Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002273.1 Hibiscus syriacus cultivar Beakdansim tig00004620_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: 802197
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:670 original size:36 final size:35
Alignment explanation
Indices: 625--692 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
615 TATCGTTTAA
*
625 AAGTTAAGATAATAACAAAAATATA-TTTATATTTTT
1 AAGTGAAGATAA-AA-AAAAATATATTTTATATTTTT
*
661 AAGTGAAGATAAGAAAAAATATATTTTATATT
1 AAGTGAAGATAAAAAAAAATATATTTTATATT
693 AAATTAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 9 0.31
35 9 0.31
36 11 0.38
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (35 bp):
AAGTGAAGATAAAAAAAAATATATTTTATATTTTT
Found at i:738 original size:77 final size:82
Alignment explanation
Indices: 657--810 Score: 239
Period size: 80 Copynumber: 1.9 Consensus size: 82
647 ATATTTATAT
*
657 TTTTAAGTGA-AGAT-AAGA-AAAAATATA-TTTTATATTAAATTAATAATAAAAT-TTTAAATA
1 TTTTAAGTGATA-ATAAAGATAAAAATACATTTTTATATTAAATTAATAATAAAATATTTAAATA
717 TA-TTCAAGTTAAGATAA
65 TATTTCAAGTTAAGATAA
*
734 TTTTAAGTGATAATAAAGATAAATATACATTTTTATATTAAATTAATAATAAAATATTTAAATAT
1 TTTTAAGTGATAATAAAGATAAAAATACATTTTTATATTAAATTAATAATAAAATATTTAAATAT
799 ATTTCAAGTTAA
66 ATTTCAAGTTAA
811 AAAAATTTAA
Statistics
Matches: 69, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
77 12 0.17
78 5 0.07
79 7 0.10
80 25 0.36
81 10 0.14
82 10 0.14
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (82 bp):
TTTTAAGTGATAATAAAGATAAAAATACATTTTTATATTAAATTAATAATAAAATATTTAAATAT
ATTTCAAGTTAAGATAA
Found at i:1417 original size:13 final size:12
Alignment explanation
Indices: 1399--1433 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1389 TAGTTTACCC
1399 AAAAAAAATTACA
1 AAAAAAAATTA-A
*
1412 AAAAAAAATGAA
1 AAAAAAAATTAA
1424 AAAAAAAATT
1 AAAAAAAATT
1434 CAATCTCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTAA
Found at i:3986 original size:226 final size:218
Alignment explanation
Indices: 3594--4023 Score: 670
Period size: 226 Copynumber: 1.9 Consensus size: 218
3584 TTATCTATCC
*
3594 TTTTTAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTATTATCTTTAGTTAATATTGTTA
1 TTTTTAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTATTATATTTAGTTAATATTGTTA
*
3659 AATTTAAAATCTAAATATATGTTATAAAAATATCAAAACAATCAAATAATTTTTGTGTAAATGAA
66 AATTTAAAATCTAAATATATGTTATAAAAATATCAAAACAATCAAATAAATTTTGTGTAAATGAA
3724 ATTATTAAATAATATTGTAGGTGGAAACATGAAACACTATTAAAAATTAAAACATAAATTACATA
131 ATTATTAAATAATATTGTAGGTGGAAACATGAAACACTATTAAAAATTAAAACATAAATTACATA
3789 ACTTTCAAAAAAGGTATATATCAT
196 ACTTT-AAAAAAGGTATATATCAT
*
3813 TTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTTATTATTATATTTGGTTAAT
1 TTTT-TAAAAGTGTCCATACTTATTTCACTG-TG-AAA-ATA---TATTATTATATTTAGTTAAT
*
3878 ATTGTTAAA-TTAAATTCT-AATAATAT-TTAT-AAAATATCAAAACAATCAAATAAAATTTTGT
59 ATTGTTAAATTTAAAATCTAAAT-ATATGTTATAAAAATATCAAAACAATCAAAT-AAATTTTGT
* *
3939 GTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAATTGAAACA
122 GTAAATGAAATTATTAAA-TAATATTGTAGGTGG-AAACATGAAACACTATTAAAAATTAAAACA
4004 TAAATTACATAACTTTAAAA
185 TAAATTACATAACTTTAAAA
4024 GCAGTTTTAA
Statistics
Matches: 194, Mismatches: 6, Indels: 16
0.90 0.03 0.07
Matches are distributed among these distances:
219 4 0.02
220 26 0.13
221 2 0.01
222 3 0.02
223 24 0.12
224 32 0.16
225 31 0.16
226 72 0.37
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.39
Consensus pattern (218 bp):
TTTTTAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTATTATATTTAGTTAATATTGTTA
AATTTAAAATCTAAATATATGTTATAAAAATATCAAAACAATCAAATAAATTTTGTGTAAATGAA
ATTATTAAATAATATTGTAGGTGGAAACATGAAACACTATTAAAAATTAAAACATAAATTACATA
ACTTTAAAAAAGGTATATATCAT
Found at i:4112 original size:20 final size:19
Alignment explanation
Indices: 4089--4134 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
4079 CGATATACCA
4089 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
4109 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
*
4129 GATAAA
1 GGTAAA
4135 TTTAAAAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.57, C:0.11, G:0.15, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:8413 original size:19 final size:19
Alignment explanation
Indices: 8389--8437 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
8379 AATGTAGGGT
8389 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
8408 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
8427 TATTTTTGTAT
1 TAATTTTGTAT
8438 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:8969 original size:198 final size:198
Alignment explanation
Indices: 8556--10107 Score: 2853
Period size: 198 Copynumber: 7.9 Consensus size: 198
8546 CAATATGGCC
8556 AACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
8618 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
8683 AATATGTATAAATAATATGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGAATGAAT
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTT-TTTTCCAGAATGAAT
8748 GGAA
195 GGAA
*
8752 AAAAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
8817 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
8882 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
**
8947 GCC
196 GAA
8950 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
9015 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
9080 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGAATGAAT
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTT-TTTTCCAGAATGAAT
9145 GGAA
195 GGAA
9149 AACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
9212 CAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
9276 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
**
9341 GCC
196 GAA
9344 AACAGGGTGCACCCATAAAGTGTCGATCCATATA-AAAAAG-GTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
9407 CAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
9471 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
9536 GGAA
195 GGAA
9540 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
9605 CAAAAG--TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
* *
9668 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-CTTTTTCCAGAATGAATG
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
9732 G-A
196 GAA
9734 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
9799 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
* *
9864 AATATGTCTAAA-AATGTATCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
9928 GGAA
195 GGAA
*
9932 AACAGGGTGCACCCATAAAGTGTCGATCCATATATTAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
9997 CAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
10062 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
10108 CTAATTTAAA
Statistics
Matches: 1322, Mismatches: 18, Indels: 29
0.97 0.01 0.02
Matches are distributed among these distances:
194 72 0.05
195 229 0.17
196 262 0.20
197 170 0.13
198 385 0.29
199 204 0.15
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
GAA
Found at i:9705 original size:392 final size:396
Alignment explanation
Indices: 8550--10107 Score: 2890
Period size: 392 Copynumber: 4.0 Consensus size: 396
8540 AATTTACAAT
8550 ATGGCCAACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCC-AAATCAT
1 ATGGCCAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
8612 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
66 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
*
8677 TGAGAGAATATGTATAAATAATATGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGA
131 TGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGA
*
8742 ATGAATGGAAAAAAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAA
196 ATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAA
8807 TCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGT
261 TCATCGAACCCAAAAG-ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGT
8872 TTTATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCC
325 TTTATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCC
8937 AGAATGA
390 AGAATGA
8944 ATGGCCAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
1 ATGGCCAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
9009 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
66 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
9074 TGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGA
131 TGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGA
9139 ATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAA
196 ATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAA
9202 TCATCGAACCCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGT
261 TCATCGAACCCAAAAG-ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGT
9266 TTTATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCC
325 TTTATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCC
9331 AGAATGA
390 AGAATGA
9338 ATGGCCAACAGGGTGCACCCATAAAGTGTCGATCCATATA-AAAAAG-GTCGATCCCAAAATCAT
1 ATGGCCAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
9401 CGAACCCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTA
66 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
*
9465 TGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGA
131 TGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGA
9530 ATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAA
196 ATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAA
9595 TCATCGAACCCAAAAG-TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTT
261 TCATCGAACCCAAAAGATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTT
* *
9659 TTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-CTTTTTCCA
326 TTATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCA
9723 GAATGA
391 GAATGA
*
9729 ATGG-AAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
1 ATGGCCAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
9793 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
66 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
* * *
9858 TGAGAGAATATGTCTAAA-AATGTATCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGA
131 TGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGA
*
9922 ATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATTAAAAGTGTCGATCCCAAAA
196 ATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAA
*
9987 TCATCGAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAATTATACCGGT
261 TCATCGAACCCAAAAG-ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGT
*
10052 TTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
325 TTTATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
10108 CTAATTTAAA
Statistics
Matches: 1143, Mismatches: 10, Indels: 22
0.97 0.01 0.02
Matches are distributed among these distances:
390 34 0.03
391 177 0.15
392 303 0.27
393 98 0.09
394 280 0.24
395 57 0.05
396 20 0.02
397 174 0.15
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (396 bp):
ATGGCCAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
TGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGA
ATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAA
TCATCGAACCCAAAAGATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTT
TTATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCA
GAATGA
Found at i:11586 original size:12 final size:12
Alignment explanation
Indices: 11569--11621 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
11559 GGTCGCAGAA
*
11569 GATGAAGCTGAC
1 GATGAAGATGAC
11581 GATGAAGATGAC
1 GATGAAGATGAC
*
11593 GATGATGATGAC
1 GATGAAGATGAC
* *
11605 GATGATGATGAT
1 GATGAAGATGAC
11617 GATGA
1 GATGA
11622 TGAAGATGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.36, C:0.08, G:0.34, T:0.23
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:11601 original size:3 final size:3
Alignment explanation
Indices: 11581--11634 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
11571 TGAAGCTGAC
* * * *
11581 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
11629 GAT GAT
1 GAT GAT
11635 CCAAACAAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:11602 original size:18 final size:18
Alignment explanation
Indices: 11566--11634 Score: 72
Period size: 18 Copynumber: 4.0 Consensus size: 18
11556 AGCGGTCGCA
* *
11566 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
11584 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
*
11602 GACGAT---GATGATGAT
1 GAAGATGAAGATGATGAT
*
11617 GATGATGAAGATGATGAT
1 GAAGATGAAGATGATGAT
11635 CCAAACAAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
15 14 0.33
18 29 0.67
ACGTcount: A:0.38, C:0.06, G:0.33, T:0.23
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:11622 original size:12 final size:12
Alignment explanation
Indices: 11577--11634 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
11567 AAGATGAAGC
*
11577 TGACGATGAAGA
1 TGACGATGATGA
11589 TGACGATGATGA
1 TGACGATGATGA
11601 TGACGATGATGA
1 TGACGATGATGA
*
11613 TGATGATGATGA
1 TGACGATGATGA
* *
11625 AGATGATGAT
1 TGACGATGAT
11635 CCAAACAAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.36, C:0.05, G:0.33, T:0.26
Consensus pattern (12 bp):
TGACGATGATGA
Found at i:13360 original size:183 final size:182
Alignment explanation
Indices: 13052--13755 Score: 1234
Period size: 183 Copynumber: 3.9 Consensus size: 182
13042 CTTTCAACAT
** * * * *
13052 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGTGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
13117 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AA
*
13182 AATGTGTCGATACGATTTAAAAAAGTGTCGATATTTACACATCGGAACCCATA
130 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
13235 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
13300 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AA
13365 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
130 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* *
13418 ATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATACGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
13483 GGTCTAC-A-CTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
13545 ATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGA
131 ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
*
13597 TTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
* *
13662 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
13727 ATGTGTCGATACCATTTAAAAAAGTGTCG
131 ATGTGTCGATACGATTTAAAAAAGTGTCG
13756 GTAATTTTAA
Statistics
Matches: 500, Mismatches: 18, Indels: 7
0.95 0.03 0.01
Matches are distributed among these distances:
179 122 0.24
180 40 0.08
181 24 0.05
182 68 0.14
183 246 0.49
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34
Consensus pattern (182 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:13722 original size:362 final size:365
Alignment explanation
Indices: 13077--13755 Score: 1240
Period size: 362 Copynumber: 1.9 Consensus size: 365
13067 GTAAATTTGC
* *
13077 AATATAACCGGTATAAATATACCGGTTTTATGCGTGAATAGGTCTACAACCTATATCGACACTTT
1 AATATAACCGGTATAAATATACCGGTTTTATACGCGAATAGGTCTACAACCTATATCGACACTTT
13142 TTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAG
66 TTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAG
* * *
13207 TGTCGATATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGT
131 TATCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGT
*
13272 ATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGT
196 ATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGT
* *
13337 CGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTA
261 CGGTACTTTATGTCCAGATTGGAAG-AAAATGTGTCGATACCATTTAAAAAAGTGTCGACATTTA
13402 CACATCGGAACCCATAATTATAATGTAATAGATAATTTTAT
325 CACATCGGAACCCATAATTATAATGTAATAGATAATTTTAT
13443 AATATAACCGGTATAAATATACCGGTTTTATACGCGAATAGGTCTAC-A-CTATATCGACAC-TT
1 AATATAACCGGTATAAATATACCGGTTTTATACGCGAATAGGTCTACAACCTATATCGACACTTT
13505 TTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AAAATGTGTCGATACGATTTAAAAAAG
66 TTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAG
*
13569 TATCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGT
131 TATCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGT
13634 ATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGT
196 ATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGT
13699 CGGTACTTTATGTCCAGATTGGAAGAAAATGTGTCGATACCATTTAAAAAAGTGTCG
261 CGGTACTTTATGTCCAGATTGGAAGAAAATGTGTCGATACCATTTAAAAAAGTGTCG
13756 GTAATTTTAA
Statistics
Matches: 304, Mismatches: 9, Indels: 5
0.96 0.03 0.02
Matches are distributed among these distances:
361 31 0.10
362 176 0.58
363 39 0.13
364 12 0.04
365 1 0.00
366 45 0.15
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (365 bp):
AATATAACCGGTATAAATATACCGGTTTTATACGCGAATAGGTCTACAACCTATATCGACACTTT
TTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAG
TATCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGT
ATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGT
CGGTACTTTATGTCCAGATTGGAAGAAAATGTGTCGATACCATTTAAAAAAGTGTCGACATTTAC
ACATCGGAACCCATAATTATAATGTAATAGATAATTTTAT
Found at i:15751 original size:13 final size:13
Alignment explanation
Indices: 15733--15757 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15723 TGTAATTTGA
15733 AATAAATAAAAAG
1 AATAAATAAAAAG
15746 AATAAATAAAAA
1 AATAAATAAAAA
15758 ACTATATACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AATAAATAAAAAG
Found at i:16368 original size:26 final size:26
Alignment explanation
Indices: 16305--16371 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
16295 GGCCACCTAA
* *
16305 ACGACGCCGTTCTGGAATTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
16331 ACGACGCCGTTTTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
16357 ACGACGCCGTTTTGG
1 ACGACGCCGTTTTGG
16372 CGTACGAGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.21
Consensus pattern (26 bp):
ACGACGCCGTTTTGGAACTAAACGGG
Found at i:18488 original size:55 final size:55
Alignment explanation
Indices: 17850--18493 Score: 940
Period size: 55 Copynumber: 11.7 Consensus size: 55
17840 TGGTTTTATC
* * **
17850 CCCTATTGCTTCAGGGAGTA-AA-ACTCGAA-AATCTTCGTCAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* * * * * * *
17902 CCCCATTT-TTCCAGAGAGTACAAGACTCAAACGAT-TCTCGATAATCATGTCTGCT
1 CCCTATTTCTT-CAGAGAGTATAAGACTCGAACAATCT-TCAACAATCGTGTCTGCT
* * * *
17957 CCCTATTTTTTCAGAGAGTATGAGACTCGAACAAT-TCTCAATAATCGTGCCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCT-TCAACAATCGTGTCTGCT
* *
18012 CCCTATTTTCTTCAGAGAGAATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
1 CCCTA-TTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* * *
18068 CCCTATCTCTTCAGAGAGTATGAGACTCGAACAATCTTCGACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
18123 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* * *
18178 CCCTATCTCTTCAGAGAGTATGAGACTCGAACAATCTTCGACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
18233 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
18288 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
18343 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* *
18398 CCCTATTTCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAATCGCGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
18453 CCCTATTTCTTCAGAGAGTATAAGACTCGATCAATCTTCAA
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
18494 TTATCGTTGG
Statistics
Matches: 540, Mismatches: 44, Indels: 13
0.90 0.07 0.02
Matches are distributed among these distances:
51 2 0.00
52 14 0.03
53 2 0.00
54 7 0.01
55 463 0.86
56 51 0.09
57 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (55 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
Found at i:19509 original size:8 final size:8
Alignment explanation
Indices: 19496--19548 Score: 55
Period size: 8 Copynumber: 7.4 Consensus size: 8
19486 TGAACCCTCA
19496 TTTTTCAT
1 TTTTTCAT
19504 TTTTTCA-
1 TTTTTCAT
19511 ---TTCAT
1 TTTTTCAT
19516 TTTTT-AT
1 TTTTTCAT
*
19523 TTTTTTA-
1 TTTTTCAT
19530 TTTTTCAT
1 TTTTTCAT
19538 TTTTTCAT
1 TTTTTCAT
19546 TTT
1 TTT
19549 CACTCATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
4 4 0.11
7 13 0.34
8 21 0.55
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCAT
Found at i:19534 original size:15 final size:15
Alignment explanation
Indices: 19511--19548 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
19501 CATTTTTTCA
*
19511 TTCATTTTTTATTTT
1 TTCATTTTTCATTTT
*
19526 TTTATTTTTCATTTT
1 TTCATTTTTCATTTT
19541 TTCATTTT
1 TTCATTTT
19549 CACTCATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (15 bp):
TTCATTTTTCATTTT
Found at i:19556 original size:40 final size:41
Alignment explanation
Indices: 19496--19575 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 41
19486 TGAACCCTCA
*
19496 TTTTTCATTTTTTCATTCATTTTTTATT-TTTTTATTTTTCAT
1 TTTTTCA-TTTTTCACTCATTTTTTATTCTTTTT-TTTTTCAT
*
19538 TTTTTCA-TTTTCACTCATTTTTTCTTCTTTTTTTTTTC
1 TTTTTCATTTTTCACTCATTTTTTATTCTTTTTTTTTTC
19576 TTCAAGCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 23 0.66
41 5 0.14
42 7 0.20
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (41 bp):
TTTTTCATTTTTCACTCATTTTTTATTCTTTTTTTTTTCAT
Found at i:31224 original size:13 final size:13
Alignment explanation
Indices: 31206--31230 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31196 TGTAATTTGA
31206 AATAAATAAAAAG
1 AATAAATAAAAAG
31219 AATAAATAAAAA
1 AATAAATAAAAA
31231 ACTATATACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AATAAATAAAAAG
Found at i:31836 original size:26 final size:26
Alignment explanation
Indices: 31773--31839 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
31763 GGCCACCTAA
* *
31773 ACGACGCCGTTCTGGAATTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
31799 ACGACGCCGTTTTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
31825 ACGACGCCGTTTTGG
1 ACGACGCCGTTTTGG
31840 CGTACGAGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.21
Consensus pattern (26 bp):
ACGACGCCGTTTTGGAACTAAACGGG
Found at i:34567 original size:25 final size:25
Alignment explanation
Indices: 34533--34596 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
34523 TTATCATTAA
34533 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
34558 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
34583 A-TTAGGTATATACA
1 ATTTAGGTATGTACA
34597 TCTTTTGAGT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
24 9 0.29
25 22 0.71
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:34963 original size:23 final size:23
Alignment explanation
Indices: 34932--34995 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
34922 ATAGGTAAAC
*
34932 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
34955 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
34978 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
34996 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:35002 original size:23 final size:23
Alignment explanation
Indices: 34932--35004 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
34922 ATAGGTAAAC
* **
34932 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
34955 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
34978 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
35001 ATAT
1 ATAT
35005 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:35302 original size:25 final size:24
Alignment explanation
Indices: 35269--35318 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
35259 ACAACAAATC
*
35269 AATTAACATTGTTGTGGGTACATT
1 AATTAACATTGTTATGGGTACATT
35293 AATTGAACATTGTTATGGGTACATT
1 AATT-AACATTGTTATGGGTACATT
35318 A
1 A
35319 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (24 bp):
AATTAACATTGTTATGGGTACATT
Found at i:35726 original size:18 final size:18
Alignment explanation
Indices: 35705--35741 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35695 GTAATTGGAG
35705 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
35723 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
35741 T
1 T
35742 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:35749 original size:24 final size:24
Alignment explanation
Indices: 35697--35743 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
35687 TTTCATATGT
* *
35697 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
35721 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
35744 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:36040 original size:39 final size:39
Alignment explanation
Indices: 35997--36083 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
35987 TCCGATGCTC
*
35997 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
36036 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
36075 ATCAAAATC
1 ATCAAAATC
36084 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:36445 original size:22 final size:23
Alignment explanation
Indices: 36415--36457 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
36405 CATAAATTAC
36415 ATAACTTTTAAAAAAAAGTATCG
1 ATAACTTTTAAAAAAAAGTATCG
* *
36438 ATAA-TTTTTATAAAAAGTAT
1 ATAACTTTTAAAAAAAAGTAT
36458 GGACACTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (23 bp):
ATAACTTTTAAAAAAAAGTATCG
Found at i:36515 original size:23 final size:23
Alignment explanation
Indices: 36484--36556 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
36474 ATAGGTAAAC
* *
36484 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGATT
* * *
36507 ATATAATGTAATAAGTATCGTTT
1 ATATAATGTAATAGGTAGCGATT
*
36530 ATATAATGTAATAGGTAGTGATT
1 ATATAATGTAATAGGTAGCGATT
36553 ATAT
1 ATAT
36557 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGATT
Found at i:37235 original size:330 final size:326
Alignment explanation
Indices: 36599--37264 Score: 1154
Period size: 330 Copynumber: 2.0 Consensus size: 326
36589 CATACTTTTT
36599 TCACTGTGGAAAAAATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
1 TCACTGTGGAAAAAATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
*
36664 TATAGGCGTCTAATGATTTATTTTTTTCGTTACGATATATATTATTATTAAATTAAAAATTCTAA
66 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAA
*
36729 ATATTATTTTAAAATATCAAAACAATCAAATAATTTTTTGTGCAATGAAATTATTAAATTAATAT
131 ATAATATTTTAAAATATCAAAACAATCAAATAATTTTTTGTGCAATGAAATTATTAAATTAATAT
36794 TGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAA
196 TGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAA
*
36859 GTATCGATCCTTTTTATAAAAAGTATGACACTTTCAATATAATATAATGTAATAGGTAAATTTGC
261 GTATCGATCATTTTTATAAAAAGTATGACACTTTC---A-AATATAATGTAATAGGTAAATTTGC
36924 AATGC
322 AATGC
*
36929 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
1 TCACTGTGGAAAAAATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
36994 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAA
66 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAA
37059 ATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
131 ATAATA-TTT-TAAAATATCAAAACAATCAAATAATTTTTTGTGC-AATGAAATTATTAAATTAA
37124 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAA
193 TATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTTTAAA
*
37189 AGAAA-TATCGATCATTTTTATAAAAAGTATGGACCCTTTCAATATAATATAATGTAATAGGTAA
257 A-AAAGTATCGATCATTTTTATAAAAAGTAT-GACACTTTC---A-AATATAATGTAATAGGTAA
37253 ATTTGCAATGC
316 ATTTGCAATGC
37264 T
1 T
37265 ATCGGTATAA
Statistics
Matches: 325, Mismatches: 5, Indels: 7
0.96 0.01 0.02
Matches are distributed among these distances:
330 133 0.41
331 3 0.01
332 34 0.10
333 49 0.15
334 59 0.18
335 47 0.14
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (326 bp):
TCACTGTGGAAAAAATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAA
ATAATATTTTAAAATATCAAAACAATCAAATAATTTTTTGTGCAATGAAATTATTAAATTAATAT
TGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAA
GTATCGATCATTTTTATAAAAAGTATGACACTTTCAAATATAATGTAATAGGTAAATTTGCAATG
C
Found at i:39327 original size:21 final size:23
Alignment explanation
Indices: 39303--39350 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
39293 TTATTAAAAA
*
39303 ATTAATAATTTTTTAAT-TTA-T
1 ATTAATAATTATTTAATATTATT
*
39324 ATTAATTATTATTTAATATTATT
1 ATTAATAATTATTTAATATTATT
39347 ATTA
1 ATTA
39351 TGTAACTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 15 0.65
22 3 0.13
23 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTAATAATTATTTAATATTATT
Found at i:39347 original size:16 final size:16
Alignment explanation
Indices: 39318--39351 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
39308 TAATTTTTTA
39318 ATTTATATTAATTATT
1 ATTTATATTAATTATT
39334 ATTTAATATT-ATTATT
1 ATTT-ATATTAATTATT
39350 AT
1 AT
39352 GTAACTTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTATATTAATTATT
Found at i:43661 original size:45 final size:45
Alignment explanation
Indices: 43597--43692 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 45
43587 CCTTTGGAAA
* *
43597 TATTACATGAATGGCATTTCTTTCTTGTATTTCAAACACTTCGTG
1 TATTACATGAATGGCATTTCTTTCTTATATTTCAAACACTCCGTG
* * *
43642 TATTACTTGAATGGTATTTCTTTCTTATATTTCAAATACTCCGTG
1 TATTACATGAATGGCATTTCTTTCTTATATTTCAAACACTCCGTG
43687 TATTAC
1 TATTAC
43693 CTAACAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (45 bp):
TATTACATGAATGGCATTTCTTTCTTATATTTCAAACACTCCGTG
Found at i:50513 original size:30 final size:28
Alignment explanation
Indices: 50469--50525 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
50459 TTGTTTTAAG
*
50469 TTTTTTTTAGTTCAAGTCGAGATTAAAT
1 TTTTTTTTAGTTCAAATCGAGATTAAAT
*
50497 TTTTATTTTGAGTTCAAATCGAGCTTAAA
1 TTTT-TTTT-AGTTCAAATCGAGATTAAA
50526 AATTTTAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.16
29 4 0.16
30 17 0.68
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (28 bp):
TTTTTTTTAGTTCAAATCGAGATTAAAT
Found at i:50618 original size:20 final size:20
Alignment explanation
Indices: 50593--50661 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
50583 TGAGCTCAAT
50593 TATCGCAACGCGAAAATGGC
1 TATCGCAACGCGAAAATGGC
** **
50613 TATCGCAATTCG-AAATGAAA
1 TATCGCAACGCGAAAATG-GC
*
50633 AATCGCAACGCGAAAATGGC
1 TATCGCAACGCGAAAATGGC
*
50653 TATCCCAAC
1 TATCGCAAC
50662 TAGAAAATCG
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (20 bp):
TATCGCAACGCGAAAATGGC
Found at i:50774 original size:19 final size:19
Alignment explanation
Indices: 50707--50773 Score: 116
Period size: 19 Copynumber: 3.5 Consensus size: 19
50697 GATTTTCTTG
50707 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTAATTTCGCA
50726 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTAATTTCGCA
*
50745 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTAATTTCGCA
*
50764 TTGCAATTTT
1 TTGCGATTTT
50774 CTCGTTGCGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.19, C:0.16, G:0.15, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTAATTTCGCA
Found at i:50782 original size:33 final size:33
Alignment explanation
Indices: 50688--50784 Score: 104
Period size: 38 Copynumber: 2.8 Consensus size: 33
50678 GAAATGAAAA
* *
50688 TCGCATTGCGATTTTCTTGTTGCGATTTTAATT
1 TCGCATTGCAATTTTCTCGTTGCGATTTTAATT
* * *
50721 TCGCATTGCGATTTTAATTTCGCATTGCGATTTTCATT
1 TCGCATTGC-AATTT--TCTCG--TTGCGATTTTAATT
50759 TCGCATTGCAATTTTCTCGTTGCGAT
1 TCGCATTGCAATTTTCTCGTTGCGAT
50785 AGTCAGTTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
33 16 0.31
34 3 0.06
35 4 0.08
36 3 0.06
37 4 0.08
38 22 0.42
ACGTcount: A:0.16, C:0.19, G:0.18, T:0.47
Consensus pattern (33 bp):
TCGCATTGCAATTTTCTCGTTGCGATTTTAATT
Found at i:52834 original size:20 final size:20
Alignment explanation
Indices: 52811--52864 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
52801 GAAACTTAAA
52811 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
52831 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
52851 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
52865 TGCAAATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:52887 original size:14 final size:14
Alignment explanation
Indices: 52868--52957 Score: 72
Period size: 14 Copynumber: 5.8 Consensus size: 14
52858 TGCGAAATGC
52868 AAATCGCAACGACA
1 AAATCGCAACGACA
* *
52882 AAATCGTAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
52901 AAATCGCAACGACA
1 AAATCGCAACGACA
*
52915 AAATCGCAATGCGAAA
1 AAATCGCAA--CGACA
52931 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
52947 AAATCGCAACG
1 AAATCGCAACG
52958 CGAAACACAA
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 29 0.48
15 1 0.02
16 10 0.16
17 2 0.03
18 10 0.16
19 9 0.15
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:52898 original size:33 final size:33
Alignment explanation
Indices: 52851--52973 Score: 194
Period size: 33 Copynumber: 3.8 Consensus size: 33
52841 GGAAATGGCT
52851 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
* *
52884 ATCGTAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
52917 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
* **
52949 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAATGCGAAATGCAAATCGCA
52974 TTGCGACTTT
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
32 29 0.35
33 54 0.65
ACGTcount: A:0.46, C:0.24, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGCAAATCGCAACGACAAA
Found at i:52970 original size:65 final size:66
Alignment explanation
Indices: 52851--52973 Score: 196
Period size: 65 Copynumber: 1.9 Consensus size: 66
52841 GGAAATGGCT
* * *
52851 ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGTAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
52916 A
66 A
52917 ATCGCAATGCGAAATG-AAATCGCAACGACAAAATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAACGCGAAATCA-AAATCGCA
52974 TTGCGACTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
64 1 0.02
65 36 0.68
66 16 0.30
ACGTcount: A:0.46, C:0.24, G:0.18, T:0.12
Consensus pattern (66 bp):
ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:52991 original size:19 final size:18
Alignment explanation
Indices: 52969--53029 Score: 67
Period size: 19 Copynumber: 3.5 Consensus size: 18
52959 GAAACACAAA
52969 TCGCATTGCGACTTTCATT
1 TCGCATTGCGA-TTTCATT
*
52988 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
53004 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
53021 TCGCATTGC
1 TCGCATTGC
53030 AATAGCCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 6 0.17
15 3 0.09
16 4 0.11
17 4 0.11
18 3 0.09
19 15 0.43
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:53039 original size:19 final size:20
Alignment explanation
Indices: 53017--53060 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
53007 TTGCGATTTT
53017 CATTT-CGCATTGCAATAGC
1 CATTTCCGCATTGCAATAGC
* * *
53036 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCAATAGC
53056 CATTT
1 CATTT
53061 TCATGTTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCAATAGC
Found at i:53579 original size:18 final size:18
Alignment explanation
Indices: 53553--53597 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
53543 GTCGATCAGA
*
53553 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
53571 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
53589 TGATGGCTC
1 TGATGGCTC
53598 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:54942 original size:20 final size:20
Alignment explanation
Indices: 54917--54990 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
54907 AATAGTTTCT
*
54917 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
54937 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
54957 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
54977 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
54991 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:55480 original size:20 final size:20
Alignment explanation
Indices: 55454--55565 Score: 84
Period size: 20 Copynumber: 5.5 Consensus size: 20
55444 GATTATGTAT
55454 TATCGCGTTGCGAAAGTCAGA
1 TATCGCGTTGCGAAAGTCA-A
55475 -ATCGCGTTGCGAAAGTCAA
1 TATCGCGTTGCGAAAGTCAA
* ** *
55494 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAA
* * *
55515 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAA
* * *
55535 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAA
*
55555 TATCGCATTGC
1 TATCGCGTTGC
55566 AATTTTCCCA
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
19 4 0.05
20 61 0.77
21 12 0.15
22 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAA
Found at i:55571 original size:61 final size:61
Alignment explanation
Indices: 55434--55571 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
55424 CGCTTTGAAA
* * *
55434 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAAT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAAT
* * * * * *
55495 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAAT
*
55556 ATCGCATTGCAATTTT
1 ATCGCATTGCGATTTT
55572 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAAT
Found at i:55587 original size:61 final size:61
Alignment explanation
Indices: 55454--55589 Score: 148
Period size: 61 Copynumber: 2.2 Consensus size: 61
55444 GATTATGTAT
* * * * * ** *
55454 TATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAATATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAATATCGCATTGCAATTTTCCAA
* * * *
55515 TATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCAATTTTCCCAA
1 TATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAATATCGCATTGCAATTTT-CCAA
55577 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
55590 TTACTTATTC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (61 bp):
TATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAATATCGCATTGCAATTTTCCAA
Found at i:62342 original size:26 final size:26
Alignment explanation
Indices: 62320--62370 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
62310 AGAGGTAATT
62320 GAAGTGTAAAACTAGATTAGGTAACA
1 GAAGTGTAAAACTAGATTAGGTAACA
*
62346 GAATTGTAAAACTAGATTAGGTAAC
1 GAAGTGTAAAACTAGATTAGGTAAC
62371 TTTGTTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.25
Consensus pattern (26 bp):
GAAGTGTAAAACTAGATTAGGTAACA
Found at i:70756 original size:12 final size:13
Alignment explanation
Indices: 70707--70755 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
70697 TTTGGTAATC
70707 CCCGCCCCGATTA
1 CCCGCCCCGATTA
70720 CCCGCCCCGATTA
1 CCCGCCCCGATTA
*
70733 CCGGCCCCGA-TA
1 CCCGCCCCGATTA
*
70745 CCCGACCCGAT
1 CCCGCCCCGAT
70756 AAATATTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
12 10 0.31
13 22 0.69
ACGTcount: A:0.16, C:0.53, G:0.18, T:0.12
Consensus pattern (13 bp):
CCCGCCCCGATTA
Found at i:70882 original size:24 final size:24
Alignment explanation
Indices: 70855--70909 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
70845 ATATATATAT
* * *
70855 ATACCCGACCCGATTCTCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
70879 ATACCCGACCCAATACCCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
70903 ATACCCG
1 ATACCCG
70910 TTTAAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.47, G:0.15, T:0.13
Consensus pattern (24 bp):
ATACCCGACCCAATACCCGGCCCA
Found at i:70892 original size:12 final size:12
Alignment explanation
Indices: 70855--70909 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
70845 ATATATATAT
*
70855 ATACCCGACCCG
1 ATACCCGACCCA
* * *
70867 ATTCTCGGCCCA
1 ATACCCGACCCA
70879 ATACCCGACCCA
1 ATACCCGACCCA
*
70891 ATACCCGGCCCA
1 ATACCCGACCCA
70903 ATACCCG
1 ATACCCG
70910 TTTAAATAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.25, C:0.47, G:0.15, T:0.13
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:78451 original size:15 final size:15
Alignment explanation
Indices: 78425--78461 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
78415 TAATTTATAA
78425 TTATACATTTAATATT
1 TTATA-ATTTAATATT
*
78441 TTATAATTTAATGTT
1 TTATAATTTAATATT
78456 TTATAA
1 TTATAA
78462 AGTAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (15 bp):
TTATAATTTAATATT
Found at i:78910 original size:22 final size:22
Alignment explanation
Indices: 78882--78933 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
78872 TGAGTACCAG
* *
78882 GAATGTCATGGGTATAAACGTT
1 GAATGTCATGAGTATAAACGAT
78904 GAATGTCATGAGTATAAACGAT
1 GAATGTCATGAGTATAAACGAT
78926 GAATGTCA
1 GAATGTCA
78934 AATGATTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.29
Consensus pattern (22 bp):
GAATGTCATGAGTATAAACGAT
Found at i:82452 original size:16 final size:15
Alignment explanation
Indices: 82426--82455 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
82416 ACAATTACAC
82426 ATTTGATATTTTATT
1 ATTTGATATTTTATT
82441 ATTTGTATATTTTAT
1 ATTTG-ATATTTTAT
82456 CAATTTGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
ATTTGATATTTTATT
Found at i:90731 original size:19 final size:19
Alignment explanation
Indices: 90696--90741 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
90686 TTATAACTTT
90696 TATAATATTTGAATTTAAGAA
1 TATAA-ATTTGAATTTAA-AA
90717 TATAAATTT-AATTTAAAA
1 TATAAATTTGAATTTAAAA
90735 T-TAAATT
1 TATAAATT
90742 ATAAATCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.24
18 3 0.12
19 7 0.28
20 4 0.16
21 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (19 bp):
TATAAATTTGAATTTAAAA
Found at i:93396 original size:16 final size:16
Alignment explanation
Indices: 93373--93459 Score: 120
Period size: 16 Copynumber: 5.4 Consensus size: 16
93363 GGTATTACCC
*
93373 GACCTGTTTTCAACCT
1 GACCTGTTTTTAACCT
*
93389 GGCCTGTTTTTAACCT
1 GACCTGTTTTTAACCT
* *
93405 TACATGTTTTTAACCT
1 GACCTGTTTTTAACCT
* *
93421 GACATGTTTTCAACCT
1 GACCTGTTTTTAACCT
93437 GACCTGTTTTTAACCT
1 GACCTGTTTTTAACCT
93453 GACCTGT
1 GACCTGT
93460 AAATGATCCG
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 62 1.00
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (16 bp):
GACCTGTTTTTAACCT
Found at i:93725 original size:12 final size:14
Alignment explanation
Indices: 93690--93727 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
93680 TGCAAAGGAA
* *
93690 AATTAATATAGTTT
1 AATTTATATAGATT
93704 AATTTATATAGATT
1 AATTTATATAGATT
93718 AATTTATATA
1 AATTTATATA
93728 AAAAATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (14 bp):
AATTTATATAGATT
Found at i:96981 original size:24 final size:24
Alignment explanation
Indices: 96947--97003 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
96937 TTTACCGAAA
*
96947 ATAAAAAAAGTACAATATCA-AAGG
1 ATAAAACAAGTACAATATCAGAA-G
*
96971 ATAAAACAAGTACAATTTCAGAAG
1 ATAAAACAAGTACAATATCAGAAG
*
96995 ATAATACAA
1 ATAAAACAA
97004 TAAGGAAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.19
Consensus pattern (24 bp):
ATAAAACAAGTACAATATCAGAAG
Found at i:98367 original size:62 final size:61
Alignment explanation
Indices: 98255--98403 Score: 165
Period size: 62 Copynumber: 2.4 Consensus size: 61
98245 GTTATCTATT
* *
98255 AATTTTAAATTTATTTAATTTAGTCTAAATTTAATGATTTAATATATTAATTTAAGCTTCA
1 AATTTTAAATTTATTTAATTTAATCCAAATTTAATGATTTAATATATTAATTTAAGCTTCA
* * * * *
98316 AATTTTAATTTTTTTTCAATTTAATCCAATTTTAATG-TTATAATTTTTTAATTTAAGCTTCA
1 AATTTTAAATTTATTT-AATTTAATCCAAATTTAATGATT-TAATATATTAATTTAAGCTTCA
* * * * *
98378 TATTTAAAATTTGTTCAATTTGATCC
1 AATTTTAAATTTATTTAATTTAATCC
98404 TTATATATTT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
61 25 0.34
62 48 0.66
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (61 bp):
AATTTTAAATTTATTTAATTTAATCCAAATTTAATGATTTAATATATTAATTTAAGCTTCA
Found at i:98491 original size:33 final size:33
Alignment explanation
Indices: 98450--98568 Score: 137
Period size: 33 Copynumber: 3.8 Consensus size: 33
98440 TTTATATTAA
98450 TATATTAATATATAGTTTATATATACTAATGAAC
1 TATA-TAATATATAGTTTATATATACTAATGAAC
* *
98484 TATTTAATATATAG-TT-TGTATA-T-AT---C
1 TATATAATATATAGTTTATATATACTAATGAAC
* *
98510 -ATATACTATATAGGTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
98542 TATATAATATATAGTTTATATATACTA
1 TATATAATATATAGTTTATATATACTA
98569 TATAGTTTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
25 11 0.16
26 3 0.04
27 5 0.07
28 1 0.01
29 4 0.06
30 1 0.01
31 5 0.07
32 3 0.04
33 34 0.49
34 3 0.04
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (33 bp):
TATATAATATATAGTTTATATATACTAATGAAC
Found at i:98531 original size:18 final size:18
Alignment explanation
Indices: 98510--98586 Score: 81
Period size: 18 Copynumber: 4.4 Consensus size: 18
98500 TGTATATATC
98510 ATATACTATATAGGTTAT
1 ATATACTATATAGGTTAT
*
98528 ATATACTA-AT--G-AACT
1 ATATACTATATAGGTTA-T
* *
98543 ATATAATATATAGTTTAT
1 ATATACTATATAGGTTAT
*
98561 ATATACTATATAGTTTAT
1 ATATACTATATAGGTTAT
98579 ATATACTA
1 ATATACTA
98587 ATGAACTGTA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
14 1 0.02
15 9 0.18
16 2 0.04
17 2 0.04
18 34 0.69
19 1 0.02
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.44
Consensus pattern (18 bp):
ATATACTATATAGGTTAT
Found at i:98531 original size:58 final size:56
Alignment explanation
Indices: 98429--98631 Score: 236
Period size: 51 Copynumber: 3.6 Consensus size: 56
98419 TTCTTTCAAT
* * *
98429 TAATATATATTTTTATATTAATATATTAATATATAGTTTATATATACTAATGAACTATT
1 TAATATATATTTGTATA-T-ATATA-TACTATATAGTTTATATATACTAATGAACTATA
*
98488 TAATATATAGTTTGTATATATCATATACTATATAGGTTATATATACTAATGAACTATA
1 TAATATATA-TTTGTATATAT-ATATACTATATAGTTTATATATACTAATGAACTATA
*
98546 TAATATATA---GT-T-TATATATACTATATAGTTTATATATACTAATGAACTGTA
1 TAATATATATTTGTATATATATATACTATATAGTTTATATATACTAATGAACTATA
* *
98597 TAATATATAGTTTATATATACTAATAAACTATATA
1 TAATATATA-TTTGTATATA-T-ATATACTATATA
98632 ATGTATAGTT
Statistics
Matches: 126, Mismatches: 8, Indels: 20
0.82 0.05 0.13
Matches are distributed among these distances:
51 43 0.34
52 3 0.02
53 1 0.01
54 2 0.02
55 1 0.01
56 1 0.01
57 2 0.02
58 42 0.33
59 24 0.19
60 7 0.06
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (56 bp):
TAATATATATTTGTATATATATATACTATATAGTTTATATATACTAATGAACTATA
Found at i:98609 original size:33 final size:33
Alignment explanation
Indices: 98560--98643 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
98550 ATATAGTTTA
* *
98560 TATATACTATATAGTTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATAAAC
*
98593 TGTATAATATATAGTTTATATATACTAATAAAC
1 TATATAATATATAGTTTATATATACTAATAAAC
*
98626 TATATAATGTATAGTTTA
1 TATATAATATATAGTTTA
98644 GGGTTTAGGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (33 bp):
TATATAATATATAGTTTATATATACTAATAAAC
Found at i:98697 original size:2 final size:2
Alignment explanation
Indices: 98680--98750 Score: 54
Period size: 2 Copynumber: 33.0 Consensus size: 2
98670 ATGTGTAAAT
*
98680 TA TA CTA TA TA GTA TA TA TA GTT TA TA TA TA TA -A TA TA TA GTA
1 TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
* *
98723 TA TA AA TA TA AA CTA TA GTA TA TA TA TA
1 TA TA TA TA TA TA -TA TA -TA TA TA TA TA
98751 GGTCATATGT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
1 1 0.02
2 45 0.80
3 10 0.18
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.44
Consensus pattern (2 bp):
TA
Found at i:98699 original size:9 final size:9
Alignment explanation
Indices: 98685--98748 Score: 51
Period size: 9 Copynumber: 6.7 Consensus size: 9
98675 TAAATTATAC
98685 TATATAGTA
1 TATATAGTA
98694 TATATAGTTTA
1 TATATAG--TA
98705 TATATA-TAA
1 TATATAGT-A
98714 TATATAGTA
1 TATATAGTA
98723 TATAAATA-TA
1 TAT--ATAGTA
*
98733 AACTATAGTA
1 TA-TATAGTA
98743 TATATA
1 TATATA
98749 TAGGTCATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
8 1 0.02
9 25 0.56
10 7 0.16
11 12 0.27
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (9 bp):
TATATAGTA
Found at i:98710 original size:20 final size:19
Alignment explanation
Indices: 98680--98750 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 19
98670 ATGTGTAAAT
98680 TATACTATATAGTATATATAG
1 TATA-TATATA-TATATATAG
*
98701 TTTATATATATAATATATAG
1 TATATATATAT-ATATATAG
* *
98721 TATATAAATATAAACTATAG
1 TATATATATATATA-TATAG
98741 TATATATATA
1 TATATATATA
98751 GGTCATATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.44
Consensus pattern (19 bp):
TATATATATATATATATAG
Found at i:98739 original size:29 final size:29
Alignment explanation
Indices: 98675--98751 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
98665 AGTTCATGTG
* * *
98675 TAAAT-TATACTATATAGTATATATAGTT
1 TAAATATATAATATATAGTATATATAATA
*
98703 TATATATATAATATATAGTATATA-AATA
1 TAAATATATAATATATAGTATATATAATA
98731 TAAACTATAGTATATATATAG
1 TAAA-TATA-TA-ATATATAG
98752 GTCATATGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 9 0.22
29 21 0.52
30 2 0.05
31 8 0.20
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (29 bp):
TAAATATATAATATATAGTATATATAATA
Found at i:98763 original size:29 final size:29
Alignment explanation
Indices: 98731--98819 Score: 95
Period size: 29 Copynumber: 3.3 Consensus size: 29
98721 TATATAAATA
98731 TAAACTATAGTATATATATAGGTCATATG
1 TAAACTATAGTATATATATAGGTCATATG
98760 TAAACTATA-TAGTATATA-A----ATA--
1 TAAACTATAGTA-TATATATAGGTCATATG
* *
98782 TCAACTCTAGTATATATATAGGTCATATG
1 TAAACTATAGTATATATATAGGTCATATG
98811 TAAACTATA
1 TAAACTATA
98820 TAGTTTATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 18
0.68 0.06 0.26
Matches are distributed among these distances:
22 13 0.28
23 3 0.06
24 3 0.06
27 3 0.06
28 3 0.06
29 22 0.47
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (29 bp):
TAAACTATAGTATATATATAGGTCATATG
Found at i:98769 original size:51 final size:51
Alignment explanation
Indices: 98675--98828 Score: 206
Period size: 51 Copynumber: 3.0 Consensus size: 51
98665 AGTTCATGTG
* * * *
98675 TAAAT-TATACTATA-TAGTATATATAGTTTATATATATAA-TATATAGTATA
1 TAAATATAAACTATAGTA-TATATATAGGTCATATGTA-AACTATATAGTATA
98725 TAAATATAAACTATAGTATATATATAGGTCATATGTAAACTATATAGTATA
1 TAAATATAAACTATAGTATATATATAGGTCATATGTAAACTATATAGTATA
* * *
98776 TAAATATCAACTCTAGTATATATATAGGTCATATGTAAACTATATAGTTTA
1 TAAATATAAACTATAGTATATATATAGGTCATATGTAAACTATATAGTATA
98827 TA
1 TA
98829 TATGTAGTAT
Statistics
Matches: 94, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
50 7 0.07
51 85 0.90
52 2 0.02
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (51 bp):
TAAATATAAACTATAGTATATATATAGGTCATATGTAAACTATATAGTATA
Found at i:98770 original size:20 final size:18
Alignment explanation
Indices: 98737--98822 Score: 58
Period size: 20 Copynumber: 4.8 Consensus size: 18
98727 AATATAAACT
*
98737 ATAGTATATATATAGGTC
1 ATAGTAAATATATAGGTC
98755 ATATGTAAACTATATA-GT-
1 ATA-GTAAA-TATATAGGTC
*
98773 ATA-TAAATATCA-A-CTC
1 ATAGTAAATAT-ATAGGTC
*
98789 -TAGTATATATATAGGTC
1 ATAGTAAATATATAGGTC
98806 ATATGTAAACTATATAG
1 ATA-GTAAA-TATATAG
98823 TTTATATATG
Statistics
Matches: 53, Mismatches: 5, Indels: 18
0.70 0.07 0.24
Matches are distributed among these distances:
15 8 0.15
16 12 0.23
17 2 0.04
18 8 0.15
19 10 0.19
20 13 0.25
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (18 bp):
ATAGTAAATATATAGGTC
Found at i:98938 original size:22 final size:22
Alignment explanation
Indices: 98920--98982 Score: 117
Period size: 22 Copynumber: 2.9 Consensus size: 22
98910 TACTATATAT
98920 ATAAACTATATAATTTATATTA
1 ATAAACTATATAATTTATATTA
98942 ATAAACTATATAATTTATATTA
1 ATAAACTATATAATTTATATTA
*
98964 ATAAACTACATAATTTATA
1 ATAAACTATATAATTTATA
98983 CGATATATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (22 bp):
ATAAACTATATAATTTATATTA
Found at i:99064 original size:13 final size:11
Alignment explanation
Indices: 99035--99066 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
99025 ATTGTATAGC
99035 TTATATATAAT
1 TTATATATAAT
*
99046 TCATATATAAT
1 TTATATATAAT
99057 TTATATATAA
1 TTATATATAA
99067 ACTATGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
TTATATATAAT
Found at i:99162 original size:25 final size:26
Alignment explanation
Indices: 99108--99238 Score: 82
Period size: 25 Copynumber: 5.2 Consensus size: 26
99098 ATATATAAAC
* **
99108 TATATAGTATTATAGTTTATACATGG
1 TATATAGTATTATACTTTATACATAA
99134 TATATAGT-TTATACTTTATACATAA
1 TATATAGTATTATACTTTATACATAA
* *
99159 TATATA-TAATATA-TGTTATATAT-A
1 TATATAGTATTATACT-TTATACATAA
* *
99183 TA-ATA-CA-TATACTTTATATATAAA
1 TATATAGTATTATACTTTATACAT-AA
*
99207 CTATATAGT-TTATA-TTATATATATATA
1 -TATATAGTATTATACTT-TATACATA-A
99234 TATAT
1 TATAT
99239 GTAACATCCC
Statistics
Matches: 87, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
22 12 0.14
23 5 0.06
24 6 0.07
25 33 0.38
26 19 0.22
27 12 0.14
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (26 bp):
TATATAGTATTATACTTTATACATAA
Found at i:99165 original size:2 final size:2
Alignment explanation
Indices: 99158--99238 Score: 62
Period size: 2 Copynumber: 41.0 Consensus size: 2
99148 TTTATACATA
* * *
99158 AT AT AT AT A- AT AT AT GT -T AT AT AT AT A- AT AC AT AT ACT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* *
99198 AT AT AT AA ACT AT AT AGT TT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
99239 GTAACATCCC
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
1 4 0.06
2 56 0.89
3 3 0.05
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:99172 original size:9 final size:9
Alignment explanation
Indices: 99150--99238 Score: 65
Period size: 9 Copynumber: 9.8 Consensus size: 9
99140 GTTTATACTT
*
99150 TATACATAA
1 TATATATAA
99159 TATATATAA
1 TATATATAA
* *
99168 TATATGTTA
1 TATATATAA
99177 TATATATAA
1 TATATATAA
* *
99186 TACATATACTT
1 TATATATA--A
99197 TATATATAA
1 TATATATAA
*
99206 -ACTATATAG
1 TA-TATATAA
* *
99215 TTTATATTA
1 TATATATAA
99224 TATATAT-A
1 TATATATAA
99232 TATATAT
1 TATATAT
99239 GTAACATCCC
Statistics
Matches: 62, Mismatches: 14, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
8 9 0.15
9 46 0.74
11 7 0.11
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.47
Consensus pattern (9 bp):
TATATATAA
Found at i:99181 original size:20 final size:21
Alignment explanation
Indices: 99158--99236 Score: 69
Period size: 22 Copynumber: 3.8 Consensus size: 21
99148 TTTATACATA
99158 ATATATATA-ATATATGTTAT
1 ATATATATACATATATGTTAT
99178 ATATATAATACATATACT-TTAT
1 ATATAT-ATACATATA-TGTTAT
99200 ATATA-A-AC-TATATAGTTTAT
1 ATATATATACATATAT-G-TTAT
*
99220 ATTATATATATATATAT
1 A-TATATATACATATAT
99237 ATGTAACATC
Statistics
Matches: 48, Mismatches: 1, Indels: 16
0.74 0.02 0.25
Matches are distributed among these distances:
17 1 0.02
18 4 0.08
19 2 0.04
20 12 0.25
21 7 0.15
22 15 0.31
23 2 0.04
24 5 0.10
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.48
Consensus pattern (21 bp):
ATATATATACATATATGTTAT
Found at i:102548 original size:29 final size:29
Alignment explanation
Indices: 102514--102585 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
102504 CATATTATGA
* *
102514 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
102543 TACATGACATGAATTCATATGATATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
102572 TGCATGACATGAAT
1 TACATGACATGAAT
102586 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATGAAATGTAT
Found at i:102642 original size:30 final size:30
Alignment explanation
Indices: 102600--102676 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
102590 AGAAAAAGTT
* *
102600 ATATGAGCTATGTGATAAAGGTATGTAAATG
1 ATATGA-CTATGTGATAAAGGTATGGAAATA
102631 ATATGACTATGTGATAAAGGTATGGAAATA
1 ATATGACTATGTGATAAAGGTATGGAAATA
*
102661 ATATGACTACGTGATA
1 ATATGACTATGTGATA
102677 TGAACTACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
ATATGACTATGTGATAAAGGTATGGAAATA
Found at i:102953 original size:23 final size:23
Alignment explanation
Indices: 102887--102945 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
102877 ATCATTATAT
*
102887 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
102909 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
102932 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
102946 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:109463 original size:34 final size:29
Alignment explanation
Indices: 109395--109466 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
109385 CATATTATGA
*
109395 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTTATATGAAATGTAT
*
109424 TACATGACATGAATTTATATGATATGTAT
1 TACATGACATGAATTTATATGAAATGTAT
*
109453 TGCATGACATGAAT
1 TACATGACATGAAT
109467 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTTATATGAAATGTAT
Found at i:109523 original size:30 final size:30
Alignment explanation
Indices: 109481--109557 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
109471 AGAAAAAGTT
* *
109481 ATATGAGCTATGTGATAAAGGTATGTAAATG
1 ATATGA-CTATGTGATAAAGGTATGGAAATA
109512 ATATGACTATGTGATAAAGGTATGGAAATA
1 ATATGACTATGTGATAAAGGTATGGAAATA
*
109542 ATATGACTACGTGATA
1 ATATGACTATGTGATA
109558 TGAACTACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
ATATGACTATGTGATAAAGGTATGGAAATA
Found at i:109800 original size:22 final size:23
Alignment explanation
Indices: 109768--109826 Score: 93
Period size: 22 Copynumber: 2.6 Consensus size: 23
109758 ATCATTATAT
*
109768 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
109790 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
*
109813 GGCACTTCAGTGCA
1 GGCACTTCGGTGCA
109827 TTTATACGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 20 0.59
23 14 0.41
ACGTcount: A:0.20, C:0.27, G:0.29, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:109834 original size:23 final size:23
Alignment explanation
Indices: 109768--109834 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 23
109758 ATCATTATAT
* * *
109768 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCAGTGCAATTATACGG
* *
109790 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCAGTGCAATTATACGG
*
109813 GGCACTTCAGTGCATTTATACG
1 GGCACTTCAGTGCAATTATACG
109835 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 20 0.50
23 20 0.50
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTTCAGTGCAATTATACGG
Found at i:116025 original size:23 final size:23
Alignment explanation
Indices: 115962--116030 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
115952 GACATTATTA
115962 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * * *
115985 CGGCACTCCAGTGTAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
116008 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
116031 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:117178 original size:207 final size:206
Alignment explanation
Indices: 116790--117578 Score: 1040
Period size: 207 Copynumber: 3.8 Consensus size: 206
116780 TTTTTTCTCA
* *
116790 ACTTATTACTTATTTATATTTATTAATTGGCCCATAACTTTTTAAA-TGAGTATAATTTAGTACA
1 ACTTATTACTTATTTCTATTT-TTAATTGGCCCATAACTTTTTAAATTG-GTATAATTTAGTACT
*
116854 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTT-GATTTGATCCCTTTTGTG-TGTATAA
64 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTTTTGTGTTGTTTAA
**
116917 -ATATTTAATTTTTA-TTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCACC
129 TATATTTAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATA
116980 TGAAATTGACACAT
194 TGAAATTGAC-CAT
*
116994 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAA-TTTTTAAATAGGTATAATTTAGTAC-T
1 ACTTATTACTTATTTCTATTTTT-AATTGGCCCATAACTTTTTAAATTGGTATAATTTAGTACTT
* *
117057 TTTGTATTAATTTTAACCTCAAAATTTAAAATTATTTCGGTTTGATCCCTTTTGTGTTGTTTAAT
65 TTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTTTTGTGTTGTTTAAT
*
117122 ATATTTAAATTTTTATTTGTAATTTCATATTTGTTTAATTTAGTCCTCCAAATTTTATTTGCATA
130 ATATTT-AATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATA
117187 TGAAATTGACCTAT
194 TGAAATTGACC-AT
* *
117201 ACTTATTACTTATTTCTATTTTTAAATTTGCCCATAACTTTTTAAATTGATATAATTTAGTACTT
1 ACTTATTACTTATTTCTATTTTT-AATTGGCCCATAACTTTTTAAATTGGTATAATTTAGTAC-T
* * ** *** * *
117266 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCAT-CAATGTGT-G
64 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTTTTGTGTTGTTTAA
* *
117329 T-TGTTTAA--TTT-TTT-TAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTTATTTGCGT
129 TATATTTAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA-TTTTATTTGCAT
117389 ATGAAATTGATCCAT
193 ATGAAATTGA-CCAT
*
117404 ACTTATTACTTGA-TT-T-TTTTTAATTGGCCCATAA-TTTTTAAATTGGTATAATTTAGTATTT
1 ACTTATTACTT-ATTTCTATTTTTAATTGGCCCATAACTTTTTAAATTGGTATAATTTAGTA-CT
* *
117465 TTTTGTATTAACTTCAACCTCATAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
64 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT--T---T-TGTGTT
117530 GTTTAATAT-TGTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
123 GTTTAATATAT-TT-AATTTTTATTTGTAATTTCATATTTGTTCAATTTA
117579 ATTCTTAAAT
Statistics
Matches: 517, Mismatches: 38, Indels: 51
0.85 0.06 0.08
Matches are distributed among these distances:
199 72 0.14
200 12 0.02
201 5 0.01
202 70 0.14
203 80 0.15
204 46 0.09
205 7 0.01
206 15 0.03
207 100 0.19
208 27 0.05
209 6 0.01
210 48 0.09
211 3 0.01
212 3 0.01
213 23 0.04
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.50
Consensus pattern (206 bp):
ACTTATTACTTATTTCTATTTTTAATTGGCCCATAACTTTTTAAATTGGTATAATTTAGTACTTT
TTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTTTTGTGTTGTTTAATA
TATTTAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATATG
AAATTGACCAT
Found at i:125151 original size:24 final size:24
Alignment explanation
Indices: 125089--125151 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
125079 CGTTCGTGAA
* *
125089 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGATTATGTTTGTTTATGTT
125113 CGTTCGATTATGTTTGTTTATGTT
1 CGTTCGATTATGTTTGTTTATGTT
*
125137 CTTTC-ATTTATGTTT
1 CGTTCGA-TTATGTTT
125152 AACCCAATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (24 bp):
CGTTCGATTATGTTTGTTTATGTT
Found at i:126148 original size:16 final size:16
Alignment explanation
Indices: 126127--126201 Score: 81
Period size: 16 Copynumber: 5.1 Consensus size: 16
126117 CCAACGTTGA
126127 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
126143 TGTTCGCTTATGTT--
1 TGTTCGTTTATGTTCG
*
126157 TGTTCATTTATGTTC-
1 TGTTCGTTTATGTTCG
*
126172 --AT-GTTTATGTTCG
1 TGTTCGTTTATGTTCG
126185 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
126201 T
1 T
126202 TTATTTAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
12 9 0.19
13 1 0.02
14 12 0.25
15 1 0.02
16 25 0.52
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:126287 original size:16 final size:16
Alignment explanation
Indices: 126266--126298 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
126256 CAAAAAATTT
126266 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
126282 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
126298 T
1 T
126299 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:131324 original size:1 final size:1
Alignment explanation
Indices: 131318--131342 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
131308 GAGAGTAGAA
131318 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
131343 AAAGGATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:138160 original size:18 final size:17
Alignment explanation
Indices: 138128--138161 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
138118 AAACTTGAAC
*
138128 TCAAAAAAGAATAGAAT
1 TCAAAAAAAAATAGAAT
138145 TCAAAAAAAAATTAGAA
1 TCAAAAAAAAA-TAGAA
138162 GCTCGATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.06, G:0.09, T:0.18
Consensus pattern (17 bp):
TCAAAAAAAAATAGAAT
Found at i:151673 original size:42 final size:42
Alignment explanation
Indices: 151612--151699 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
151602 CTGCAAGGAA
*
151612 GAAAAACAGAAACTTGAAGCATCTTTGCATA-AATGTAATGAG
1 GAAAAACAGAAACTAGAAGCATCTTTGCA-AGAATGTAATGAG
*
151654 GAAAAACAGAAACTAGAAGCGTCTTTGCAAGAATGTAATGAG
1 GAAAAACAGAAACTAGAAGCATCTTTGCAAGAATGTAATGAG
151696 GAAA
1 GAAA
151700 TATCTAGAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
41 1 0.02
42 42 0.98
ACGTcount: A:0.47, C:0.11, G:0.22, T:0.20
Consensus pattern (42 bp):
GAAAAACAGAAACTAGAAGCATCTTTGCAAGAATGTAATGAG
Found at i:155237 original size:46 final size:46
Alignment explanation
Indices: 155185--155279 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
155175 TCGAAACTTT
155185 AGATTACACAATGGAATCTGTATAATCATAGGCGTTCTTGAAAGGC
1 AGATTACACAATGGAATCTGTATAATCATAGGCGTTCTTGAAAGGC
155231 AGATTACACAATGGAATCTGTATAATCATAGGCGTTCTTGAAAGGC
1 AGATTACACAATGGAATCTGTATAATCATAGGCGTTCTTGAAAGGC
155277 AGA
1 AGA
155280 CAACAAAATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (46 bp):
AGATTACACAATGGAATCTGTATAATCATAGGCGTTCTTGAAAGGC
Found at i:157015 original size:2 final size:2
Alignment explanation
Indices: 157010--157035 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
157000 ATTTTAAAAA
157010 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
157036 TAAAACTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:160917 original size:18 final size:18
Alignment explanation
Indices: 160894--160928 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
160884 TTCCATCCGG
*
160894 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
160912 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
160929 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:162251 original size:19 final size:19
Alignment explanation
Indices: 162224--162260 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
162214 ACATAGTCAA
*
162224 CGGTTCGGTCCAGGCGGTT
1 CGGTCCGGTCCAGGCGGTT
162243 CGGTCCGGTCCAGGCGGT
1 CGGTCCGGTCCAGGCGGT
162261 CCAGTCCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.05, C:0.30, G:0.43, T:0.22
Consensus pattern (19 bp):
CGGTCCGGTCCAGGCGGTT
Found at i:162267 original size:19 final size:19
Alignment explanation
Indices: 162229--162267 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
162219 GTCAACGGTT
* *
162229 CGGTCCAGGCGGTTCGGTC
1 CGGTCCAGGCGGTCCAGTC
162248 CGGTCCAGGCGGTCCAGTC
1 CGGTCCAGGCGGTCCAGTC
162267 C
1 C
162268 AAGCGGCTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.08, C:0.36, G:0.38, T:0.18
Consensus pattern (19 bp):
CGGTCCAGGCGGTCCAGTC
Found at i:162335 original size:22 final size:22
Alignment explanation
Indices: 162275--162360 Score: 84
Period size: 22 Copynumber: 3.9 Consensus size: 22
162265 TCCAAGCGGC
162275 TCGATCGGCTCGGTCGGCTCGG
1 TCGATCGGCTCGGTCGGCTCGG
* * *
162297 TCTGCTC-GATCGATCGGCTCGG
1 TC-GATCGGCTCGGTCGGCTCGG
* * **
162319 TCGATCGGCTCAGTCGGTTTAG
1 TCGATCGGCTCGGTCGGCTCGG
*
162341 TCGGTCGGCTCGGTCGGCTC
1 TCGATCGGCTCGGTCGGCTC
162361 AACTGGTTCA
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
21 3 0.06
22 42 0.88
23 3 0.06
ACGTcount: A:0.07, C:0.30, G:0.36, T:0.27
Consensus pattern (22 bp):
TCGATCGGCTCGGTCGGCTCGG
Found at i:162353 original size:9 final size:9
Alignment explanation
Indices: 162271--162360 Score: 58
Period size: 9 Copynumber: 9.7 Consensus size: 9
162261 CCAGTCCAAG
*
162271 CGGCTCGAT
1 CGGCTCGGT
162280 CGGCTCGGT
1 CGGCTCGGT
162289 CGGCTCGGT
1 CGGCTCGGT
* *
162298 CTGCTCGAT
1 CGGCTCGGT
*
162307 C-GATCGGCT
1 CGGCTCGG-T
*
162316 CGG-TCGAT
1 CGGCTCGGT
*
162324 CGGCTCAGT
1 CGGCTCGGT
*
162333 CGGTTTAGTCGGT
1 CGG----CTCGGT
162346 CGGCTCGGT
1 CGGCTCGGT
162355 CGGCTC
1 CGGCTC
162361 AACTGGTTCA
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
8 8 0.13
9 47 0.75
10 1 0.02
13 7 0.11
ACGTcount: A:0.07, C:0.31, G:0.37, T:0.26
Consensus pattern (9 bp):
CGGCTCGGT
Found at i:162356 original size:13 final size:13
Alignment explanation
Indices: 162271--162336 Score: 53
Period size: 13 Copynumber: 5.0 Consensus size: 13
162261 CCAGTCCAAG
*
162271 CGGCTCGATCGGCT
1 CGGCTCGGTCGG-T
162285 CGG-TCGGCTCGGT
1 CGGCTCGG-TCGGT
* * *
162298 CTGCTCGATCGAT
1 CGGCTCGGTCGGT
*
162311 CGGCTCGGTCGAT
1 CGGCTCGGTCGGT
*
162324 CGGCTCAGTCGGT
1 CGGCTCGGTCGGT
162337 TTAGTCGGTC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
13 32 0.76
14 10 0.24
ACGTcount: A:0.08, C:0.32, G:0.36, T:0.24
Consensus pattern (13 bp):
CGGCTCGGTCGGT
Found at i:168040 original size:20 final size:19
Alignment explanation
Indices: 168015--168054 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
168005 ATACAATTAG
168015 AATTTTAAAAATATACAAAT
1 AATTTTAAAAATATA-AAAT
*
168035 AATTTTAATAATATAAAAT
1 AATTTTAAAAATATAAAAT
168054 A
1 A
168055 TTAGATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTTTAAAAATATAAAAT
Found at i:170007 original size:13 final size:13
Alignment explanation
Indices: 169991--170035 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
169981 TAAAATTAAT
169991 TTAATGATTATAA
1 TTAATGATTATAA
170004 TTAA-GATTTATAA
1 TTAATGA-TTATAA
*
170017 TGTAAAGATTATAA
1 T-TAATGATTATAA
170031 TTAAT
1 TTAAT
170036 ATATAAAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 2 0.07
13 14 0.50
14 10 0.36
15 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (13 bp):
TTAATGATTATAA
Found at i:170046 original size:25 final size:27
Alignment explanation
Indices: 169996--170047 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
169986 TTAATTTAAT
* *
169996 GATTATAATTAAGATTTATAATGTAAA
1 GATTATAATTAAGATATATAAAGTAAA
170023 GATTATAATT-A-ATATATAAAGTAAA
1 GATTATAATTAAGATATATAAAGTAAA
170048 TTTATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 12 0.52
26 1 0.04
27 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (27 bp):
GATTATAATTAAGATATATAAAGTAAA
Found at i:175919 original size:20 final size:21
Alignment explanation
Indices: 175894--175986 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
175884 TTTTCCCAAT
*
175894 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
175914 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
175935 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
175955 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
175976 TCGCAATGCGA
1 TCGCAATGCGA
175987 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:175939 original size:41 final size:41
Alignment explanation
Indices: 175894--175986 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
175884 TTTTCCCAAT
175894 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
175935 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
175976 TCGCAATGCGA
1 TCGCAATGCGA
175987 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:175999 original size:41 final size:41
Alignment explanation
Indices: 175913--176047 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
175903 GAATAAGTAA
* *
175913 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
175954 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
175995 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
176036 TTCGCAACGCGA
1 ATCGCAACGCGA
176048 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:176000 original size:20 final size:20
Alignment explanation
Indices: 175975--176069 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
175965 AATTGGGAAA
*
175975 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
175995 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
176016 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
176036 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
176056 TTCGCAACGCGATA
1 ATCGCAACGCGATA
176070 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:176285 original size:22 final size:22
Alignment explanation
Indices: 176257--176300 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
176247 CACTCTCTCA
176257 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
176279 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
176301 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:176437 original size:14 final size:14
Alignment explanation
Indices: 176418--176444 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
176408 ATTATTAGGT
176418 TTTGTGTTTCGCGA
1 TTTGTGTTTCGCGA
176432 TTTGTGTTTCGCG
1 TTTGTGTTTCGCG
176445 TTGCGATTTT
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:0.04, C:0.15, G:0.30, T:0.52
Consensus pattern (14 bp):
TTTGTGTTTCGCGA
Found at i:176460 original size:14 final size:14
Alignment explanation
Indices: 176443--176500 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
176433 TTGTGTTTCG
176443 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
176457 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
176473 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
176489 CGTTGCGATTTT
1 CGTTGCGATTTT
176501 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:176466 original size:33 final size:32
Alignment explanation
Indices: 176428--176516 Score: 133
Period size: 32 Copynumber: 2.7 Consensus size: 32
176418 TTTGTGTTTC
*
176428 GCGATTTGTGTTTCGCGTTGCGATTTTGTCGTT
1 GCGATTT-TATTTCGCGTTGCGATTTTGTCGTT
*
176461 GCGATTTCATTTCGCGTTGCGATTTTGTCGTT
1 GCGATTTTATTTCGCGTTGCGATTTTGTCGTT
*
176493 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTT-ATTTCGCGTTGCGAT
176517 AGCCATTTCC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 30 0.59
33 21 0.41
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.46
Consensus pattern (32 bp):
GCGATTTTATTTCGCGTTGCGATTTTGTCGTT
Found at i:176476 original size:32 final size:33
Alignment explanation
Indices: 176438--176516 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
176428 GCGATTTGTG
176438 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
176470 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
176503 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
176517 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:176515 original size:19 final size:19
Alignment explanation
Indices: 176457--176574 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
176447 GCGATTTTGT
176457 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
176475 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
176489 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
176508 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
176528 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
176547 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
176567 TGTTGCGA
1 CGTTGCGA
176575 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:178567 original size:33 final size:36
Alignment explanation
Indices: 178522--178623 Score: 120
Period size: 38 Copynumber: 2.8 Consensus size: 36
178512 AAAACAGACT
* ***
178522 ATCGCAACGCGAAATGGCTATCGCAA-CG-A-GAAA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
178555 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
178593 ATCGCAATGCGAAATGAAAATCGCAATGCGA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCGA
178624 TTTTCTCGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
33 22 0.37
35 2 0.03
37 2 0.03
38 34 0.57
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:178573 original size:19 final size:19
Alignment explanation
Indices: 178551--178623 Score: 146
Period size: 19 Copynumber: 3.8 Consensus size: 19
178541 ATCGCAACGA
178551 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
178570 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
178589 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
178608 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
178624 TTTTCTCGTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 54 1.00
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:178680 original size:20 final size:20
Alignment explanation
Indices: 178623--178680 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
178613 TCGCAATGCG
* *
178623 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
178643 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
178663 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
178681 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:179767 original size:24 final size:24
Alignment explanation
Indices: 179740--179793 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
179730 GTATTCGAAA
* *
179740 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
179764 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
179788 TTTGAT
1 TTTGAT
179794 GATGTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:179985 original size:12 final size:12
Alignment explanation
Indices: 179968--179992 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
179958 ATATAATCCT
179968 GAAGAAGAAAAA
1 GAAGAAGAAAAA
179980 GAAGAAGAAAAA
1 GAAGAAGAAAAA
179992 G
1 G
179993 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Done.