Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 89
Found at i:5572245 original size:25 final size:25
Alignment explanation
Indices: 5572090--5572271 Score: 90
Period size: 23 Copynumber: 7.8 Consensus size: 25
5572080 AAAATATTAT
5572090 ATATTATATATATA-AT-TAATATAAA
1 ATATTATATATATATATAT-ATAT-AA
* * *
5572115 ATATAAAAAATAT-TATATATATAA
1 ATATTATATATATATATATATATAA
* * * *
5572139 TTAATATA-AAATAT-TATATATAT
1 ATATTATATATATATATATATATAA
* *
5572162 A-ATTA-ATATA-AAATAT-TAAAA
1 ATATTATATATATATATATATATAA
5572183 ATATTATATATATA-AT-TAATATAA
1 ATATTATATATATATATAT-ATATAA
* * * *
5572207 AAAATATA-AAATAT-TATATATAT
1 ATATTATATATATATATATATATAA
5572230 ATA-TATATATATATATATATAT-A
1 ATATTATATATATATATATATATAA
**
5572253 AT-CGATATATATATATATA
1 ATATTATATATATATATATA
5572272 ATCGGGGCGG
Statistics
Matches: 118, Mismatches: 24, Indels: 32
0.68 0.14 0.18
Matches are distributed among these distances:
21 6 0.05
22 17 0.14
23 52 0.44
24 26 0.22
25 16 0.14
26 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (25 bp):
ATATTATATATATATATATATATAA
Found at i:5572248 original size:34 final size:34
Alignment explanation
Indices: 5572080--5572271 Score: 168
Period size: 34 Copynumber: 5.7 Consensus size: 34
5572070 ATTAATATAA
*
5572080 AAAATATTATATAT-TATATATATA-ATTAATAT
1 AAAATATTATATATATATATATATATATAAATAT
* * * *
5572112 AAAATATAAAAAATAT-TATATATATAATTAATAT
1 AAAATATTATATATATATATATATAT-ATAAATAT
5572146 AAAATATTATATATATA-AT-TA-ATATAAAATATT
1 AAAATATTATATATATATATATATATAT-AAATA-T
*
5572179 AAAAATATTATATATATA-AT-TAATATAAAAAATAT
1 -AAAATATTATATATATATATAT-ATAT-ATAAATAT
*
5572214 AAAATATTATATATATATATATATATATATATAT
1 AAAATATTATATATATATATATATATATAAATAT
* * **
5572248 -ATATAATCGATATATATATATATA
1 AAAATATTATATATATATATATATA
5572272 ATCGGGGCGG
Statistics
Matches: 134, Mismatches: 14, Indels: 23
0.78 0.08 0.13
Matches are distributed among these distances:
31 2 0.01
32 25 0.19
33 24 0.18
34 66 0.49
35 8 0.06
36 8 0.06
37 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (34 bp):
AAAATATTATATATATATATATATATATAAATAT
Found at i:5572364 original size:21 final size:21
Alignment explanation
Indices: 5572339--5572392 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
5572329 CCGATACTGG
5572339 ACCCGACCCGATATTATTCAA
1 ACCCGACCCGATATTATTCAA
*
5572360 ACCCGACCTGATATTATTCAA
1 ACCCGACCCGATATTATTCAA
*
5572381 ACCCGACTCGAT
1 ACCCGACCCGAT
5572393 CCGAACTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.33, G:0.11, T:0.24
Consensus pattern (21 bp):
ACCCGACCCGATATTATTCAA
Found at i:5573170 original size:2 final size:2
Alignment explanation
Indices: 5573165--5573236 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
5573155 ACACACACAC
5573165 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5573207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5573237 TCTTTTCACA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5580395 original size:78 final size:78
Alignment explanation
Indices: 5580285--5580443 Score: 187
Period size: 77 Copynumber: 2.0 Consensus size: 78
5580275 CCGAATATAG
* * * *
5580285 TAAATAAACATTAAAAGAATGTAATTCTGATTACAACTCTTTTAATGGATATTTAATTCAGAA-T
1 TAAATAAACATTAAAAGAATATAATTCGGATTACAAAT-ATTTAATGGATATTTAATT-AGAATT
*
5580349 AATTAAATAAGAGTT
64 AATTAAATAAGAATT
* * * * * *
5580364 TAAATAAACGTT-AAAGAGTATAATTCGGATTATAAATATTTAATGGGTATTTAGTTTGAATTAA
1 TAAATAAACATTAAAAGAATATAATTCGGATTACAAATATTTAATGGATATTTAATTAGAATTAA
5580428 TTAAATAAGAATT
66 TTAAATAAGAATT
5580441 TAA
1 TAA
5580444 TTAATTCAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
76 3 0.04
77 34 0.50
78 20 0.29
79 11 0.16
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (78 bp):
TAAATAAACATTAAAAGAATATAATTCGGATTACAAATATTTAATGGATATTTAATTAGAATTAA
TTAAATAAGAATT
Found at i:5581941 original size:20 final size:20
Alignment explanation
Indices: 5581896--5581942 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
5581886 ACTACACATC
5581896 ATTCTCAACCATTCCAATTCA
1 ATTC-CAACCATTCCAATTCA
*
5581917 TTTCCAACCACTTCCAA-TCA
1 ATTCCAACCA-TTCCAATTCA
5581937 ATTCCA
1 ATTCCA
5581943 TATCACAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (20 bp):
ATTCCAACCATTCCAATTCA
Found at i:5584625 original size:24 final size:24
Alignment explanation
Indices: 5584593--5584643 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
5584583 AAATTTTTCC
5584593 GTTGCATTAGATGTAATGTTGTTG
1 GTTGCATTAGATGTAATGTTGTTG
5584617 GTTGCATTAGATGTAATGTTGTTG
1 GTTGCATTAGATGTAATGTTGTTG
5584641 GTT
1 GTT
5584644 TTGTGATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.04, G:0.29, T:0.47
Consensus pattern (24 bp):
GTTGCATTAGATGTAATGTTGTTG
Found at i:5584904 original size:23 final size:23
Alignment explanation
Indices: 5584874--5584920 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
5584864 CACCAGCCTC
* *
5584874 ACTTCGGTCTTTTCTTGATTGTA
1 ACTTCGGTCCTTTCCTGATTGTA
*
5584897 ACTTCGGTCCTTTCCTGGTTGTA
1 ACTTCGGTCCTTTCCTGATTGTA
5584920 A
1 A
5584921 GATTAGGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (23 bp):
ACTTCGGTCCTTTCCTGATTGTA
Found at i:5597827 original size:19 final size:19
Alignment explanation
Indices: 5597803--5597840 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5597793 CAAAACCAAC
5597803 AAGATGGACATTACAATGA
1 AAGATGGACATTACAATGA
5597822 AAGATGGACATTACAATGA
1 AAGATGGACATTACAATGA
5597841 GAATTCATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (19 bp):
AAGATGGACATTACAATGA
Found at i:5599470 original size:32 final size:32
Alignment explanation
Indices: 5599434--5599516 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 32
5599424 GGGGCCGTGA
*
5599434 GGCCTACCTAAGAGCACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAGCACATCTCAGGGCCGCAG
* * *
5599466 GGCCTACC--CGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAGCA-CATCTCAGGGCCGCAG
*
5599497 AGCCTACCTAAGAGTCACAT
1 GGCCTACCTAAGAG-CACAT
5599517 TAGGTTTGTA
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
30 4 0.10
31 21 0.54
32 8 0.21
33 5 0.13
34 1 0.03
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.16
Consensus pattern (32 bp):
GGCCTACCTAAGAGCACATCTCAGGGCCGCAG
Found at i:5599492 original size:63 final size:63
Alignment explanation
Indices: 5599377--5599516 Score: 160
Period size: 63 Copynumber: 2.2 Consensus size: 63
5599367 AAAGCGTTAC
* * * * *
5599377 CCTAAGGGAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTA
1 CCTAAGAGCACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTA
* *
5599440 CCTAAGAGCACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTA
1 CCTAAGAGCACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTA
5599503 CCTAAGAGTCACAT
1 CCTAAGAG-CACAT
5599517 TAGGTTTGTA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
62 2 0.03
63 57 0.86
64 7 0.11
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
CCTAAGAGCACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTA
Found at i:5600391 original size:7 final size:7
Alignment explanation
Indices: 5600379--5600409 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
5600369 GTCAAAGAAA
5600379 GTCAACG
1 GTCAACG
5600386 GTCAACG
1 GTCAACG
*
5600393 GTCAACA
1 GTCAACG
5600400 GTCAACG
1 GTCAACG
5600407 GTC
1 GTC
5600410 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:5600428 original size:22 final size:22
Alignment explanation
Indices: 5600400--5600441 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
5600390 ACGGTCAACA
5600400 GTCAACGGTCGGGTCGGGTCGG
1 GTCAACGGTCGGGTCGGGTCGG
5600422 GTCAACGGTCGGGTCGGGTC
1 GTCAACGGTCGGGTCGGGTC
5600442 AGACCGGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.10, C:0.24, G:0.48, T:0.19
Consensus pattern (22 bp):
GTCAACGGTCGGGTCGGGTCGG
Found at i:5600456 original size:9 final size:9
Alignment explanation
Indices: 5600438--5600536 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
5600428 GGTCGGGTCG
*
5600438 GGTCAGACC
1 GGTCAAACC
5600447 GGTCAAACC
1 GGTCAAACC
* *
5600456 GATTCAGACC
1 G-GTCAAACC
5600466 GGTCAAACC
1 GGTCAAACC
*
5600475 GGTTCGAACC
1 GG-TCAAACC
*
5600485 GGTTGAAACC
1 GG-TCAAACC
5600495 GGTCAAACC
1 GGTCAAACC
5600504 GGTCAGAACC
1 GGTCA-AACC
*
5600514 GGTTGAAAACC
1 GG-T-CAAACC
5600525 GGTCAAACC
1 GGTCAAACC
5600534 GGT
1 GGT
5600537 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:5600462 original size:19 final size:19
Alignment explanation
Indices: 5600440--5600537 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
5600430 TCGGGTCGGG
*
5600440 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
5600459 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
5600478 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
5600497 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* *
5600517 TGAAAACCGGTCAAACCGGT
1 T-CAGACCGGTCAAACCGGT
5600537 T
1 T
5600538 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 38 0.56
20 17 0.25
21 10 0.15
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:5600495 original size:29 final size:31
Alignment explanation
Indices: 5600463--5600537 Score: 129
Period size: 29 Copynumber: 2.5 Consensus size: 31
5600453 ACCGATTCAG
5600463 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
5600492 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
5600522 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
5600538 TCCAGCAGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.56
30 16 0.37
31 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:5606802 original size:32 final size:31
Alignment explanation
Indices: 5606766--5606841 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
5606756 GGGGCCGTGA
*
5606766 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
5606798 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
5606829 AGCCTACCTAAGA
1 GGCCTACCTAAGA
5606842 GTCACATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:5606824 original size:63 final size:63
Alignment explanation
Indices: 5606718--5606841 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
5606708 CCCTAAGGGA
* * *
5606718 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
* *
5606781 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
5606842 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 2 0.04
63 49 0.92
64 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:5607752 original size:22 final size:22
Alignment explanation
Indices: 5607724--5607766 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
5607714 AACGGTCAAC
5607724 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
5607746 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
5607767 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:5607810 original size:19 final size:19
Alignment explanation
Indices: 5607795--5607891 Score: 108
Period size: 19 Copynumber: 4.9 Consensus size: 19
5607785 CAGACCGGTC
*
5607795 AAACCGGTTCGAACCGGTTG
1 AAACCGG-TCAAACCGGTTG
5607815 AAACCGGTCAAACCGGTTCG
1 AAACCGGTCAAACCGGTT-G
* *
5607835 -AACCGGTTGAAACCGG-TC
1 AAACCGG-TCAAACCGGTTG
5607853 AAACCGGTCAGAACCGGTTG
1 AAACCGGTCA-AACCGGTTG
5607873 AAAACCGGTCAAACCGGTT
1 -AAACCGGTCAAACCGGTT
5607892 TCCAGCAGCC
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
18 2 0.03
19 29 0.44
20 25 0.38
21 10 0.15
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (19 bp):
AAACCGGTCAAACCGGTTG
Found at i:5607811 original size:10 final size:10
Alignment explanation
Indices: 5607796--5607871 Score: 72
Period size: 10 Copynumber: 7.8 Consensus size: 10
5607786 AGACCGGTCA
5607796 AACCGGTTCG
1 AACCGGTTCG
5607806 AACCGGTT-G
1 AACCGGTTCG
*
5607815 AAACCGG-TCA
1 -AACCGGTTCG
5607825 AACCGGTTCG
1 AACCGGTTCG
5607835 AACCGGTT-G
1 AACCGGTTCG
*
5607844 AAACCGG-TCA
1 -AACCGGTTCG
5607854 AACCGG-TCAG
1 AACCGGTTC-G
5607864 AACCGGTT
1 AACCGGTT
5607872 GAAAACCGGT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
9 18 0.33
10 36 0.65
11 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (10 bp):
AACCGGTTCG
Found at i:5607821 original size:29 final size:29
Alignment explanation
Indices: 5607788--5607891 Score: 183
Period size: 29 Copynumber: 3.6 Consensus size: 29
5607778 ACCAATTCAG
5607788 ACCGGTCAAACCGGTTCGAACCGGTTGAA
1 ACCGGTCAAACCGGTTCGAACCGGTTGAA
5607817 ACCGGTCAAACCGGTTCGAACCGGTTGAA
1 ACCGGTCAAACCGGTTCGAACCGGTTGAA
5607846 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
5607876 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
5607892 TCCAGCAGCC
Statistics
Matches: 72, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
28 2 0.03
29 53 0.74
30 16 0.22
31 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (29 bp):
ACCGGTCAAACCGGTTCGAACCGGTTGAA
Found at i:5611336 original size:79 final size:80
Alignment explanation
Indices: 5611217--5611377 Score: 243
Period size: 80 Copynumber: 2.0 Consensus size: 80
5611207 TTAATATTTT
* *
5611217 TTTAACATTTCTGGTAAAGCGCTACATAAAACATTA-TTTTTTCTACCGAAAATGTTAATATTGG
1 TTTAACATTTCCGGTAAAGCGCTACATAAAACATTATTTTTTTCTACCGAAAATATTAATATTGG
*
5611281 GCGCTACCTAAAATG
66 GCGCTACCGAAAATG
* * *
5611296 TTTAACATTTCCGGTAAAGCGTTACCTAAAACATTATTTTTTTCTACTGAAAATATTAATATTGG
1 TTTAACATTTCCGGTAAAGCGCTACATAAAACATTATTTTTTTCTACCGAAAATATTAATATTGG
**
5611361 GTTCTACCGAAAATG
66 GCGCTACCGAAAATG
5611376 TT
1 TT
5611378 AATATTGGGT
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
79 33 0.45
80 40 0.55
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.38
Consensus pattern (80 bp):
TTTAACATTTCCGGTAAAGCGCTACATAAAACATTATTTTTTTCTACCGAAAATATTAATATTGG
GCGCTACCGAAAATG
Found at i:5611365 original size:25 final size:25
Alignment explanation
Indices: 5611337--5611399 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
5611327 CATTATTTTT
*
5611337 TTCTACTGAAAATATTAATATTGGG
1 TTCTACCGAAAATATTAATATTGGG
*
5611362 TTCTACCGAAAATGTTAATATTGGG
1 TTCTACCGAAAATATTAATATTGGG
*
5611387 TTCTACCGGAAAT
1 TTCTACCGAAAAT
5611400 TAGTTAGCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (25 bp):
TTCTACCGAAAATATTAATATTGGG
Found at i:5615155 original size:31 final size:31
Alignment explanation
Indices: 5615119--5615199 Score: 112
Period size: 31 Copynumber: 2.6 Consensus size: 31
5615109 CGCTACTAAG
5615119 ACAAGCAATCACAC-TAATGTCACTAAGGCCA
1 ACAAGCAATCACACTTAA-GTCACTAAGGCCA
*
5615150 ACAAGCAATCCCACTTAAGTCACTAAGGCCA
1 ACAAGCAATCACACTTAAGTCACTAAGGCCA
*
5615181 ACAAACAAAT-ACACTTAAG
1 ACAAGC-AATCACACTTAAG
5615200 CTACTCAGGT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
31 39 0.87
32 6 0.13
ACGTcount: A:0.44, C:0.28, G:0.11, T:0.16
Consensus pattern (31 bp):
ACAAGCAATCACACTTAAGTCACTAAGGCCA
Found at i:5616723 original size:15 final size:15
Alignment explanation
Indices: 5616705--5616747 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
5616695 AACAACCAAA
*
5616705 TTTTCCTTTCTTT-TT
1 TTTTCCTTT-TTTCCT
5616720 TTTTCCTTTTTTCCT
1 TTTTCCTTTTTTCCT
5616735 TTTTCCTTTTTTC
1 TTTTCCTTTTTTC
5616748 GATTTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 3 0.12
15 23 0.88
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTCCTTTTTTCCT
Found at i:5616731 original size:8 final size:8
Alignment explanation
Indices: 5616705--5616747 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
5616695 AACAACCAAA
5616705 TTTTCCTT
1 TTTTCCTT
5616713 TCTTT--TT
1 T-TTTCCTT
5616720 TTTTCCTT
1 TTTTCCTT
5616728 TTTTCC-T
1 TTTTCCTT
5616735 TTTTCCTT
1 TTTTCCTT
5616743 TTTTC
1 TTTTC
5616748 GATTTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 3 0.10
7 10 0.32
8 15 0.48
9 3 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTCCTT
Found at i:5616753 original size:15 final size:15
Alignment explanation
Indices: 5616720--5616753 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5616710 CTTTCTTTTT
*
5616720 TTTTCCTTTTTTCCT
1 TTTTCCTTTTTTCCA
*
5616735 TTTTCCTTTTTTCGA
1 TTTTCCTTTTTTCCA
5616750 TTTT
1 TTTT
5616754 TTTATGCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTCCTTTTTTCCA
Found at i:5616753 original size:23 final size:23
Alignment explanation
Indices: 5616705--5616754 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
5616695 AACAACCAAA
* *
5616705 TTTTCCTTTCTTTTTTTTTCCTT
1 TTTTCCTTTCTTCTTTTTTCCAT
*
5616728 TTTTCCTTT-TTCCTTTTTTCGAT
1 TTTTCCTTTCTT-CTTTTTTCCAT
5616751 TTTT
1 TTTT
5616755 TTATGCTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTTCCTTTCTTCTTTTTTCCAT
Found at i:5618047 original size:22 final size:23
Alignment explanation
Indices: 5618012--5618056 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
5618002 GTGTCACGTC
5618012 AAGAAAGGTAAAATATTTCTATT
1 AAGAAAGGTAAAATATTTCTATT
*
5618035 AAGAAA-GTAAAATATTTTTATT
1 AAGAAAGGTAAAATATTTCTATT
5618057 GTATTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (23 bp):
AAGAAAGGTAAAATATTTCTATT
Found at i:5620441 original size:23 final size:22
Alignment explanation
Indices: 5620403--5620445 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
5620393 CAATTCATTT
5620403 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTTCTTTATCTTGTTTTA
*
5620425 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
5620446 CCAGCACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTA
Found at i:5626607 original size:23 final size:22
Alignment explanation
Indices: 5626569--5626611 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
5626559 CAATTCATTT
5626569 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTTCTTTATCTTGTTTTA
*
5626591 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
5626612 CCAGCTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTA
Found at i:5627134 original size:21 final size:21
Alignment explanation
Indices: 5627087--5627135 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5627077 TGTATATTCT
*
5627087 ACAGTCATTTCAGATGGCACC
1 ACAGTCGTTTCAGATGGCACC
* *
5627108 ATAGTCGTTTTAGATGGCACC
1 ACAGTCGTTTCAGATGGCACC
*
5627129 GCAGTCG
1 ACAGTCG
5627136 GGTCAGACGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (21 bp):
ACAGTCGTTTCAGATGGCACC
Found at i:5627680 original size:17 final size:17
Alignment explanation
Indices: 5627658--5627690 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5627648 GTTCAAATTG
5627658 TTTTTATTATTTAGTTC
1 TTTTTATTATTTAGTTC
*
5627675 TTTTTATTTTTTAGTT
1 TTTTTATTATTTAGTT
5627691 GCATCGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTTATTATTTAGTTC
Found at i:5628957 original size:20 final size:20
Alignment explanation
Indices: 5628893--5628962 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
5628883 AAAACTTTTT
*
5628893 TATGAATAGTAAC-ATATTA
1 TATGAATAGTACCGATATTA
* *
5628912 TATGAATAGTACCGATACTG
1 TATGAATAGTACCGATATTA
**
5628932 TATGAATAGTTTCGATATTA
1 TATGAATAGTACCGATATTA
* *
5628952 TGTGAACAGTA
1 TATGAATAGTA
5628963 GTATCAATAC
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 12 0.30
20 28 0.70
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.36
Consensus pattern (20 bp):
TATGAATAGTACCGATATTA
Found at i:5628978 original size:21 final size:21
Alignment explanation
Indices: 5628954--5629022 Score: 120
Period size: 21 Copynumber: 3.3 Consensus size: 21
5628944 CGATATTATG
* *
5628954 TGAACAGTAGTATCAATACCA
1 TGAACAGTAGTACCGATACCA
5628975 TGAACAGTAGTACCGATACCA
1 TGAACAGTAGTACCGATACCA
5628996 TGAACAGTAGTACCGATACCA
1 TGAACAGTAGTACCGATACCA
5629017 TGAACA
1 TGAACA
5629023 ATACCGATGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (21 bp):
TGAACAGTAGTACCGATACCA
Found at i:5629105 original size:21 final size:21
Alignment explanation
Indices: 5629073--5629129 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
5629063 CGATACTGCT
5629073 ACAATAGTATCGATACCATGA
1 ACAATAGTATCGATACCATGA
* * *
5629094 ACAGTGGTATCGATACCGTGA
1 ACAATAGTATCGATACCATGA
5629115 ACAATAGTATCGATA
1 ACAATAGTATCGATA
5629130 ATATCAAGCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25
Consensus pattern (21 bp):
ACAATAGTATCGATACCATGA
Found at i:5629528 original size:34 final size:34
Alignment explanation
Indices: 5629471--5629537 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
5629461 TGTAAAAGGA
*
5629471 AAGGTTCTAATTGAGCCCTTGAAAAGCTAGGGAT
1 AAGGTTCTAATTGAGCCCTTGAAAAACTAGGGAT
* *
5629505 AAGGTTCTAGTTTAG-CCTGTGAAAAACTAGGGA
1 AAGGTTCTAATTGAGCCCT-TGAAAAACTAGGGA
5629538 GTTTTAAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 3 0.10
34 26 0.90
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (34 bp):
AAGGTTCTAATTGAGCCCTTGAAAAACTAGGGAT
Found at i:5631918 original size:21 final size:21
Alignment explanation
Indices: 5631892--5631945 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
5631882 ACTGCTACAG
*
5631892 TAGTATCGATACCATGAATAA
1 TAGTATCGATACCATAAATAA
* *
5631913 TAGTATCGATACCGTAAATAG
1 TAGTATCGATACCATAAATAA
*
5631934 TAGTATCAATAC
1 TAGTATCGATAC
5631946 TATCAAGCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (21 bp):
TAGTATCGATACCATAAATAA
Found at i:5635854 original size:16 final size:17
Alignment explanation
Indices: 5635833--5635866 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5635823 AGAAAAATAG
5635833 AAATAAAACAT-ATAAA
1 AAATAAAACATAATAAA
*
5635849 AAATAAAATATAATAAA
1 AAATAAAACATAATAAA
5635866 A
1 A
5635867 TCGACAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AAATAAAACATAATAAA
Found at i:5641309 original size:20 final size:21
Alignment explanation
Indices: 5641280--5641323 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
5641270 TTTTTTCTCT
*
5641280 TTTTTTAAATGTT-AATTT-TA
1 TTTTTAAAAT-TTAAATTTCTA
5641300 TTTTTAAAATTTAAATTTCTA
1 TTTTTAAAATTTAAATTTCTA
5641321 TTT
1 TTT
5641324 AAATTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 14 0.67
21 5 0.24
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTTAAAATTTAAATTTCTA
Found at i:5641313 original size:19 final size:19
Alignment explanation
Indices: 5641280--5641338 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
5641270 TTTTTTCTCT
*
5641280 TTTTTTAAATGTTAATTTTA
1 TTTTTAAAAT-TTAATTTTA
* *
5641300 TTTTTAAAATTTAAATTTC
1 TTTTTAAAATTTAATTTTA
*
5641319 TATTTAAATTATTTAATTTT
1 TTTTTAAA--ATTTAATTTT
5641339 TGAAATTAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
19 14 0.44
20 9 0.28
21 9 0.28
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTTAAAATTTAATTTTA
Found at i:5641704 original size:39 final size:37
Alignment explanation
Indices: 5641628--5641739 Score: 163
Period size: 39 Copynumber: 3.0 Consensus size: 37
5641618 TTATTTACTT
* *
5641628 TAATTTTATTTATAATTTTGTA-TTTTTATTTTAAAG
1 TAATTTTATTTCTAATTTTGTATTTTTTATTTCAAAG
*
5641664 TAGTTTTATTTCTAATTTTGTATTTTTTTTATTTCAAAG
1 TAATTTTATTTCTAATTTTGTA--TTTTTTATTTCAAAG
*
5641703 TAAATTTATTTCTAATTTTGTATTTTTTATTTCAAAG
1 TAATTTTATTTCTAATTTTGTATTTTTTATTTCAAAG
5641740 AAATGATAGA
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
36 20 0.29
37 15 0.22
39 33 0.49
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (37 bp):
TAATTTTATTTCTAATTTTGTATTTTTTATTTCAAAG
Found at i:5641755 original size:37 final size:38
Alignment explanation
Indices: 5641675--5641755 Score: 94
Period size: 37 Copynumber: 2.1 Consensus size: 38
5641665 AGTTTTATTT
* ***
5641675 CTAATTTTGTATTTTTTTTATTTCAAAGTAAATTTATTT
1 CTAATTTTGTA-TTTTTTTATTTCAAAGTAAATATAGAA
5641714 CTAATTTTGTA-TTTTTTATTTCAAAG-AAATGATAGAA
1 CTAATTTTGTATTTTTTTATTTCAAAGTAAAT-ATAGAA
5641751 CTAAT
1 CTAAT
5641756 ATAAATACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 4 0.11
37 22 0.59
39 11 0.30
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.53
Consensus pattern (38 bp):
CTAATTTTGTATTTTTTTATTTCAAAGTAAATATAGAA
Found at i:5642098 original size:21 final size:21
Alignment explanation
Indices: 5642074--5642124 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
5642064 GTTTGTTTTC
5642074 ATTCAATTCTCTAATATTCGG
1 ATTCAATTCTCTAATATTCGG
*
5642095 ATTCAATTCTCTATTATTCGG
1 ATTCAATTCTCTAATATTCGG
5642116 ATTCAATTC
1 ATTCAATTC
5642125 GGCTTATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.45
Consensus pattern (21 bp):
ATTCAATTCTCTAATATTCGG
Found at i:5643750 original size:20 final size:20
Alignment explanation
Indices: 5643721--5643759 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5643711 AGGGCTTATA
*
5643721 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
5643741 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
5643760 ATGATGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:5644857 original size:15 final size:15
Alignment explanation
Indices: 5644837--5644865 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5644827 ATACCAAAGG
5644837 AAGGGTATCGATACC
1 AAGGGTATCGATACC
5644852 AAGGGTATCGATAC
1 AAGGGTATCGATAC
5644866 TAATGTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (15 bp):
AAGGGTATCGATACC
Found at i:5645788 original size:23 final size:23
Alignment explanation
Indices: 5645744--5645788 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
5645734 GAGTCGAGGG
* *
5645744 TTCTACGCGGTCCTTTGTGACAT
1 TTCTACGCGGTCCTTCGGGACAT
* *
5645767 TTCTACGTGGTTCTTCGGGACA
1 TTCTACGCGGTCCTTCGGGACA
5645789 ATACTATGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.13, C:0.24, G:0.24, T:0.38
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAT
Found at i:5645849 original size:24 final size:24
Alignment explanation
Indices: 5645812--5645890 Score: 131
Period size: 24 Copynumber: 3.3 Consensus size: 24
5645802 ATTCAAGACA
**
5645812 TTCTATGTGGCACTTCGGTGCAAT
1 TTCTATGTAACACTTCGGTGCAAT
5645836 TTCTATGTAACACTTCGGTGCAAT
1 TTCTATGTAACACTTCGGTGCAAT
5645860 TTCTATGTAACACTTCGGTGCAAT
1 TTCTATGTAACACTTCGGTGCAAT
*
5645884 TTATATG
1 TTCTATG
5645891 AGTTGTGCTG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (24 bp):
TTCTATGTAACACTTCGGTGCAAT
Found at i:5646120 original size:6 final size:6
Alignment explanation
Indices: 5646109--5646167 Score: 64
Period size: 6 Copynumber: 9.8 Consensus size: 6
5646099 TCTTGAATAG
* * * * *
5646109 TGATAA TGATAA TTATAG TGACAA TGATAA TGATAA TGATGA TGATGA
1 TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA
*
5646157 TGATAT TGATA
1 TGATAA TGATA
5646168 TATATATATA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.36
Consensus pattern (6 bp):
TGATAA
Found at i:5646128 original size:18 final size:18
Alignment explanation
Indices: 5646105--5646167 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 18
5646095 ATTATCTTGA
*
5646105 ATAGTGATAATGATAATT
1 ATAGTGATAATGATAATG
*
5646123 ATAGTGACAATGATAATG
1 ATAGTGATAATGATAATG
* * *
5646141 ATAATGATGATGATGATG
1 ATAGTGATAATGATAATG
*
5646159 ATATTGATA
1 ATAGTGATA
5646168 TATATATATA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.35
Consensus pattern (18 bp):
ATAGTGATAATGATAATG
Found at i:5650170 original size:23 final size:23
Alignment explanation
Indices: 5650144--5650241 Score: 90
Period size: 23 Copynumber: 4.3 Consensus size: 23
5650134 GAGTCGAGAG
*
5650144 TTCTATGCGGTCATTCGGGACAA
1 TTCTATGTGGTCATTCGGGACAA
* ** * * *
5650167 TTCTACGTGGTTTTTTGGGATAT
1 TTCTATGTGGTCATTCGGGACAA
* *
5650190 TTCTACGTGGTCATTTGGGACAA
1 TTCTATGTGGTCATTCGGGACAA
* *
5650213 TACTATGTGGTCCTTCGGGAC-A
1 TTCTATGTGGTCATTCGGGACAA
5650235 TTCTATG
1 TTCTATG
5650242 CGGCACTTCA
Statistics
Matches: 59, Mismatches: 16, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
22 7 0.12
23 52 0.88
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (23 bp):
TTCTATGTGGTCATTCGGGACAA
Found at i:5650263 original size:24 final size:24
Alignment explanation
Indices: 5650235--5650289 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
5650225 CTTCGGGACA
*
5650235 TTCTATGCGGCACTTCAGTGCAAT
1 TTCTACGCGGCACTTCAGTGCAAT
* * *
5650259 TTCTACGTGTCACTTCGGTGCAAT
1 TTCTACGCGGCACTTCAGTGCAAT
*
5650283 TTATACG
1 TTCTACG
5650290 AGCTGTGGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (24 bp):
TTCTACGCGGCACTTCAGTGCAAT
Found at i:5650520 original size:6 final size:6
Alignment explanation
Indices: 5650509--5650572 Score: 56
Period size: 6 Copynumber: 10.7 Consensus size: 6
5650499 TCTTGAACAG
* * * * **
5650509 TGATAA TGATAA TTACAG TGACAA TGATAA TGATAA TGATGT TGATAA
1 TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA
* *
5650557 TGATAT TGATGA TGAT
1 TGATAA TGATAA TGAT
5650573 GATGCTGATG
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36
Consensus pattern (6 bp):
TGATAA
Found at i:5650528 original size:18 final size:18
Alignment explanation
Indices: 5650505--5650539 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5650495 ATTGTCTTGA
*
5650505 ACAGTGATAATGATAATT
1 ACAGTGACAATGATAATT
5650523 ACAGTGACAATGATAAT
1 ACAGTGACAATGATAAT
5650540 GATAATGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.29
Consensus pattern (18 bp):
ACAGTGACAATGATAATT
Found at i:5650554 original size:18 final size:18
Alignment explanation
Indices: 5650532--5650572 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
5650522 TACAGTGACA
5650532 ATGATAATGATAATGATG
1 ATGATAATGATAATGATG
* *
5650550 TTGATAATGATATTGATG
1 ATGATAATGATAATGATG
5650568 ATGAT
1 ATGAT
5650573 GATGCTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.22, T:0.39
Consensus pattern (18 bp):
ATGATAATGATAATGATG
Found at i:5650558 original size:24 final size:23
Alignment explanation
Indices: 5650509--5650573 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
5650499 TCTTGAACAG
* *
5650509 TGATAATGATAATTACAGTGACAA
1 TGATAATGATAATGA-TGTGACAA
*
5650533 TGATAATGATAATGATGTTGATAA
1 TGATAATGATAATGATG-TGACAA
* *
5650557 TGATATTGATGATGATG
1 TGATAATGATAATGATG
5650574 ATGCTGATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (23 bp):
TGATAATGATAATGATGTGACAA
Found at i:5665832 original size:19 final size:19
Alignment explanation
Indices: 5665808--5665849 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5665798 ATTAGTTGGG
*
5665808 AAAAAAGAC-AAAAATAA-T
1 AAAAAAAACTAAAAA-AACT
5665826 AAAAAAAACTAAAAAAACT
1 AAAAAAAACTAAAAAAACT
5665845 AAAAA
1 AAAAA
5665850 TTTGAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.81, C:0.07, G:0.02, T:0.10
Consensus pattern (19 bp):
AAAAAAAACTAAAAAAACT
Found at i:5668997 original size:18 final size:20
Alignment explanation
Indices: 5668957--5668994 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5668947 TAAGACATTA
5668957 AACATCATAAACAAAACAAAC
1 AACATCAT-AACAAAACAAAC
5668978 AACATCAT-ACAAAACAA
1 AACATCATAACAAAACAA
5668995 CAATCCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.66, C:0.24, G:0.00, T:0.11
Consensus pattern (20 bp):
AACATCATAACAAAACAAAC
Found at i:5671219 original size:16 final size:16
Alignment explanation
Indices: 5671194--5671226 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5671184 AATCATAAAT
5671194 TTAATAATAATAATAA
1 TTAATAATAATAATAA
*
5671210 TTAATGATAATAATAA
1 TTAATAATAATAATAA
5671226 T
1 T
5671227 ATGCAAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
TTAATAATAATAATAA
Found at i:5671414 original size:22 final size:22
Alignment explanation
Indices: 5671386--5671428 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5671376 AATTTTGAGT
5671386 TATTAAAAA-AATATATCTTATA
1 TATTAAAAATAATATAT-TTATA
5671408 TATTAAAAATAATATATTTAT
1 TATTAAAAATAATATATTTAT
5671429 CTACTCACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TATTAAAAATAATATATTTATA
Found at i:5684509 original size:42 final size:41
Alignment explanation
Indices: 5684416--5684509 Score: 95
Period size: 42 Copynumber: 2.3 Consensus size: 41
5684406 GAACTTGAAC
5684416 ATTTTTC--GCCTTAGAAACTTTTATTTACTTACTATTGCA
1 ATTTTTCTTGCCTTAGAAACTTTTATTTACTTACTATTGCA
* * ** *
5684455 ATTAATTT-TTGCCTTAGCAATTTTTATTTGTTTACTCTTGCA
1 ATT--TTTCTTGCCTTAGAAACTTTTATTTACTTACTATTGCA
5684497 TATTTTTCTTGCC
1 -ATTTTTCTTGCC
5684510 ACGAAAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
39 3 0.07
41 6 0.14
42 32 0.73
43 3 0.07
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (41 bp):
ATTTTTCTTGCCTTAGAAACTTTTATTTACTTACTATTGCA
Found at i:5686217 original size:21 final size:21
Alignment explanation
Indices: 5686191--5686246 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
5686181 CCTGAAAGAA
5686191 TTCATGGCTTCAA-AAAATGAT
1 TTCATGGCTTCAACAAAAT-AT
5686212 TTCATGGCTTCAACAAAATAT
1 TTCATGGCTTCAACAAAATAT
5686233 TTCATGGCTTCAAC
1 TTCATGGCTTCAAC
5686247 TAAGGCCTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 29 0.85
22 5 0.15
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (21 bp):
TTCATGGCTTCAACAAAATAT
Found at i:5687294 original size:42 final size:41
Alignment explanation
Indices: 5687208--5687363 Score: 113
Period size: 42 Copynumber: 3.8 Consensus size: 41
5687198 AGGAAGCCGA
* * * **
5687208 AGTA-GACATTTTTTGCCATGGCAAATTTTTACATTTGGAA-G
1 AGTATGACAATTTTTGCCAAGACAAATTTTT-CAACT-GAAGG
*
5687249 AGTATGACAATTTTTGCCAAGGCAATATTTTTCAACTGAAGG
1 AGTATGACAATTTTTGCCAAGACAA-ATTTTTCAACTGAAGG
* * * * *
5687291 AGTATGACAACTTTGGCCACGACGATATTTTAT-AGCCTG-AGG
1 AGTATGACAATTTTTGCCAAGAC-AAATTTT-TCA-ACTGAAGG
* *
5687333 AGCATGACAATTTTTGTCAAGACAAATTTTT
1 AGTATGACAATTTTTGCCAAGACAAATTTTT
5687364 TTAGAAGGAG
Statistics
Matches: 93, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
40 1 0.01
41 13 0.14
42 68 0.73
43 11 0.12
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (41 bp):
AGTATGACAATTTTTGCCAAGACAAATTTTTCAACTGAAGG
Found at i:5695984 original size:7 final size:7
Alignment explanation
Indices: 5695971--5696001 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
5695961 GTCAAAGAAA
5695971 GTCAACG
1 GTCAACG
*
5695978 ATCAACG
1 GTCAACG
5695985 GTCAACG
1 GTCAACG
5695992 GTCAACG
1 GTCAACG
5695999 GTC
1 GTC
5696002 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:5696008 original size:5 final size:5
Alignment explanation
Indices: 5695998--5696065 Score: 82
Period size: 5 Copynumber: 12.8 Consensus size: 5
5695988 AACGGTCAAC
* *
5695998 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
5696047 GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC
5696066 AGACCGGTCA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
5 47 0.85
7 8 0.15
ACGTcount: A:0.06, C:0.22, G:0.53, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:5696019 original size:22 final size:22
Alignment explanation
Indices: 5695991--5696060 Score: 140
Period size: 22 Copynumber: 3.2 Consensus size: 22
5695981 AACGGTCAAC
5695991 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
5696013 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
5696035 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
5696057 GGTC
1 GGTC
5696061 GGGTCAGACC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.09, C:0.23, G:0.50, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:5696080 original size:9 final size:9
Alignment explanation
Indices: 5696062--5696160 Score: 72
Period size: 9 Copynumber: 10.3 Consensus size: 9
5696052 GGTCGGGTCG
*
5696062 GGTCAGACC
1 GGTCAAACC
5696071 GGTCAAACC
1 GGTCAAACC
* * *
5696080 GATTCAGACA
1 G-GTCAAACC
5696090 GGTCAAACC
1 GGTCAAACC
*
5696099 GGTTCGAACC
1 GG-TCAAACC
*
5696109 GGTTGAAACC
1 GG-TCAAACC
5696119 GGTCAAACC
1 GGTCAAACC
5696128 GGTCAGAACC
1 GGTCA-AACC
*
5696138 GGTTGAAAACC
1 GG-T-CAAACC
*
5696149 GGTTAAACC
1 GGTCAAACC
5696158 GGT
1 GGT
5696161 TTCCAGCAGC
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
9 35 0.49
10 29 0.40
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:5696122 original size:29 final size:31
Alignment explanation
Indices: 5696090--5696161 Score: 114
Period size: 29 Copynumber: 2.4 Consensus size: 31
5696080 GATTCAGACA
5696090 GGTCAAACCGGTTC-GAACCGGTTG-AAACC
1 GGTCAAACCGGTTCAGAACCGGTTGAAAACC
5696119 GGTCAAACCGG-TCAGAACCGGTTGAAAACC
1 GGTCAAACCGGTTCAGAACCGGTTGAAAACC
*
5696149 GGTTAAACCGGTT
1 GGTCAAACCGGTT
5696162 TCCAGCAGCC
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 21 0.54
30 15 0.38
31 1 0.03
ACGTcount: A:0.29, C:0.25, G:0.28, T:0.18
Consensus pattern (31 bp):
GGTCAAACCGGTTCAGAACCGGTTGAAAACC
Found at i:5696139 original size:19 final size:19
Alignment explanation
Indices: 5696062--5696160 Score: 71
Period size: 19 Copynumber: 5.2 Consensus size: 19
5696052 GGTCGGGTCG
5696062 GGTCAG-ACCGGTCAAACC
1 GGTCAGAACCGGTCAAACC
* *
5696080 GATTCAG-ACAGGTCAAACC
1 G-GTCAGAACCGGTCAAACC
*
5696099 GGTTC-GAACCGGTTGAAACC
1 GG-TCAGAACCGG-TCAAACC
5696119 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
* * *
5696138 GGTTGAAAACCGGTTAAACC
1 GG-TCAGAACCGGTCAAACC
5696158 GGT
1 GGT
5696161 TTCCAGCAGC
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
18 4 0.06
19 37 0.57
20 16 0.25
21 8 0.12
ACGTcount: A:0.30, C:0.26, G:0.27, T:0.16
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:5703324 original size:7 final size:7
Alignment explanation
Indices: 5703312--5703342 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
5703302 GTCAAAGAAA
5703312 GTCAACG
1 GTCAACG
5703319 GTCAACG
1 GTCAACG
5703326 GTCAACG
1 GTCAACG
5703333 GTCAACG
1 GTCAACG
5703340 GTC
1 GTC
5703343 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:5703349 original size:5 final size:5
Alignment explanation
Indices: 5703339--5703401 Score: 63
Period size: 5 Copynumber: 11.8 Consensus size: 5
5703329 AACGGTCAAC
* * *
5703339 GGTCG GGTCG GGTCG GGTCAAC GATCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
5703388 GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC
5703402 AACGGTCAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 41 0.85
7 7 0.15
ACGTcount: A:0.08, C:0.22, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:5703360 original size:22 final size:22
Alignment explanation
Indices: 5703332--5703408 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
5703322 AACGGTCAAC
5703332 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
5703354 GGTCAACGATCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
5703376 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
5703398 GGTCAACGGTC
1 GGTCAACGGTC
5703409 AAACCGATTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:5703453 original size:29 final size:31
Alignment explanation
Indices: 5703421--5703495 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
5703411 ACCGATTCAG
5703421 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
5703450 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
5703480 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
5703496 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:5703473 original size:19 final size:19
Alignment explanation
Indices: 5703404--5703494 Score: 71
Period size: 19 Copynumber: 4.7 Consensus size: 19
5703394 GTCGGGTCAA
*
5703404 CGGTCAAACCGATTCAG-AC
1 CGGTCAAACCG-GTCAGAAC
5703423 CGGTCAAACCGGTTC-GAAC
1 CGGTCAAACCGG-TCAGAAC
*
5703442 CGGTTGAAACCGGTCA-AAC
1 CGG-TCAAACCGGTCAGAAC
* *
5703461 CGGTCAGAACCGGTTGAAAAC
1 CGGTCA-AACCGG-TCAGAAC
*
5703482 CGGTTAAACCGGT
1 CGGTCAAACCGGT
5703495 TTCCAGCAGC
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
18 3 0.05
19 33 0.55
20 16 0.27
21 8 0.13
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.16
Consensus pattern (19 bp):
CGGTCAAACCGGTCAGAAC
Found at i:5703495 original size:9 final size:9
Alignment explanation
Indices: 5703421--5703495 Score: 69
Period size: 9 Copynumber: 7.8 Consensus size: 9
5703411 ACCGATTCAG
*
5703421 ACCGGTCAA
1 ACCGGTTAA
*
5703430 ACCGGTTCGA
1 ACCGGTT-AA
5703440 ACCGGTTGAA
1 ACCGGTT-AA
*
5703450 ACCGGTCAA
1 ACCGGTTAA
*
5703459 ACCGGTCAGA
1 ACCGGTTA-A
5703469 ACCGGTTGAAA
1 ACCGGTT--AA
5703480 ACCGGTTAA
1 ACCGGTTAA
5703489 ACCGGTT
1 ACCGGTT
5703496 TCCAGCAGCC
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
9 25 0.45
10 22 0.39
11 8 0.14
12 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:5706577 original size:17 final size:17
Alignment explanation
Indices: 5706533--5706578 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
5706523 ATCAAACATT
5706533 CAAAACACA-AAATATC
1 CAAAACACACAAATATC
5706549 C-AAACA-ACCAAATATC
1 CAAAACACA-CAAATATC
5706565 CAAAACACACAAAT
1 CAAAACACACAAAT
5706579 CCATCGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.04
15 5 0.19
16 9 0.35
17 10 0.38
18 1 0.04
ACGTcount: A:0.61, C:0.28, G:0.00, T:0.11
Consensus pattern (17 bp):
CAAAACACACAAATATC
Found at i:5708058 original size:18 final size:18
Alignment explanation
Indices: 5708035--5708069 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5708025 AAAACAATAT
5708035 AATTAAATCAAAAACAAC
1 AATTAAATCAAAAACAAC
*
5708053 AATTAAGTCAAAAACAA
1 AATTAAATCAAAAACAA
5708070 TTTTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.14, G:0.03, T:0.17
Consensus pattern (18 bp):
AATTAAATCAAAAACAAC
Found at i:5714248 original size:20 final size:20
Alignment explanation
Indices: 5714223--5714272 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
5714213 AAACCAACAA
5714223 TATCGATACTGG-CAATGGGG
1 TATCGATACTGGTC-ATGGGG
5714243 TATCGATACTGGTCATGGGG
1 TATCGATACTGGTCATGGGG
5714263 TATCGATACT
1 TATCGATACT
5714273 ACTATGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (20 bp):
TATCGATACTGGTCATGGGG
Found at i:5714667 original size:18 final size:18
Alignment explanation
Indices: 5714644--5714679 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5714634 ATTTGAATAA
5714644 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
5714662 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
5714680 CTTAAAAATT
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:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (18 bp):
TTGAATCGAATATAAAAT
Found at i:5715757 original size:32 final size:31
Alignment explanation
Indices: 5715707--5715768 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
5715697 AAAGAATATA
*
5715707 ATTCTGATTACAACTCTTTTAATGAATATTTT
1 ATTCAGATTACAACTC-TTTAATGAATATTTT
* * *
5715739 ATTCAGATTATAAGTCTTTAATGGATATTT
1 ATTCAGATTACAACTCTTTAATGAATATTT
5715769 AATTTAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (31 bp):
ATTCAGATTACAACTCTTTAATGAATATTTT
Found at i:5719653 original size:17 final size:17
Alignment explanation
Indices: 5719631--5719672 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5719621 GCGTTTCTTG
* *
5719631 CTCGAATGAGAGTTTTT
1 CTCGAATGAGAATTTCT
*
5719648 CTCGAAAGAGAATTTCT
1 CTCGAATGAGAATTTCT
5719665 CTC-AATGA
1 CTCGAATGA
5719673 AAGGAAATGG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (17 bp):
CTCGAATGAGAATTTCT
Found at i:5723990 original size:45 final size:45
Alignment explanation
Indices: 5723935--5724027 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
5723925 TATTTCTCTC
5723935 ACTATGTTGGAGCTATTACCAACATTACCCAACTTATTTCCTAAG
1 ACTATGTTGGAGCTATTACCAACATTACCCAACTTATTTCCTAAG
* *
5723980 ACTATGTTGGAGCTATTACCAACGTTACCTAACTTATTTCCTAAG
1 ACTATGTTGGAGCTATTACCAACATTACCCAACTTATTTCCTAAG
5724025 ACT
1 ACT
5724028 CACATCATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (45 bp):
ACTATGTTGGAGCTATTACCAACATTACCCAACTTATTTCCTAAG
Found at i:5741174 original size:55 final size:55
Alignment explanation
Indices: 5741035--5741436 Score: 481
Period size: 55 Copynumber: 7.3 Consensus size: 55
5741025 TTTACTAAGA
* * * *
5741035 TGCACACGTAGTGCCA--TACGG-TAGTTCATCAACTCATGATGAATTTCGTGG-GT
1 TGCACACATAGTG-CATGTACGGTTA-TTCATCAACTCATGATGAATTCCATGGATT
* * * *
5741088 TGCACATATCGTGCATGTACGATTATTCATCAACTCATGATGAATTCTATGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
* * * * * *
5741143 TGCACACATATTACTTGTATGTTTATTCATCAACTCATGATGAATTCTATGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
* * *
5741198 TGCACACATAGTGCATGTGCGGTTATTCATCAACTCATAATGAATTCCGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
* * * *
5741253 TGCACACATAGTGCATGTTCGGTAACTCATCAACACATGATGAATTCCATGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
*
5741308 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATTT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCATGGA-TT
* * * * **
5741364 TG-ACACATAGTGCATGCACGATTATTTATCAACTCATGCTGAATTCTGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
*
5741418 TGCACACATAGTGCCTGTA
1 TGCACACATAGTGCATGTA
5741437 TAACACTTAG
Statistics
Matches: 301, Mismatches: 42, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
52 2 0.01
53 10 0.03
54 32 0.11
55 253 0.84
56 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (55 bp):
TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
Found at i:5749234 original size:55 final size:55
Alignment explanation
Indices: 5749155--5749459 Score: 477
Period size: 55 Copynumber: 5.5 Consensus size: 55
5749145 ATCGTGTCGA
*
5749155 TACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCATG
1 TACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCTTG
* * *
5749210 TACAGTTATTCATCAACTCATGATGAATTCTATAGATTTGCACACATAGTGCTTG
1 TACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCTTG
*** *
5749265 TACGGTTATTCATCAACTCATGATGAATTTTGTGTATTTGCACACATAGTGCTTG
1 TACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCTTG
* * *
5749320 TACTGTTATTCATCAACTCATGATGAATTTCATGGATTTGCACACATAGTGCCTG
1 TACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCTTG
*
5749375 TACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTG-TCTG
1 TACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCT-TG
*
5749430 CACGGTTATTCATCAACTCATGATGAATTC
1 TACGGTTATTCATCAACTCATGATGAATTC
5749460 TGTAGAATTA
Statistics
Matches: 230, Mismatches: 19, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
55 230 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (55 bp):
TACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCTTG
Found at i:5749357 original size:165 final size:164
Alignment explanation
Indices: 5749084--5749458 Score: 531
Period size: 165 Copynumber: 2.3 Consensus size: 164
5749074 TTTATTAAGA
* * * * ** *
5749084 TGCACACGTAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATTTTGTGGGTTGAACGTATC
1 TGCACACATAGTGCTTGTACGGTTA-TTCATCAACTCATGATGAATTTTGTGAGTTGAACACATA
5749148 GTGTCGATACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCATGTAC
65 GTGTCGATACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCATGTAC
*
5749213 AGTTATTCATCAACTCATGATGAATTCTATAGATT
130 AGTTATTCATCAACTCATGATGAATTCCATAGATT
* *
5749248 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTTTGTGTATTTGCACACATA
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTTTGTG-AGTTGAACACATA
* * * *
5749313 GTGCTTG-TACTGTTATTCATCAACTCATGATGAATTTCATGGATTTGCACACATAGTGCCTGTA
65 GTG-TCGATACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCATGTA
* * *
5749377 CGGTTATTCATCAACTCATGATGAATTCCGTGGATT
129 CAGTTATTCATCAACTCATGATGAATTCCATAGATT
*
5749413 TGCACACATAGTG-TCTGCACGGTTATTCATCAACTCATGATGAATT
1 TGCACACATAGTGCT-TGTACGGTTATTCATCAACTCATGATGAATT
5749459 CTGTAGAATT
Statistics
Matches: 189, Mismatches: 18, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
164 46 0.24
165 141 0.75
166 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (164 bp):
TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTTTGTGAGTTGAACACATAG
TGTCGATACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCATGTACA
GTTATTCATCAACTCATGATGAATTCCATAGATT
Found at i:5749474 original size:55 final size:54
Alignment explanation
Indices: 5749084--5749479 Score: 469
Period size: 55 Copynumber: 7.2 Consensus size: 54
5749074 TTTATTAAGA
* * * * **
5749084 TGCACACGTAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATTTTGTGGGT
1 TGCACACATAGTGCTTGTACGGTTA-TTCATCAACTCATGATGAATTCTGTGATT
* ** * *
5749138 TGAACGTATCGTG-TCGATACGGTTATTCATCAACTCATGATGAATTCCATG-GATT
1 TGCACACATAGTGCTTG-TACGGTTATTCATCAACTCATGATGAATT-C-TGTGATT
* * *
5749193 TGCACACATAGTGCATGTACAGTTATTCATCAACTCATGATGAATTCTATAGATT
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCTGT-GATT
*
5749248 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTTTGTGTATT
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCTGTG-ATT
*
5749303 TGCACACATAGTGCTTGTACTGTTATTCATCAACTCATGATGAATTTCATG-GATT
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAA-TTC-TGTGATT
* *
5749358 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCTGT-GATT
* *
5749413 TGCACACATAGTG-TCTGCACGGTTATTCATCAACTCATGATGAATTCTGTAGAAT
1 TGCACACATAGTGCT-TGTACGGTTATTCATCAACTCATGATGAATTCTGT-GATT
*
5749468 TACACACATAGT
1 TGCACACATAGT
5749480 CCCTATAGTA
Statistics
Matches: 295, Mismatches: 34, Indels: 25
0.83 0.10 0.07
Matches are distributed among these distances:
53 2 0.01
54 39 0.13
55 246 0.83
56 6 0.02
57 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (54 bp):
TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCTGTGATT
Found at i:5752187 original size:25 final size:25
Alignment explanation
Indices: 5752153--5752200 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
5752143 AGGGATGCAG
*
5752153 CAGTGGTCCCCTCCTGGGTAGCTAA
1 CAGTGGTCCCCTCCTGGGCAGCTAA
*
5752178 CAGTGGTCCCCTTCTGGGCAGCT
1 CAGTGGTCCCCTCCTGGGCAGCT
5752201 GGGCATACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.12, C:0.33, G:0.29, T:0.25
Consensus pattern (25 bp):
CAGTGGTCCCCTCCTGGGCAGCTAA
Found at i:5752520 original size:20 final size:20
Alignment explanation
Indices: 5752491--5752529 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5752481 TTTCCACCAC
*
5752491 ATGCAACTATATGCTCTTAA
1 ATGCAACTATATGATCTTAA
*
5752511 ATGCATCTATATGATCTTA
1 ATGCAACTATATGATCTTA
5752530 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (20 bp):
ATGCAACTATATGATCTTAA
Found at i:5766452 original size:20 final size:21
Alignment explanation
Indices: 5766412--5766453 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
5766402 ACAAATGATA
5766412 ATGTTGTGGCAAAATGAGATGG
1 ATGTTGTGG-AAAATGAGATGG
*
5766434 ATGTTGTGG-AAATGGGATGG
1 ATGTTGTGGAAAATGAGATGG
5766454 TGGTAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.40, T:0.29
Consensus pattern (21 bp):
ATGTTGTGGAAAATGAGATGG
Found at i:5771226 original size:18 final size:19
Alignment explanation
Indices: 5771181--5771226 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
5771171 CCCATATGGA
5771181 GAGTATCGATACTACCCCCTT
1 GAGTATCGATACT--CCCCTT
5771202 G-GTATCGATACT-CCCTT
1 GAGTATCGATACTCCCCTT
5771219 GAGTATCG
1 GAGTATCG
5771227 GTACCAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.25
18 6 0.25
20 11 0.46
21 1 0.04
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (19 bp):
GAGTATCGATACTCCCCTT
Found at i:5781456 original size:11 final size:11
Alignment explanation
Indices: 5781442--5781493 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
5781432 ATTAATATAA
5781442 ATTATATTTAT
1 ATTATATTTAT
*
5781453 ATTATAATTAT
1 ATTATATTTAT
5781464 -TT-TATTTAT
1 ATTATATTTAT
*
5781473 -TTATATTTTT
1 ATTATATTTAT
5781483 ATTATAATTTA
1 ATTAT-ATTTA
5781494 AGTTAATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
9 8 0.24
10 8 0.24
11 14 0.41
12 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTATATTTAT
Found at i:5792715 original size:35 final size:35
Alignment explanation
Indices: 5792676--5792786 Score: 177
Period size: 35 Copynumber: 3.2 Consensus size: 35
5792666 AACACAGCCC
* * * *
5792676 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
1 TCAATTACATTTTAAACCCCAAATTTTAAAATACT
5792711 TCAATTACATTTTAAACCCCAAATTTTAAAATACT
1 TCAATTACATTTTAAACCCCAAATTTTAAAATACT
5792746 TCAATTACATTTTAAACCCCAAATTTTAAAATACT
1 TCAATTACATTTTAAACCCCAAATTTTAAAATACT
*
5792781 TTAATT
1 TCAATT
5792787 TAGGGTTTAG
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 71 1.00
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (35 bp):
TCAATTACATTTTAAACCCCAAATTTTAAAATACT
Found at i:5792822 original size:35 final size:35
Alignment explanation
Indices: 5792790--5792857 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
5792780 TTTAATTTAG
*
5792790 GGTTTAGAATGTAATTAAAGTATTTTGGAATTTGA
1 GGTTTAGAATATAATTAAAGTATTTTGGAATTTGA
* *
5792825 GGTTTAGAATATAATTGAAGTGTTTTGGAATTT
1 GGTTTAGAATATAATTAAAGTATTTTGGAATTT
5792858 TAAACATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (35 bp):
GGTTTAGAATATAATTAAAGTATTTTGGAATTTGA
Found at i:5804517 original size:64 final size:64
Alignment explanation
Indices: 5804407--5804565 Score: 169
Period size: 64 Copynumber: 2.5 Consensus size: 64
5804397 TTAATATGTT
* * * * *
5804407 CATCGATGCACTACTCATGCATCGATACACAAATCACCTTCAATGTTTTCA-TTTTAAGGGGGTG
1 CATCGATGCACTCCTTATGCATCGATACACAAATCACATTCAATGTTTCCATTTTTAA-GGGATG
* * ** * *
5804471 CATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGGATG
1 CATCGATGCACTCCTTATGCATCGATACACAAATCACATTCAATGTTTCCATTTTTAAGGGATG
* *
5804535 TATCGATGCACTTCC-TGTGCATCGATACACA
1 CATCGATGCAC-TCCTTATGCATCGATACACA
5804566 CTGAACAATT
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
64 69 0.88
65 9 0.12
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (64 bp):
CATCGATGCACTCCTTATGCATCGATACACAAATCACATTCAATGTTTCCATTTTTAAGGGATG
Found at i:5808119 original size:20 final size:20
Alignment explanation
Indices: 5808094--5808131 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5808084 TTCCCTTTGA
*
5808094 AGTGCATTGATGCATTCTAT
1 AGTGCATCGATGCATTCTAT
5808114 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
5808132 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAT
Found at i:5808250 original size:18 final size:20
Alignment explanation
Indices: 5808204--5808250 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
5808194 TTTAAGGGTG
*
5808204 TGCATT-GATGCACTCCTTA
1 TGCATTCGATGCACTCATTA
5808223 TGCA-TCGATGCACT-ATT-
1 TGCATTCGATGCACTCATTA
5808240 TGCATTCGATG
1 TGCATTCGATG
5808251 TTTCCATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.16
18 9 0.36
19 12 0.48
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (20 bp):
TGCATTCGATGCACTCATTA
Found at i:5808252 original size:64 final size:65
Alignment explanation
Indices: 5808138--5808300 Score: 179
Period size: 64 Copynumber: 2.5 Consensus size: 65
5808128 TTCTTTAACA
* * * *
5808138 TGTGCATCGATGCACTACTCATGCATCGATACACAAATCACCTTCAATGTTTTCA-TTTTAAGGG
1 TGTGCATCGATGCACTCCTTATGCATCGATACACAAATCACATTCAATGTTTCCATTTTTAAGGG
* * * * ** * *
5808202 TGTGCATTGATGCACTCCTTATGCATCGATGCACTATTTGCATTCGATGTTTCCATTTTTAATGG
1 TGTGCATCGATGCACTCCTTATGCATCGATACACAAATCACATTCAATGTTTCCATTTTTAAGGG
*
5808267 -GTGCATCGATGCACTTCC-TGTGCATCGATACACA
1 TGTGCATCGATGCAC-TCCTTATGCATCGATACACA
5808301 CTGAACAATT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
64 70 0.86
65 11 0.14
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (65 bp):
TGTGCATCGATGCACTCCTTATGCATCGATACACAAATCACATTCAATGTTTCCATTTTTAAGGG
Found at i:5810972 original size:35 final size:35
Alignment explanation
Indices: 5810931--5811011 Score: 153
Period size: 35 Copynumber: 2.3 Consensus size: 35
5810921 GGGAAGAACA
*
5810931 GTATCGATACCCAGGGTACCAATACCTTAAAGAAT
1 GTATCGATACCCAGGGTACCAATACCTTAAAGAAG
5810966 GTATCGATACCCAGGGTACCAATACCTTAAAGAAG
1 GTATCGATACCCAGGGTACCAATACCTTAAAGAAG
5811001 GTATCGATACC
1 GTATCGATACC
5811012 TTCTTTGAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (35 bp):
GTATCGATACCCAGGGTACCAATACCTTAAAGAAG
Found at i:5811879 original size:25 final size:25
Alignment explanation
Indices: 5811845--5811906 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
5811835 TTCTATGTGA
5811845 TCCTTCGGGACATATGTGATAGTGG
1 TCCTTCGGGACATATGTGATAGTGG
5811870 TCCTTCGGGACATATGTGATAGTGG
1 TCCTTCGGGACATATGTGATAGTGG
5811895 TCCTTCGGGACA
1 TCCTTCGGGACA
5811907 AATTCTACGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (25 bp):
TCCTTCGGGACATATGTGATAGTGG
Found at i:5824507 original size:21 final size:21
Alignment explanation
Indices: 5824481--5824599 Score: 163
Period size: 21 Copynumber: 5.8 Consensus size: 21
5824471 AGAACCACTA
5824481 TGTCCCGAAGGACCACTGATT
1 TGTCCCGAAGGACCACTGATT
*
5824502 TGTCCCGAAAGACCACTGATT
1 TGTCCCGAAGGACCACTGATT
*
5824523 TGTTCCGAAGGACCACTGATT
1 TGTCCCGAAGGACCACTGATT
*
5824544 TGCCCCGAAGGACCACTGATT
1 TGTCCCGAAGGACCACTGATT
* *
5824565 TGCCCCGAAAGACCACT-A--
1 TGTCCCGAAGGACCACTGATT
*
5824583 TGTCCCGAAGGATCACT
1 TGTCCCGAAGGACCACT
5824600 CCTTAAGAAC
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
18 14 0.16
20 1 0.01
21 74 0.83
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (21 bp):
TGTCCCGAAGGACCACTGATT
Found at i:5824559 original size:63 final size:60
Alignment explanation
Indices: 5824460--5824581 Score: 181
Period size: 63 Copynumber: 2.0 Consensus size: 60
5824450 GGCACTGTAT
* * *
5824460 ATTTGTTTCGAAGAACCACTATGTCCCGAAGGACCACTGATTTGTCCCGAAAGACCACTG
1 ATTTGTTCCGAAGAACCACTATGCCCCGAAGGACCACTGATTTGCCCCGAAAGACCACTG
*
5824520 ATTTGTTCCGAAGGACCACTGATTTGCCCCGAAGGACCACTGATTTGCCCCGAAAGACCACT
1 ATTTGTTCCGAAGAACCACT-A--TGCCCCGAAGGACCACTGATTTGCCCCGAAAGACCACT
5824582 ATGTCCCGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
60 18 0.33
61 1 0.02
63 36 0.65
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (60 bp):
ATTTGTTCCGAAGAACCACTATGCCCCGAAGGACCACTGATTTGCCCCGAAAGACCACTG
Found at i:5829876 original size:18 final size:18
Alignment explanation
Indices: 5829853--5829887 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5829843 ACTGTATATT
5829853 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
5829871 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
5829888 CCTTAAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:5834242 original size:21 final size:21
Alignment explanation
Indices: 5834216--5834258 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5834206 AGCACTTCCA
5834216 AGAATTACCTTTGATGAGATT
1 AGAATTACCTTTGATGAGATT
5834237 AGAATTACCTTTGATGAGATT
1 AGAATTACCTTTGATGAGATT
5834258 A
1 A
5834259 TATCCAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (21 bp):
AGAATTACCTTTGATGAGATT
Found at i:5838651 original size:3 final size:3
Alignment explanation
Indices: 5838643--5838670 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5838633 AATCCAAAAT
5838643 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5838671 CTTTTCTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5845096 original size:29 final size:30
Alignment explanation
Indices: 5845027--5845104 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
5845017 ATTTTAAAAA
* * *
5845027 TTACATTTTTAGTCCCTAAACTTTTCCAAGT
1 TTACA-TTTTGGTCACTAAACTTTTCAAAGT
* * *
5845058 TTATACTTTGGTCACTAAAC-TTTCAAATT
1 TTACATTTTGGTCACTAAACTTTTCAAAGT
5845087 TTACATTTTGGTCACTAA
1 TTACATTTTGGTCACTAA
5845105 CTAAAATTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 23 0.59
30 12 0.31
31 4 0.10
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.45
Consensus pattern (30 bp):
TTACATTTTGGTCACTAAACTTTTCAAAGT
Found at i:5848448 original size:42 final size:45
Alignment explanation
Indices: 5848357--5848450 Score: 104
Period size: 46 Copynumber: 2.1 Consensus size: 45
5848347 TAACTTAAAA
* *
5848357 ACCCGACCCGACCCGAGTTAATTTTTTATTTAATAAAACTCGACTCG
1 ACCCGACCAGACCCGAGTTAATTTTTTATTTAATAAAA--CAACTCG
* * *
5848404 ACCCGACCATACCCGA-TTTATTTTTTATTTACTAAAA-AAC-CG
1 ACCCGACCAGACCCGAGTTAATTTTTTATTTAATAAAACAACTCG
5848446 ACCCG
1 ACCCG
5848451 GATCGACCCA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
42 7 0.17
43 2 0.05
46 19 0.45
47 14 0.33
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.30
Consensus pattern (45 bp):
ACCCGACCAGACCCGAGTTAATTTTTTATTTAATAAAACAACTCG
Found at i:5848706 original size:18 final size:18
Alignment explanation
Indices: 5848683--5848717 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5848673 TATCAAGAAA
5848683 GAAGTATAATT-ATAATAT
1 GAAGTA-AATTGATAATAT
5848701 GAAGTAAATTGATAATA
1 GAAGTAAATTGATAATA
5848718 ACAATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (18 bp):
GAAGTAAATTGATAATAT
Found at i:5857192 original size:19 final size:19
Alignment explanation
Indices: 5857168--5857208 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
5857158 TGAAAAAATT
5857168 GTATCGGTACCATAGCATA
1 GTATCGGTACCATAGCATA
*
5857187 GTATCGGTACCATAGTATA
1 GTATCGGTACCATAGCATA
5857206 GTA
1 GTA
5857209 GTGTCGATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (19 bp):
GTATCGGTACCATAGCATA
Found at i:5857219 original size:22 final size:22
Alignment explanation
Indices: 5857185--5857239 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
5857175 TACCATAGCA
*
5857185 TAGTATCGGTACCATAGTATAG
1 TAGTATCGATACCATAGTATAG
* *
5857207 TAGTGTCGATACCATGGTAT-G
1 TAGTATCGATACCATAGTATAG
*
5857228 -GGTATCGATACC
1 TAGTATCGATACC
5857240 GAGGAGTCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 10 0.36
21 1 0.04
22 17 0.61
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (22 bp):
TAGTATCGATACCATAGTATAG
Found at i:5857686 original size:55 final size:55
Alignment explanation
Indices: 5857602--5857961 Score: 392
Period size: 55 Copynumber: 6.6 Consensus size: 55
5857592 ATAATGCTTT
**
5857602 AGTTGATGAATAACTATAC-AGACACTATGTGTGTAAACCCACGAAATTCATCATG
1 AGTTGATGAATAACCGTACAAG-CACTATGTGTGTAAACCCACGAAATTCATCATG
* *
5857657 AGTTGATGAATAACCGTACAAGCAATATGTGTGCAAACCCAC-AGAATTCATCATG
1 AGTTGATGAATAACCGTACAAGCACTATGTGTGTAAACCCACGA-AATTCATCATG
* * **
5857712 AGTTGATGAATAACAGTAC-GGACACTATGTGCATAAACCCAC-AGAATTCATCATG
1 AGTTGATGAATAACCGTACAAG-CACTATGTGTGTAAACCCACGA-AATTCATCATG
* * * *
5857767 AGTTGATGAATAACTGTACATGCACTATGTGTGCAAACCCATGAAATTCATCATG
1 AGTTGATGAATAACCGTACAAGCACTATGTGTGTAAACCCACGAAATTCATCATG
* * * * * *
5857822 AGTTTATGAATAACCATACATGCACTAT-TGTG-CAACCCACGAGATTCATCATA
1 AGTTGATGAATAACCGTACAAGCACTATGTGTGTAAACCCACGAAATTCATCATG
* * * * *
5857875 AGTTGGTGAATAACCTTAGAAGAACTATGTGTGT-AACCCACAAAATTCATCATG
1 AGTTGATGAATAACCGTACAAGCACTATGTGTGTAAACCCACGAAATTCATCATG
* * * *
5857929 AGTTGATGAATTACCGTATAGGCACTATTTGTG
1 AGTTGATGAATAACCGTACAAGCACTATGTGTG
5857962 CATTCTAATA
Statistics
Matches: 259, Mismatches: 39, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
53 39 0.15
54 53 0.20
55 163 0.63
56 4 0.02
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (55 bp):
AGTTGATGAATAACCGTACAAGCACTATGTGTGTAAACCCACGAAATTCATCATG
Found at i:5869444 original size:30 final size:29
Alignment explanation
Indices: 5869410--5869467 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
5869400 TTACCTCATT
*
5869410 CATACATAAAGTATGTCAAATTCTCAGTTG
1 CATACATAAAGT-TGTAAAATTCTCAGTTG
* *
5869440 CATACATAATGTTTTAAAATTCTCAGTT
1 CATACATAAAGTTGTAAAATTCTCAGTT
5869468 TCATGCATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (29 bp):
CATACATAAAGTTGTAAAATTCTCAGTTG
Found at i:5869464 original size:29 final size:29
Alignment explanation
Indices: 5869427--5869487 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
5869417 AAAGTATGTC
5869427 AAATTCTCAGTTGCATACATAATGTTTTA
1 AAATTCTCAGTTGCATACATAATGTTTTA
* * **
5869456 AAATTCTCAGTTTCATGCATGGTGTTTTA
1 AAATTCTCAGTTGCATACATAATGTTTTA
5869485 AAA
1 AAA
5869488 ATGACGCGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (29 bp):
AAATTCTCAGTTGCATACATAATGTTTTA
Found at i:5879464 original size:12 final size:12
Alignment explanation
Indices: 5879449--5879485 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
5879439 AAAAAAATCA
5879449 TCATCATCATCT
1 TCATCATCATCT
*
5879461 TCATCAACATCT
1 TCATCATCATCT
*
5879473 TCATCTTCATCT
1 TCATCATCATCT
5879485 T
1 T
5879486 ATGCTTCCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.43
Consensus pattern (12 bp):
TCATCATCATCT
Found at i:5880167 original size:62 final size:62
Alignment explanation
Indices: 5880092--5880213 Score: 167
Period size: 62 Copynumber: 2.0 Consensus size: 62
5880082 TAAAATTTTG
*
5880092 AAAATTTCAAAGTTAAAAATAATATCAA-ACTTTTA-GAAATTTTAACAAATTTGAAAAAAATT
1 AAAATTTCAAAGTTAAAAA-AATATCAATA-TTGTAGGAAATTTTAACAAATTTGAAAAAAATT
** * *
5880154 AAAATTTTGAAGTTAAAAAAATATGAATATTGTAGGAATTTTTAACAAATTTGAAAAAAA
1 AAAATTTCAAAGTTAAAAAAATATCAATATTGTAGGAAATTTTAACAAATTTGAAAAAAA
5880214 AGAAAAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
61 11 0.21
62 42 0.79
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.34
Consensus pattern (62 bp):
AAAATTTCAAAGTTAAAAAAATATCAATATTGTAGGAAATTTTAACAAATTTGAAAAAAATT
Found at i:5881302 original size:22 final size:22
Alignment explanation
Indices: 5881255--5881356 Score: 113
Period size: 22 Copynumber: 4.8 Consensus size: 22
5881245 GTTCAGTATT
*
5881255 CGTCACGAAAGACCACT--AT-
1 CGTCCCGAAAGACCACTAGATA
5881274 -GTCCCGAAAGACCACTAGATA
1 CGTCCCGAAAGACCACTAGATA
* * *
5881295 CGTCCCGAAGGACCATTGGATA
1 CGTCCCGAAAGACCACTAGATA
* *
5881317 CGTCCCGAAGGACCACTGGATA
1 CGTCCCGAAAGACCACTAGATA
*
5881339 CGTCCCGAATGACCACTA
1 CGTCCCGAAAGACCACTA
5881357 TACCCTCGAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
18 15 0.21
20 2 0.03
22 55 0.76
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (22 bp):
CGTCCCGAAAGACCACTAGATA
Found at i:5885902 original size:22 final size:21
Alignment explanation
Indices: 5885855--5885959 Score: 96
Period size: 22 Copynumber: 5.0 Consensus size: 21
5885845 GTTCAGTATT
*
5885855 CGTCACGAAAGACCACT-AT-
1 CGTCCCGAAAGACCACTGATA
5885874 -GTCCCGAAAGACCACTAGATA
1 CGTCCCGAAAGACCACT-GATA
*
5885895 CGTCCCG-AAGAACCATTGGATA
1 CGTCCCGAAAG-ACCACT-GATA
*
5885917 CGTCCCGAAGGACCACTGTATA
1 CGTCCCGAAAGACCACTG-ATA
5885939 CGTCCC-AAAGGACCACT-ATA
1 CGTCCCGAAA-GACCACTGATA
5885959 C
1 C
5885960 CCTCGACTCT
Statistics
Matches: 72, Mismatches: 6, Indels: 15
0.77 0.06 0.16
Matches are distributed among these distances:
18 15 0.21
20 6 0.08
21 6 0.08
22 43 0.60
23 2 0.03
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.16
Consensus pattern (21 bp):
CGTCCCGAAAGACCACTGATA
Found at i:5891170 original size:32 final size:32
Alignment explanation
Indices: 5891129--5891198 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
5891119 GTTTTTTGTT
* *
5891129 AGATGAAAGGAGTTTGTTGTGTAAGAGATTGA
1 AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
5891161 AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
1 AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
5891193 AGATGA
1 AGATGA
5891199 TGTGCACAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.37, C:0.00, G:0.34, T:0.29
Consensus pattern (32 bp):
AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
Found at i:5908019 original size:18 final size:18
Alignment explanation
Indices: 5907996--5908064 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
5907986 TCGAGTTGTT
5907996 TGAAATGACTAAATTATA
1 TGAAATGACTAAATTATA
*
5908014 TGAAATGAGTAAATTATA
1 TGAAATGACTAAATTATA
* * * *
5908032 TAAAAAGACTAAATCAAA
1 TGAAATGACTAAATTATA
*
5908050 TGAAAGGACATAAAT
1 TGAAATGAC-TAAAT
5908065 ACCATCGATT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
18 37 0.88
19 5 0.12
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (18 bp):
TGAAATGACTAAATTATA
Found at i:5913402 original size:123 final size:123
Alignment explanation
Indices: 5913183--5913425 Score: 441
Period size: 123 Copynumber: 2.0 Consensus size: 123
5913173 GGATCTGTTA
5913183 GTTTAATTTTGACTAAAAATCCTGATAATTCAATATAAATCTCGAATGCTACAAATTATCGTTTT
1 GTTTAATTTTGACTAAAAATCCTGATAATTCAATATAAATCTCGAATGCTACAAATTATCGTTTT
5913248 ACCCTTAATGGGTTAAATTACAAAGAATTCTTCGAAAATTAAAATATCTAAAATGCTT
66 ACCCTTAATGGGTTAAATTACAAAGAATTCTTCGAAAATTAAAATATCTAAAATGCTT
** *
5913306 GTTTAATTTTGACTCGAAATCCTGATAATTCAATATAATTCTCGAATGCTACAAATTATCGTTTT
1 GTTTAATTTTGACTAAAAATCCTGATAATTCAATATAAATCTCGAATGCTACAAATTATCGTTTT
* *
5913371 ACCCTTATTGGGTTAAATTACAAAGAATTCTTCGAGAATTAAAATATCTAAAATG
66 ACCCTTAATGGGTTAAATTACAAAGAATTCTTCGAAAATTAAAATATCTAAAATG
5913426 TATCTCATGA
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 115 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (123 bp):
GTTTAATTTTGACTAAAAATCCTGATAATTCAATATAAATCTCGAATGCTACAAATTATCGTTTT
ACCCTTAATGGGTTAAATTACAAAGAATTCTTCGAAAATTAAAATATCTAAAATGCTT
Done.