Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006423.1 Hibiscus syriacus cultivar Beakdansim tig00015498_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: 772901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:339616 original size:35 final size:34
Alignment explanation
Indices: 339570--339682 Score: 156
Period size: 35 Copynumber: 3.2 Consensus size: 34
339560 AAAACAATCC
*
339570 TCAATTTCATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
339605 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* *
339640 TCAATTAT-ATTCTAAAACCCAAATTCTAAAATACT
1 TCAATT-TCATTCT-AAACCCAAATTCCAAAATAAT
339675 TCAATTTC
1 TCAATTTC
339683 TGTCTTTTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
34 2 0.03
35 62 0.87
36 7 0.10
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:340785 original size:35 final size:34
Alignment explanation
Indices: 340737--340848 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 34
340727 ATTCCTCCTT
* *
340737 AAATTGAAATATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGG-TTTAGAATG
*
340772 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
*
340807 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
340842 AAATTGA
1 AAATTGA
340849 TGAATGTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
35 67 0.96
36 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:341541 original size:31 final size:31
Alignment explanation
Indices: 341505--341595 Score: 85
Period size: 31 Copynumber: 2.9 Consensus size: 31
341495 TACCGTACCA
341505 ATTAAA-TGATGATGTGATATGTGTCACATC
1 ATTAAAGTGATGATGTGATATGTGTCACATC
* * * * *
341535 ATTTAAAGTAATAACGTGATGTGTATCACATC
1 A-TTAAAGTGATGATGTGATATGTGTCACATC
* * * *
341567 ATCAAAGTGAGGGTGTGATATATGTCACA
1 ATTAAAGTGATGATGTGATATGTGTCACA
341596 CGCTACTAAT
Statistics
Matches: 45, Mismatches: 14, Indels: 3
0.73 0.23 0.05
Matches are distributed among these distances:
30 1 0.02
31 24 0.53
32 20 0.44
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (31 bp):
ATTAAAGTGATGATGTGATATGTGTCACATC
Found at i:349685 original size:72 final size:72
Alignment explanation
Indices: 349554--349734 Score: 217
Period size: 72 Copynumber: 2.5 Consensus size: 72
349544 CAGCAACTCA
* *
349554 TCGGTTTCCATGT-CGACCTTAGTCTGTTTGAACCGAAAATCGGGTTTCATTTATCAGTTTGTGG
1 TCGGTTTCCTTGTCCGACCTTAGTCTGTTTGAACCGAAAATCAGGTTTCATTTATCAGTTTGTGG
349618 TGTGTCT
66 TGTGTCT
* * * * *
349625 TTGGTTTCCTTGTCCGACCGTT-GTTTGTTGTGGACCGAATATCAGGTTTCGTTT-TCAGTTTGT
1 TCGGTTTCCTTGTCCGACC-TTAGTCTGTT-TGAACCGAAAATCAGGTTTCATTTATCAGTTTGT
349688 GGTGTGTCT
64 GGTGTGTCT
* * *
349697 TCGGCTTCCTTGTCCGA-ATATTGTCTGTTTGAACCGAA
1 TCGGTTTCCTTGTCCGACCT-TAGTCTGTTTGAACCGAA
349735 CATCGTGTCT
Statistics
Matches: 93, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
70 1 0.01
71 20 0.22
72 50 0.54
73 22 0.24
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.42
Consensus pattern (72 bp):
TCGGTTTCCTTGTCCGACCTTAGTCTGTTTGAACCGAAAATCAGGTTTCATTTATCAGTTTGTGG
TGTGTCT
Found at i:351777 original size:34 final size:39
Alignment explanation
Indices: 351701--351777 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 39
351691 ATGAAATCAT
351701 TATAATATATGTTTTTCCACATGTTTTCTTAATTTAAGC
1 TATAATATATGTTTTTCCACATGTTTTCTTAATTTAAGC
351740 TATAA-ATATG-TTTT-C-CATGTTTTCTTAA-TTAAGC
1 TATAATATATGTTTTTCCACATGTTTTCTTAATTTAAGC
351774 TATA
1 TATA
351778 GTGGTTTAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
34 10 0.26
35 13 0.34
36 1 0.03
37 4 0.11
38 5 0.13
39 5 0.13
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.51
Consensus pattern (39 bp):
TATAATATATGTTTTTCCACATGTTTTCTTAATTTAAGC
Found at i:354684 original size:48 final size:50
Alignment explanation
Indices: 354574--354698 Score: 182
Period size: 48 Copynumber: 2.5 Consensus size: 50
354564 AAACTCCTGT
* * * *
354574 AAGATCTGATATTCTCTTCAGAGTAAACGGAACATGTATCTCTCTTTCTC
1 AAGATCTGATATTCCCTTCAGAGTAAGCGGAACATGTACCTCTCTTTCCC
*
354624 AAGATCTGATATTCCCTTCAGAGTAAGCGGAACA-G-GCCTCTCTTTCCC
1 AAGATCTGATATTCCCTTCAGAGTAAGCGGAACATGTACCTCTCTTTCCC
*
354672 AAGATGTGATATTCCCTTCAGAGTAAG
1 AAGATCTGATATTCCCTTCAGAGTAAG
354699 TGGAGATAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
48 36 0.52
49 1 0.01
50 32 0.46
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (50 bp):
AAGATCTGATATTCCCTTCAGAGTAAGCGGAACATGTACCTCTCTTTCCC
Found at i:355922 original size:71 final size:73
Alignment explanation
Indices: 355806--355978 Score: 255
Period size: 71 Copynumber: 2.4 Consensus size: 73
355796 AAAAATATAT
355806 AATATATGAAATCATTATAATATTTGTTTTCTCACATGTTTCCTTAATTT-AGC-TAGTGGTTTA
1 AATATATGAAATCATTATAATATTTGTTTTCTCACATGTTTCCTTAATTTAAGCATAGTGGTTTA
355869 GTTTTTTA
66 GTTTTTTA
* * *
355877 AATATATGGAGTCATTATATTATTTGTTTTC-CTACATGTTTCCTTAATTTAAGCTATAGTGGTT
1 AATATATGAAATCATTATAATATTTGTTTTCTC-ACATGTTTCCTTAATTTAAGC-ATAGTGGTT
355941 TAGTTTTTT-
64 TAGTTTTTTA
* *
355950 AATATATAAAATTATTATAATATTTGTTT
1 AATATATGAAATCATTATAATATTTGTTT
355979 CTTCACTTTC
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
70 1 0.01
71 45 0.50
72 3 0.03
73 24 0.27
74 17 0.19
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.51
Consensus pattern (73 bp):
AATATATGAAATCATTATAATATTTGTTTTCTCACATGTTTCCTTAATTTAAGCATAGTGGTTTA
GTTTTTTA
Found at i:359646 original size:26 final size:26
Alignment explanation
Indices: 359610--359665 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
359600 TATTGACTCG
* *
359610 TTTATAACATT-AATTTTAGTTATACA
1 TTTATAACATTAAACTTTAATT-TACA
359636 TTTATAACATTAAACTTTAATTTACA
1 TTTATAACATTAAACTTTAATTTACA
359662 TTTA
1 TTTA
359666 ATTGTACAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 19 0.70
27 8 0.30
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTATAACATTAAACTTTAATTTACA
Found at i:360891 original size:197 final size:195
Alignment explanation
Indices: 360500--360892 Score: 727
Period size: 196 Copynumber: 2.0 Consensus size: 195
360490 AATTGATGTA
360500 TATTGATAAAATTAAAGTTTAACTATACAAACTAGTCAACAAATAAAATTTAATAGTATTTGAAT
1 TATTGATAAAATTAAAGTTTAACTATACAAACTAGTCAACAAATAAAATTTAATAGTATTTGAAT
360565 CAGTTTGCCCTAAAATACTAAATAAACTATCCATTAATCACTAACTATTTAGCCCTTTTACTTGT
66 CAGTTTGCCCTAAAATACTAAATAAACTATCCATTAATCACTAACTATTTAGCCCTTTTACTTGT
360630 ACCATTGATCTTTCAGTTTGTCAATCAGACCACCTAACTATTTAATTATATTCAATCAAGGTACT
131 ACCATTGATCTTTCAGTTTGTCAATCAGACCACCTAACTATTTAATTATATTCAATCAAGGTACT
360695 TATTGATAAAATTAAAAGTTTAACTATACAAACTAGTCAACAAATAAAATTTAATAGTATTTGAA
1 TATTGATAAAATT-AAAGTTTAACTATACAAACTAGTCAACAAATAAAATTTAATAGTATTTGAA
360760 TCAGTTTGCCCTAAAA-ACTAAATAAACTATACCATTAATCACTTAACTATTTAGCCCTTTTACT
65 TCAGTTTGCCCTAAAATACTAAATAAACTAT-CCATTAATCAC-TAACTATTTAGCCCTTTTACT
*
360824 TGTACCATTGATCTTTCAGTTTTGTCAATCA-CCCACCTAACTATTTAATTATATTCAATCAAGG
128 TGTACCATTGATCTTTCAG-TTTGTCAATCAGACCACCTAACTATTTAATTATATTCAATCAAGG
360888 TACT
192 TACT
360892 T
1 T
360893 GCCGTAATAT
Statistics
Matches: 193, Mismatches: 1, Indels: 6
0.96 0.00 0.03
Matches are distributed among these distances:
195 27 0.14
196 78 0.40
197 77 0.40
198 11 0.06
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (195 bp):
TATTGATAAAATTAAAGTTTAACTATACAAACTAGTCAACAAATAAAATTTAATAGTATTTGAAT
CAGTTTGCCCTAAAATACTAAATAAACTATCCATTAATCACTAACTATTTAGCCCTTTTACTTGT
ACCATTGATCTTTCAGTTTGTCAATCAGACCACCTAACTATTTAATTATATTCAATCAAGGTACT
Found at i:362748 original size:20 final size:20
Alignment explanation
Indices: 362723--362770 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
362713 TTATTCCCTA
362723 GTAATCTTTTA-TTCTCATTG
1 GTAATCTTTTATTTC-CATTG
362743 GTAATCTTTTATTTCCATTG
1 GTAATCTTTTATTTCCATTG
*
362763 ATAATCTT
1 GTAATCTT
362771 ACATTCCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (20 bp):
GTAATCTTTTATTTCCATTG
Found at i:362780 original size:20 final size:20
Alignment explanation
Indices: 362733--362797 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
362723 GTAATCTTTT
* * **
362733 ATTCTCATTGGTAATCTTTT
1 ATTCCCATTGATAATCTTAC
*
362753 ATTTCCATTGATAATCTTAC
1 ATTCCCATTGATAATCTTAC
*
362773 ATTCCCATTAATAATCTTAC
1 ATTCCCATTGATAATCTTAC
362793 ATTCC
1 ATTCC
362798 GTGAACAAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.28, C:0.22, G:0.05, T:0.46
Consensus pattern (20 bp):
ATTCCCATTGATAATCTTAC
Found at i:363223 original size:30 final size:30
Alignment explanation
Indices: 363169--363232 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 30
363159 TTAGGGATTA
*
363169 AAATTATCAATTAAAATAAAATTAA-GACC
1 AAATTATCAAATAAAATAAAATTAATGACC
*
363198 AAATTGATCAAAT-AAATAAATATTAATGATC
1 AAATT-ATCAAATAAAATAAA-ATTAATGACC
363229 AAAT
1 AAAT
363233 ATAAATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 12 0.40
30 11 0.37
31 7 0.23
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTATCAAATAAAATAAAATTAATGACC
Found at i:368169 original size:30 final size:31
Alignment explanation
Indices: 368103--368169 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 31
368093 AACGATTAGT
* * *
368103 TAAAATATTATTATTAAATATTTAAGAATGA
1 TAAAATAGTAGTATTAAATATTTAAGAATAA
368134 T-AAATAGTAGTATTAAATA-TTAA-AATAAA
1 TAAAATAGTAGTATTAAATATTTAAGAAT-AA
368163 TAAAATA
1 TAAAATA
368170 TCTCTGATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 3 0.10
29 6 0.19
30 21 0.68
31 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (31 bp):
TAAAATAGTAGTATTAAATATTTAAGAATAA
Found at i:372330 original size:31 final size:31
Alignment explanation
Indices: 372287--372355 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
372277 GTGAAAGGTT
* *
372287 AAATTAACATTTTATATAAAGTTTAGGGATC
1 AAATTAACATTTTATATAAACTTTAGAGATC
* *
372318 AAATTAAGATTTTATCTAAACTTTAGAGATC
1 AAATTAACATTTTATATAAACTTTAGAGATC
372349 AAATTAA
1 AAATTAA
372356 AAATTAACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (31 bp):
AAATTAACATTTTATATAAACTTTAGAGATC
Found at i:380062 original size:3 final size:3
Alignment explanation
Indices: 380056--380091 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
380046 TTTAATACAT
380056 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TA
380092 TGTAAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:381796 original size:7 final size:7
Alignment explanation
Indices: 381784--381809 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
381774 GATAGTGCCT
381784 TAAAATG
1 TAAAATG
381791 TAAAATG
1 TAAAATG
381798 TAAAATG
1 TAAAATG
381805 TAAAA
1 TAAAA
381810 CTGTTTCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.27
Consensus pattern (7 bp):
TAAAATG
Found at i:384377 original size:10 final size:10
Alignment explanation
Indices: 384362--384428 Score: 53
Period size: 10 Copynumber: 6.1 Consensus size: 10
384352 CATTTAAACG
384362 ATAAACGAAC
1 ATAAACGAAC
* *
384372 ATAAACAAATGTA
1 ATAAACGAA---C
384385 ATAAACGAACGC
1 ATAAACGAA--C
384397 AATAAACGAAC
1 A-TAAACGAAC
*
384408 GTAAACGAAC
1 ATAAACGAAC
384418 ATAAACGAAC
1 ATAAACGAAC
384428 A
1 A
384429 ACACAAACAC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
10 27 0.60
11 1 0.02
12 1 0.02
13 16 0.36
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:384400 original size:13 final size:13
Alignment explanation
Indices: 384384--384408 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
384374 AAACAAATGT
384384 AATAAACGAACGC
1 AATAAACGAACGC
384397 AATAAACGAACG
1 AATAAACGAACG
384409 TAAACGAACA
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:0.56, C:0.20, G:0.16, T:0.08
Consensus pattern (13 bp):
AATAAACGAACGC
Found at i:384720 original size:14 final size:14
Alignment explanation
Indices: 384701--384790 Score: 61
Period size: 14 Copynumber: 7.0 Consensus size: 14
384691 CCCTCTGTTA
384701 GAACATAAATGAAC
1 GAACATAAATGAAC
384715 GAACATAAAT----
1 GAACATAAATGAAC
* *
384725 GTACATAACTGAAC
1 GAACATAAATGAAC
384739 GAACATAAAT----
1 GAACATAAATGAAC
* **
384749 GAATATAACCGAAC
1 GAACATAAATGAAC
*
384763 GACCATAAATGAAC
1 GAACATAAATGAAC
*
384777 GAACATAAACGAAC
1 GAACATAAATGAAC
384791 ATATAATCGA
Statistics
Matches: 55, Mismatches: 13, Indels: 16
0.65 0.15 0.19
Matches are distributed among these distances:
10 15 0.27
14 40 0.73
ACGTcount: A:0.53, C:0.18, G:0.13, T:0.16
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:384737 original size:24 final size:24
Alignment explanation
Indices: 384701--384802 Score: 107
Period size: 24 Copynumber: 4.2 Consensus size: 24
384691 CCCTCTGTTA
*
384701 GAACATAAATGAACGAACATAAAT
1 GAACATAACTGAACGAACATAAAT
*
384725 GTACATAACTGAACGAACATAAAT
1 GAACATAACTGAACGAACATAAAT
* * *
384749 GAATATAACCGAACGACCATAAAT
1 GAACATAACTGAACGAACATAAAT
* *
384773 GAAC-GAACATAAACGAACATATAAT
1 GAACATAAC-TGAACGAACATA-AAT
384798 CGAAC
1 -GAAC
384803 GTTCACGAAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
23 3 0.05
24 54 0.84
25 3 0.05
26 4 0.06
ACGTcount: A:0.53, C:0.18, G:0.13, T:0.17
Consensus pattern (24 bp):
GAACATAACTGAACGAACATAAAT
Found at i:384770 original size:38 final size:40
Alignment explanation
Indices: 384728--384803 Score: 111
Period size: 38 Copynumber: 1.9 Consensus size: 40
384718 CATAAATGTA
* *
384728 CATAACTGAACGAACATAAATG-A-ATATAACCGAACGAC
1 CATAAATGAACGAACATAAACGAACATATAACCGAACGAC
*
384766 CATAAATGAACGAACATAAACGAACATATAATCGAACG
1 CATAAATGAACGAACATAAACGAACATATAACCGAACG
384804 TTCACGAACG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 20 0.61
39 1 0.03
40 12 0.36
ACGTcount: A:0.51, C:0.20, G:0.13, T:0.16
Consensus pattern (40 bp):
CATAAATGAACGAACATAAACGAACATATAACCGAACGAC
Found at i:386704 original size:23 final size:21
Alignment explanation
Indices: 386676--386726 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
386666 GAAAAATATC
386676 AAAAAAAAATTTAACTCGATTT
1 AAAAAAAAA-TTAACTCGATTT
* *
386698 AATAAAAAAATTAATTTGATTT
1 AA-AAAAAAATTAACTCGATTT
386720 AAAAAAA
1 AAAAAAA
386727 TTATTCAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 5 0.19
22 14 0.54
23 7 0.27
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAAAAAAATTAACTCGATTT
Found at i:391298 original size:29 final size:29
Alignment explanation
Indices: 391273--391332 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
391263 ATTATAATTG
391273 TTATTATCTATTATATAGTATAATAATAT
1 TTATTATCTATTATATAGTATAATAATAT
391302 TTATTATCTATTATATAGTATAATAATAT
1 TTATTATCTATTATATAGTATAATAATAT
391331 TT
1 TT
391333 GTATGGTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (29 bp):
TTATTATCTATTATATAGTATAATAATAT
Found at i:394426 original size:3 final size:3
Alignment explanation
Indices: 394418--394456 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
394408 AAAGGACGAG
394418 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
394457 ACTACAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:395100 original size:14 final size:14
Alignment explanation
Indices: 395081--395109 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
395071 TCAAACCAAT
395081 GAATATGAATGTAC
1 GAATATGAATGTAC
395095 GAATATGAATGTAC
1 GAATATGAATGTAC
395109 G
1 G
395110 TAAGATGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.28
Consensus pattern (14 bp):
GAATATGAATGTAC
Found at i:398513 original size:20 final size:21
Alignment explanation
Indices: 398472--398513 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
398462 CTTTGACTTA
* *
398472 AAACTCTAATTTATCTATCTT
1 AAACTCTAAATTATCAATCTT
398493 AAACTCTAAATTAT-AATCTT
1 AAACTCTAAATTATCAATCTT
398513 A
1 A
398514 TGATCTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (21 bp):
AAACTCTAAATTATCAATCTT
Found at i:398541 original size:22 final size:21
Alignment explanation
Indices: 398490--398547 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
398480 ATTTATCTAT
* *
398490 CTTAAA-CTCTAAATTATAAT
1 CTTAAATCTTTAAATTATAAC
*
398510 CTTATGATCTTTAAATTATAAAC
1 CTTA-AATCTTTAAATTAT-AAC
398533 CTTAAATC-TTAAATT
1 CTTAAATCTTTAAATT
398548 TTAATTTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 4 0.13
21 8 0.26
22 13 0.42
23 6 0.19
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (21 bp):
CTTAAATCTTTAAATTATAAC
Found at i:400677 original size:22 final size:22
Alignment explanation
Indices: 400621--400678 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
400611 CGCGATTCTG
*
400621 ACTATCGCATTGCGATTTTTTA
1 ACTATCGCATTGCGATTTTTCA
* *
400643 AAT-TCGCGTTGCGATTTTTCA
1 ACTATCGCATTGCGATTTTTCA
*
400664 ACTATCGCAATGCGA
1 ACTATCGCATTGCGA
400679 ATATGTCGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (22 bp):
ACTATCGCATTGCGATTTTTCA
Found at i:400689 original size:16 final size:16
Alignment explanation
Indices: 400668--400700 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
400658 TTTTCAACTA
400668 TCGCAATGCGAATATG
1 TCGCAATGCGAATATG
400684 TCGCAATGCGAATATG
1 TCGCAATGCGAATATG
400700 T
1 T
400701 AAATCGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (16 bp):
TCGCAATGCGAATATG
Found at i:400709 original size:20 final size:20
Alignment explanation
Indices: 400667--400759 Score: 122
Period size: 20 Copynumber: 4.8 Consensus size: 20
400657 TTTTTCAACT
400667 ATCGCAATGCGAATATG---
1 ATCGCAATGCGAATATGTAA
400684 -TCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
400703 ATCGCAATGCGATTATGTAA
1 ATCGCAATGCGAATATGTAA
* *
400723 ATCACAATACGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
400743 ATCGCAATGCGATTATG
1 ATCGCAATGCGAATATG
400760 ACTATCGCAA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
16 16 0.25
20 49 0.75
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:400766 original size:20 final size:20
Alignment explanation
Indices: 400664--400829 Score: 112
Period size: 20 Copynumber: 8.5 Consensus size: 20
400654 CGATTTTTCA
400664 ACTATCGCAATGCGA--AT-
1 ACTATCGCAATGCGATTATG
* *
400681 A-TGTCGCAATGCGAATATG
1 ACTATCGCAATGCGATTATG
*
400700 TA-AATCGCAATGCGATTATG
1 -ACTATCGCAATGCGATTATG
* * * *
400720 TA-AATCACAATACGAATATG
1 -ACTATCGCAATGCGATTATG
*
400740 TA-AATCGCAATGCGATTATG
1 -ACTATCGCAATGCGATTATG
* *
400760 ACTATCGCAACGCGATTCTG
1 ACTATCGCAATGCGATTATG
* * *
400780 ACTATCGCAACGAGATTCTG
1 ACTATCGCAATGCGATTATG
* *
400800 ACTATCGCAACGCGATTCTG
1 ACTATCGCAATGCGATTATG
*
400820 ACTGTCGCAA
1 ACTATCGCAA
400830 CACTGAATTT
Statistics
Matches: 128, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
16 12 0.09
17 1 0.01
18 2 0.02
19 1 0.01
20 112 0.88
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (20 bp):
ACTATCGCAATGCGATTATG
Found at i:400830 original size:20 final size:20
Alignment explanation
Indices: 400743--400830 Score: 140
Period size: 20 Copynumber: 4.4 Consensus size: 20
400733 GAATATGTAA
* *
400743 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
400763 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
400783 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
400803 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
400823 GTCGCAAC
1 ATCGCAAC
400831 ACTGAATTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:401682 original size:24 final size:24
Alignment explanation
Indices: 401650--401703 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
401640 GTATTCAAAA
401650 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
401674 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
401698 TTTGAT
1 TTTGAT
401704 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:401911 original size:12 final size:13
Alignment explanation
Indices: 401896--401928 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
401886 AAAAGAAGAA
401896 GAAGAAA-TCCCC
1 GAAGAAAGTCCCC
401908 GAAGAATAGTCCCC
1 GAAGAA-AGTCCCC
401922 GAAGAAA
1 GAAGAAA
401929 ATGTCACGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 2 0.11
14 11 0.58
ACGTcount: A:0.45, C:0.24, G:0.21, T:0.09
Consensus pattern (13 bp):
GAAGAAAGTCCCC
Found at i:403765 original size:6 final size:6
Alignment explanation
Indices: 403744--403796 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
403734 AGAAAAAGGC
** ** *
403744 AATCAA AATCGC AATCAA AATCAA AATCGC AATCAA AATCAA AATCCA
1 AATCAA AATCAA AATCAA AATCAA AATCAA AATCAA AATCAA AATCAA
403792 AATCA
1 AATCA
403797 CAACCGGCTT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.57, C:0.23, G:0.04, T:0.17
Consensus pattern (6 bp):
AATCAA
Found at i:403796 original size:18 final size:18
Alignment explanation
Indices: 403744--403789 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
403734 AGAAAAAGGC
403744 AATCAAAATCGCAATCAA
1 AATCAAAATCGCAATCAA
403762 AATCAAAATCGCAATCAA
1 AATCAAAATCGCAATCAA
403780 AATCAAAATC
1 AATCAAAATC
403790 CAAATCACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.57, C:0.22, G:0.04, T:0.17
Consensus pattern (18 bp):
AATCAAAATCGCAATCAA
Found at i:403981 original size:20 final size:20
Alignment explanation
Indices: 403956--404142 Score: 181
Period size: 20 Copynumber: 9.7 Consensus size: 20
403946 TTACACATTC
* *
403956 ATTTGAATATCGTAACGCGA
1 ATTTGACTATCGCAACGCGA
*
403976 ATTTGATTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
*
403995 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
404010 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
404030 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
404050 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
404070 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
* *
404090 ATTTGACTATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
404110 ATTAGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
404129 AATTGACTTTCGCA
1 ATTTGACTATCGCA
404143 TTGCGATTTT
Statistics
Matches: 137, Mismatches: 24, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
14 10 0.07
15 3 0.02
19 13 0.09
20 111 0.81
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:404160 original size:20 final size:20
Alignment explanation
Indices: 404135--404228 Score: 161
Period size: 20 Copynumber: 4.7 Consensus size: 20
404125 CGCAAATTGA
404135 CTTTCGCATTGCGATTTTGT
1 CTTTCGCATTGCGATTTTGT
404155 CTTTCGCATTGCGATTTTGT
1 CTTTCGCATTGCGATTTTGT
*
404175 CTTTCGCATTGCAATTTTGT
1 CTTTCGCATTGCGATTTTGT
*
404195 CTTTCGCATTGTGATTTTGT
1 CTTTCGCATTGCGATTTTGT
*
404215 CTTTCGCGTTGCGA
1 CTTTCGCATTGCGA
404229 AAGTGTACCT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.49
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGT
Found at i:404369 original size:14 final size:14
Alignment explanation
Indices: 404350--404386 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
404340 TCAATATTAA
*
404350 ACAAATCAACTTTT
1 ACAAATCAAATTTT
404364 ACAAATCAAATTTT
1 ACAAATCAAATTTT
*
404378 ATAAATCAA
1 ACAAATCAA
404387 TTAAACAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAAATTTT
Found at i:405880 original size:21 final size:21
Alignment explanation
Indices: 405779--405883 Score: 104
Period size: 21 Copynumber: 5.0 Consensus size: 21
405769 AGAATGTTGG
* * *
405779 GAGGGACCTCTTCAACGATTA
1 GAGGGGCCTCTTGAACGATGA
* * *
405800 CAGTGGCCTCTTGAACGGTGA
1 GAGGGGCCTCTTGAACGATGA
* **
405821 GAGGGGACTCTTGAGGGATGA
1 GAGGGGCCTCTTGAACGATGA
*
405842 TAGGGGCCTCTTGAACGAT-A
1 GAGGGGCCTCTTGAACGATGA
405862 GAGGAGGCCTCTTGAACGATGA
1 GAGG-GGCCTCTTGAACGATGA
405884 CAGGTGAGTC
Statistics
Matches: 65, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 4 0.06
21 60 0.92
22 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.22
Consensus pattern (21 bp):
GAGGGGCCTCTTGAACGATGA
Found at i:405883 original size:42 final size:42
Alignment explanation
Indices: 405779--405887 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
405769 AGAATGTTGG
* * * * *
405779 GAGGGACCTCTTCAACGATTACAGTGGCCTCTTGAACGGTGA
1 GAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGATGA
* ** *
405821 GAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGAT-A
1 GAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGATGA
405862 GAGGAGGCCTCTTGAACGATGACAGG
1 GAGG-GGCCTCTTGAACGATGACAGG
405888 TGAGTCGGGC
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 5 0.09
42 48 0.91
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.21
Consensus pattern (42 bp):
GAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGATGA
Found at i:406453 original size:20 final size:20
Alignment explanation
Indices: 406428--406473 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
406418 GCGATTCTTT
406428 CGTTGCAATAGTCAAATTCG
1 CGTTGCAATAGTCAAATTCG
**
406448 CGTTGCAATAGTCATTTTCG
1 CGTTGCAATAGTCAAATTCG
406468 CGTTGC
1 CGTTGC
406474 GAAAGTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (20 bp):
CGTTGCAATAGTCAAATTCG
Found at i:406701 original size:19 final size:19
Alignment explanation
Indices: 406666--406715 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
406656 TAGTTTACTT
* **
406666 TCGCAACGCGAAAATGACTA
1 TCGCAATGCG-AAATGAAAA
406686 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
406705 TCGCATTGCGA
1 TCGCAATGCGA
406716 TTCTTTCGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:406747 original size:20 final size:20
Alignment explanation
Indices: 406722--406769 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
406712 GCGATTCTTT
406722 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
406742 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
406762 CATTGCGA
1 CGTTGCGA
406770 AAGTAAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:406872 original size:294 final size:294
Alignment explanation
Indices: 406320--407228 Score: 1363
Period size: 294 Copynumber: 3.0 Consensus size: 294
406310 TTGAAGTAAT
* * *
406320 GCAATTCATTCAAGTTTCAATTTGCAGAAGAAGAATAGAATCTAAAACTTAAAATCGCAACACG-
1 GCAATCCATTCAAGTTTCAATTTGCAGAAGAAGAATAG--T-T--TACTT----TCGCAACGCGA
** ** ** *
406384 -AATGACTATCGCAATGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCAATAGTCAAATTCG
57 AAATGACTATCGCAATGCGAAATGAAAATCGCATTGCGATTCTTTCGTTGCGATAGTCAAATTCG
*
406448 CGTTGCAATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAG
122 CGTTGCAATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAA
* * *
406513 TGGATTGCATTACTTCAACCAAAAGATAACAAAAAACAAATACTAACTTCACAGGGTTGAAGAAT
187 TGGATTGCATTACTTCAACCAAAAGACAACCAAAAACAAATACTAACTTCACAGGGTTAAAGAAT
406578 AAACAGTTTAGCAGTATTGGCAGCAACCGAATGAATTTACTAA
252 AAACAGTTTAGCAGTATTGGCAGCAACCGAATGAATTTACTAA
*
406621 GTAATCCATTCAAGTTTCAATTTGCAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTA
1 GCAATCCATTCAAGTTTCAATTTGCAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTA
*
406686 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCGTTGCGAT
66 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCGTTGCAAT
*
406751 AGTCATTTTCGCATTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAATGGATTGCA
131 AGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAATGGATTGCA
* *
406816 TTACTTCAACCAAAAGACAACCAAAAACAAATACTAACTTCACATGGTTAAAGAATAAACAATTT
196 TTACTTCAACCAAAAGACAACCAAAAACAAATACTAACTTCACAGGGTTAAAGAATAAACAGTTT
*
406881 AGCAGTATTGGCAGCAACCAAATGAATTTACTAA
261 AGCAGTATTGGCAGCAACCGAATGAATTTACTAA
406915 GCAATCCATTCAAGTTTCAATTTGCAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTA
1 GCAATCCATTCAAGTTTCAATTTGCAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTA
* * *
406980 TCGTAACGCGAGAATCGCAATGGGATTTTCATTTCGCATTGTGATTCTTTCGTTGCGATAGTCAA
66 TCGCAATGCGA-AAT-G-AA----A-----A--TCGCATTGCGATTCTTTCGTTGCGATAGTCAA
407045 ATTCGCGTTGCAATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAAC
117 ATTCGCGTTGCAATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAAC
*
407110 TTGAATGGATTGCATTATTTCAACCAAAAGACAACCAAAAACAAATACTAACTTCACAGGGTTAA
182 TTGAATGGATTGCATTACTTCAACCAAAAGACAACCAAAAACAAATACTAACTTCACAGGGTTAA
* *
407175 AGAATAAACAGTTTAGCAGTTTTGGCAGCAATCGAATGAATTTACTAA
247 AGAATAAACAGTTTAGCAGTATTGGCAGCAACCGAATGAATTTACTAA
407223 GCAATC
1 GCAATC
407229 TAAGTGAAAT
Statistics
Matches: 560, Mismatches: 32, Indels: 25
0.91 0.05 0.04
Matches are distributed among these distances:
292 9 0.02
294 294 0.52
295 3 0.01
296 5 0.01
297 2 0.00
298 1 0.00
299 1 0.00
301 37 0.07
306 1 0.00
308 207 0.37
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (294 bp):
GCAATCCATTCAAGTTTCAATTTGCAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTA
TCGCAATGCGAAATGAAAATCGCATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCGTTGCAAT
AGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAATGGATTGCA
TTACTTCAACCAAAAGACAACCAAAAACAAATACTAACTTCACAGGGTTAAAGAATAAACAGTTT
AGCAGTATTGGCAGCAACCGAATGAATTTACTAA
Found at i:407055 original size:20 final size:20
Alignment explanation
Indices: 407030--407077 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
407020 GTGATTCTTT
407030 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
407050 CGTTGCAATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
407070 CGTTGCGA
1 CGTTGCGA
407078 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:409012 original size:20 final size:20
Alignment explanation
Indices: 408989--409076 Score: 88
Period size: 20 Copynumber: 4.5 Consensus size: 20
408979 TCTGAAACTT
408989 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
409009 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
409029 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** * *
409049 ACTATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
409068 AAAATCGCA
1 AAAATCGCA
409077 TAGCGATTCT
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 7 0.12
20 52 0.88
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:409490 original size:22 final size:22
Alignment explanation
Indices: 409463--409504 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
409453 GAGATAGACG
409463 GATTTCGCCGGAGATGGGGACT
1 GATTTCGCCGGAGATGGGGACT
*
409485 GATTTCGTCGGAGATGGGGA
1 GATTTCGCCGGAGATGGGGA
409505 TGGATGTCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.43, T:0.24
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACT
Found at i:409716 original size:20 final size:20
Alignment explanation
Indices: 409686--409796 Score: 159
Period size: 20 Copynumber: 5.5 Consensus size: 20
409676 GCGCTTTAAA
*
409686 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
409706 CATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
*
409726 CATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
409746 AATCTCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
409766 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
*
409786 AATCGCATTGC
1 AATCGCGTTGC
409797 AATTTACATA
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:409817 original size:60 final size:60
Alignment explanation
Indices: 409686--409823 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 60
409676 GCGCTTTAAA
* * * *
409686 AATCGCATTGCGATAGTCAGCATCGCGTTGCGATAGTCATCATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAGAATCGCGTTGCGATAGTCATAATCGCATTGCAATAGTCAG
* * * *
409746 AATCTCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCATAATCGCATTGCAAT-TTACAT
1 AATCGCATTGCGATAGTCAGAATCGCGTTGCGATAGTCATAATCGCATTGCAATAGT-CAG
*
409806 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
409824 GGAAAATCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
59 1 0.02
60 65 0.98
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (60 bp):
AATCGCATTGCGATAGTCAGAATCGCGTTGCGATAGTCATAATCGCATTGCAATAGTCAG
Found at i:415483 original size:42 final size:41
Alignment explanation
Indices: 415420--415534 Score: 176
Period size: 42 Copynumber: 2.8 Consensus size: 41
415410 TTCCTCGAAA
* * *
415420 TTCCGTGTTTGTTTCATGTAATTCGTTTTCTGGAAAATGTT
1 TTCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTT
*
415461 TTCCTGTGTTTGTTTCACGTAATTCATTTTCCGAAAAATGTT
1 TTCC-GTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTT
415503 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCC
1 TT-CCGTGTTTGTTTCACGTAATTCGTTTTCC
415535 AGAATGTAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (41 bp):
TTCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTT
Found at i:415761 original size:24 final size:23
Alignment explanation
Indices: 415734--415787 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
415724 AAATATTGAA
*
415734 AATATATTTATTAATATTTATAAT
1 AATATATATA-TAATATTTATAAT
*
415758 AATATA-ATATAATATTTTTAAT
1 AATATATATATAATATTTATAAT
*
415780 ATTATATA
1 AATATATA
415788 AAATAATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 17 0.65
23 3 0.12
24 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATATATATAATATTTATAAT
Found at i:415770 original size:22 final size:22
Alignment explanation
Indices: 415745--415825 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 22
415735 ATATATTTAT
415745 TAATATTTATAATAATATAATA
1 TAATATTTATAATAATATAATA
* *
415767 TAATATTTTTAATATTATATAAAA
1 TAATATTTATAATA--ATATAATA
* *
415791 TAATCAATTAT-ATTATAATAATA
1 TAAT-ATTTATAATAAT-ATAATA
*
415814 TAAGATATTATA
1 TAATAT-TTATA
415826 TTTTTATTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
22 16 0.36
23 12 0.27
24 13 0.29
25 4 0.09
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (22 bp):
TAATATTTATAATAATATAATA
Found at i:415780 original size:31 final size:30
Alignment explanation
Indices: 415737--415903 Score: 96
Period size: 29 Copynumber: 5.8 Consensus size: 30
415727 TATTGAAAAT
415737 ATATTTATTAATATTTATAATAATATAATATA
1 ATATTT-TT-ATATTTATAATAATATAATATA
*
415769 ATATTTTTA-A--TAT--T-ATATAAAATA
1 ATATTTTTATATTTATAATAATATAATATA
* *
415793 ATCA--ATTATA-TTATAATAATATAAGATATT
1 AT-ATTTTTATATTTATAATAATAT-A-ATATA
415823 ATATTTTTAT-TTTAATAAT-ATATAATA-A
1 ATATTTTTATATTT-ATAATAATATAATATA
*
415851 ATTTTTTTATATATT-TAATAATGAATAATAT-
1 ATATTTTTATAT-TTATAATAAT--ATAATATA
*
415882 -TATTTATATATTT-TAATAATAT
1 ATATTTTTATATTTATAATAATAT
415904 TTTAATAAAG
Statistics
Matches: 108, Mismatches: 9, Indels: 41
0.68 0.06 0.26
Matches are distributed among these distances:
23 3 0.03
24 12 0.11
25 5 0.05
27 6 0.06
28 17 0.16
29 18 0.17
30 18 0.17
31 18 0.17
32 11 0.10
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (30 bp):
ATATTTTTATATTTATAATAATATAATATA
Found at i:415861 original size:54 final size:52
Alignment explanation
Indices: 415750--415861 Score: 129
Period size: 54 Copynumber: 2.1 Consensus size: 52
415740 TTTATTAATA
*
415750 TTTATAATAATATAATATAATATTTTTAATATTATATAAAATAATCAATTAT
1 TTTATAATAATATAATATAATATTTTTAATATTATATAAAATAATAAATTAT
* * * *
415802 ATTATAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAATAAATTTT
1 TTTATAATAATAT-A-ATATAATATTTTTAATATTATATAA-A-ATAATAAATTAT
415856 TTTATA
1 TTTATA
415862 TATTTAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
52 16 0.32
53 7 0.14
54 27 0.54
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (52 bp):
TTTATAATAATATAATATAATATTTTTAATATTATATAAAATAATAAATTAT
Found at i:415869 original size:28 final size:29
Alignment explanation
Indices: 415830--415901 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 29
415820 ATTATATTTT
*
415830 TATTTTAATAAT-ATATAATAAATT-TTTTTA
1 TATTTTAATAATGA-ATAAT--ATTATTTATA
415860 TATATTTAATAATGAATAATATTATTTATA
1 TAT-TTTAATAATGAATAATATTATTTATA
415890 TATTTTAATAAT
1 TATTTTAATAAT
415902 ATTTTAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 12 0.32
30 11 0.29
31 14 0.37
32 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (29 bp):
TATTTTAATAATGAATAATATTATTTATA
Found at i:415881 original size:19 final size:19
Alignment explanation
Indices: 415859--415911 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
415849 AAATTTTTTT
415859 ATATATTTAATAATGAATA
1 ATATATTTAATAATGAATA
* *
415878 ATATTATTTATATATTTTAATA
1 ATA-TATTTA-ATA-ATGAATA
415900 ATAT-TTTAATAA
1 ATATATTTAATAA
415912 AGATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATATATTTAATAATGAATA
Found at i:415919 original size:14 final size:11
Alignment explanation
Indices: 415874--415911 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
415864 TTTAATAATG
415874 AATAATATTATT
1 AATAATATT-TT
*
415886 TAT-ATATTTT
1 AATAATATTTT
415896 AATAATATTTT
1 AATAATATTTT
415907 AATAA
1 AATAA
415912 AGATATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 4 0.17
11 17 0.74
12 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATAATATTTT
Found at i:415932 original size:23 final size:23
Alignment explanation
Indices: 415906--415950 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
415896 AATAATATTT
415906 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
415929 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
415951 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:416031 original size:90 final size:86
Alignment explanation
Indices: 415919--416088 Score: 202
Period size: 91 Copynumber: 1.9 Consensus size: 86
415909 TAAAGATATT
* * * * *
415919 TAAAATATACTAATTAATATTTTTA-AAATATAA-TATAACACTATTAATTTAATAA-ATAATAA
1 TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATAAT-ATTTAATAATA-AATAA
415981 ATATAATTTATAATATTTTATCTCAC
64 AT-T-ATTT-TAATATTTTATCTCAC
*
416007 TAAAATATACCAATATTAATATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAA
1 TAAAATATA-CAA-ATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAA
416072 ATTATTTTAATATTTTA
64 ATTATTTTAATATTTTA
416089 AAATAATAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
88 19 0.27
89 6 0.08
90 14 0.20
91 22 0.31
92 10 0.14
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (86 bp):
TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAAAT
TATTTTAATATTTTATCTCAC
Found at i:416314 original size:14 final size:15
Alignment explanation
Indices: 416294--416336 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
416284 TTCCAGAAAT
416294 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
** *
416309 -TAATTCAAATTACA
1 GTAATTCATTTTCCA
416323 GTAATTCATTTTCC
1 GTAATTCATTTTCC
416337 GAAAAACCAA
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:416348 original size:29 final size:29
Alignment explanation
Indices: 416294--416352 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
416284 TTCCAGAAAT
**
416294 GTAATTCATTTTCCATAATTCAAATTACA
1 GTAATTCATTTTCCATAAAACAAATTACA
*
416323 GTAATTCATTTTCCGA-AAAACCAATTACA
1 GTAATTCATTTTCC-ATAAAACAAATTACA
416352 G
1 G
416353 CCAAACAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.36
Consensus pattern (29 bp):
GTAATTCATTTTCCATAAAACAAATTACA
Found at i:417337 original size:2 final size:2
Alignment explanation
Indices: 417330--417355 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
417320 TATGATAATC
417330 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
417356 GACTATGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:417850 original size:16 final size:18
Alignment explanation
Indices: 417829--417861 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
417819 AATATAATAT
417829 TTATAAA-A-TTTTAAAG
1 TTATAAATAGTTTTAAAG
417845 TTATAAATAGTTTTAAA
1 TTATAAATAGTTTTAAA
417862 TCAATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (18 bp):
TTATAAATAGTTTTAAAG
Found at i:424075 original size:3 final size:3
Alignment explanation
Indices: 424064--424124 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
424054 TTTTTTATCG
** * *
424064 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TCA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
424109 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
424125 CATATTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 4 0.08
3 41 0.85
4 3 0.06
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:424119 original size:29 final size:30
Alignment explanation
Indices: 424057--424119 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
424047 TCCGGGTTTT
* *
424057 TTTATCGTTATTTTATTATTATTATTATTA
1 TTTATCGTCATCTTATTATTATTATTATTA
424087 -TTATCGTCATCTTATTATT-TTATTATTA
1 TTTATCGTCATCTTATTATTATTATTATTA
424115 TTTAT
1 TTTAT
424120 TATTACATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 9 0.30
29 21 0.70
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.65
Consensus pattern (30 bp):
TTTATCGTCATCTTATTATTATTATTATTA
Found at i:432350 original size:24 final size:22
Alignment explanation
Indices: 432311--432355 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
432301 CAATATTTGA
* *
432311 ATCTTTAAAACGATTTTTTTTT
1 ATCTTTAAAACAATTTCTTTTT
432333 ATCTCTTAAAGACAATTTCTTTT
1 ATCT-TTAAA-ACAATTTCTTTT
432356 GAGAAAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 5 0.26
24 10 0.53
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.53
Consensus pattern (22 bp):
ATCTTTAAAACAATTTCTTTTT
Found at i:432394 original size:27 final size:26
Alignment explanation
Indices: 432358--432416 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 26
432348 TTTCTTTTGA
432358 GAAAAATCTTTGAGTTTGTTCCTCTT
1 GAAAAATCTTTGAGTTTGTTCCTCTT
432384 GAAAAAGTCTTTGAGTTTGTTCCTCTT
1 GAAAAA-TCTTTGAGTTTGTTCCTCTT
*
432411 TAAAAA
1 GAAAAA
432417 AAAAAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 6 0.19
27 25 0.81
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (26 bp):
GAAAAATCTTTGAGTTTGTTCCTCTT
Found at i:432453 original size:29 final size:28
Alignment explanation
Indices: 432419--432577 Score: 135
Period size: 29 Copynumber: 5.6 Consensus size: 28
432409 TTTAAAAAAA
432419 AAAAAAATCTTTGAGTTTGTTCCTTTTG
1 AAAAAAATCTTTGAGTTTGTTCCTTTTG
* *
432447 AATAAAAATCTTGGAGTTTGTTCCTTTGG
1 AA-AAAAATCTTTGAGTTTGTTCCTTTTG
* * *
432476 AATAAAAATCTGTGAG-TTGTTTCGTTTG
1 AA-AAAAATCTTTGAGTTTGTTCCTTTTG
* * *
432504 AAAAAAATCTTCGAGTCTAT-TTACTTGTGG
1 AAAAAAATCTTTGAGT-T-TGTTCCTT-TTG
* * *
432534 AATAAAAATCTGTGAG-TTGTTTCGTTTG
1 AA-AAAAATCTTTGAGTTTGTTCCTTTTG
*
432562 AAAAAAATCTTCGAGT
1 AAAAAAATCTTTGAGT
432578 CTATTTACTT
Statistics
Matches: 104, Mismatches: 19, Indels: 16
0.75 0.14 0.12
Matches are distributed among these distances:
27 22 0.21
28 18 0.17
29 48 0.46
30 5 0.05
31 11 0.11
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.40
Consensus pattern (28 bp):
AAAAAAATCTTTGAGTTTGTTCCTTTTG
Found at i:432535 original size:58 final size:57
Alignment explanation
Indices: 432421--432589 Score: 243
Period size: 58 Copynumber: 2.9 Consensus size: 57
432411 TAAAAAAAAA
* * * * *
432421 AAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGT-T-TGTTCCTTTGGAAT
1 AAAAATCTGTGAG-TTGTTTCGTTTGAA-AAAAATCTTCGAGTCTAT-TTACTTTGGAAT
432479 AAAAATCTGTGAGTTGTTTCGTTTGAAAAAAATCTTCGAGTCTATTTACTTGTGGAAT
1 AAAAATCTGTGAGTTGTTTCGTTTGAAAAAAATCTTCGAGTCTATTTACTT-TGGAAT
432537 AAAAATCTGTGAGTTGTTTCGTTTGAAAAAAATCTTCGAGTCTATTTACTTTG
1 AAAAATCTGTGAGTTGTTTCGTTTGAAAAAAATCTTCGAGTCTATTTACTTTG
432590 AAACAAAGTT
Statistics
Matches: 103, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
56 13 0.13
57 20 0.19
58 70 0.68
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.42
Consensus pattern (57 bp):
AAAAATCTGTGAGTTGTTTCGTTTGAAAAAAATCTTCGAGTCTATTTACTTTGGAAT
Found at i:432670 original size:29 final size:29
Alignment explanation
Indices: 432625--432691 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 29
432615 CAATTGTGTG
*
432625 AAAATCTTTGAGATTGTTTCTTTTGAAAC
1 AAAATCTTTGAGATTGTTTCTTTGGAAAC
*
432654 AAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAATCTTTGAGATTGTTTCTTTGGAAAC
432683 AAAAT-TTTG
1 AAAATCTTTG
432692 TCTCTTGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 4 0.11
29 32 0.89
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (29 bp):
AAAATCTTTGAGATTGTTTCTTTGGAAAC
Found at i:432729 original size:67 final size:63
Alignment explanation
Indices: 432641--432822 Score: 190
Period size: 67 Copynumber: 2.9 Consensus size: 63
432631 TTTGAGATTG
* * *
432641 TTTCTTTTGAAACAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTGAAACAT
1 TTTC-TTTAAAACAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTAAAACAA
* ** * *
432705 TTTCTCTTAAAACAAGATCATCTTTGAGTTTGTTTCTCTGGAAACAAGGTTTTATCCCTTAAAAC
1 TTTCT-TTAAAACAA-A--ATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTAAAAC
432770 AA
62 AA
** * *
432772 TTTCTTTTGAAGAAAATC--TGAGTCTGTTTCTTTGGAAAC-AAATTTTGTCTC
1 TTTCTTTAAAACAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTC
432823 ACTAAGATAC
Statistics
Matches: 97, Mismatches: 17, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
60 8 0.08
61 19 0.20
63 4 0.04
64 12 0.12
65 2 0.02
66 6 0.06
67 46 0.47
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (63 bp):
TTTCTTTAAAACAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTAAAACAA
Found at i:433372 original size:28 final size:28
Alignment explanation
Indices: 433322--433375 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
433312 TCAAAATCCA
* *
433322 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTTCCTATTGAAACAC
433350 ATCTTTGAGTTGGTCTCCT-TTGAAAC
1 ATCTTTGAGTTGGT-TCCTATTGAAAC
433376 CATTATCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (28 bp):
ATCTTTGAGTTGGTTCCTATTGAAACAC
Found at i:433583 original size:46 final size:45
Alignment explanation
Indices: 433489--433826 Score: 268
Period size: 46 Copynumber: 7.9 Consensus size: 45
433479 CCAGATCTCT
* *
433489 TCATCACGTAGGAGCCGTGTCA--ACCATAGATAACCAGCCGTCC
1 TCATCACGTAGGAACCGTGTCATCACCTTAGATAACCAGCCGTCC
* * **
433532 CCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGCCGTCC
1 TCATCACGTAGGAACCGTGTCATCACC-TTAGATAACCAGCCGTCC
* * * *
433578 TCATCATGTAGGAACCGTGTCATC-CC-CAG---ACCAGATC-TCT
1 TCATCACGTAGGAACCGTGTCATCACCTTAGATAACCAG-CCGTCC
* *
433618 TCATCACGTAGGAGCCGTGTCA--ACCATAGATAACCAGCCGTCC
1 TCATCACGTAGGAACCGTGTCATCACCTTAGATAACCAGCCGTCC
* * **
433661 CCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGCCGTCC
1 TCATCACGTAGGAACCGTGTCATCACC-TTAGATAACCAGCCGTCC
* * * *
433707 TCATCATGTAGGAACCGTGTCATC-CC-CAG---ACCAGATC-TCT
1 TCATCACGTAGGAACCGTGTCATCACCTTAGATAACCAG-CCGTCC
* **
433747 TCATCACGTATGAGTCGTGTCA-C-CC-TAGATAACCAGCCGTCC
1 TCATCACGTAGGAACCGTGTCATCACCTTAGATAACCAGCCGTCC
*
433789 TCATCACGTA-GAACCGTGT-ATCACCTTTAGATAGCCAG
1 TCATCACGTAGGAACCGTGTCATCACC-TTAGATAACCAG
433827 AACTCTTCAT
Statistics
Matches: 232, Mismatches: 41, Indels: 43
0.73 0.13 0.14
Matches are distributed among these distances:
39 7 0.03
40 53 0.23
41 11 0.05
42 20 0.09
43 49 0.21
44 10 0.04
45 10 0.04
46 72 0.31
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (45 bp):
TCATCACGTAGGAACCGTGTCATCACCTTAGATAACCAGCCGTCC
Found at i:433617 original size:129 final size:129
Alignment explanation
Indices: 433387--433909 Score: 727
Period size: 129 Copynumber: 4.1 Consensus size: 129
433377 ATTATCCTAG
* * *
433387 AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCCCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCCTCA
** * ** *
433452 TTGCGTATGAGTCGTGTCATTTCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTAGGAACCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCAT
*
433516 AGATAACCAGCCGTCCCCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAG-CCGTCCTC
1 AGATAACCAGCCGTCCCCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC-TCCTC
*
433580 ATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCA
65 ATCACGTAGGAACCGTGTCATTCCCC-GACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCA
433644 T
129 T
*
433645 AGATAACCAGCCGTCCCCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAG-CCGTCCTC
1 AGATAACCAGCCGTCCCCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC-TCCTC
* * * *
433709 ATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTCATCACGTATGAGTCGTGTC-ACCC
65 ATCACGTAGGAACCGTGTCATTCCCC-GACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCA
433772 T
129 T
* * *
433773 AGATAACCAGCCGTCCTCATCACGTA-GAACCGTG-TATCACCTTTAGATAGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCCCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCCTCA
* ** * * *
433836 TCACGTATGAGTCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTT
66 TCACGTAGGAACCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCAT
*
433900 AGATGACCAG
1 AGATAACCAG
433910 ACCTCTTCAT
Statistics
Matches: 363, Mismatches: 26, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
126 71 0.20
127 26 0.07
128 34 0.09
129 232 0.64
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (129 bp):
AGATAACCAGCCGTCCCCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCCTCA
TCACGTAGGAACCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCAT
Found at i:433636 original size:40 final size:40
Alignment explanation
Indices: 433578--434024 Score: 221
Period size: 40 Copynumber: 10.7 Consensus size: 40
433568 CCAGCCGTCC
* * * *
433578 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCATCCCCAGACCAGACCTCT
* * ** *
433618 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTCATCCCCAG---ACCAGACC-TCT
* * * * * *
433661 CCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTCATC-CC--CAGA---CCAGACC-TCT
* * * *
433707 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCATCCCCAGACCAGACCTCT
* * *
433747 TCATCACGTATGAGTCGTGTCA-CCCTAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTCATCCCCAG---ACCAGACC-TCT
* * *
433789 TCATCACGTA-GAACCGTGT-ATCACCTTTAGATAGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTCATC-CC--CAG--A-CCAGACCTCT
* *
433833 TCATCACGTATGAGTCGTGTCATTCCCC-GACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCA-TCCCCAGACCAGACCTCT
*
433873 TCATCACGTATGAGCCGTGTCA-CCCTTAGATGACCAGACCTCT
1 TCATCACGTATGAGCCGTGTCATCCC---CA-GACCAGACCTCT
** * * *
433916 TCATTGCGTATGAGTCGTGTCATTTCCC-GACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCA-TCCCCAGACCAGACCTCT
*
433956 TCATCACGTATGAGCCGTGTCA-CCCTTATGACCAGACCTCT
1 TCATCACGTATGAGCCGTGTCATCCC-CA-GACCAGACCTCT
** * *
433997 TCATTGCGTATGAGCAGTGTCGTCCCCA
1 TCATCACGTATGAGCCGTGTCATCCCCA
434025 CCAACAGAAC
Statistics
Matches: 317, Mismatches: 55, Indels: 69
0.72 0.12 0.16
Matches are distributed among these distances:
38 5 0.02
39 5 0.02
40 109 0.34
41 41 0.13
42 23 0.07
43 63 0.20
44 20 0.06
45 12 0.04
46 37 0.12
47 2 0.01
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (40 bp):
TCATCACGTATGAGCCGTGTCATCCCCAGACCAGACCTCT
Found at i:433833 original size:86 final size:86
Alignment explanation
Indices: 433479--433854 Score: 285
Period size: 86 Copynumber: 4.4 Consensus size: 86
433469 CATTTCCCGA
* * *
433479 CCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCCCATCACGTAGG
1 CCAGACCTCTTCATCACGTAGGAGCCGTGTC-ACCCTAGATAACCAGCCGTCCTCATCACGTAGG
*
433544 AACCGTGTTATCACCTTTAGATGG
65 AACCGTG-TATCACC-TTAGATAG
* * * * * *
433568 CCAG-CCGTCCTCATCATGTAGGAACCGTGTCATCCCCAG---ACCAGATC-TCTTCATCACGTA
1 CCAGACC-TCTTCATCACGTAGGAGCCGTGTCA-CCCTAGATAACCAG-CCGTCCTCATCACGTA
* * *
433628 GGAGCCGTG--TCAACCATAGATAA
63 GGAACCGTGTATC-ACCTTAGATAG
** * * ** *
433651 CCAG-CCGTCCCCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGCCGTCCTCATCATG
1 CCAGACC-TCTTCATCACGTAGGAGCCGTG---TCACC-CTAGATAACCAGCCGTCCTCATCACG
*
433715 TAGGAACCGTGTCATC-CC-CAG--A-
61 TAGGAACCGTGT-ATCACCTTAGATAG
* * *
433737 CCAGATCTCTTCATCACGTATGAGTCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTA-GA
1 CCAGACCTCTTCATCACGTAGGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGA
433801 ACCGTGTATCACCTTTAGATAG
66 ACCGTGTATCACC-TTAGATAG
* * *
433823 CCAGAACTCTTCATCACGTATGAGTCGTGTCA
1 CCAGACCTCTTCATCACGTAGGAGCCGTGTCA
433855 TTCCCCGACC
Statistics
Matches: 230, Mismatches: 35, Indels: 47
0.74 0.11 0.15
Matches are distributed among these distances:
80 3 0.01
81 11 0.05
82 24 0.10
83 41 0.18
84 3 0.01
85 3 0.01
86 81 0.35
87 3 0.01
88 3 0.01
89 54 0.23
90 2 0.01
92 2 0.01
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (86 bp):
CCAGACCTCTTCATCACGTAGGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGA
ACCGTGTATCACCTTAGATAG
Found at i:433926 original size:83 final size:83
Alignment explanation
Indices: 433789--434010 Score: 335
Period size: 83 Copynumber: 2.7 Consensus size: 83
433779 CCAGCCGTCC
* * * **
433789 TCATCACGTA-GAACCGTGTATCACCTTTAGAT-AGCCAGAACTCTTCATCACGTATGAGTCGTG
1 TCATCACGTATGAGCCGTG--TCACCCTTAGATGA-CCAGACCTCTTCATTGCGTATGAGTCGTG
433852 TCATTCCCCGACCAGATCTCT
63 TCATTCCCCGACCAGATCTCT
433873 TCATCACGTATGAGCCGTGTCACCCTTAGATGACCAGACCTCTTCATTGCGTATGAGTCGTGTCA
1 TCATCACGTATGAGCCGTGTCACCCTTAGATGACCAGACCTCTTCATTGCGTATGAGTCGTGTCA
*
433938 TTTCCCGACCAGATCTCT
66 TTCCCCGACCAGATCTCT
433956 TCATCACGTATGAGCCGTGTCACCCTT--ATGACCAGACCTCTTCATTGCGTATGAG
1 TCATCACGTATGAGCCGTGTCACCCTTAGATGACCAGACCTCTTCATTGCGTATGAG
434011 CAGTGTCGTC
Statistics
Matches: 130, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
81 28 0.22
83 84 0.65
84 11 0.08
85 7 0.05
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (83 bp):
TCATCACGTATGAGCCGTGTCACCCTTAGATGACCAGACCTCTTCATTGCGTATGAGTCGTGTCA
TTCCCCGACCAGATCTCT
Found at i:434210 original size:29 final size:30
Alignment explanation
Indices: 434167--434228 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
434157 CGGGTTTTTT
* *
434167 TTATCGTTATTTTATTATTATTATTA-TTA
1 TTATCGTCATCTTATTATTATTATTATTTA
*
434196 TTATCGTCATCTTATTATTTTTATTATTTA
1 TTATCGTCATCTTATTATTATTATTATTTA
434226 TTA
1 TTA
434229 CATATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (30 bp):
TTATCGTCATCTTATTATTATTATTATTTA
Found at i:435458 original size:38 final size:40
Alignment explanation
Indices: 435415--435493 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
435405 CTATTTATAT
435415 TAGTATTTTGTATG-TTAAATA-TT-GATTTTAGCTGTTAA
1 TAGTA-TTTGTATGTTTAAATATTTAGATTTTAGCTGTTAA
435453 TAGTATTTGTATGTTTAAATATTTAGATTTTAGCTGTTAA
1 TAGTATTTGTATGTTTAAATATTTAGATTTTAGCTGTTAA
435493 T
1 T
435494 CTTGTGTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
37 8 0.21
38 12 0.32
39 2 0.05
40 16 0.42
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (40 bp):
TAGTATTTGTATGTTTAAATATTTAGATTTTAGCTGTTAA
Found at i:435502 original size:38 final size:37
Alignment explanation
Indices: 435423--435502 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 37
435413 ATTAGTATTT
* *
435423 TGTATGTTAAATATTGATTTTAGCTGTTAATAGTATT
1 TGTATGTTAAATATTGATTTTAGCTGTTAATACTATG
435460 TGTATGTTTAAATATTTAGATTTTAGCTGTTAAT-CT-TG
1 TGTATG-TTAAATA-TT-GATTTTAGCTGTTAATACTATG
435498 TGTAT
1 TGTAT
435503 TATTCATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
37 6 0.16
38 13 0.34
39 3 0.08
40 16 0.42
ACGTcount: A:0.28, C:0.04, G:0.16, T:0.53
Consensus pattern (37 bp):
TGTATGTTAAATATTGATTTTAGCTGTTAATACTATG
Found at i:440821 original size:13 final size:13
Alignment explanation
Indices: 440784--440822 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
440774 TTATTTTTTA
*
440784 AAAAATA-AAAAA
1 AAAAATAGAAAAT
*
440796 AAAAACAGAAAAT
1 AAAAATAGAAAAT
440809 AAAAATAGAAAAT
1 AAAAATAGAAAAT
440822 A
1 A
440823 TTTTCTAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.82, C:0.03, G:0.05, T:0.10
Consensus pattern (13 bp):
AAAAATAGAAAAT
Found at i:443826 original size:17 final size:17
Alignment explanation
Indices: 443804--443837 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
443794 GAAATTACTC
443804 CTACCATATGACCTCAA
1 CTACCATATGACCTCAA
443821 CTACCATATGACCTCAA
1 CTACCATATGACCTCAA
443838 AGGTAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.35, G:0.06, T:0.24
Consensus pattern (17 bp):
CTACCATATGACCTCAA
Found at i:444605 original size:26 final size:26
Alignment explanation
Indices: 444576--444628 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
444566 CAGAAACATG
444576 AATTTAAGTCCTTATCCGTAATATAT
1 AATTTAAGTCCTTATCCGTAATATAT
* *
444602 AATTTAAGTCCTTTTCTGTAATATAT
1 AATTTAAGTCCTTATCCGTAATATAT
444628 A
1 A
444629 CTTATTACTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (26 bp):
AATTTAAGTCCTTATCCGTAATATAT
Found at i:450029 original size:21 final size:21
Alignment explanation
Indices: 450005--450071 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
449995 GAGAAAAAGT
450005 AAAAGTTAAGAATGAAAGAGA
1 AAAAGTTAAGAATGAAAGAGA
*
450026 AAAA-ATAAGAATGAAAGAGA
1 AAAAGTTAAGAATGAAAGAGA
*
450046 AAAAGTTAAGAATGAAAGATA
1 AAAAGTTAAGAATGAAAGAGA
450067 AAAAG
1 AAAAG
450072 AAAAAGTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
20 19 0.45
21 23 0.55
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.13
Consensus pattern (21 bp):
AAAAGTTAAGAATGAAAGAGA
Found at i:458202 original size:21 final size:21
Alignment explanation
Indices: 458176--458227 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
458166 TTGTTTATGG
*
458176 GTAATGTAATGGAAGTTGTTT
1 GTAATGTAATGAAAGTTGTTT
458197 GTAATGTAATGAAAGTTGTTT
1 GTAATGTAATGAAAGTTGTTT
* *
458218 TTTATGTAAT
1 GTAATGTAAT
458228 CTATCTTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (21 bp):
GTAATGTAATGAAAGTTGTTT
Found at i:458440 original size:18 final size:19
Alignment explanation
Indices: 458417--458459 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
458407 AAAGTTAGCT
*
458417 AAATGTAATG-AAAAAAGG
1 AAATGTAATGTAAAAAAGA
*
458435 AAATGT-ATGTACAAAAGA
1 AAATGTAATGTAAAAAAGA
458453 AAATGTA
1 AAATGTA
458460 TGTGCATAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.58, C:0.02, G:0.19, T:0.21
Consensus pattern (19 bp):
AAATGTAATGTAAAAAAGA
Found at i:458471 original size:23 final size:23
Alignment explanation
Indices: 458445--458491 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
458435 AAATGTATGT
458445 ACAAAAGAAAATGTA-TGTGCATA
1 ACAAAAGAAAATG-ACTGTGCATA
**
458468 ACAAAAGGTAATGACTGTGCATA
1 ACAAAAGAAAATGACTGTGCATA
458491 A
1 A
458492 GGACATTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.21
Consensus pattern (23 bp):
ACAAAAGAAAATGACTGTGCATA
Found at i:458473 original size:18 final size:18
Alignment explanation
Indices: 458435--458473 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
458425 TGAAAAAAGG
*
458435 AAATGTATGTACAAAAGA
1 AAATGTATGTACAAAACA
* *
458453 AAATGTATGTGCATAACA
1 AAATGTATGTACAAAACA
458471 AAA
1 AAA
458474 GGTAATGACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (18 bp):
AAATGTATGTACAAAACA
Found at i:459946 original size:14 final size:15
Alignment explanation
Indices: 459927--459964 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
459917 GTTATTAGTT
459927 AACAAAATG-TAATA
1 AACAAAATGATAATA
459941 AACAAAATGCATAATA
1 AACAAAATG-ATAATA
*
459957 AACCAAAT
1 AACAAAAT
459965 AATGCAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
16 12 0.57
ACGTcount: A:0.63, C:0.13, G:0.05, T:0.18
Consensus pattern (15 bp):
AACAAAATGATAATA
Found at i:460908 original size:12 final size:12
Alignment explanation
Indices: 460893--460924 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
460883 TGTTTCTTCC
460893 TCAACTTCATCA
1 TCAACTTCATCA
*
460905 TCAACTTCCTCA
1 TCAACTTCATCA
460917 TCAACTTC
1 TCAACTTC
460925 TACTTCTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.38, G:0.00, T:0.34
Consensus pattern (12 bp):
TCAACTTCATCA
Found at i:462175 original size:6 final size:6
Alignment explanation
Indices: 462164--462205 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
462154 GACACGTATT
462164 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
462206 CGAGACGGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.29, C:0.55, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:462196 original size:5 final size:5
Alignment explanation
Indices: 462168--462208 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
462158 CGTATTACCA
462168 CGACC ACGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
462209 GACGGACAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.27, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:462877 original size:20 final size:20
Alignment explanation
Indices: 462852--462899 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
462842 ACTGTAGACT
* *
462852 ATCGCAAGGCGAAATGGAAA
1 ATCGCAACGCGAAATAGAAA
462872 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATAGAAA
*
462892 AGCGCAAC
1 ATCGCAAC
462900 ATGATTTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.21, G:0.25, T:0.08
Consensus pattern (20 bp):
ATCGCAACGCGAAATAGAAA
Found at i:462926 original size:21 final size:21
Alignment explanation
Indices: 462902--462945 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
462892 AGCGCAACAT
*
462902 GATTTTCAAGTATCGCAAAGC
1 GATTTTCAACTATCGCAAAGC
*
462923 GATTTTCAACTATCGCAACGC
1 GATTTTCAACTATCGCAAAGC
462944 GA
1 GA
462946 ATTTGCGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (21 bp):
GATTTTCAACTATCGCAAAGC
Found at i:463563 original size:59 final size:60
Alignment explanation
Indices: 463488--463620 Score: 205
Period size: 59 Copynumber: 2.2 Consensus size: 60
463478 AATTAAAAAG
* * *
463488 AACAAAATTGACCACGTGTTAACTAGTTTGAAACGAGTGACCTTAAGTTT-AAAAAACGA
1 AACAAAAGTGACCACGTGTTAAATAGTTTGAAACGAGTGACCATAAGTTTAAAAAAACGA
* * *
463547 AACAAAAGTGATCACGTGTTAAATAGTTTGAAACGAGTGACCATATGTTTAAAAAAATGA
1 AACAAAAGTGACCACGTGTTAAATAGTTTGAAACGAGTGACCATAAGTTTAAAAAAACGA
463607 AACAAAAGTGACCA
1 AACAAAAGTGACCA
463621 ACGACGTAGT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
59 45 0.68
60 21 0.32
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (60 bp):
AACAAAAGTGACCACGTGTTAAATAGTTTGAAACGAGTGACCATAAGTTTAAAAAAACGA
Found at i:465897 original size:35 final size:35
Alignment explanation
Indices: 465789--465920 Score: 142
Period size: 35 Copynumber: 3.8 Consensus size: 35
465779 AGAAGAACGA
*
465789 AAGG-AGCATCAGCACTTTCGATTCAAAGTGAATGG
1 AAGGAAGCATCGGCACTTTCGATTC-AAGTGAATGG
* * * * *
465824 AAGGAAACATCGACACTTTCAATTCAAGAAGAA-CG
1 AAGGAAGCATCGGCACTTTCGATTCAAG-TGAATGG
*
465859 AAGGAAGCACCGGCACTTTCGATTCAAGTGAATGG
1 AAGGAAGCATCGGCACTTTCGATTCAAGTGAATGG
* * *
465894 AAGGAAGCGTCAGCATTTTCGATTCAA
1 AAGGAAGCATCGGCACTTTCGATTCAA
465921 TTGTTCATTT
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
34 3 0.04
35 56 0.72
36 19 0.24
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.21
Consensus pattern (35 bp):
AAGGAAGCATCGGCACTTTCGATTCAAGTGAATGG
Found at i:466939 original size:54 final size:56
Alignment explanation
Indices: 466738--466953 Score: 231
Period size: 57 Copynumber: 3.8 Consensus size: 56
466728 AGAGGGAGGG
** * * *
466738 ATAAATCGTTGGATTTATTTCGTCGTT-AGAATCTTGCATTCATTCTAACTTTATAAAGAAA
1 ATAAATCGTTAAATTTATTT--TC-TTGAGAATCTTG-AATGATTCT-ACTTTGT-AAGAAA
** * * * *
466799 GCAAATCATTGAATTTATTTTCTTGAGAAACTTGAATGATTTTAACTTTGTAAGAAA
1 ATAAATCGTTAAATTTATTTTCTTGAGAATCTTGAATGATTCT-ACTTTGTAAGAAA
*
466856 ATAAATCGTTAAATTTATTTTCATGAGAATCTTGAATGATTCTACTTTGTAAG-AA
1 ATAAATCGTTAAATTTATTTTCTTGAGAATCTTGAATGATTCTACTTTGTAAGAAA
*
466911 AT-AATCGTTAAATTTATTTTCTTAAGAATCTTGAATGATTCTA
1 ATAAATCGTTAAATTTATTTTCTTGAGAATCTTGAATGATTCTA
466954 AACTTTTTAA
Statistics
Matches: 136, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
54 39 0.29
55 4 0.03
56 10 0.07
57 42 0.31
58 15 0.11
59 10 0.07
61 16 0.12
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (56 bp):
ATAAATCGTTAAATTTATTTTCTTGAGAATCTTGAATGATTCTACTTTGTAAGAAA
Found at i:470588 original size:29 final size:29
Alignment explanation
Indices: 470551--470614 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
470541 TAAAAAATAT
470551 TGAAA-AGGAGTAATCAAATTAAATCAAA
1 TGAAATAGGAGTAATCAAATTAAATCAAA
470579 TGAAATAGGAGTAATCAAATTAAATCAAA
1 TGAAATAGGAGTAATCAAATTAAATCAAA
470608 TGAAATA
1 TGAAATA
470615 CTAACAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 5 0.14
29 30 0.86
ACGTcount: A:0.56, C:0.06, G:0.14, T:0.23
Consensus pattern (29 bp):
TGAAATAGGAGTAATCAAATTAAATCAAA
Found at i:471948 original size:15 final size:15
Alignment explanation
Indices: 471928--471958 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
471918 AGTACTTTTG
471928 TGATCAGTGTCTGTT
1 TGATCAGTGTCTGTT
471943 TGATCAGTGTCTGTT
1 TGATCAGTGTCTGTT
471958 T
1 T
471959 AACGGTACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.48
Consensus pattern (15 bp):
TGATCAGTGTCTGTT
Found at i:478846 original size:18 final size:18
Alignment explanation
Indices: 478812--478847 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
478802 TTTATTTTTT
* *
478812 TATTTTTAATAATAAAAA
1 TATTTTTAAAAAAAAAAA
478830 TATTTTTAAAAAAAAAAA
1 TATTTTTAAAAAAAAAAA
478848 AGAAAGAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TATTTTTAAAAAAAAAAA
Found at i:481581 original size:21 final size:21
Alignment explanation
Indices: 481556--481606 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
481546 ATCGTTTCTC
*
481556 CCGATCGAACTAATTTAGTGG
1 CCGATCGAACTAATTTAGTGA
* *
481577 TCGATCGAACTAATTTGGTGA
1 CCGATCGAACTAATTTAGTGA
481598 CCGATCGAA
1 CCGATCGAA
481607 TTAACTGAAC
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:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (21 bp):
CCGATCGAACTAATTTAGTGA
Found at i:482416 original size:22 final size:22
Alignment explanation
Indices: 482385--482427 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
482375 AAAATCATTT
*
482385 TATTACAAATTTATAATGTTAG
1 TATTACAAATTGATAATGTTAG
*
482407 TATTATAAATTGATAATGTTA
1 TATTACAAATTGATAATGTTA
482428 ATTACCAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (22 bp):
TATTACAAATTGATAATGTTAG
Found at i:484877 original size:19 final size:22
Alignment explanation
Indices: 484834--484881 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
484824 TTGTTGTAAA
484834 TATTTATTTCACATATTTCTATT
1 TATTTATTTCACATATTTC-ATT
484857 TATTTATTTC-CAT-TTTC-TT
1 TATTTATTTCACATATTTCATT
484876 TATTTA
1 TATTTA
484882 AATATTATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
21 4 0.16
22 3 0.12
23 10 0.40
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (22 bp):
TATTTATTTCACATATTTCATT
Found at i:489747 original size:11 final size:11
Alignment explanation
Indices: 489719--489756 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
489709 AAGAGCAAAG
489719 AGAAAAATCAA
1 AGAAAAATCAA
489730 AGCAAAAATCAA
1 AG-AAAAATCAA
*
489742 AGAAAAAGCAA
1 AGAAAAATCAA
489753 AGAA
1 AGAA
489757 CAAAAAGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:491131 original size:94 final size:96
Alignment explanation
Indices: 490985--491186 Score: 358
Period size: 94 Copynumber: 2.1 Consensus size: 96
490975 GAGATTATTT
490985 TCTTTAAA-AAAATAAAAAAAATAAATAAGTGTCGTCTCACTTGAGATAGTTTTCTT-AAAACAA
1 TCTTTAAACAAAATAAAAAAAATAAATAAGTGTCGTCTCACTTGAGATAGTTTTCTTAAAAACAA
491048 ATTTT-TTTAGTCTCGCTTGAGACAATTTTC
66 ATTTTATTTAGTCTCGCTTGAGACAATTTTC
491078 TCTTTAAACAAAA-AAAAAAAATAAATAAAGTGTCGTCTCACTTGAGATAGTTTTCTTAAAAACA
1 TCTTTAAACAAAATAAAAAAAATAAAT-AAGTGTCGTCTCACTTGAGATAGTTTTCTTAAAAACA
491142 AATTTTATTTAGTCTCGCTTGAGACAATTTTC
65 AATTTTATTTAGTCTCGCTTGAGACAATTTTC
491174 TCTTTAAAACAAA
1 TCTTT-AAACAAA
491187 TTATGTCTCG
Statistics
Matches: 104, Mismatches: 0, Indels: 6
0.95 0.00 0.05
Matches are distributed among these distances:
93 21 0.20
94 34 0.33
95 12 0.12
96 30 0.29
97 7 0.07
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (96 bp):
TCTTTAAACAAAATAAAAAAAATAAATAAGTGTCGTCTCACTTGAGATAGTTTTCTTAAAAACAA
ATTTTATTTAGTCTCGCTTGAGACAATTTTC
Found at i:491412 original size:101 final size:98
Alignment explanation
Indices: 491230--491460 Score: 254
Period size: 101 Copynumber: 2.3 Consensus size: 98
491220 TTGAGAATTT
* * * *
491230 AAAACAAATTGCGTATCGCTTGAGACATTTTTCCTTTGAGATAAAATTTTGAATTTGATTCACTT
1 AAAAC-AATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATAAAATTTCGAATTTGATTCACTT
*
491295 AAAACAAAATTAATCTCA-TT-AGATGTTGTTTCTTTC
65 AAAACAAAATTAATCTCACTTGAGA--TCGTTTC--TC
* * *
491331 AAAACAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACAT
1 AAAACAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGAT-AAAATTTCGAATTTGATTCAC-T
* *
491396 T-AAACAAAGTTGATCTCACTTGAGATCGTTTCTC
64 TAAAACAAAATTAATCTCACTTGAGATCGTTTCTC
* *
491430 AAAAAAACTTT-GTCTCGCTTGAGACAATTTC
1 AAAACAA-TTTCGTCTCGCTTGAGACATTTTC
491461 TCTAAAAACA
Statistics
Matches: 112, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
99 26 0.23
100 35 0.31
101 44 0.39
102 4 0.04
103 3 0.03
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (98 bp):
AAAACAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATAAAATTTCGAATTTGATTCACTTA
AAACAAAATTAATCTCACTTGAGATCGTTTCTC
Found at i:491488 original size:36 final size:34
Alignment explanation
Indices: 491430--491525 Score: 113
Period size: 34 Copynumber: 2.8 Consensus size: 34
491420 ATCGTTTCTC
* *
491430 AAAA-AAACTTTGTCTCGCTTGAGACAATTTCTCT
1 AAAACAAATTTTGTCTCGCTTGAGACAATATCT-T
** *
491464 AAAAACAAATTTTGTCTCATTTGAGACTATATCTT
1 -AAAACAAATTTTGTCTCGCTTGAGACAATATCTT
*
491499 AAAGCAAATTTTGTCTCGCTTGAGACA
1 AAAACAAATTTTGTCTCGCTTGAGACA
491526 TCATTTTCTC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
34 23 0.45
35 5 0.10
36 23 0.45
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (34 bp):
AAAACAAATTTTGTCTCGCTTGAGACAATATCTT
Found at i:491814 original size:29 final size:29
Alignment explanation
Indices: 491775--491985 Score: 171
Period size: 29 Copynumber: 7.4 Consensus size: 29
491765 TTTCTCTTGG
*
491775 AAAAATCTTTGAGTTTGTTCCTCTTGAAA
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAA
*
491804 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAA
*
491833 AAAAATCTTTGAG-TTGTTTCTTTTG-AA
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAA
* * **
491860 AAAAATCTTTGAGTCTATTTATTTTGAAA
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAA
* * ** * * ** **
491889 CAAAGT-TTTGTCTCTCTTGACAATTTGTGA
1 AAAAATCTTTGAGTTTGTT--CCTTTTGAAA
* *
491919 AAAAATCTTTGAGATTGTT-CTTTTGAAC
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAA
* *
491947 AAAAATCTTTGAGTTTGTTTCTTTGGAAA
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAA
*
491976 CAAAAT-TTTG
1 AAAAATCTTTG
491986 TATCTCTTAA
Statistics
Matches: 144, Mismatches: 32, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
27 14 0.10
28 55 0.38
29 58 0.40
30 10 0.07
31 7 0.05
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (29 bp):
AAAAATCTTTGAGTTTGTTCCTTTTGAAA
Found at i:491850 original size:28 final size:28
Alignment explanation
Indices: 491775--491985 Score: 171
Period size: 28 Copynumber: 7.4 Consensus size: 28
491765 TTTCTCTTGG
*
491775 AAAAATCTTTGAGTTTGTTCCTCTTGAAA
1 AAAAATCTTTGAGTTTGTTCCTTTTG-AA
491804 AAAAATCTTTGAGTTTGTTCCTTTTGAA
1 AAAAATCTTTGAGTTTGTTCCTTTTGAA
*
491832 TAAAAATCTTTGAG-TTGTTTCTTTTGAA
1 -AAAAATCTTTGAGTTTGTTCCTTTTGAA
* * **
491860 AAAAATCTTTGAGTCTATTTATTTTGAA
1 AAAAATCTTTGAGTTTGTTCCTTTTGAA
* ** * * *
491888 ACAAAGT-TTTGTCTCTCTTGACAATTTGTG-A
1 A-AAAATCTTTGAGTTTGTT--C-CTTT-TGAA
*
491919 AAAAATCTTTGAGATTGTT-CTTTTGAA
1 AAAAATCTTTGAGTTTGTTCCTTTTGAA
* *
491946 CAAAAATCTTTGAGTTTGTTTCTTTGGAA
1 -AAAAATCTTTGAGTTTGTTCCTTTTGAA
491975 ACAAAAT-TTTG
1 A-AAAATCTTTG
491986 TATCTCTTAA
Statistics
Matches: 151, Mismatches: 19, Indels: 25
0.77 0.10 0.13
Matches are distributed among these distances:
26 2 0.01
27 17 0.11
28 59 0.39
29 54 0.36
30 4 0.03
31 13 0.09
32 2 0.01
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (28 bp):
AAAAATCTTTGAGTTTGTTCCTTTTGAA
Found at i:491978 original size:87 final size:86
Alignment explanation
Indices: 491833--492051 Score: 244
Period size: 87 Copynumber: 2.4 Consensus size: 86
491823 CCTTTTGAAT
* *
491833 AAAAATCTTTGAGTTGTTTCTTTTGAAAAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTTTT
1 AAAAATCTTTGAGTTGTTTCTTTTGAAAAAAATCTTTGAGTCTATTTATTTGGAAACAAAATTTT
*
491898 GTCTCTCTTGACAATTTGTGA
66 GTATCTCTTGACAATTTGTGA
* * *
491919 AAAAATCTTTGAGATTG-TTCTTTTGAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATT
1 AAAAATCTTTGAG-TTGTTTCTTTTGAA-AAAAATCTTTGAGTCTATTTATTTGGAAACAAAATT
* *
491983 TTGTATCTCTTAAGATAATTTCTTTTGAA
64 TTGTATCTCTT--GACAA--T-TTGTG-A
*
492012 ACAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAAT-TTTG
1 A-AAAATCTTTGAGT-TGTTTCTTTTGAAA-AAAATCTTTG
492052 TCTCTCTTAA
Statistics
Matches: 112, Mismatches: 9, Indels: 16
0.82 0.07 0.12
Matches are distributed among these distances:
86 23 0.21
87 44 0.39
89 4 0.04
91 1 0.01
92 4 0.04
93 3 0.03
94 19 0.17
95 14 0.12
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.44
Consensus pattern (86 bp):
AAAAATCTTTGAGTTGTTTCTTTTGAAAAAAATCTTTGAGTCTATTTATTTGGAAACAAAATTTT
GTATCTCTTGACAATTTGTGA
Found at i:492006 original size:66 final size:65
Alignment explanation
Indices: 491936--492153 Score: 271
Period size: 66 Copynumber: 3.3 Consensus size: 65
491926 TTTGAGATTG
*
491936 TTCTTTTGAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTATCTCTTAAGATAA
1 TTCTTTTGAA-AAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTATCTCTTAAGATAA
492001 T
65 T
* *
492002 TTCTTTTGAAACAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAAATAA
1 TTCTTTTGAAA-AAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTATCTCTTAAGATAA
492067 T
65 T
* * * * *
492068 TTCTTTTGAAAAAAGTCTTTGAATCTGTTTCTCTT--AAA-ATGAATTTTGTATCTCTTGAGACA
1 TTCTTTTGAAAAAAATCTTTGAGTCTGTTTCT-TTGGAAACA-AAATTTTGTATCTCTTAAGATA
*
492130 GT
64 AT
* **
492132 TTCTCTTGAAGTAAATCTTTGA
1 TTCTTTTGAAAAAAATCTTTGA
492154 ATATGTTCAT
Statistics
Matches: 134, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
63 1 0.01
64 39 0.29
65 20 0.15
66 74 0.55
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (65 bp):
TTCTTTTGAAAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTATCTCTTAAGATAAT
Found at i:492014 original size:37 final size:37
Alignment explanation
Indices: 491964--492078 Score: 113
Period size: 37 Copynumber: 3.3 Consensus size: 37
491954 TTTGAGTTTG
491964 TTTCTTTGGAAACAAAATTTTGTATCTCTTAAGATAA
1 TTTCTTTGGAAACAAAATTTTGTATCTCTTAAGATAA
* *
492001 TTTCTTTTGAAACAAAATCTTTG-A-GTC-T--G----
1 TTTCTTTGGAAACAAAAT-TTTGTATCTCTTAAGATAA
* *
492030 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAAATAA
1 TTTCTTTGGAAACAAAATTTTGTATCTCTTAAGATAA
*
492067 TTTCTTTTGAAA
1 TTTCTTTGGAAA
492079 AAAGTCTTTG
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
28 4 0.07
29 17 0.28
30 2 0.03
31 1 0.02
33 1 0.02
35 1 0.02
36 2 0.03
37 29 0.48
38 4 0.07
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.45
Consensus pattern (37 bp):
TTTCTTTGGAAACAAAATTTTGTATCTCTTAAGATAA
Found at i:492336 original size:120 final size:116
Alignment explanation
Indices: 492198--492418 Score: 266
Period size: 116 Copynumber: 1.9 Consensus size: 116
492188 TTAACAAAAT
* * * *
492198 CATCTTTGAGTCTATTTCTTTAAAA-ACAAATGTTGTCTCTCTT-GAGACAGTTTCTAATGAAAA
1 CATCTTAGAGTCTATTTCTTTAAAACA-AAAT-TT-TATCTCTTAAAGACAATTTCTAATGAAAA
492261 ACTAACTTTTGAGATTGTTTCATTTGAAACAAATTTGGTCTCACTTAAGATGTGATC
63 A--AAC-TTTGAGATTGTTTCATTTGAAACAAATTTGGTCTCACTTAAGATGTGATC
* * ** *
492318 CATCTTAGAGTCTGTTTCTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAAT
1 CATCTTAGAGTCTATTTCTTTAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAAAA
* * *
492383 CTTTGAGTTTGTTTCCTTTGAAACAAATTTTGTCTC
66 CTTTGAGATTGTTTCATTTGAAACAAATTTGGTCTC
492419 GAGACAACTT
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
116 32 0.37
117 2 0.02
118 7 0.08
119 19 0.22
120 26 0.30
121 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (116 bp):
CATCTTAGAGTCTATTTCTTTAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAAAA
CTTTGAGATTGTTTCATTTGAAACAAATTTGGTCTCACTTAAGATGTGATC
Found at i:492438 original size:59 final size:60
Alignment explanation
Indices: 492319--492438 Score: 154
Period size: 62 Copynumber: 2.0 Consensus size: 60
492309 GATGTGATCC
*
492319 ATCTTAGAGTCTGTTTCTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAA
1 ATCTTAGAGTCTGTTTCTTTGAAACAAAATTTTATCTC-T-AAGACAACTTCTTTTGAAAAA
* * * *
492381 ATCTTTGAGTTTGTTTCCTTTGAAAC-AAATTTTGTCTC-GAGACAACTTCTTTTGAAAA
1 ATCTTAGAGTCTGTTT-CTTTGAAACAAAATTTTATCTCTAAGACAACTTCTTTTGAAAA
492439 TACCCACCTT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
59 18 0.35
62 25 0.48
63 9 0.17
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (60 bp):
ATCTTAGAGTCTGTTTCTTTGAAACAAAATTTTATCTCTAAGACAACTTCTTTTGAAAAA
Found at i:492483 original size:40 final size:40
Alignment explanation
Indices: 492420--492499 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
492410 TTTTGTCTCG
492420 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
* *
492460 AGACAATTTCTTTT-AAAACTACCCACCTTTGAGATTGTTT
1 AGACAACTTCTTTTGAAAA-TACCCACCTTTGAGATCGTTT
492500 TTATTAAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 4 0.11
40 33 0.89
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
Found at i:492611 original size:14 final size:15
Alignment explanation
Indices: 492600--492630 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
492590 GTCGTTTCAT
492600 TTGAA-CATTTTCTC
1 TTGAAGCATTTTCTC
492614 TTGAAGCATTTTCTC
1 TTGAAGCATTTTCTC
492629 TT
1 TT
492631 AAAACAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.52
Consensus pattern (15 bp):
TTGAAGCATTTTCTC
Found at i:493401 original size:43 final size:44
Alignment explanation
Indices: 493311--493545 Score: 179
Period size: 40 Copynumber: 5.5 Consensus size: 44
493301 TGGCCAGTAG
* * ** *
493311 TCCTCATCACATAGGAACCGTGTCAT-CCCCAG---ACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
493351 TCCTCATCACGTAGGAGCCGTGTCA-ACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
* * * ** *
493393 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCAT-ACC-ATAGATAACCAGACC
* * * ** *
493440 TCTTCATCACGTATGAGCCGTGTCATTCC-CCG---ACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
*
493480 TCTTCATCACGTAGGAGCCGTGTCA-ACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
*
493522 GTCCTCATCACGTAGGAACCGTGT
1 -TCCTCATCACGTAGGAGCCGTGT
493546 TATCGCCCTT
Statistics
Matches: 154, Mismatches: 27, Indels: 25
0.75 0.13 0.12
Matches are distributed among these distances:
39 2 0.01
40 58 0.38
42 2 0.01
43 55 0.36
45 5 0.03
46 31 0.20
47 1 0.01
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (44 bp):
TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
Found at i:493527 original size:129 final size:131
Alignment explanation
Indices: 493297--493604 Score: 442
Period size: 129 Copynumber: 2.3 Consensus size: 131
493287 CCATTATCCC
* * * * * *
493297 TAGATGGCCAGTAGTCCTCATCACATAGGAACCGTGTCATCCCCAGACCAGATCTCCTCATCACG
1 TAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACG
493362 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTAT-C-ACCT
66 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCCTACCT
493425 T
131 T
*
493426 TAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTCATCAC
1 TAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCA-TCCCCAGACCAGATCTCCTCATCAC
493490 GTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGCCCT
65 GTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTAT---CCT
*
493555 TCCTT
127 ACCTT
* * * * *
493560 TAGACGACCAGAACTCTTCATCATGTATGAGCAGTGTCGTCCCCA
1 TAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCA
493605 ACAACCAACA
Statistics
Matches: 159, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
129 110 0.69
130 5 0.03
133 6 0.04
134 38 0.24
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.24
Consensus pattern (131 bp):
TAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACG
TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCCTACCT
T
Found at i:493774 original size:3 final size:3
Alignment explanation
Indices: 493760--493806 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
493750 TCTAATTGTA
*
493760 ATT ATA ATT ATT ATT ATT A-T ATT ATT ATT ATT A-T ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
493805 AT
1 AT
493807 GCTTATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 6 0.15
3 33 0.85
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Done.