Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007703.1 Hibiscus syriacus cultivar Beakdansim tig00109916_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: 1017536
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:811861 original size:36 final size:36
Alignment explanation
Indices: 811821--811892 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
811811 TAAAATTTAA
* *
811821 AATAAGTATGTAAGTTATGGTAAATACGAAAGTTAT
1 AATAAGTATGAAAGTTATGATAAATACGAAAGTTAT
* *
811857 AATAAGTATGAAAGTTATGATACATATGAAAGTTAT
1 AATAAGTATGAAAGTTATGATAAATACGAAAGTTAT
811893 GAAATATGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.33
Consensus pattern (36 bp):
AATAAGTATGAAAGTTATGATAAATACGAAAGTTAT
Found at i:812279 original size:31 final size:30
Alignment explanation
Indices: 812241--812305 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
812231 GTAAGTTTTG
*
812241 AAAGTTTAAGGA-ATAAAATATAAATTTTGTA
1 AAAGTTTAAGGACA-AAAATAT-AATTTTGAA
*
812272 AAAGTTTAGGGACCAAAAATATAATTTTGAA
1 AAAGTTTAAGGA-CAAAAATATAATTTTGAA
812303 AAA
1 AAA
812306 TTATAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 22 0.73
32 7 0.23
33 1 0.03
ACGTcount: A:0.52, C:0.03, G:0.14, T:0.31
Consensus pattern (30 bp):
AAAGTTTAAGGACAAAAATATAATTTTGAA
Found at i:814443 original size:27 final size:27
Alignment explanation
Indices: 814411--814474 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
814401 TGAAGTTGTC
*
814411 TAGAAATTTAAATTCGAACAGTTAGTT
1 TAGAAATTTAAATTCGAACAATTAGTT
814438 TAGAAATTTAAATTCGAACAATTAGTT
1 TAGAAATTTAAATTCGAACAATTAGTT
814465 TAGAAATTTA
1 TAGAAATTTA
814475 CCATAAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (27 bp):
TAGAAATTTAAATTCGAACAATTAGTT
Found at i:815205 original size:17 final size:16
Alignment explanation
Indices: 815168--815228 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 16
815158 TCTTTATAGA
815168 TATCAGATGATTATA-AT
1 TATCAGAT-ATT-TACAT
815185 TATCAGATATTTACAT
1 TATCAGATATTTACAT
*
815201 ATATCAAATATTTTACAGT
1 -TATCAGATA-TTTACA-T
815220 TATCAGATA
1 TATCAGATA
815229 CATGTTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
15 2 0.05
16 5 0.13
17 16 0.42
18 14 0.37
19 1 0.03
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (16 bp):
TATCAGATATTTACAT
Found at i:815224 original size:35 final size:36
Alignment explanation
Indices: 815133--815228 Score: 101
Period size: 35 Copynumber: 2.8 Consensus size: 36
815123 TGTTTATAGT
* * * *
815133 TATCATATGATTTT-CAGTTATAAGATCTTTATAGA
1 TATCAAATGATTTTACAGTTATCAGATATTTACAGA
* * *
815168 TATCAGATGATTATA-A-TTATCAGATATTTACATA
1 TATCAAATGATTTTACAGTTATCAGATATTTACAGA
815202 TATCAAAT-ATTTTACAGTTATCAGATA
1 TATCAAATGATTTTACAGTTATCAGATA
815229 CATGTTAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
33 5 0.10
34 22 0.44
35 23 0.46
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (36 bp):
TATCAAATGATTTTACAGTTATCAGATATTTACAGA
Found at i:815391 original size:43 final size:42
Alignment explanation
Indices: 815329--815416 Score: 122
Period size: 43 Copynumber: 2.1 Consensus size: 42
815319 GTGCTTATCC
* *
815329 GTTATCAATTATCAAATCAGCTTTGGTACATTCTTGTATCAAT
1 GTTATCAACTATCAAATCAGCTTTGGTA-ATTCATGTATCAAT
* * *
815372 GTTATCAGCTATCATATCAGCTTTGGTAATTCATGTATTAAT
1 GTTATCAACTATCAAATCAGCTTTGGTAATTCATGTATCAAT
815414 GTT
1 GTT
815417 TAGTATCGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 15 0.38
43 25 0.62
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (42 bp):
GTTATCAACTATCAAATCAGCTTTGGTAATTCATGTATCAAT
Found at i:821979 original size:17 final size:17
Alignment explanation
Indices: 821957--822019 Score: 67
Period size: 17 Copynumber: 3.7 Consensus size: 17
821947 GGTTTTTAGT
*
821957 TATCAGATCTTTACATA
1 TATCAGATATTTACATA
821974 TATCAGATGA-TTACAGT-
1 TATCAGAT-ATTTACA-TA
*
821991 TATAAGATATTTACATA
1 TATCAGATATTTACATA
*
822008 TATTAGATATTT
1 TATCAGATATTT
822020 TACAGTTATC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
16 2 0.05
17 36 0.92
18 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (17 bp):
TATCAGATATTTACATA
Found at i:821992 original size:34 final size:34
Alignment explanation
Indices: 821954--822030 Score: 102
Period size: 34 Copynumber: 2.2 Consensus size: 34
821944 TATGGTTTTT
*
821954 AGTTATCAGATCTTTACATATATCAGATGA-TTAC
1 AGTTATCAGATATTTACATATATCAGAT-ATTTAC
* *
821988 AGTTATAAGATATTTACATATATTAGATATTTTAC
1 AGTTATCAGATATTTACATATATCAGATA-TTTAC
822023 AGTTATCA
1 AGTTATCA
822031 TATACAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 1 0.03
34 25 0.68
35 11 0.30
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (34 bp):
AGTTATCAGATATTTACATATATCAGATATTTAC
Found at i:823671 original size:44 final size:44
Alignment explanation
Indices: 823608--823697 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
823598 AAAGATGAAC
823608 ACAGGTGCCTCTGGCAATGGCATTTACTTGAAGAAACATCATTA
1 ACAGGTGCCTCTGGCAATGGCATTTACTTGAAGAAACATCATTA
823652 ACAGGTGCCTCTGGCAATGGCATTTACTTGAAGAAACATCATTA
1 ACAGGTGCCTCTGGCAATGGCATTTACTTGAAGAAACATCATTA
823696 AC
1 AC
823698 CAATGAATAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (44 bp):
ACAGGTGCCTCTGGCAATGGCATTTACTTGAAGAAACATCATTA
Found at i:824173 original size:37 final size:36
Alignment explanation
Indices: 824100--824203 Score: 111
Period size: 37 Copynumber: 2.8 Consensus size: 36
824090 GTATGTAGCG
*
824100 GCAACAAACATAACACAACGAAA-AAGCGATCTCAACC
1 GCAACAAACATAACACAAC-AAATAAGTGA-CTCAACC
824137 GCAACAAACATAACACAACAAATAAGTGACTGCAACC
1 GCAACAAACATAACACAACAAATAAGTGACT-CAACC
* * * * * *
824174 ACAATAAACACAGCACATCGAATAAGTGAC
1 GCAACAAACATAACACAACAAATAAGTGAC
824204 CACAAATACA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 5 0.09
37 53 0.91
ACGTcount: A:0.51, C:0.27, G:0.12, T:0.11
Consensus pattern (36 bp):
GCAACAAACATAACACAACAAATAAGTGACTCAACC
Found at i:826418 original size:12 final size:10
Alignment explanation
Indices: 826377--826417 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
826367 TTTATCACAC
826377 CAAATTCTCT
1 CAAATTCTCT
826387 CAAATTCTCT
1 CAAATTCTCT
826397 -AAATTTCTCT
1 CAAA-TTCTCT
*
826407 CAAATACTCT
1 CAAATTCTCT
826417 C
1 C
826418 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:826466 original size:13 final size:14
Alignment explanation
Indices: 826438--826466 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
826428 ATATTTTATA
826438 ATATTTTTACTATT
1 ATATTTTTACTATT
826452 ATATTTTTACT-TT
1 ATATTTTTACTATT
826465 AT
1 AT
826467 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTACTATT
Found at i:832507 original size:49 final size:51
Alignment explanation
Indices: 832400--832522 Score: 171
Period size: 49 Copynumber: 2.5 Consensus size: 51
832390 TTATACAAAA
* *
832400 CGCGGTACCTGCCCCGTGCTATATAAAATTATGTCAGGAGTAAATGTATGT
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
*
832451 CGCGGTACCTGCCCTGCGCTATATAAAATTAT-T-AGGAGTAAAGGTATAG-
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTAT-GT
**
832500 CGCGGTACCTGATCCGCGCTATA
1 CGCGGTACCTGCCCCGCGCTATA
832523 CCCCTACGTG
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
49 33 0.51
50 2 0.03
51 30 0.46
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (51 bp):
CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
Found at i:832611 original size:50 final size:51
Alignment explanation
Indices: 832546--832661 Score: 153
Period size: 51 Copynumber: 2.3 Consensus size: 51
832536 TATAGCACGC
* * ** *
832546 TGCAGGGGCCACGCTATA-CCCACGTGGCGCCAGCTCACCGTATAGCGCAG
1 TGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCACCGTATAACGCAG
* * *
832596 TGCAGGGGGCGCGCTATACCCCACGTGGTGCCAAATCATCGTATAACGCGG
1 TGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCACCGTATAACGCAG
832647 TGCAGGGGGCGCGCT
1 TGCAGGGGGCGCGCT
832662 TTACTGCTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 16 0.28
51 41 0.72
ACGTcount: A:0.19, C:0.32, G:0.34, T:0.16
Consensus pattern (51 bp):
TGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCACCGTATAACGCAG
Found at i:842283 original size:15 final size:16
Alignment explanation
Indices: 842258--842308 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
842248 CATAATTTAT
*
842258 ATAATTTTAATATTAA
1 ATAATATTAATATTAA
* *
842274 ATATTA-TAATAGTATTA
1 ATAATATTAATA-T-TAA
842291 ATAATATTAATATTAA
1 ATAATATTAATATTAA
842307 AT
1 AT
842309 TTTCAGTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
15 5 0.19
16 9 0.33
17 8 0.30
18 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATAATATTAATATTAA
Found at i:848931 original size:23 final size:24
Alignment explanation
Indices: 848904--848994 Score: 132
Period size: 24 Copynumber: 3.9 Consensus size: 24
848894 ATAAAGATCA
*
848904 TGCATTT-CATTAATACATTTGAT
1 TGCATTTGCATAAATACATTTGAT
* *
848927 TGCATTT-CATTAATACATTTGCT
1 TGCATTTGCATAAATACATTTGAT
*
848950 TGCATTTGCATAAATACATTTTAT
1 TGCATTTGCATAAATACATTTGAT
848974 TGCATTTGCATAAATACATTT
1 TGCATTTGCATAAATACATTT
848995 TGTTAGAAGA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
23 29 0.46
24 34 0.54
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (24 bp):
TGCATTTGCATAAATACATTTGAT
Found at i:848966 original size:47 final size:47
Alignment explanation
Indices: 848904--848994 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 47
848894 ATAAAGATCA
* *
848904 TGCATTTCATTAATACATTTGATTGCATTT-CATTAATACATTTGCT
1 TGCATTTCATAAATACATTTGATTGCATTTGCATAAATACATTTGCT
*
848950 TGCATTTGCATAAATACATTTTATTGCATTTGCATAAATACATTT
1 TGCATTT-CATAAATACATTTGATTGCATTTGCATAAATACATTT
848995 TGTTAGAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 7 0.17
47 21 0.52
48 12 0.30
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (47 bp):
TGCATTTCATAAATACATTTGATTGCATTTGCATAAATACATTTGCT
Found at i:860412 original size:32 final size:32
Alignment explanation
Indices: 860376--860445 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
860366 ACTCATATAT
860376 TTAAAAATCAATAAAAATACAAT-AAAAAAGAA
1 TTAAAAATCAAT-AAAATACAATAAAAAAAGAA
* * **
860408 TTAAAAGTGAATAAAATTTAATAAAAAAAGAA
1 TTAAAAATCAATAAAATACAATAAAAAAAGAA
860440 TGTAAA
1 T-TAAA
860446 GCTAAAGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 8 0.25
32 20 0.62
33 4 0.12
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.23
Consensus pattern (32 bp):
TTAAAAATCAATAAAATACAATAAAAAAAGAA
Found at i:862558 original size:24 final size:22
Alignment explanation
Indices: 862509--862573 Score: 62
Period size: 24 Copynumber: 2.9 Consensus size: 22
862499 TTATATATTT
*
862509 TTATAAAAATTATA-TGAAATA
1 TTATAAAAATTATATTTAAATA
*
862530 ATATAAAAATGTATATTTATAATA
1 TTATAAAAAT-TATATTTA-AATA
862554 TTATACAAATATT-TATTTAA
1 TTATA-AAA-ATTATATTTAA
862574 TTTTTAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 9 0.25
22 4 0.11
23 3 0.08
24 14 0.39
25 4 0.11
26 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (22 bp):
TTATAAAAATTATATTTAAATA
Found at i:862613 original size:23 final size:23
Alignment explanation
Indices: 862561--862613 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
862551 ATATTATACA
*
862561 AATATTTATTTAATTTTTAAAATC
1 AATA-TTAATTAATTTTTAAAATC
862585 AA-ATTAATTAATTATTTAAAAT-
1 AATATTAATTAATT-TTTAAAATC
862607 AATATTA
1 AATATTA
862614 TTTTTATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 11 0.42
23 13 0.50
24 2 0.08
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
AATATTAATTAATTTTTAAAATC
Found at i:862756 original size:23 final size:23
Alignment explanation
Indices: 862726--862780 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
862716 ATAAATAATT
862726 TAAA-AATATTATTTAAAATAAA
1 TAAATAATATTATTTAAAATAAA
*
862748 TAAATAATATTATTTCAAATAAA
1 TAAATAATATTATTTAAAATAAA
862771 TAAATAATAT
1 TAAATAATAT
862781 GGTTTTAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 4 0.13
23 27 0.87
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAATAATATTATTTAAAATAAA
Found at i:862775 original size:27 final size:25
Alignment explanation
Indices: 862712--862777 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 25
862702 ATATTTAAAA
*
862712 TTAAATAAATAATTTAAAAATATTAT
1 TTAAATAAATAA-ATAAAAATATTAT
862738 TT--A-AAATAAATAAATAATATTAT
1 TTAAATAAATAAATAAA-AATATTAT
862761 TTCAAATAAATAAATAA
1 TT-AAATAAATAAATAA
862778 TATGGTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
22 4 0.12
23 16 0.47
24 1 0.03
26 3 0.09
27 10 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
TTAAATAAATAAATAAAAATATTAT
Found at i:862844 original size:31 final size:33
Alignment explanation
Indices: 862799--862866 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 33
862789 ACATTAAATT
*
862799 AATA-TTTTAAAATAATTTCATA-ATAT-TATA
1 AATATTTTTAAAATAATTTCATATAAATATATA
*
862829 AATATTTTTAGAATAATTTCATATAAATATATA
1 AATATTTTTAAAATAATTTCATATAAATATATA
862862 AATAT
1 AATAT
862867 AACAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 4 0.12
31 17 0.52
32 3 0.09
33 9 0.27
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (33 bp):
AATATTTTTAAAATAATTTCATATAAATATATA
Found at i:877653 original size:27 final size:28
Alignment explanation
Indices: 877623--877675 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
877613 TAATTAAACT
* *
877623 TTAAATTTTTTATCTTAAA-ATAAAATA
1 TTAAATTATATATCTTAAATATAAAATA
*
877650 TTAAATTATATATTTTAAATATAAAA
1 TTAAATTATATATCTTAAATATAAAA
877676 ATAATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
TTAAATTATATATCTTAAATATAAAATA
Found at i:878291 original size:37 final size:38
Alignment explanation
Indices: 878244--878317 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
878234 TTTTGTTCGG
878244 GTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA
878281 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCG
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCG
878318 GGGTTGGGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 11 0.31
38 25 0.69
ACGTcount: A:0.12, C:0.11, G:0.38, T:0.39
Consensus pattern (38 bp):
GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:878536 original size:42 final size:41
Alignment explanation
Indices: 878489--878586 Score: 132
Period size: 38 Copynumber: 2.4 Consensus size: 41
878479 TTTATTTTGT
*
878489 TCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTC-G---GG
1 TCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCAGTCAAG
*
878526 TCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGTCAAG
1 TCGGGTCGGGTCGGG-TTTTTTAAGTGTGATATTCAGTCAAG
878568 TCGGGTCGGGTTCGGGTTT
1 TCGGGTCGGG-TCGGGTTT
878587 AGGGTGAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
37 14 0.27
38 19 0.37
39 1 0.02
42 13 0.25
43 5 0.10
ACGTcount: A:0.12, C:0.12, G:0.38, T:0.38
Consensus pattern (41 bp):
TCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCAGTCAAG
Found at i:878549 original size:249 final size:250
Alignment explanation
Indices: 878020--878625 Score: 873
Period size: 249 Copynumber: 2.4 Consensus size: 250
878010 TTTTGATCGG
* *
878020 GTCGGATCGGGTTTTTTTAAGTGTGATATTCAAGTCGGGTCGAGTCGGGTTCGGGTTTAGGGTGA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATA-T----TCGGGTC-AG-CGGGTTCGGGTTTAGGGTAA
* *
878085 AAAAAACGGATCGACCCGAAAATATATAATTCAGGTCGGGTCAGATTAAGTCACTGTTTTTATTG
59 AAAAAACGGACCGACCCGAAAATATATAATTCAGGTCGGGTCAGATTAAGTCACTGTTTTTATTA
*
878150 AATAAAAATAATTTTTTATTATTTCGGGTCGGGTCAGGTTGGATTTCTAATTCATATATTCGGGT
124 AATAAAAATAATTTTTTATTATTTCAGGTCGGGTC--G--GGATTTCTAATTCATATATTCGGGT
878215 CGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCG
185 CGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCG
878280 A
250 A
878281 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC-G-GGGTT-GGGTTTAGGGTAAAAAAAAC
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGCGGGTTCGGGTTTAGGGTAAAAAAAA-
* *
878343 CGGACCGACCCGAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATA
65 CGGACCGACCCG-AAA-ATATATAATTCAGGTCGGGTCAGATTAAGTCACTGTTTTTATTAAATA
878408 AAAATAATTTTTTATTATTTCAGGTCGGGTC-GGATTTCTAATTCATATATTCGGGTCGGGTCGG
128 AAAATAATTTTTTATTATTTCAGGTCGGGTCGGGATTTCTAATTCATATATTCGGGTCGGGTCGG
878472 ATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
193 ATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
* *
878530 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGTCAAGTCGGGTCGGGTTCGGGTTTAGGGTGAA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTC-G---GGTC-AG-CGGGTTCGGGTTTAGGGT-AA
*
878595 AAAAAA--GACCAACCCGAAAAAATATATAATT
59 AAAAAACGGACCGACCCG--AAAATATATAATT
878626 TTAGGAATAA
Statistics
Matches: 322, Mismatches: 9, Indels: 33
0.88 0.02 0.09
Matches are distributed among these distances:
249 122 0.38
250 1 0.00
251 18 0.06
252 16 0.05
253 6 0.02
254 76 0.24
255 1 0.00
256 26 0.08
257 9 0.03
258 11 0.03
259 8 0.02
260 1 0.00
261 27 0.08
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.35
Consensus pattern (250 bp):
GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGCGGGTTCGGGTTTAGGGTAAAAAAAAC
GGACCGACCCGAAAATATATAATTCAGGTCGGGTCAGATTAAGTCACTGTTTTTATTAAATAAAA
ATAATTTTTTATTATTTCAGGTCGGGTCGGGATTTCTAATTCATATATTCGGGTCGGGTCGGATG
AAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:878555 original size:38 final size:37
Alignment explanation
Indices: 878493--878579 Score: 140
Period size: 37 Copynumber: 2.4 Consensus size: 37
878483 TTTTGTTCGG
* *
878493 GTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTC-AGTCAA
878530 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGTCAA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGTCAA
878567 GTCGGGTCGGGTT
1 GTCGGGTCGGGTT
878580 CGGGTTTAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 28 0.60
38 19 0.40
ACGTcount: A:0.14, C:0.11, G:0.37, T:0.38
Consensus pattern (37 bp):
GTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGTCAA
Found at i:883714 original size:12 final size:12
Alignment explanation
Indices: 883697--883761 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
883687 ACAAAAATAT
883697 TTTATTATATTA
1 TTTATTATATTA
883709 TTTATTATTATTA
1 TTTATTA-TATTA
883722 TTACTATTA-A-TA
1 TT--TATTATATTA
*
883734 TTTTTTAT-TTA
1 TTTATTATATTA
* *
883745 TTTATTTTATTT
1 TTTATTATATTA
883757 TTTAT
1 TTTAT
883762 AGACCCCATG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 4 0.09
11 8 0.19
12 18 0.42
13 8 0.19
15 5 0.12
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTATTATATTA
Found at i:884275 original size:11 final size:11
Alignment explanation
Indices: 884251--884284 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
884241 AATTTTCATC
884251 CATATATAATAT
1 CATATAT-ATAT
884263 CATATATATAT
1 CATATATATAT
*
884274 CACATATATAT
1 CATATATATAT
884285 ATTACTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (11 bp):
CATATATATAT
Found at i:885284 original size:15 final size:16
Alignment explanation
Indices: 885264--885296 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
885254 ATATATTTTA
*
885264 TTTATTTCTT-TTATT
1 TTTATTACTTATTATT
885279 TTTATTACTTATTATT
1 TTTATTACTTATTATT
885295 TT
1 TT
885297 ATTGTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTACTTATTATT
Found at i:885312 original size:21 final size:21
Alignment explanation
Indices: 885272--885339 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
885262 TATTTATTTC
*
885272 TTTTATT-TTTATTACTTATTA
1 TTTTATTGTTTTTTAC-TATTA
885293 TTTTATTGTTTTTTACTATT-
1 TTTTATTGTTTTTTACTATTA
* * *
885313 TTCTTTTTGGTTTTTATTATTTA
1 TT-TTATTGTTTTTTACTA-TTA
885336 TTTT
1 TTTT
885340 CCATACGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 2 0.05
21 24 0.62
22 11 0.28
23 2 0.05
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.75
Consensus pattern (21 bp):
TTTTATTGTTTTTTACTATTA
Found at i:885452 original size:2 final size:2
Alignment explanation
Indices: 885445--885487 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
885435 GTAATATTTG
885445 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
885487 T
1 T
885488 CTTTATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:885633 original size:20 final size:21
Alignment explanation
Indices: 885588--885633 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
885578 TATATTATTT
*
885588 ATTCCTTTTTATCTTATTTTT
1 ATTCCTTTTTATCTTATTTTA
*
885609 GTTCCTGTTTT-T-TTATTTTA
1 ATTCCT-TTTTATCTTATTTTA
885629 ATTCC
1 ATTCC
885634 ATTATTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.52
21 6 0.29
22 4 0.19
ACGTcount: A:0.13, C:0.15, G:0.04, T:0.67
Consensus pattern (21 bp):
ATTCCTTTTTATCTTATTTTA
Found at i:888757 original size:17 final size:15
Alignment explanation
Indices: 888723--888806 Score: 62
Period size: 16 Copynumber: 5.3 Consensus size: 15
888713 AGATCCAATC
*
888723 AAGAACAAAAAAGAA
1 AAGAACAAAAAAAAA
888738 AAGAAGCAAAAAAAACA
1 AAGAA-CAAAAAAAA-A
* *
888755 AAGAA-AAAGAGAAAC
1 AAGAACAAA-AAAAAA
*
888770 AAGAACAAAAGGAAAA
1 AAGAACAAAA-AAAAA
* *
888786 AAGAGCAAAAATCAAA
1 AAGAACAAAAA-AAAA
888802 AAGAA
1 AAGAA
888807 AAAGGGATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
15 14 0.25
16 35 0.64
17 6 0.11
ACGTcount: A:0.75, C:0.08, G:0.15, T:0.01
Consensus pattern (15 bp):
AAGAACAAAAAAAAA
Found at i:889491 original size:23 final size:22
Alignment explanation
Indices: 889449--889491 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
889439 CCATCAATCT
* *
889449 TTTGAGCATCCAATGCCAAACC
1 TTTGAGCATCAAATGACAAACC
889471 TTTGAGCATCAAATGAACAAA
1 TTTGAGCATCAAATG-ACAAA
889492 AATGCCAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (22 bp):
TTTGAGCATCAAATGACAAACC
Found at i:890579 original size:106 final size:106
Alignment explanation
Indices: 890450--891297 Score: 1309
Period size: 106 Copynumber: 8.0 Consensus size: 106
890440 ATATCGTGCC
* * * *
890450 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAGCAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
890515 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
890556 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
890621 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
890662 ACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTT-T
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTCC
890726 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
890768 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
890833 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
890874 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTT-T
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTCC
*
890938 TAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
890980 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAAAACAACTTC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC--AACAAACAATTTC
* *
891045 CCAATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGG
64 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
891088 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AA-AATTT--C
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
891149 -A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
891188 ACTCGAGACAGCGCAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * * *
891253 GATTCCAAAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
891294 ACTC
1 ACTC
891298 GGAACAATAC
Statistics
Matches: 688, Mismatches: 41, Indels: 26
0.91 0.05 0.03
Matches are distributed among these distances:
100 85 0.12
101 3 0.00
102 6 0.01
104 5 0.01
105 6 0.01
106 480 0.70
107 7 0.01
108 96 0.14
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:893147 original size:15 final size:16
Alignment explanation
Indices: 893127--893159 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
893117 ATTTTATTTA
*
893127 TTTATTTCTT-TTATT
1 TTTATTACTTATTATT
893142 TTTATTACTTATTATT
1 TTTATTACTTATTATT
893158 TT
1 TT
893160 ATTGTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTACTTATTATT
Found at i:893153 original size:22 final size:22
Alignment explanation
Indices: 893118--893182 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
893108 ATTCTATATA
*
893118 TTTTATTTATTTATTTCTTTTAT
1 TTTTA-TTACTTATTTCTTTTAT
*
893141 TTTTATTACTTA-TTATTTTAT
1 TTTTATTACTTATTTCTTTTAT
*
893162 TGTTTTTTAC-TATTTTCTTTT
1 T-TTTATTACTTA-TTTCTTTT
893183 TGGTTTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 11 0.31
22 13 0.37
23 11 0.31
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTTATTACTTATTTCTTTTAT
Found at i:893175 original size:21 final size:21
Alignment explanation
Indices: 893103--893172 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 21
893093 TGTTTTGCTA
*
893103 TTATTATTCTATATATTTTATTTAT
1 TTATTATT-T-TAT-TTTTA-TTAC
*
893128 TTATTTCTTTTATTTTTATTAC
1 TTA-TTATTTTATTTTTATTAC
*
893150 TTATTATTTTATTGTTTTTTAC
1 TTATTATTTTATT-TTTATTAC
893172 T
1 T
893173 ATTTTCTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 9 0.23
22 14 0.36
23 5 0.13
24 3 0.08
25 4 0.10
26 4 0.10
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.71
Consensus pattern (21 bp):
TTATTATTTTATTTTTATTAC
Found at i:893181 original size:44 final size:43
Alignment explanation
Indices: 893131--893272 Score: 112
Period size: 44 Copynumber: 3.2 Consensus size: 43
893121 TATTTATTTA
893131 TTTCTTTTATTTTTATTACTTATTATTTTATTGTTTTTTACTAT
1 TTTCTTTTATTTTTATTACTTATTATTTTATTGTTTTTTA-TAT
* *
893175 TTTCTTTTTGGTTTTTATTA-TT-TTATTTTCCATACGTTTTTTATAT
1 TTTC-TTTT-ATTTTTATTACTTATTATTTT--AT-TGTTTTTTATAT
* * * * *
893221 ATTT-TTTAATAATTTT-TTCCTTATTATTTTCTTATTATTTATAT
1 -TTTCTTT--TATTTTTATTACTTATTATTTTATTGTTTTTTATAT
893265 TTTCTTTT
1 TTTCTTTT
893273 TCTTTCATTT
Statistics
Matches: 78, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
42 1 0.01
43 3 0.04
44 23 0.29
45 12 0.15
46 20 0.26
47 19 0.24
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.71
Consensus pattern (43 bp):
TTTCTTTTATTTTTATTACTTATTATTTTATTGTTTTTTATAT
Found at i:895089 original size:24 final size:25
Alignment explanation
Indices: 895062--895124 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
895052 TTCTTTTGAC
895062 TTATTTATTTTTTTCA-AATTTTTA
1 TTATTTATTTTTTTCACAATTTTTA
**
895086 TTA-TTATTATTTTT-ACGTTTTTTA
1 TTATTTATT-TTTTTCACAATTTTTA
895110 TT-TTTATATTTTTTC
1 TTATTTAT-TTTTTTC
895125 TTTCATTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
23 6 0.19
24 25 0.78
25 1 0.03
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.73
Consensus pattern (25 bp):
TTATTTATTTTTTTCACAATTTTTA
Found at i:899619 original size:23 final size:23
Alignment explanation
Indices: 899593--899643 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
899583 CAGCTCATAT
*
899593 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* **
899616 AATTGCACCGGAGTGCTGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
899639 AATTG
1 AATTG
899644 AACTGTAGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:899843 original size:103 final size:103
Alignment explanation
Indices: 899672--899889 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
899662 TAATGTCCAT
*
899672 AAGGACCGCATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
899737 GACCTCACACATGTTCCAAAGAATACATATATGTCTCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
*
899775 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
899840 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
899878 AAGGACCACATA
1 AAGGACCACATA
899890 GACCCTCTAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:900448 original size:64 final size:67
Alignment explanation
Indices: 900338--900465 Score: 201
Period size: 64 Copynumber: 2.0 Consensus size: 67
900328 ATTTTCATCT
900338 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGATGTTTG
1 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGATGTTTG
900403 TA
66 TA
* *
900405 TTTAATGG-GG-ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCTATTCGATGTTT
1 TTTAATGGAGGTATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCATATTCGATGTTT
900466 TCTTTTTAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
63 1 0.02
64 32 0.55
65 15 0.26
66 2 0.03
67 8 0.14
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (67 bp):
TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGATGTTTG
TA
Found at i:900503 original size:64 final size:63
Alignment explanation
Indices: 900350--900510 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 63
900340 TAATGGAGGT
* * *
900350 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACA-TATGCATCGATGCATAAATCATATTCGATGTTTCTATTTAAT-GGA
* * * * *
900415 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTACATATGCATCGATGCATAAATCATATTCGATG-TTTCTATTT-AATGGA
* * *
900479 ATGCATCGATGCACTGCATGTGCATTGATGCA
1 ATGCATCGATGCACTACATATGCATCGATGCA
900511 CCTTAAACAA
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 56 0.68
65 23 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACATATGCATCGATGCATAAATCATATTCGATGTTTCTATTTAATGGA
Found at i:906641 original size:23 final size:22
Alignment explanation
Indices: 906615--906678 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
906605 CAGCTCATAT
906615 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
** *
906638 AATTGCACAGGAGTGCCGCGTAG
1 AATTGCAC-CTAGTGCCACGTAG
*
906661 AATTGAACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
906679 TATAATAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:906820 original size:103 final size:103
Alignment explanation
Indices: 906694--906911 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
906684 TAATGTCCAT
906694 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
906759 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
906797 AAGGACCACATATCATTTCTTAAGAATCATATACATATGCCAATGATCAAGTGTGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
906862 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
906900 AAGGACCACATA
1 AAGGACCACATA
906912 GACCCTCTAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:907461 original size:19 final size:19
Alignment explanation
Indices: 907437--907487 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
907427 TTTAATGGGG
907437 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
907456 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
907475 ATGCATCGATGCA
1 ATGCATCGATGCA
907488 TAAATCCTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTT
Found at i:907524 original size:83 final size:83
Alignment explanation
Indices: 907371--907552 Score: 217
Period size: 83 Copynumber: 2.2 Consensus size: 83
907361 TTAATGGAGG
*
907371 TATGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGATGTTTGTATTTAATGGG
1 TATGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGATGTTTCTATTTAAT-GG
* *
907436 GATGCATCGATGCACTCCT
65 AATGCATCGATGCACTCCA
* * * *
907455 TATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCTATTTGATGTTTTCTTTTTAAAT
1 TATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCATATTCGATG-TTTCTATTT-AAT
* *
907518 -TAATGCATCGATGCACTGCA
63 GGAATGCATCGATGCACTCCA
*
907538 TGTGCATCGATGCAC
1 TATGCATCGATGCAC
907553 CTTAAACAAT
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
82 1 0.01
83 58 0.68
84 23 0.27
85 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (83 bp):
TATGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGATGTTTCTATTTAATGGA
ATGCATCGATGCACTCCA
Found at i:909571 original size:30 final size:30
Alignment explanation
Indices: 909536--909605 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
909526 CGTATATATG
909536 AGCTATGTGATCATATGAGAATATGAAAAA
1 AGCTATGTGATCATATGAGAATATGAAAAA
909566 AGCTATGTGATCATATGAGAATATGAAAAA
1 AGCTATGTGATCATATGAGAATATGAAAAA
909596 AGCTATGTGA
1 AGCTATGTGA
909606 ACAAGTGAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.27
Consensus pattern (30 bp):
AGCTATGTGATCATATGAGAATATGAAAAA
Found at i:910866 original size:58 final size:58
Alignment explanation
Indices: 910796--910997 Score: 160
Period size: 58 Copynumber: 3.3 Consensus size: 58
910786 CCATCCACGG
910796 TTTCAACTTCACGACGAAGGGAATTGTGCTCACCAACAACATTCATCTTTAGATTGGA
1 TTTCAACTTCACGACGAAGGGAATTGTGCTCACCAACAACATTCATCTTTAGATTGGA
* * * * ** **
910854 TTTCAACTTCACGACGAAGGATATCCAATTCAAG-GCTCAACTTC-ACAACGAATGAGCCATCCA
1 TTTCAACTTCACGACGAAGG-----GAATT---GTGCTC-AC--CAACAAC-ATTCATCTTTAGA
**
910917 -CAG-
54 TTGGA
* *
910920 TTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTTAGATTGGA
1 TTTCAACTTCACGACGAAGGGAATTGTGCTCACCAACAACATTCATCTTTAGATTGGA
910978 TTTCAACTTCACGACGAAGG
1 TTTCAACTTCACGACGAAGG
910998 ATATCCAATT
Statistics
Matches: 106, Mismatches: 22, Indels: 32
0.66 0.14 0.20
Matches are distributed among these distances:
56 7 0.07
57 5 0.05
58 43 0.41
59 4 0.04
61 3 0.03
63 4 0.04
65 4 0.04
66 23 0.22
67 6 0.06
68 7 0.07
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (58 bp):
TTTCAACTTCACGACGAAGGGAATTGTGCTCACCAACAACATTCATCTTTAGATTGGA
Found at i:910930 original size:124 final size:124
Alignment explanation
Indices: 910710--911773 Score: 1593
Period size: 124 Copynumber: 8.6 Consensus size: 124
910700 GGGGTGTTAC
* * *
910710 ACATTCATCTTTAGATTGGATTTCAACTTCACGATGAAGGATTTTCAATTCAAGGCTCAACTTCA
1 ACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCA
* * * *
910775 CAATGAAGGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATTGTGCTCACCAACA
66 CAACGAATGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCA
910834 ACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCA
1 ACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCA
* *
910899 CAACGAATGAGCCATCCACAGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCA
66 CAACGAATGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCA
910958 ACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCA
1 ACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCA
* * *
911023 CAATGAAGGGGACATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCA
66 CAACGAATGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCA
* * * *
911082 ATATTCATCTTTAGATTGAATTTCAAATTCACGACGAAGGATATCCAATTCAAGGCTCAACTTTA
1 ACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCA
* * *
911147 CAACGAATGGGTCATCCACGGTTTCAACTTCACGACGAAAGGAATCGTGCTCACCAGTA
66 CAACGAATGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCA
* *
911206 ACATTCATCTTTAGATTGGATTTCAACTTCACGGA-AAATGATATCCAATTCAAGGCTCAACTTC
1 ACATTCATCTTTAGATTGGATTTCAACTTCAC-GACGAAGGATATCCAATTCAAGGCTCAACTTC
* * * *
911270 ACAACGAAGGGGCCATCCACGGTTTCAACTTCACGACAAAGGAAATCGTGCTTACCAGCA
65 ACAACGAATGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCA
* * *
911330 AGATTCATCTTTAGATTGGATTTCAACTTAACGACGAAGGATATCCAATTCAAGGCTTAACTTCA
1 ACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCA
* * * *
911395 CAACGAAT-GG---TCCA--TTTTCAACTTCACGACAAAGGGAATCGTTCTCATCAGCA
66 CAACGAATGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCA
* * * *
911448 ACATTCATCTTAAGATTGGATTTCAACTTCACGACGAATGCTATACAATTCAAGGCTCAACTTCA
1 ACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCA
* * * * *
911513 AAATGAATGGGCCATCCATGGTTTCAACTTCACGACGAAGGGAATCGTACTCACCAGTA
66 CAACGAATGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCA
* *
911572 ACATTCATCTTTAGATTAGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAAATTCA
1 ACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCA
* * * * *
911637 CAACGAATAGGCCATCCACGGTTTTAACTTCATGACGAAGGGAATCGTGCCCACTAGCA
66 CAACGAATGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCA
* * *
911696 ACATTCATCTTCAGATTGGATTTCAATTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCA
1 ACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCA
* *
911761 TAACGAAAGGGCC
66 CAACGAATGGGCC
911774 CTCTTCGATC
Statistics
Matches: 847, Mismatches: 85, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
118 98 0.12
119 2 0.00
120 4 0.00
122 4 0.00
123 4 0.00
124 733 0.87
125 2 0.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (124 bp):
ACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCA
CAACGAATGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCA
Found at i:911642 original size:490 final size:494
Alignment explanation
Indices: 910710--911773 Score: 1654
Period size: 490 Copynumber: 2.2 Consensus size: 494
910700 GGGGTGTTAC
* * * *
910710 ACATTCATCTTTAGATTGGATTTCAACTTCACGATGAAGGATTTTCAATTCAAGGCTCAACTTCA
1 ACATTCATCTTTAGATTGGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCA
* * * *
910775 CAATGAAGGGGCCATCCACGGTTTCAACTTCACGACGAAGGGAATTGTGCTCACCAACAACATTC
66 CAACGAAGGGGCCATCCACGGTTTCAACTTCACGACAAAGGAAATCGTGCTCACCAACAACATTC
*
910840 ATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGA
131 ATCTTTAGATTGGATTTCAACTTAACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGA
* *
910905 ATGAGCCATCCACAGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTT
196 ATGAG-C-TCCACAGTTTCAACTTCACGACAAAGGGAATCGTGCTCACCAGCAACATTCATCTTA
* *
910970 AGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGGA
259 AGATTGGATTTCAACTTCACGACGAAGGATATACAATTCAAGGCTCAACTTCAAAATGAAGGGGA
* *
911035 CATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAATATTCATCTTTAGATTG
324 CATCCACGGTTTCAACTTCACGACGAAGGGAATCGTACTCACCAGCAACATTCATCTTTAGATTG
* * * *
911100 AATTTCAAATTCACGACGAAGGATATCCAATTCAAGGCTCAACTTTACAACGAATGGGTCATCCA
389 AATTTCAAATTCACGACGAAGGATATCCAATTCAAGGCTCAAATTCACAACGAATAGGCCATCCA
* *
911165 CGGTTTCAACTTCACGACGAAAGGAATCGTGCTCACCAGTA
454 CGGTTTCAACTTCACGACGAAAGGAATCGTGCCCACCAGCA
*
911206 ACATTCATCTTTAGATTGGATTTCAACTTCACGGA-AAATGATATCCAATTCAAGGCTCAACTTC
1 ACATTCATCTTTAGATTGGATTTCAACTTCAC-GACGAATGATATCCAATTCAAGGCTCAACTTC
* * *
911270 ACAACGAAGGGGCCATCCACGGTTTCAACTTCACGACAAAGGAAATCGTGCTTACCAGCAAGATT
65 ACAACGAAGGGGCCATCCACGGTTTCAACTTCACGACAAAGGAAATCGTGCTCACCAACAACATT
*
911335 CATCTTTAGATTGGATTTCAACTTAACGACGAAGGATATCCAATTCAAGGCTTAACTTCACAACG
130 CATCTTTAGATTGGATTTCAACTTAACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACG
* * *
911400 AATG-G-T-C-CATTTTCAACTTCACGACAAAGGGAATCGTTCTCATCAGCAACATTCATCTTAA
195 AATGAGCTCCACAGTTTCAACTTCACGACAAAGGGAATCGTGCTCACCAGCAACATTCATCTTAA
* * * *
911461 GATTGGATTTCAACTTCACGACGAATGCTATACAATTCAAGGCTCAACTTCAAAATGAATGGGCC
260 GATTGGATTTCAACTTCACGACGAAGGATATACAATTCAAGGCTCAACTTCAAAATGAAGGGGAC
* *
911526 ATCCATGGTTTCAACTTCACGACGAAGGGAATCGTACTCACCAGTAACATTCATCTTTAGATT-A
325 ATCCACGGTTTCAACTTCACGACGAAGGGAATCGTACTCACCAGCAACATTCATCTTTAGATTGA
*
911590 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAAATTCACAACGAATAGGCCATCCA
390 -ATTTCAAATTCACGACGAAGGATATCCAATTCAAGGCTCAAATTCACAACGAATAGGCCATCCA
* * * *
911655 CGGTTTTAACTTCATGACGAAGGGAATCGTGCCCACTAGCA
454 CGGTTTCAACTTCACGACGAAAGGAATCGTGCCCACCAGCA
* *
911696 ACATTCATCTTCAGATTGGATTTCAATTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCA
1 ACATTCATCTTTAGATTGGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCA
* *
911761 TAACGAAAGGGCC
66 CAACGAAGGGGCC
911774 CTCTTCGATC
Statistics
Matches: 521, Mismatches: 44, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
489 3 0.01
490 331 0.64
491 1 0.00
492 1 0.00
495 1 0.00
496 182 0.35
497 2 0.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (494 bp):
ACATTCATCTTTAGATTGGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCA
CAACGAAGGGGCCATCCACGGTTTCAACTTCACGACAAAGGAAATCGTGCTCACCAACAACATTC
ATCTTTAGATTGGATTTCAACTTAACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGA
ATGAGCTCCACAGTTTCAACTTCACGACAAAGGGAATCGTGCTCACCAGCAACATTCATCTTAAG
ATTGGATTTCAACTTCACGACGAAGGATATACAATTCAAGGCTCAACTTCAAAATGAAGGGGACA
TCCACGGTTTCAACTTCACGACGAAGGGAATCGTACTCACCAGCAACATTCATCTTTAGATTGAA
TTTCAAATTCACGACGAAGGATATCCAATTCAAGGCTCAAATTCACAACGAATAGGCCATCCACG
GTTTCAACTTCACGACGAAAGGAATCGTGCCCACCAGCA
Found at i:912023 original size:3 final size:3
Alignment explanation
Indices: 912011--912061 Score: 61
Period size: 3 Copynumber: 16.7 Consensus size: 3
912001 CAAAAACATT
912011 TTA TTA -TA TTA TTTA TTTA TTTA TTA TTA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA -TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
912057 TTA TT
1 TTA TT
912062 TTTTGTAGGC
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 30 0.67
4 11 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:912740 original size:39 final size:39
Alignment explanation
Indices: 912697--912772 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
912687 AACTGCCTCC
912697 ACCAAACAACCATTTCCCGACAATCACCAAACAGTCTCT
1 ACCAAACAACCATTTCCCGACAATCACCAAACAGTCTCT
*
912736 ACCAAACAACCATTTCCCGACAATCACCAAACGGTCT
1 ACCAAACAACCATTTCCCGACAATCACCAAACAGTCT
912773 TCACCACTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.38, C:0.38, G:0.07, T:0.17
Consensus pattern (39 bp):
ACCAAACAACCATTTCCCGACAATCACCAAACAGTCTCT
Found at i:913716 original size:39 final size:39
Alignment explanation
Indices: 913672--913777 Score: 101
Period size: 39 Copynumber: 2.6 Consensus size: 39
913662 TTTTGACTTA
913672 TTTAATTT-TTTTAATT-TTATTTTAT-TTCATGTTTTTTTC
1 TTTAATTTATTTTAATTATT-TTTTATCTT-A-GTTTTTTTC
*
913711 TTTAATTTATTTTTATTATTTTTTATCTTAGTTTTTTTCC
1 TTTAATTTATTTTAATTATTTTTTATCTTAGTTTTTTT-C
* *
913751 TTTTGATTTATTATTATTTATTATTTT
1 -TTTAATTTATT-TTAATTATT-TTTT
913778 TACGTTTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
39 16 0.29
40 15 0.27
41 14 0.25
42 7 0.12
43 4 0.07
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.74
Consensus pattern (39 bp):
TTTAATTTATTTTAATTATTTTTTATCTTAGTTTTTTTC
Found at i:919830 original size:82 final size:82
Alignment explanation
Indices: 919662--919845 Score: 205
Period size: 82 Copynumber: 2.3 Consensus size: 82
919652 AATAGCGATT
* * *
919662 TTTGAATAAAAATGCCACTAAAGTATGAGTCTATAGCATCGTTTGTAAAAAAACGCCGCTAAAGC
1 TTTGTATAAAAATGCCACTAAAGGATGAGTCTATAGCATCGTTTGTAAAAAAACGCCACTAAAGC
* * *
919727 ACGGATCTATAGCATCC
66 ACAGATCTATAGCAGCA
* *
919744 TTTGTATAAAAATGCCACTAAAGGACT-AGTCTATAGTGA-CGTTTGTATAAAAACGCCACTAAA
1 TTTGTATAAAAATGCCACTAAAGGA-TGAGTCTATAG-CATCGTTTGTAAAAAAACGCCACTAAA
* * *
919807 GTACTAG-TCTTTAGCGGCA
64 GCAC-AGATCTATAGCAGCA
*
919826 TTTGTAT-AAAACGCCACTAA
1 TTTGTATAAAAATGCCACTAA
919846 TGTACTAATA
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
81 12 0.14
82 72 0.83
83 3 0.03
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (82 bp):
TTTGTATAAAAATGCCACTAAAGGATGAGTCTATAGCATCGTTTGTAAAAAAACGCCACTAAAGC
ACAGATCTATAGCAGCA
Found at i:919851 original size:40 final size:41
Alignment explanation
Indices: 919653--919852 Score: 176
Period size: 41 Copynumber: 4.9 Consensus size: 41
919643 ACCACTAAAA
** * *
919653 ATAGCGATTTTTGAATAAAAATGCCACTAAAGTA-TGAGTCT
1 ATAGCGACATTTGTATAAAAACGCCACTAAAGTACT-AGTCT
* * * * *
919694 ATAGC-ATCGTTTGTAAAAAAACGCCGCTAAAGCAC-GGATCT
1 ATAGCGA-CATTTGTATAAAAACGCCACTAAAGTACTAG-TCT
* * *
919735 ATAGC-ATCCTTTGTATAAAAATGCCACTAAAGGACTAGTCT
1 ATAGCGA-CATTTGTATAAAAACGCCACTAAAGTACTAGTCT
* *
919776 ATAGTGACGTTTGTATAAAAACGCCACTAAAGTACTAGTCT
1 ATAGCGACATTTGTATAAAAACGCCACTAAAGTACTAGTCT
* * *
919817 TTAGCGGCATTTGTAT-AAAACGCCACTAATGTACTA
1 ATAGCGACATTTGTATAAAAACGCCACTAAAGTACTA
919853 ATAAATTGCG
Statistics
Matches: 131, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
40 21 0.16
41 108 0.82
42 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (41 bp):
ATAGCGACATTTGTATAAAAACGCCACTAAAGTACTAGTCT
Found at i:919868 original size:40 final size:41
Alignment explanation
Indices: 919744--919882 Score: 115
Period size: 41 Copynumber: 3.4 Consensus size: 41
919734 TATAGCATCC
* * * * * *
919744 TTTGTATAAAAATGCCACTAAAGGACTAGT-CTATAGTGACG
1 TTTGTATAAAAACGCCACTAAAGTACTAATAAT-TAGCGACA
* ** *
919785 TTTGTATAAAAACGCCACTAAAGTACTAGTCTTTAGCGGCA
1 TTTGTATAAAAACGCCACTAAAGTACTAATAATTAGCGACA
*
919826 TTTGTAT-AAAACGCCACTAATGTACTAATAAATT-GCGACA
1 TTTGTATAAAAACGCCACTAAAGTACTAAT-AATTAGCGACA
*
919866 TTTAT-TCAAAAACGCCA
1 TTTGTAT-AAAAACGCCA
919883 TTACATTATG
Statistics
Matches: 82, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
39 1 0.01
40 29 0.35
41 51 0.62
42 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Consensus pattern (41 bp):
TTTGTATAAAAACGCCACTAAAGTACTAATAATTAGCGACA
Found at i:919993 original size:41 final size:40
Alignment explanation
Indices: 919948--920024 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 40
919938 TATTATGGTG
* *
919948 TTTGTATAAAAACGCCACTAAAGTACAAGTCTTTAGCGGCA
1 TTTGTATAAAAACACCACGAAAGTACAAG-CTTTAGCGGCA
* *
919989 TTTGTATACAAACACCACGAAAGTACGAGCTTTAGC
1 TTTGTATAAAAACACCACGAAAGTACAAGCTTTAGC
920025 AGCGTTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 7 0.22
41 25 0.78
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (40 bp):
TTTGTATAAAAACACCACGAAAGTACAAGCTTTAGCGGCA
Found at i:926526 original size:32 final size:32
Alignment explanation
Indices: 926485--926549 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
926475 TCCAAATTCC
926485 TTACCTTCGAATAAATGACTCAATTTTTAGAT
1 TTACCTTCGAATAAATGACTCAATTTTTAGAT
*
926517 TTACCTTCGAATAAATGACTTAATTTTTAGAT
1 TTACCTTCGAATAAATGACTCAATTTTTAGAT
926549 T
1 T
926550 CAGAGCGATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (32 bp):
TTACCTTCGAATAAATGACTCAATTTTTAGAT
Found at i:927822 original size:22 final size:22
Alignment explanation
Indices: 927797--927838 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
927787 TAATAATTTT
* *
927797 CTTTTCTTTTTTTATTATTTCA
1 CTTTTATTTTTATATTATTTCA
927819 CTTTTATTTTTATATTATTT
1 CTTTTATTTTTATATTATTT
927839 GATATTACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.74
Consensus pattern (22 bp):
CTTTTATTTTTATATTATTTCA
Found at i:933501 original size:60 final size:60
Alignment explanation
Indices: 933393--933511 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
933383 TTGGGTGATC
* * * *
933393 ATTTTATATCTTTTAATAGTCAATAGACTCAACAAAGCAACGCCTTATACTCGAGAGACT
1 ATTTTATAACTTTTAATAGTCAATAGACTCAACAAAACAACGCATTATACTCAAGAGACT
* * *
933453 ATTTTATAACTTTTAATAGTCAATGGACTCAACAAAACAACGTATTATAGTCAAGAGAC
1 ATTTTATAACTTTTAATAGTCAATAGACTCAACAAAACAACGCATTATACTCAAGAGAC
933512 CATTCCTATC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTCAATAGACTCAACAAAACAACGCATTATACTCAAGAGACT
Found at i:934056 original size:29 final size:29
Alignment explanation
Indices: 934023--934085 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
934013 AAAAATATAG
* * *
934023 TAAAAATGAATAAAATAAAGAAGGTGAAA
1 TAAAAATAAATAAAATAAAGAAGATAAAA
** *
934052 TAAAAATAAATGCAATAAAGTAGATAAAA
1 TAAAAATAAATAAAATAAAGAAGATAAAA
934081 TAAAA
1 TAAAA
934086 CAGATAAAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.67, C:0.02, G:0.13, T:0.19
Consensus pattern (29 bp):
TAAAAATAAATAAAATAAAGAAGATAAAA
Found at i:934157 original size:2 final size:2
Alignment explanation
Indices: 934150--934184 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
934140 CAAATATAAA
934150 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
934185 AATAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:934228 original size:18 final size:18
Alignment explanation
Indices: 934188--934229 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
934178 ATATATAAAT
*
934188 AAATAAATAAAATACATA
1 AAATAAAGAAAATACATA
*
934206 AAATAAAGAAGATA-ATA
1 AAATAAAGAAAATACATA
934223 ACAATAA
1 A-AATAA
934230 CAATACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.19
Consensus pattern (18 bp):
AAATAAAGAAAATACATA
Found at i:934248 original size:20 final size:19
Alignment explanation
Indices: 934205--934289 Score: 59
Period size: 20 Copynumber: 4.4 Consensus size: 19
934195 TAAAATACAT
* *
934205 AAAATAAAGA-AGATAATA
1 AAAATAAAGATAAAAAATA
*
934223 ACAATAACA-ATACAAAAATA
1 AAAATAA-AGATA-AAAAATA
934243 AAAATAGAAGATAAAAAATA
1 AAAATA-AAGATAAAAAATA
* *
934263 AAAGATAAA-ATGAAATATA
1 AAA-ATAAAGATAAAAAATA
934282 TAAAATAA
1 -AAAATAA
934290 TAAATATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
18 7 0.13
19 14 0.26
20 26 0.48
21 7 0.13
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.18
Consensus pattern (19 bp):
AAAATAAAGATAAAAAATA
Found at i:934259 original size:14 final size:14
Alignment explanation
Indices: 934242--934272 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
934232 ATACAAAAAT
*
934242 AAAAATAGAAGATA
1 AAAAATAAAAGATA
934256 AAAAATAAAAGATA
1 AAAAATAAAAGATA
934270 AAA
1 AAA
934273 TGAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (14 bp):
AAAAATAAAAGATA
Found at i:934296 original size:16 final size:17
Alignment explanation
Indices: 934275--934430 Score: 91
Period size: 18 Copynumber: 9.4 Consensus size: 17
934265 AGATAAAATG
934275 AAATATATA-AAATAAT
1 AAATATATATAAATAAT
934291 AAATATATATAACAT-AT
1 AAATATATATAA-ATAAT
934308 -AAT-TATAGT-AAT-A-
1 AAATATATA-TAAATAAT
934321 AAA-ATATAT-AATAAT
1 AAATATATATAAATAAT
* *
934336 ATATATGATATATATAA-
1 AAATAT-ATATAAATAAT
*
934353 AAATATATATATATATAT
1 AAATATATATAAATA-AT
* *
934371 ATATATATATATATATAT
1 AAATATATATAAATA-AT
* *
934389 ATATATATATATATACGAT
1 AAATATATATAAATA--AT
* *
934408 AAATATAGA-AAATAAA
1 AAATATATATAAATAAT
934424 AAATATA
1 AAATATA
934431 AAAAAATAGC
Statistics
Matches: 118, Mismatches: 9, Indels: 26
0.77 0.06 0.17
Matches are distributed among these distances:
13 4 0.03
14 10 0.08
15 7 0.06
16 32 0.27
17 14 0.12
18 42 0.36
19 9 0.08
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (17 bp):
AAATATATATAAATAAT
Found at i:934307 original size:9 final size:9
Alignment explanation
Indices: 934275--934401 Score: 60
Period size: 10 Copynumber: 13.0 Consensus size: 9
934265 AGATAAAATG
934275 AAATATATA
1 AAATATATA
934284 AAATA-ATA
1 AAATATATA
934292 AATATATATA
1 AA-ATATATA
*
934302 ACATATA-A
1 AAATATATA
**
934310 TTATAGTAATAA
1 AAATA-T-AT-A
934322 AAATATATA
1 AAATATATA
934331 ATAATATATA
1 A-AATATATA
*
934341 TGATATATATAA
1 --AAATATAT-A
934353 AAATATATA
1 AAATATATA
*
934362 TATATATATA
1 -AAATATATA
*
934372 TATATATATA
1 -AAATATATA
*
934382 TATATATATA
1 -AAATATATA
*
934392 TATATATATA
1 -AAATATATA
934402 TACGATAAAT
Statistics
Matches: 99, Mismatches: 8, Indels: 21
0.77 0.06 0.16
Matches are distributed among these distances:
8 9 0.09
9 17 0.17
10 60 0.61
11 7 0.07
12 6 0.06
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (9 bp):
AAATATATA
Found at i:934329 original size:31 final size:29
Alignment explanation
Indices: 934277--934402 Score: 103
Period size: 31 Copynumber: 4.1 Consensus size: 29
934267 ATAAAATGAA
*
934277 ATAT-ATAAAATAATAAATATATATAACAT
1 ATATGATATAATAA-AAATATATATAACAT
* *
934306 ATAATTATAGTAATAAAAATATATAATAATAT
1 AT-ATGATA-TAATAAAAATATAT-ATAACAT
*
934338 ATATGATATATATAAAAATATATATATATAT
1 ATATGATATA-ATAAAAATATATATA-ACAT
* * *
934369 ATAT-ATATATATATATATATATATATATAT
1 ATATGATATA-ATAAAAATATATATA-ACAT
934399 ATAT
1 ATAT
934403 ACGATAAATA
Statistics
Matches: 86, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
29 2 0.02
30 35 0.41
31 36 0.42
32 13 0.15
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (29 bp):
ATATGATATAATAAAAATATATATAACAT
Found at i:934339 original size:2 final size:2
Alignment explanation
Indices: 934324--934403 Score: 119
Period size: 2 Copynumber: 40.5 Consensus size: 2
934314 AGTAATAAAA
* *
934324 AT AT AT A- AT A- AT AT AT AT GAT AT AT AT AA AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
934365 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
934404 CGATAAATAT
Statistics
Matches: 73, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
1 2 0.03
2 69 0.95
3 2 0.03
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:934462 original size:2 final size:2
Alignment explanation
Indices: 934455--934480 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
934445 TGAAGATAAT
934455 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
934481 ATAAGAATAA
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):
TA
Found at i:936029 original size:110 final size:110
Alignment explanation
Indices: 935896--936094 Score: 299
Period size: 110 Copynumber: 1.8 Consensus size: 110
935886 GCTCTGGAAA
* *
935896 TTGTTTGTTGACAGTCAGCCGCCCCTTCGCTATGAAGTTGAGCTTGTATTGTCTCGAGTTCAATA
1 TTGTTTGTTGACAATCAGCCGCCCCTTCGCTATGAAGTTGAGCTTGTATTGTCTCGAGTCCAATA
*
935961 TCCTTCACTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAG
66 TCCCTCACTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAG
* * * * *
936006 TTGTTTGTTGACAATCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATA
1 TTGTTTGTTGACAATCAGCCGCCCCTTCGCTATGAAGTTGAGCTTGTATTGTCTCGAGTCCAATA
** *
936071 TCCCTCGTTGTGAAGTTGAAATTG
66 TCCCTCACTGTGAAGTTAAAATTG
936095 CTGAAACTGG
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
110 78 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.36
Consensus pattern (110 bp):
TTGTTTGTTGACAATCAGCCGCCCCTTCGCTATGAAGTTGAGCTTGTATTGTCTCGAGTCCAATA
TCCCTCACTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAG
Found at i:937089 original size:15 final size:16
Alignment explanation
Indices: 937069--937104 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
937059 CCCACCTTAT
937069 TTTTTG-TTCTTTCTC
1 TTTTTGTTTCTTTCTC
*
937084 TTTTTGTTTTTTTCTC
1 TTTTTGTTTCTTTCTC
937100 TTTTT
1 TTTTT
937105 TCAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.81
Consensus pattern (16 bp):
TTTTTGTTTCTTTCTC
Found at i:943854 original size:22 final size:22
Alignment explanation
Indices: 943829--943871 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
943819 AAGTTTGCAC
943829 CTTT-ACAGCAGATGATGTTTTT
1 CTTTGACAGCAGATGA-GTTTTT
* *
943851 CTTTGATAGTAGATGAGTTTT
1 CTTTGACAGCAGATGAGTTTT
943872 CTTGTGGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.47
Consensus pattern (22 bp):
CTTTGACAGCAGATGAGTTTTT
Found at i:947530 original size:29 final size:29
Alignment explanation
Indices: 947472--947534 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
947462 AAAAATATAG
*
947472 TAAAAATAAATAAAATAAAGAAGGTGAAA
1 TAAAAATAAATAAAATAAAGAAGGTAAAA
** *
947501 TAAAAATAAATGCAATAAAGTAGAG-AAAA
1 TAAAAATAAATAAAATAAAGAAG-GTAAAA
947530 TAAAA
1 TAAAA
947535 CATATAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.13, T:0.17
Consensus pattern (29 bp):
TAAAAATAAATAAAATAAAGAAGGTAAAA
Found at i:947599 original size:2 final size:2
Alignment explanation
Indices: 947592--947650 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
947582 ACAAAAACAA
947592 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
947634 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
947651 ATACATAAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:947714 original size:15 final size:15
Alignment explanation
Indices: 947694--947724 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
947684 ATACAAAAAT
*
947694 AAAATAGAAGATAAA
1 AAAATAAAAGATAAA
947709 AAAATAAAAGATAAA
1 AAAATAAAAGATAAA
947724 A
1 A
947725 TGTAATATAA
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:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (15 bp):
AAAATAAAAGATAAA
Found at i:947747 original size:14 final size:15
Alignment explanation
Indices: 947728--947862 Score: 59
Period size: 16 Copynumber: 8.8 Consensus size: 15
947718 GATAAAATGT
947728 AATATA-AAATAATA
1 AATATATAAATAATA
*
947742 AATATATATAACATATA
1 AATATATA-AATA-ATA
*
947759 ATTATAGT-AATAA-A
1 AATATA-TAAATAATA
947773 AATATATAAATAATA
1 AATATATAAATAATA
*
947788 ATGATATATGAAA-AA-G
1 A--ATATAT-AAATAATA
947804 AAT-TA-AAAGTATATA
1 AATATATAAA-TA-ATA
* *
947819 TATATATATATATATA
1 AATATATAAATA-ATA
* *
947835 TATATATATATATATA
1 AATATATAAATA-ATA
*
947851 TATATATAAATA
1 AATATATAAATA
947863 GAATAAAAAA
Statistics
Matches: 97, Mismatches: 9, Indels: 28
0.72 0.07 0.21
Matches are distributed among these distances:
11 3 0.03
13 4 0.04
14 20 0.21
15 6 0.06
16 42 0.43
17 18 0.19
18 4 0.04
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.37
Consensus pattern (15 bp):
AATATATAAATAATA
Found at i:947820 original size:2 final size:2
Alignment explanation
Indices: 947813--947858 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
947803 GAATTAAAAG
947813 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
947855 TA TA
1 TA TA
947859 AATAGAATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:950448 original size:20 final size:21
Alignment explanation
Indices: 950407--950462 Score: 78
Period size: 20 Copynumber: 2.6 Consensus size: 21
950397 TTTTCCTAAT
950407 TCGCAATGCGAATACGACGTAAA
1 TCGCAATGCGAATA--ACGTAAA
950430 TCGCAATGCGAAT-ACGTAAA
1 TCGCAATGCGAATAACGTAAA
*
950450 TCGCAACGCGAAT
1 TCGCAATGCGAAT
950463 CTGACTATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 19 0.59
23 13 0.41
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATAACGTAAA
Found at i:950472 original size:20 final size:20
Alignment explanation
Indices: 950449--950515 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
950439 GAATACGTAA
* *
950449 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
*
950469 ATCGCAACGAGATTTTGACT
1 ATCGCAACGAGATTCTGACT
950489 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
950509 ATCGCAA
1 ATCGCAA
950516 TACTGAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:951384 original size:24 final size:24
Alignment explanation
Indices: 951357--951410 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
951347 GTATTCAAAA
*
951357 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGATCAATACCCGGAC
* *
951381 TTTGATCTTGATCAATACTCGGAT
1 TTTGATCTTGATCAATACCCGGAC
951405 TTTGAT
1 TTTGAT
951411 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGATCAATACCCGGAC
Found at i:953936 original size:20 final size:20
Alignment explanation
Indices: 953843--953936 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
953833 CAACGCGGAA
*
953843 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAAAATGACT
* *
953863 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
953883 ATCGCAACGCGGAATTGACT
1 ATCGCAACGCGAAAATGACT
953903 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
953923 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
953937 TAAAAATCGC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:954056 original size:33 final size:33
Alignment explanation
Indices: 954001--954094 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
953991 TAGTTTCGCG
954001 TTGCGATTTTCATTTTCGCATTGCGATTCTCTCA
1 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCA
*
954035 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCA
** *
954068 TTGCGATAGTCATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTT-CGCATTGCGAT
954095 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 33 0.60
34 22 0.40
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCA
Found at i:954219 original size:14 final size:14
Alignment explanation
Indices: 954200--954236 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
954190 CATCAATTAA
954200 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
954214 ACAAATCATCTTTT
1 ACAAATCAACATTT
954228 ACAAATCAA
1 ACAAATCAA
954237 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:955715 original size:42 final size:42
Alignment explanation
Indices: 955636--955717 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
955626 CCTCTTCAAC
* * *
955636 GATGACAGTGGCCTCTTGAACGCTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* *
955678 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGA
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGA
955718 ATTATGACAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.21, C:0.18, G:0.39, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:956232 original size:20 final size:20
Alignment explanation
Indices: 956209--956277 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
956199 GAAACTTAAA
956209 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
956229 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
956249 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
956269 ATCGCAACG
1 ATCGCAACG
956278 AGAGAATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:956347 original size:20 final size:20
Alignment explanation
Indices: 956322--956408 Score: 111
Period size: 20 Copynumber: 4.3 Consensus size: 20
956312 GATTCTTTCG
956322 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
**
956342 TTGCGATAGTCAAATTCATA
1 TTGCGATAGTCAAATTCGCA
**
956362 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
956382 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
956402 TTGCGAT
1 TTGCGAT
956409 TTTGTTGTTG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:956406 original size:40 final size:40
Alignment explanation
Indices: 956320--956498 Score: 134
Period size: 40 Copynumber: 4.8 Consensus size: 40
956310 GCGATTCTTT
** ** *
956320 CGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCG
**
956360 TATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCG
* **
956400 CGTTGCGAT--T--TTGTT-G--TTGCGTTTTTCA-TTTCG
1 CGTTGCGATAGTCATT-TTCGCATTGCGATAGTCATTTTCG
* * *
956433 CATTGCGAT--TC--TCTCG--TTGCTATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCG
956467 CGTTGCGATAGTCATTTTCGCATTGCGATAGT
1 CGTTGCGATAGTCATTTTCGCATTGCGATAGT
956499 AAACTATTCT
Statistics
Matches: 108, Mismatches: 21, Indels: 20
0.72 0.14 0.13
Matches are distributed among these distances:
32 1 0.01
33 24 0.22
34 22 0.20
36 5 0.05
37 2 0.02
38 5 0.05
40 49 0.45
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.41
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCG
Found at i:956472 original size:20 final size:20
Alignment explanation
Indices: 956447--956498 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
956437 GCGATTCTCT
*
956447 CGTTGCTATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
956467 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
956487 CATTGCGATAGT
1 CGTTGCGATAGT
956499 AAACTATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:958428 original size:20 final size:20
Alignment explanation
Indices: 958383--958422 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
958373 ATGAAATTTT
* *
958383 AAATCGCAACACGAAAATGA
1 AAATTGCAACACAAAAATGA
958403 AAATTGCAACACAAAAATGA
1 AAATTGCAACACAAAAATGA
958423 CTATTGAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.57, C:0.17, G:0.12, T:0.12
Consensus pattern (20 bp):
AAATTGCAACACAAAAATGA
Found at i:958856 original size:22 final size:22
Alignment explanation
Indices: 958822--958881 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
958812 TGACCGTGAA
*
958822 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGAGAC
* *
958844 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGAGAC
958866 TGATTTCGTCGGAGAT
1 TGATTTCGTCGGAGAT
958882 AGGGACGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.22, C:0.15, G:0.37, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGAGAC
Found at i:959108 original size:26 final size:26
Alignment explanation
Indices: 959068--959146 Score: 135
Period size: 26 Copynumber: 3.1 Consensus size: 26
959058 TGTAAATCGC
959068 ATTGCGA--TACGTATTCGCATTGCG
1 ATTGCGATTTACGTATTCGCATTGCG
*
959092 ATTGCGATTTACGTATTCGTATTGCG
1 ATTGCGATTTACGTATTCGCATTGCG
959118 ATTGCGATTTACGTATTCGCATTGCG
1 ATTGCGATTTACGTATTCGCATTGCG
959144 ATT
1 ATT
959147 TACGGCAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
24 7 0.14
26 44 0.86
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (26 bp):
ATTGCGATTTACGTATTCGCATTGCG
Found at i:959117 original size:20 final size:20
Alignment explanation
Indices: 959109--959150 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
959099 TTTACGTATT
959109 CGTATTGCGATTGCGATTTA
1 CGTATTGCGATTGCGATTTA
959129 CGTATT-CGCATTGCGATTTA
1 CGTATTGCG-ATTGCGATTTA
959149 CG
1 CG
959151 GCAAAATCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTATTGCGATTGCGATTTA
Found at i:960801 original size:3 final size:3
Alignment explanation
Indices: 960793--960825 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
960783 GCCTGTAAAG
*
960793 CTT CTT CTT CTT CTT CTT CTT CTT CAT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
960826 TTTGTTGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:968446 original size:18 final size:18
Alignment explanation
Indices: 968415--968465 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
968405 ACTTTACTCA
*
968415 TCACATACATAATTTCAT
1 TCACATACAAAATTTCAT
* *
968433 TTATATACAAAATTTCAT
1 TCACATACAAAATTTCAT
*
968451 TCACATGCAAAATTT
1 TCACATACAAAATTT
968466 GGCTTACATC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.41, C:0.18, G:0.02, T:0.39
Consensus pattern (18 bp):
TCACATACAAAATTTCAT
Found at i:973272 original size:10 final size:10
Alignment explanation
Indices: 973257--973313 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
973247 ATTTTTTTCA
973257 AAAAAAAAAC
1 AAAAAAAAAC
973267 AAAAAAAAAAC
1 -AAAAAAAAAC
**
973278 AAAAAAAATT
1 AAAAAAAAAC
***
973288 GGCAAAAAAC
1 AAAAAAAAAC
973298 AAAAAAAAAC
1 AAAAAAAAAC
973308 AAAAAA
1 AAAAAA
973314 GCCAAAATTT
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
10 26 0.72
11 10 0.28
ACGTcount: A:0.84, C:0.09, G:0.04, T:0.04
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:973305 original size:11 final size:11
Alignment explanation
Indices: 973255--973285 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
973245 CTATTTTTTT
973255 CAAAAAAAAAA
1 CAAAAAAAAAA
973266 CAAAAAAAAAA
1 CAAAAAAAAAA
973277 CAAAAAAAA
1 CAAAAAAAA
973286 TTGGCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:978235 original size:12 final size:12
Alignment explanation
Indices: 978217--978262 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
978207 AAAATATGGT
978217 ATGAACAGTACC
1 ATGAACAGTACC
* *
978229 GTGAACA-T-CA
1 ATGAACAGTACC
*
978239 ATGAACATTACC
1 ATGAACAGTACC
978251 ATGAACAGTACC
1 ATGAACAGTACC
978263 CGTGAAATCA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
10 7 0.26
11 2 0.07
12 18 0.67
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:978315 original size:21 final size:22
Alignment explanation
Indices: 978291--978337 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
978281 CAGATTGCAA
978291 ACAGGGTACCGATT-CCCTACT
1 ACAGGGTACCGATTCCCCTACT
978312 ACAGGGTACCGATTCCCCTACT
1 ACAGGGTACCGATTCCCCTACT
978334 ACAG
1 ACAG
978338 TACTGCTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.26, C:0.34, G:0.19, T:0.21
Consensus pattern (22 bp):
ACAGGGTACCGATTCCCCTACT
Found at i:979085 original size:23 final size:23
Alignment explanation
Indices: 979058--979101 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
979048 AATACATATA
*
979058 TGTCCTGAAAGACCACGTAGAAT
1 TGTCCCGAAAGACCACGTAGAAT
* *
979081 TGTCCCGAAGGACCGCGTAGA
1 TGTCCCGAAAGACCACGTAGA
979102 CCCTCTACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAAGACCACGTAGAAT
Found at i:979215 original size:30 final size:31
Alignment explanation
Indices: 979179--979249 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
979169 ATATAATTTA
979179 TATCACATAGACATATCA-TTTCCATACCTT
1 TATCACATAGACATATCATTTTCCATACCTT
*
979209 TTTCACATAGACATATCATTTTCCATACCTT
1 TATCACATAGACATATCATTTTCCATACCTT
979240 TATCACATAG
1 TATCACATAG
979250 CTCATATAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 17 0.45
31 21 0.55
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.38
Consensus pattern (31 bp):
TATCACATAGACATATCATTTTCCATACCTT
Found at i:981066 original size:196 final size:199
Alignment explanation
Indices: 980833--981211 Score: 496
Period size: 199 Copynumber: 1.9 Consensus size: 199
980823 TTTTAACATG
* *
980833 TTATATTGTCATGTATCGATACATGTGTCTAAGGTATCGATACTTAATAGAC-GCTA-TTATTGC
1 TTATATTGCCATGTATCGATACATGTGTCTAAGGTATCGATACTTAAGAGACAGCTATTTATTGC
*
980896 AATTCTTTTAAATTCCTAAAATACC-ATTACTTTGGTGCATATACTTATAAAAGTATCGATACAA
66 AATTCTTTTAAATTCCTAAAATACCGA-TACTTTGGTACATATACTTATAAAAGTATCGATACAA
* * * * *
980960 ATTTCAACCATT-TGGTATCTCTTTATTGGTTTTGTCAAACTGAAACCGATTTTGTCAAACTTCA
130 ATTTCAACAATTCTGGTAGCTCTTTATCGATTTTCTCAAACTGAAACCGATTTTGTCAAACTTCA
981024 ATGTA
195 ATGTA
* ** ** * *
981029 TTATATTGCCATGTATCGATACATGTGTGTAAGGTATCGATACTTTCGAGACATTTTATTTTTTT
1 TTATATTGCCATGTATCGATACATGTGTCTAAGGTATCGATACTTAAGAGACA-GCTATTTATTG
* * * * * * *
981094 CATTTCTTTTAAATTCTTACAGTACCGATACTTTGGTACATATATTTATACATGTATCGATACAA
65 CAATTCTTTTAAATTCCTAAAATACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAA
* *
981159 ATTTCAACAATTCTGGTAGCTCTTTATCGATTTTCTCAAATTGAAATCGATTT
130 ATTTCAACAATTCTGGTAGCTCTTTATCGATTTTCTCAAACTGAAACCGATTT
981212 CTCAAATTGA
Statistics
Matches: 154, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
196 47 0.31
198 2 0.01
199 70 0.45
200 35 0.23
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.42
Consensus pattern (199 bp):
TTATATTGCCATGTATCGATACATGTGTCTAAGGTATCGATACTTAAGAGACAGCTATTTATTGC
AATTCTTTTAAATTCCTAAAATACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAA
TTTCAACAATTCTGGTAGCTCTTTATCGATTTTCTCAAACTGAAACCGATTTTGTCAAACTTCAA
TGTA
Found at i:981238 original size:19 final size:20
Alignment explanation
Indices: 981184--981258 Score: 91
Period size: 19 Copynumber: 3.9 Consensus size: 20
981174 GTAGCTCTTT
981184 ATCGATTTTCTCAAATTGAA
1 ATCGATTTTCTCAAATTGAA
981204 ATCGA-TTTCTCAAATTGAA
1 ATCGATTTTCTCAAATTGAA
* **
981223 ATCGATTTTATC-AATTTCA
1 ATCGATTTTCTCAAATTGAA
* *
981242 ATCGGTTTTTTCAAATT
1 ATCGATTTTCTCAAATT
981259 CGTTACCTGT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 34 0.71
20 14 0.29
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (20 bp):
ATCGATTTTCTCAAATTGAA
Found at i:988899 original size:29 final size:28
Alignment explanation
Indices: 988867--988939 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 28
988857 TTTTTAAAAA
***
988867 AATTACCAAAATAGCACCCATTTCGAATT
1 AATT-CCAAAATAGCACCCAAAACGAATT
*
988896 AATTCCCAGAATAGCA-CCAAAACGAATT
1 AATT-CCAAAATAGCACCCAAAACGAATT
*
988924 AATTCCCAAATAGCAC
1 AATTCCAAAATAGCAC
988940 TAGTCAAGGG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 9 0.25
28 13 0.36
29 14 0.39
ACGTcount: A:0.44, C:0.26, G:0.08, T:0.22
Consensus pattern (28 bp):
AATTCCAAAATAGCACCCAAAACGAATT
Found at i:996156 original size:13 final size:13
Alignment explanation
Indices: 996124--996170 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
996114 GAATAGCACC
996124 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
996137 GGT---CGGGTTG
1 GGTCAACGGGTCG
996147 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
996160 GGTAAACGGGT
1 GGTCAACGGGT
996171 AAACGGGTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
10 9 0.32
13 19 0.68
ACGTcount: A:0.15, C:0.17, G:0.49, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:998995 original size:22 final size:23
Alignment explanation
Indices: 998951--998996 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
998941 ATTGAAAAAT
*
998951 AAATAAATATTAAAATATGATAA
1 AAATAAATATTAAAAAATGATAA
998974 AAAT-AATATATAAAAAAT-ATAA
1 AAATAAATAT-TAAAAAATGATAA
998996 A
1 A
998997 TTATTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATAAATATTAAAAAATGATAA
Found at i:999061 original size:23 final size:23
Alignment explanation
Indices: 998948--999066 Score: 57
Period size: 22 Copynumber: 5.1 Consensus size: 23
998938 GATATTGAAA
*
998948 AATAAATA-AATATTAAAAT-AT
1 AATAAATATAATATTTAAATAAT
* * * *
998969 GATAAAAATAATATATAAAAAAT
1 AATAAATATAATATTTAAATAAT
* *
998992 -ATAAAT-TATTATTTATTATATAT
1 AATAAATATAATATTTA-AATA-AT
** * *
999015 ATATATTTATATTACTATATAATAAT
1 A-ATAAATATAATA-TTTA-AATAAT
999041 AATAAATATAATATTTAAATATAT
1 AATAAATATAATATTTAAATA-AT
999065 AA
1 AA
999067 ACAAGTAAAA
Statistics
Matches: 71, Mismatches: 18, Indels: 15
0.68 0.17 0.14
Matches are distributed among these distances:
21 13 0.18
22 15 0.21
23 8 0.11
24 7 0.10
25 13 0.18
26 8 0.11
27 7 0.10
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (23 bp):
AATAAATATAATATTTAAATAAT
Found at i:1000480 original size:3 final size:3
Alignment explanation
Indices: 1000474--1000522 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
1000464 TAATATTTTT
1000474 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
1000518 TAA TA
1 TAA TA
1000523 TTTAAATGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1000827 original size:38 final size:38
Alignment explanation
Indices: 1000782--1000861 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
1000772 TATGAGTTTC
1000782 TTCTTTCTTTTTCGGATGAGTTCTTCTCATTATGAACT
1 TTCTTTCTTTTTCGGATGAGTTCTTCTCATTATGAACT
*
1000820 TTCTTTCTTTTTCTGATGAGTTCTTCTCATTATGAACT
1 TTCTTTCTTTTTCGGATGAGTTCTTCTCATTATGAACT
1000858 TTCT
1 TTCT
1000862 CTGGAAAAGC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.15, C:0.19, G:0.11, T:0.55
Consensus pattern (38 bp):
TTCTTTCTTTTTCGGATGAGTTCTTCTCATTATGAACT
Found at i:1000961 original size:112 final size:111
Alignment explanation
Indices: 1000802--1001546 Score: 883
Period size: 112 Copynumber: 6.6 Consensus size: 111
1000792 TTCGGATGAG
* * *
1000802 TTCTTCTCATTATGAACT-TTCTTTCTTTTTCTGATGAGTTCTTCTCATTATGAACT-TTCTCTG
1 TTCTTCTCATTATGAACTCTTC-TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTG
* * * ** *
1000865 GAAAAGCTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTGAACAAA
64 GCAATGTTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
* *
1000913 TTCTTCTCATTGTGAA-T-TTATTCTTCTTCAGATGACGATTTCTTCTCATTATGAACTCTACCT
1 TTCTTCTCATTATGAACTCTTCTTCTTCTTCAGATGA-G--TTCTTCTCATTATGAACTCTACCT
* * *
1000976 GGCAATGTTGATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAA
63 GGCAATGTTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
* * **
1001025 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCAAAATG
1 TTCTTCTCATTATGAAC-TCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
* * * * * * *
1001090 GTAATGCTGATCAATTGAA-TGATGAATTCAAGCAAAAAGTTGAACAAG
64 GCAATGTTGATCCA-TCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
*
1001138 TTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAAATCTACCT-G
1 TTCTTCTCATTATGAAC-TCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGG
* * *
1001202 CAATGTTGATCCACCGAGAGATGAATTCAAACAAAAGGTTGAACAAA
65 CAATGTTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
* **
1001249 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAAATG
1 TTCTTCTCATTATGAAC-TCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
* * * * * * *
1001314 GTAATGATGATCAATTGAA-TGATGAATTCAAGCAAAAAGTTGAACAAG
64 GCAATGTTGATCCA-TCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
* *
1001362 TTCTTCTCATTATGAACTTCTTCTTTTTCTTCAGATGAGTTCTTCTCATTATGAAATCTACCTGG
1 TTCTTCTCATTATGAAC-TCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGG
* *
1001427 CAATGTTGATCCACCGAGTGATGAATTCAAACAAAAGGTTGAACAAA
65 CAATGTTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
* * *
1001474 TTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAAC-TCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
*
1001539 GAAATGTT
64 GCAATGTT
1001547 AATGCTGATC
Statistics
Matches: 543, Mismatches: 76, Indels: 28
0.84 0.12 0.04
Matches are distributed among these distances:
109 13 0.02
110 5 0.01
111 77 0.14
112 239 0.44
113 186 0.34
114 5 0.01
115 5 0.01
116 13 0.02
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (111 bp):
TTCTTCTCATTATGAACTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGC
AATGTTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
Found at i:1001303 original size:224 final size:225
Alignment explanation
Indices: 1000802--1001717 Score: 1120
Period size: 225 Copynumber: 4.0 Consensus size: 225
1000792 TTCGGATGAG
* * * *****
1000802 TTCTTCTCATTATGAAC-T-TTCTTTCTTTTTCTGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAAATG
* * * * ** * * *
1000865 GAAAAGCTGATCCA-TCAAGTGATGAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTGTGAA
66 GTAATGCTGATCAATTGAA-TGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAA
* *
1000929 --T-TTATTCTTCTTCAGATGACGATTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCA
130 CTTCTTCTTCTTCTTCAGATGA-G--TTCTTCTCATTATGAAATCTACCTGGCAATGTTGATCCA
* * * *
1000991 TC-AAATAATGAATTTAAACAAAAGGTTGAACAAA
192 CCGAGA-GATGAATTCAAACAAAAGGTTGAACAAA
*
1001025 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCAAAATG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAAATG
1001090 GTAATGCTGATCAATTGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
66 GTAATGCTGATCAATTGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
1001155 TTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAAATCTACCT-GCAATGTTGATCCACCGA
131 TTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAAATCTACCTGGCAATGTTGATCCACCGA
1001219 GAGATGAATTCAAACAAAAGGTTGAACAAA
196 GAGATGAATTCAAACAAAAGGTTGAACAAA
1001249 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAAATG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAAATG
*
1001314 GTAATGATGATCAATTGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
66 GTAATGCTGATCAATTGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
*
1001379 TTCTTCTTTTTCTTCAGATGAGTTCTTCTCATTATGAAATCTACCTGGCAATGTTGATCCACCGA
131 TTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAAATCTACCTGGCAATGTTGATCCACCGA
*
1001444 GTGATGAATTCAAACAAAAGGTTGAACAAA
196 GAGATGAATTCAAACAAAAGGTTGAACAAA
*
1001474 TTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC--A---
* * *** * * *
1001539 GAAATGTTAATGCTGATCTATCTTCTTTTG-TGATAGAGTCAAAGAAAAAAGTTTGAACAAGCTC
61 -AAATGGTAATGCTGATC-A-ATT-GAATGATG--A-ATTC-AAGCAAAAAG-TTGAACAAGTTC
* * *
1001603 TTCTCATTTATGAACTTCTTCTT-TCTCTTCAGATAAGTTCTTCTCATTATG-AACCT-TCTGGC
117 TTCTCA-TTATGAACTTCTTCTTCT-TCTTCAGATGAGTTCTTCTCATTATGAAATCTACCTGGC
* * * ** ** *
1001665 AACGCTGATCTATTGA-ATGATGAATTTGAGCAAAAGGTTGAACAAA
180 AATGTTGATCCACCGAGA-GATGAATTCAAACAAAAGGTTGAACAAA
1001711 TTCTTCT
1 TTCTTCT
1001718 TTCTTCAGAT
Statistics
Matches: 618, Mismatches: 50, Indels: 36
0.88 0.07 0.05
Matches are distributed among these distances:
223 17 0.03
224 215 0.35
225 217 0.35
226 3 0.00
227 3 0.00
228 17 0.03
231 15 0.02
232 1 0.00
233 4 0.01
234 2 0.00
235 1 0.00
236 3 0.00
237 57 0.09
238 22 0.04
239 41 0.07
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (225 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAAATG
GTAATGCTGATCAATTGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
TTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAAATCTACCTGGCAATGTTGATCCACCGA
GAGATGAATTCAAACAAAAGGTTGAACAAA
Found at i:1002627 original size:113 final size:114
Alignment explanation
Indices: 1002478--1002692 Score: 360
Period size: 113 Copynumber: 1.9 Consensus size: 114
1002468 ATCTTTTAAT
* * * * *
1002478 TCCAATGATTGGTTTTGTGGTTCCTACCGAACCAGATCAGATGACTCAAAGAACACTTCCAGAAG
1 TCCAATGATTGATTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1002543 ATGCTATTGGGTC-TCTTATTTCTACTATGAGCACATTCATATTTCAAA
66 ATGCTATTGGGTCTTCTTATTTCTACTATGAGCACATTCATATTTCAAA
* *
1002591 TCCAATGATTGATTTTGGGGTTCATATCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 TCCAATGATTGATTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1002656 ATGCTATTGGGTCTTCTTATTTCTACTATGAGCACAT
66 ATGCTATTGGGTCTTCTTATTTCTACTATGAGCACAT
1002693 GGCACTTGCT
Statistics
Matches: 94, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
113 71 0.76
114 23 0.24
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (114 bp):
TCCAATGATTGATTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
ATGCTATTGGGTCTTCTTATTTCTACTATGAGCACATTCATATTTCAAA
Found at i:1003884 original size:19 final size:17
Alignment explanation
Indices: 1003860--1003908 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 17
1003850 AAAATAAAAG
1003860 AATAAATTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
1003879 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
1003895 AATAAATTGAATTT
1 AATAAATTGAATTT
1003909 AAAGAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 3 0.11
19 11 0.41
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:1004278 original size:15 final size:15
Alignment explanation
Indices: 1004260--1004310 Score: 65
Period size: 16 Copynumber: 3.6 Consensus size: 15
1004250 TCTTGACCCC
1004260 TCTTTTCTTTTTCTT
1 TCTTTTCTTTTTCTT
1004275 TCTTTTTCTTTTT-TT
1 TC-TTTTCTTTTTCTT
1004290 TC-TTT-TTTTTCTT
1 TCTTTTCTTTTTCTT
1004303 T-TTTTCTT
1 TCTTTTCTT
1004311 CAAGCATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 5 0.16
13 9 0.28
14 2 0.06
15 6 0.19
16 10 0.31
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TCTTTTCTTTTTCTT
Found at i:1004289 original size:9 final size:9
Alignment explanation
Indices: 1004267--1004307 Score: 73
Period size: 9 Copynumber: 4.4 Consensus size: 9
1004257 CCCTCTTTTC
1004267 TTTTTCTTT
1 TTTTTCTTT
1004276 CTTTTTCTTT
1 -TTTTTCTTT
1004286 TTTTTCTTT
1 TTTTTCTTT
1004295 TTTTTCTTT
1 TTTTTCTTT
1004304 TTTT
1 TTTT
1004308 CTTCAAGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 22 0.71
10 9 0.29
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:1014862 original size:25 final size:25
Alignment explanation
Indices: 1014806--1014859 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
1014796 TGACAGAAAA
1014806 AATAAAT--AATGAAATAAAATACT
1 AATAAATAAAATGAAATAAAATACT
**
1014829 TGTAAATAAAATGAAATATAAATACT
1 AATAAATAAAATGAAATA-AAATACT
1014855 AATAA
1 AATAA
1014860 TAAGTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 5 0.21
25 9 0.38
26 10 0.42
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.28
Consensus pattern (25 bp):
AATAAATAAAATGAAATAAAATACT
Done.