Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009137.1 Hibiscus syriacus cultivar Beakdansim tig00112637_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: 390993
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 1 of 2
Found at i:1172 original size:37 final size:36
Alignment explanation
Indices: 1111--1185 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 36
1101 TCATTAAACT
* *
1111 ATTTTATATTTTCAATTTTGTAAAAAA-ATTATATAA
1 ATTTTATAATTTAAATTTTGTAAAAAATA-TATATAA
*
1147 ATTTTATGAATTTAAATTTTTTAAAAAATATATATAA
1 ATTTTAT-AATTTAAATTTTGTAAAAAATATATATAA
1184 AT
1 AT
1186 ATTTTCCAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 7 0.21
37 26 0.76
38 1 0.03
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (36 bp):
ATTTTATAATTTAAATTTTGTAAAAAATATATATAA
Found at i:1358 original size:18 final size:19
Alignment explanation
Indices: 1335--1377 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1325 CCAATAATGC
*
1335 TATTCT-CTGGTAATCTTT
1 TATTCTACTGGTAATCTTA
1353 TATTCTCACTGGTAATCTTA
1 TATTCT-ACTGGTAATCTTA
1373 TATTC
1 TATTC
1378 CGTGAACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.21, C:0.19, G:0.09, T:0.51
Consensus pattern (19 bp):
TATTCTACTGGTAATCTTA
Found at i:1630 original size:2 final size:2
Alignment explanation
Indices: 1618--1649 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1608 ATAAAATTGA
1618 AT AT A- 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 A
1650 ATTTTGTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3541 original size:2 final size:2
Alignment explanation
Indices: 3536--3560 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3526 CTCTCCCCCC
3536 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
3561 GCATAAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:8793 original size:2 final size:2
Alignment explanation
Indices: 8754--8782 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8744 TGTGTGTGTG
8754 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8783 GCACATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11856 original size:15 final size:15
Alignment explanation
Indices: 11809--11865 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
11799 TTAAAATTTA
*
11809 AAATTTAAAATATAC-
1 AAATATAAAA-ATACT
*
11824 AAATATAAGAAAAAACT
1 AAATAT-A-AAAATACT
11841 AAATATAAAAATACT
1 AAATATAAAAATACT
*
11856 AAAAATAAAA
1 AAATATAAAA
11866 GTTAAATTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 21 0.60
16 5 0.14
17 9 0.26
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (15 bp):
AAATATAAAAATACT
Found at i:11864 original size:21 final size:21
Alignment explanation
Indices: 11834--11890 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
11824 AAATATAAGA
11834 AAAAACTAAATATAAAAATACT
1 AAAAA-TAAATATAAAAATACT
* *
11856 AAAAATAAA-AGTTAAATTACT
1 AAAAATAAATA-TAAAAATACT
11877 AAAAA-AAATA-AAAA
1 AAAAATAAATATAAAA
11891 TATTAATCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.10
20 4 0.13
21 18 0.60
22 5 0.17
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (21 bp):
AAAAATAAATATAAAAATACT
Found at i:29464 original size:229 final size:227
Alignment explanation
Indices: 29059--29507 Score: 785
Period size: 229 Copynumber: 2.0 Consensus size: 227
29049 GTAAATTATC
* * *
29059 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
29124 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
29189 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA-AAATTT
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAA-TT
29253 GAAACATAAATTACATAACTTTCAAAAAAGTATA
195 GAAACATAAATTACATAACTTT-AAAAAAGTATA
*
29287 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
29352 TTAATATTGTTAAATTT-AAATGCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
65 TTAATATTGTTAAATTTAAAAT-CTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
*
29416 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
129 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
29481 TGAAACATAAATTACATAACTTTAAAA
194 TGAAACATAAATTACATAACTTTAAAA
29508 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
228 44 0.21
229 164 0.78
230 3 0.01
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:29595 original size:20 final size:19
Alignment explanation
Indices: 29572--29617 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
29562 CGATATACCA
29572 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
29592 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
29612 GGTAAA
1 GGTAAA
29618 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:29761 original size:20 final size:19
Alignment explanation
Indices: 29738--29784 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
29728 CGATATAACA
*
29738 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
29758 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
29778 GGTAAAA
1 GGTAAAA
29785 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:32034 original size:33 final size:33
Alignment explanation
Indices: 31992--32057 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
31982 AAATAGATGG
*
31992 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
32025 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
32058 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:33888 original size:19 final size:19
Alignment explanation
Indices: 33844--33887 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
33834 AATGTCGAGT
33844 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
33863 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
33882 T-ATTTT
1 TAATTTT
33888 TTTATGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:34411 original size:198 final size:199
Alignment explanation
Indices: 33970--34988 Score: 1845
Period size: 198 Copynumber: 5.1 Consensus size: 199
33960 TTAAGGGTCA
*
33970 TGTCGATACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAA-TAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
*
34033 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
34098 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
34163 TAATG
195 TAATG
*
34168 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
34232 AATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
34296 TAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
34361 AATG
196 AATG
*
34365 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
34430 -ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
34494 TAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
34559 AATG
196 AATG
34563 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCCAGAATGAATTAAAAACAAGGTGCAC
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTTCCAGAATGAATTAAAAACAAGGTGCAC
34628 CAATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAAT
65 CAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* *
34691 GTAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
34756 TAATG
195 TAATG
* *
34761 TGTCGACACTAATATAGTTTGTTTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
*
34826 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATTGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
34891 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
34956 AATG
196 AATG
*
34960 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
34989 CTAATTTAAA
Statistics
Matches: 799, Mismatches: 15, Indels: 13
0.97 0.02 0.02
Matches are distributed among these distances:
197 216 0.27
198 355 0.44
199 207 0.26
200 21 0.03
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:34914 original size:397 final size:394
Alignment explanation
Indices: 33970--34988 Score: 1853
Period size: 397 Copynumber: 2.6 Consensus size: 394
33960 TTAAGGGTCA
*
33970 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA-TAAAAACAAGGTGCACCC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCA-CC
34034 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
65 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
34099 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
129 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
34164 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGC
194 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGC
*
34229 ATCAATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
259 ACCAATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
* *
34294 TGTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAA
324 TGTAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATAAGTCTAA
34359 ATAATG
389 ATAATG
*
34365 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
34430 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
65 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
34495 AATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
130 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
34560 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCCAGAATGAATTAAAAACAAGGTG
195 ATGTGTCGACACTAATATAGTTTGTGTCGATA--TTTTTTTCCAGAATGAATTAAAAACAAGGTG
34625 CACCAATAAAGTGTCGATCCATATATAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATA
258 CACCAATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
*
34689 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTA
323 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATAAGTCTA
34754 AATAATG
388 AATAATG
*
34761 TGTCGACACTAATATAGTTTGTTTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCACC
*
34826 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATTGAACCCAAAAGTATAATG
65 -ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
34891 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
129 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
*
34956 AATGTGTCGACACTAATATATTTTGTGTCGATA
194 AATGTGTCGACACTAATATAGTTTGTGTCGATA
34989 CTAATTTAAA
Statistics
Matches: 604, Mismatches: 14, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
395 174 0.29
396 186 0.31
397 244 0.40
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (394 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
ATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAA
TGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCAC
CAATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:36465 original size:18 final size:18
Alignment explanation
Indices: 36442--36509 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
36432 ATCGGTCGCA
36442 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
36460 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
36481 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
36502 GAAGATGA
1 GAAGATGA
36510 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:36466 original size:6 final size:6
Alignment explanation
Indices: 36442--36539 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
36432 ATCGGTCGCA
* * * * * *
36442 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
36490 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
36538 GA
1 GA
36540 TGATCCAAAC
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:36477 original size:3 final size:3
Alignment explanation
Indices: 36457--36543 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
36447 TGAAGCTGAC
* * * * * ** *
36457 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
36505 GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
36544 CCAAACAAGT
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:36492 original size:42 final size:42
Alignment explanation
Indices: 36445--36535 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
36435 GGTCGCAGAA
*
36445 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* * *
36487 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
36529 GATGAAG
1 GATGAAG
36536 ATGATGATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
Found at i:36543 original size:18 final size:18
Alignment explanation
Indices: 36442--36539 Score: 88
Period size: 18 Copynumber: 5.4 Consensus size: 18
36432 ATCGGTCGCA
* *
36442 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
36460 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
36478 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
** *
36496 GGCGATGAAGATGATGAC
1 GAAGATGAAGATGATGAT
* *
36514 GATGATGATGATGATGAT
1 GAAGATGAAGATGATGAT
36532 GAAGATGA
1 GAAGATGA
36540 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:38458 original size:183 final size:184
Alignment explanation
Indices: 38011--38679 Score: 1236
Period size: 183 Copynumber: 3.7 Consensus size: 184
38001 CTTTCAACAT
** *
38011 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
38076 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
38141 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
38195 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGT-TTATGAGCCAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
38259 GGTCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
38323 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
38377 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
38442 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTAC-TTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
38506 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
38560 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCAAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
*
38625 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
38680 CCATTTAAAA
Statistics
Matches: 470, Mismatches: 12, Indels: 6
0.96 0.02 0.01
Matches are distributed among these distances:
182 146 0.31
183 244 0.52
184 80 0.17
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:41265 original size:23 final size:23
Alignment explanation
Indices: 41234--41296 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
41224 ATAGGTAAAC
*
41234 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
41257 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
41280 ATATAATGT-ATAGGTAG
1 ATATAATGTAATAGGTAG
41297 TGGTTATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 7 0.20
23 28 0.80
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:41303 original size:22 final size:23
Alignment explanation
Indices: 41234--41305 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
41224 ATAGGTAAAC
* * **
41234 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
41257 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
41280 ATATAATGT-ATAGGTAGT-GGTT
1 ATATAATGTAATAGGTA-TCGGTT
41302 ATAT
1 ATAT
41306 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
22 14 0.33
23 29 0.67
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:41494 original size:29 final size:30
Alignment explanation
Indices: 41451--41517 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
41441 GTTACGGTAT
* *
41451 ATATTATTATTAAAT-TAAAA-ATTCTAAATA
1 ATATT-TTATAAAATATAAAACAATC-AAATA
41481 ATATTTTATAAAATATAAAACAATCAAATA
1 ATATTTTATAAAATATAAAACAATCAAATA
*
41511 ATTTTTT
1 ATATTTT
41518 GTGCAAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 21 0.66
31 3 0.09
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (30 bp):
ATATTTTATAAAATATAAAACAATCAAATA
Found at i:41692 original size:23 final size:23
Alignment explanation
Indices: 41660--41724 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
41650 AATAGGTAAA
*
41660 TATATGATGTAATAGGTAGCCCT
1 TATATAATGTAATAGGTAGCCCT
* **
41683 TATATAATGTAATAGGTATCGTT
1 TATATAATGTAATAGGTAGCCCT
41706 TATATAATGTAATAGGTAG
1 TATATAATGTAATAGGTAG
41725 TGGTTATATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
TATATAATGTAATAGGTAGCCCT
Found at i:41731 original size:23 final size:23
Alignment explanation
Indices: 41660--41733 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
41650 AATAGGTAAA
* **
41660 TATATGATGTAATAGGTAGCCCT
1 TATATAATGTAATAGGTAGTGCT
*
41683 TATATAATGTAATAGGTA-TCGTT
1 TATATAATGTAATAGGTAGT-GCT
*
41706 TATATAATGTAATAGGTAGTGGT
1 TATATAATGTAATAGGTAGTGCT
41729 TATAT
1 TATAT
41734 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
23 43 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (23 bp):
TATATAATGTAATAGGTAGTGCT
Found at i:42153 original size:23 final size:23
Alignment explanation
Indices: 42090--42154 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
42080 ATAGGTAAAC
* *
42090 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCCCTT
**
42113 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
42136 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
42155 TATCTCGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:42379 original size:18 final size:18
Alignment explanation
Indices: 42358--42394 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42348 GTAATTGGAG
42358 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
42376 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
42394 T
1 T
42395 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:42402 original size:24 final size:24
Alignment explanation
Indices: 42350--42396 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
42340 TTTCATATGT
* *
42350 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
42374 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
42397 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:61046 original size:32 final size:32
Alignment explanation
Indices: 61008--61078 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
60998 GTCTGCATGT
*
61008 GCCATGCACGTCTCCAACA-CCCAACACAGGTC
1 GCCATGCAC-TCCCCAACACCCCAACACAGGTC
*
61040 GTCATGCACTCCCCAACACCCCAACACAGGTC
1 GCCATGCACTCCCCAACACCCCAACACAGGTC
61072 GCCATGC
1 GCCATGC
61079 CTACAAGGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 8 0.23
32 27 0.77
ACGTcount: A:0.27, C:0.45, G:0.15, T:0.13
Consensus pattern (32 bp):
GCCATGCACTCCCCAACACCCCAACACAGGTC
Found at i:61373 original size:29 final size:29
Alignment explanation
Indices: 61336--61392 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
61326 GTAATGACCA
*
61336 TAGGTCGCCATGCAATCCAGGCGACCTTG
1 TAGGCCGCCATGCAATCCAGGCGACCTTG
** *
61365 TAGGCCGCCATGCCTTTCAGGCGACCTT
1 TAGGCCGCCATGCAATCCAGGCGACCTT
61393 TGTGGGGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.18, C:0.33, G:0.26, T:0.23
Consensus pattern (29 bp):
TAGGCCGCCATGCAATCCAGGCGACCTTG
Found at i:61724 original size:26 final size:26
Alignment explanation
Indices: 61691--61748 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
61681 ACATAAAAGA
*
61691 AAGAAAGGGAGAAGAGATTGCAGCAG
1 AAGAAAGGGAGAAGAAATTGCAGCAG
61717 AAGAAAGGGAGAAGAAATTGCAGCAG
1 AAGAAAGGGAGAAGAAATTGCAGCAG
61743 -AGAAAG
1 AAGAAAG
61749 AAAGAAAGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 6 0.19
26 25 0.81
ACGTcount: A:0.50, C:0.07, G:0.36, T:0.07
Consensus pattern (26 bp):
AAGAAAGGGAGAAGAAATTGCAGCAG
Found at i:61749 original size:29 final size:27
Alignment explanation
Indices: 61688--61752 Score: 96
Period size: 26 Copynumber: 2.4 Consensus size: 27
61678 AGAACATAAA
*
61688 AGAAAGAAAGGGAGAAGAGATTGCAGC
1 AGAAAGAAAGGGAGAAGAAATTGCAGC
61715 AG-AAGAAAGGGAGAAGAAATTGCAGC
1 AGAAAGAAAGGGAGAAGAAATTGCAGC
61741 AGAGAAAGAAAG
1 --AGAAAGAAAG
61753 AAAGTGAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
26 23 0.68
27 2 0.06
28 2 0.06
29 7 0.21
ACGTcount: A:0.52, C:0.06, G:0.35, T:0.06
Consensus pattern (27 bp):
AGAAAGAAAGGGAGAAGAAATTGCAGC
Found at i:62229 original size:15 final size:14
Alignment explanation
Indices: 62209--62239 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
62199 GTTTGTTAGT
62209 TTATTATATTATAAG
1 TTATTATATTA-AAG
62224 TTATTATATTAAAG
1 TTATTATATTAAAG
62238 TT
1 TT
62240 TAATGTTGTA
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:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:64464 original size:14 final size:14
Alignment explanation
Indices: 64445--64491 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
64435 TTCAAGTCGT
64445 AAATCATTACTATC
1 AAATCATTACTATC
64459 AAATCATTAC--T-
1 AAATCATTACTATC
*
64470 -AATCATTAATATC
1 AAATCATTACTATC
64483 AAATCATTA
1 AAATCATTA
64492 AATATTAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
10 8 0.29
12 2 0.07
14 18 0.64
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:64473 original size:24 final size:24
Alignment explanation
Indices: 64446--64636 Score: 135
Period size: 24 Copynumber: 7.9 Consensus size: 24
64436 TCAAGTCGTA
*
64446 AATCATTACTATCAAATCATTACT
1 AATCATTAATATCAAATCATTACT
64470 AATCATTAATATCAAATCATTA--
1 AATCATTAATATCAAATCATTACT
* *
64492 AAT-ATTAATAATAAATTATTATTACT
1 AATCATTAAT-ATCAA--ATCATTACT
64518 AATCATTAATATCAAATCATTA--
1 AATCATTAATATCAAATCATTACT
*
64540 AAT-ATTAATAAT-AAATTTTTATTACT
1 AATCATTAAT-ATCAAA---TCATTACT
* **
64566 AATCATTACTATCAAATCATTAAA
1 AATCATTAATATCAAATCATTACT
* * *** *
64590 AATTAATAATAATTTTATTATTACT
1 AATCATTAAT-ATCAAATCATTACT
*
64615 AATCATTACTATCAAATCATTA
1 AATCATTAATATCAAATCATTA
64637 AATATTAATA
Statistics
Matches: 126, Mismatches: 26, Indels: 30
0.69 0.14 0.16
Matches are distributed among these distances:
21 15 0.12
22 12 0.10
24 58 0.46
25 15 0.12
26 12 0.10
27 14 0.11
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (24 bp):
AATCATTAATATCAAATCATTACT
Found at i:64492 original size:14 final size:14
Alignment explanation
Indices: 64445--64540 Score: 56
Period size: 14 Copynumber: 6.7 Consensus size: 14
64435 TTCAAGTCGT
*
64445 AAATCATTACTATC
1 AAATCATTAATATC
64459 AAATCA-T--TA-C
1 AAATCATTAATATC
*
64469 TAATCATTAATATC
1 AAATCATTAATATC
*
64483 AAATCATTAAATATTA
1 AAATCATT-AATA-TC
* *
64499 ATAATAAATTATTATTAC
1 A-AAT-CATTAATA-T-C
*
64517 TAATCATTAATATC
1 AAATCATTAATATC
64531 AAATCATTAA
1 AAATCATTAA
64541 ATATTAATAA
Statistics
Matches: 63, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
10 6 0.10
11 3 0.05
13 3 0.05
14 24 0.38
15 5 0.08
16 8 0.13
17 11 0.17
18 3 0.05
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATCATTAATATC
Found at i:64526 original size:34 final size:34
Alignment explanation
Indices: 64484--64622 Score: 87
Period size: 34 Copynumber: 4.2 Consensus size: 34
64474 ATTAATATCA
64484 AATCATTAAATATTAATAATAAATTATTATTACT
1 AATCATTAAATATTAATAATAAATTATTATTACT
* * * *
64518 AATCATT-AATATCAAATCATTAAA-TATTAATAAT
1 AATCATTAAATAT-TAAT-AATAAATTATTATTACT
** * * * *
64552 AA--ATT-TTTATTACTAAT-CATTACTA-T-CA
1 AATCATTAAATATTAATAATAAATTATTATTACT
* *
64580 AATCATTAAAAATTAATAATAATTTTATTATTACT
1 AATCATTAAATATTAATAATAA-ATTATTATTACT
64615 AATCATTA
1 AATCATTA
64623 CTATCAAATC
Statistics
Matches: 74, Mismatches: 21, Indels: 19
0.65 0.18 0.17
Matches are distributed among these distances:
28 2 0.03
29 2 0.03
30 9 0.12
31 10 0.14
32 6 0.08
33 10 0.14
34 21 0.28
35 14 0.19
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (34 bp):
AATCATTAAATATTAATAATAAATTATTATTACT
Found at i:64630 original size:49 final size:49
Alignment explanation
Indices: 64464--64674 Score: 354
Period size: 48 Copynumber: 4.3 Consensus size: 49
64454 CTATCAAATC
* *
64464 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAA-ATTATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATT
* *
64512 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAAATTT-TT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATT
*
64560 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATT
*
64609 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATT
64658 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
64675 AATCATTATT
Statistics
Matches: 155, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
48 87 0.56
49 68 0.44
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATT
Found at i:64775 original size:14 final size:14
Alignment explanation
Indices: 64756--64803 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
64746 TTCAAGTCGT
64756 AAATCATTACTATC
1 AAATCATTACTATC
64770 AAATCATTAC--T-
1 AAATCATTACTATC
*
64781 AAATCATTAATATC
1 AAATCATTACTATC
64795 AAATCATTA
1 AAATCATTA
64804 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:64783 original size:25 final size:25
Alignment explanation
Indices: 64755--64803 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
64745 GTTCAAGTCG
*
64755 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
64780 TAAATCATTAATATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
64804 AATATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:64819 original size:21 final size:22
Alignment explanation
Indices: 64755--64813 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 22
64745 GTTCAAGTCG
*
64755 TAAATCATTACTATCAAATCATT
1 TAAATCATTAATATCAAATCA-T
64778 ACTAAATCATTAATATCAAATCAT
1 --TAAATCATTAATATCAAATCAT
64802 TAAAT-ATTAATA
1 TAAATCATTAATA
64814 ATAAATTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 7 0.21
22 5 0.15
24 1 0.03
25 20 0.61
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATCATTAATATCAAATCAT
Found at i:64824 original size:21 final size:22
Alignment explanation
Indices: 64755--64824 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 22
64745 GTTCAAGTCG
* *
64755 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATC-AA--ATTAT
*
64780 TAAATCATTAATATCAAATCAT
1 TAAATCATTAATATCAAATTAT
64802 TAAAT-ATTAATAAT-AAATTAT
1 TAAATCATTAAT-ATCAAATTAT
64823 TA
1 TA
64825 TTACTAATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 14 0.35
22 10 0.25
24 2 0.05
25 14 0.35
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATCATTAATATCAAATTAT
Found at i:64902 original size:21 final size:21
Alignment explanation
Indices: 64878--65022 Score: 58
Period size: 21 Copynumber: 7.2 Consensus size: 21
64868 TAATTTTATT
64878 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
* * *
64899 ATTAAT-ATCAAATCATTAAAT-
1 ATTACTAATC--ATTACTAAATC
* * * *
64920 ATTAATAATAATT--T-CATT
1 ATTACTAATCATTACTAAATC
*
64938 ATTACTAATGATTACTAAATC
1 ATTACTAATCATTACTAAATC
* *
64959 ATTACT-ATCAAATCATTAAAT-
1 ATTACTAATC--ATTACTAAATC
* * * *
64980 ATTAATAATAATT--T-CATT
1 ATTACTAATCATTACTAAATC
64998 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
65019 ATTA
1 ATTA
65023 ATATCAAATC
Statistics
Matches: 89, Mismatches: 21, Indels: 28
0.64 0.15 0.20
Matches are distributed among these distances:
17 4 0.04
18 24 0.27
20 11 0.12
21 30 0.34
22 20 0.22
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (21 bp):
ATTACTAATCATTACTAAATC
Found at i:65014 original size:120 final size:120
Alignment explanation
Indices: 64771--65424 Score: 724
Period size: 120 Copynumber: 5.6 Consensus size: 120
64761 ATTACTATCA
*
64771 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTACTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
* * *
64835 TTAC----T-ATTACTATC-AATCATTAAAAATTAATAATAATTTTATTATTACT
66 TTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
*
64884 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATGA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
*
64949 TTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
66 TTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* *
65004 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTTATTATTATTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
* * * * * ** *
65069 TTACTAAATCATTATTAT-AATTTCATTACTAGTTATGTAACGAA-AATATGGTTAATTGAACC
66 TTACTAAATCATTAATATCAA-ATCATTA--A-ATAT-TAA-TAATAATTTCATT-ATT--ACT
* * * * * * *
65131 AAACATT-GT---TCATT-GT-TCAAGTC-GTAAAGCA-T--TACT-A--TC------A--AATC
1 AATCATTACTAAATCATTAATATCAAATCATTAAA-TATTAATAATAATTTCATTATTACTAATC
*
65175 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTACT
65 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* * *
65230 AATCATTACT-AATTATTACTATCAAATCATTAAAAATTAATAATAAATTTCATTATTACTAATC
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAAT-AATTTCATTATTACTAATC
*
65294 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATATTTTCATTATTACT
65 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
*
65350 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
65415 TTACTAAATC
66 TTACTAAATC
65425 TTAGAAATAC
Statistics
Matches: 456, Mismatches: 43, Indels: 77
0.79 0.07 0.13
Matches are distributed among these distances:
99 8 0.02
100 1 0.00
101 3 0.01
102 8 0.02
103 7 0.02
104 10 0.02
105 6 0.01
107 31 0.07
108 2 0.00
109 2 0.00
111 2 0.00
113 49 0.11
114 17 0.04
115 1 0.00
117 2 0.00
118 4 0.01
119 59 0.13
120 172 0.38
121 39 0.09
122 2 0.00
123 8 0.02
124 9 0.02
125 5 0.01
126 1 0.00
127 8 0.02
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (120 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
TTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
Found at i:65096 original size:60 final size:60
Alignment explanation
Indices: 64771--65082 Score: 503
Period size: 60 Copynumber: 5.3 Consensus size: 60
64761 ATTACTATCA
*
64771 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* * *
64830 AATCATTAC----T-ATTACTATC-AATCATTAAAAATTAATAATAATTTTATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
64884 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* *
64944 AATGATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* *
65004 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTTATTATTATT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
65064 AATCATTACTAAATCATTA
1 AATCATTACTAAATCATTA
65083 TTATAATTTC
Statistics
Matches: 234, Mismatches: 12, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
53 23 0.10
54 26 0.11
55 1 0.00
58 1 0.00
59 17 0.07
60 166 0.71
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.42
Consensus pattern (60 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
Found at i:65179 original size:14 final size:14
Alignment explanation
Indices: 65160--65203 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
65150 AGTCGTAAAG
65160 CATTACTATCAAAT
1 CATTACTATCAAAT
65174 CATTAC--T-AAAT
1 CATTACTATCAAAT
*
65185 CATTAATATCAAAT
1 CATTACTATCAAAT
65199 CATTA
1 CATTA
65204 AATATTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 9 0.35
12 1 0.04
13 1 0.04
14 15 0.58
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (14 bp):
CATTACTATCAAAT
Found at i:65183 original size:25 final size:25
Alignment explanation
Indices: 65155--65203 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
65145 GTTCAAGTCG
*
65155 TAAAGCATTACTATCAAATCATTAC
1 TAAAGCATTAATATCAAATCATTAC
*
65180 TAAATCATTAATATCAAATCATTA
1 TAAAGCATTAATATCAAATCATTA
65204 AATATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (25 bp):
TAAAGCATTAATATCAAATCATTAC
Found at i:65189 original size:400 final size:403
Alignment explanation
Indices: 64560--65424 Score: 1508
Period size: 400 Copynumber: 2.2 Consensus size: 403
64550 ATAAATTTTT
*
64560 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAAT-A----ATT-TTA-T--T-ATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
*
64614 T-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAAT
66 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAAT
* *
64678 CATTATTATAATTTCATTACTAGTTATGTAACTAAAATATGGTTAATTGAACTAAACATTGTTCA
131 CATTATTATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAAACATTGTTCA
*
64743 TTGTTCAAGTCGTAAATCATTACTATCAAATCATTACTAAATCATTAATATCAAATCATTAAATA
196 TTGTTCAAGTCGTAAAGCATTACTATCAAATCATTACTAAATCATTAATATCAAATCATTAAATA
64808 TTAATAATAAATTATTATTACTAATCATTAC-TATTACTATC-AATCATTAAAAATTAATAAT-A
261 TTAATAATAAATTATTATTACTAATCATTACATATTACTATCAAATCATTAAAAATTAATAATAA
*
64870 ATTTTATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTC
326 ATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTC
*
64935 ATTATTACTAATG
391 ATTATTACTAATC
64948 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
* *
65013 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTTATTATTATTAATCATTACTAAAT
66 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAAT
65078 CATTATTATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAAACATTGTTCA
131 CATTATTATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAAACATTGTTCA
65143 TTGTTCAAGTCGTAAAGCATTACTATCAAATCATTACTAAATCATTAATATCAAATCATTAAATA
196 TTGTTCAAGTCGTAAAGCATTACTATCAAATCATTACTAAATCATTAATATCAAATCATTAAATA
65208 TTAATAATAAATTATTATTACTAATCATTACTAATTATTACTATCAAATCATTAAAAATTAATAA
261 TTAATAATAAATTATTATTACTAATCATTAC--A-TATTACTATCAAATCATTAAAAATTAATAA
*
65273 TAAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATATT
323 TAAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAT
65338 TTCATTATTACTAATC
388 TTCATTATTACTAATC
65354 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
65419 TAAATC
66 TAAATC
65425 TTAGAAATAC
Statistics
Matches: 449, Mismatches: 10, Indels: 18
0.94 0.02 0.04
Matches are distributed among these distances:
388 6 0.01
389 33 0.07
390 1 0.00
394 3 0.01
395 3 0.01
396 1 0.00
398 1 0.00
399 6 0.01
400 218 0.49
404 10 0.02
405 20 0.04
406 147 0.33
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.41
Consensus pattern (403 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAAT
CATTATTATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAAACATTGTTCA
TTGTTCAAGTCGTAAAGCATTACTATCAAATCATTACTAAATCATTAATATCAAATCATTAAATA
TTAATAATAAATTATTATTACTAATCATTACATATTACTATCAAATCATTAAAAATTAATAATAA
ATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTC
ATTATTACTAATC
Found at i:65243 original size:23 final size:24
Alignment explanation
Indices: 65217--65261 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
65207 ATTAATAATA
* *
65217 AATTATTATTA-CTAATCATTACT
1 AATTATTACTATCAAATCATTACT
65240 AATTATTACTATCAAATCATTA
1 AATTATTACTATCAAATCATTA
65262 AAAATTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (24 bp):
AATTATTACTATCAAATCATTACT
Found at i:65267 original size:24 final size:23
Alignment explanation
Indices: 65216--65268 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
65206 TATTAATAAT
* * *
65216 AAATTATTATTACTAATCATTAC
1 AAATTATTACTACAAATCATTAA
*
65239 TAATTATTACTATCAAATCATTAA
1 AAATTATTACTA-CAAATCATTAA
65263 AAATTA
1 AAATTA
65269 ATAATAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATTATTACTACAAATCATTAA
Found at i:65293 original size:60 final size:60
Alignment explanation
Indices: 65171--65424 Score: 431
Period size: 60 Copynumber: 4.2 Consensus size: 60
65161 ATTACTATCA
*
65171 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* * *
65230 AATCATTACT-AATTATTACTATCAAATCATTAAAAATTAATAATAAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAAT-AATTTCATTATTACT
*
65290 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATATTTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
*
65350 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
65410 AATCATTACTAAATC
1 AATCATTACTAAATC
65425 TTAGAAATAC
Statistics
Matches: 182, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
58 31 0.17
59 14 0.08
60 106 0.58
61 31 0.17
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (60 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
Found at i:65368 original size:21 final size:21
Alignment explanation
Indices: 65284--65371 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 21
65274 AAATTTCATT
65284 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
* * *
65305 ATTAAT-ATCAAATCATTAAAT-
1 ATTACTAATC--ATTACTAAATC
* ** *
65326 ATTAATAAT-ATT--TTCATT
1 ATTACTAATCATTACTAAATC
65344 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
65365 ATTACTA
1 ATTACTA
65372 TCAAATCATT
Statistics
Matches: 50, Mismatches: 10, Indels: 14
0.68 0.14 0.19
Matches are distributed among these distances:
17 3 0.06
18 8 0.16
19 5 0.10
20 3 0.06
21 21 0.42
22 10 0.20
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTACTAATCATTACTAAATC
Found at i:66963 original size:19 final size:20
Alignment explanation
Indices: 66934--66971 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
66924 ATAAATTTGT
66934 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
66954 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
66972 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:67083 original size:62 final size:61
Alignment explanation
Indices: 66939--67096 Score: 178
Period size: 62 Copynumber: 2.5 Consensus size: 61
66929 TTTGTTGAAG
* * * * *
66939 GTGCATCGATGCATATGAAGTGCATCGATGCATTAATTTAAATACAAATATCGAATGTCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATT-ATCTAAATACAAATAACGAATGCCCTCA
*
67002 GTGCATCGATACATAAGGAGTGCATCGATGCATT-TCT-AATA-AAATGAACATGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTATCTAAATACAAAT-AAC--GAATGCCCTCA
67064 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
67097 GCCTCCATTA
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
59 4 0.05
60 6 0.07
61 2 0.02
62 40 0.48
63 30 0.36
64 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (61 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTATCTAAATACAAATAACGAATGCCCTCA
Found at i:68435 original size:18 final size:18
Alignment explanation
Indices: 68412--68447 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
68402 AGGAATGATA
68412 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
68430 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
68448 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:68462 original size:121 final size:121
Alignment explanation
Indices: 68309--68672 Score: 665
Period size: 121 Copynumber: 3.0 Consensus size: 121
68299 CGAGGGTCTA
68309 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
68374 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
68430 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGGGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
68495 GATCCCTAGCATATGTATATAATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
* *
68551 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* **
68616 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
68672 T
1 T
68673 ATTATATGGC
Statistics
Matches: 234, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
121 234 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:68556 original size:18 final size:18
Alignment explanation
Indices: 68533--68568 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
68523 AGGAATGATA
68533 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
*
68551 TGTGGTCCTTTGGGACAT
1 TGTGGTCCTTCGGGACAT
68569 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:68710 original size:23 final size:23
Alignment explanation
Indices: 68680--68739 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
68670 ATTATTATAT
68680 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
68703 GGCACTACGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
*
68726 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
68740 TTTATGAGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:71900 original size:17 final size:17
Alignment explanation
Indices: 71847--71909 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
71837 ATAATATAAA
71847 TTAAACAAAATA-TTTT
1 TTAAACAAAATATTTTT
* * *
71863 TAAAACAACACTAAATATTT
1 TTAAACAA-A--ATATTTTT
71883 TTAAACAAAATATTTTT
1 TTAAACAAAATATTTTT
71900 TTAAACAAAA
1 TTAAACAAAA
71910 ATTATATCGC
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
16 7 0.19
17 17 0.46
19 3 0.08
20 10 0.27
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAAACAAAATATTTTT
Found at i:72710 original size:22 final size:23
Alignment explanation
Indices: 72685--72734 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
72675 AATTTGACTG
72685 TTGAAGCAAATAA-TATTGAGCA
1 TTGAAGCAAATAACTATTGAGCA
* ** *
72707 TTGAATCATGTAACTATTGAGCG
1 TTGAAGCAAATAACTATTGAGCA
72730 TTGAA
1 TTGAA
72735 AGGCTGCAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (23 bp):
TTGAAGCAAATAACTATTGAGCA
Found at i:72889 original size:23 final size:23
Alignment explanation
Indices: 72859--72902 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
72849 GATTGGCTAC
*
72859 AATCTCCCAGCTATGGATGCAGG
1 AATCTCCCAGCTATAGATGCAGG
72882 AATCTCCCAGCTATAGATGCA
1 AATCTCCCAGCTATAGATGCA
72903 ACGCATGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (23 bp):
AATCTCCCAGCTATAGATGCAGG
Found at i:73033 original size:28 final size:28
Alignment explanation
Indices: 72971--73077 Score: 93
Period size: 26 Copynumber: 4.0 Consensus size: 28
72961 TCGCCAGCTT
* * *
72971 GGTCGCCGGGACTGCTTGGCGACC--TA
1 GGTCGCTGGGAGTGCATGGCGACCTGTA
72997 GGTCGCTGGGAGTGCATGGCGACCTGTA
1 GGTCGCTGGGAGTGCATGGCGACCTGTA
*
73025 GGTCGCT-GG-GTG--TGGCGACCTGTGG
1 GGTCGCTGGGAGTGCATGGCGACCTGT-A
*
73050 GGT-GTTGGGGACGTGCATGGCGACCTGT
1 GGTCGCT-GGGA-GTGCATGGCGACCTGT
73078 GTTGGGTGTT
Statistics
Matches: 67, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
24 13 0.19
25 3 0.04
26 26 0.39
27 2 0.03
28 12 0.18
30 11 0.16
ACGTcount: A:0.10, C:0.22, G:0.45, T:0.22
Consensus pattern (28 bp):
GGTCGCTGGGAGTGCATGGCGACCTGTA
Found at i:73045 original size:24 final size:27
Alignment explanation
Indices: 72987--73047 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 27
72977 CGGGACTGCT
72987 TGGCGACC--TAGGTCGCTGGGAGTGCA
1 TGGCGACCTGTAGGTCGCTGGGAGTG-A
73013 TGGCGACCTGTAGGTCGCT-GG-GTG-
1 TGGCGACCTGTAGGTCGCTGGGAGTGA
73037 TGGCGACCTGT
1 TGGCGACCTGT
73048 GGGGTGTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
24 11 0.33
26 11 0.33
27 2 0.06
28 9 0.27
ACGTcount: A:0.11, C:0.23, G:0.43, T:0.23
Consensus pattern (27 bp):
TGGCGACCTGTAGGTCGCTGGGAGTGA
Found at i:73073 original size:30 final size:31
Alignment explanation
Indices: 73037--73102 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 31
73027 TCGCTGGGTG
73037 TGGCGACCTGTG-GGGTGTTGGGGACGTGCA
1 TGGCGACCTGTGTGGGTGTTGGGGACGTGCA
*
73067 TGGCGACCTGTGTTGGGTGTTGGGGATGTGCA
1 TGGCGACCTGTG-TGGGTGTTGGGGACGTGCA
73099 TGGC
1 TGGC
73103 ATATGCAGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 12 0.36
32 21 0.64
ACGTcount: A:0.09, C:0.15, G:0.48, T:0.27
Consensus pattern (31 bp):
TGGCGACCTGTGTGGGTGTTGGGGACGTGCA
Found at i:74391 original size:41 final size:41
Alignment explanation
Indices: 74235--74473 Score: 143
Period size: 41 Copynumber: 5.8 Consensus size: 41
74225 AAAATAAAAC
* *
74235 TTTAGCGGAGTTTTT-TCAACAAACGCCGCAATAGGGT-GTTAA
1 TTTAGCGGCGTTTTTAT-AA-AAACGCCGCAATAGAGTAG-TAA
* * * * * *
74277 GTTAGCGGCGTTTATAGCT-CAAACGCCGGAATATAGTTGT--
1 TTTAGCGGCGTTTTTA--TAAAAACGCCGCAATAGAGTAGTAA
* * *
74317 TTATAGTGGCGTTTTCTAAAAAAACACCGCAATAGAGTAGTAA
1 TT-TAGCGGCGTTTT-TATAAAAACGCCGCAATAGAGTAGTAA
* *
74360 TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGT--
1 TTTAGCGGCGTTTTTATAAAAACGCCGCAATAGAGTAGTAA
* ** * *
74399 TTATAGTGGCGTTTGTGCTAAAAATGCCGCAA-AGAGTAATAA
1 TT-TAGCGGCGTTT-TTATAAAAACGCCGCAATAGAGTAGTAA
** *
74441 TTTAGCGGCGATTTTCCTACAAACGCCGCAATA
1 TTTAGCGGCG-TTTTTATAAAAACGCCGCAATA
74474 TGTTTGTCTG
Statistics
Matches: 150, Mismatches: 32, Indels: 30
0.71 0.15 0.14
Matches are distributed among these distances:
39 2 0.01
40 17 0.11
41 81 0.54
42 46 0.31
43 3 0.02
45 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.30
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTATAAAAACGCCGCAATAGAGTAGTAA
Found at i:74410 original size:82 final size:82
Alignment explanation
Indices: 74255--74473 Score: 248
Period size: 82 Copynumber: 2.7 Consensus size: 82
74245 TTTTTTCAAC
* * * ** * *
74255 AAACGCCGCAATAGGGT-GTTAAGTTAGCGGCGTTTATAGCTCAAACGCCGGAATATAGTTGTTT
1 AAACGCCGCAATAGAGTAG-TAATTTAGCGGCGTTTTTATAT-AAACGCCGCAATAGAGTTGTTT
74319 ATAGTGGCGTTT-T-CTAAAA
64 ATAGTGGCGTTTGTGCT--AA
*
74338 AAACACCGCAATAGAGTAGTAATTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTAT
1 AAACGCCGCAATAGAGTAGTAATTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTAT
74403 AGTGGCGTTTGTGCTAA
66 AGTGGCGTTTGTGCTAA
* * ** *
74420 AAATGCCGCAA-AGAGTAATAATTTAGCGGCGATTTTCCTACAAACGCCGCAATA
1 AAACGCCGCAATAGAGTAGTAATTTAGCGGCG-TTTTTATATAAACGCCGCAATA
74474 TGTTTGTCTG
Statistics
Matches: 118, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
81 19 0.16
82 62 0.53
83 34 0.29
84 3 0.03
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.29
Consensus pattern (82 bp):
AAACGCCGCAATAGAGTAGTAATTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTAT
AGTGGCGTTTGTGCTAA
Found at i:74488 original size:82 final size:80
Alignment explanation
Indices: 74296--74503 Score: 231
Period size: 82 Copynumber: 2.5 Consensus size: 80
74286 GTTTATAGCT
* *
74296 CAAACGCCGGAATATAGTTGTTTATAGTGGCGTTTTCTAAAAAAACACCGCAATAGAGTAGTAAT
1 CAAACGCCGCAATAT-GTTGTTTATAGTGGCGTTTTCT-AAAAAACACCGCAATAGAGTAATAAT
*
74361 TTAGCGGCGTTTTTATA
64 TTAGCGGCGTTTTCATA
* * **
74378 TAAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTGTGCT-AAAAATGCCGCAA-AGAGTAATAA
1 CAAACGCCGCAATA-TGTTGTTTATAGTGGCGTTT-T-CTAAAAAACACCGCAATAGAGTAATAA
*
74441 TTTAGCGGCGATTTTCCTA
63 TTTAGCGGCG-TTTTCATA
* * *
74460 CAAACGCCGCAATATGTTTGTCTGTAGTGGCGCTTTTATAAAAA
1 CAAACGCCGCAATATG-TTGTTTATAGTGGCG-TTTTCTAAAAA
74504 CGCCACAAAA
Statistics
Matches: 106, Mismatches: 13, Indels: 14
0.80 0.10 0.11
Matches are distributed among these distances:
81 21 0.20
82 79 0.75
83 4 0.04
84 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (80 bp):
CAAACGCCGCAATATGTTGTTTATAGTGGCGTTTTCTAAAAAACACCGCAATAGAGTAATAATTT
AGCGGCGTTTTCATA
Found at i:76009 original size:18 final size:18
Alignment explanation
Indices: 75986--76021 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
75976 AGCGTCGTTT
75986 GTAGCTAAAACGCCGCAA
1 GTAGCTAAAACGCCGCAA
76004 GTAGCTAAAACGCCGCAA
1 GTAGCTAAAACGCCGCAA
76022 TAGAGTAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.28, G:0.22, T:0.11
Consensus pattern (18 bp):
GTAGCTAAAACGCCGCAA
Found at i:76018 original size:60 final size:60
Alignment explanation
Indices: 75944--76063 Score: 195
Period size: 60 Copynumber: 2.0 Consensus size: 60
75934 AGCGGCGTTT
* * * *
75944 GTAGCTCAAACGCCGTAATAGAGTAGTAATATAGCGTCGTTTGTAGCTAAAACGCCGCAA
1 GTAGCTAAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTAAAACGCCGCAA
*
76004 GTAGCTAAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTAAAATGCCGCAA
1 GTAGCTAAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTAAAACGCCGCAA
76064 TAGAGTAGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (60 bp):
GTAGCTAAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTAAAACGCCGCAA
Found at i:76064 original size:42 final size:42
Alignment explanation
Indices: 76005--76358 Score: 487
Period size: 42 Copynumber: 8.5 Consensus size: 42
75995 ACGCCGCAAG
* *
76005 TAGCTAAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTA
1 TAGCTCAAACGCCGTAATAGAGTAGTAATATAGCGGCGTTTA
* * *
76047 TAGCTAAAATGCCGCAATAGAGTAGTAATATAGCGGCGTTT-
1 TAGCTCAAACGCCGTAATAGAGTAGTAATATAGCGGCGTTTA
*
76088 GAGCTACAAACGCCGTAATAGAGTAGTAATATAGCGGCGTTTA
1 TAGCT-CAAACGCCGTAATAGAGTAGTAATATAGCGGCGTTTA
* * * *
76131 T-GATCAAACACCATAATAGAGTTGTAATATAGCGGCGTTTA
1 TAGCTCAAACGCCGTAATAGAGTAGTAATATAGCGGCGTTTA
* * *
76172 TAGCTCAAACGTCATAATAGAGTTGTAATATAGCGGCGTTTA
1 TAGCTCAAACGCCGTAATAGAGTAGTAATATAGCGGCGTTTA
*
76214 TAGCTCAAACGCCGTAATAGAGTAGTAATATAGCAGCGTTTA
1 TAGCTCAAACGCCGTAATAGAGTAGTAATATAGCGGCGTTTA
* * * * * *
76256 TAGATAAAACGCCGCAATAGAGTTGTAATATAACGACGTTTA
1 TAGCTCAAACGCCGTAATAGAGTAGTAATATAGCGGCGTTTA
* *
76298 TAGCTCAAACGCCGTAATAGAGTTGTAATATAGCGGCTTTTA
1 TAGCTCAAACGCCGTAATAGAGTAGTAATATAGCGGCGTTTA
76340 TAGCTCAAACGCCGTAATA
1 TAGCTCAAACGCCGTAATA
76359 TGGTTAACAT
Statistics
Matches: 279, Mismatches: 30, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
41 39 0.14
42 240 0.86
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (42 bp):
TAGCTCAAACGCCGTAATAGAGTAGTAATATAGCGGCGTTTA
Found at i:76379 original size:126 final size:124
Alignment explanation
Indices: 76009--76358 Score: 513
Period size: 125 Copynumber: 2.8 Consensus size: 124
75999 CGCAAGTAGC
* * * * *
76009 TAAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTAAAATGCCGCAATAGAGTAGTA
1 TAAAACGCCGCAATAGAGTTGTAATATAGCGGCGTTTATAGCTCAAACGCCGTAATAGAGTTGTA
*
76074 ATATAGCGGCGTTT-GAGCTACAAACGCCGTAATAGAGTAGTAATATAGCGGCGTTTATGA
66 ATATAGCGGCGTTTATAGCT-CAAACGCCGTAATAGAGTAG-AATATAGCGGCGTTTATGA
* * ** * *
76134 TCAAACACCATAATAGAGTTGTAATATAGCGGCGTTTATAGCTCAAACGTCATAATAGAGTTGTA
1 TAAAACGCCGCAATAGAGTTGTAATATAGCGGCGTTTATAGCTCAAACGCCGTAATAGAGTTGTA
*
76199 ATATAGCGGCGTTTATAGCTCAAACGCCGTAATAGAGTAGTAATATAGCAGCGTTTATAGA
66 ATATAGCGGCGTTTATAGCTCAAACGCCGTAATAGAGTAG-AATATAGCGGCGTTTAT-GA
* *
76260 TAAAACGCCGCAATAGAGTTGTAATATAACGACGTTTATAGCTCAAACGCCGTAATAGAGTTGTA
1 TAAAACGCCGCAATAGAGTTGTAATATAGCGGCGTTTATAGCTCAAACGCCGTAATAGAGTTGTA
*
76325 ATATAGCGGCTTTTATAGCTCAAACGCCGTAATA
66 ATATAGCGGCGTTTATAGCTCAAACGCCGTAATA
76359 TGGTTAACAT
Statistics
Matches: 201, Mismatches: 22, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
125 105 0.52
126 96 0.48
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (124 bp):
TAAAACGCCGCAATAGAGTTGTAATATAGCGGCGTTTATAGCTCAAACGCCGTAATAGAGTTGTA
ATATAGCGGCGTTTATAGCTCAAACGCCGTAATAGAGTAGAATATAGCGGCGTTTATGA
Found at i:76767 original size:23 final size:23
Alignment explanation
Indices: 76719--76767 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
76709 TTCACTGCGC
* *
76719 CGTGCCTTCTTCGTCTCCGGCGT
1 CGTGCCTTCTTCGTCTCCGACAT
76742 CGTGCCTTCTTCGTCTCCGACAT
1 CGTGCCTTCTTCGTCTCCGACAT
76765 CGT
1 CGT
76768 CGCATTTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.04, C:0.39, G:0.22, T:0.35
Consensus pattern (23 bp):
CGTGCCTTCTTCGTCTCCGACAT
Found at i:83614 original size:21 final size:21
Alignment explanation
Indices: 83580--83662 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 21
83570 ATGAAGCAAG
*
83580 GGAAGCAAAGAGAGCAGCAGT
1 GGAAGCAGAGAGAGCAGCAGT
** *
83601 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGT
* *
83622 GGAAGTAGAGAGAGAAGCAGT
1 GGAAGCAGAGAGAGCAGCAGT
* * *
83643 GGCAGCACAGAGAGAAGCAG
1 GGAAGCAGAGAGAGCAGCAG
83663 CGACAGCACA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.40, C:0.16, G:0.40, T:0.05
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGT
Found at i:83669 original size:21 final size:21
Alignment explanation
Indices: 83630--83676 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
83620 GCGGAAGTAG
* *
83630 AGAGAGAAGCAGTGGCAGCAC
1 AGAGAGAAGCAGCGACAGCAC
83651 AGAGAGAAGCAGCGACAGCAC
1 AGAGAGAAGCAGCGACAGCAC
83672 AGAGA
1 AGAGA
83677 TGCGCAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.43, C:0.19, G:0.36, T:0.02
Consensus pattern (21 bp):
AGAGAGAAGCAGCGACAGCAC
Found at i:84194 original size:85 final size:86
Alignment explanation
Indices: 84090--84270 Score: 213
Period size: 85 Copynumber: 2.1 Consensus size: 86
84080 CAAGACATAT
* * * * * * *
84090 TGCGGCTTTTGCGACGAAAACGCCGCTAAATATCAACATCT-TCTGCGGTGTTTGT-GGGAAAAC
1 TGCGGCGTTTGTGAAGAAAACGCCGCTAAACATCAACACCTAT-TGCGGCGTTTGTCGGCAAAAC
*
84153 GCCGGTAAAAATCAACACCTAC
65 GCCGCTAAAAATCAACACCTAC
* * * *
84175 TGCGGTGTTTGTGAAGAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTCTGCCAAATG
1 TGCGGCGTTTGTGAAGAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTCGGCAAAACG
* *
84240 CCGCTAAATATCAACACCTAT
66 CCGCTAAAAATCAACACCTAC
84261 TGCGGCGTTT
1 TGCGGCGTTT
84271 TTCTGTCAAA
Statistics
Matches: 79, Mismatches: 15, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
85 46 0.58
86 33 0.42
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (86 bp):
TGCGGCGTTTGTGAAGAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTCGGCAAAACG
CCGCTAAAAATCAACACCTAC
Found at i:84210 original size:43 final size:42
Alignment explanation
Indices: 84090--84270 Score: 191
Period size: 43 Copynumber: 4.2 Consensus size: 42
84080 CAAGACATAT
* * * *
84090 TGCGGCTTTTGCGACGAAAACGCCGCTAAATATCAACATCTTC
1 TGCGGCGTTTGTGA-GAAAACGCCGCTAAATATCAACACCTAC
* * * *
84133 TGCGGTGTTTGTGGGAAAACGCCGGTAAAAATCAACACCTAC
1 TGCGGCGTTTGTGAGAAAACGCCGCTAAATATCAACACCTAC
* * *
84175 TGCGGTGTTTGTGAAGAAAACGCCGCTAAACATCAACACCTAT
1 TGCGGCGTTTGTG-AGAAAACGCCGCTAAATATCAACACCTAC
** * * *
84218 TGCGGCGTTTGTCTGCCAAATGCCGCTAAATATCAACACCTAT
1 TGCGGCGTTTGTGAG-AAAACGCCGCTAAATATCAACACCTAC
84261 TGCGGCGTTT
1 TGCGGCGTTT
84271 TTCTGTCAAA
Statistics
Matches: 118, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
42 38 0.32
43 80 0.68
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (42 bp):
TGCGGCGTTTGTGAGAAAACGCCGCTAAATATCAACACCTAC
Found at i:84286 original size:43 final size:42
Alignment explanation
Indices: 84105--84315 Score: 172
Period size: 43 Copynumber: 5.0 Consensus size: 42
84095 CTTTTGCGAC
* * * **
84105 GAAAACGCCGCTAAATATCAACATCT-TCTGCGGTGTTTGTGG
1 GAAAACGCCGCTAAATATCAACACCTAT-TGCGGCGTTTTTCT
* * * * ***
84147 GAAAACGCCGGTAAAAATCAACACCTACTGCGGTGTTTGTGAA
1 GAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTT-TTCT
* *
84190 GAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTCT
1 GAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTCT
* *
84232 GCCAAATGCCGCTAAATATCAACACCTATTGCGGCGTTTTTCT
1 G-AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTCT
* * * * * * *
84275 GTCAAACGCCGCTATATGTTATCACCTATTGAGGCATTTTT
1 G-AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTT
84316 TGTTGAAAAA
Statistics
Matches: 138, Mismatches: 28, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
42 34 0.25
43 104 0.75
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (42 bp):
GAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTCT
Found at i:84424 original size:20 final size:21
Alignment explanation
Indices: 84382--84432 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
84372 AACGGCGCTT
84382 AAAAACGCCGTTATAAGTAAA
1 AAAAACGCCGTTATAAGTAAA
*
84403 AAAAATGCCGTTATAAGT-AA
1 AAAAACGCCGTTATAAGTAAA
84423 AAAAACGCCG
1 AAAAACGCCG
84433 CAACAAGCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.18
Consensus pattern (21 bp):
AAAAACGCCGTTATAAGTAAA
Found at i:85515 original size:19 final size:18
Alignment explanation
Indices: 85491--85526 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
85481 TCGAATCAAG
*
85491 AAAATAAGATTTAAAAAAA
1 AAAATAA-AATTAAAAAAA
85510 AAAATAAAATTAAAAAA
1 AAAATAAAATTAAAAAA
85527 TAAATACGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (18 bp):
AAAATAAAATTAAAAAAA
Found at i:94487 original size:28 final size:28
Alignment explanation
Indices: 94438--94507 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
94428 TAACTTGTAT
*
94438 ACATACATATATACTTAAGCTATGGACAC
1 ACATATATATA-ACTTAAGCTATGGACAC
*
94467 ACATATATATAACTTAAGCTATGGGCAC
1 ACATATATATAACTTAAGCTATGGACAC
94495 ACATATATATAAC
1 ACATATATATAAC
94508 CTTATTTAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 29 0.74
29 10 0.26
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.29
Consensus pattern (28 bp):
ACATATATATAACTTAAGCTATGGACAC
Found at i:99245 original size:84 final size:84
Alignment explanation
Indices: 99099--99276 Score: 230
Period size: 84 Copynumber: 2.1 Consensus size: 84
99089 TTTTTTTAAA
* * * * *
99099 CAAAACTTTCTTTTTCTTCAATTTACAAGGCGAATCTACTTTAAAATCGGAAAACATGCTAACCA
1 CAAAACTTCCTTTTTCTTCAATTTACAAGGCGAATCAACTTCAAAATCAGAAAACATACTAACCA
*
99164 GAGCAATAACAATAAACTG
66 GAGCAAAAACAATAAACTG
** * **
99183 CAAAACTTCCTTTTTCTTCGGTTTACAAGGCGACTCAACTTCAAAATCAGAAAACATACTAACGG
1 CAAAACTTCCTTTTTCTTCAATTTACAAGGCGAATCAACTTCAAAATCAGAAAACATACTAACCA
* **
99248 GAGCAAAAACGATAGGCTG
66 GAGCAAAAACAATAAACTG
99267 CAAAACTTCC
1 CAAAACTTCC
99277 CCTTCGATAT
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (84 bp):
CAAAACTTCCTTTTTCTTCAATTTACAAGGCGAATCAACTTCAAAATCAGAAAACATACTAACCA
GAGCAAAAACAATAAACTG
Found at i:103898 original size:17 final size:17
Alignment explanation
Indices: 103878--103917 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
103868 TATAATCTCC
*
103878 TATTAATTATTTGTAGG
1 TATTAATTATTTGTAGA
*
103895 TATTAATTATTTTTAGA
1 TATTAATTATTTGTAGA
103912 TATTAA
1 TATTAA
103918 ATGTTATTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (17 bp):
TATTAATTATTTGTAGA
Found at i:113847 original size:29 final size:29
Alignment explanation
Indices: 113805--113864 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
113795 CCTCCATCTA
113805 GCCAAAACTTTCTAGTCTTGCCCCCCTTG
1 GCCAAAACTTTCTAGTCTTGCCCCCCTTG
113834 GCCAAAACTTTCTAGTCTTGCCCCCCTTG
1 GCCAAAACTTTCTAGTCTTGCCCCCCTTG
113863 GC
1 GC
113865 AAGCTCAATC
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:0.17, C:0.38, G:0.15, T:0.30
Consensus pattern (29 bp):
GCCAAAACTTTCTAGTCTTGCCCCCCTTG
Found at i:118764 original size:130 final size:130
Alignment explanation
Indices: 118531--118811 Score: 420
Period size: 130 Copynumber: 2.2 Consensus size: 130
118521 TATATTCAAA
* * *
118531 AGATGGAATGACTACTATACTTGAGAGGTATAGCAAACCTCATCGTCAAAGGCTGGACCATGGAG
1 AGATGGAATGACTACCATACTTGAGAGCTATAGCAAACCTCATCGTCAAAGGCTGGACCATAGAG
* * *
118596 TTCCAGAAAGTATACCGAGAAGCAAATGTCGCAGCGGATTTTATATCCAAGATGGAC-TCCGCAC
66 TTCCAGAAAGTATACCGAGAAGCAAATGCCGCAACGGATTTTATATCCAAGATGAACTTCC-CAC
118660 T
130 T
* * * **
118661 AGATGGAATGAGTACCATACTTGAGAGCTATTGTAATTCTCATCGTCAAAGGCTGGACCATAGAG
1 AGATGGAATGACTACCATACTTGAGAGCTATAGCAAACCTCATCGTCAAAGGCTGGACCATAGAG
*
118726 TTCCAGAAAGTATACCGAGAAGTAAATGCCGCAACGGATTTTATATCCAAGATGAACTTCCCACT
66 TTCCAGAAAGTATACCGAGAAGCAAATGCCGCAACGGATTTTATATCCAAGATGAACTTCCCACT
* *
118791 AGATGGAATGCCTACTATACT
1 AGATGGAATGACTACCATACT
118812 CTCGGCATAC
Statistics
Matches: 135, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
130 132 0.98
131 3 0.02
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (130 bp):
AGATGGAATGACTACCATACTTGAGAGCTATAGCAAACCTCATCGTCAAAGGCTGGACCATAGAG
TTCCAGAAAGTATACCGAGAAGCAAATGCCGCAACGGATTTTATATCCAAGATGAACTTCCCACT
Found at i:126118 original size:45 final size:45
Alignment explanation
Indices: 126040--126255 Score: 281
Period size: 45 Copynumber: 4.8 Consensus size: 45
126030 CCAAGTGGGG
*
126040 CTATACCTGATGAGAGTCATTCCGAAAAGGCTGCACTGCCAATGA
1 CTATACCTGATGAGAGTCATTCCGAAAAGGCTGCACAGCCAATGA
* * * * *
126085 CTATGCTTGATGAGAGTCATTCCAAAAATGCTGCACAG-CAAGGA
1 CTATACCTGATGAGAGTCATTCCGAAAAGGCTGCACAGCCAATGA
* * * *
126129 CTATACCTGATGATAGTCATTCCGAAAAGGTTGCGCAGCCGATGA
1 CTATACCTGATGAGAGTCATTCCGAAAAGGCTGCACAGCCAATGA
* ** *
126174 CTATACCTGATGATAGTCATTTTGAAAAGGCTGCACAACCAATGA
1 CTATACCTGATGAGAGTCATTCCGAAAAGGCTGCACAGCCAATGA
* *
126219 CTATACCTGATGTGAGTCATTCTGAAAAGGCTGCACA
1 CTATACCTGATGAGAGTCATTCCGAAAAGGCTGCACA
126256 ACCAGAAAGA
Statistics
Matches: 146, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
44 36 0.25
45 110 0.75
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (45 bp):
CTATACCTGATGAGAGTCATTCCGAAAAGGCTGCACAGCCAATGA
Found at i:126192 original size:89 final size:90
Alignment explanation
Indices: 126040--126255 Score: 274
Period size: 89 Copynumber: 2.4 Consensus size: 90
126030 CCAAGTGGGG
* * * *
126040 CTATACCTGATGAGAGTCATTCCGAAAAGGCTGCACTGCCAATGACTATGCTTGATGAGAGTCAT
1 CTATACCTGATGATAGTCATTCCGAAAAGGCTGCACAGCCAATGACTATACCTGATGAGAGTCAT
* *
126105 TCCAAAAATGCTGCAC-AGCAAGGA
66 TCCAAAAAGGCTGCACAACCAAGGA
* * * *
126129 CTATACCTGATGATAGTCATTCCGAAAAGGTTGCGCAGCCGATGACTATACCTGATGATAGTCAT
1 CTATACCTGATGATAGTCATTCCGAAAAGGCTGCACAGCCAATGACTATACCTGATGAGAGTCAT
*** *
126194 TTTGAAAAGGCTGCACAACCAATGA
66 TCCAAAAAGGCTGCACAACCAAGGA
*
126219 CTATACCTGATG-TGAGTCATTCTGAAAAGGCTGCACA
1 CTATACCTGATGAT-AGTCATTCCGAAAAGGCTGCACA
126256 ACCAGAAAGA
Statistics
Matches: 108, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
89 70 0.65
90 38 0.35
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (90 bp):
CTATACCTGATGATAGTCATTCCGAAAAGGCTGCACAGCCAATGACTATACCTGATGAGAGTCAT
TCCAAAAAGGCTGCACAACCAAGGA
Found at i:146725 original size:16 final size:16
Alignment explanation
Indices: 146704--146737 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
146694 TTACTATTAA
*
146704 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
146720 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
146736 CG
1 CG
146738 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:159966 original size:34 final size:34
Alignment explanation
Indices: 159923--160047 Score: 111
Period size: 34 Copynumber: 3.8 Consensus size: 34
159913 TTCGTCCTAC
*
159923 TAGGATTCAAACTCCTAAAAATAGGATATAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
159957 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
159992 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * * *
160021 TATGATTTAAATTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
160048 CCACAAGCAC
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 38 0.52
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:160420 original size:13 final size:13
Alignment explanation
Indices: 160406--160442 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
160396 TATATGGATA
160406 TTTTATTTATTTAT
1 TTTTA-TTATTTAT
160420 TTTTATTATTTAT
1 TTTTATTATTTAT
160433 TTATTATTAT
1 TT-TTATTAT
160443 ATGTATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:160425 original size:14 final size:14
Alignment explanation
Indices: 160406--160440 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
160396 TATATGGATA
160406 TTTTATTTATTTAT
1 TTTTATTTATTTAT
160420 TTTTA-TTATTTAT
1 TTTTATTTATTTAT
160433 TTATTATT
1 TT-TTATT
160441 ATATGTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.53
14 8 0.42
15 1 0.05
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTTATTTAT
Found at i:160428 original size:17 final size:17
Alignment explanation
Indices: 160404--160442 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
160394 ATTATATGGA
160404 TATT-TTATTTATTTAT
1 TATTATTATTTATTTAT
*
160420 TTTTATTATTTATTTAT
1 TATTATTATTTATTTAT
160437 TATTAT
1 TATTAT
160443 ATGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTATTATTTATTTAT
Found at i:160453 original size:2 final size:2
Alignment explanation
Indices: 160440--160476 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
160430 TATTTATTAT
*
160440 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
160477 TTCTTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:160617 original size:14 final size:14
Alignment explanation
Indices: 160598--160624 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
160588 TATATTCTTA
160598 ATTATTTTTATTTG
1 ATTATTTTTATTTG
160612 ATTATTTTTATTT
1 ATTATTTTTATTT
160625 ACGTAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (14 bp):
ATTATTTTTATTTG
Found at i:160947 original size:9 final size:9
Alignment explanation
Indices: 160926--160959 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
160916 TATTTTTTCC
160926 TTTATCTTA-
1 TTTAT-TTAT
160935 TTTATTTAT
1 TTTATTTAT
160944 TTTATTTAT
1 TTTATTTAT
160953 TTTATTT
1 TTTATTT
160960 TTCCCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:160948 original size:13 final size:14
Alignment explanation
Indices: 160926--160960 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
160916 TATTTTTTCC
*
160926 TTTATCTTATTTA-
1 TTTATTTTATTTAT
160939 TTTATTTTATTTAT
1 TTTATTTTATTTAT
160953 TTTATTTT
1 TTTATTTT
160961 TCCCTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:162944 original size:18 final size:18
Alignment explanation
Indices: 162921--162960 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
162911 TTCCTTTAAG
162921 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
162939 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
162957 TCTG
1 TCTG
162961 AAAGACTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (18 bp):
TCTGGATTCACATCCACT
Found at i:164692 original size:16 final size:16
Alignment explanation
Indices: 164666--164747 Score: 59
Period size: 16 Copynumber: 5.1 Consensus size: 16
164656 AGATCCAATC
164666 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
164681 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
*
164698 AA-AA-AAACAAAGAAA
1 AAGAACAAA-AAAGCAA
164713 AAGAGA-AACAAGAA-CAA
1 AAGA-ACAA-AA-AAGCAA
164730 AAGGAA-AAAAAAGCAA
1 AA-GAACAAAAAAGCAA
164746 AA
1 AA
164748 ATCAAAAAGA
Statistics
Matches: 56, Mismatches: 2, Indels: 17
0.75 0.03 0.23
Matches are distributed among these distances:
14 3 0.05
15 15 0.27
16 18 0.32
17 15 0.27
18 5 0.09
ACGTcount: A:0.77, C:0.09, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:164713 original size:22 final size:22
Alignment explanation
Indices: 164672--164739 Score: 52
Period size: 22 Copynumber: 3.0 Consensus size: 22
164662 AATCAAGAAC
164672 AAAAAAGAAA-AGAAGCAAAAAAG
1 AAAAAAGAAACA-AAG-AAAAAAG
164695 CAAAAAA-AAACAAAGAAAAAGAG
1 -AAAAAAGAAACAAAGAAAAA-AG
*
164718 AAACAAG-AACAAAAGGAAAAAA
1 AAAAAAGAAAC-AAA-GAAAAAA
164740 AAGCAAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
22 13 0.34
23 12 0.32
24 13 0.34
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAACAAAGAAAAAAG
Found at i:164732 original size:38 final size:37
Alignment explanation
Indices: 164673--164746 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
164663 ATCAAGAACA
*
164673 AAAAAGAAAAGAAGCAAAAAAGCAAAAAAAAACAAAG
1 AAAAAGAAAACAAGCAAAAAAGCAAAAAAAAACAAAG
* *
164710 AAAAAGAGAAACAAG-AACAAAAGGAAAAAAAAGCAAA
1 AAAAAGA-AAACAAGCAA-AAAAGCAAAAAAAAACAAA
164747 AATCAAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 9 0.28
38 23 0.72
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (37 bp):
AAAAAGAAAACAAGCAAAAAAGCAAAAAAAAACAAAG
Found at i:164739 original size:8 final size:7
Alignment explanation
Indices: 164672--164739 Score: 57
Period size: 8 Copynumber: 8.9 Consensus size: 7
164662 AATCAAGAAC
164672 AAAAAAG
1 AAAAAAG
164679 AAAAGAAG
1 AAAA-AAG
164687 CAAAAAAG
1 -AAAAAAG
164695 CAAAAAA-
1 -AAAAAAG
164702 AAACAAAG
1 AAA-AAAG
164710 AAAAAGAG
1 AAAAA-AG
*
164718 AAACAAG
1 AAAAAAG
164725 AACAAAAGG
1 AA-AAAA-G
164734 AAAAAA
1 AAAAAA
164740 AAGCAAAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
6 3 0.06
7 13 0.25
8 29 0.56
9 7 0.13
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:165422 original size:22 final size:22
Alignment explanation
Indices: 165397--165445 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
165387 CCATCAATCT
* *
165397 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
165419 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
165441 TTTGA
1 TTTGA
165446 CCAAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:165883 original size:18 final size:18
Alignment explanation
Indices: 165860--165895 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
165850 TCAACATCAA
* *
165860 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
165878 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
165896 GGATTCAACA
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:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:166414 original size:36 final size:36
Alignment explanation
Indices: 166373--166654 Score: 267
Period size: 36 Copynumber: 8.0 Consensus size: 36
166363 ACTAGAAGAG
166373 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
166409 TTTTGTCTCTCTTGAGACAGCTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
166445 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
166481 TTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
166517 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
** * ** * *
166546 TTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
166583 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * *
166618 TTTTCGTTTATGTTGAGATAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
166655 ATCTTTGAAT
Statistics
Matches: 198, Mismatches: 36, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.01
29 18 0.09
30 2 0.01
35 6 0.03
36 136 0.69
37 34 0.17
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:166646 original size:138 final size:137
Alignment explanation
Indices: 166393--166717 Score: 393
Period size: 138 Copynumber: 2.4 Consensus size: 137
166383 CTTGAGACAG
*
166393 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGCTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACAAATTTCGTCTATCTT
*
166458 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTAAAACAAAATATTT
*
166523 GAATATG
131 GAATATA
* * ** * * * * * *
166530 TTTTCTTTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAAC-AAATTTCGTCTATCT
* * * * * * *
166595 TGAGACAGTTTCTCTTGAAA-CAATTTTCGTTTATGTTGAGATAGTTTCCCTTGAAACAAAATCT
65 TGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTAAAACAAAATAT
*
166659 TTGAATTTA
129 TTGAATATA
* * *
166668 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACA-ATTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTT-CTCTTGAAACA
166718 CAAAATCTTC
Statistics
Matches: 155, Mismatches: 30, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
137 50 0.32
138 105 0.68
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTAAAACAAAATATTT
GAATATA
Found at i:167515 original size:105 final size:105
Alignment explanation
Indices: 167389--168047 Score: 999
Period size: 105 Copynumber: 6.3 Consensus size: 105
167379 GGCCATCCGT
* *
167389 AATTTCAACTTCACAATGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCATGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGG
167454 GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCC
*
167494 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGG
167559 GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCC
167599 AATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
167664 GACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCC
* * * *
167704 AATTTCAACTTCACAACGAATGATATTAGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
167769 GACCGCTGCTTGTCAACAACAACTTCCCAATCTAAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCC
* *
167809 AATTTCAACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGG
* **
167874 GACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTAAGATTC
66 GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCC
* *
167909 AATTTCAACTTCACAACGAAGGATATTGGAC-TCGAGACAACACAAGTTCAACTTCACAACGAAG
1 AATTTCAACTTCACAACGAAGGATATTGGACTTC-AGACAACGCAAGTTCAACTTCACGACGAAG
* * * ** *
167973 GGACGGCTGGTTGTCAACAAACAA-TTTTCCGGTTCCAGAGCC
65 GGACCGCTGCTTGTCAAC-AACAACTTCT-CAATTTCAGAGCC
* *
168015 AATTTCAACTTCACGACGGAGGATATTGGACTT
1 AATTTCAACTTCACAACGAAGGATATTGGACTT
168048 GGACAATGCT
Statistics
Matches: 514, Mismatches: 32, Indels: 14
0.92 0.06 0.03
Matches are distributed among these distances:
99 1 0.00
100 80 0.16
101 3 0.01
102 5 0.01
103 3 0.01
104 3 0.01
105 384 0.75
106 34 0.07
107 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCC
Found at i:168637 original size:34 final size:34
Alignment explanation
Indices: 168594--168718 Score: 120
Period size: 34 Copynumber: 3.8 Consensus size: 34
168584 TTCGTCCTAC
168594 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
168628 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
168663 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * * *
168692 TATGATTTAAATTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
168719 CCACAAGCAC
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 39 0.53
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:169096 original size:14 final size:13
Alignment explanation
Indices: 169077--169115 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
169067 TATATGGATA
169077 TTTTATTCATTTAT
1 TTTTATT-ATTTAT
169091 TTTTATTATTTAT
1 TTTTATTATTTAT
169104 GTTATTATTATT
1 -TT-TTATTATT
169116 ATATGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:169114 original size:18 final size:17
Alignment explanation
Indices: 169075--169117 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
169065 ATTATATGGA
169075 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
* *
169091 TTTTATTATTTATGTTAT
1 TATTATTATTCAT-TTAT
169109 TATTATTAT
1 TATTATTAT
169118 ATGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:169128 original size:2 final size:2
Alignment explanation
Indices: 169115--169153 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
169105 TTATTATTAT
*
169115 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
169154 TTCTTTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:169628 original size:9 final size:9
Alignment explanation
Indices: 169607--169640 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
169597 TATTTTTTCC
169607 TTTATCTTA-
1 TTTAT-TTAT
169616 TTTATTTAT
1 TTTATTTAT
169625 TTTATTTAT
1 TTTATTTAT
169634 TTTATTT
1 TTTATTT
169641 TTCCCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:169629 original size:13 final size:14
Alignment explanation
Indices: 169607--169641 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
169597 TATTTTTTCC
*
169607 TTTATCTTATTTA-
1 TTTATTTTATTTAT
169620 TTTATTTTATTTAT
1 TTTATTTTATTTAT
169634 TTTATTTT
1 TTTATTTT
169642 TCCCTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:171611 original size:7 final size:7
Alignment explanation
Indices: 171599--171708 Score: 220
Period size: 7 Copynumber: 15.7 Consensus size: 7
171589 TTCCTGACTT
171599 GCTTCTA
1 GCTTCTA
171606 GCTTCTA
1 GCTTCTA
171613 GCTTCTA
1 GCTTCTA
171620 GCTTCTA
1 GCTTCTA
171627 GCTTCTA
1 GCTTCTA
171634 GCTTCTA
1 GCTTCTA
171641 GCTTCTA
1 GCTTCTA
171648 GCTTCTA
1 GCTTCTA
171655 GCTTCTA
1 GCTTCTA
171662 GCTTCTA
1 GCTTCTA
171669 GCTTCTA
1 GCTTCTA
171676 GCTTCTA
1 GCTTCTA
171683 GCTTCTA
1 GCTTCTA
171690 GCTTCTA
1 GCTTCTA
171697 GCTTCTA
1 GCTTCTA
171704 GCTTC
1 GCTTC
171709 GATTCAGTGT
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 103 1.00
ACGTcount: A:0.14, C:0.29, G:0.15, T:0.43
Consensus pattern (7 bp):
GCTTCTA
Found at i:192546 original size:14 final size:14
Alignment explanation
Indices: 192529--192556 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
192519 ATCATAACAA
192529 AATTATATAACTAT
1 AATTATATAACTAT
192543 AATTATATAACTAT
1 AATTATATAACTAT
192557 TTTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:198755 original size:75 final size:74
Alignment explanation
Indices: 198572--198823 Score: 194
Period size: 64 Copynumber: 3.6 Consensus size: 74
198562 TATATATGTA
* * * * * *
198572 TATAATATATAGTTTTGAAAACATA-TTTG-AAAC-ATTTATATATTATATAGTTTTTAAAACAC
1 TATAATATATAGTTTTAAAAAAAAATTTTGAAAACTATATATATATTATATAGTTTTAAAAACAT
198634 TTTGAAAA-
66 TTTGAAAAC
* *** *
198642 TA-AATATA-A-TTTT-TAAAACGTTTTTG--AA--A-ATATATATTATATGGTTTTAAAAACAT
1 TATAATATATAGTTTTAAAAAAAAATTTTGAAAACTATATATATATTATATAGTTTTAAAAACAT
*
198698 TTTTAAAA-
66 TTTGAAAAC
* *
198706 TA-AATATA-ATTTTTAAAAAGAAACATTTTGAAAACATATATATATTATTATATAGTTTTGAAA
1 TATAATATATAGTTTTAAAAA-AAA-ATTTTGAAAAC-TATATATA-TATTATATAGTTTTAAAA
*
198769 TCATTTTGAAAAC
62 ACATTTTGAAAAC
* *
198782 TTATAATATATAGTTTTAAAAAATATTTTTGAAAACTATATA
1 -TATAATATATAGTTTTAAAAAAAAATTTTGAAAACTATATA
198824 ATTTTGAAAA
Statistics
Matches: 145, Mismatches: 21, Indels: 26
0.76 0.11 0.14
Matches are distributed among these distances:
64 39 0.27
65 5 0.03
66 8 0.06
67 9 0.06
68 6 0.04
69 6 0.04
70 4 0.03
73 1 0.01
74 5 0.03
75 26 0.18
76 6 0.04
77 12 0.08
78 8 0.06
79 10 0.07
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (74 bp):
TATAATATATAGTTTTAAAAAAAAATTTTGAAAACTATATATATATTATATAGTTTTAAAAACAT
TTTGAAAAC
Found at i:198795 original size:34 final size:35
Alignment explanation
Indices: 198570--198897 Score: 121
Period size: 34 Copynumber: 9.5 Consensus size: 35
198560 CATATATATG
* *
198570 TATATAATATATAGTTTTGAAA-ACATATTTGAAACATT
1 TATATAATATATAGTTTTAAAATAC-T-TTTGAAA-A-C
* *
198608 TATATATTATATAGTTTTTAAAACAC-TTTG-AAA-
1 TATATAATATATAG-TTTTAAAATACTTTTGAAAAC
* ***
198641 -ATA-AATATA-ATTTTTAAAACGTTTTTGAAAA-
1 TATATAATATATAGTTTTAAAATACTTTTGAAAAC
* * *
198672 TATATATTATATGGTTTTAAAA-ACATTTT-TAAA-
1 TATATAATATATAGTTTTAAAATAC-TTTTGAAAAC
* *
198705 -ATA-AATATA-ATTTTTAAAAAGAAACATTTTGAAAAC
1 TATATAATATATAGTTTT--AAA-ATAC-TTTTGAAAAC
*
198741 ATATATATATTATTATATAGTTTTGAAAT-CATTTTGAAAAC
1 ---TATATA--A-TATATAGTTTTAAAATAC-TTTTGAAAAC
*
198782 T-TATAATATATAGTTTTAAAAAATATTTTTGAAAAC
1 TATATAATATATAGTTTT--AAAATACTTTTGAAAAC
* *
198818 ----T-ATATA-A-TTTTGAAA-ACGTTTTAGAAAAA
1 TATATAATATATAGTTTTAAAATAC-TTTT-GAAAAC
*
198847 TATATAATATATAATTTTAAAATACTTTTGAAAA-
1 TATATAATATATAGTTTTAAAATACTTTTGAAAAC
*
198881 TATATATTATATAGTTT
1 TATATAATATATAGTTT
198898 GTAGAAAATA
Statistics
Matches: 227, Mismatches: 27, Indels: 76
0.69 0.08 0.23
Matches are distributed among these distances:
27 1 0.00
28 7 0.03
29 14 0.06
30 13 0.06
31 14 0.06
32 17 0.07
33 11 0.05
34 50 0.22
35 11 0.05
36 27 0.12
37 10 0.04
38 14 0.06
39 7 0.03
40 5 0.02
41 13 0.06
42 1 0.00
43 3 0.01
44 4 0.02
45 5 0.02
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (35 bp):
TATATAATATATAGTTTTAAAATACTTTTGAAAAC
Found at i:198857 original size:64 final size:62
Alignment explanation
Indices: 198754--198886 Score: 144
Period size: 64 Copynumber: 2.1 Consensus size: 62
198744 TATATATTAT
* * * *
198754 TATATAGTTTTGAAATCATTTTGAAAACTTATAATATATAGT-TTTAAAAAATATTTTTGAAAA
1 TATATAATTTTGAAAACATTTTGAAAACATATAATATATA-TATTT-AAAAATACTTTTGAAAA
* * *
198817 CTATATAATTTTGAAAACGTTTTAGAAAAATATATAATATATA-ATTTTAAAATACTTTTGAAAA
1 -TATATAATTTTGAAAACATTTT-G-AAAACATATAATATATATATTTAAAAATACTTTTGAAAA
198881 TATATA
1 TATATA
198887 TTATATAGTT
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
63 6 0.10
64 34 0.58
65 4 0.07
66 15 0.25
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.43
Consensus pattern (62 bp):
TATATAATTTTGAAAACATTTTGAAAACATATAATATATATATTTAAAAATACTTTTGAAAA
Found at i:198859 original size:36 final size:34
Alignment explanation
Indices: 198818--198893 Score: 100
Period size: 36 Copynumber: 2.2 Consensus size: 34
198808 TTTTGAAAAC
*
198818 TATATAATTTTGAAA-ACGTTTTAGAAAAATATATAA
1 TATATAATTTTAAAATAC-TTTT-G-AAAATATATAA
*
198854 TATATAATTTTAAAATACTTTTGAAAATATATAT
1 TATATAATTTTAAAATACTTTTGAAAATATATAA
198888 TATATA
1 TATATA
198894 GTTTGTAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
34 16 0.43
35 1 0.03
36 18 0.49
37 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (34 bp):
TATATAATTTTAAAATACTTTTGAAAATATATAA
Found at i:198867 original size:175 final size:177
Alignment explanation
Indices: 198563--198887 Score: 421
Period size: 175 Copynumber: 1.8 Consensus size: 177
198553 ATATATACAT
* * *
198563 ATATATGTATATAATATATAGTTTTGAAAACATATTTGAAACATTTATATATTATATAGTTTTTA
1 ATATATATATATAATATATAGTTTTGAAAACATATTTGAAACACTTATATATTATATAGTTTTAA
* * * **
198628 AAACACTTTGAAAATAAATATAATTTTTAAAACGTTTTTGAAAATATATATTATATGGTTTTAAA
66 AAACACTTTGAAAAT-AATATAATTTTGAAAACGTTTTAGAAAATATATAATATATAATTTTAAA
*
198693 A-ACATTTTTAAAATAAATATAATTTTTAAAAAGAAACATTTTGAAAAC
130 ATAC-TTTTGAAAATAAATATAATTTTTAAAAAGAAACATTTTGAAAAC
* *
198741 ATATATATAT-TATTATATAGTTTTGAAATCAT-TTTGAAA-ACTTATA-A-TATATAGTTTTAA
1 ATATATATATATAATATATAGTTTTGAAAACATATTTGAAACACTTATATATTATATAGTTTT-A
* *
198801 AAAATATTTTTGAAAACT-ATATAATTTTGAAAACGTTTTAGAAAAATATATAATATATAATTTT
65 AAAACA-CTTTGAAAA-TAATATAATTTTGAAAACGTTTTAG-AAAATATATAATATATAATTTT
*
198865 AAAATACTTTTGAAAATATATAT
127 AAAATACTTTTGAAAATAAATAT
198888 TATATAGTTT
Statistics
Matches: 128, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
173 11 0.09
174 27 0.21
175 51 0.40
176 10 0.08
177 20 0.16
178 9 0.07
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (177 bp):
ATATATATATATAATATATAGTTTTGAAAACATATTTGAAACACTTATATATTATATAGTTTTAA
AAACACTTTGAAAATAATATAATTTTGAAAACGTTTTAGAAAATATATAATATATAATTTTAAAA
TACTTTTGAAAATAAATATAATTTTTAAAAAGAAACATTTTGAAAAC
Found at i:198952 original size:14 final size:14
Alignment explanation
Indices: 198933--198962 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
198923 ATTATCGTTG
198933 TTATTTATTTTTAT
1 TTATTTATTTTTAT
198947 TTATTTATTTTTAT
1 TTATTTATTTTTAT
198961 TT
1 TT
198963 TACTTTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TTATTTATTTTTAT
Found at i:201997 original size:19 final size:19
Alignment explanation
Indices: 201963--202007 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
201953 ATTTAGACAT
201963 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
201981 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
202000 TTTGCATT
1 TTTGCATT
202008 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Done.