Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009071.1 Hibiscus syriacus cultivar Beakdansim tig00112501_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: 822590
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:430296 original size:14 final size:14
Alignment explanation
Indices: 430277--430308 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
430267 GTCCCCGAAA
430277 AAAAGAAAAAGAAG
1 AAAAGAAAAAGAAG
430291 AAAAGAAAAAGAAG
1 AAAAGAAAAAGAAG
430305 AAAA
1 AAAA
430309 TGCCACGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAGAAG
Found at i:431701 original size:159 final size:159
Alignment explanation
Indices: 431410--431730 Score: 615
Period size: 159 Copynumber: 2.0 Consensus size: 159
431400 AATACAAATG
431410 GACATACTGGAAGGCTGTAAAAGCTTATCGGAAAGTGGATTTTAATAAGCATATAAATTGTTTAA
1 GACATACTGGAAGGCTGTAAAAGCTTATCGGAAAGTGGATTTTAATAAGCATATAAATTGTTTAA
*
431475 GACGTGTTTTGCCTCAATGTGCTCAAACACTAGAAGATGTCGGGTTTGAAAGATGGTCAAGATTA
66 GACGTGTTTTGCCTCAATGTGCTCAAACACTAGAAGATGTCGGGTTTGAAAGATGGTCAAGAGTA
*
431540 CATCAACTTGGAGTAAGATATGGTTTCGT
131 CATCAACTTGGAGCAAGATATGGTTTCGT
*
431569 GACATACTGGAAGGCTGTAAAAGCTTATCGGGAAGTGGATTTTAATAAGCATATAAATTGTTTAA
1 GACATACTGGAAGGCTGTAAAAGCTTATCGGAAAGTGGATTTTAATAAGCATATAAATTGTTTAA
431634 GACGTGTTTTGCCTCAATGTGCTCAAACACTAGAAGATGTCGGGTTTGAAAGATGGTCAAGAGTA
66 GACGTGTTTTGCCTCAATGTGCTCAAACACTAGAAGATGTCGGGTTTGAAAGATGGTCAAGAGTA
431699 CATCAACTTGGAGCAAGATATGGTTTCGT
131 CATCAACTTGGAGCAAGATATGGTTTCGT
431728 GAC
1 GAC
431731 GTCTAATAGT
Statistics
Matches: 159, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
159 159 1.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (159 bp):
GACATACTGGAAGGCTGTAAAAGCTTATCGGAAAGTGGATTTTAATAAGCATATAAATTGTTTAA
GACGTGTTTTGCCTCAATGTGCTCAAACACTAGAAGATGTCGGGTTTGAAAGATGGTCAAGAGTA
CATCAACTTGGAGCAAGATATGGTTTCGT
Found at i:432532 original size:18 final size:18
Alignment explanation
Indices: 432509--432544 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
432499 AAGCAAAAGG
432509 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
432527 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
432545 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:432787 original size:20 final size:20
Alignment explanation
Indices: 432748--432789 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
432738 TTTTATGTAG
**
432748 TCAAATATGCAACGTGAAAA
1 TCAAATATGCAACGCAAAAA
*
432768 TCAAATTTGCAACGCAAAAA
1 TCAAATATGCAACGCAAAAA
432788 TC
1 TC
432790 GCAATGTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (20 bp):
TCAAATATGCAACGCAAAAA
Found at i:432813 original size:29 final size:29
Alignment explanation
Indices: 432780--432840 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
432770 AAATTTGCAA
**
432780 CGCAAAAATCGCAATGTGAATTTAACTTT
1 CGCAAAAATCGCAATGCAAATTTAACTTT
* *
432809 CGCAACAATCGCAATGCAAATTTTACTTT
1 CGCAAAAATCGCAATGCAAATTTAACTTT
432838 CGC
1 CGC
432841 GTTACGAATT
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:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (29 bp):
CGCAAAAATCGCAATGCAAATTTAACTTT
Found at i:434110 original size:16 final size:15
Alignment explanation
Indices: 434082--434115 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
434072 TCGGAAGACA
434082 TTTTTTTACATAATT
1 TTTTTTTACATAATT
*
434097 TTTTTTCTATATAATT
1 TTTTTT-TACATAATT
434113 TTT
1 TTT
434116 CAATGATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTTTACATAATT
Found at i:436258 original size:26 final size:26
Alignment explanation
Indices: 436222--436312 Score: 129
Period size: 26 Copynumber: 3.7 Consensus size: 26
436212 ACGGTAGGAG
436222 GAGCCTCTTGAACGATGAGATGAGAT
1 GAGCCTCTTGAACGATGAGATGAGAT
*
436248 GAGCCTCTTGAACGATGAAATGAGAT
1 GAGCCTCTTGAACGATGAGATGAGAT
436274 GAGCCTCTTGAACGAT-AG--GAG--
1 GAGCCTCTTGAACGATGAGATGAGAT
*
436295 GCGCCTCTTGAACGATGA
1 GAGCCTCTTGAACGATGA
436313 AATGTGAATT
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.25
22 1 0.02
23 3 0.05
25 1 0.02
26 41 0.67
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.22
Consensus pattern (26 bp):
GAGCCTCTTGAACGATGAGATGAGAT
Found at i:436270 original size:21 final size:22
Alignment explanation
Indices: 436163--436312 Score: 110
Period size: 21 Copynumber: 6.6 Consensus size: 22
436153 GTGAATTGGG
* * *
436163 CTCTTGAACGGTGGGAGGGA-C
1 CTCTTGAACGATGAGAAGGAGC
* *
436184 CTCTTGAACGATGA-CAGGGGC
1 CTCTTGAACGATGAGAAGGAGC
* *
436205 CTCTTGAACGGT-AGGAGGAGC
1 CTCTTGAACGATGAGAAGGAGC
436226 CTCTTGAACGATGAGATGAGATGAGC
1 CTCTTGAACGATGAGA--AG--GAGC
*
436252 CTCTTGAACGATGAAATGAGATGAGC
1 CTCTTGAACGATG--A-GA-AGGAGC
* *
436278 CTCTTGAACGAT-AGGAGGCGC
1 CTCTTGAACGATGAGAAGGAGC
436299 CTCTTGAACGATGA
1 CTCTTGAACGATGA
436313 AATGTGAATT
Statistics
Matches: 104, Mismatches: 14, Indels: 21
0.75 0.10 0.15
Matches are distributed among these distances:
20 3 0.03
21 56 0.54
22 4 0.04
23 1 0.01
24 2 0.02
26 33 0.32
28 3 0.03
29 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.21
Consensus pattern (22 bp):
CTCTTGAACGATGAGAAGGAGC
Found at i:436301 original size:47 final size:50
Alignment explanation
Indices: 436222--436316 Score: 142
Period size: 47 Copynumber: 1.9 Consensus size: 50
436212 ACGGTAGGAG
436222 GAGCCTCTTGAACGATGAGATGAGATGAGCCTCTTGAACGATGAAATGAGAT
1 GAGCCTCTTGAACGATGAGA-GAGA-GAGCCTCTTGAACGATGAAATGAGAT
*
436274 GAGCCTCTTGAACGAT-AG-GAG-GCGCCTCTTGAACGATGAAATG
1 GAGCCTCTTGAACGATGAGAGAGAGAGCCTCTTGAACGATGAAATG
436317 TGAATTGGGC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
47 21 0.50
49 3 0.07
51 2 0.05
52 16 0.38
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (50 bp):
GAGCCTCTTGAACGATGAGAGAGAGAGCCTCTTGAACGATGAAATGAGAT
Found at i:436927 original size:14 final size:14
Alignment explanation
Indices: 436908--436935 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
436898 TGAGAAGAGG
436908 CTCGATCAGGTGAT
1 CTCGATCAGGTGAT
436922 CTCGATCAGGTGAT
1 CTCGATCAGGTGAT
436936 GGCTCTCGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (14 bp):
CTCGATCAGGTGAT
Found at i:439033 original size:20 final size:20
Alignment explanation
Indices: 438983--439074 Score: 80
Period size: 20 Copynumber: 4.6 Consensus size: 20
438973 CAAACGTGCT
* *
438983 TTGCAAATTTAACTTATGTG
1 TTGCGAATTTGACTTATGTG
*
439003 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTATGTG
* * *
439023 TTGTGAATTTGGA--AATCGCG
1 TTGCGAATTT-GACTTAT-GTG
* *
439043 TTACGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTATGTG
439063 TTGCGAATTTGA
1 TTGCGAATTTGA
439075 GATCGCATTG
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
19 3 0.05
20 49 0.89
21 3 0.05
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:441821 original size:21 final size:21
Alignment explanation
Indices: 441797--441846 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
441787 TAATAATATT
441797 AATGAAAATAAAATAAA-ATAA
1 AATGAAAA-AAAATAAATATAA
* *
441818 AATGATAAAAAGTAAATATAA
1 AATGAAAAAAAATAAATATAA
*
441839 AATCAAAA
1 AATGAAAA
441847 GAAAGCACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (21 bp):
AATGAAAAAAAATAAATATAA
Found at i:450072 original size:12 final size:11
Alignment explanation
Indices: 450041--450075 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
450031 ATTATTATTT
450041 AATATAAAATA
1 AATATAAAATA
450052 AATATAAAATA
1 AATATAAAATA
450063 AATAATAAAATA
1 AAT-ATAAAATA
450075 A
1 A
450076 TATTTCTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATATAAAATA
Found at i:451841 original size:29 final size:29
Alignment explanation
Indices: 451808--452016 Score: 297
Period size: 29 Copynumber: 7.4 Consensus size: 29
451798 GACCCGACCC
*
451808 AGTGATTTTTTGGTAATTATTTTGAAAAA
1 AGTGATATTTTGGTAATTATTTTGAAAAA
*
451837 AGTGATAATTTGGTAATTATTTTGAAAAA
1 AGTGATATTTTGGTAATTATTTTGAAAAA
451866 TA-TGATATTTTGGTAATTATTTTG--AAA
1 -AGTGATATTTTGGTAATTATTTTGAAAAA
451893 AGTGATATTTTGGTAATTATTTTG-AAAA
1 AGTGATATTTTGGTAATTATTTTGAAAAA
451921 AGTGATATTTTGGTAATTATTTTGAAAAA
1 AGTGATATTTTGGTAATTATTTTGAAAAA
*
451950 GGTGATATTTTGGTAATTATTTT-AAAAA
1 AGTGATATTTTGGTAATTATTTTGAAAAA
* *
451978 A-TGATATTTTTGTAATT-TTTTTAAAAA
1 AGTGATATTTTGGTAATTATTTTGAAAAA
*
452005 TAGTGCTATTTT
1 -AGTGATATTTT
452017 CATTATAATT
Statistics
Matches: 166, Mismatches: 7, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
26 5 0.03
27 45 0.27
28 33 0.20
29 82 0.49
30 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (29 bp):
AGTGATATTTTGGTAATTATTTTGAAAAA
Found at i:451911 original size:56 final size:56
Alignment explanation
Indices: 451810--452016 Score: 301
Period size: 56 Copynumber: 3.7 Consensus size: 56
451800 CCCGACCCAG
* *
451810 TGATTTTTTGGTAATTATTTTGAAAAAAGTGATAATTTGGTAATTATTTTGAAAAATA
1 TGATATTTTGGTAATTATTTTG-AAAAAGTGATATTTTGGTAATTATTTTGAAAAA-A
*
451868 TGATATTTTGGTAATTATTTTG-AAAAGTGATATTTTGGTAATTATTTTGAAAAAG
1 TGATATTTTGGTAATTATTTTGAAAAAGTGATATTTTGGTAATTATTTTGAAAAAA
451923 TGATATTTTGGTAATTATTTTGAAAAAGGTGATATTTTGGTAATTATTTT-AAAAAA
1 TGATATTTTGGTAATTATTTTGAAAAA-GTGATATTTTGGTAATTATTTTGAAAAAA
* * * *
451979 TGATATTTTTGTAATTTTTTTAAAAATAGTGCTATTTT
1 TGATATTTTGGTAATTATTTTGAAAA-AGTGATATTTT
452017 CATTATAATT
Statistics
Matches: 138, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
55 22 0.16
56 72 0.52
57 23 0.17
58 21 0.15
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.49
Consensus pattern (56 bp):
TGATATTTTGGTAATTATTTTGAAAAAGTGATATTTTGGTAATTATTTTGAAAAAA
Found at i:451956 original size:84 final size:84
Alignment explanation
Indices: 451808--452016 Score: 310
Period size: 84 Copynumber: 2.5 Consensus size: 84
451798 GACCCGACCC
* * *
451808 AGTGATTTTTTGGTAATTATTTTGAAAAAAGTGATAATTTGGTAATTATTTTGAAAAATATGATA
1 AGTGATATTTTGGTAATTATTTTG-AAAAAGTGATATTTTGGTAATTATTTTGAAAAAGATGATA
*
451873 TTTTGGTAATTATTTTGAAA
65 TTTTGGTAATTATTTTAAAA
*
451893 AGTGATATTTTGGTAATTATTTTGAAAAAGTGATATTTTGGTAATTATTTTGAAAAAGGTGATAT
1 AGTGATATTTTGGTAATTATTTTGAAAAAGTGATATTTTGGTAATTATTTTGAAAAAGATGATAT
451958 TTTGGTAATTATTTTAAAA
66 TTTGGTAATTATTTTAAAA
* * * * *
451977 AATGATATTTTTGTAATTTTTTTAAAAATAGTGCTATTTT
1 AGTGATATTTTGGTAATTATTTTGAAAA-AGTGATATTTT
452017 CATTATAATT
Statistics
Matches: 113, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
84 80 0.71
85 33 0.29
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (84 bp):
AGTGATATTTTGGTAATTATTTTGAAAAAGTGATATTTTGGTAATTATTTTGAAAAAGATGATAT
TTTGGTAATTATTTTAAAA
Found at i:453082 original size:25 final size:25
Alignment explanation
Indices: 453030--453082 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
453020 ATGGTAACTC
* *
453030 TTTTATGAGATTTACTATAGTATAA
1 TTTTATGAGATTTACTAGACTATAA
* * *
453055 TTTTATGAGATTTGCTGGACTATGA
1 TTTTATGAGATTTACTAGACTATAA
453080 TTT
1 TTT
453083 GTTTAGTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.49
Consensus pattern (25 bp):
TTTTATGAGATTTACTAGACTATAA
Found at i:457755 original size:28 final size:28
Alignment explanation
Indices: 457715--457842 Score: 143
Period size: 28 Copynumber: 4.6 Consensus size: 28
457705 ACCCGTCTTG
*
457715 GTGATATTTTGGTAATTATTTTGAAAAA
1 GTGATATTTTGGTAATTATTTTTAAAAA
* *
457743 GTGATAGTTTGGTAATTATTTTTAAACA
1 GTGATATTTTGGTAATTATTTTTAAAAA
* *
457771 -TGATATTTTTGTAATT-TTTTTTAAAA
1 GTGATATTTTGGTAATTATTTTTAAAAA
* *
457797 GTGATATTTTTGTAAATATTTTTAAAAATA
1 GTGATATTTTGGTAATTATTTTT-AAAA-A
* *
457827 GTGCTATTTTCGTAAT
1 GTGATATTTTGGTAAT
457843 AATTGTTGTG
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
26 8 0.10
27 29 0.35
28 30 0.36
29 3 0.04
30 14 0.17
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (28 bp):
GTGATATTTTGGTAATTATTTTTAAAAA
Found at i:457784 original size:27 final size:27
Alignment explanation
Indices: 457715--457823 Score: 139
Period size: 27 Copynumber: 4.0 Consensus size: 27
457705 ACCCGTCTTG
*
457715 GTGATATTTTGGTAATTATTTTGAAAAA
1 GTGATATTTTGGTAATTATTTT-TAAAA
*
457743 GTGATAGTTTGGTAATTATTTTTAAACA
1 GTGATATTTTGGTAATTATTTTTAAA-A
* *
457771 -TGATATTTTTGTAATTTTTTTTAAAA
1 GTGATATTTTGGTAATTATTTTTAAAA
* *
457797 GTGATATTTTTGTAAATATTTTTAAAA
1 GTGATATTTTGGTAATTATTTTTAAAA
457824 ATAGTGCTAT
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 1 0.01
27 49 0.68
28 22 0.31
ACGTcount: A:0.34, C:0.01, G:0.14, T:0.51
Consensus pattern (27 bp):
GTGATATTTTGGTAATTATTTTTAAAA
Found at i:458924 original size:25 final size:25
Alignment explanation
Indices: 458872--458924 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
458862 AGGGTAACTC
*
458872 TTTTATGAGATTTACTGTAGTATAA
1 TTTTATGAGATTTACTGGAGTATAA
* * *
458897 TTTTATGAGATTTATTGGATTATGA
1 TTTTATGAGATTTACTGGAGTATAA
458922 TTT
1 TTT
458925 GTTTAGTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.53
Consensus pattern (25 bp):
TTTTATGAGATTTACTGGAGTATAA
Found at i:459514 original size:18 final size:18
Alignment explanation
Indices: 459485--459521 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
459475 ATGATTAGAA
459485 AGTTTTATTTA-TTAATT
1 AGTTTTATTTATTTAATT
459502 AGTTTTAATTTATTTAATT
1 AGTTTT-ATTTATTTAATT
459521 A
1 A
459522 AATATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 5 0.28
19 7 0.39
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
AGTTTTATTTATTTAATT
Found at i:459530 original size:23 final size:22
Alignment explanation
Indices: 459488--459530 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
459478 ATTAGAAAGT
*
459488 TTTATTTATTAATTAGTTTTAA
1 TTTATTTATTAAATAGTTTTAA
*
459510 TTTATTTAATTAAATATTTTT
1 TTTATTT-ATTAAATAGTTTT
459531 TTTATCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTATTTATTAAATAGTTTTAA
Found at i:460436 original size:13 final size:13
Alignment explanation
Indices: 460418--460443 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
460408 TTGCTCTCTT
460418 ACTAGTTTAAGGG
1 ACTAGTTTAAGGG
460431 ACTAGTTTAAGGG
1 ACTAGTTTAAGGG
460444 GGAGAGAGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (13 bp):
ACTAGTTTAAGGG
Found at i:461220 original size:15 final size:15
Alignment explanation
Indices: 461200--461231 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
461190 CCGCCTCCTC
461200 AACCTTTTTCGACCG
1 AACCTTTTTCGACCG
461215 AACCTTTTTCGACCG
1 AACCTTTTTCGACCG
461230 AA
1 AA
461232 AGTCTCGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.31
Consensus pattern (15 bp):
AACCTTTTTCGACCG
Found at i:464364 original size:16 final size:16
Alignment explanation
Indices: 464343--464378 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
464333 TGATCGTAAT
464343 TGCTAGATTAATGGCC
1 TGCTAGATTAATGGCC
464359 TGCTAGATTAATGGCC
1 TGCTAGATTAATGGCC
464375 TGCT
1 TGCT
464379 CATGTGAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (16 bp):
TGCTAGATTAATGGCC
Found at i:465353 original size:14 final size:12
Alignment explanation
Indices: 465335--465364 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
465325 CCTCCCCTCC
*
465335 TCCCTCTCACTG
1 TCCCCCTCACTG
465347 TCCCCCTCACTG
1 TCCCCCTCACTG
465359 TCCCCC
1 TCCCCC
465365 ACTGTCCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.60, G:0.07, T:0.27
Consensus pattern (12 bp):
TCCCCCTCACTG
Found at i:466167 original size:20 final size:20
Alignment explanation
Indices: 466131--466168 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
466121 CTTTAATATT
* *
466131 AAATTATAAATATTTTAAAA
1 AAATTATAAAAAATTTAAAA
466151 AAATTATAAAAAATTTAA
1 AAATTATAAAAAATTTAA
466169 TTGTTACAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATTATAAAAAATTTAAAA
Found at i:470829 original size:32 final size:32
Alignment explanation
Indices: 470788--470853 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
470778 TGTTGTAACT
470788 TTCCTCCTTATGTAATAGCTGGTTGATGAAGG
1 TTCCTCCTTATGTAATAGCTGGTTGATGAAGG
*
470820 TTCCTCCTTATGTAATCGCTGGTTGATGAAGG
1 TTCCTCCTTATGTAATAGCTGGTTGATGAAGG
470852 TT
1 TT
470854 TTAACACGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (32 bp):
TTCCTCCTTATGTAATAGCTGGTTGATGAAGG
Found at i:474482 original size:73 final size:74
Alignment explanation
Indices: 474357--474496 Score: 246
Period size: 73 Copynumber: 1.9 Consensus size: 74
474347 CCAACATTTA
* *
474357 ATTTTCTTCATCTAACGGTCTTAAAAAAGGTGTAAATACTCTAGAAACAACAATGATTCTTTTAA
1 ATTTCCTTCATCTAACGATCTTAAAAAAGGTGTAAATACTCTAGAAACAACAATGATTCTTTTAA
474422 CACGCACAC
66 CACGCACAC
*
474431 ATTTCCTTCATCTAACGATCTT-AAAAAGGTGTAAATACTCTAGGAACAACAATGATTCTTTTAA
1 ATTTCCTTCATCTAACGATCTTAAAAAAGGTGTAAATACTCTAGAAACAACAATGATTCTTTTAA
474495 CA
66 CA
474497 TACACAATTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
73 43 0.68
74 20 0.32
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (74 bp):
ATTTCCTTCATCTAACGATCTTAAAAAAGGTGTAAATACTCTAGAAACAACAATGATTCTTTTAA
CACGCACAC
Found at i:481614 original size:6 final size:6
Alignment explanation
Indices: 481603--481637 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
481593 CAGGGCCCCT
481603 CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC CCTTT
1 CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC CCTTT
481638 TTTCTCTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (6 bp):
CCTTTC
Found at i:485234 original size:22 final size:22
Alignment explanation
Indices: 485206--485346 Score: 210
Period size: 22 Copynumber: 6.4 Consensus size: 22
485196 TATTTAAATC
*
485206 TATTTTAAAATATTGATTGATT
1 TATTTTAAAATATGGATTGATT
485228 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
** *** *
485250 TATTTTAAAATATAAAAAAAAT
1 TATTTTAAAATATGGATTGATT
485272 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
485294 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGGATTGATT
*
485316 TATTTTAAAATATAGATTGATT
1 TATTTTAAAATATGGATTGATT
485338 TATTTTAAA
1 TATTTTAAA
485347 TATTTTATTA
Statistics
Matches: 105, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 105 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (22 bp):
TATTTTAAAATATGGATTGATT
Found at i:485294 original size:66 final size:67
Alignment explanation
Indices: 485201--485329 Score: 242
Period size: 66 Copynumber: 1.9 Consensus size: 67
485191 AAAATTATTT
*
485201 AAATCTATTTTAAAATATTGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATAAA
1 AAATCTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATAAA
485266 AA
66 AA
485268 AAAT-TATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATA
1 AAATCTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATA
485330 GATTGATTTA
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
66 57 0.93
67 4 0.07
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.47
Consensus pattern (67 bp):
AAATCTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATAAA
AA
Found at i:485407 original size:31 final size:31
Alignment explanation
Indices: 485370--485429 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
485360 TAGTTGTATG
* *
485370 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATTTAAGTATTGCAAAACTAA
485401 AATTATTTAAATTTAAGTATTGCAAAACT
1 AATTATTTAAATTTAAGTATTGCAAAACT
485430 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATTTAAGTATTGCAAAACTAA
Found at i:487293 original size:2 final size:2
Alignment explanation
Indices: 487286--487310 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
487276 AATTATGTTA
487286 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
487311 CCCATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:491082 original size:18 final size:18
Alignment explanation
Indices: 491033--491083 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
491023 AAAATTTTCT
491033 TTCGTATCCAAGTTTAAA
1 TTCGTATCCAAGTTTAAA
* *
491051 TT-GATAACTC-AGTTTATA
1 TTCG-TATC-CAAGTTTAAA
491069 TTCGTATCCAAGTTT
1 TTCGTATCCAAGTTT
491084 CCCATGGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 8
0.70 0.08 0.22
Matches are distributed among these distances:
17 2 0.08
18 22 0.85
19 2 0.08
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (18 bp):
TTCGTATCCAAGTTTAAA
Found at i:498485 original size:147 final size:147
Alignment explanation
Indices: 498216--498511 Score: 441
Period size: 147 Copynumber: 2.0 Consensus size: 147
498206 TAGTTTTATT
* *
498216 TCATTTAAGTATCTAAACTTTATTTGTTTCAAAGTCATACTCGACTTTTACTTTTTGTTTCATTT
1 TCATTTAAGTATCTAAACTTTATTTGTTTCAAAATCATACTCGACGTTTACTTTTTGTTTCATTT
* ** * * *
498281 TAATATTTGGCCGTTAAAAACTTAACAGAATTGTTGTACATGACTTTTTTATGAGTAAATTATAT
66 TAATACTCAGCCGTTAAAAACTTAACAGAATTGTTGCACATGACTTTTTTATAAGTAAATTACAT
498346 TATTCATCACTAAATTA
131 TATTCATCACTAAATTA
* *
498363 TCATTTGAGTATTTAAACTTTCA-TTGTTTCAAAATCATACTCGACGTTTACTTTTTGTTTCATT
1 TCATTTAAGTATCTAAACTTT-ATTTGTTTCAAAATCATACTCGACGTTTACTTTTTGTTTCATT
* * * *
498427 TTAGTACTCAGCCTTTAAAAACTTAACGGAATTGTTGCACATGATTTTTTTATAAGTAAATTACA
65 TTAATACTCAGCCGTTAAAAACTTAACAGAATTGTTGCACATGACTTTTTTATAAGTAAATTACA
*
498492 TTATTCATCACTTAATTA
130 TTATTCATCACTAAATTA
498510 TC
1 TC
498512 TTTTCACTCC
Statistics
Matches: 133, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
147 132 0.99
148 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (147 bp):
TCATTTAAGTATCTAAACTTTATTTGTTTCAAAATCATACTCGACGTTTACTTTTTGTTTCATTT
TAATACTCAGCCGTTAAAAACTTAACAGAATTGTTGCACATGACTTTTTTATAAGTAAATTACAT
TATTCATCACTAAATTA
Found at i:501165 original size:15 final size:15
Alignment explanation
Indices: 501145--501196 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 15
501135 AAATAAATAA
501145 AATATAATTAATATT
1 AATATAATTAATATT
*
501160 AATAT-ATTAAAATT
1 AATATAATTAATATT
*
501174 TATATAATATAAATTATT
1 AATATAAT-T-AA-TATT
501192 AATAT
1 AATAT
501197 GTTAAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 12 0.41
15 7 0.24
16 1 0.03
17 2 0.07
18 7 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATAATTAATATT
Found at i:501170 original size:25 final size:24
Alignment explanation
Indices: 501142--501193 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
501132 TGAAAATAAA
*
501142 TAAAATATAAT-TAATATTAATATAT
1 TAAAAT-TAATATAATATAAAT-TAT
*
501167 TAAAATTTATATAATATAAATTAT
1 TAAAATTAATATAATATAAATTAT
501191 TAA
1 TAA
501194 TATGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAAATTAATATAATATAAATTAT
Found at i:502321 original size:6 final size:6
Alignment explanation
Indices: 502310--502340 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
502300 ATGAAAGGTT
502310 GGGGGA GGGGGA GGGGGA GGGGGA GGGGGA G
1 GGGGGA GGGGGA GGGGGA GGGGGA GGGGGA G
502341 TTGAGAGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.84, T:0.00
Consensus pattern (6 bp):
GGGGGA
Found at i:521054 original size:3 final size:3
Alignment explanation
Indices: 521046--521073 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
521036 AATCTGAAAC
521046 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
521074 AAAGAAGCCT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:537536 original size:20 final size:20
Alignment explanation
Indices: 537511--537550 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
537501 AGCAATAGAA
*
537511 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
537531 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
537551 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:537593 original size:20 final size:21
Alignment explanation
Indices: 537564--537603 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
537554 TAATAGAATA
*
537564 AAAAATTGATTCTATCTAATT
1 AAAAATTGATCCTATCTAATT
537585 AAAAA-TGATCCTATCTAAT
1 AAAAATTGATCCTATCTAAT
537604 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
AAAAATTGATCCTATCTAATT
Found at i:537642 original size:20 final size:20
Alignment explanation
Indices: 537617--537655 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
537607 TAATAGAATA
*
537617 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
537637 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
537656 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:537646 original size:52 final size:51
Alignment explanation
Indices: 537504--537656 Score: 270
Period size: 53 Copynumber: 2.9 Consensus size: 51
537494 TAAAATTAGC
537504 AATAGAATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACT
1 AATAGAATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACT
537555 AATAGAATAAAAAATTGATTCTATCTAATTAAAAATGATCCTATCTAATAACT
1 AATAGAAT-AAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACT
*
537608 AATAGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AATAGAATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATA
537657 TTTAATTTAG
Statistics
Matches: 98, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
51 8 0.08
52 44 0.45
53 46 0.47
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (51 bp):
AATAGAATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACT
Found at i:542251 original size:20 final size:20
Alignment explanation
Indices: 542226--542265 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
542216 AGCAACAGAA
*
542226 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
542246 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
542266 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:542308 original size:20 final size:21
Alignment explanation
Indices: 542279--542318 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
542269 TAATAGAATA
*
542279 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
542300 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
542319 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:542357 original size:20 final size:20
Alignment explanation
Indices: 542332--542370 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
542322 TAATAGAATA
*
542332 AAAACTGATTATATCTAATT
1 AAAACTGATCATATCTAATT
*
542352 AAAACTGATCCTATCTAAT
1 AAAACTGATCATATCTAAT
542371 ATTTAATTTA
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:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCATATCTAATT
Found at i:542361 original size:52 final size:52
Alignment explanation
Indices: 542222--542371 Score: 266
Period size: 53 Copynumber: 2.9 Consensus size: 52
542212 AATTAGCAAC
542222 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
542273 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
* *
542326 AGAATAAAAACTGATTATATCTAATTAAAACTGATCCTATCTAATA
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
542372 TTTAATTTAG
Statistics
Matches: 95, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
51 5 0.05
52 44 0.46
53 46 0.48
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.33
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:543436 original size:13 final size:13
Alignment explanation
Indices: 543418--543448 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
543408 ACCCGACCCG
543418 ACCCGACCCGTTT
1 ACCCGACCCGTTT
543431 ACCCGACCCGTTT
1 ACCCGACCCGTTT
543444 ACCCG
1 ACCCG
543449 GCCAGTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.48, G:0.16, T:0.19
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:543481 original size:7 final size:7
Alignment explanation
Indices: 543469--543499 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
543459 CTGACCCGAC
543469 CCGTTGA
1 CCGTTGA
543476 CCGTTGA
1 CCGTTGA
543483 CCCGTTGA
1 -CCGTTGA
543491 CCGTTGA
1 CCGTTGA
543498 CC
1 CC
543500 CACGTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.13, C:0.35, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:543486 original size:15 final size:15
Alignment explanation
Indices: 543466--543500 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
543456 GACCTGACCC
543466 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
543481 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
543496 GACCC
1 GACCC
543501 ACGTTGACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.37, G:0.26, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:543520 original size:10 final size:9
Alignment explanation
Indices: 543466--543520 Score: 50
Period size: 7 Copynumber: 6.6 Consensus size: 9
543456 GACCTGACCC
543466 GACC-CGTT
1 GACCACGTT
543474 GA-C-CGTT
1 GACCACGTT
543481 GACC-CGTT
1 GACCACGTT
543489 GA-C-CGTT
1 GACCACGTT
543496 GACCCACGTT
1 GA-CCACGTT
543506 GACCACTGTT
1 GACCAC-GTT
543516 GACCA
1 GACCA
543521 AAACTTTGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
7 14 0.33
8 9 0.21
9 5 0.12
10 14 0.33
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (9 bp):
GACCACGTT
Found at i:544822 original size:18 final size:18
Alignment explanation
Indices: 544796--544831 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
544786 TCGAAAGGAC
*
544796 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
544814 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
544832 CGGATGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:548178 original size:13 final size:13
Alignment explanation
Indices: 548160--548208 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
548150 ACCCGACCCG
548160 ACCCGACCCGTTT
1 ACCCGACCCGTTT
548173 ACCCGACCCGTTT
1 ACCCGACCCGTTT
* *
548186 ACCCGACCAGTTG
1 ACCCGACCCGTTT
*
548199 ACCTGACCCG
1 ACCCGACCCG
548209 ACCCGTTGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.18, C:0.45, G:0.18, T:0.18
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:548223 original size:7 final size:7
Alignment explanation
Indices: 548211--548241 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
548201 CTGACCCGAC
548211 CCGTTGA
1 CCGTTGA
548218 CCGTTGA
1 CCGTTGA
548225 CCCGTTGA
1 -CCGTTGA
548233 CCGTTGA
1 CCGTTGA
548240 CC
1 CC
548242 CACGTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.13, C:0.35, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:548228 original size:15 final size:15
Alignment explanation
Indices: 548208--548242 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
548198 GACCTGACCC
548208 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
548223 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
548238 GACCC
1 GACCC
548243 ACGTTGACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.37, G:0.26, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:548262 original size:10 final size:9
Alignment explanation
Indices: 548208--548262 Score: 50
Period size: 7 Copynumber: 6.6 Consensus size: 9
548198 GACCTGACCC
548208 GACC-CGTT
1 GACCACGTT
548216 GA-C-CGTT
1 GACCACGTT
548223 GACC-CGTT
1 GACCACGTT
548231 GA-C-CGTT
1 GACCACGTT
548238 GACCCACGTT
1 GA-CCACGTT
548248 GACCACTGTT
1 GACCAC-GTT
548258 GACCA
1 GACCA
548263 AAACTTTGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
7 14 0.33
8 9 0.21
9 5 0.12
10 14 0.33
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (9 bp):
GACCACGTT
Found at i:549564 original size:18 final size:18
Alignment explanation
Indices: 549538--549573 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
549528 TCGAAAGGAC
*
549538 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
549556 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
549574 CGGATGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:563622 original size:16 final size:16
Alignment explanation
Indices: 563601--563639 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
563591 TTTCTAAAAG
*
563601 CTAAAAGCTTTTGCAA
1 CTAAAAGCTATTGCAA
563617 CTAAAAGCTATTGCAA
1 CTAAAAGCTATTGCAA
*
563633 CAAAAAG
1 CTAAAAG
563640 AACTTATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (16 bp):
CTAAAAGCTATTGCAA
Found at i:565217 original size:20 final size:21
Alignment explanation
Indices: 565192--565284 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
565182 TTTTCCCAAT
*
565192 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
565212 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
565233 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* * **
565253 TCACAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
565274 TCGCAATGCGA
1 TCGCAATGCGA
565285 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:565237 original size:41 final size:41
Alignment explanation
Indices: 565192--565284 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
565182 TTTTCCCAAT
*
565192 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAA
565233 TCGCAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAA
565274 TCGCAATGCGA
1 TCGCAATGCGA
565285 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAA
Found at i:565298 original size:20 final size:20
Alignment explanation
Indices: 565273--565366 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
565263 AATTGGGAAA
*
565273 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
565293 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
565314 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
565334 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
565354 TTCGCAACGCGAT
1 ATCGCAACGCGAT
565367 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:565315 original size:41 final size:41
Alignment explanation
Indices: 565270--565347 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
565260 GCGAATTGGG
* * *
565270 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
565311 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
565348 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:565920 original size:19 final size:19
Alignment explanation
Indices: 565882--565948 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
565872 TTCGAGAATG
565882 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
565902 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
565921 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
565940 AAAATCGCA
1 AAAATCGCA
565949 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:565966 original size:19 final size:19
Alignment explanation
Indices: 565944--566089 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
565934 GAAACCAAAA
*
565944 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
565963 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
565982 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
565998 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
566015 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
566029 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
566048 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
566068 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
566088 TC
1 TC
566090 AACCAAAAGA
Statistics
Matches: 100, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
14 20 0.20
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 40 0.40
20 31 0.31
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:566059 original size:34 final size:33
Alignment explanation
Indices: 565979--566064 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
565969 TGCGATTTTT
* *
565979 ATTTCGCGTTGCGATTGTCTGGTCGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
*
566012 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
566045 ATTTCCGCGTTGCGATTCTC
1 ATTT-CGCGTTGCGATTCTC
566065 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 34 0.69
34 15 0.31
ACGTcount: A:0.12, C:0.24, G:0.26, T:0.38
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
Found at i:566066 original size:20 final size:20
Alignment explanation
Indices: 566032--566089 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
566022 GCGATTCTCT
**
566032 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
566052 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
566072 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
566090 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:568147 original size:42 final size:42
Alignment explanation
Indices: 568088--568209 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 42
568078 CCCGACTCGT
* * *
568088 CTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCC
* * * *
568130 CTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCC
* ** * *
568172 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
568210 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 61 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
CTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCC
Found at i:568167 original size:21 final size:21
Alignment explanation
Indices: 568143--568209 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
568133 TCATTCCTCG
568143 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
568164 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
568185 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
568206 AGAG
1 AGAG
568210 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:569587 original size:14 final size:14
Alignment explanation
Indices: 569568--569603 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
569558 ATTGTTTAAT
569568 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
569582 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
569596 TGATTTGT
1 TGATTTGT
569604 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:569804 original size:19 final size:19
Alignment explanation
Indices: 569782--569898 Score: 119
Period size: 19 Copynumber: 6.7 Consensus size: 19
569772 CGAAATTAAA
*
569782 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
569801 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
569820 TTCTCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
569836 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
569853 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
569869 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
569886 TTCGCATTGCGAT
1 TTCGCATTGCGAT
569899 AGTAATTTCC
Statistics
Matches: 79, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
14 12 0.15
16 12 0.15
17 13 0.16
19 42 0.53
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:569849 original size:33 final size:33
Alignment explanation
Indices: 569807--569898 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
569797 TCATTTCGCA
*
569807 TTGCGATTTTCATTTCTCATTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
*
569840 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
569873 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
569899 AGTAATTTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
Found at i:569898 original size:52 final size:50
Alignment explanation
Indices: 569782--569880 Score: 123
Period size: 52 Copynumber: 2.0 Consensus size: 50
569772 CGAAATTAAA
569782 TTCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCTCATTGCGATTCC
1 TTCGC-TTGCGATTTTCATTTCGCATTGCGA-TTTC--TTCTCATTGCGATTCC
* *
569836 CTCG-TTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCGTTGCGATT
1 TTCGCTTGCGATTTTCATTTCGCATTGCGATTTCTTCTCATTGCGATT
569881 TTCATTTCGC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
47 12 0.28
50 3 0.07
52 25 0.58
54 3 0.07
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.45
Consensus pattern (50 bp):
TTCGCTTGCGATTTTCATTTCGCATTGCGATTTCTTCTCATTGCGATTCC
Found at i:572208 original size:12 final size:12
Alignment explanation
Indices: 572191--572215 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
572181 TCTTCGGGGA
572191 CTTTTTCTTCTT
1 CTTTTTCTTCTT
572203 CTTTTTCTTCTT
1 CTTTTTCTTCTT
572215 C
1 C
572216 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:572424 original size:24 final size:24
Alignment explanation
Indices: 572390--572443 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
572380 CTGAAACATC
* *
572390 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
* *
572414 ATCAAAGTCCGGGTATTGACTAAG
1 ATCAAAATCCGGGTATTGACCAAG
572438 ATCAAA
1 ATCAAA
572444 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:573570 original size:39 final size:38
Alignment explanation
Indices: 573503--573576 Score: 121
Period size: 39 Copynumber: 1.9 Consensus size: 38
573493 ATTCATTTGA
573503 CTATCGCAACGCGAAATGACTATCGCAACGCGAAATGG
1 CTATCGCAACGCGAAATGACTATCGCAACGCGAAATGG
**
573541 CTATCGCAACGCGAAAATGGTTATCGCAACGCGAAA
1 CTATCGCAACGCG-AAATGACTATCGCAACGCGAAA
573577 ATCGCAATGC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
38 13 0.39
39 20 0.61
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (38 bp):
CTATCGCAACGCGAAATGACTATCGCAACGCGAAATGG
Found at i:573578 original size:20 final size:19
Alignment explanation
Indices: 573503--573576 Score: 121
Period size: 19 Copynumber: 3.8 Consensus size: 19
573493 ATTCATTTGA
*
573503 CTATCGCAACGCGAAATGA
1 CTATCGCAACGCGAAATGG
573522 CTATCGCAACGCGAAATGG
1 CTATCGCAACGCGAAATGG
573541 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCG-AAATGG
*
573561 TTATCGCAACGCGAAA
1 CTATCGCAACGCGAAA
573577 ATCGCAATGC
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 34 0.65
20 18 0.35
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (19 bp):
CTATCGCAACGCGAAATGG
Found at i:573638 original size:19 final size:19
Alignment explanation
Indices: 573597--573664 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
573587 GAAATGAAAA
573597 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
573613 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
573630 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
573649 TCGCAATGCAATTTTC
1 TCGCATTGCGATTTTC
573665 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 28 0.62
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:575717 original size:20 final size:19
Alignment explanation
Indices: 575682--575748 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
575672 GAAACTTAAA
575682 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
575701 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
575721 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
575740 ATCGCAACG
1 ATCGCAACG
575749 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:575756 original size:14 final size:14
Alignment explanation
Indices: 575737--575794 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
575727 ATGCGAAATG
575737 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
575751 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
*
575767 ATGAAATCGCAATGAC
1 A--AAATCGCAACGAC
575783 AAAATCGCAACG
1 AAAATCGCAACG
575795 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 7 0.19
18 9 0.25
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:575784 original size:32 final size:33
Alignment explanation
Indices: 575721--575799 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
575711 GGAAATGGCT
*
575721 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
575754 ATCGCAACGCGAAATG-AAATCGCAATGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
575786 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
575800 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:575828 original size:19 final size:19
Alignment explanation
Indices: 575806--575922 Score: 92
Period size: 19 Copynumber: 6.6 Consensus size: 19
575796 GAAACACAAA
575806 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
575825 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
575841 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
575858 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
575874 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* ***
575891 TCTCATTGCGATAGCCATT
1 TCGCATTGCGATTTTCATT
575910 TCCGCATTGCGAT
1 T-CGCATTGCGAT
575923 AGTCATTTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 21
0.71 0.09 0.19
Matches are distributed among these distances:
14 12 0.16
15 6 0.08
16 8 0.10
17 7 0.09
18 6 0.08
19 28 0.36
20 10 0.13
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:575847 original size:14 final size:14
Alignment explanation
Indices: 575828--575886 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
575818 TTTCATTTCG
575828 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
575842 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
575859 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
575875 CGTTGCGATTTT
1 CGTTGCGATTTT
575887 CATTTCTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:575853 original size:33 final size:33
Alignment explanation
Indices: 575811--575902 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
575801 ACAAATCGCA
*
575811 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
575844 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
575877 TTGCGATTTTCATTTCTCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
575903 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:576440 original size:18 final size:18
Alignment explanation
Indices: 576414--576458 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
576404 GTCGATCAGA
*
576414 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
576432 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
576450 TGATGGCTC
1 TGATGGCTC
576459 CTGAAGTGGA
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:577803 original size:20 final size:20
Alignment explanation
Indices: 577778--577816 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
577768 AATAGTTTCT
577778 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
577798 GAAAATGACTATCGCAACA
1 GAAAATGAAAATCGCAACA
577817 AGAGAATCAC
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:0.51, C:0.21, G:0.15, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:578104 original size:22 final size:22
Alignment explanation
Indices: 578079--578122 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
578069 GATTTAGATA
578079 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
578101 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
578123 TGAGAGAGTG
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:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:578335 original size:20 final size:20
Alignment explanation
Indices: 578310--578403 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
578300 GATTATGTAT
578310 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
578330 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
578350 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
578371 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
578391 TATCGCATTGCGA
1 TATCGCGTTGCGA
578404 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:578404 original size:20 final size:20
Alignment explanation
Indices: 578290--578404 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
578280 CGCTTTGAAA
*
578290 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
578311 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
578331 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
578351 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
578372 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
578392 ATCGCATTGCGAT
1 ATCGCATTGCGAT
578405 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:578422 original size:21 final size:21
Alignment explanation
Indices: 578393--578468 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
578383 ATAGTCAGTA
578393 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
578414 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
578434 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
578455 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
578469 ACTTATTCGC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:578423 original size:41 final size:41
Alignment explanation
Indices: 578332--578466 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
578322 AAAGTCAGTA
* * * ** *
578332 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
578372 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
578414 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
578455 TCGCGTTGCGAT
1 TCGCGTTGCGAT
578467 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:578437 original size:20 final size:20
Alignment explanation
Indices: 578412--578478 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
578402 GATTTTCCCA
578412 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* * **
578432 ATTCGCATTGCGATTTTCCCA
1 ATTCGCGTTGCGA-TTTACTT
578453 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
578473 ATTCGC
1 ATTCGC
578479 ATTACGAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:578467 original size:41 final size:41
Alignment explanation
Indices: 578393--578481 Score: 178
Period size: 41 Copynumber: 2.2 Consensus size: 41
578383 ATAGTCAGTA
578393 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
578434 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
578475 TCGCATT
1 TCGCATT
578482 ACGAATTGGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.42
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:583752 original size:21 final size:21
Alignment explanation
Indices: 583723--583775 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
583713 ATTCTGACTA
583723 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
583744 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
583765 TCGCAATGCGA
1 TCGCATTGCGA
583776 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:583836 original size:20 final size:20
Alignment explanation
Indices: 583784--583837 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
583774 GAATACGTAA
* * *
583784 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTAACT
583804 ATCGCAACGAGATTCTAACT
1 ATCGCAACGAGATTCTAACT
583824 ATCGCAACGAGATT
1 ATCGCAACGAGATT
583838 TATGTCGAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGATTCTAACT
Found at i:584346 original size:20 final size:20
Alignment explanation
Indices: 584324--584409 Score: 95
Period size: 20 Copynumber: 4.3 Consensus size: 20
584314 AGCGGAAATT
*
584324 GCAACGC-GAATATGACTATT
1 GCAACGCGGAA-ATGACTATC
*
584344 GCAACACGGAAATGACTATC
1 GCAACGCGGAAATGACTATC
*
584364 GCAACGC-GAAATTTACTATC
1 GCAACGCGGAAA-TGACTATC
* *
584384 GCAACGCGGAATTTACTATC
1 GCAACGCGGAAATGACTATC
584404 GCAACG
1 GCAACG
584410 AGAGAATCGC
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
19 4 0.07
20 48 0.83
21 6 0.10
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (20 bp):
GCAACGCGGAAATGACTATC
Found at i:584382 original size:40 final size:40
Alignment explanation
Indices: 584324--584409 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
584314 AGCGGAAATT
*
584324 GCAACGCGAATATGACTATTGCAACACGGAAATGACTATC
1 GCAACGCGAATATGACTATCGCAACACGGAAATGACTATC
* * * *
584364 GCAACGCGAA-ATTTACTATCGCAACGCGGAATTTACTATC
1 GCAACGCGAATA-TGACTATCGCAACACGGAAATGACTATC
584404 GCAACG
1 GCAACG
584410 AGAGAATCGC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 1 0.03
40 39 0.98
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (40 bp):
GCAACGCGAATATGACTATCGCAACACGGAAATGACTATC
Found at i:584438 original size:19 final size:19
Alignment explanation
Indices: 584414--584532 Score: 132
Period size: 19 Copynumber: 6.7 Consensus size: 19
584404 GCAACGAGAG
584414 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
584433 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
584452 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
584466 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
584485 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
584499 AATCGCAATGCGAAAGTGAA
1 AATCGCAATGCGAAA-TGAA
*
584519 AATCGCAACGCGAA
1 AATCGCAATGCGAA
584533 TTTAGTTTCG
Statistics
Matches: 84, Mismatches: 5, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
14 20 0.24
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 37 0.44
20 15 0.18
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:584470 original size:33 final size:33
Alignment explanation
Indices: 584433--584528 Score: 183
Period size: 33 Copynumber: 2.9 Consensus size: 33
584423 GCGAAATGAA
584433 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
584466 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
584499 AATCGCAATGCGAAAGTGAAAATCGCAACG
1 AATCGCAATGCGAAA-TGAAAATCGCAACG
584529 CGAATTTAGT
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 48 0.77
34 14 0.23
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:584471 original size:14 final size:14
Alignment explanation
Indices: 584452--584506 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
584442 GCGAAATGAA
584452 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
584466 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
584485 AATCGCAACGAGAG
1 AATCGCAACGAGAG
584499 AATCGCAA
1 AATCGCAA
584507 TGCGAAAGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:584710 original size:14 final size:14
Alignment explanation
Indices: 584691--584727 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
584681 CATCAATTAA
584691 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
584705 ACAAATCATCTTTT
1 ACAAATCAACATTT
584719 ACAAATCAA
1 ACAAATCAA
584728 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:586461 original size:41 final size:40
Alignment explanation
Indices: 586366--586461 Score: 95
Period size: 41 Copynumber: 2.3 Consensus size: 40
586356 AATTTTCTAA
* * * *
586366 TTTATATAAAAATTAAATATTTTATAATTCAAAAAAAACAG
1 TTTATAT-AAATTTAAATAATATATAATTCAAAAAAAAAAG
* *
586407 TTTATAATTAATTTAAATAATATATAATT-ATAAAATAAAAAT
1 TTTAT-ATAAATTTAAATAATATATAATTCA-AAAA-AAAAAG
586449 TTTATATAAATTT
1 TTTATATAAATTT
586462 TTTAATTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
40 1 0.02
41 33 0.73
42 11 0.24
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (40 bp):
TTTATATAAATTTAAATAATATATAATTCAAAAAAAAAAG
Found at i:586673 original size:180 final size:187
Alignment explanation
Indices: 586368--586754 Score: 655
Period size: 180 Copynumber: 2.1 Consensus size: 187
586358 TTTTCTAATT
* * *
586368 TATATAA-AAATTAAATATTTTATAATTCAAAAAAAACAGTTTATAATTAATTTAAATAATATAT
1 TATATAATATATTTAATATTTTATAATTCAAAAAAAACAGTTTACAATTAATTTAAATAATATAT
586432 AATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
66 AATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
*
586497 ATTGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
131 ATTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
*
586554 TATATAATATATTTAATATTTTTTAATTC-AAAAAAA-AGTTTACAATTAATTTAAAT-A-ATAT
1 TATATAATATATTTAATATTTTATAATTCAAAAAAAACAGTTTACAATTAATTTAAATAATATAT
586615 -ATTATAAAAT-AAAATTTTATATAAA-TTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
66 AATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
*
586677 ATTGGATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
131 ATTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
*
586734 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
586755 AAAATTTTAT
Statistics
Matches: 193, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
180 112 0.58
181 15 0.08
182 10 0.05
183 4 0.02
184 1 0.01
185 19 0.10
186 14 0.07
187 18 0.09
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (187 bp):
TATATAATATATTTAATATTTTATAATTCAAAAAAAACAGTTTACAATTAATTTAAATAATATAT
AATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
ATTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
Found at i:587496 original size:20 final size:20
Alignment explanation
Indices: 587471--587554 Score: 141
Period size: 20 Copynumber: 4.2 Consensus size: 20
587461 CAAAATCAAA
587471 AACGCGAAAATGACTATCGC
1 AACGCGAAAATGACTATCGC
587491 AACGCGAAAATGACTATCGC
1 AACGCGAAAATGACTATCGC
**
587511 AACGCGAATTTGACTATCGC
1 AACGCGAAAATGACTATCGC
*
587531 AACGTGAAAATGACTATCGC
1 AACGCGAAAATGACTATCGC
587551 AACG
1 AACG
587555 AGAGAATCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (20 bp):
AACGCGAAAATGACTATCGC
Found at i:587622 original size:34 final size:34
Alignment explanation
Indices: 587577--587732 Score: 136
Period size: 34 Copynumber: 4.4 Consensus size: 34
587567 TGTGATTTTC
587577 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
1 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
*
587611 AATTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCA
1 ATTTCGCATTGCGAT--TC--TTTCG--TTGCGATAGTCA
* ** * * **
587651 TTTTCGTGTTGCGATT-TTGTTGTTGCAATTTTC-
1 ATTTCGCATTGCGATTCTT-TCGTTGCGATAGTCA
*
587684 ATTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
1 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
* *
587718 TTTTCACATTGCGAT
1 ATTTCGCATTGCGAT
587733 AGTCATTTTC
Statistics
Matches: 94, Mismatches: 19, Indels: 18
0.72 0.15 0.14
Matches are distributed among these distances:
33 23 0.24
34 36 0.38
35 2 0.02
36 4 0.04
38 6 0.06
40 23 0.24
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.43
Consensus pattern (34 bp):
ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
Found at i:587651 original size:20 final size:20
Alignment explanation
Indices: 587599--587755 Score: 126
Period size: 20 Copynumber: 8.5 Consensus size: 20
587589 GATTCTTTCG
**
587599 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
587619 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
**
587639 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCA
587659 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
* **
587673 TTGCAATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
587692 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
587706 TTGCGATAGTCATTTTCACA
1 TTGCGATAGTCATTTTCGCA
587726 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
587746 TTGCGATAGT
1 TTGCGATAGT
587756 AAACTATTCT
Statistics
Matches: 113, Mismatches: 10, Indels: 28
0.75 0.07 0.19
Matches are distributed among these distances:
14 13 0.12
16 12 0.11
17 6 0.05
18 4 0.04
19 6 0.05
20 72 0.64
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:589484 original size:21 final size:21
Alignment explanation
Indices: 589459--589514 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
589449 TACATATATC
* *
589459 ATCATCTATTTTCTTAGCATT
1 ATCATCTATATTATTAGCATT
* *
589480 ATCATATATATTATTATCATT
1 ATCATCTATATTATTAGCATT
589501 ATC-TCTATCATTAT
1 ATCATCTAT-ATTAT
589515 CATCAAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.30, C:0.16, G:0.02, T:0.52
Consensus pattern (21 bp):
ATCATCTATATTATTAGCATT
Found at i:589519 original size:21 final size:21
Alignment explanation
Indices: 589476--589519 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
589466 ATTTTCTTAG
*
589476 CATTATCATATATATTATTAT
1 CATTATCATATATATTATCAT
*
589497 CATTATC-TCTATCATTATCAT
1 CATTATCATATAT-ATTATCAT
589518 CA
1 CA
589520 AATTATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (21 bp):
CATTATCATATATATTATCAT
Found at i:590001 original size:149 final size:149
Alignment explanation
Indices: 589731--590182 Score: 789
Period size: 149 Copynumber: 3.0 Consensus size: 149
589721 CCGAAGTGCA
*
589731 CGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
589796 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
*
589861 TATATATCCCGAAGGACTG
131 TATATATCCCGAAGGACCG
589880 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
589945 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
590010 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
590029 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
* * * * * * * *
590094 CATATACATATACTAAGGACCAAGTATGTGCCTCA-AAGACCTCATAAATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
* *
590158 CATATGTCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
590177 CGTAGA
1 CGTAGA
590183 CCCTCGACTC
Statistics
Matches: 291, Mismatches: 12, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
148 48 0.16
149 243 0.84
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCG
Found at i:591301 original size:64 final size:62
Alignment explanation
Indices: 591196--591352 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 62
591186 TAATGAAGGT
* * * **
591196 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATG-TTGTATTATTATAGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTTCTATT-TTA-AAAG
* *
591260 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATGTTTCTATTTTAAAAG
*
591323 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
591353 ACACCTTCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
63 4 0.05
64 68 0.85
65 8 0.10
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (62 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTTCTATTTTAAAAG
Found at i:592805 original size:20 final size:20
Alignment explanation
Indices: 592782--592851 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
592772 TCTGAAACTT
592782 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
592802 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
592822 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
592841 AAAATCACAAC
1 AAAATCGCAAC
592852 GATAGAATCG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 13 0.30
20 31 0.70
ACGTcount: A:0.51, C:0.23, G:0.14, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:593050 original size:21 final size:21
Alignment explanation
Indices: 593001--593057 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
592991 CAGTATTGGC
*
593001 AGCAATCAAATGAATATAATA
1 AGCAATCTAATGAATATAATA
593022 AGCAATCTAATGAATATAATA
1 AGCAATCTAATGAATATAATA
593043 AGCAATCTAAGTGAA
1 AGCAATCTAA-TGAA
593058 ATGGTTAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 30 0.88
22 4 0.12
ACGTcount: A:0.53, C:0.11, G:0.12, T:0.25
Consensus pattern (21 bp):
AGCAATCTAATGAATATAATA
Found at i:593242 original size:22 final size:22
Alignment explanation
Indices: 593217--593284 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 22
593207 AATGATTTCT
*
593217 CCGGAGATGGAGACTGATATCG
1 CCGGAGATGGGGACTGATATCG
*
593239 CCGGAGATGGGGACTGATTTCG
1 CCGGAGATGGGGACTGATATCG
* * *
593261 TCGGAGATGGGGACGGATGTCG
1 CCGGAGATGGGGACTGATATCG
593283 CC
1 CC
593285 TTAGAGAGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.19, G:0.41, T:0.19
Consensus pattern (22 bp):
CCGGAGATGGGGACTGATATCG
Found at i:593525 original size:21 final size:20
Alignment explanation
Indices: 593501--593547 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
593491 TATTCGCATT
593501 GCGATTTAGGAAAATCGCAAC
1 GCGATTT-GGAAAATCGCAAC
*
593522 GCGAATTTGGAAAATCGCAAT
1 GCG-ATTTGGAAAATCGCAAC
593543 GCGAT
1 GCGAT
593548 AGTCAGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 2 0.08
21 18 0.75
22 4 0.17
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (20 bp):
GCGATTTGGAAAATCGCAAC
Found at i:594245 original size:24 final size:23
Alignment explanation
Indices: 594213--594263 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
594203 TCGTGAATGC
* *
594213 TAAATGAACATGTTCGT-GAACATA
1 TAAACGAACACGTTC-TCGAACA-A
594237 TAAACGAACACGTTCTCGAACAA
1 TAAACGAACACGTTCTCGAACAA
594260 TAAA
1 TAAA
594264 TAAAAGAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.24
Consensus pattern (23 bp):
TAAACGAACACGTTCTCGAACAA
Found at i:594279 original size:33 final size:31
Alignment explanation
Indices: 594258--594322 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
594248 GTTCTCGAAC
594258 AATAAATAAAAGAACATGAACAC-ATTCAAA
1 AATAAATAAAAGAACATGAACACGATTCAAA
* *
594288 AATAAATAAACGAACATGAACACGATACTAAA
1 AATAAATAAAAGAACATGAACACGATTC-AAA
594320 AAT
1 AAT
594323 TTAAACGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 22 0.71
31 3 0.10
32 6 0.19
ACGTcount: A:0.62, C:0.14, G:0.08, T:0.17
Consensus pattern (31 bp):
AATAAATAAAAGAACATGAACACGATTCAAA
Found at i:594328 original size:30 final size:29
Alignment explanation
Indices: 594262--594338 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
594252 TCGAACAATA
* *
594262 AATAAAAGAACATGAACACATTCAAAAAT
1 AATAAACGAACATGAACACATACAAAAAT
594291 AAATAAACGAACATGAACACGATACTAAAAAT
1 -AATAAACGAACATGAACAC-ATAC-AAAAAT
* *
594323 -TTAAACGAACACGAAC
1 AATAAACGAACATGAAC
594339 CGAACTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 32 0.78
31 3 0.07
32 6 0.15
ACGTcount: A:0.58, C:0.17, G:0.09, T:0.16
Consensus pattern (29 bp):
AATAAACGAACATGAACACATACAAAAAT
Found at i:595752 original size:135 final size:133
Alignment explanation
Indices: 595517--595828 Score: 328
Period size: 132 Copynumber: 2.3 Consensus size: 133
595507 CTTGCTATGG
* * * *
595517 TGTAATCACCTCATATTATTAATTTTTTTATATTATGTACTATAACTATTCTTGACTAGGTTGTT
1 TGTAATCACCTAATAGTATTAATTTTTTTATATAATGTACTATAACTATTCTTGACTAGGTTATT
* * * * *
595582 GCGTGTAGGAATAAGTAAAATTCGACTCGACTCATAATAATTATATAAACTCGACTCGACTCATA
66 GCGTGTAGGAATAAGCAAAACTCAACTC-A--AATCATAATTATATAAACTCGACTCGACTCATA
595647 TTTCGT
128 TTTCGT
* *
595653 TGTAATCACCTAATAGTATTAA-TTTTTTATACTAAT-TACTATAATTATTCTTGGCTAGGTTAT
1 TGTAATCACCTAATAGTATTAATTTTTTTATA-TAATGTACTATAACTATTCTTGACTAGGTTAT
* ** * * *
595716 TGTGTGTAGGGGTGAGCAAAACTCAACTCAAATCATAATTGTATAAACTCGACTCGACTTATATT
65 TGCGTGTAGGAATAAGCAAAACTCAACTCAAATCATAATTATATAAACTCGACTCGACTCATATT
595781 AT-GT
130 -TCGT
* * ** **
595785 TCTAATCATCTCTTCCTATT-ATTTTTTTATA-ATATGTACTATAA
1 TGTAATCACCTAATAGTATTAATTTTTTTATATA-ATGTACTATAA
595829 TTTTTTTATT
Statistics
Matches: 148, Mismatches: 23, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
130 1 0.01
131 3 0.02
132 64 0.43
133 1 0.01
134 1 0.01
135 55 0.37
136 23 0.16
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.42
Consensus pattern (133 bp):
TGTAATCACCTAATAGTATTAATTTTTTTATATAATGTACTATAACTATTCTTGACTAGGTTATT
GCGTGTAGGAATAAGCAAAACTCAACTCAAATCATAATTATATAAACTCGACTCGACTCATATTT
CGT
Found at i:596211 original size:2 final size:2
Alignment explanation
Indices: 596194--596236 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
596184 ATTATATCAA
596194 AT AT AT GAT AT A- 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
596236 A
1 A
596237 ATCAAAACTA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:611266 original size:15 final size:15
Alignment explanation
Indices: 611246--611311 Score: 96
Period size: 15 Copynumber: 4.4 Consensus size: 15
611236 TTCCAGAAAA
611246 TGAATTACTGAAATT
1 TGAATTACTGAAATT
*
611261 TGAATTACTGGAATT
1 TGAATTACTGAAATT
**
611276 TGAATTACTGAAAAA
1 TGAATTACTGAAATT
*
611291 TGAATTACTGGAATT
1 TGAATTACTGAAATT
611306 TGAATT
1 TGAATT
611312 CTGGAAAATG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.38
Consensus pattern (15 bp):
TGAATTACTGAAATT
Done.