTAT-TATTTTTCTCTT
1 TTTTATATATTTTTCTCTT
55350983 TTTT
1 TTTT
55350987 TTAGAGAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTATATATTTTTCTCTT
Found at i:55352008 original size:11 final size:11
Alignment explanation
Indices: 55351994--55352023 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
55351984 ATAAAAATAA
55351994 AAATAAAACAT
1 AAATAAAACAT
55352005 AAATAAAACAT
1 AAATAAAACAT
55352016 AAACTAAA
1 AAA-TAAA
55352024 TGAAATAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (11 bp):
AAATAAAACAT
Found at i:55356526 original size:22 final size:22
Alignment explanation
Indices: 55356501--55356545 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
55356491 CAAAATATTG
55356501 AAAAAAAAACA-AAAAAATAGC
1 AAAAAAAAACATAAAAAATAGC
* *
55356522 AAAAAAATACATATAAAATAGC
1 AAAAAAAAACATAAAAAATAGC
55356544 AA
1 AA
55356546 GAATAGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.76, C:0.09, G:0.04, T:0.11
Consensus pattern (22 bp):
AAAAAAAAACATAAAAAATAGC
Found at i:55356529 original size:11 final size:11
Alignment explanation
Indices: 55356501--55356562 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
55356491 CAAAATATTG
*
55356501 AAAAAAA-AAC
1 AAAAAAATAGC
55356511 AAAAAAATAGC
1 AAAAAAATAGC
55356522 AAAAAAATA-C
1 AAAAAAATAGC
*
55356532 ATATAAAATAGC
1 A-AAAAAATAGC
* *
55356544 --AAGAATAGT
1 AAAAAAATAGC
55356553 AAAAAAATAG
1 AAAAAAATAG
55356563 TTTTTTCTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
9 6 0.15
10 9 0.22
11 25 0.61
12 1 0.02
ACGTcount: A:0.73, C:0.06, G:0.08, T:0.13
Consensus pattern (11 bp):
AAAAAAATAGC
Found at i:55357043 original size:6 final size:6
Alignment explanation
Indices: 55357032--55357057 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
55357022 GATCCGCGTA
55357032 TCCGAG TCCGAG TCCGAG TCCGAG TC
1 TCCGAG TCCGAG TCCGAG TCCGAG TC
55357058 ATGTTAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.31, T:0.19
Consensus pattern (6 bp):
TCCGAG
Found at i:55365906 original size:22 final size:22
Alignment explanation
Indices: 55365878--55365922 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
55365868 AAGAAAAATT
*
55365878 AAAATGTAAAAATTAAATTAAA
1 AAAATGTAAAAATTAAAATAAA
*
55365900 AAAATGTTAAAATTAAAATAAA
1 AAAATGTAAAAATTAAAATAAA
55365922 A
1 A
55365923 TTAGCTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAATGTAAAAATTAAAATAAA
Found at i:55367890 original size:128 final size:129
Alignment explanation
Indices: 55367724--55368122 Score: 653
Period size: 128 Copynumber: 3.1 Consensus size: 129
55367714 TCATTTTCTA
* *
55367724 ACACCACT-AATTTTAGGGTCGTTACACTTGTTCCTTAGTTAACTATCCAATTGTCAAAATTAAA
1 ACACCACTGACTTTTAGGGTCGTTACACTTGTACCTTAGTTAACTATCCAATTGTCAAAATTAAA
*
55367788 AGGCCAAACTTTAATTAAACTTTATACTAACCTCGGAAATGGGTTTCCAAAATCACCGTTTTCG
66 AGACCAAACTTTAATTAAACTTTATACTAACCTCGGAAATGGGTTTCCAAAATCACCGTTTTCG
* *
55367852 ACACTACTGA-TTTTAGGGTCGTTACACTTGTACTTTAGTTAACTATCCAATTGTCAAAATTAAA
1 ACACCACTGACTTTTAGGGTCGTTACACTTGTACCTTAGTTAACTATCCAATTGTCAAAATTAAA
* * *
55367916 AGACCAAACTTTAATTAAACTTTATACTAACTTTGGAAATGGGTTTCCAAAATTACCGTTTTCG
66 AGACCAAACTTTAATTAAACTTTATACTAACCTCGGAAATGGGTTTCCAAAATCACCGTTTTCG
*
55367980 ACACCACT-AGC-TTTATGGTCGTTACACTTGTACCTTAGTTAACTATCCAATTGTCAAAATTAA
1 ACACCACTGA-CTTTTAGGGTCGTTACACTTGTACCTTAGTTAACTATCCAATTGTCAAAATTAA
** *
55368043 AAGACCAAACTTTAATTAAACTTTATACTAACCTCAAAAATGGATTTCCAAAATCACCGTTTTCG
65 AAGACCAAACTTTAATTAAACTTTATACTAACCTCGGAAATGGGTTTCCAAAATCACCGTTTTCG
55368108 ACACCACTGACTTTT
1 ACACCACTGACTTTT
55368123 GAGTCATTAC
Statistics
Matches: 250, Mismatches: 16, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
127 1 0.00
128 244 0.98
129 5 0.02
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (129 bp):
ACACCACTGACTTTTAGGGTCGTTACACTTGTACCTTAGTTAACTATCCAATTGTCAAAATTAAA
AGACCAAACTTTAATTAAACTTTATACTAACCTCGGAAATGGGTTTCCAAAATCACCGTTTTCG
Found at i:55374778 original size:21 final size:21
Alignment explanation
Indices: 55374746--55374786 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
55374736 GAACATTTGG
55374746 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
55374767 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
55374787 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:55379045 original size:15 final size:15
Alignment explanation
Indices: 55379025--55379055 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55379015 CATGTGTCTC
*
55379025 ATGTATGCTTAGTGG
1 ATGTATACTTAGTGG
55379040 ATGTATACTTAGTGG
1 ATGTATACTTAGTGG
55379055 A
1 A
55379056 GATGTGATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.39
Consensus pattern (15 bp):
ATGTATACTTAGTGG
Found at i:55383846 original size:110 final size:111
Alignment explanation
Indices: 55383704--55384288 Score: 399
Period size: 110 Copynumber: 5.5 Consensus size: 111
55383694 CAAATAAATT
* * * *
55383704 TACATTATAACAAATCACAATACACATTAAACTAAA-A-AAATAATTTATAATCAAATCATAAAT
1 TACATTATAACAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCAAATCATAAAT
* *
55383767 TACTAACAAAATAACTTTAAAATAATTTAAAAAACACAAAAAAAAA
66 TACTAACAAAATAACTTTAAAAAAATTAAAAAAACACAAAAAAAAA
* * *
55383813 TACATTTATAATAAGTCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAA
1 TACA-TTATAACAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCAAATCATAAA
* ** *
55383878 TTACTAACAAAATAACTTTAAAAAAATTAAAAAAATTTACATTCATAAAA
65 TTACTAACAAAATAACTTTAAAAAAATTAAAAAAA--CACA-AAAAAAAA
* * * * * *
55383928 -A-ATCACAATAAA-CAC--T-AA-ACTAAGC-ACAA-AC--A--ATTTATAACCTAATGATAAA
1 TACATTATAACAAATCACAATAAACACTAAACTA-AACACAAACAATTTATAACCAAATCATAAA
* *
55383980 TTACTAACAAAATAACTTTCAAATAATTAAAAAAA-AC-AAAAAAAA
65 TTACTAACAAAATAACTTTAAAAAAATTAAAAAAACACAAAAAAAAA
* * * * * *
55384025 TATATTCATAAAAAATCACAATAAACATTAAACTAATCACAAACAATTTATAACCTAACCATAAA
1 TACATT-ATAACAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCAAATCATAAA
* * * * *** *
55384090 TTACTAAGAAAATGACTTTAAAATAATTTTAAAAAAATTACATTCATAAA
65 TTACTAACAAAATAACTTTAAAA-AA-ATTAAAAAAA-CACAAAAAAAAA
* * * *
55384140 -A-A--ATCACAAA--ACACT-AA-ACTAAAC-ACA----AACAATTTATAACCTAATCATAAAT
1 TACATTATAACAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCAAATCATAAAT
* * * ****
55384192 TACTAACAAAATAACTTTCAAATAATTAAAATAAA-ATAAAAATTTT
66 TACTAACAAAATAACTTTAAAAAAATTAAAA-AAACACAAAAAAAAA
* * *
55384238 TACATTCATAAAAAATAAC-A-AAACACTAAACTAAACACAAATAATTTATAA
1 TACATT-ATAACAAATCACAATAAACACTAAACTAAACACAAACAATTTATAA
55384289 TAATTGATAA
Statistics
Matches: 371, Mismatches: 64, Indels: 81
0.72 0.12 0.16
Matches are distributed among these distances:
97 5 0.01
98 5 0.01
99 11 0.03
100 11 0.03
101 46 0.12
102 52 0.14
103 7 0.02
104 5 0.01
105 16 0.04
106 14 0.04
107 10 0.03
108 7 0.02
109 5 0.01
110 83 0.22
111 5 0.01
112 71 0.19
113 2 0.01
114 7 0.02
115 9 0.02
ACGTcount: A:0.58, C:0.15, G:0.01, T:0.26
Consensus pattern (111 bp):
TACATTATAACAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCAAATCATAAAT
TACTAACAAAATAACTTTAAAAAAATTAAAAAAACACAAAAAAAAA
Found at i:55383919 original size:102 final size:102
Alignment explanation
Indices: 55383785--55384288 Score: 588
Period size: 110 Copynumber: 4.8 Consensus size: 102
55383775 AAATAACTTT
* * * *
55383785 AAAATAA-TTTAAAAAACA-CAAAAAAAAATACATTTATAATAAGTCACAATAAACACTAAACTA
1 AAAATAACTTTAAAAAA-ATTAAAAAAAAATACATTCATAAAAAATCACAATAAACACTAAACTA
55383848 AACACAAACAATTTATAACCTAATCATAAATTACTAAC
65 AACACAAACAATTTATAACCTAATCATAAATTACTAAC
**
55383886 AAAATAACTTTAAAAAAATTAAAAAAATTTACATTCATAAAAAATCACAATAAACACTAAACTAA
1 AAAATAACTTTAAAAAAATTAAAAAAAAATACATTCATAAAAAATCACAATAAACACTAAACTAA
* *
55383951 GCACAAACAATTTATAACCTAATGATAAATTACTAAC
66 ACACAAACAATTTATAACCTAATCATAAATTACTAAC
** * *
55383988 AAAATAACTTTCAAATAATTAAAAAAAACAAAAAAAATATATTCATAAAAAATCACAATAAACAT
1 AAAATAAC-TT----TAA--AAAAATTA-AAAAAAAATACATTCATAAAAAATCACAATAAACAC
* * *
55384053 TAAACTAATCACAAACAATTTATAACCTAACCATAAATTACTAAG
58 TAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAAC
* * * *
55384098 AAAATGACTTTAAAATAATTTTAAAAAAATTACATTCATAAAAAATCAC-A-AAACACTAAACTA
1 AAAATAACTTTAAAA-AAATTAAAAAAAAATACATTCATAAAAAATCACAATAAACACTAAACTA
55384161 AACACAAACAATTTATAACCTAATCATAAATTACTAAC
65 AACACAAACAATTTATAACCTAATCATAAATTACTAAC
* *
55384199 AAAATAACTTTCAAATAATTAAAATAAAATAAAAATTTTTACATTCATAAAAAATAAC-A-AAAC
1 AAAATAACTTT--AA-AA--AAATTAAAA-AAAAA----TACATTCATAAAAAATCACAATAAAC
*
55384262 ACTAAACTAAACACAAATAATTTATAA
56 ACTAAACTAAACACAAACAATTTATAA
55384289 TAATTGATAA
Statistics
Matches: 347, Mismatches: 36, Indels: 31
0.84 0.09 0.07
Matches are distributed among these distances:
101 65 0.19
102 93 0.27
103 31 0.09
104 4 0.01
105 10 0.03
106 4 0.01
107 3 0.01
109 8 0.02
110 129 0.37
ACGTcount: A:0.59, C:0.14, G:0.01, T:0.26
Consensus pattern (102 bp):
AAAATAACTTTAAAAAAATTAAAAAAAAATACATTCATAAAAAATCACAATAAACACTAAACTAA
ACACAAACAATTTATAACCTAATCATAAATTACTAAC
Found at i:55384059 original size:212 final size:213
Alignment explanation
Indices: 55383699--55384288 Score: 829
Period size: 212 Copynumber: 2.8 Consensus size: 213
55383689 AAAAACAAAT
* * * * * * *
55383699 AAATTTACATT-ATAACAAATCACAATACACATTAAACTAA-AAAAATAATTTATAATCAAATCA
1 AAATTTACATTCATAAAAAATCACAATAAACACTAAACTAACACAAACAATTTATAACCTAATCA
* * * *
55383762 TAAATTACTAACAAAATAACTTTAAAATAATTTAAAAAACACAAAAAAAAATACATTTATAATAA
66 TAAATTACTAACAAAATAACTTTCAAATAA-TTAAAAAAAAC-AAAAAAAATACATTCATAAAAA
* *
55383827 GTCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAATA
129 ATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAACCATAAATTACTAACAAAATA
55383892 ACTTTAAAA-AA-ATTAAAA
194 ACTTTAAAATAATATTAAAA
*
55383910 AAATTTACATTCATAAAAAATCACAATAAACACTAAACTAAGCACAAACAATTTATAACCTAATG
1 AAATTTACATTCATAAAAAATCACAATAAACACTAAACTAA-CACAAACAATTTATAACCTAATC
*
55383975 ATAAATTACTAACAAAATAACTTTCAAATAATTAAAAAAAACAAAAAAAATATATTCATAAAAAA
65 ATAAATTACTAACAAAATAACTTTCAAATAATTAAAAAAAACAAAAAAAATACATTCATAAAAAA
* * * *
55384040 TCACAATAAACATTAAACTAATCACAAACAATTTATAACCTAACCATAAATTACTAAGAAAATGA
130 TCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAACCATAAATTACTAACAAAATAA
*
55384105 CTTTAAAATAATTTTAAAA
195 CTTTAAAATAATATTAAAA
55384124 AAA-TTACATTCATAAAAAATCAC-A-AAACACTAAACTAAACACAAACAATTTATAACCTAATC
1 AAATTTACATTCATAAAAAATCACAATAAACACTAAACT-AACACAAACAATTTATAACCTAATC
* ***
55384186 ATAAATTACTAACAAAATAACTTTCAAATAATTAAAATAAAATAAAAATTTTTACATTCATAAAA
65 ATAAATTACTAACAAAATAACTTTCAAATAATTAAAA-AAAACAAAAA-AAATACATTCATAAAA
* *
55384251 AATAAC-A-AAACACTAAACTAAACACAAATAATTTATAA
128 AATCACAATAAACACTAAACTAAACACAAACAATTTATAA
55384289 TAATTGATAA
Statistics
Matches: 341, Mismatches: 30, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
211 110 0.32
212 126 0.37
213 49 0.14
214 56 0.16
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.26
Consensus pattern (213 bp):
AAATTTACATTCATAAAAAATCACAATAAACACTAAACTAACACAAACAATTTATAACCTAATCA
TAAATTACTAACAAAATAACTTTCAAATAATTAAAAAAAACAAAAAAAATACATTCATAAAAAAT
CACAATAAACACTAAACTAAACACAAACAATTTATAACCTAACCATAAATTACTAACAAAATAAC
TTTAAAATAATATTAAAA
Found at i:55384215 original size:101 final size:103
Alignment explanation
Indices: 55384017--55384288 Score: 352
Period size: 101 Copynumber: 2.6 Consensus size: 103
55384007 TAAAAAAAAC
* * *
55384017 AAAAAAAA-TATATTCATAAAAAATCACAATAAACATTAAACTAATCACAAACAATTTATAACCT
1 AAAAAAAATTACATTCATAAAAAATCAC-A-AAACACTAAACTAAACACAAACAATTTATAACCT
* *
55384081 AACCATAAATTACTAAGAAAATGACTTTAAAATAATT-T-
64 AACCATAAATTACTAACAAAATAACTTTAAAATAATTATA
*
55384119 TAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAA
1 AAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAA
* *
55384184 TCATAAATTACTAACAAAATAACTTTCAAATAATTAAAATA
66 CCATAAATTACTAACAAAATAACTTTAAAATAATT---ATA
* *
55384225 AAATAAAAATTTTTACATTCATAAAAAATAACAAAACACTAAACTAAACACAAATAATTTATAA
1 AAA-AAAAA---TTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAA
55384289 TAATTGATAA
Statistics
Matches: 149, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
101 65 0.44
102 8 0.05
103 18 0.12
105 1 0.01
106 2 0.01
107 5 0.03
110 50 0.34
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.26
Consensus pattern (103 bp):
AAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAA
CCATAAATTACTAACAAAATAACTTTAAAATAATTATA
Found at i:55384335 original size:211 final size:208
Alignment explanation
Indices: 55383699--55384337 Score: 710
Period size: 211 Copynumber: 3.0 Consensus size: 208
55383689 AAAAACAAAT
* * * * *
55383699 AAATTTACATT-ATAACAAATCACAATACACATTAAACTAAA-A-AAATAATTTATAATCAAATC
1 AAATTTACATTCATAAAAAATCACAA-A-ACACTAAACTAAACACAAACAATTTATAACCTAATC
* * * *
55383761 ATAAATTACTAACAAAATAACTTTAAAATAATTTAAAAAACACAAAAAAAAATACATTTATAATA
64 ATAAATTACTAACAAAATAACTTTCAAATAA-TTAAAAAAAAC-AAAAAAAATACATTCATAAAA
* *
55383826 AGTCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAA-AA
127 AATCACAATAAACACTAAACTAAACACAAACAATTTATAA-CTAATCATAAATTACTAAAAATAA
55383890 -TAA-CTTTAAAAAAATTAAAA
191 CTAATCTTT----AAATTAAAA
* *
55383910 AAATTTACATTCATAAAAAATCACAATAAACACTAAACTAAGCACAAACAATTTATAACCTAATG
1 AAATTTACATTCATAAAAAATCAC-A-AAACACTAAACTAAACACAAACAATTTATAACCTAATC
*
55383975 ATAAATTACTAACAAAATAACTTTCAAATAATTAAAAAAAACAAAAAAAATATATTCATAAAAAA
64 ATAAATTACTAACAAAATAACTTTCAAATAATTAAAAAAAACAAAAAAAATACATTCATAAAAAA
* * * *
55384040 TCACAATAAACATTAAACTAATCACAAACAATTTATAACCTAACCATAAATTACTAAGAA-AA-T
129 TCACAATAAACACTAAACTAAACACAAACAATTTATAA-CTAATCATAAATTACTAAAAATAACT
*
55384103 GA-CTTTAAAATAATTTTAAAA
193 AATCTTT---A-AA--TTAAAA
55384124 AAA-TTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAATCAT
1 AAATTTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAATCAT
* ***
55384188 AAATTACTAACAAAATAACTTTCAAATAATTAAAATAAAATAAAAATTTTTACATTCATAAAAAA
66 AAATTACTAACAAAATAACTTTCAAATAATTAAAA-AAAACAAAAA-AAATACATTCATAAAAAA
* * * **
55384253 TAAC-A-AAACACTAAACTAAACACAAATAATTTATAA-TAATTGATAAAAAAACATAAAAATAA
129 TCACAATAAACACTAAACTAAACACAAACAATTTATAACTAA-TCAT-AAATTAC-TAAAAATAA
55384315 CTAATCCCTTTAAATTAAAA
191 CTAAT--CTTTAAATTAAAA
55384335 AAA
1 AAA
55384338 ATTAATTACT
Statistics
Matches: 375, Mismatches: 35, Indels: 36
0.84 0.08 0.08
Matches are distributed among these distances:
209 3 0.01
210 2 0.01
211 130 0.35
212 123 0.33
213 54 0.14
214 59 0.16
217 4 0.01
ACGTcount: A:0.59, C:0.14, G:0.01, T:0.26
Consensus pattern (208 bp):
AAATTTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAATCAT
AAATTACTAACAAAATAACTTTCAAATAATTAAAAAAAACAAAAAAAATACATTCATAAAAAATC
ACAATAAACACTAAACTAAACACAAACAATTTATAACTAATCATAAATTACTAAAAATAACTAAT
CTTTAAATTAAAA
Found at i:55385569 original size:57 final size:57
Alignment explanation
Indices: 55385412--55385580 Score: 194
Period size: 57 Copynumber: 2.9 Consensus size: 57
55385402 TAAAGTGGAC
* * * * ***
55385412 TTAAAATAAATCACCTCTTTAAAGAAAAGCTGATGATCACACCACCTTAAGGTGAAA
1 TTAAACTAAATCACCTCTTTAAGGCAAAGATGATGATCACACCTTTTTAAGGTGAAA
* * * * * *
55385469 TTAAACTTAATCACTTCTTTAGGGCGAAGATGATGATCACACCTTTTTAAGTTGAAC
1 TTAAACTAAATCACCTCTTTAAGGCAAAGATGATGATCACACCTTTTTAAGGTGAAA
* *
55385526 TTCAACTAAATCACCTCCTTAAGGCAAAGATGATGATCACACCTGTTTTAAGGTG
1 TTAAACTAAATCACCTCTTTAAGGCAAAGATGATGATCACACCT-TTTTAAGGTG
55385581 GATTTTATTG
Statistics
Matches: 91, Mismatches: 20, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
57 82 0.90
58 9 0.10
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.30
Consensus pattern (57 bp):
TTAAACTAAATCACCTCTTTAAGGCAAAGATGATGATCACACCTTTTTAAGGTGAAA
Found at i:55386289 original size:17 final size:17
Alignment explanation
Indices: 55386253--55386304 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
55386243 CTATTTCCCA
*
55386253 AAATAAATATTATTTATTT
1 AAATAAAT-TAATTT-TTT
55386272 AAATAAATTAATTTTTT
1 AAATAAATTAATTTTTT
* *
55386289 AATTAAATAAATTTTT
1 AAATAAATTAATTTTT
55386305 CAGTCCAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 17 0.57
18 5 0.17
19 8 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AAATAAATTAATTTTTT
Found at i:55386294 original size:21 final size:20
Alignment explanation
Indices: 55386253--55386301 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
55386243 CTATTTCCCA
*
55386253 AAATAAA-TATTATTTATTT
1 AAATAAATTATTATTTAATT
*
55386272 AAATAAATTAATTTTTTAATT
1 AAATAAATT-ATTATTTAATT
55386293 AAATAAATT
1 AAATAAATT
55386302 TTTCAGTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 7 0.27
20 1 0.04
21 18 0.69
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATAAATTATTATTTAATT
Found at i:55397330 original size:12 final size:12
Alignment explanation
Indices: 55397313--55397338 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55397303 GTTCTTTCAT
55397313 AATTTTTGTTAA
1 AATTTTTGTTAA
55397325 AATTTTTGTTAA
1 AATTTTTGTTAA
55397337 AA
1 AA
55397339 GAAGATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (12 bp):
AATTTTTGTTAA
Found at i:55397529 original size:11 final size:11
Alignment explanation
Indices: 55397513--55397537 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55397503 GGAATGTAAT
55397513 TTAAGCTTAAA
1 TTAAGCTTAAA
55397524 TTAAGCTTAAA
1 TTAAGCTTAAA
55397535 TTA
1 TTA
55397538 TTTGATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
TTAAGCTTAAA
Found at i:55401047 original size:24 final size:24
Alignment explanation
Indices: 55401019--55401070 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
55401009 TTAGTAGGTC
* *
55401019 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
55401043 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
55401067 AAAT
1 AAAT
55401071 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:55404282 original size:21 final size:22
Alignment explanation
Indices: 55404256--55404308 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
55404246 TGTGGGGTCA
*
55404256 ACACGCCCATAT-AAAGGAGGC
1 ACACGCCCATATGAAAGAAGGC
* *
55404277 ACACGCCTAAATGAAAGAAGGC
1 ACACGCCCATATGAAAGAAGGC
*
55404299 ACACGACCAT
1 ACACGCCCAT
55404309 GTGACTATGA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
ACACGCCCATATGAAAGAAGGC
Found at i:55407066 original size:9 final size:9
Alignment explanation
Indices: 55407049--55407085 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
55407039 TGAGTTTTCG
55407049 AATTCGAAT
1 AATTCGAAT
*
55407058 AACTCGAAT
1 AATTCGAAT
*
55407067 AATTCAAAT
1 AATTCGAAT
55407076 AATTCGAAT
1 AATTCGAAT
55407085 A
1 A
55407086 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:55407497 original size:19 final size:19
Alignment explanation
Indices: 55407448--55407508 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
55407438 TATTTACTTT
55407448 CCCTCAAACTTTTA--TT-C
1 CCCT-AAACTTTTATTTTCC
*
55407465 CCCAAAACTTTTTATTTTCC
1 CCCTAAAC-TTTTATTTTCC
*
55407485 CCCTAAACTTTTACTTTTCA
1 CCCTAAACTTTTA-TTTTCC
55407505 CCCT
1 CCCT
55407509 TTACTCTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
16 4 0.11
17 8 0.22
19 7 0.19
20 17 0.47
ACGTcount: A:0.23, C:0.34, G:0.00, T:0.43
Consensus pattern (19 bp):
CCCTAAACTTTTATTTTCC
Found at i:55408011 original size:5 final size:5
Alignment explanation
Indices: 55408001--55408026 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
55407991 GAACAAATAT
55408001 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
55408027 ATTTCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:55412341 original size:9 final size:9
Alignment explanation
Indices: 55412327--55412353 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
55412317 TTAAATGTTG
55412327 ATACTATTA
1 ATACTATTA
55412336 ATACTATTA
1 ATACTATTA
55412345 ATACTATTA
1 ATACTATTA
55412354 GTATTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (9 bp):
ATACTATTA
Found at i:55412473 original size:22 final size:22
Alignment explanation
Indices: 55412448--55412494 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
55412438 ATTAATCGAA
*
55412448 TATTTTTTAATATTGTTATT-AT
1 TATTTCTTAATATTG-TATTAAT
*
55412470 TATTTCTTATTATTGTATTAAT
1 TATTTCTTAATATTGTATTAAT
55412492 TAT
1 TAT
55412495 AGTATTGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (22 bp):
TATTTCTTAATATTGTATTAAT
Found at i:55413380 original size:27 final size:27
Alignment explanation
Indices: 55413348--55413401 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
55413338 AACATTTATC
*
55413348 CCTCTAAGTTCCTTTCAAGACTGTCTT
1 CCTCTAAGTTCCTTTCAAGACTCTCTT
55413375 CCTCTAAGTTCCTTTCAAGACTCTCTT
1 CCTCTAAGTTCCTTTCAAGACTCTCTT
55413402 TCACTAACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.31, G:0.09, T:0.41
Consensus pattern (27 bp):
CCTCTAAGTTCCTTTCAAGACTCTCTT
Found at i:55413408 original size:27 final size:27
Alignment explanation
Indices: 55413351--55413408 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
55413341 ATTTATCCCT
* *
55413351 CTAAGTTCCTTTCAAGACTGTCTTCCT
1 CTAAGTTCCTTTCAAGACTCTCTTCCA
*
55413378 CTAAGTTCCTTTCAAGACTCTCTTTCA
1 CTAAGTTCCTTTCAAGACTCTCTTCCA
55413405 CTAA
1 CTAA
55413409 CCTTTCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.29, G:0.09, T:0.40
Consensus pattern (27 bp):
CTAAGTTCCTTTCAAGACTCTCTTCCA
Found at i:55413492 original size:15 final size:15
Alignment explanation
Indices: 55413472--55413549 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
55413462 TTTATGGAAA
55413472 ATCAAATATATGGGT
1 ATCAAATATATGGGT
* **
55413487 ATCAAATA-ATAGAA
1 ATCAAATATATGGGT
*
55413501 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
**
55413517 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
*
55413531 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
55413547 ATC
1 ATC
55413550 GAGATATTGG
Statistics
Matches: 46, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
14 8 0.17
15 30 0.65
16 8 0.17
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.27
Consensus pattern (15 bp):
ATCAAATATATGGGT
Found at i:55413513 original size:30 final size:30
Alignment explanation
Indices: 55413468--55413549 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
55413458 CATATTTATG
* *
55413468 GAAAATCAAATATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
55413498 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
55413528 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
55413550 GAGATATTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.26
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:55417354 original size:15 final size:15
Alignment explanation
Indices: 55417334--55417411 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
55417324 TTTATGGAAA
55417334 ATCAAATATATGGGT
1 ATCAAATATATGGGT
* **
55417349 ATCAAATA-ATAGAA
1 ATCAAATATATGGGT
*
55417363 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
**
55417379 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
*
55417393 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
55417409 ATC
1 ATC
55417412 GAGATATTGG
Statistics
Matches: 46, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
14 8 0.17
15 30 0.65
16 8 0.17
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.27
Consensus pattern (15 bp):
ATCAAATATATGGGT
Found at i:55417375 original size:30 final size:30
Alignment explanation
Indices: 55417330--55417411 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
55417320 CATATTTATG
* *
55417330 GAAAATCAAATATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
55417360 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
55417390 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
55417412 GAGATATTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.26
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:55434895 original size:29 final size:30
Alignment explanation
Indices: 55434825--55434895 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
55434815 ATAATTGAAT
* *
55434825 CTAAATTTTCAAATTTAAAAAGTAAAGAAA
1 CTAAATTTTTAAATATAAAAAGTAAAGAAA
* **
55434855 CTAAATTCTTAAATAT-AAAAGTAGGGAAA
1 CTAAATTTTTAAATATAAAAAGTAAAGAAA
55434884 CTAAATTTTTAA
1 CTAAATTTTTAA
55434896 TGTACGAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.32
Consensus pattern (30 bp):
CTAAATTTTTAAATATAAAAAGTAAAGAAA
Found at i:55442233 original size:26 final size:26
Alignment explanation
Indices: 55442154--55442233 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
55442144 TTTTGGAGTT
55442154 AAATTGATTCCATGAAGTGAAACTAC
1 AAATTGATTCCATGAAGTGAAACTAC
*
55442180 AAATTG--TCCAT----TGACACAGCGT-T
1 AAATTGATTCCATGAAGTGA-A-A-C-TAC
55442203 AAATTGATTCCATGAAGTGAAACTAC
1 AAATTGATTCCATGAAGTGAAACTAC
55442229 AAATT
1 AAATT
55442234 CTTTTCACCC
Statistics
Matches: 41, Mismatches: 2, Indels: 22
0.63 0.03 0.34
Matches are distributed among these distances:
20 3 0.07
21 1 0.02
22 1 0.02
23 7 0.17
24 6 0.15
25 6 0.15
26 12 0.29
27 1 0.02
28 1 0.02
29 3 0.07
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (26 bp):
AAATTGATTCCATGAAGTGAAACTAC
Found at i:55443251 original size:142 final size:142
Alignment explanation
Indices: 55442995--55443260 Score: 383
Period size: 142 Copynumber: 1.9 Consensus size: 142
55442985 ATATAGACAA
** * * *
55442995 GAGGAAAACTTGGGCATCTAAAGCAAAACTGATTTAAAAGGGAACAACAGTCTTTCACTCTCATC
1 GAGGAAAACCAGGGCATCTAAAACAAAACTCATTTAAAAGGGAACAACAGTCTATCACTCTCATC
** *
55443060 ACCTACCATCTCCTTCGAGACTCGATTACGTTAGGAAACAGAAGATATATGAATGAAAATTTATA
66 ACCTACCATCTCCCCCGAGACTCAATTACGTTAGGAAACAGAAGATATATGAATGAAAATTTATA
55443125 CAAAACAAATAT
131 CAAAACAAATAT
* *
55443137 GAGGAAAACCAGGGCATCTAAAACAAAAC-CATTTTAAAAGGGACCAACAGTCTATCATTCTCAT
1 GAGGAAAACCAGGGCATCTAAAACAAAACTCA-TTTAAAAGGGAACAACAGTCTATCACTCTCAT
* * *
55443201 CACCTACCATCTCCCCCGAGACTCAATTA-TTATATGAAACAGAAGTTATATGAATGAAAA
65 CACCTACCATCTCCCCCGAGACTCAATTACGT-TAGGAAACAGAAGATATATGAATGAAAA
55443261 CTGATAATAA
Statistics
Matches: 109, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
141 2 0.02
142 107 0.98
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.24
Consensus pattern (142 bp):
GAGGAAAACCAGGGCATCTAAAACAAAACTCATTTAAAAGGGAACAACAGTCTATCACTCTCATC
ACCTACCATCTCCCCCGAGACTCAATTACGTTAGGAAACAGAAGATATATGAATGAAAATTTATA
CAAAACAAATAT
Found at i:55448786 original size:27 final size:27
Alignment explanation
Indices: 55448750--55448815 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
55448740 TAATAATTTT
**
55448750 TAAATAAAAAATTAACTCTTTAATTTAA
1 TAAAT-AAAAATTAACTAATTAATTTAA
* **
55448778 TAAATAAAAATTAATTAATTAATTTTT
1 TAAATAAAAATTAACTAATTAATTTAA
55448805 TAAATAAAAAT
1 TAAATAAAAAT
55448816 AAAATATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
27 28 0.85
28 5 0.15
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (27 bp):
TAAATAAAAATTAACTAATTAATTTAA
Found at i:55448836 original size:29 final size:27
Alignment explanation
Indices: 55448778--55448838 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 27
55448768 TTTAATTTAA
* * *
55448778 TAAATAAAAATTAATTAATTAATTTTT
1 TAAATAAAAATAAATTAATTAATCTCT
*
55448805 TAAATAAAAATAAAATATAATTTATCTCT
1 TAAATAAAAAT-AAAT-TAATTAATCTCT
55448834 TAAAT
1 TAAAT
55448839 TCCTACATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 11 0.39
28 3 0.11
29 14 0.50
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (27 bp):
TAAATAAAAATAAATTAATTAATCTCT
Found at i:55453830 original size:90 final size:90
Alignment explanation
Indices: 55453709--55454035 Score: 408
Period size: 90 Copynumber: 3.6 Consensus size: 90
55453699 TTTGTATCTG
* *
55453709 TAAATTTAATTTAGTCAGTATTCTATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTAACC
1 TAAATTTAATTTAATCAGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTAACC
55453774 ATCTGTTTGTAGTTTGTTGGGTGTT
66 ATCTGTTTGTAGTTTGTTGGGTGTT
* * * * * * *
55453799 TAAATTTAATTTAATCTGTGTTATATATAGTTTGAATTTAAAATTTTCATGCACTAATTTTATCC
1 TAAATTTAATTTAATCAGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTAACC
*
55453864 ATCTGTTTGTAGTTTGTTGAGTGTT
66 ATCTGTTTGTAGTTTGTTGGGTGTT
* * * * ** *
55453889 TAAATTTAATTTAGA-CCGTATTATATGTAGTTTAAATTTAAATTTTTTGTGTATTAAACTTACC
1 TAAATTTAATTTA-ATCAGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTAAC
55453953 CATCTGTTTGTAGTTTGTTGGGTGTT
65 CATCTGTTTGTAGTTTGTTGGGTGTT
* * * * * *
55453979 TAAATTTAATTTAGTGCA-TATTAT-TTTTGTTTGAATTTTATATTTTTGTGTATTAAT
1 TAAATTTAATTTAAT-CAGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAAT
55454036 ATTGTAGAAT
Statistics
Matches: 202, Mismatches: 32, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
89 26 0.13
90 174 0.86
91 2 0.01
ACGTcount: A:0.27, C:0.06, G:0.14, T:0.52
Consensus pattern (90 bp):
TAAATTTAATTTAATCAGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTAACC
ATCTGTTTGTAGTTTGTTGGGTGTT
Found at i:55455878 original size:24 final size:23
Alignment explanation
Indices: 55455843--55455895 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
55455833 TCTTTTTAAC
*
55455843 TTTTTTTACCATTTCATTTAAAT
1 TTTTTTTACCATTTAATTTAAAT
* *
55455866 TATTTTTTCCCATTTAATTTTAAT
1 T-TTTTTTACCATTTAATTTAAAT
55455890 TTTTTT
1 TTTTTT
55455896 CTTATTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTTTTACCATTTAATTTAAAT
Found at i:55455887 original size:25 final size:22
Alignment explanation
Indices: 55455837--55455895 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 22
55455827 GCCCTATCTT
* *
55455837 TTTAACTTTTTTTACCATTTCA
1 TTTAATTTTTTTTACCATTTAA
*
55455859 TTTAAATTATTTTTTCCCATTTAA
1 TTT-AATT-TTTTTTACCATTTAA
55455883 TTTTAATTTTTTT
1 -TTTAATTTTTTT
55455896 CTTATTTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 3 0.10
23 8 0.26
24 17 0.55
25 3 0.10
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTAATTTTTTTTACCATTTAA
Found at i:55455907 original size:17 final size:17
Alignment explanation
Indices: 55455882--55455941 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 17
55455872 TTCCCATTTA
*
55455882 ATTTTAATTTTTTTCTT
1 ATTTCAATTTTTTTCTT
55455899 ATTTCAA-TTTTTT-TT
1 ATTTCAATTTTTTTCTT
55455914 ATTTCAGTATTTGTTTTC--
1 ATTTCA--ATTT-TTTTCTT
55455932 ATTTCAATTT
1 ATTTCAATTT
55455942 ATAATTTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
15 8 0.22
16 10 0.27
17 7 0.19
18 8 0.22
19 4 0.11
ACGTcount: A:0.20, C:0.08, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTCAATTTTTTTCTT
Found at i:55455930 original size:18 final size:15
Alignment explanation
Indices: 55455890--55455941 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 15
55455880 TAATTTTAAT
55455890 TTTTTTCTTATTTCAA
1 TTTTTT-TTATTTCAA
55455906 TTTTTTTTATTTCAGTA
1 TTTTTTTTATTTCA--A
*
55455923 TTTGTTTTCATTTCAA
1 TTT-TTTTTATTTCAA
55455939 TTT
1 TTT
55455942 ATAATTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 8 0.25
16 10 0.31
17 4 0.12
18 10 0.31
ACGTcount: A:0.17, C:0.10, G:0.04, T:0.69
Consensus pattern (15 bp):
TTTTTTTTATTTCAA
Found at i:55455992 original size:5 final size:5
Alignment explanation
Indices: 55455963--55456087 Score: 83
Period size: 5 Copynumber: 23.4 Consensus size: 5
55455953 TCATTTAAAC
* * *
55455963 TTTCA TTCCA TTTCA TAATCA --TCA TTTCA TTTTA TATTCA TTTAACA
1 TTTCA TTTCA TTTCA T-TTCA TTTCA TTTCA TTTCA T-TTCA TTT--CA
* *
55456010 TTTCA TTTCA TTTCA TTTCA TTTCA TATTCA TTACAAA TTACA TTTCA
1 TTTCA TTTCA TTTCA TTTCA TTTCA T-TTCA TTTC--A TTTCA TTTCA
* *
55456058 TTTCG TATTCA TTTAAAA TTTCA TTTCA TT
1 TTTCA T-TTCA TTT--CA TTTCA TTTCA TT
55456088 AATTGTTTTC
Statistics
Matches: 97, Mismatches: 11, Indels: 24
0.73 0.08 0.18
Matches are distributed among these distances:
3 3 0.03
5 64 0.66
6 16 0.16
7 14 0.14
ACGTcount: A:0.29, C:0.18, G:0.01, T:0.53
Consensus pattern (5 bp):
TTTCA
Found at i:55456038 original size:38 final size:38
Alignment explanation
Indices: 55455984--55456071 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 38
55455974 TTCATAATCA
* * *
55455984 TCATTTCATTTTATATTCATTTA-ACATTTCATTTCATT
1 TCATTTCATTTCATATTCA-TTACAAATTACATTTCATT
55456022 TCATTTCATTTCATATTCATTACAAATTACATTTCATT
1 TCATTTCATTTCATATTCATTACAAATTACATTTCATT
*
55456060 TCGTATTCATTT
1 TCAT-TTCATTT
55456072 AAAATTTCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
37 3 0.07
38 34 0.77
39 7 0.16
ACGTcount: A:0.27, C:0.17, G:0.01, T:0.55
Consensus pattern (38 bp):
TCATTTCATTTCATATTCATTACAAATTACATTTCATT
Found at i:55456057 original size:28 final size:28
Alignment explanation
Indices: 55456023--55456087 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
55456013 CATTTCATTT
55456023 CATTTCATTTCATATTCA-TTACAAATTA
1 CATTTCATTTCATATTCATTTA-AAATTA
* *
55456051 CATTTCATTTCGTATTCATTTAAAATTT
1 CATTTCATTTCATATTCATTTAAAATTA
55456079 CATTTCATT
1 CATTTCATT
55456088 AATTGTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 31 0.91
29 3 0.09
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.51
Consensus pattern (28 bp):
CATTTCATTTCATATTCATTTAAAATTA
Found at i:55456179 original size:15 final size:16
Alignment explanation
Indices: 55456159--55456199 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
55456149 AGTAGTCTCA
*
55456159 TTTCAATT-TATCTTT
1 TTTCAATTCAATCTTT
*
55456174 TTTCAATTCAATTTTT
1 TTTCAATTCAATCTTT
55456190 TTTCAATTCA
1 TTTCAATTCA
55456200 TTCCATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTCAATTCAATCTTT
Done.