Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009460.1 Hibiscus syriacus cultivar Beakdansim tig00113722_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: 2853300
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 3 of 14
Found at i:437553 original size:39 final size:39
Alignment explanation
Indices: 437479--437554 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
437469 GAGTTTATTT
* * *
437479 ATTAAATGAACGAACATGAACAATATTTTTATTCGTTTA
1 ATTAAATGAACGAACATGAACAATAGTCTCATTCGTTTA
*
437518 ATTAAATGAACGAACATGAAC-ATAGGTCTCGTTCGTT
1 ATTAAATGAACGAACATGAACAATA-GTCTCATTCGTT
437555 CATTTACGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.09
39 29 0.91
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (39 bp):
ATTAAATGAACGAACATGAACAATAGTCTCATTCGTTTA
Found at i:437613 original size:24 final size:24
Alignment explanation
Indices: 437571--437619 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
437561 CGTTCGTGAA
437571 CGTTCGGTTATGTTCGTTTACGTT
1 CGTTCGGTTATGTTCGTTTACGTT
*
437595 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTACGTT
437619 C
1 C
437620 ATTCATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.16, G:0.24, T:0.51
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTACGTT
Found at i:437629 original size:24 final size:24
Alignment explanation
Indices: 437577--437632 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
437567 TGAACGTTCG
* *
437577 GTTATGTTCGTTTACGTTCGTTCG
1 GTTATGTTCGTTTACGTTCATTCA
*
437601 GTTATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTTTACGTTCATTCA
*
437625 TTTATGTT
1 GTTATGTT
437633 TAACCCAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTATGTTCGTTTACGTTCATTCA
Found at i:438383 original size:16 final size:16
Alignment explanation
Indices: 438362--438445 Score: 105
Period size: 16 Copynumber: 5.2 Consensus size: 16
438352 GGTCTCCAAC
438362 GTTTATGTTCGTTTAT
1 GTTTATGTTCGTTTAT
438378 GTTTATGTTCGTTTAT
1 GTTTATGTTCGTTTAT
* *
438394 GTTTGTGTTCATTTAT
1 GTTTATGTTCGTTTAT
* *
438410 ATTTCTGTTCGTTTAT
1 GTTTATGTTCGTTTAT
**
438426 GTTCGTGTTCGTTTTAT
1 GTTTATGTTCG-TTTAT
438443 GTT
1 GTT
438446 CGTTTATTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
16 51 0.86
17 8 0.14
ACGTcount: A:0.11, C:0.08, G:0.19, T:0.62
Consensus pattern (16 bp):
GTTTATGTTCGTTTAT
Found at i:441148 original size:30 final size:29
Alignment explanation
Indices: 441114--441220 Score: 108
Period size: 30 Copynumber: 3.6 Consensus size: 29
441104 CATATTGATC
441114 AAATTTAGAAGTCAAATTATATTTTATTTA
1 AAATTTA-AAGTCAAATTATATTTTATTTA
*
441144 AAATTTAAGAGTCAAAATGATATTTTATTTA
1 AAATTTAA-AGTC-AAATTATATTTTATTTA
* **
441175 AAATTT-AAGATCAAATTAATATTGTATCCA
1 AAATTTAAAG-TCAAATT-ATATTTTATTTA
* *
441205 AATTTTAAAGTAAAAT
1 AAATTTAAAGTCAAAT
441221 AAAGAATTAA
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
29 7 0.11
30 33 0.51
31 25 0.38
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (29 bp):
AAATTTAAAGTCAAATTATATTTTATTTA
Found at i:441170 original size:31 final size:31
Alignment explanation
Indices: 441114--441189 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
441104 CATATTGATC
*
441114 AAATTT-AGAAGTC-AAATTATATTTTATTTA
1 AAATTTAAG-AGTCAAAATGATATTTTATTTA
441144 AAATTTAAGAGTCAAAATGATATTTTATTTA
1 AAATTTAAGAGTCAAAATGATATTTTATTTA
441175 AAATTTAAGA-TCAAA
1 AAATTTAAGAGTCAAA
441190 TTAATATTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
30 15 0.35
31 28 0.65
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (31 bp):
AAATTTAAGAGTCAAAATGATATTTTATTTA
Found at i:443278 original size:22 final size:23
Alignment explanation
Indices: 443242--443286 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
443232 TTAATAATAA
443242 TTAAATATTAAAGTATATACTAT
1 TTAAATATTAAAGTATATACTAT
*
443265 TTAAA-ATTGAAGTATATACTAT
1 TTAAATATTAAAGTATATACTAT
443287 ATAGTGTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (23 bp):
TTAAATATTAAAGTATATACTAT
Found at i:448146 original size:25 final size:25
Alignment explanation
Indices: 448112--448160 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
448102 TAGTACCAAA
*
448112 AGCCGAATATTTAGGGATTTAGGAC
1 AGCCGAATATTTAGGAATTTAGGAC
448137 AGCCGAATATTTAGGAATTTAGGA
1 AGCCGAATATTTAGGAATTTAGGA
448161 TTATTTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.29
Consensus pattern (25 bp):
AGCCGAATATTTAGGAATTTAGGAC
Found at i:448339 original size:25 final size:27
Alignment explanation
Indices: 448287--448339 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
448277 GGCACTCACT
* *
448287 CGGCTGAGAGGCTGGAACGTCAAGCGG
1 CGGCTGAGAGGCTGGAACGCCAAACGG
*
448314 CGGCTG-GA-GCTGGAAGGCCAAACGG
1 CGGCTGAGAGGCTGGAACGCCAAACGG
448339 C
1 C
448340 TGAGCGGCGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 15 0.65
26 2 0.09
27 6 0.26
ACGTcount: A:0.23, C:0.25, G:0.43, T:0.09
Consensus pattern (27 bp):
CGGCTGAGAGGCTGGAACGCCAAACGG
Found at i:448480 original size:3 final size:3
Alignment explanation
Indices: 448467--448523 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
448457 GTAATATGTA
* * *
448467 AAT AA- AAT AAT AAT AAT AAC ACT AAT AAT AAT AATT AA- AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
448511 GAT AAT AAT AAT A
1 AAT AAT AAT AAT A
448524 TACAAAAAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:448530 original size:24 final size:24
Alignment explanation
Indices: 448467--448523 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
448457 GTAATATGTA
448467 AATAA-AATAAT-AATAATAACACT
1 AATAATAATAATCAA-AATAACACT
*
448490 AATAATAATAATTAAAATAACGA-T
1 AATAATAATAATCAAAATAAC-ACT
448514 AATAATAATA
1 AATAATAATA
448524 TACAAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 5 0.16
24 23 0.74
25 3 0.10
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (24 bp):
AATAATAATAATCAAAATAACACT
Found at i:448792 original size:40 final size:40
Alignment explanation
Indices: 448684--448792 Score: 112
Period size: 40 Copynumber: 2.6 Consensus size: 40
448674 GGGACGCCAC
*
448684 TGCTCATACGTGATGAAGAGTTCGGGTCGTCTAAGGGTGACAT
1 TGCTCATACGTGATGAAGAGTTCTGGTCG--T-AGGGTGACAT
* * * * **
448727 GGTTCCTACGTGATGAGGAAATCTGGTCG-AGGGTTGACAT
1 TGCTCATACGTGATGAAGAGTTCTGGTCGTAGGG-TGACAT
448767 TGCTCATACGTGATGAAGAGTTCTGG
1 TGCTCATACGTGATGAAGAGTTCTGG
448793 CCATCTAAAG
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
39 4 0.08
40 26 0.50
43 22 0.42
ACGTcount: A:0.23, C:0.16, G:0.33, T:0.28
Consensus pattern (40 bp):
TGCTCATACGTGATGAAGAGTTCTGGTCGTAGGGTGACAT
Found at i:449102 original size:128 final size:128
Alignment explanation
Indices: 448708--449103 Score: 596
Period size: 128 Copynumber: 3.1 Consensus size: 128
448698 GAAGAGTTCG
* * * * **
448708 GGTCGTCTAAGGGTGACATGGTTCCTACGTGATGAGGAAATCTGGTCGAGGGT-TGACATTGCTC
1 GGTCATCT-AGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCG-GGGTATGACACGGCTC
448772 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCT
64 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCT
* * * * *
448837 GGTTATCTATGGTTGACACGGCTCCTACGTGGTGAGGAGATCTGGTCTGGAGAATGACACGGCTC
1 GGTCATCTA-GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTC-GGGGTATGACACGGCTC
448902 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCT
64 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCT
* *
448967 GGTCATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGTATGACACGGCTCAT
1 GGTCATCTAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGTATGACACGGCTCAT
* * *
449032 ACGTAATGAAGAGGTCTGGTCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCT
66 ACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCT
*
449095 GGCCATCTA
1 GGTCATCTA
449104 AAAGTTATGG
Statistics
Matches: 242, Mismatches: 22, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
128 86 0.36
129 73 0.30
130 83 0.34
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (128 bp):
GGTCATCTAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGTATGACACGGCTCAT
ACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCT
Found at i:449105 original size:46 final size:44
Alignment explanation
Indices: 448768--449104 Score: 209
Period size: 46 Copynumber: 7.7 Consensus size: 44
448758 GGTTGACATT
* * * *
448768 GCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACG
1 GCTCCTACGTGATGAGGAG-GCTGGCCATCT-AAGGTGATGACACG
* ** *
448814 GTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT--TGACACG
1 GCTCCTACGTGATGAGGA-GGCTGGCCATCTAAGGTGATGACACG
* * *
448857 GCTCCTACGTGGTGAGGAGATCTGG---TCT--GGAGAATGACACG
1 GCTCCTACGTGATGAGGAG-GCTGGCCATCTAAGGTG-ATGACACG
* * * *
448898 GCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACG
1 GCTCCTACGTGATGAGGAG-GCTGGCCATCT-AAGGTGATGACACG
* *
448944 GTTCCTACGTGATGAGGACGGCTGGTCATCT-AGG-G-TGACACG
1 GCTCCTACGTGATGAGGA-GGCTGGCCATCTAAGGTGATGACACG
* * * **
448986 GCTCATACGTGATGAAGAGATCTGG---TC-GGGGT-ATGACACG
1 GCTCCTACGTGATGAGGAG-GCTGGCCATCTAAGGTGATGACACG
* * * * *
449026 GCTCATACGTAATGAAGAGGTCTGGTCATCTAAAGGTGATAACACG
1 GCTCCTACGTGATGAGGAGG-CTGGCCATCT-AAGGTGATGACACG
*
449072 GTTCCTACGTGATGAGGACGGCTGGCCATCTAA
1 GCTCCTACGTGATGAGGA-GGCTGGCCATCTAA
449105 AAGTTATGGT
Statistics
Matches: 228, Mismatches: 39, Indels: 49
0.72 0.12 0.16
Matches are distributed among these distances:
38 2 0.01
39 4 0.02
40 32 0.14
41 29 0.13
42 26 0.11
43 29 0.13
44 6 0.03
45 9 0.04
46 84 0.37
47 7 0.03
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (44 bp):
GCTCCTACGTGATGAGGAGGCTGGCCATCTAAGGTGATGACACG
Found at i:449260 original size:36 final size:36
Alignment explanation
Indices: 449220--449294 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
449210 GTTTCAAAGG
*
449220 AAATGACTCAAAGATT-GTTTAAAGGAAAACTG-TCTC
1 AAATGACACAAA-ATTCGTTTAAAGGAAAA-TGATCTC
* *
449256 AAATGAGACAAAATTCGTTTAAAGGGAAATGATCTC
1 AAATGACACAAAATTCGTTTAAAGGAAAATGATCTC
449292 AAA
1 AAA
449295 GATGTTTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 5 0.15
36 29 0.85
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.25
Consensus pattern (36 bp):
AAATGACACAAAATTCGTTTAAAGGAAAATGATCTC
Found at i:449293 original size:63 final size:63
Alignment explanation
Indices: 449182--449301 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
449172 TTTCAAAAGC
*
449182 AACTGTCTCTTAAAAGAGACAAAATTTTGTTTCAAAGGAAATGACTCAAAGATTGTTTAAAGGAA
1 AACTGTCTC-TAAAAGAGACAAAATTTCGTTTCAAAGGAAATGACTCAAAGA-TGTTTAAAGGAA
*
449247 AACTGTCTC-AAATGAGACAAAA-TTCGTTT-AAAGGGAAATGATCTCAAAGATGTTT
1 AACTGTCTCTAAAAGAGACAAAATTTCGTTTCAAA-GGAAATGA-CTCAAAGATGTTT
449302 GTTTTGTTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
61 3 0.06
62 19 0.37
63 20 0.39
65 9 0.18
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (63 bp):
AACTGTCTCTAAAAGAGACAAAATTTCGTTTCAAAGGAAATGACTCAAAGATGTTTAAAGGAA
Found at i:449328 original size:35 final size:35
Alignment explanation
Indices: 449289--449368 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 35
449279 GGGAAATGAT
* * *
449289 CTCAAAGATGTTTG-TTTTGTT-TCAAAGGAAACAGA
1 CTCAAAGATG-GTGATTTTGTTCCCAAA-GAAACAAA
449324 CTCAAAGATGGTGAATTTTGTTCCCAAAGAAACAAA
1 CTCAAAGATGGTG-ATTTTGTTCCCAAAGAAACAAA
449360 CTCAAAGAT
1 CTCAAAGAT
449369 TTTATATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
34 2 0.05
35 10 0.26
36 23 0.59
37 4 0.10
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (35 bp):
CTCAAAGATGGTGATTTTGTTCCCAAAGAAACAAA
Found at i:449520 original size:62 final size:63
Alignment explanation
Indices: 449442--449564 Score: 185
Period size: 63 Copynumber: 2.0 Consensus size: 63
449432 ATGTGGGTGG
* * *
449442 TTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTT
1 TTTCAAAAGAAATTGTCGTCAAGAGACAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATTT
* * *
449504 TTTCAAAAGAAATTGTCGTTAAGAGATAAAATTTTGTTTTAAAAGAAACAGACTCAAAGAT
1 TTTCAAAAGAAATTGTCGTCAAGAGACAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
449565 GGATTACATC
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
62 16 0.30
63 38 0.70
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (63 bp):
TTTCAAAAGAAATTGTCGTCAAGAGACAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATTT
Found at i:449858 original size:38 final size:37
Alignment explanation
Indices: 449811--449932 Score: 114
Period size: 37 Copynumber: 3.5 Consensus size: 37
449801 GATTTTTTTT
*
449811 TTTTTTTTCCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCC-AAAGAAATTATCTTAAGAGAGACAAAA
** * * *
449849 TTTTGTTTCCAAAGAAACAAAC-TCA-A-AG----AT
1 TTTTGTTTCCAAAGAAATTATCTTAAGAGAGACAAAA
*
449879 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCCAAAGAAATTATCTTAAGAGAGACAAAA
*
449916 TTTTATTTCCAAAGAAA
1 TTTTGTTTCCAAAGAAA
449933 CCAACTCAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 15
0.68 0.15 0.16
Matches are distributed among these distances:
30 19 0.30
31 2 0.03
32 1 0.02
33 2 0.03
34 2 0.03
35 1 0.02
36 2 0.03
37 25 0.40
38 9 0.14
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (37 bp):
TTTTGTTTCCAAAGAAATTATCTTAAGAGAGACAAAA
Found at i:449891 original size:67 final size:68
Alignment explanation
Indices: 449810--449949 Score: 246
Period size: 67 Copynumber: 2.1 Consensus size: 68
449800 AGATTTTTTT
* *
449810 TTTTTTTTTCCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAA
1 TTTTTGTTTCCAAAAGAAATTATCTTAAGAGAGACAAAATTTTATTTCCAAAGAAACAAACTCAA
449875 AGA
66 AGA
*
449878 TTTTTGTTT-CAAAAGAAATTATCTTAAGAGAGACAAAATTTTATTTCCAAAGAAACCAACTCAA
1 TTTTTGTTTCCAAAAGAAATTATCTTAAGAGAGACAAAATTTTATTTCCAAAGAAACAAACTCAA
449942 AGA
66 AGA
449945 TTTTT
1 TTTTT
449950 TCAAAAGAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
67 61 0.88
68 8 0.12
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (68 bp):
TTTTTGTTTCCAAAAGAAATTATCTTAAGAGAGACAAAATTTTATTTCCAAAGAAACAAACTCAA
AGA
Found at i:449975 original size:26 final size:27
Alignment explanation
Indices: 449921--449977 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
449911 CAAAATTTTA
*
449921 TTTCCAAAGAAACCAACTCAAAGATTT
1 TTTCAAAAGAAACCAACTCAAAGATTT
449948 TTTCAAAAGAAA-CAATCTCAAAGATTT
1 TTTCAAAAGAAACCAA-CTCAAAGATTT
449975 TTT
1 TTT
449978 TCACAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.32
Consensus pattern (27 bp):
TTTCAAAAGAAACCAACTCAAAGATTT
Found at i:450039 original size:52 final size:53
Alignment explanation
Indices: 449964--450067 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
449954 AAGAAACAAT
449964 CTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
1 CTCAAAGA-TTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
450018 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
450068 AAATAAATAG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 41 0.84
54 8 0.16
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:450112 original size:27 final size:28
Alignment explanation
Indices: 450063--450245 Score: 199
Period size: 28 Copynumber: 6.4 Consensus size: 28
450053 CAAAACTTTG
* * * *
450063 TTTCAAAATAAATAGACTCAAAGATATT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
450091 TTTCAAAAGAAAC-AACTCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
* *
450118 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAACAAACTCAAAGATTTT
* *
450147 TATTCAAAAGGAGCAAACTCAAAGA-TTT
1 T-TTCAAAAGAAACAAACTCAAAGATTTT
* *
450175 TTTCAAGAGGAACAAACTCAAAGATTTTTTT
1 TTTCAAAAGAAACAAACTCAAAGA---TTTT
* *
450206 TTTCAAGAGAAACAAACCCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
450234 TTTCAAAAGAAA
1 TTTCAAAAGAAA
450246 TTGTCTTTAA
Statistics
Matches: 136, Mismatches: 13, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
27 34 0.25
28 41 0.30
29 36 0.26
31 25 0.18
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.29
Consensus pattern (28 bp):
TTTCAAAAGAAACAAACTCAAAGATTTT
Found at i:450146 original size:29 final size:28
Alignment explanation
Indices: 450078--450242 Score: 199
Period size: 29 Copynumber: 5.8 Consensus size: 28
450068 AAATAAATAG
* *
450078 ACTCAAAGATATTTTTCAAAAGAAAC-A
1 ACTCAAAGATTTTTTTCAAAAGGAACAA
450105 ACTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTT-TTCAAAAGGAACAA
* *
450134 ACTCCAAGATTTTTATTCAAAAGGAGCAA
1 ACTCAAAGATTTTT-TTCAAAAGGAACAA
*
450163 ACTCAAAGA-TTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTTTCAAAAGGAACAA
* *
450190 ACTCAAAGATTTTTTTTTTCAAGAGAAACAA
1 ACTCAAAGA---TTTTTTTCAAAAGGAACAA
*
450221 ACCCAAAGATTTTTTTCAAAAG
1 ACTCAAAGATTTTTTTCAAAAG
450243 AAATTGTCTT
Statistics
Matches: 122, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
27 34 0.28
28 27 0.22
29 36 0.30
31 25 0.20
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (28 bp):
ACTCAAAGATTTTTTTCAAAAGGAACAA
Found at i:450568 original size:36 final size:36
Alignment explanation
Indices: 450484--450587 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
450474 GAGAAAATGA
* * *
450484 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
450518 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
450554 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
450588 CGATTTCAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:450741 original size:105 final size:100
Alignment explanation
Indices: 450555--450786 Score: 259
Period size: 105 Copynumber: 2.3 Consensus size: 100
450545 TAGAGAAATT
* * **
450555 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAACGATTTCAAGTGAGATCAACTTTGTTTAATGT
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAGAAACAAAATCAAGTGAGATCAACTTTGTTTAATGT
* *
450620 GAAACAAATCCGAAATTTGGATCTCAAAGGGAAAAG
65 GAAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
* *
450656 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTAATTTTGTTT-
1 GTCTCAAGCGAGACAAAATTTGTTTTG--AGAAACAA-AATC-AA-GTGAGATCAACTTTGTTTA
* * * * *
450720 TTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
61 AT-GTGAAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
* *
450761 GTCTCAAGCGAAACACAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
450787 AAAATTCTCA
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
100 5 0.05
101 21 0.19
102 7 0.06
103 2 0.02
104 3 0.03
105 72 0.65
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (100 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAGAAACAAAATCAAGTGAGATCAACTTTGTTTAATGTG
AAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:451261 original size:4 final size:4
Alignment explanation
Indices: 451252--451287 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
451242 TGTATCATGG
451252 ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
451288 ATACTTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
4 28 0.93
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:453156 original size:26 final size:24
Alignment explanation
Indices: 453126--453196 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 24
453116 CAAGGTGGAA
453126 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
* *
453150 AGGGAATGTTTCAAGG--TCGAA-A-
1 A--GAATATTTCAAGGTCTCAAAGAG
453172 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
453196 A
1 A
453197 TAGAATGTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
20 12 0.32
22 5 0.14
23 2 0.05
24 6 0.16
26 12 0.32
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (24 bp):
AGAATATTTCAAGGTCTCAAAGAG
Found at i:453181 original size:20 final size:20
Alignment explanation
Indices: 453113--453187 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
453103 AAATACAGTG
*
453113 TTTCAAGGT-GGAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
* *
453132 TTTCAAGGTCTCAAAGAGAGGGAATG
1 TTTCAAGG--TCGAA-A-A--GAATA
453158 TTTCAAGGTCGAAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
453178 TTTCAAGGTC
1 TTTCAAGGTC
453188 TCAAAGAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 8 0.18
20 14 0.32
21 1 0.02
22 2 0.05
23 2 0.05
24 5 0.11
26 12 0.27
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (20 bp):
TTTCAAGGTCGAAAAGAATA
Found at i:453201 original size:26 final size:26
Alignment explanation
Indices: 453123--453202 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
453113 TTTCAAGGTG
453123 GAAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
** *
453149 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATATTTCAAGGTCTCAAAGA
453170 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
*
453195 GATAGAAT
1 GAAAGAAT
453203 GTCAAAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 2 0.05
24 2 0.05
25 2 0.05
26 20 0.49
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (26 bp):
GAAAGAATATTTCAAGGTCTCAAAGA
Found at i:453203 original size:46 final size:45
Alignment explanation
Indices: 453111--453204 Score: 152
Period size: 46 Copynumber: 2.1 Consensus size: 45
453101 ATAAATACAG
* *
453111 TGTTTCAAGGTGGAAAGAATATTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
*
453156 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
453202 TGT
1 TGT
453205 CAAAAATTGG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 11 0.24
46 34 0.76
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:455697 original size:31 final size:32
Alignment explanation
Indices: 455641--455702 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
455631 TGACAAAATG
455641 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
455673 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
455703 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:459289 original size:25 final size:25
Alignment explanation
Indices: 459255--459303 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
459245 TAGTACCAAA
*
459255 AGCCAAATATTTAGGGATTTAGGAC
1 AGCCAAATATTTAGGAATTTAGGAC
*
459280 AGCCGAATATTTAGGAATTTAGGA
1 AGCCAAATATTTAGGAATTTAGGA
459304 TTATTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (25 bp):
AGCCAAATATTTAGGAATTTAGGAC
Found at i:459482 original size:25 final size:27
Alignment explanation
Indices: 459430--459482 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
459420 GGCACTCACT
* *
459430 CGGCTGAGAGGCTGGAACGTCAAGCGG
1 CGGCTGAGAGGCTGGAACGCCAAACGG
*
459457 CGGCTG-GA-GCTGGAAGGCCAAACGG
1 CGGCTGAGAGGCTGGAACGCCAAACGG
459482 C
1 C
459483 TGAGCGGCGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 15 0.65
26 2 0.09
27 6 0.26
ACGTcount: A:0.23, C:0.25, G:0.43, T:0.09
Consensus pattern (27 bp):
CGGCTGAGAGGCTGGAACGCCAAACGG
Found at i:459623 original size:3 final size:3
Alignment explanation
Indices: 459610--459666 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
459600 GTAATATGTA
* * *
459610 AAT AA- AAT AAT AAT AAT AAC ACT AAT AAT AAT AATT AA- AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
459654 GAT AAT AAT AAT A
1 AAT AAT AAT AAT A
459667 TACAAAAAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:459673 original size:24 final size:24
Alignment explanation
Indices: 459610--459666 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
459600 GTAATATGTA
459610 AATAA-AATAAT-AATAATAACACT
1 AATAATAATAATCAA-AATAACACT
*
459633 AATAATAATAATTAAAATAACGA-T
1 AATAATAATAATCAAAATAAC-ACT
459657 AATAATAATA
1 AATAATAATA
459667 TACAAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 5 0.16
24 23 0.74
25 3 0.10
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (24 bp):
AATAATAATAATCAAAATAACACT
Found at i:459788 original size:41 final size:40
Alignment explanation
Indices: 459703--460107 Score: 342
Period size: 41 Copynumber: 10.3 Consensus size: 40
459693 GTGTCTACAG
*
459703 AAAC-TATATA-ATATATATAG-TTTT-GAAAACATTTT-A
1 AAACATATATATAT-TATATAGTTTTTAAAAAACATTTTGA
*
459739 GAAA-ATATATATATTATATAGTTTTT-AAAACCATTTTGA
1 -AAACATATATATATTATATAGTTTTTAAAAAACATTTTGA
* * * *
459778 AAAC-T-TATATAATATAAAGTTTTTTAAAATA-TTTTTG-
1 AAACATATATATATTATATAG-TTTTTAAAAAACATTTTGA
* *
459815 AAA-ATTTATATAATATATAGTTCTTTAAAAAAAACATTTTGA
1 AAACATATATATATTATATAGTT-TTT--AAAAAACATTTTGA
* *
459857 AAACATTTATATATTATATAGTATTTTAAAAAATATTTTGA
1 AAACATATATATATTATATAGT-TTTTAAAAAACATTTTGA
* *
459898 AAACATTTACATATTATATAGTTTTTAAAAAAACATTTTGA
1 AAACATATATATATTATATAGTTTTT-AAAAAACATTTTGA
* *
459939 AAACATTTATATATTATATAGTTTTTTAAAAAATATTTTGA
1 AAACATATATATATTATATAG-TTTTTAAAAAACATTTTGA
* *
459980 AAAC-T-TATATAATATATAGTTTTTTAAAAAACATTTTGG
1 AAACATATATATATTATATAG-TTTTTAAAAAACATTTTGA
* * * **
460019 AAA-ATATATATAATATGTA-ATTTTAAAAATATTTTTTGA
1 AAACATATATATATTATATAGTTTTTAAAAA-ACATTTTGA
* * * *
460058 AAATATAT-TATATTATAT-GATTTTGAAAAACATTTTTTA
1 AAACATATATATATTATATAGTTTTTAAAAAACA-TTTTGA
*
460097 AATCATATATA
1 AAACATATATA
460108 AAATATAATT
Statistics
Matches: 311, Mismatches: 32, Indels: 47
0.80 0.08 0.12
Matches are distributed among these distances:
37 34 0.11
38 55 0.18
39 76 0.24
40 28 0.09
41 89 0.29
42 8 0.03
43 20 0.06
44 1 0.00
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (40 bp):
AAACATATATATATTATATAGTTTTTAAAAAACATTTTGA
Found at i:460144 original size:4 final size:4
Alignment explanation
Indices: 460135--460185 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
460125 ATAATTTTCT
* *
460135 TTTA TTTA TTTA TTTA TTT- GTTA TTTTA TTTTA TTTA -TTA TTTA TTAA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA
460183 TTT
1 TTT
460186 TCCTTTTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 5 0.12
4 27 0.68
5 8 0.20
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:460164 original size:24 final size:25
Alignment explanation
Indices: 460134--460186 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
460124 AATAATTTTC
*
460134 TTTTA-TTTATTTATTTATTTGTT-A
1 TTTTATTTTATTTA-TTATTTATTAA
460158 TTTTATTTTATTTATTATTTATTAA
1 TTTTATTTTATTTATTATTTATTAA
460183 TTTT
1 TTTT
460187 CCTTTTTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (25 bp):
TTTTATTTTATTTATTATTTATTAA
Found at i:460169 original size:17 final size:16
Alignment explanation
Indices: 460143--460177 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
460133 CTTTTATTTA
*
460143 TTTATTTATTTGTTAT
1 TTTATTTATTTATTAT
460159 TTTATTTTATTTATTAT
1 TTTA-TTTATTTATTAT
460176 TT
1 TT
460178 ATTAATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTATTTATTTATTAT
Found at i:460179 original size:21 final size:19
Alignment explanation
Indices: 460134--460180 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
460124 AATAATTTTC
460134 TTTTA-TTTATTTATTTAT
1 TTTTATTTTATTTATTTAT
460152 TTGTTATTTTATTTTATTTAT
1 TT-TTATTTTA-TTTATTTAT
460173 TATTTATT
1 T-TTTATT
460181 AATTTTCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 4 0.16
21 15 0.60
22 1 0.04
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTTATTTTATTTATTTAT
Found at i:461361 original size:13 final size:13
Alignment explanation
Indices: 461345--461392 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
461335 TTATTTAACA
461345 TTTTTATTTTTAT
1 TTTTTATTTTTAT
461358 TTTTTA---TTAT
1 TTTTTATTTTTAT
461368 TTTTT-TCTTTTAT
1 TTTTTAT-TTTTAT
461381 TTATTTATTTTT
1 TT-TTTATTTTT
461393 TTATCATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
10 9 0.31
13 12 0.41
14 7 0.24
15 1 0.03
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:461370 original size:8 final size:7
Alignment explanation
Indices: 461345--461393 Score: 55
Period size: 8 Copynumber: 6.7 Consensus size: 7
461335 TTATTTAACA
461345 TTTTTA-
1 TTTTTAT
461351 TTTTTAT
1 TTTTTAT
461358 TTTTTAT
1 TTTTTAT
*
461365 TATTTTTT
1 T-TTTTAT
461373 TCTTTTAT
1 T-TTTTAT
461381 TTATTTAT
1 TT-TTTAT
461389 TTTTT
1 TTTTT
461394 TATCATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
6 6 0.16
7 12 0.32
8 19 0.51
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTAT
Found at i:461402 original size:21 final size:20
Alignment explanation
Indices: 461360--461403 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
461350 ATTTTTATTT
* **
461360 TTTATTATTTTTTTCTTTTA
1 TTTATTATTTTTTTATCATA
461380 TTTATTTATTTTTTTATCATA
1 TTTA-TTATTTTTTTATCATA
461401 TTT
1 TTT
461404 CCTTTTGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTATTATTTTTTTATCATA
Found at i:461403 original size:17 final size:15
Alignment explanation
Indices: 461345--461396 Score: 63
Period size: 16 Copynumber: 3.5 Consensus size: 15
461335 TTATTTAACA
461345 TTTTTATT-TTTA-T
1 TTTTTATTATTTATT
*
461358 TTTTTATTATTTTTT
1 TTTTTATTATTTATT
461373 TCTTTTATTTATTTATT
1 T-TTTTA-TTATTTATT
461390 TTTTTAT
1 TTTTTAT
461397 CATATTTCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 8 0.24
14 3 0.09
15 3 0.09
16 10 0.30
17 9 0.27
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTATTATTTATT
Found at i:461409 original size:31 final size:33
Alignment explanation
Indices: 461347--461422 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 33
461337 ATTTAACATT
* * * *
461347 TTTATTTTTATTTTTTATTATTTTTTTCTTTT-A
1 TTTATTTAT-TTTTTTATCATTATTTCCTTTTGA
461380 TTTATTTATTTTTTTATCA-TATTTCCTTTTGA
1 TTTATTTATTTTTTTATCATTATTTCCTTTTGA
461412 TTTA-TTATTTT
1 TTTATTTATTTT
461423 GTTTTTTCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 16 0.42
32 14 0.37
33 8 0.21
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.76
Consensus pattern (33 bp):
TTTATTTATTTTTTTATCATTATTTCCTTTTGA
Found at i:462891 original size:16 final size:16
Alignment explanation
Indices: 462872--462905 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
462862 TACTTTTGGG
462872 TCGGGTTAAATTCGGT
1 TCGGGTTAAATTCGGT
**
462888 TCGGGTTACTTTCGGT
1 TCGGGTTAAATTCGGT
462904 TC
1 TC
462906 TGATTGATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.18, G:0.29, T:0.41
Consensus pattern (16 bp):
TCGGGTTAAATTCGGT
Found at i:467875 original size:35 final size:35
Alignment explanation
Indices: 467802--467875 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
467792 AATGAATTCA
*
467802 TTTTTAAAAATTAAATTTATACCAAAACAACGTTG
1 TTTTTAAAAATTAAATTTATACCAAAACAACGTCG
* * *
467837 TTTTTAAAATTTAAATTTATACCAAAACGATGTCG
1 TTTTTAAAAATTAAATTTATACCAAAACAACGTCG
467872 TTTT
1 TTTT
467876 GCATCTATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.42
Consensus pattern (35 bp):
TTTTTAAAAATTAAATTTATACCAAAACAACGTCG
Found at i:469856 original size:5 final size:5
Alignment explanation
Indices: 469846--469880 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
469836 TTTGATTCTA
469846 AATTT AATTT AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT
469881 TTTTATGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:469943 original size:27 final size:27
Alignment explanation
Indices: 469908--469964 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
469898 TTGATAATAA
*
469908 AATATTTATTCATATTA-ATTTATTATT
1 AATAATTATTCATA-TAGATTTATTATT
469935 AATAATTATTCATATAGATTTATTATT
1 AATAATTATTCATATAGATTTATTATT
469962 AAT
1 AAT
469965 TATAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (27 bp):
AATAATTATTCATATAGATTTATTATT
Found at i:474734 original size:20 final size:20
Alignment explanation
Indices: 474640--475008 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
474630 GATTTTCCAT
* ** *
474640 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
474660 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
474680 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
474700 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
474720 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
474740 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
474760 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
474780 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
474800 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
474820 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
474840 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
474860 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
474880 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
474900 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
474920 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
474940 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
474960 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
474980 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
475000 AATCACAAC
1 AATCGCAAC
475009 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:475721 original size:24 final size:24
Alignment explanation
Indices: 475682--475728 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
475672 AAATTTGGTC
475682 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
475706 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
475729 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:475920 original size:12 final size:12
Alignment explanation
Indices: 475903--475927 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
475893 ATATAATCCT
475903 GAAGAAGAAAAA
1 GAAGAAGAAAAA
475915 GAAGAAGAAAAA
1 GAAGAAGAAAAA
475927 G
1 G
475928 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:478252 original size:19 final size:19
Alignment explanation
Indices: 478230--478517 Score: 329
Period size: 19 Copynumber: 16.4 Consensus size: 19
478220 CGGAAAATAC
*
478230 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
478249 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
478263 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
478283 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
478297 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
478316 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
478335 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
478349 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
478368 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
478382 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
478401 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
478420 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
478439 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
478458 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
478472 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
478491 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
478510 AATCGCAA
1 AATCGCAA
478518 CGAGATAATC
Statistics
Matches: 231, Mismatches: 12, Indels: 52
0.78 0.04 0.18
Matches are distributed among these distances:
14 50 0.22
15 3 0.01
16 13 0.06
17 12 0.05
18 4 0.02
19 136 0.59
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:478317 original size:33 final size:33
Alignment explanation
Indices: 478230--478498 Score: 193
Period size: 33 Copynumber: 7.8 Consensus size: 33
478220 CGGAAAATAC
* *
478230 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
478263 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
478297 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
478335 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
478368 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
478401 AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAA
478439 AATCGCAATGCGAAATGAAAATCGCAACGA-AA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
478471 GAATCGCAATGCGAAATGAAAATCGCAA
1 -AATCGCAATGCGAAATGAAAATCGCAA
478499 TGCGAAATGA
Statistics
Matches: 213, Mismatches: 8, Indels: 30
0.85 0.03 0.12
Matches are distributed among these distances:
32 2 0.01
33 115 0.54
34 31 0.15
35 5 0.02
36 5 0.02
37 3 0.01
38 50 0.23
39 1 0.00
40 1 0.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:478345 original size:52 final size:52
Alignment explanation
Indices: 478258--478498 Score: 273
Period size: 52 Copynumber: 4.6 Consensus size: 52
478248 AAATCCCAAC
478258 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
478311 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * * * *
478363 ATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAA
* * *
478415 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
478470 A-G--AATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
478499 TGCGAAATGA
Statistics
Matches: 163, Mismatches: 14, Indels: 23
0.81 0.07 0.12
Matches are distributed among these distances:
50 5 0.03
51 6 0.04
52 107 0.66
53 23 0.14
54 8 0.05
55 5 0.03
56 1 0.01
57 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:478354 original size:14 final size:14
Alignment explanation
Indices: 478335--478389 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
478325 GCGAAATGAA
478335 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
478349 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
478368 AATCGCAACGAGAG
1 AATCGCAACGAGAG
478382 AATCGCAA
1 AATCGCAA
478390 TGCGAAATGA
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:478528 original size:33 final size:34
Alignment explanation
Indices: 478313--478539 Score: 245
Period size: 33 Copynumber: 6.6 Consensus size: 34
478303 AATGCGAAAT
478313 GAAAATCGCAATGCGAAATGAAAATCGCAA-CGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAAGCGA
*
478346 GAGAATCGCAATGCGAAATGAAAATCGCAA-CGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAAGCGA
*
478379 GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
1 GAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A
* *
478416 TTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAA
1 -GAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A
478454 TGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAA
1 -GAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A
478487 TGAAAATCGCAATGCGAAATGAAAATCGCAA-CGA
1 -GAAAATCGCAATGCGAAATGAAAATCGCAAGCGA
*
478521 GATAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
478540 TATAAACGCA
Statistics
Matches: 178, Mismatches: 6, Indels: 20
0.87 0.03 0.10
Matches are distributed among these distances:
33 107 0.60
34 1 0.01
35 8 0.04
36 8 0.04
37 1 0.01
38 53 0.30
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (34 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAAGCGA
Found at i:478555 original size:52 final size:52
Alignment explanation
Indices: 478230--478539 Score: 267
Period size: 52 Copynumber: 5.9 Consensus size: 52
478220 CGGAAAATAC
* *
478230 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA-AATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA--AATAATCGCAATGC-GAAATGAA
*
478283 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAAT---AATCGCAATGCGAAATGAA
* *
478335 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAAT---AATCGCAATGCGAAATGAA
*
478382 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-T--AATCGCAATGCGAAATGAA
*
478439 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATAATCGCAATGCGAAATGAA
*
478491 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATAATCGCAATGCGAAAT
478540 TATAAACGCA
Statistics
Matches: 230, Mismatches: 9, Indels: 37
0.83 0.03 0.13
Matches are distributed among these distances:
47 10 0.04
48 10 0.04
49 5 0.02
50 3 0.01
51 4 0.02
52 141 0.61
53 20 0.09
54 2 0.01
55 5 0.02
56 1 0.00
57 29 0.13
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAATAATCGCAATGCGAAATGAA
Found at i:478655 original size:19 final size:19
Alignment explanation
Indices: 478546--478647 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
478536 AAATTATAAA
478546 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
478565 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
478585 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
478601 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
478618 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
478637 CGCATTGCGAT
1 CGCATTGCGAT
478648 AGTCATTTTG
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:478772 original size:14 final size:14
Alignment explanation
Indices: 478753--478789 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
478743 CATCAATTAC
478753 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
478767 ACAAATCATCTTTT
1 ACAAATCAACTTTT
478781 ACAAATCAA
1 ACAAATCAA
478790 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:478801 original size:12 final size:12
Alignment explanation
Indices: 478784--478856 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
478774 ATCTTTTACA
478784 AATCAATTAAAC
1 AATCAATTAAAC
*
478796 AATCAA--AAATTG
1 AATCAATTAAA--C
**
478808 AATCAACTTTTAC
1 AATCAA-TTAAAC
478821 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
478834 AATCAA-AAAAC
1 AATCAATTAAAC
478845 AATCAATTAAAC
1 AATCAATTAAAC
478857 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:478818 original size:38 final size:38
Alignment explanation
Indices: 478770--478842 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
478760 AACTTTTACA
*
478770 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
478808 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
478843 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:480698 original size:19 final size:19
Alignment explanation
Indices: 480658--480792 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
480648 TAGTTTACTT
* *
480658 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
480678 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
480697 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
480716 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
480730 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
480749 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
480763 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
480782 TCGCAATGCGA
1 TCGCAACGCGA
480793 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:480733 original size:14 final size:14
Alignment explanation
Indices: 480714--480770 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
480704 GCGAAATGAA
*
480714 AATCGCAACGACAG
1 AATCGCAACGAAAG
480728 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
480745 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
480761 AATCGCAACG
1 AATCGCAACG
480771 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:480737 original size:33 final size:33
Alignment explanation
Indices: 480695--480787 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
480685 GCGAAACCAA
*
480695 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
480728 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
480761 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
480788 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:480784 original size:52 final size:54
Alignment explanation
Indices: 480658--480792 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
480648 TAGTTTACTT
*
480658 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
480716 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
480763 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
480793 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:480810 original size:19 final size:19
Alignment explanation
Indices: 480788--480916 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
480778 AAAATCGCAA
480788 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
480807 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
480821 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
480840 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
480854 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
480873 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
480892 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
480912 TGCGA
1 TGCGA
480917 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:480830 original size:33 final size:33
Alignment explanation
Indices: 480788--480879 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
480778 AAAATCGCAA
480788 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
480821 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
480854 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
480880 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:481119 original size:93 final size:93
Alignment explanation
Indices: 480960--481339 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
480950 TTGAATGGAT
480960 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
481025 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
481053 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
481118 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
481146 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
481210 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
481238 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
481303 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
481331 AAATTTACT
1 AAATTTACT
481340 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:481273 original size:185 final size:186
Alignment explanation
Indices: 480960--481339 Score: 744
Period size: 185 Copynumber: 2.0 Consensus size: 186
480950 TTGAATGGAT
480960 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
481025 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
481090 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
481146 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
481210 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
481275 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
481331 AAATTTACT
1 AAATTTACT
481340 AAGCAATCTA
Statistics
Matches: 193, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
185 154 0.80
186 39 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:483065 original size:14 final size:14
Alignment explanation
Indices: 483046--483135 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
483036 TTGAAATGAA
483046 AATCGCAACGAGAG
1 AATCGCAACGAGAG
483060 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
483077 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
483093 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
483112 AATCGCAACGAGAG
1 AATCGCAACGAGAG
483126 AATCGCAACG
1 AATCGCAACG
483136 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:483083 original size:33 final size:33
Alignment explanation
Indices: 483038--483152 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
483028 TCTTTTGGTT
483038 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
483071 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
483104 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
483137 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
483153 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:483084 original size:19 final size:18
Alignment explanation
Indices: 483045--483157 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
483035 GTTGAAATGA
483045 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
483060 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
483077 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
483093 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
483110 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
483126 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
483143 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
483158 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:483188 original size:14 final size:14
Alignment explanation
Indices: 483169--483223 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
483159 TTTGGTTTCG
483169 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
483183 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
483202 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
483216 CGTTGCGA
1 CGTTGCGA
483224 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:483386 original size:33 final size:33
Alignment explanation
Indices: 483344--483414 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
483334 AATACTAACT
*
483344 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
483377 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
483410 TGAAA
1 TGAAA
483415 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:483648 original size:22 final size:22
Alignment explanation
Indices: 483596--483650 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
483586 TGGTTGTGAG
**
483596 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
483618 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
483640 GGATTTCTTCG
1 GGATTTCTTCG
483651 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:483821 original size:20 final size:20
Alignment explanation
Indices: 483796--483989 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
483786 CTTTAAATAT
483796 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
483816 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
483838 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
483857 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
483877 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
483897 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
483917 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
483937 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
483957 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
483977 CGCGTTGCGATTT
1 CGCGTTGCGATTT
483990 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:483983 original size:60 final size:60
Alignment explanation
Indices: 483796--483989 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
483786 CTTTAAATAT
**
483796 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
483857 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
483917 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
483977 CGCGTTGCGATTT
1 CGCGTTGCGATTT
483990 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:484006 original size:21 final size:20
Alignment explanation
Indices: 483982--484058 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
483972 ATATTCGCGT
483982 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
484003 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
484023 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
484045 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
484059 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:484069 original size:20 final size:20
Alignment explanation
Indices: 484044--484095 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
484034 AAGAATCGCG
*
484044 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
484064 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
484084 TTGCGATTCTGG
1 TTGCGATTCTGG
484096 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:484828 original size:7 final size:7
Alignment explanation
Indices: 484816--484858 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
484806 TGTAATGAAT
484816 CCTAAAC
1 CCTAAAC
*
484823 CCTAAAA
1 CCTAAAC
*
484830 CCTAAAT
1 CCTAAAC
484837 CCTAAAC
1 CCTAAAC
*
484844 CCTAAAT
1 CCTAAAC
484851 CCTAAAC
1 CCTAAAC
484858 C
1 C
484859 ATGAATTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (7 bp):
CCTAAAC
Found at i:484839 original size:21 final size:21
Alignment explanation
Indices: 484813--484856 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
484803 ATTTGTAATG
484813 AATCCTAAACCCTAAAACCTA
1 AATCCTAAACCCTAAAACCTA
*
484834 AATCCTAAACCCTAAATCCTA
1 AATCCTAAACCCTAAAACCTA
484855 AA
1 AA
484857 CCATGAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (21 bp):
AATCCTAAACCCTAAAACCTA
Found at i:484857 original size:14 final size:14
Alignment explanation
Indices: 484816--484858 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
484806 TGTAATGAAT
* *
484816 CCTAAACCCTAAAA
1 CCTAAATCCTAAAC
484830 CCTAAATCCTAAAC
1 CCTAAATCCTAAAC
484844 CCTAAATCCTAAAC
1 CCTAAATCCTAAAC
484858 C
1 C
484859 ATGAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (14 bp):
CCTAAATCCTAAAC
Found at i:484884 original size:14 final size:14
Alignment explanation
Indices: 484827--484884 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
484817 CTAAACCCTA
484827 AAACC-TAAATCCT
1 AAACCATAAATCCT
*
484840 AAACCCTAAATCCT
1 AAACCATAAATCCT
* **
484854 AAACCATGAATTAT
1 AAACCATAAATCCT
*
484868 AAACCATAAACCCT
1 AAACCATAAATCCT
484882 AAA
1 AAA
484885 TCCGATTATA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
13 5 0.14
14 31 0.86
ACGTcount: A:0.50, C:0.28, G:0.02, T:0.21
Consensus pattern (14 bp):
AAACCATAAATCCT
Found at i:487333 original size:16 final size:16
Alignment explanation
Indices: 487308--487338 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
487298 CTCTTGAATT
*
487308 TTTTTTGAGTTCGAGC
1 TTTTTCGAGTTCGAGC
487324 TTTTTCGAGTTCGAG
1 TTTTTCGAGTTCGAG
487339 TCAAGTTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.48
Consensus pattern (16 bp):
TTTTTCGAGTTCGAGC
Found at i:500809 original size:2 final size:2
Alignment explanation
Indices: 500804--500836 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
500794 ATTCTTTTTC
500804 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
500837 AAGCTCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:504434 original size:69 final size:68
Alignment explanation
Indices: 504317--504497 Score: 179
Period size: 69 Copynumber: 2.6 Consensus size: 68
504307 CGAATATAAC
* * ** * *
504317 AATAA-TATGATTAGGTGCTCCTGTGTGAGTCACTCTAATTTTTTGGGACTCCCGTACGAGTCA-
1 AATAATTATGATTATGTGCT-CTGTGCGAGTCACTCTAATCCTTCGGGACTCCCATACGAGTCAC
504380 CTCAG
65 CT-AG
* * **
504385 AATAATTATGATTATGTGCTCTAGTGCAAGTCACTCTAATCCTTCGGGACTCCTATGGGAGTCAC
1 AATAATTATGATTATGTGCTCT-GTGCGAGTCACTCTAATCCTTCGGGACTCCCATACGAGTCAC
*
504450 CTAT
65 CTAG
* *
504454 AGTAGTTATGATTATGTGCTCCCT-TGCGAGTCACTCTAATCCTT
1 AATAATTATGATTATGTGCT--CTGTGCGAGTCACTCTAATCCTT
504498 TGTAGAATCT
Statistics
Matches: 94, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
68 7 0.07
69 83 0.88
70 2 0.02
71 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (68 bp):
AATAATTATGATTATGTGCTCTGTGCGAGTCACTCTAATCCTTCGGGACTCCCATACGAGTCACC
TAG
Found at i:504533 original size:20 final size:19
Alignment explanation
Indices: 504503--504802 Score: 90
Period size: 19 Copynumber: 15.7 Consensus size: 19
504493 TCCTTTGTAG
*
504503 AATCTGGTTTCCAATCCCAA
1 AATCAGGTTTCCAA-CCCAA
* * *
504523 AGTCAGGTTTCTAACTCAA
1 AATCAGGTTTCCAACCCAA
* *
504542 AATCAAGTTTCCAACCTAA
1 AATCAGGTTTCCAACCCAA
* * **
504561 AA-CTTGCTTTCCAAACTAAA
1 AATC-AGGTTTCC-AACCCAA
*
504581 AATCAGGTTTCCAACCTAA
1 AATCAGGTTTCCAACCCAA
* ** * **
504600 AACCTATTTTTCAAACTAAA
1 AATC-AGGTTTCCAACCCAA
* * *
504620 AATTAGGCTTCCAACCTAA
1 AATCAGGTTTCCAACCCAA
* *
504639 AATCAGTTTTCCAA-CCTA
1 AATCAGGTTTCCAACCCAA
*
504657 AA-CATGTTTCCAATCCCAA
1 AATCAGGTTTCCAA-CCCAA
** * *
504676 AATCAACTTTCTAACTCAA
1 AATCAGGTTTCCAACCCAA
* * *
504695 ACTCAGGCTT-CAACCTAA
1 AATCAGGTTTCCAACCCAA
* **
504713 AA-CATGTTTTCCAAACAAAA
1 AATCA-GGTTTCC-AACCCAA
* *
504733 AACCAGGTTTCCAACCTAA
1 AATCAGGTTTCCAACCCAA
* * * *
504752 AACCTGCTTT-CAATCCAAA
1 AATCAGGTTTCCAA-CCCAA
* * *
504771 AATTAGGTTTTCAACTCAA
1 AATCAGGTTTCCAACCCAA
* *
504790 AATTAAGTTTCCA
1 AATCAGGTTTCCA
504803 CGTTAATCAC
Statistics
Matches: 197, Mismatches: 70, Indels: 27
0.67 0.24 0.09
Matches are distributed among these distances:
17 11 0.06
18 17 0.09
19 106 0.54
20 60 0.30
21 3 0.02
ACGTcount: A:0.38, C:0.26, G:0.07, T:0.29
Consensus pattern (19 bp):
AATCAGGTTTCCAACCCAA
Found at i:504562 original size:19 final size:19
Alignment explanation
Indices: 504503--504753 Score: 122
Period size: 19 Copynumber: 13.1 Consensus size: 19
504493 TCCTTTGTAG
* *
504503 AATCTGGTTTCCAATCCCAA
1 AATCAGGTTTCCAA-CCTAA
* *
504523 AGTCAGGTTTCTAA-CTCAA
1 AATCAGGTTTCCAACCT-AA
*
504542 AATCAAGTTTCCAACCTAA
1 AATCAGGTTTCCAACCTAA
* * *
504561 AA-CTTGCTTTCCAAACTAAA
1 AATC-AGGTTTCCAACCT-AA
504581 AATCAGGTTTCCAACCTAA
1 AATCAGGTTTCCAACCTAA
* * * *
504600 AACCTA-TTTTTCAAACTAAA
1 AATC-AGGTTTCCAACCT-AA
* *
504620 AATTAGGCTTCCAACCTAA
1 AATCAGGTTTCCAACCTAA
*
504639 AATCAGTTTTCCAACCT-A
1 AATCAGGTTTCCAACCTAA
* *
504657 AA-CATGTTTCCAATCCCAA
1 AATCAGGTTTCCAA-CCTAA
** *
504676 AATCAACTTTCTAA-CTCAA
1 AATCAGGTTTCCAACCT-AA
* *
504695 ACTCAGGCTT-CAACCTAA
1 AATCAGGTTTCCAACCTAA
* **
504713 AA-CATGTTTTCCAAACAAAA
1 AATCA-GGTTTCC-AACCTAA
*
504733 AACCAGGTTTCCAACCTAA
1 AATCAGGTTTCCAACCTAA
504752 AA
1 AA
504754 CCTGCTTTCA
Statistics
Matches: 167, Mismatches: 47, Indels: 35
0.67 0.19 0.14
Matches are distributed among these distances:
17 11 0.07
18 16 0.10
19 77 0.46
20 60 0.36
21 3 0.02
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.28
Consensus pattern (19 bp):
AATCAGGTTTCCAACCTAA
Found at i:504583 original size:39 final size:39
Alignment explanation
Indices: 504535--504785 Score: 167
Period size: 39 Copynumber: 6.6 Consensus size: 39
504525 TCAGGTTTCT
* *
504535 AACTCAAAATCAAGTTTCCAACCTAAAACTTGCTTTCCA
1 AACTAAAAATCAGGTTTCCAACCTAAAACTTGCTTTCCA
* ** *
504574 AACTAAAAATCAGGTTTCCAACCTAAAACCTATTTTTCA
1 AACTAAAAATCAGGTTTCCAACCTAAAACTTGCTTTCCA
* * * *
504613 AACTAAAAATTAGGCTTCCAACCTAAAA-TCAGTTTTCCA
1 AACTAAAAATCAGGTTTCCAACCTAAAACT-TGCTTTCCA
* * * ** *
504652 ACCT--AAA-CATGTTTCCAATCCCAAAA-TCAACTTT-CT
1 AACTAAAAATCAGGTTTCCAA-CCTAAAACT-TGCTTTCCA
* * * * *
504688 AACTCAAACTCAGGCTT-CAACCTAAAACATGTTTTCCA
1 AACTAAAAATCAGGTTTCCAACCTAAAACTTGCTTTCCA
* * *
504726 AACAAAAAACCAGGTTTCCAACCTAAAACCTGCTTT-CA
1 AACTAAAAATCAGGTTTCCAACCTAAAACTTGCTTTCCA
* * * *
504764 ATCCAAAAATTAGGTTTTCAAC
1 AACTAAAAATCAGGTTTCCAAC
504786 TCAAAATTAA
Statistics
Matches: 162, Mismatches: 42, Indels: 17
0.73 0.19 0.08
Matches are distributed among these distances:
36 12 0.07
37 24 0.15
38 37 0.23
39 89 0.55
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.28
Consensus pattern (39 bp):
AACTAAAAATCAGGTTTCCAACCTAAAACTTGCTTTCCA
Found at i:506077 original size:26 final size:24
Alignment explanation
Indices: 506030--506077 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
506020 TATGAACAAG
*
506030 ATATAAGAGATAGAAAGGATAATC
1 ATATAAGAGATAGAAAAGATAATC
*
506054 ATATAAGAGTATGAGAAAATATAA
1 ATATAAGAG-AT-AGAAAAGATAA
506078 ATGATGACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 2 0.10
26 9 0.45
ACGTcount: A:0.56, C:0.02, G:0.19, T:0.23
Consensus pattern (24 bp):
ATATAAGAGATAGAAAAGATAATC
Found at i:510016 original size:21 final size:21
Alignment explanation
Indices: 509990--510029 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
509980 ATATGTGTTA
* *
509990 TAAGTGGTCCTTTGGGACATC
1 TAAGTGGTCATTCGGGACATC
510011 TAAGTGGTCATTCGGGACA
1 TAAGTGGTCATTCGGGACA
510030 AATTCTACGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
TAAGTGGTCATTCGGGACATC
Found at i:513372 original size:18 final size:19
Alignment explanation
Indices: 513349--513389 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
513339 ACGAAATATA
513349 CATCGAATGCA-AT-GAGTG
1 CATCG-ATGCATATGGAGTG
513367 CATCGATGCATATGGAGTG
1 CATCGATGCATATGGAGTG
513386 CATC
1 CATC
513390 AATACACCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.24
18 7 0.33
19 9 0.43
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (19 bp):
CATCGATGCATATGGAGTG
Found at i:517918 original size:36 final size:35
Alignment explanation
Indices: 517854--517922 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 35
517844 GAACACCATT
*
517854 CATACGTAGAGCACAAGGTACATGTATATATATTTA
1 CATACGTAGAGCACAAGATACA-GTATATATATTTA
517890 CATACGTAGAGCACAAGATATGCA-TATATATAT
1 CATACGTAGAGCACAAGATA--CAGTATATATAT
517923 AAATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 28 0.93
38 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (35 bp):
CATACGTAGAGCACAAGATACAGTATATATATTTA
Found at i:517920 original size:2 final size:2
Alignment explanation
Indices: 517913--517948 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
517903 CAAGATATGC
*
517913 AT AT AT AT AT AA 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
517949 CATACATGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:519052 original size:2 final size:2
Alignment explanation
Indices: 519045--519072 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
519035 ATTGAATAAT
519045 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
519073 ATTATTCTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:520648 original size:30 final size:29
Alignment explanation
Indices: 520608--520665 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
520598 AGTAACGAGC
* * *
520608 TTAATGAGCACGAGTTGAGCAATAATTTTT
1 TTAAAGAGCACAAGTCGAGCAA-AATTTTT
*
520638 TTAAAGAGCACAAGTCGAGTAAAATTTT
1 TTAAAGAGCACAAGTCGAGCAAAATTTT
520666 AACGAGCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (29 bp):
TTAAAGAGCACAAGTCGAGCAAAATTTTT
Found at i:521480 original size:20 final size:20
Alignment explanation
Indices: 521455--521495 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
521445 ACAACCTTAA
521455 TCAAATTTGTACGGTTTTCT
1 TCAAATTTGTACGGTTTTCT
521475 TCAAATTTGTACGGTTTTCT
1 TCAAATTTGTACGGTTTTCT
521495 T
1 T
521496 TTTAATAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.51
Consensus pattern (20 bp):
TCAAATTTGTACGGTTTTCT
Found at i:522507 original size:25 final size:25
Alignment explanation
Indices: 522479--522534 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
522469 TTTTGAAAAA
*
522479 ATCAAAAAATAAAATATTAAAACAG
1 ATCAAAAAATAAAATATTAAAACAC
*
522504 ATCAAAAAATAAAATATTAAAATAC
1 ATCAAAAAATAAAATATTAAAACAC
522529 ATCAAA
1 ATCAAA
522535 TTAATAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.68, C:0.09, G:0.02, T:0.21
Consensus pattern (25 bp):
ATCAAAAAATAAAATATTAAAACAC
Found at i:526940 original size:20 final size:20
Alignment explanation
Indices: 526904--526941 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
526894 ATCCTATTCC
**
526904 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
526924 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
526942 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:531556 original size:41 final size:39
Alignment explanation
Indices: 531511--531639 Score: 114
Period size: 42 Copynumber: 3.4 Consensus size: 39
531501 ATTTTTCAAA
531511 TAATAATATAATAAAATACTGTTAAAATAGTTAAATATATT
1 TAATAA-ATAATAAAATACTGTTAAAATA-TTAAATATATT
* *
531552 TAATAAAATAAGTAAATTA-T-TT-TAATATT-AA-A-A--
1 TAAT-AAATAA-TAAAATACTGTTAAAATATTAAATATATT
531585 TAAT-AATAATAAAATACTGTTAAAATATTTAAATATATT
1 TAATAAATAATAAAATACTGTTAAAATA-TTAAATATATT
531624 TAATATAATAAATAAA
1 TAATA-AAT-AATAAA
531640 TAATCTTATT
Statistics
Matches: 70, Mismatches: 4, Indels: 27
0.69 0.04 0.27
Matches are distributed among these distances:
30 6 0.09
31 6 0.09
32 2 0.03
33 8 0.11
34 2 0.03
35 3 0.04
36 2 0.03
37 3 0.04
38 2 0.03
39 8 0.11
40 2 0.03
41 12 0.17
42 14 0.20
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.39
Consensus pattern (39 bp):
TAATAAATAATAAAATACTGTTAAAATATTAAATATATT
Found at i:531557 original size:33 final size:33
Alignment explanation
Indices: 531519--531633 Score: 99
Period size: 33 Copynumber: 3.3 Consensus size: 33
531509 AATAATAATA
*
531519 TAATAAAATACTGTTAAAATAGTTAAATATATT
1 TAATAAAATACTGTTAAAATATTTAAATATATT
* * *
531552 TAATAAAATA-AG-TAAATTATTTTAATATTAAAATAATAA
1 TAATAAAATACTGTTAAAATA-TTTAA-A-T---AT-AT-T
531591 TAATAAAATACTGTTAAAATATTTAAATATATT
1 TAATAAAATACTGTTAAAATATTTAAATATATT
*
531624 TAATATAATA
1 TAATAAAATA
531634 AATAAATAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
31 6 0.09
32 5 0.08
33 20 0.31
34 3 0.05
35 2 0.03
37 2 0.03
38 3 0.05
39 11 0.17
40 6 0.09
41 6 0.09
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (33 bp):
TAATAAAATACTGTTAAAATATTTAAATATATT
Found at i:531561 original size:22 final size:22
Alignment explanation
Indices: 531533--531578 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
531523 AAAATACTGT
531533 TAAAAT-AGTTAAA-TATATTTAA
1 TAAAATAAG-TAAATTAT-TTTAA
531555 TAAAATAAGTAAATTATTTTAA
1 TAAAATAAGTAAATTATTTTAA
531577 TA
1 TA
531579 TTAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (22 bp):
TAAAATAAGTAAATTATTTTAA
Found at i:542758 original size:15 final size:15
Alignment explanation
Indices: 542738--542780 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
542728 ATATATTTTC
542738 TTTAAAAAATTTAAA
1 TTTAAAAAATTTAAA
542753 TTTAAAAAATTTAAA
1 TTTAAAAAATTTAAA
542768 -TTAATAAAATTTA
1 TTTAA-AAAATTTA
542781 TATAATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTTAAAAAATTTAAA
Found at i:546831 original size:3 final size:3
Alignment explanation
Indices: 546825--546863 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
546815 CTTTTCTTAA
546825 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
546864 GCTACCATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:549872 original size:23 final size:23
Alignment explanation
Indices: 549846--549925 Score: 142
Period size: 23 Copynumber: 3.5 Consensus size: 23
549836 ACGAACGAAA
* *
549846 ATAAACGAACATAATAAGTGAAC
1 ATAAACGAACACAATAAATGAAC
549869 ATAAACGAACACAATAAATGAAC
1 ATAAACGAACACAATAAATGAAC
549892 ATAAACGAACACAATAAATGAAC
1 ATAAACGAACACAATAAATGAAC
549915 ATAAACGAACA
1 ATAAACGAACA
549926 ACACAAACAC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.60, C:0.16, G:0.10, T:0.14
Consensus pattern (23 bp):
ATAAACGAACACAATAAATGAAC
Found at i:549878 original size:10 final size:10
Alignment explanation
Indices: 549839--549925 Score: 57
Period size: 10 Copynumber: 7.8 Consensus size: 10
549829 ATGATAAACG
*
549839 AACGAAAATA
1 AACGAACATA
549849 AACGAACATAA
1 AACGAACAT-A
*
549860 TAAGTGAACATA
1 -AA-CGAACATA
549872 AACGAACACAATA
1 AACG-A-AC-ATA
*
549885 AATGAACATA
1 AACGAACATA
549895 AACGAACACAATA
1 AACG-A-AC-ATA
*
549908 AATGAACATA
1 AACGAACATA
549918 AACGAACA
1 AACGAACA
549926 ACACAAACAC
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
10 25 0.41
11 9 0.15
12 9 0.15
13 18 0.30
ACGTcount: A:0.61, C:0.16, G:0.10, T:0.13
Consensus pattern (10 bp):
AACGAACATA
Found at i:549885 original size:13 final size:13
Alignment explanation
Indices: 549832--549915 Score: 63
Period size: 13 Copynumber: 6.8 Consensus size: 13
549822 CATTTAAATG
*
549832 ATAAACGAACGAAA
1 ATAAACGAAC-ACA
*
549846 ATAAACGAACATA
1 ATAAACGAACACA
**
549859 ATAAGTG-A-AC-
1 ATAAACGAACACA
549869 ATAAACGAACACA
1 ATAAACGAACACA
*
549882 ATAAATG-A-AC-
1 ATAAACGAACACA
549892 ATAAACGAACACA
1 ATAAACGAACACA
*
549905 ATAAATGAACA
1 ATAAACGAACA
549916 TAAACGAACA
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
10 11 0.20
11 5 0.09
12 6 0.11
13 23 0.42
14 10 0.18
ACGTcount: A:0.61, C:0.15, G:0.11, T:0.13
Consensus pattern (13 bp):
ATAAACGAACACA
Found at i:554809 original size:23 final size:23
Alignment explanation
Indices: 554774--554817 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
554764 TTATACATAT
*
554774 CACATATACCATT-TCATCAAAAA
1 CACACATACCATTAT-ATCAAAAA
*
554797 CACACATATCATTATATCAAA
1 CACACATACCATTATATCAAA
554818 TTATGTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.94
24 1 0.06
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (23 bp):
CACACATACCATTATATCAAAAA
Found at i:555008 original size:18 final size:18
Alignment explanation
Indices: 554939--554997 Score: 91
Period size: 18 Copynumber: 3.3 Consensus size: 18
554929 GCGTAGAATT
* * *
554939 TGTCCCGTAGGACCACTG
1 TGTCCCGAAGCACCACTA
554957 TGTCCCGAAGCACCACTA
1 TGTCCCGAAGCACCACTA
554975 TGTCCCGAAGCACCACTA
1 TGTCCCGAAGCACCACTA
554993 TGTCC
1 TGTCC
554998 TAAAGGACCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.22, C:0.37, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGCACCACTA
Found at i:555008 original size:36 final size:36
Alignment explanation
Indices: 554939--555008 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
554929 GCGTAGAATT
* * * *
554939 TGTCCCGTAGGACCACTGTGTCCCGAAGCACCACTA
1 TGTCCCGAAGCACCACTATGTCCCAAAGCACCACTA
* *
554975 TGTCCCGAAGCACCACTATGTCCTAAAGGACCAC
1 TGTCCCGAAGCACCACTATGTCCCAAAGCACCAC
555009 GTAGAACCCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.26, C:0.36, G:0.20, T:0.19
Consensus pattern (36 bp):
TGTCCCGAAGCACCACTATGTCCCAAAGCACCACTA
Found at i:556866 original size:2 final size:2
Alignment explanation
Indices: 556859--556886 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
556849 TCGATACTCA
556859 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
556887 CTTTCTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:562567 original size:4 final size:4
Alignment explanation
Indices: 562517--562603 Score: 56
Period size: 4 Copynumber: 21.8 Consensus size: 4
562507 TTAAATAGTA
* * *
562517 TATT TA-T TATT ATATG TATT TACT TATA TATT T-TCAT TATT TA-T TATT
1 TATT TATT TATT -TATT TATT TATT TATT TATT TAT--T TATT TATT TATT
* * *
562565 TATT TCTT TATT TCTT T-TT TATTT TATT TTTT TATT TAT
1 TATT TATT TATT TATT TATT TA-TT TATT TATT TATT TAT
562604 ATATATATAT
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
3 10 0.16
4 44 0.69
5 9 0.14
6 1 0.02
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:562606 original size:2 final size:2
Alignment explanation
Indices: 562601--562666 Score: 57
Period size: 2 Copynumber: 32.5 Consensus size: 2
562591 TTTTTTTATT
* *
562601 TA TA TA TA TA TA TA TA TA TA T- TA TA CCA CTA CTA TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA -TA -TA TA TA TA TA
562642 TCA T- TA TA TA TA TA TA TA TA TA TA T
1 T-A TA TA TA TA TA TA TA TA TA TA TA T
562667 CCTTTTAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
1 3 0.05
2 45 0.80
3 8 0.14
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:562699 original size:3 final size:3
Alignment explanation
Indices: 562691--562721 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
562681 ATTTATACGT
562691 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
562722 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:562769 original size:2 final size:2
Alignment explanation
Indices: 562759--562793 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
562749 TTTTCAGCAT
*
562759 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
562794 CGTTTCCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:562991 original size:22 final size:22
Alignment explanation
Indices: 562965--563017 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
562955 CCATTGTCTG
562965 TATTTTATTTATTTATTATTAT
1 TATTTTATTTATTTATTATTAT
** * *
562987 TATTTCCTTTATTTTTTATTCT
1 TATTTTATTTATTTATTATTAT
563009 T-TTTTATTT
1 TATTTTATTT
563018 TCTTTATCTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (22 bp):
TATTTTATTTATTTATTATTAT
Found at i:563015 original size:26 final size:26
Alignment explanation
Indices: 562968--563039 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
562958 TTGTCTGTAT
*
562968 TTTATTTATTTATT-ATTATTATTTCC
1 TTTATTT-TTTATTCTTTATTATTTCC
* *
562994 TTTATTTTTTATTCTTTTTTATTTTC
1 TTTATTTTTTATTCTTTATTATTTCC
563020 TTTATCTTTTTA-TCTTTATT
1 TTTAT-TTTTTATTCTTTATT
563040 TTCTTTGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
25 6 0.15
26 28 0.70
27 6 0.15
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTATTTTTTATTCTTTATTATTTCC
Found at i:563016 original size:17 final size:17
Alignment explanation
Indices: 562965--563077 Score: 69
Period size: 18 Copynumber: 6.8 Consensus size: 17
562955 CCATTGTCTG
* *
562965 TATTTTA-TTTATTTAT
1 TATTTTATTTTCTTTTT
* *
562981 TATTATTATTTCCTTTAT
1 TATT-TTATTTTCTTTTT
562999 T-TTTTA--TTCTTTTT
1 TATTTTATTTTCTTTTT
*
563013 TATTTTCTTTATC-TTTT
1 TATTTTATTT-TCTTTTT
563030 TATCTTTATTTTCTTTGTT
1 TAT-TTTATTTTCTTT-TT
* * *
563049 TCTTTT-GTTT-TTCTT
1 TATTTTATTTTCTTTTT
563064 TATTTTATTTTCTT
1 TATTTTATTTTCTT
563078 CCTTTAATAC
Statistics
Matches: 75, Mismatches: 11, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
14 7 0.09
15 11 0.15
16 12 0.16
17 20 0.27
18 21 0.28
19 4 0.05
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.76
Consensus pattern (17 bp):
TATTTTATTTTCTTTTT
Done.