Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 193 of 206
Found at i:58450269 original size:50 final size:50
Alignment explanation
Indices: 58450171--58450281 Score: 116
Period size: 50 Copynumber: 2.2 Consensus size: 50
58450161 CCAGTGAGAT
* * * ** *
58450171 AAGATTCGCTGTTGTAGCTTCAATCTATTTAATTGCAATGTCAGGGAAGC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTCAACTACAATCACAAGGAAGC
* * *
58450221 AAGATTTGCTGTTGTAGCTTCAATCTATTCCACTAC-ATCACTAAGGAAGT
1 AAGATTCGCTGTTGTAGCTTCAATCTATTCAACTACAATCAC-AAGGAAGC
*
58450271 AAAATTCGCTG
1 AAGATTCGCTG
58450282 CCTTTAGCTT
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
49 3 0.06
50 46 0.94
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (50 bp):
AAGATTCGCTGTTGTAGCTTCAATCTATTCAACTACAATCACAAGGAAGC
Found at i:58450278 original size:136 final size:136
Alignment explanation
Indices: 58450034--58450317 Score: 428
Period size: 136 Copynumber: 2.1 Consensus size: 136
58450024 ACCAAGGAAG
* *
58450034 TAAGATTCGCTGTTGTAGCTTCAATCTGTTTAACTGCAATGTCGAGGAAGCAAGATTCGTTGTCT
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGAGGAAGCAAGATTCGCTGTCT
* * * *
58450099 TAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAAATTCGCTGCCTTCAGCTTTAATGCCA
66 TAGCTTCAATCTATTCCACTACACCACCAAGGAAGTAAAATTCGCTGCCTTCAGCTTTAACGCCA
*
58450164 GTGAGA
131 GGGAGA
* *
58450170 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAATTGCAATGTC-AGGGAAGCAAGATTTGCTGT-
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGA-GGAAGCAAGATTCGCTGTC
* * *
58450233 TGTAGCTTCAATCTATTCCACTACATCACTAAGGAAGTAAAATTCGCTGCCTTTAGCTTTAACGC
65 T-TAGCTTCAATCTATTCCACTACACCACCAAGGAAGTAAAATTCGCTGCCTTCAGCTTTAACGC
58450298 CAGGGAGA
129 CAGGGAGA
58450306 TAAGATTCGCTG
1 TAAGATTCGCTG
58450318 CCTTCAGCTT
Statistics
Matches: 134, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
135 2 0.01
136 132 0.99
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (136 bp):
TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGAGGAAGCAAGATTCGCTGTCT
TAGCTTCAATCTATTCCACTACACCACCAAGGAAGTAAAATTCGCTGCCTTCAGCTTTAACGCCA
GGGAGA
Found at i:58450393 original size:49 final size:49
Alignment explanation
Indices: 58450297--58450395 Score: 119
Period size: 49 Copynumber: 2.0 Consensus size: 49
58450287 AGCTTTAACG
* * * * *
58450297 CCAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTTCGCTGCAA
1 CCAGGGAAATAAGAATCGCTACCTTCAGATTTAATCTGCTTCACTGCAA
* *
58450346 CCAGGGAAATATGAATCGCTACCTTTAGATTTAATCTG-TTCCACTGCAA
1 CCAGGGAAATAAGAATCGCTACCTTCAGATTTAATCTGCTT-CACTGCAA
58450395 C
1 C
58450396 ACCAAAGAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 2 0.05
49 40 0.95
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (49 bp):
CCAGGGAAATAAGAATCGCTACCTTCAGATTTAATCTGCTTCACTGCAA
Found at i:58450444 original size:21 final size:21
Alignment explanation
Indices: 58450420--58450462 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
58450410 ATTCACTGCT
58450420 TTCAGCTTTAATCCACTCCAC
1 TTCAGCTTTAATCCACTCCAC
* *
58450441 TTCAGCTTTAATCTATTCCAC
1 TTCAGCTTTAATCCACTCCAC
58450462 T
1 T
58450463 GCAACACCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.33, G:0.05, T:0.40
Consensus pattern (21 bp):
TTCAGCTTTAATCCACTCCAC
Found at i:58450541 original size:123 final size:121
Alignment explanation
Indices: 58450319--58450542 Score: 279
Period size: 123 Copynumber: 1.8 Consensus size: 121
58450309 GATTCGCTGC
* * * *
58450319 CTTCAGCTTTAATCTGCTTCGCTGCAACCAGGGAAATATGAATCGCTACCTTTAGATTTAATCTG
1 CTTCAGCTTTAATCTGATTCACTGCAACCAGGGAAACAAGAATCGCTACCTTTAGATTTAATCTG
* *
58450384 TTCCACTGCAACACCAAAGAGATAGGATTCACTGCTTTCAGCTTTAATCCACTCCA
66 TTCCACTGCAACACCAAAGAAATAAGATTCACTGCTTTCAGCTTTAATCCACTCCA
* * *
58450440 CTTCAGCTTTAATCT-ATTCCACTGCAACACCAGGGAAACAAGATTCGTTACCTTTAGCTTTAAT
1 CTTCAGCTTTAATCTGATT-CACTGC-A-ACCAGGGAAACAAGAATCGCTACCTTTAGATTTAAT
* ** ** *
58450504 CTGTTCCGCTGCAACGTCAGGGAAATAAGATTTACTGCT
63 CTGTTCCACTGCAACACCAAAGAAATAAGATTCACTGCT
58450543 CTTTTCAAAC
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
120 2 0.02
121 20 0.24
122 1 0.01
123 62 0.73
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (121 bp):
CTTCAGCTTTAATCTGATTCACTGCAACCAGGGAAACAAGAATCGCTACCTTTAGATTTAATCTG
TTCCACTGCAACACCAAAGAAATAAGATTCACTGCTTTCAGCTTTAATCCACTCCA
Found at i:58453040 original size:593 final size:593
Alignment explanation
Indices: 58451913--58453085 Score: 2328
Period size: 593 Copynumber: 2.0 Consensus size: 593
58451903 TCAAAGCTCT
58451913 TCCAGAAAAGGCCTTCTTTAGAACATAAGGCCCTTCCCAATTTGGCATCCACTTCCCTCTAAAAT
1 TCCAGAAAAGGCCTTCTTTAGAACATAAGGCCCTTCCCAATTTGGCATCCACTTCCCTCTAAAAT
58451978 CCTTTTGTAGAGGAAGAATCTTCTTCAACACCAGGTCCCCCTCATGAAATTCTCTAGGGCGAACC
66 CCTTTTGTAGAGGAAGAATCTTCTTCAACACCAGGTCCCCCTCATGAAATTCTCTAGGGCGAACC
58452043 CTTTTGCTATAGGCTCGTATCATTCGTTTCTAATACATCTGACCGTGATGAATAAATTTTAGCCT
131 CTTTTGCTATAGGCTCGTATCATTCGTTTCTAATACATCTGACCGTGATGAATAAATTTTAGCCT
58452108 ATTTTCTTCTGTCAGGTTCAACTGGTCATATCGAGATTGAATCTATTCGGCCTTATCTAACTTTA
196 ATTTTCTTCTGTCAGGTTCAACTGGTCATATCGAGATTGAATCTATTCGGCCTTATCTAACTTTA
58452173 GCTCAGCTAATACCCGAAGAGAAAGGATCTCAACTTTAATGGGTAACACTACCTCCATCCCGTAA
261 GCTCAGCTAATACCCGAAGAGAAAGGATCTCAACTTTAATGGGTAACACTACCTCCATCCCGTAA
58452238 ACTAGAAAGAAAGGTGTTGCCCCAGTAGAAGTCCTAATAGATGTTCGATATGCAAGGAGAGCGAA
326 ACTAGAAAGAAAGGTGTTGCCCCAGTAGAAGTCCTAATAGATGTTCGATATGCAAGGAGAGCGAA
58452303 AGGTAATTTCTCATGTCAGTCCTTGTAGGTTTTAGTCATTTTCCCTACAATTCTCTTGATGTTTC
391 AGGTAATTTCTCATGTCAGTCCTTGTAGGTTTTAGTCATTTTCCCTACAATTCTCTTGATGTTTC
58452368 CACGGCACCATTCATTTTGGGGCGATACGGTGACGAATTATGGTGTCTGATCTTGAACTGACTAC
456 CACGGCACCATTCATTTTGGGGCGATACGGTGACGAATTATGGTGTCTGATCTTGAACTGACTAC
*
58452433 AAACTTCTACTATTAAGCTGTTGTTCAAATTCAGCACATTGTCAGATATAATTCTTTCAGCACAT
521 AAACTTCTACTATTAAGCTGTTGTTCAAATTCAGCACATTATCAGATATAATTCTTTCAGCACAT
58452498 TGTTCAAA
586 TGTTCAAA
58452506 TCCAGAAAAGGCCTTCTTTAGAACATAAGGCCCTTCCCAATTTGGCATCCACTTCCCTCTAAAAT
1 TCCAGAAAAGGCCTTCTTTAGAACATAAGGCCCTTCCCAATTTGGCATCCACTTCCCTCTAAAAT
58452571 CCTTTTGTAGAGGAAGAATCTTCTTCAACACCAGGTCCCCCTCATGAAATTCTCTAGGGCGAACC
66 CCTTTTGTAGAGGAAGAATCTTCTTCAACACCAGGTCCCCCTCATGAAATTCTCTAGGGCGAACC
*
58452636 CTTTTGCTATAGGCTCGTATCATTCGTTTCTAATACATCTGACCGTGATGAATAACTTTTAGCCT
131 CTTTTGCTATAGGCTCGTATCATTCGTTTCTAATACATCTGACCGTGATGAATAAATTTTAGCCT
58452701 ATTTTCTTCTGTCAGGTTCAACTGGTCATATCGAGATTGAATCTATTCGGCCTTATCTAACTTTA
196 ATTTTCTTCTGTCAGGTTCAACTGGTCATATCGAGATTGAATCTATTCGGCCTTATCTAACTTTA
58452766 GCTCAGCTAATACCCGAAGAGAAAGGATCTCAACTTTAATGGGTAACACTACCTCCATCCCGTAA
261 GCTCAGCTAATACCCGAAGAGAAAGGATCTCAACTTTAATGGGTAACACTACCTCCATCCCGTAA
58452831 ACTAGAAAGAAAGGTGTTGCCCCAGTAGAAGTCCTAATAGATGTTCGATATGCAAGGAGAGCGAA
326 ACTAGAAAGAAAGGTGTTGCCCCAGTAGAAGTCCTAATAGATGTTCGATATGCAAGGAGAGCGAA
58452896 AGGTAATTTCTCATGTCAGTCCTTGTAGGTTTTAGTCATTTTCCCTACAATTCTCTTGATGTTTC
391 AGGTAATTTCTCATGTCAGTCCTTGTAGGTTTTAGTCATTTTCCCTACAATTCTCTTGATGTTTC
58452961 CACGGCACCATTCATTTTGGGGCGATACGGTGACGAATTATGGTGTCTGATCTTGAACTGACTAC
456 CACGGCACCATTCATTTTGGGGCGATACGGTGACGAATTATGGTGTCTGATCTTGAACTGACTAC
58453026 AAACTTCTACTATTAAGCTGTTGTTCAAATTCAGCACATTATCAGATATAATTCTTTCAG
521 AAACTTCTACTATTAAGCTGTTGTTCAAATTCAGCACATTATCAGATATAATTCTTTCAG
58453086 GCATCCCATA
Statistics
Matches: 578, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
593 578 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (593 bp):
TCCAGAAAAGGCCTTCTTTAGAACATAAGGCCCTTCCCAATTTGGCATCCACTTCCCTCTAAAAT
CCTTTTGTAGAGGAAGAATCTTCTTCAACACCAGGTCCCCCTCATGAAATTCTCTAGGGCGAACC
CTTTTGCTATAGGCTCGTATCATTCGTTTCTAATACATCTGACCGTGATGAATAAATTTTAGCCT
ATTTTCTTCTGTCAGGTTCAACTGGTCATATCGAGATTGAATCTATTCGGCCTTATCTAACTTTA
GCTCAGCTAATACCCGAAGAGAAAGGATCTCAACTTTAATGGGTAACACTACCTCCATCCCGTAA
ACTAGAAAGAAAGGTGTTGCCCCAGTAGAAGTCCTAATAGATGTTCGATATGCAAGGAGAGCGAA
AGGTAATTTCTCATGTCAGTCCTTGTAGGTTTTAGTCATTTTCCCTACAATTCTCTTGATGTTTC
CACGGCACCATTCATTTTGGGGCGATACGGTGACGAATTATGGTGTCTGATCTTGAACTGACTAC
AAACTTCTACTATTAAGCTGTTGTTCAAATTCAGCACATTATCAGATATAATTCTTTCAGCACAT
TGTTCAAA
Found at i:58455390 original size:26 final size:26
Alignment explanation
Indices: 58455361--58455412 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
58455351 TTTCTTAGGA
58455361 ACGGGTACAATATTGGCTACCCATTC
1 ACGGGTACAATATTGGCTACCCATTC
58455387 ACGGGTACAATATTGGCTACCCATTC
1 ACGGGTACAATATTGGCTACCCATTC
58455413 TGAGTACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (26 bp):
ACGGGTACAATATTGGCTACCCATTC
Found at i:58457742 original size:12 final size:12
Alignment explanation
Indices: 58457725--58457755 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
58457715 CATATGCTTC
58457725 CTTCTTCTTAGA
1 CTTCTTCTTAGA
*
58457737 CTTCTTCTTGGA
1 CTTCTTCTTAGA
58457749 CTTCTTC
1 CTTCTTC
58457756 ACAGAACTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.29, G:0.10, T:0.52
Consensus pattern (12 bp):
CTTCTTCTTAGA
Found at i:58461848 original size:16 final size:16
Alignment explanation
Indices: 58461824--58461855 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
58461814 CCTTTCATGA
58461824 TGAAATGCCATGTAGT
1 TGAAATGCCATGTAGT
*
58461840 TGAAGTGCCATGTAGT
1 TGAAATGCCATGTAGT
58461856 CAAAGTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.31
Consensus pattern (16 bp):
TGAAATGCCATGTAGT
Found at i:58463457 original size:26 final size:26
Alignment explanation
Indices: 58463424--58463473 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
58463414 TACAAAAGTT
58463424 AAAATATGTACGTATATAT-TATAAA
1 AAAATATGTACGTATATATGTATAAA
**
58463449 AAAATTATGTGTGTATATATGTATA
1 AAAA-TATGTACGTATATATGTATA
58463474 TTTTTTGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 13 0.62
27 4 0.19
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (26 bp):
AAAATATGTACGTATATATGTATAAA
Found at i:58465565 original size:15 final size:15
Alignment explanation
Indices: 58465547--58465586 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
58465537 GTGATTGAAG
*
58465547 TTTTTATTTTTGTTA
1 TTTTTATTTTTGTAA
*
58465562 TTTTTATGTTTGTAA
1 TTTTTATTTTTGTAA
*
58465577 TTTATATTTT
1 TTTTTATTTT
58465587 AATAGATTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.75
Consensus pattern (15 bp):
TTTTTATTTTTGTAA
Found at i:58470138 original size:43 final size:42
Alignment explanation
Indices: 58470058--58470138 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 42
58470048 AAATAAGTTT
*
58470058 AAGAAAATAAATAAAAAATAAAGCAACAAAAACAAAATTAAA
1 AAGAAAATAAATAAAAAATAAAGCAACAAAAAAAAAATTAAA
58470100 AAGAAAGATAAATAAAAAATAAAAG-AA-AAAAGAAAAAAT
1 AAGAAA-ATAAATAAAAAAT-AAAGCAACAAAA-AAAAAAT
58470139 AATAAACTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
42 10 0.29
43 21 0.60
44 4 0.11
ACGTcount: A:0.78, C:0.04, G:0.07, T:0.11
Consensus pattern (42 bp):
AAGAAAATAAATAAAAAATAAAGCAACAAAAAAAAAATTAAA
Found at i:58470258 original size:5 final size:5
Alignment explanation
Indices: 58470248--58470319 Score: 51
Period size: 5 Copynumber: 13.6 Consensus size: 5
58470238 TAAGAATAAT
*
58470248 AAATA AAATA AAATAGGA AAATA AAA-A TAAATA ATATA AAA-A ATAATA
1 AAATA AAATA AAAT---A AAATA AAATA -AAATA AAATA AAATA A-AATA
58470296 ACAA-A TAAATA AAATA AAATA AAA
1 A-AATA -AAATA AAATA AAATA AAA
58470320 GGGGTAGTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
4 3 0.05
5 40 0.73
6 7 0.13
8 5 0.09
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:58470930 original size:11 final size:12
Alignment explanation
Indices: 58470914--58470939 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58470904 GTCAAAAACA
58470914 TTTTTTAAAATT
1 TTTTTTAAAATT
58470926 TTTTTTAAAATT
1 TTTTTTAAAATT
58470938 TT
1 TT
58470940 GAAAATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTTAAAATT
Found at i:58477865 original size:35 final size:35
Alignment explanation
Indices: 58477826--58477897 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
58477816 TCAATTTAAT
58477826 TCTTCATAAAATTTGAACAAGAATTCAATATCACA
1 TCTTCATAAAATTTGAACAAGAATTCAATATCACA
*
58477861 TCTTCATAAAATTTTAACAAGAATTCAATATCACA
1 TCTTCATAAAATTTGAACAAGAATTCAATATCACA
58477896 TC
1 TC
58477898 AATTAACAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.33
Consensus pattern (35 bp):
TCTTCATAAAATTTGAACAAGAATTCAATATCACA
Found at i:58481828 original size:25 final size:24
Alignment explanation
Indices: 58481800--58482040 Score: 172
Period size: 25 Copynumber: 10.4 Consensus size: 24
58481790 GGAGTTTAGC
58481800 GTGCTCTCTGATTATTAGCACATCA
1 GTGCTCTCTGA-TATTAGCACATCA
*
58481825 GTGCTCTCTGATTATTAGCACGTCA
1 GTGCTCTCTGA-TATTAGCACATCA
58481850 GTGCTCTCTG-T-TTAGCACAT-A
1 GTGCTCTCTGATATTAGCACATCA
* *
58481871 TGTGCTCTCTGATATTTATCACGTCA
1 -GTGCTCTCTGATA-TTAGCACATCA
58481897 GTGCTCTCTG-T-TTAGCACATCTA
1 GTGCTCTCTGATATTAGCACATC-A
* *
58481920 -TGTTCTCTGATATTTAGCACGTCA
1 GTGCTCTCTGATA-TTAGCACATCA
*
58481944 GTGCTCTCTGATTACTAG--CA-C-
1 GTGCTCTCTGA-TATTAGCACATCA
* * *
58481965 --GCTCTCTGATCACTAGCGCATTA
1 GTGCTCTCTGAT-ATTAGCACATCA
* **
58481988 GTGCTCTCCG-T-TTAGCACATTT
1 GTGCTCTCTGATATTAGCACATCA
* *
58482010 GTGCTCTCTG-TA-TAGCACTTTA
1 GTGCTCTCTGATATTAGCACATCA
58482032 GTGCTCTCT
1 GTGCTCTCT
58482041 CTTTAATAGT
Statistics
Matches: 178, Mismatches: 19, Indels: 41
0.75 0.08 0.17
Matches are distributed among these distances:
18 1 0.01
19 14 0.08
21 3 0.02
22 70 0.39
23 5 0.03
24 3 0.02
25 79 0.44
26 3 0.02
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (24 bp):
GTGCTCTCTGATATTAGCACATCA
Found at i:58481876 original size:47 final size:46
Alignment explanation
Indices: 58481800--58482045 Score: 213
Period size: 47 Copynumber: 5.3 Consensus size: 46
58481790 GGAGTTTAGC
58481800 GTGCTCTCTGATTATTAGCACATCA-GTGCTCTCTGATTATTAGCACGTCA
1 GTGCTCTCTG--T-TTAGCACAT-ATGTGCTCTCTGA-TATTAGCACGTCA
*
58481850 GTGCTCTCTGTTTAGCACATATGTGCTCTCTGATATTTATCACGTCA
1 GTGCTCTCTGTTTAGCACATATGTGCTCTCTGATA-TTAGCACGTCA
* * *
58481897 GTGCTCTCTGTTTAGCACATCTATGTTCTCTGATATTTAGCACGTCA
1 GTGCTCTCTGTTTAGCACATATGTGCTCTCTGATA-TTAGCACGTCA
* * * *
58481944 GTGCTCTCTGATTACTAGCAC------GCTCTCTGATCACTAGCGCATTA
1 GTGCTCTCTG-TT--TAGCACATATGTGCTCTCTGAT-ATTAGCACGTCA
* * * *
58481988 GTGCTCTCCGTTTAGCACATTTGTGCTCTCTG-TA-TAGCACTTTA
1 GTGCTCTCTGTTTAGCACATATGTGCTCTCTGATATTAGCACGTCA
*
58482032 GTGCTCTCTCTTTA
1 GTGCTCTCTGTTTA
58482046 ATAGTGCATA
Statistics
Matches: 169, Mismatches: 15, Indels: 30
0.79 0.07 0.14
Matches are distributed among these distances:
41 6 0.04
43 2 0.01
44 45 0.27
45 2 0.01
46 4 0.02
47 91 0.54
48 3 0.02
50 16 0.09
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (46 bp):
GTGCTCTCTGTTTAGCACATATGTGCTCTCTGATATTAGCACGTCA
Found at i:58482008 original size:22 final size:22
Alignment explanation
Indices: 58481978--58482039 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
58481968 CTCTGATCAC
* *
58481978 TAGCGCATTAGTGCTCTCCGTT
1 TAGCACATTAGTGCTCTCCGTA
* *
58482000 TAGCACATTTGTGCTCTCTGTA
1 TAGCACATTAGTGCTCTCCGTA
*
58482022 TAGCACTTTAGTGCTCTC
1 TAGCACATTAGTGCTCTC
58482040 TCTTTAATAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (22 bp):
TAGCACATTAGTGCTCTCCGTA
Found at i:58482040 original size:22 final size:23
Alignment explanation
Indices: 58481985--58482040 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
58481975 CACTAGCGCA
* *
58481985 TTAGTGCTCTCCGTTTAGCACAT
1 TTAGTGCTCTCTGTATAGCACAT
58482008 TT-GTGCTCTCTGTATAGCAC-T
1 TTAGTGCTCTCTGTATAGCACAT
58482029 TTAGTGCTCTCT
1 TTAGTGCTCTCT
58482041 CTTTAATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 3 0.10
22 25 0.83
23 2 0.07
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (23 bp):
TTAGTGCTCTCTGTATAGCACAT
Found at i:58485691 original size:17 final size:16
Alignment explanation
Indices: 58485669--58485702 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58485659 ATTATATAAT
58485669 TAATGATAATTAAATTA
1 TAATGAT-ATTAAATTA
*
58485686 TAATGATATTATATTA
1 TAATGATATTAAATTA
58485702 T
1 T
58485703 TAAATAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TAATGATATTAAATTA
Found at i:58486821 original size:21 final size:21
Alignment explanation
Indices: 58486795--58486862 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
58486785 TATTTTTGAG
58486795 TACTGAATTGAATTGTGAAGT
1 TACTGAATTGAATTGTGAAGT
* *
58486816 TACTGAA-T--ATTGTTATGT
1 TACTGAATTGAATTGTGAAGT
* * *
58486834 GTACTGCATTGAACTGTGAAAT
1 -TACTGAATTGAATTGTGAAGT
58486856 TACTGAA
1 TACTGAA
58486863 GTAATGAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
18 8 0.23
19 6 0.17
20 2 0.06
21 13 0.37
22 6 0.17
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (21 bp):
TACTGAATTGAATTGTGAAGT
Found at i:58486838 original size:40 final size:41
Alignment explanation
Indices: 58486775--58486862 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 41
58486765 CATTATGGAA
* * * *
58486775 TACTGAATATTATTTTTGAGTACTGAATTGAATTGTGAAGT
1 TACTGAATATTAGTTATGAGTACTGAATTGAACTGTGAAAT
* *
58486816 TACTGAATATT-GTTATGTGTACTGCATTGAACTGTGAAAT
1 TACTGAATATTAGTTATGAGTACTGAATTGAACTGTGAAAT
58486856 TACTGAA
1 TACTGAA
58486863 GTAATGAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
40 30 0.73
41 11 0.27
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (41 bp):
TACTGAATATTAGTTATGAGTACTGAATTGAACTGTGAAAT
Found at i:58487164 original size:43 final size:45
Alignment explanation
Indices: 58487064--58487164 Score: 127
Period size: 43 Copynumber: 2.3 Consensus size: 45
58487054 ATGCCGGCTA
* * *
58487064 CTGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATACTGTTAC
1 CTGTTACTGTTACAGATTCAACAC-TTGTATGTCGAATACTGTTAC
* *
58487110 C-GTTACGGTTACAGATTCAACAC-TGTATGTTGAATACTGTT-C
1 CTGTTACTGTTACAGATTCAACACTTGTATGTCGAATACTGTTAC
58487152 CTGTTACTGTTAC
1 CTGTTACTGTTAC
58487165 TATTACTACT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
42 2 0.04
43 26 0.54
45 19 0.40
46 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.39
Consensus pattern (45 bp):
CTGTTACTGTTACAGATTCAACACTTGTATGTCGAATACTGTTAC
Found at i:58489376 original size:16 final size:16
Alignment explanation
Indices: 58489355--58489385 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58489345 ATGTCCAGAG
*
58489355 GAGGTTCTGTTTTGAT
1 GAGGTTCTATTTTGAT
58489371 GAGGTTCTATTTTGA
1 GAGGTTCTATTTTGA
58489386 GGAGAGGAGG
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:0.16, C:0.06, G:0.29, T:0.48
Consensus pattern (16 bp):
GAGGTTCTATTTTGAT
Found at i:58493196 original size:17 final size:16
Alignment explanation
Indices: 58493174--58493207 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58493164 ATTATATAAT
58493174 TAATGATAATTAAATTA
1 TAATGAT-ATTAAATTA
*
58493191 TAATGATATTATATTA
1 TAATGATATTAAATTA
58493207 T
1 T
58493208 TAAATAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TAATGATATTAAATTA
Found at i:58493627 original size:7 final size:7
Alignment explanation
Indices: 58493617--58493664 Score: 71
Period size: 7 Copynumber: 7.0 Consensus size: 7
58493607 AACTTGAAAG
*
58493617 GGTTTAG
1 GGTTTAA
*
58493624 GGTTTAG
1 GGTTTAA
58493631 GGTTTAA
1 GGTTTAA
58493638 GGTTT-A
1 GGTTTAA
58493644 GGTTTAA
1 GGTTTAA
58493651 GGTTTAA
1 GGTTTAA
58493658 GGTTTAA
1 GGTTTAA
58493665 TTGGTAAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
6 6 0.15
7 33 0.85
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (7 bp):
GGTTTAA
Found at i:58493649 original size:20 final size:21
Alignment explanation
Indices: 58493617--58493663 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
58493607 AACTTGAAAG
*
58493617 GGTTTAGGGTTTAGGGTTTAA
1 GGTTTAGGGTTTAAGGTTTAA
58493638 GGTTTA-GGTTTAAGGTTTAA
1 GGTTTAGGGTTTAAGGTTTAA
58493658 GGTTTA
1 GGTTTA
58493664 ATTGGTAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (21 bp):
GGTTTAGGGTTTAAGGTTTAA
Found at i:58494724 original size:18 final size:19
Alignment explanation
Indices: 58494701--58494745 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
58494691 TTGAATATTG
*
58494701 TTACTGTTACTGTTACT-A
1 TTACTGTTACCGTTACTAA
*
58494719 TTACTGCTACCGTTACTAA
1 TTACTGTTACCGTTACTAA
58494738 TTACTGTT
1 TTACTGTT
58494746 TAGGTGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (19 bp):
TTACTGTTACCGTTACTAA
Found at i:58496433 original size:11 final size:11
Alignment explanation
Indices: 58496417--58496459 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
58496407 CCATTTTCTA
58496417 AATAAAATACT
1 AATAAAATACT
58496428 AAT-AAATATCT
1 AATAAAATA-CT
*
58496439 AAGTAAAATATT
1 AA-TAAAATACT
58496451 AATAAAATA
1 AATAAAATA
58496460 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 14 0.50
12 4 0.14
13 5 0.18
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATACT
Found at i:58496439 original size:23 final size:23
Alignment explanation
Indices: 58496413--58496456 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
58496403 ATAACCATTT
58496413 TCTAAATAAAATACTAATAAATA
1 TCTAAATAAAATACTAATAAATA
* *
58496436 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATACTAATAAA
58496457 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATACTAATAAATA
Found at i:58499216 original size:15 final size:15
Alignment explanation
Indices: 58499196--58499226 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
58499186 ATCAAGATCC
58499196 TGTAAAAAGGCTTGG
1 TGTAAAAAGGCTTGG
58499211 TGTAAAAAGGCTTGG
1 TGTAAAAAGGCTTGG
58499226 T
1 T
58499227 TCCTTATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.32, T:0.29
Consensus pattern (15 bp):
TGTAAAAAGGCTTGG
Found at i:58502318 original size:18 final size:19
Alignment explanation
Indices: 58502295--58502336 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
58502285 GAAAATACAC
58502295 ATAAAAAATA-AAGATTTA-
1 ATAAAAAATATAA-ATTTAT
58502313 ATAAAAAATATAAATTTAT
1 ATAAAAAATATAAATTTAT
58502332 ATAAA
1 ATAAA
58502337 TTTAGTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
ATAAAAAATATAAATTTAT
Found at i:58508687 original size:114 final size:112
Alignment explanation
Indices: 58508544--58509107 Score: 469
Period size: 114 Copynumber: 4.9 Consensus size: 112
58508534 TTTACCACGC
* * * * * *
58508544 AGCGCCGCAAAATATC-AAGACCAACACGCAGCGTTCTGGTCTTGATGTATATTGGCATTAATGG
1 AGCGCCGCAAAAGATCTTA-ACCAAAACGCAGCGTT-TGGTCTTGATGTATATTAGAATTAGTGG
* *
58508608 CGCTTATGAACAAACGCCGGTAATGTATAGTATTAGCGGCGCTTAGCGGA
64 CGCTTATGAA-AAACGCCGCTAAAGTATAGTATTAGCGGCGCTTAGCGGA
* * *
58508658 AGCGCCGCAAAAGATGTTAACCAAAACGCAGAGTTTAGTCTTGATGTATATT-GCAATTAGTGGC
1 AGCGCCGCAAAAGATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAG-AATTAGTGGC
* * * ** *
58508722 GCTTATAAAGAAAACGCCGCTAATGTATAGTATTAGCGGCACAGAGCGTTA
65 GCTTAT-GA-AAAACGCCGCTAAAGTATAGTATTAGCGGCGCTTAGCG-GA
* * * * * * *
58508773 AACGCCGCAAGATATCTTAATCAAAACGCACCGTTTTGGTCTTGATGTATACTATAATTAGTGGC
1 AGCGCCGCAAAAGATCTTAACCAAAACGCAGCG-TTTGGTCTTGATGTATATTAGAATTAGTGGC
* * * * * * * *
58508838 GTTTATGGAAAACGCCAG-TAAAGGATAGT-TATAGCAGTGTTTTGTGGTA
65 GCTTATGAAAAACGCC-GCTAAAGTATAGTAT-TAGCGGCGCTTAGCGG-A
* * * * * *
58508887 AGCGCCTCCAAATATCTTAACCAAAACGTAGAGTTTGGTCTTGA-GGAGTATTAGAATTAGTGGC
1 AGCGCCGCAAAAGATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTA-TATTAGAATTAGTGGC
* * *
58508951 GCTTGATGAAAAACGCCGCTAAAGTATA-TCATTAGCGGCG-TTTGTGTA
65 GCTT-ATGAAAAACGCCGCTAAAGTATAGT-ATTAGCGGCGCTTAGCGGA
* * *
58508999 ACGCGCCGC-AAAGTATCTTAACCAAAACACAGCGTTTAGTTCTTGATGTATATTGGAATTAGTG
1 A-GCGCCGCAAAAG-ATCTTAACCAAAACGCAGCGTTT-GGTCTTGATGTATATTAGAATTAGTG
** * * *
58509063 GCGCACATGGTAAAACGCCGCTGAAGCATAGTATTAGCGGCGCTT
63 GCGCTTAT-GAAAAACGCCGCTAAAGTATAGTATTAGCGGCGCTT
58509108 TTACCGAAAC
Statistics
Matches: 360, Mismatches: 68, Indels: 43
0.76 0.14 0.09
Matches are distributed among these distances:
112 8 0.02
113 95 0.26
114 189 0.52
115 36 0.10
116 32 0.09
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (112 bp):
AGCGCCGCAAAAGATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGCG
CTTATGAAAAACGCCGCTAAAGTATAGTATTAGCGGCGCTTAGCGGA
Found at i:58509231 original size:18 final size:18
Alignment explanation
Indices: 58509210--58509245 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
58509200 TCATTTTATA
58509210 TGTTT-TTTATATTTAATT
1 TGTTTATTTATA-TTAATT
58509228 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
58509246 AAAATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:58510172 original size:7 final size:7
Alignment explanation
Indices: 58510155--58510199 Score: 63
Period size: 7 Copynumber: 6.3 Consensus size: 7
58510145 TTTACTGTTC
58510155 GGGGTTTT
1 GGGG-TTT
58510163 GGGGTTT
1 GGGGTTT
58510170 GGGGTTT
1 GGGGTTT
*
58510177 AGGGTTT
1 GGGGTTT
*
58510184 AGGGTTT
1 GGGGTTT
58510191 GGGGTTT
1 GGGGTTT
58510198 GG
1 GG
58510200 TTTTTGAGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
7 31 0.89
8 4 0.11
ACGTcount: A:0.04, C:0.00, G:0.53, T:0.42
Consensus pattern (7 bp):
GGGGTTT
Found at i:58510210 original size:21 final size:21
Alignment explanation
Indices: 58510156--58510211 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
58510146 TTACTGTTCG
58510156 GGGTTTTGGGGTTTGGGGTTTA
1 GGGTTTT-GGGTTTGGGGTTTA
*
58510178 GGGTTTAGGGTTTGGGGTTT-
1 GGGTTTTGGGTTTGGGGTTTA
*
58510198 GGTTTTTGAGGTTT
1 GGGTTTTG-GGTTT
58510212 AAGGATTACA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.20
21 18 0.60
22 6 0.20
ACGTcount: A:0.05, C:0.00, G:0.46, T:0.48
Consensus pattern (21 bp):
GGGTTTTGGGTTTGGGGTTTA
Found at i:58518179 original size:13 final size:13
Alignment explanation
Indices: 58518161--58518218 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 13
58518151 AACCCAAATT
58518161 TTATTTTTATTTA
1 TTATTTTTATTTA
*
58518174 TTATTTTTCTTTA
1 TTATTTTTATTTA
58518187 CTTTATTTATTACTTTA
1 --TTATTT-TTA-TTTA
*
58518204 TT-TTATTATTTA
1 TTATTTTTATTTA
58518216 TTA
1 TTA
58518219 CTTATTTGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
12 6 0.16
13 15 0.41
14 2 0.05
15 8 0.22
16 2 0.05
17 4 0.11
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTTTTATTTA
Found at i:58518191 original size:22 final size:21
Alignment explanation
Indices: 58518166--58518225 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
58518156 AAATTTTATT
*
58518166 TTTATTTATTA-TTTTTCTTTA
1 TTTATTTATTACTTTAT-TTTA
58518187 CTTTATTTATTACTTTATTTTA
1 -TTTATTTATTACTTTATTTTA
58518209 -TTATTTATTAC-TTATTT
1 TTTATTTATTACTTTATTT
58518226 GGATATTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
19 6 0.17
20 11 0.31
22 15 0.42
23 4 0.11
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTATTTATTACTTTATTTTA
Found at i:58518199 original size:12 final size:11
Alignment explanation
Indices: 58518160--58518217 Score: 59
Period size: 12 Copynumber: 5.2 Consensus size: 11
58518150 CAACCCAAAT
58518160 TTTATT-TTTA
1 TTTATTATTTA
58518170 TTTATTATTT-
1 TTTATTATTTA
58518180 TTCT-TTACTTTA
1 TT-TATTA-TTTA
58518192 TTTATTACTTTA
1 TTTATTA-TTTA
58518204 TTTTATTATTTA
1 -TTTATTATTTA
58518216 TT
1 TT
58518218 ACTTATTTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
10 11 0.26
11 10 0.24
12 14 0.33
13 7 0.17
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:58518205 original size:8 final size:7
Alignment explanation
Indices: 58518161--58518224 Score: 55
Period size: 7 Copynumber: 9.3 Consensus size: 7
58518151 AACCCAAATT
58518161 TTATTT-
1 TTATTTA
58518167 TTATTTA
1 TTATTTA
58518174 TTATTT-
1 TTATTTA
*
58518180 TTCTTTA
1 TTATTTA
58518187 CTTTATTTA
1 --TTATTTA
58518196 TTACTTTA
1 TTA-TTTA
58518204 -T-TTTA
1 TTATTTA
58518209 TTATTTA
1 TTATTTA
*
58518216 TTACTTA
1 TTATTTA
58518223 TT
1 TT
58518225 TGGATATTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
5 4 0.08
6 12 0.25
7 22 0.46
8 4 0.08
9 6 0.12
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (7 bp):
TTATTTA
Found at i:58521883 original size:15 final size:16
Alignment explanation
Indices: 58521848--58521880 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
58521838 GTATTTATAA
*
58521848 TTATCGATTTGCAATT
1 TTATCGATTTACAATT
58521864 TTATCGATTTACAATT
1 TTATCGATTTACAATT
58521880 T
1 T
58521881 ATCCGGTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (16 bp):
TTATCGATTTACAATT
Found at i:58522020 original size:67 final size:67
Alignment explanation
Indices: 58521947--58522083 Score: 240
Period size: 67 Copynumber: 2.0 Consensus size: 67
58521937 TAATTGATTT
*
58521947 AATGTCAATGAATTATCAATTTTGGTTA-TCTAATTGATTGAATGTTTTATAAATTCATTATATA
1 AATGTCAATGAATTATCAATTTTGGTTAGT-TAATTGATTGAATGTTTAATAAATTCATTATATA
58522011 ATG
65 ATG
*
58522014 AATGTCAGTGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATATAA
1 AATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATATAA
58522079 TG
66 TG
58522081 AAT
1 AAT
58522084 TCTCAACAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
67 66 0.99
68 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.45
Consensus pattern (67 bp):
AATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATATAA
TG
Found at i:58522154 original size:19 final size:19
Alignment explanation
Indices: 58522130--58522175 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
58522120 AAATAACTTA
*
58522130 TTATATATATATTTTAA-AG
1 TTATATATA-ATTTCAATAG
*
58522149 TTATATATAATTTCAATAT
1 TTATATATAATTTCAATAG
58522168 TTATATAT
1 TTATATAT
58522176 TTTTACAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
TTATATATAATTTCAATAG
Found at i:58522155 original size:17 final size:18
Alignment explanation
Indices: 58522133--58522180 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
58522123 TAACTTATTA
58522133 TATATATATTTTAA-AGT
1 TATATATATTTTAATAGT
* *
58522150 TATATATAATTTCAATATT
1 TATATAT-ATTTTAATAGT
58522169 TATATAT-TTTTA
1 TATATATATTTTA
58522181 CAATTTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 11 0.42
18 6 0.23
19 9 0.35
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
TATATATATTTTAATAGT
Found at i:58522264 original size:34 final size:37
Alignment explanation
Indices: 58522198--58522271 Score: 91
Period size: 34 Copynumber: 2.1 Consensus size: 37
58522188 ATTTAACTTA
* *
58522198 TTAATATATATATTTTAAAATTGATATCTTACATTAC
1 TTAATATATATATTTTAAAAGTGATATCTTACATGAC
* *
58522235 TTAA-ATATATATTTT-TAAGT-ATATTTTACATGAC
1 TTAATATATATATTTTAAAAGTGATATCTTACATGAC
58522269 TTA
1 TTA
58522272 CATTACTTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 15 0.45
35 3 0.09
36 11 0.33
37 4 0.12
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (37 bp):
TTAATATATATATTTTAAAAGTGATATCTTACATGAC
Found at i:58522341 original size:72 final size:72
Alignment explanation
Indices: 58522259--58522429 Score: 308
Period size: 72 Copynumber: 2.4 Consensus size: 72
58522249 TTAAGTATAT
58522259 TTTACATGACTTACATTACTTACTAAAACATATTTTTTATGCAACATTAACTTGAATATATTACT
1 TTTACATGACTTACATTACTTACTAAAACATATTTTTTATGCAACATTAACTTGAATATATTACT
58522324 TAAATAA
66 TAAATAA
58522331 TTTACATGACTTACATTACTTACTAAAACATATTTTTTATGCAACATTAACTTGAATATATTACT
1 TTTACATGACTTACATTACTTACTAAAACATATTTTTTATGCAACATTAACTTGAATATATTACT
58522396 TAAATAA
66 TAAATAA
* **
58522403 TTTAC-TTAAATACATTACTTACTAAAA
1 TTTACATGACTTACATTACTTACTAAAA
58522430 TGTGTTTAAA
Statistics
Matches: 96, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 19 0.20
72 77 0.80
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.42
Consensus pattern (72 bp):
TTTACATGACTTACATTACTTACTAAAACATATTTTTTATGCAACATTAACTTGAATATATTACT
TAAATAA
Found at i:58522401 original size:13 final size:12
Alignment explanation
Indices: 58522380--58522423 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
58522370 TGCAACATTA
*
58522380 ACTTGAATATATT
1 ACTTAAATA-ATT
58522393 ACTTAAATAATTT
1 ACTTAAATAA-TT
58522406 ACTTAAATACATT
1 ACTTAAATA-ATT
58522419 ACTTA
1 ACTTA
58522424 CTAAAATGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 1 0.04
13 26 0.93
14 1 0.04
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (12 bp):
ACTTAAATAATT
Found at i:58522692 original size:16 final size:16
Alignment explanation
Indices: 58522671--58522995 Score: 63
Period size: 16 Copynumber: 19.8 Consensus size: 16
58522661 ACACTTATAA
58522671 AACTTACATAATACAT
1 AACTTACATAATACAT
*
58522687 AACTTACAT-GT---T
1 AACTTACATAATACAT
*
58522699 AACTTACATAATACTT
1 AACTTACATAATACAT
* * *
58522715 GACTTATATAAAATTCTCAAAT
1 AACTTACAT--AA---T-ACAT
58522737 AAACTTACATAATACAT
1 AA-CTTACATAATACAT
* *
58522754 TAGTTACATAATAACTTATAT
1 AACTTACATAAT-AC----AT
58522775 AAGCTTACATAATACA-
1 AA-CTTACATAATACAT
*
58522791 CA-TTAC-T--TACAT
1 AACTTACATAATACAT
* * *
58522803 AGCATACATAACTTACAC
1 AACTTACATAA--TACAT
* *
58522821 AACTTAAATAATACAA
1 AACTTACATAATACAT
58522837 AACTTACATAACTTACAT
1 AACTTACATAA--TACAT
*
58522855 AACCTACATAATACAT
1 AACTTACATAATACAT
*
58522871 AA-TAAC-T--TAC--
1 AACTTACATAATACAT
58522881 AACTTACATAACATACAT
1 AACTTACAT-A-ATACAT
* **
58522899 TACTTTGATAACTTACAT
1 AACTTACATAA--TACAT
* *
58522917 AACTTACATACTACAC
1 AACTTACATAATACAT
* * *
58522933 AACTTAAATAGCTTACTT
1 AACTTACATA--ATACAT
58522951 AA--TACATAACTTACAT
1 AACTTACATAA--TACAT
* * *
58522967 AACTTATACACGTACAT
1 AACTTACATA-ATACAT
58522984 AACTTACATAAT
1 AACTTACATAAT
58522996 TGACTTAATA
Statistics
Matches: 217, Mismatches: 49, Indels: 86
0.62 0.14 0.24
Matches are distributed among these distances:
10 2 0.01
11 7 0.03
12 14 0.06
13 5 0.02
14 6 0.03
15 3 0.01
16 77 0.35
17 21 0.10
18 56 0.26
21 8 0.04
22 12 0.06
23 6 0.03
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:58522819 original size:9 final size:9
Alignment explanation
Indices: 58522764--58522994 Score: 162
Period size: 9 Copynumber: 26.4 Consensus size: 9
58522754 TAGTTACATA
*
58522764 ATAACTTAT
1 ATAACTTAC
58522773 ATAAGCTTAC
1 ATAA-CTTAC
*
58522783 ATAA-TACAC
1 ATAACT-TAC
*
58522792 ATTACTTAC
1 ATAACTTAC
* *
58522801 ATAGCATAC
1 ATAACTTAC
58522810 ATAACTTAC
1 ATAACTTAC
* *
58522819 ACAACTTAA
1 ATAACTTAC
58522828 ATAA--TAC
1 ATAACTTAC
*
58522835 AAAACTTAC
1 ATAACTTAC
58522844 ATAACTTAC
1 ATAACTTAC
*
58522853 ATAACCTAC
1 ATAACTTAC
*
58522862 ATAATACATA-
1 AT-A-ACTTAC
58522872 ATAACTTAC
1 ATAACTTAC
58522881 --AACTTAC
1 ATAACTTAC
*
58522888 ATAACATAC
1 ATAACTTAC
* **
58522897 ATTACTTTG
1 ATAACTTAC
58522906 ATAACTTAC
1 ATAACTTAC
58522915 ATAACTTAC
1 ATAACTTAC
58522924 AT-AC-TAC
1 ATAACTTAC
* *
58522931 ACAACTTAA
1 ATAACTTAC
*
58522940 ATAGCTTAC
1 ATAACTTAC
*
58522949 TTAA--TAC
1 ATAACTTAC
58522956 ATAACTTAC
1 ATAACTTAC
58522965 ATAACTT--
1 ATAACTTAC
*
58522972 ATACACGTAC
1 ATA-ACTTAC
58522982 ATAACTTAC
1 ATAACTTAC
58522991 ATAA
1 ATAA
58522995 TTGACTTAAT
Statistics
Matches: 169, Mismatches: 36, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
7 25 0.15
8 12 0.07
9 113 0.67
10 15 0.09
11 4 0.02
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (9 bp):
ATAACTTAC
Found at i:58522840 original size:25 final size:25
Alignment explanation
Indices: 58522806--58522856 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
58522796 CTTACATAGC
*
58522806 ATACATAACTTACACAACTTAAATA
1 ATACAAAACTTACACAACTTAAATA
* *
58522831 ATACAAAACTTACATAACTTACATA
1 ATACAAAACTTACACAACTTAAATA
58522856 A
1 A
58522857 CCTACATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (25 bp):
ATACAAAACTTACACAACTTAAATA
Found at i:58522897 original size:62 final size:62
Alignment explanation
Indices: 58522805--58522972 Score: 152
Period size: 62 Copynumber: 2.7 Consensus size: 62
58522795 ACTTACATAG
58522805 CATACATAACTTACACAACTTAAATAATACAAAACTTACATAACTTACATAACCTACATAATA
1 CATACATAACTTA-ACAACTTAAATAATACAAAACTTACATAACTTACATAACCTACATAATA
* ** ** *
58522868 CATA-ATAACTT-ACAACTTACATAACATACATTACTTTGATAACTTACATAACTTAC---ATA
1 CATACATAACTTAACAACTTAAAT-A-ATACAAAACTTACATAACTTACATAACCTACATAATA
* ** *
58522927 C-TACACAACTTAA-ATAGCTTACTTAATACATAACTTACATAACTTA
1 CATACATAACTTAACA-A-CTTAAATAATACAAAACTTACATAACTTA
58522973 TACACGTACA
Statistics
Matches: 88, Mismatches: 11, Indels: 16
0.77 0.10 0.14
Matches are distributed among these distances:
58 2 0.02
59 29 0.33
60 13 0.15
61 7 0.08
62 33 0.38
63 4 0.05
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.31
Consensus pattern (62 bp):
CATACATAACTTAACAACTTAAATAATACAAAACTTACATAACTTACATAACCTACATAATA
Found at i:58522947 original size:25 final size:25
Alignment explanation
Indices: 58522928--58523007 Score: 54
Period size: 25 Copynumber: 3.2 Consensus size: 25
58522918 ACTTACATAC
* * *
58522928 TACACAACTTAAATAGCTTACTTAA
1 TACACAACTTACATAACTTACATAA
* * * *
58522953 TACATAACTTACATAACTTATACACG
1 TACACAACTTACATAACTTACATA-A
* *
58522979 TACATAACTTACATAA-TTGACTTAA
1 TACACAACTTACATAACTT-ACATAA
58523004 TACA
1 TACA
58523008 TAAATATATA
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
25 24 0.57
26 18 0.43
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.33
Consensus pattern (25 bp):
TACACAACTTACATAACTTACATAA
Found at i:58528549 original size:21 final size:21
Alignment explanation
Indices: 58528523--58528572 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
58528513 CTACAACTTA
*
58528523 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
* *
58528544 AAGCAGAAGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
58528565 AAGCAGAG
1 AAGCAGAG
58528573 CAGGCCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.44, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:58528957 original size:42 final size:42
Alignment explanation
Indices: 58528931--58529096 Score: 278
Period size: 42 Copynumber: 3.9 Consensus size: 42
58528921 CGCTTAAGAA
*
58528931 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCG-TTTTTTTC
*
58528974 TAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTC
*
58529016 TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGTGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTC
* *
58529058 TAAGCGCTGCTAAAGAACATGGTTTTTAGCGGCGTTTTT
1 TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
58529097 GTTTGTAAAC
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
42 84 0.72
43 32 0.28
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTC
Found at i:58529683 original size:37 final size:37
Alignment explanation
Indices: 58529619--58529707 Score: 108
Period size: 37 Copynumber: 2.4 Consensus size: 37
58529609 AGTAAACAGT
* * * * *
58529619 AATCAGTAACGGTAACAGTATTCGACACGCAGTGT-CA
1 AATCGGTAACAGTAACAATATTAGACACACAGT-TCCA
*
58529656 AATCGGTAACAGTAACAATATTAGACACACAGTTCCG
1 AATCGGTAACAGTAACAATATTAGACACACAGTTCCA
58529693 AATCGGTAACAGTAA
1 AATCGGTAACAGTAA
58529708 AAGTAGTCGG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 1 0.02
37 44 0.98
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.21
Consensus pattern (37 bp):
AATCGGTAACAGTAACAATATTAGACACACAGTTCCA
Found at i:58531979 original size:28 final size:27
Alignment explanation
Indices: 58531946--58532044 Score: 119
Period size: 28 Copynumber: 3.6 Consensus size: 27
58531936 TAATGAGATT
58531946 AGCACTAAGTGTGCGAGTTTAATTGAA
1 AGCACTAAGTGTGCGAGTTTAATTGAA
* **
58531973 ATGCACTAAGTGTGCGAGTATAAGGGTAA
1 A-GCACTAAGTGTGCGAGTTTAATTG-AA
*
58532002 AGCACTAAGTGTGCGAGTTTGATT-ATTA
1 AGCACTAAGTGTGCGAGTTTAATTGA--A
58532030 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
58532045 TACTTATTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 56 0.92
29 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTTAATTGAA
Found at i:58533111 original size:22 final size:24
Alignment explanation
Indices: 58533063--58533355 Score: 184
Period size: 24 Copynumber: 12.5 Consensus size: 24
58533053 CCAAATTTGA
* *
58533063 TGTCCATTTTGAGTGTATTGATGC
1 TGTCCATTTTGAATGTATTAATGC
58533087 TGTCCATTTT-AATGTA-TAATGC
1 TGTCCATTTTGAATGTATTAATGC
* *
58533109 TGTCCAATTTTGAGTGTATTGATGC
1 TGTCC-ATTTTGAATGTATTAATGC
* *
58533134 TGCCCATTTT-AATGT-GTAATGC
1 TGTCCATTTTGAATGTATTAATGC
* *
58533156 TGTCCAATTTTGAGTGTATTGATGC
1 TGTCC-ATTTTGAATGTATTAATGC
* *
58533181 CGCCCATTTT-AATGTA-TAATGC
1 TGTCCATTTTGAATGTATTAATGC
* * *
58533203 TGTCCAATTGTGAGTATATTTAA-GC
1 TGTCC-ATTTTGAATGTA-TTAATGC
* *
58533228 TGTCTAATTTG-ATGTA-TAATGC
1 TGTCCATTTTGAATGTATTAATGC
* * *
58533250 TGTCCAATTGTGAGTATATTTAA-GC
1 TGTCC-ATTTTGAATGTA-TTAATGC
* *
58533275 TGTCTAATTTG-ATGTA-TAATGC
1 TGTCCATTTTGAATGTATTAATGC
** *
58533297 TGTCCAATTTTGGGTATATTTAA-GC
1 TGTCC-ATTTTGAATGTA-TTAATGC
* *
58533322 TGTCTAATTTG-ATGTA-TAATGC
1 TGTCCATTTTGAATGTATTAATGC
58533344 TGTCCATTTTGA
1 TGTCCATTTTGA
58533356 GCATGTTATT
Statistics
Matches: 201, Mismatches: 46, Indels: 45
0.69 0.16 0.15
Matches are distributed among these distances:
21 9 0.04
22 50 0.25
23 46 0.23
24 52 0.26
25 35 0.17
26 9 0.04
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.43
Consensus pattern (24 bp):
TGTCCATTTTGAATGTATTAATGC
Found at i:58533122 original size:47 final size:47
Alignment explanation
Indices: 58533063--58533397 Score: 352
Period size: 47 Copynumber: 7.1 Consensus size: 47
58533053 CCAAATTTGA
* * *
58533063 TGTCC-ATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGC
1 TGTCCAATTTTGAGTATATTGAAGCTGTCCAATTTAATGTATAATGC
* * * * *
58533109 TGTCCAATTTTGAGTGTATTGATGCTGCCCATTTTAATGTGTAATGC
1 TGTCCAATTTTGAGTATATTGAAGCTGTCCAATTTAATGTATAATGC
* * * * *
58533156 TGTCCAATTTTGAGTGTATTGATGCCGCCCATTTTAATGTATAATGC
1 TGTCCAATTTTGAGTATATTGAAGCTGTCCAATTTAATGTATAATGC
* * * *
58533203 TGTCCAATTGTGAGTATATTTAAGCTGTCTAATTTGATGTATAATGC
1 TGTCCAATTTTGAGTATATTGAAGCTGTCCAATTTAATGTATAATGC
* * * *
58533250 TGTCCAATTGTGAGTATATTTAAGCTGTCTAATTTGATGTATAATGC
1 TGTCCAATTTTGAGTATATTGAAGCTGTCCAATTTAATGTATAATGC
* * * *
58533297 TGTCCAATTTTGGGTATATTTAAGCTGTCTAATTTGATGTATAATGC
1 TGTCCAATTTTGAGTATATTGAAGCTGTCCAATTTAATGTATAATGC
* * * ** *
58533344 TGTCC-ATTTTGAGCATGTT-ATTGCTGTCCAATTTGTTGAATAATTGC
1 TGTCCAATTTTGAGTATATTGA-AGCTGTCCAATTTAATGTATAA-TGC
58533391 TGTCCAA
1 TGTCCAA
58533398 AATAGAGTTG
Statistics
Matches: 263, Mismatches: 22, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
45 1 0.00
46 34 0.13
47 227 0.86
48 1 0.00
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.43
Consensus pattern (47 bp):
TGTCCAATTTTGAGTATATTGAAGCTGTCCAATTTAATGTATAATGC
Found at i:58533174 original size:94 final size:93
Alignment explanation
Indices: 58533063--58533356 Score: 399
Period size: 94 Copynumber: 3.1 Consensus size: 93
58533053 CCAAATTTGA
*
58533063 TGTCCATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTTTGAGTGTAT
1 TGTCCATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTTTGAGTATAT
* * * * * * *
58533128 TGATGCTGCCCATTTTAATGTGTAATGC
66 TTAAGCTGTCTAATTTGATGTATAATGC
* * *
58533156 TGTCCAATTTTGAGTGTATTGATGCCGCCCATTTTAATGTATAATGCTGTCCAATTGTGAGTATA
1 TGTCC-ATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTTTGAGTATA
58533221 TTTAAGCTGTCTAATTTGATGTATAATGC
65 TTTAAGCTGTCTAATTTGATGTATAATGC
* * * * * * * *
58533250 TGTCCAATTGTGAGTATATTTAAGCTGTCTAATTTGATGTATAATGCTGTCCAATTTTGGGTATA
1 TGTCC-ATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTTTGAGTATA
58533315 TTTAAGCTGTCTAATTTGATGTATAATGC
65 TTTAAGCTGTCTAATTTGATGTATAATGC
58533344 TGTCCATTTTGAG
1 TGTCCATTTTGAG
58533357 CATGTTATTG
Statistics
Matches: 177, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
93 12 0.07
94 165 0.93
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (93 bp):
TGTCCATTTTGAGTGTATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTTTGAGTATAT
TTAAGCTGTCTAATTTGATGTATAATGC
Found at i:58533230 original size:25 final size:25
Alignment explanation
Indices: 58533201--58533339 Score: 134
Period size: 25 Copynumber: 5.8 Consensus size: 25
58533191 AATGTATAAT
58533201 GCTGTCCAATTGTGA-GTATATTTAA
1 GCTGTCCAATT-TGATGTATATTTAA
* *
58533226 GCTGTCTAATTTGATGTATA---AT
1 GCTGTCCAATTTGATGTATATTTAA
58533248 GCTGTCCAATTGTGA-GTATATTTAA
1 GCTGTCCAATT-TGATGTATATTTAA
* *
58533273 GCTGTCTAATTTGATGTATA---AT
1 GCTGTCCAATTTGATGTATATTTAA
*
58533295 GCTGTCCAATTTTG-GGTATATTTAA
1 GCTGTCCAA-TTTGATGTATATTTAA
*
58533320 GCTGTCTAATTTGATGTATA
1 GCTGTCCAATTTGATGTATA
58533340 ATGCTGTCCA
Statistics
Matches: 92, Mismatches: 11, Indels: 22
0.74 0.09 0.18
Matches are distributed among these distances:
22 30 0.33
23 7 0.08
24 10 0.11
25 45 0.49
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.43
Consensus pattern (25 bp):
GCTGTCCAATTTGATGTATATTTAA
Found at i:58541630 original size:18 final size:18
Alignment explanation
Indices: 58541609--58541647 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
58541599 TAAAATTATA
58541609 AAAAAACATAAAAAATTT
1 AAAAAACATAAAAAATTT
** *
58541627 AAAAATTATAAAAATTTT
1 AAAAAACATAAAAAATTT
58541645 AAA
1 AAA
58541648 TTTATAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAAACATAAAAAATTT
Found at i:58541639 original size:17 final size:17
Alignment explanation
Indices: 58541619--58541659 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
58541609 AAAAAACATA
58541619 AAAAATTTAAAAATTAT
1 AAAAATTTAAAAATTAT
* *
58541636 AAAAATTTTAAATTTAT
1 AAAAATTTAAAAATTAT
*
58541653 AATAATT
1 AAAAATT
58541660 ATTTGAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAAATTTAAAAATTAT
Found at i:58541640 original size:10 final size:10
Alignment explanation
Indices: 58541600--58541640 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
58541590 GATTCATTCT
58541600 AAAATTATAA
1 AAAATTATAA
**
58541610 AAAAACATAA
1 AAAATTATAA
58541620 AAAATT-T-A
1 AAAATTATAA
58541628 AAAATTATAA
1 AAAATTATAA
58541638 AAA
1 AAA
58541641 TTTTAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
8 7 0.28
9 2 0.08
10 16 0.64
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAATTATAA
Found at i:58545337 original size:13 final size:13
Alignment explanation
Indices: 58545319--58545384 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
58545309 AAATTTGAAT
58545319 TATTTAGTGATAA
1 TATTTAGTGATAA
58545332 TATTTA---A-AA
1 TATTTAGTGATAA
*
58545341 TTATTTAGTGAAAA
1 -TATTTAGTGATAA
58545355 TATTTAGT-AT--
1 TATTTAGTGATAA
58545365 TATTTAGTGATAA
1 TATTTAGTGATAA
58545378 TATTTAG
1 TATTTAG
58545385 AAAAAATCTA
Statistics
Matches: 44, Mismatches: 1, Indels: 16
0.72 0.02 0.26
Matches are distributed among these distances:
9 2 0.05
10 15 0.34
11 2 0.05
12 1 0.02
13 22 0.50
14 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:58545384 original size:23 final size:23
Alignment explanation
Indices: 58545311--58545386 Score: 118
Period size: 23 Copynumber: 3.3 Consensus size: 23
58545301 AATTTTTAAA
58545311 ATTT-GAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
* *
58545333 ATTTAAAATTATTTAGTGAAAAT
1 ATTTAGAATTATTTAGTGATAAT
*
58545356 ATTTAGTATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
58545379 ATTTAGAA
1 ATTTAGAA
58545387 AAAATCTAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 4 0.09
23 43 0.91
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTGATAAT
Found at i:58545558 original size:22 final size:24
Alignment explanation
Indices: 58545533--58545585 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 24
58545523 TTTCATTCTT
*
58545533 TTTTTTTTTATTTA-CTTTCAA-C
1 TTTTTTTTTAATTATCTTTCAAGC
**
58545555 TTTTAGTTTAATTATCTTTCAAGGC
1 TTTTTTTTTAATTATCTTTCAA-GC
58545580 TTTTTT
1 TTTTTT
58545586 CCTTCCCACT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
22 11 0.48
23 7 0.30
25 5 0.22
ACGTcount: A:0.19, C:0.11, G:0.06, T:0.64
Consensus pattern (24 bp):
TTTTTTTTTAATTATCTTTCAAGC
Found at i:58548429 original size:23 final size:23
Alignment explanation
Indices: 58548403--58548447 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
58548393 TAAAATTTGA
*
58548403 ATTATTTAGTAATAATATTTAGG
1 ATTATTTAGTAATAACATTTAGG
*
58548426 ATTATTTAGTGATAACATTTAG
1 ATTATTTAGTAATAACATTTAG
58548448 AAAAAACCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (23 bp):
ATTATTTAGTAATAACATTTAGG
Found at i:58554395 original size:29 final size:30
Alignment explanation
Indices: 58554339--58554451 Score: 83
Period size: 29 Copynumber: 3.8 Consensus size: 30
58554329 TAAATACTTG
* *
58554339 AATTTAACTCTCTAATATTTACATATTTTATC
1 AATTTAA-TCT-TAATATTTAAAAATTTTATC
*
58554371 AATTTAATCTTAA-ATTTAAAAA-TTTAAC
1 AATTTAATCTTAATATTTAAAAATTTTATC
* *
58554399 CATATTAGTCTTTAATATTTATAAAATTTT-TC
1 AAT-TTAATC-TTAATATTTA-AAAATTTTATC
* *
58554431 -ATTTAATTTTAAT-TCTAAAAA
1 AATTTAATCTTAATATTTAAAAA
58554452 AATAAAATAA
Statistics
Matches: 67, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
27 4 0.06
28 10 0.15
29 17 0.25
30 11 0.16
31 10 0.15
32 12 0.18
33 3 0.04
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.49
Consensus pattern (30 bp):
AATTTAATCTTAATATTTAAAAATTTTATC
Found at i:58555396 original size:48 final size:49
Alignment explanation
Indices: 58555301--58555400 Score: 139
Period size: 49 Copynumber: 2.1 Consensus size: 49
58555291 CAAATTTTAT
* * * *
58555301 AAACAAGGGCTAAAATTATTGAATTATTGATTTTAGGATCAAATTGATA
1 AAACAAGGGCTAAAATTATTGAATTATTGAGTTCAAGACCAAATTGATA
* *
58555350 AAACGAGGGCTAAAATTATTGAATT-TTTAGTTCAAGACCAAATTGATA
1 AAACAAGGGCTAAAATTATTGAATTATTGAGTTCAAGACCAAATTGATA
58555398 AAA
1 AAA
58555401 TGTGTAAACA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
48 21 0.47
49 24 0.53
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (49 bp):
AAACAAGGGCTAAAATTATTGAATTATTGAGTTCAAGACCAAATTGATA
Found at i:58556430 original size:3 final size:3
Alignment explanation
Indices: 58556424--58556483 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
58556414 CAACAGCAAC
* * * *
58556424 AAG AAG AAG AAG AAG AAG AAG AAG ATG ATG ATG ATG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
58556472 ACA- AAG AAG AAG
1 A-AG AAG AAG AAG
58556484 CGCCAAAACC
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 1 0.02
3 51 0.96
4 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.32, T:0.07
Consensus pattern (3 bp):
AAG
Found at i:58557552 original size:3 final size:3
Alignment explanation
Indices: 58557544--58557583 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
58557534 TCAGGGACTT
* * *
58557544 ATG ATG ATG ATG ATG ATA ATA ATG ATG ATG ATA ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
58557584 CAACGGACGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:58557570 original size:15 final size:15
Alignment explanation
Indices: 58557550--58557583 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
58557540 ACTTATGATG
58557550 ATGATGATGATAATA
1 ATGATGATGATAATA
*
58557565 ATGATGATGATAATG
1 ATGATGATGATAATA
58557580 ATGA
1 ATGA
58557584 CAACGGACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (15 bp):
ATGATGATGATAATA
Found at i:58567769 original size:18 final size:18
Alignment explanation
Indices: 58567743--58567777 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58567733 TTAGTTCTTT
* *
58567743 TATATATTTATATATTTA
1 TATAAATTTATAAATTTA
58567761 TATAAATTTATAAATTT
1 TATAAATTTATAAATTT
58567778 TTATTCTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATAAATTTATAAATTTA
Found at i:58567905 original size:21 final size:21
Alignment explanation
Indices: 58567866--58567906 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
58567856 ATATTTTATA
*
58567866 AAATAAAAAAATATATAAAAC
1 AAATAAAAAAATACATAAAAC
*
58567887 AAATAAAAAAATACCTAAAA
1 AAATAAAAAAATACATAAAA
58567907 TGAATCTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (21 bp):
AAATAAAAAAATACATAAAAC
Found at i:58575343 original size:84 final size:83
Alignment explanation
Indices: 58575238--58575406 Score: 284
Period size: 84 Copynumber: 2.0 Consensus size: 83
58575228 TGTGGATAGT
* **
58575238 GATACATACAGTCTATTTCTCTAATTTGTCATTTTCATATATTCACATCATCGATCCAAACGCAA
1 GATACATACAATCTATTTCTCTAATTCATCATTTTCATATATTCACATCATCGATCCAAACGCAA
58575303 ACCGCTCAAGGATATATC
66 ACCGCTCAAGGATATATC
*
58575321 GATACATACAAATCTATTTCTCTAATTCATCATTTTCATATATTCACATCATTGATCCAAACGCA
1 GATACATAC-AATCTATTTCTCTAATTCATCATTTTCATATATTCACATCATCGATCCAAACGCA
*
58575386 AACCGCTTAAGGATATATC
65 AACCGCTCAAGGATATATC
58575405 GA
1 GA
58575407 GCTACTAGAG
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
83 9 0.11
84 71 0.89
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (83 bp):
GATACATACAATCTATTTCTCTAATTCATCATTTTCATATATTCACATCATCGATCCAAACGCAA
ACCGCTCAAGGATATATC
Found at i:58577322 original size:113 final size:114
Alignment explanation
Indices: 58577161--58577580 Score: 466
Period size: 114 Copynumber: 3.7 Consensus size: 114
58577151 TATTTGTAAG
* * * * ** * * * *
58577161 CGCCGCAAAAAAATGTTAGCCAAAACGCAGCGTTTGTTCCCGAGGTATATTAGACTTGGTGGCGT
1 CGCCGC-AAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGCGA
*
58577226 TTATGG-AAAACGCCGCTAAAGGAGAGTATTAGAGGCGCTTTGTAAGAAA
65 TTATGGAAAAACGCCGCTAAAGCAGAGTATTAGAGGCGCTTTGTAAGAAA
* * * *
58577275 CGCCGTAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTAACGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGCGAT
* * ** * * *
58577340 TGTGGAAAAACGCCGCTATAGCACCGTATTGGCGGCGTTTTG-AATGAAA
66 TATGGAAAAACGCCGCTAAAGCAGAGTATTAGAGGCGCTTTGTAA-GAAA
* * * * * *
58577389 CGCCGCAAGATATCTTAACCAAAACGCATCGTTTGGTCTTGATGAATATAAAAATTAGTGGCAAT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGCGAT
* * * *
58577454 TACGGAAAAAGGCCACTAAAGCAGAGTATTAGAGGCGCTTTGTAAGAAT
66 TATGGAAAAACGCCGCTAAAGCAGAGTATTAGAGGCGCTTTGTAAGAAA
* ** *
58577503 CACCGCAAAATATCTTAACCAAAACGCAATGTTTGGTCTTGATGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGCGAT
* *
58577568 CATGTAAAAACGC
66 TATGGAAAAACGC
58577581 ATGTAGGTTT
Statistics
Matches: 249, Mismatches: 54, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
113 54 0.22
114 193 0.78
115 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (114 bp):
CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGCGAT
TATGGAAAAACGCCGCTAAAGCAGAGTATTAGAGGCGCTTTGTAAGAAA
Found at i:58577855 original size:7 final size:7
Alignment explanation
Indices: 58577845--58577934 Score: 58
Period size: 7 Copynumber: 13.0 Consensus size: 7
58577835 GGAGTTTTGA
58577845 GTTTAGG
1 GTTTAGG
*
58577852 GTTTATG
1 GTTTAGG
* *
58577859 ATGTA-G
1 GTTTAGG
*
58577865 GTTTAGT
1 GTTTAGG
*
58577872 GTTTTGG
1 GTTTAGG
*
58577879 GTTTAGA
1 GTTTAGG
*
58577886 GTTTGGG
1 GTTTAGG
*
58577893 AGTTTTGG
1 -GTTTAGG
*
58577901 GTTTAAG
1 GTTTAGG
*
58577908 GTTTGGG
1 GTTTAGG
58577915 GTTT-GG
1 GTTTAGG
*
58577921 GTTTGGG
1 GTTTAGG
58577928 GTTTAGG
1 GTTTAGG
58577935 TCGTTTTAGT
Statistics
Matches: 62, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
6 10 0.16
7 46 0.74
8 6 0.10
ACGTcount: A:0.12, C:0.00, G:0.41, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:58577897 original size:22 final size:21
Alignment explanation
Indices: 58577863--58577924 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
58577853 TTTATGATGT
* *
58577863 AGGTTTAGTGTTTTGGGTTT-
1 AGGTTTGGGGTTTTGGGTTTA
58577883 AGAGTTTGGGAGTTTTGGGTTTA
1 AG-GTTTGGG-GTTTTGGGTTTA
58577906 AGGTTTGGGG-TTTGGGTTT
1 AGGTTTGGGGTTTTGGGTTT
58577925 GGGGTTTAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
20 11 0.30
21 6 0.16
22 18 0.49
23 2 0.05
ACGTcount: A:0.11, C:0.00, G:0.40, T:0.48
Consensus pattern (21 bp):
AGGTTTGGGGTTTTGGGTTTA
Found at i:58577914 original size:13 final size:14
Alignment explanation
Indices: 58577894--58577932 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
58577884 GAGTTTGGGA
*
58577894 GTTTTGGGTTTAAG
1 GTTTGGGGTTTAAG
*
58577908 GTTTGGGGTTT-GG
1 GTTTGGGGTTTAAG
58577921 GTTTGGGGTTTA
1 GTTTGGGGTTTA
58577933 GGTCGTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.08, C:0.00, G:0.44, T:0.49
Consensus pattern (14 bp):
GTTTGGGGTTTAAG
Found at i:58578410 original size:87 final size:87
Alignment explanation
Indices: 58578198--58578689 Score: 691
Period size: 87 Copynumber: 5.7 Consensus size: 87
58578188 CACACGTGAC
* * * * * * * *
58578198 TGCCTCTC-TCGGTTGTAGTAGAGCTGGTTGAAGACAACATATCTTGCCTTCCTGCATTGACAGT
1 TGCCTC-CATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGC
* ***
58578262 GAAGCAGATCGAAGACACAAGTGT
65 GAAGCAGATCGAAAACA-AAACCT
* * * *
58578286 TGCCTCCCTCGTTTGCAGTGGAGCTGGTCAAAGATAGCAGATCTTGCTTTCCTGCATTAACAGCG
1 TGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCG
* * * *
58578351 AAGCTGATCAAAAACAAAGCTT
66 AAGCAGATCGAAAACAAAACCT
* * *
58578373 TGCCTCCATCGGTTGTAGTGGAGCTGGATAAATATAGCAGATCTTGCCTTCCTGCATTAACAGCG
1 TGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCG
*
58578438 AAGCTGATCGAAAACAAAACCT
66 AAGCAGATCGAAAACAAAACCT
* * *
58578460 TGCCTCCGTCAGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGTCTTCCTGCATTAACAGCG
1 TGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCG
58578525 AAGCAGATCGAAAACAAAACCT
66 AAGCAGATCGAAAACAAAACCT
* *
58578547 TGCCTCCATAGGTTGCAGTGGAGCTGGTCAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCG
1 TGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCG
58578612 AAGCAGATCGAAAACAAAACCT
66 AAGCAGATCGAAAACAAAACCT
58578634 TGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCC-TCCTGCAT
1 TGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCAT
58578690 CGACAGCGGG
Statistics
Matches: 363, Mismatches: 40, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
86 8 0.02
87 290 0.80
88 65 0.18
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.25
Consensus pattern (87 bp):
TGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCG
AAGCAGATCGAAAACAAAACCT
Found at i:58578865 original size:40 final size:42
Alignment explanation
Indices: 58578762--58578916 Score: 190
Period size: 42 Copynumber: 3.6 Consensus size: 42
58578752 GAAGCCAGTA
58578762 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACCACAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACCACAG
* * * *
58578804 ATCTTATCTCCCTAAGTAGTAGTGGAGCAGATC-GTATC-GAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAGAACCACAG
* *
58578845 -TCTTATCTCTCTAAGCAGTAGTGGAGCAAACAGAAGAAACCACAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGAC---AG-AACCACAG
58578890 ATCTTATCTCCCTAAGCAGTAGTGGAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAG
58578917 TGGATCGCAT
Statistics
Matches: 94, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 1 0.01
40 27 0.29
41 2 0.02
42 33 0.35
43 2 0.02
44 2 0.02
45 2 0.02
46 25 0.27
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.24
Consensus pattern (42 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACCACAG
Found at i:58578923 original size:86 final size:82
Alignment explanation
Indices: 58578763--58578916 Score: 245
Period size: 86 Copynumber: 1.8 Consensus size: 82
58578753 AAGCCAGTAA
* *
58578763 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGTAGTAGTG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAAACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTG
58578828 GAGCAGATCGTATCGAG
66 GAGCAGATCGTATCGAG
*
58578845 TCTTATCTCTCTAAGCAGTAGTGGAGCAAACAGAAGAAACCACAGATCTTATCTCCCTAAGCAGT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAAAC---AG-AACCACAGATCTTATCTCCCTAAGCAGT
58578910 AGTGGAG
62 AGTGGAG
58578917 TGGATCGCAT
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
82 29 0.45
85 2 0.03
86 34 0.52
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (82 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAAACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTG
GAGCAGATCGTATCGAG
Found at i:58578939 original size:86 final size:82
Alignment explanation
Indices: 58578767--58578942 Score: 235
Period size: 86 Copynumber: 2.1 Consensus size: 82
58578757 CAGTAATCTT
* *
58578767 ATCTCCCTAAGCAGTAGTGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGTAGTAGTGGAGC
1 ATCTCCCTAAGCAGTAGTGGAGCAAACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGC
* * *
58578832 AGATCGTATCGAGTCTT
66 AGATCGCATCCAGTCTG
*
58578849 ATCTCTCTAAGCAGTAGTGGAGCAAACAGAAGAAACCACAGATCTTATCTCCCTAAGCAGTAGTG
1 ATCTCCCTAAGCAGTAGTGGAGCAAAC---AG-AACCACAGATCTTATCTCCCTAAGCAGTAGTG
** *
58578914 GAGTGGATCGCATCCCGTCTG
62 GAGCAGATCGCATCCAGTCTG
58578935 ATCTCCCT
1 ATCTCCCT
58578943 GAAGTTGCAG
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
82 25 0.31
85 2 0.03
86 53 0.66
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (82 bp):
ATCTCCCTAAGCAGTAGTGGAGCAAACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGC
AGATCGCATCCAGTCTG
Found at i:58581345 original size:16 final size:16
Alignment explanation
Indices: 58581313--58581346 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58581303 ATACCCTTTT
* *
58581313 AAATTTCAAACACATA
1 AAATTTCAAAAAAATA
58581329 AAATTTCAAAAAAATA
1 AAATTTCAAAAAAATA
58581345 AA
1 AA
58581347 GGCAATATTC
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:0.65, C:0.12, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATTTCAAAAAAATA
Found at i:58582435 original size:12 final size:12
Alignment explanation
Indices: 58582418--58582444 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
58582408 AATTTTTTTA
58582418 AATAATATTAAT
1 AATAATATTAAT
58582430 AATAATATTAAT
1 AATAATATTAAT
58582442 AAT
1 AAT
58582445 GTCATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:58583841 original size:13 final size:14
Alignment explanation
Indices: 58583811--58583843 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
58583801 GGCACATTAC
*
58583811 TTGGTATTCTTTTT
1 TTGGTATTCTTGTT
58583825 TTGGTATTC-TGTT
1 TTGGTATTCTTGTT
58583838 TTGGTA
1 TTGGTA
58583844 CAGTTTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.09, C:0.06, G:0.21, T:0.64
Consensus pattern (14 bp):
TTGGTATTCTTGTT
Found at i:58584408 original size:20 final size:19
Alignment explanation
Indices: 58584383--58584420 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
58584373 ATTTGGTTTG
58584383 TTTGTATACAATTCTATTTT
1 TTTGTATACAATT-TATTTT
*
58584403 TTTGTATACTATTTATTT
1 TTTGTATACAATTTATTT
58584421 ATATTTTCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTGTATACAATTTATTTT
Found at i:58584522 original size:37 final size:37
Alignment explanation
Indices: 58584469--58584542 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
58584459 TAATCCGCAG
*
58584469 TAATTTTCATAATACATAACTTACTTAAATTTCATAA
1 TAATTTTCATAATACATAACTTACATAAATTTCATAA
* *
58584506 TAATTTTCATAGTACATAACTTACATAATTTTCATAA
1 TAATTTTCATAATACATAACTTACATAAATTTCATAA
58584543 CCTACATAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.42, C:0.14, G:0.01, T:0.43
Consensus pattern (37 bp):
TAATTTTCATAATACATAACTTACATAAATTTCATAA
Found at i:58584612 original size:16 final size:15
Alignment explanation
Indices: 58584593--58584659 Score: 54
Period size: 16 Copynumber: 4.7 Consensus size: 15
58584583 TAATACATAG
58584593 CTTACATAATATTGAA
1 CTTACATAATATT-AA
*
58584609 CTTACATAAT-TT-T
1 CTTACATAATATTAA
* *
58584622 CGTA-AT-ACA-TAA
1 CTTACATAATATTAA
58584634 CTTACATAATATTGAA
1 CTTACATAATATT-AA
58584650 CTTACATAAT
1 CTTACATAAT
58584660 TTTCATAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
11 2 0.05
12 5 0.13
13 5 0.13
14 2 0.05
15 3 0.08
16 22 0.56
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.39
Consensus pattern (15 bp):
CTTACATAATATTAA
Found at i:58584613 original size:41 final size:41
Alignment explanation
Indices: 58584523--58584678 Score: 206
Period size: 41 Copynumber: 3.8 Consensus size: 41
58584513 CATAGTACAT
* * *
58584523 AACTTACATAATTTTCATAACCTACATAACTTATACAATACAT-
1 AACTTACATAATTTTCATAA--TACATAACTTACATAATA-TTG
* * * *
58584566 AGCTTACTTAAATTTCATAATACATAGCTTACATAATATTG
1 AACTTACATAATTTTCATAATACATAACTTACATAATATTG
*
58584607 AACTTACATAATTTTCGTAATACATAACTTACATAATATTG
1 AACTTACATAATTTTCATAATACATAACTTACATAATATTG
58584648 AACTTACATAATTTTCATAATACATAACTTA
1 AACTTACATAATTTTCATAATACATAACTTA
58584679 TTTAATTTTC
Statistics
Matches: 99, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
40 1 0.01
41 81 0.82
43 17 0.17
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (41 bp):
AACTTACATAATTTTCATAATACATAACTTACATAATATTG
Found at i:58584655 original size:25 final size:24
Alignment explanation
Indices: 58584627--58584712 Score: 73
Period size: 25 Copynumber: 3.5 Consensus size: 24
58584617 ATTTTCGTAA
58584627 TACATAACTTACATAATATTGAACT
1 TACATAACTTACATAATATT-AACT
* * *
58584652 TACATAATTTTCATAATACATAACT
1 TACATAACTTACATAATA-TTAACT
** * * *
58584677 TATTTAATTTTCATAATATAAAACT
1 TACATAACTTACATAATAT-TAACT
58584702 TACATAACTTA
1 TACATAACTTA
58584713 TACAGTACAC
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
25 47 0.98
26 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.41
Consensus pattern (24 bp):
TACATAACTTACATAATATTAACT
Found at i:58584702 original size:50 final size:50
Alignment explanation
Indices: 58584627--58584786 Score: 146
Period size: 50 Copynumber: 3.2 Consensus size: 50
58584617 ATTTTCGTAA
* * ** *
58584627 TACATAACTTACATAATATTGAACTTACATAATTTTCATAATACATAACT
1 TACATAATTTTCATAATATAAAACTTACATAATTTTCATAATACACAACT
** * *
58584677 TATTTAATTTTCATAATATAAAACTTACATAA-CTT-ATACAGTACACAGCT
1 TACATAATTTTCATAATATAAAACTTACATAATTTTCATA-A-TACACAACT
* * * *
58584727 TACATAATTTTCATAATACATAACTAACATAATTTTTCATAATACAGC-AGT
1 TACATAATTTTCATAATATAAAACTTACATAA-TTTTCATAATACA-CAACT
58584778 TACATAATT
1 TACATAATT
58584787 CTTAAAGAAT
Statistics
Matches: 87, Mismatches: 17, Indels: 11
0.76 0.15 0.10
Matches are distributed among these distances:
48 3 0.03
49 3 0.03
50 60 0.69
51 14 0.16
52 4 0.05
53 3 0.03
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (50 bp):
TACATAATTTTCATAATATAAAACTTACATAATTTTCATAATACACAACT
Found at i:58584706 original size:75 final size:76
Alignment explanation
Indices: 58584627--58584770 Score: 191
Period size: 75 Copynumber: 1.9 Consensus size: 76
58584617 ATTTTCGTAA
* *** * **
58584627 TACATAACTTACATAATATTGAACTTACATAATTTTCATAATACATAACTTATTTAA-TTTTCAT
1 TACATAACTTACACAATACACAACTTACATAATTTTCATAATACATAACTAACATAATTTTTCAT
58584691 AATATAAAACT
66 AATATAAAACT
* * *
58584702 TACATAACTTATACAGTACACAGCTTACATAATTTTCATAATACATAACTAACATAATTTTTCAT
1 TACATAACTTACACAATACACAACTTACATAATTTTCATAATACATAACTAACATAATTTTTCAT
58584767 AATA
66 AATA
58584771 CAGCAGTTAC
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
75 47 0.81
76 11 0.19
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.39
Consensus pattern (76 bp):
TACATAACTTACACAATACACAACTTACATAATTTTCATAATACATAACTAACATAATTTTTCAT
AATATAAAACT
Found at i:58584746 original size:25 final size:25
Alignment explanation
Indices: 58584648--58584786 Score: 131
Period size: 25 Copynumber: 5.5 Consensus size: 25
58584638 CATAATATTG
*
58584648 AACTTACATAATTTTCATAATACAT
1 AACTTACATAATTTTCATAATACAC
** * *
58584673 AACTTATTTAATTTTCATAATATAA
1 AACTTACATAATTTTCATAATACAC
*
58584698 AACTTACATAA-CTT-ATACAGTACAC
1 AACTTACATAATTTTCATA-A-TACAC
* *
58584723 AGCTTACATAATTTTCATAATACAT
1 AACTTACATAATTTTCATAATACAC
*
58584748 AACTAACATAATTTTTCATAATACAGC
1 AACTTACATAA-TTTTCATAATACA-C
*
58584775 -AGTTACATAATT
1 AACTTACATAATT
58584787 CTTAAAGAAT
Statistics
Matches: 91, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
23 3 0.03
24 3 0.03
25 58 0.64
26 24 0.26
27 3 0.03
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (25 bp):
AACTTACATAATTTTCATAATACAC
Found at i:58584782 original size:26 final size:25
Alignment explanation
Indices: 58584718--58584786 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
58584708 ACTTATACAG
58584718 TACACAGCTTACATAA-TTTTCATAA
1 TACACAG-TTACATAATTTTTCATAA
* * *
58584743 TACATAACTAACATAATTTTTCATAA
1 TACA-CAGTTACATAATTTTTCATAA
58584769 TACAGCAGTTACATAATT
1 TACA-CAGTTACATAATT
58584787 CTTAAAGAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
25 11 0.31
26 24 0.69
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.36
Consensus pattern (25 bp):
TACACAGTTACATAATTTTTCATAA
Found at i:58588550 original size:21 final size:21
Alignment explanation
Indices: 58588513--58588580 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
58588503 CAACTTAAAA
*
58588513 CAGAGGCAGCAGCGAGGGAAG
1 CAGAGGCTGCAGCGAGGGAAG
* *
58588534 CAGCGGCTGCAGTGAGGGAAG
1 CAGAGGCTGCAGCGAGGGAAG
* *
58588555 CAGAGGCTGCAGCAAGAGAAG
1 CAGAGGCTGCAGCGAGGGAAG
58588576 CAGAG
1 CAGAG
58588581 CAGAGCAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.32, C:0.19, G:0.44, T:0.04
Consensus pattern (21 bp):
CAGAGGCTGCAGCGAGGGAAG
Found at i:58588951 original size:42 final size:42
Alignment explanation
Indices: 58588897--58589057 Score: 234
Period size: 42 Copynumber: 3.8 Consensus size: 42
58588887 GTTTTTGTAT
* *
58588897 AAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
58588939 AAAAACGCCGCTAAAGATA-ATGTTCTTTAGCAGCGCTTAGAA
1 AAAAACGCCGCTAAAGA-ACATGTTCTTTAGCGGCGCTTAGAA
* * *
58588981 AAAAGCGCTGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
* *
58589023 AGAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG
58589058 TTTTTGTTTG
Statistics
Matches: 107, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
42 106 0.99
43 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
Found at i:58588985 original size:84 final size:84
Alignment explanation
Indices: 58588897--58589053 Score: 260
Period size: 84 Copynumber: 1.9 Consensus size: 84
58588887 GTTTTTGTAT
*
58588897 AAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAAAAAAAACGCCGCTAAAGATAATGT
1 AAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAAAAAAAACGCCGCTAAAGACAATGT
58588962 TCTTTAGCAGCGCTTAGAA
66 TCTTTAGCAGCGCTTAGAA
* * * * *
58588981 AAAAGCGCTGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAGAAACGCCGCTAAAGACCATGT
1 AAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAAAAAAAACGCCGCTAAAGACAATGT
58589046 TCTTTAGC
66 TCTTTAGC
58589054 GGCGTTTTTG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 67 1.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (84 bp):
AAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAAAAAAAACGCCGCTAAAGACAATGT
TCTTTAGCAGCGCTTAGAA
Found at i:58590483 original size:12 final size:12
Alignment explanation
Indices: 58590468--58590499 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
58590458 TATTGTATTA
58590468 AAAAATAAATAT
1 AAAAATAAATAT
58590480 AAAAAT--ATAT
1 AAAAATAAATAT
58590490 AAAAATAAAT
1 AAAAATAAAT
58590500 TTAATATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.56
12 8 0.44
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
AAAAATAAATAT
Found at i:58590509 original size:6 final size:6
Alignment explanation
Indices: 58590500--58590533 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
58590490 AAAAATAAAT
58590500 TTAATA TTAATA TTAATA TTAATA TTAATA TTAA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAA
58590534 ATAAAATCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:58593194 original size:20 final size:21
Alignment explanation
Indices: 58593162--58593213 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
58593152 AGATAGAACA
58593162 TTTAAATATTTA-TGTGATAT
1 TTTAAATATTTATTGTGATAT
*
58593182 TATTAAA-ATTTATTGTTATAT
1 T-TTAAATATTTATTGTGATAT
*
58593203 TTTAATTATTT
1 TTTAAATATTT
58593214 TAGGAGGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (21 bp):
TTTAAATATTTATTGTGATAT
Found at i:58596007 original size:50 final size:48
Alignment explanation
Indices: 58595948--58596181 Score: 233
Period size: 50 Copynumber: 4.8 Consensus size: 48
58595938 GGCAGTGAGT
*
58595948 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGTCTGATGA
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-G-CAGATGA
* *
58595998 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATGGACAGA-GAA
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CG-CAGATG-A
* * * *
58596048 GAGTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCG-AGATGG
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGCAGATGA
* ** * *
58596095 GTGCCAGTGTAAGACCATGTCTGGGAAATGGCATCAACAC-CGATATGT
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGC-AGATGA
* * * *
58596143 GATCCCA-TGTAAGACCATATCTGGGATATGGCATTGGCA
1 G-TGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
58596182 GTACAGGAAA
Statistics
Matches: 154, Mismatches: 24, Indels: 14
0.80 0.12 0.07
Matches are distributed among these distances:
47 37 0.24
48 33 0.21
49 6 0.04
50 78 0.51
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.22
Consensus pattern (48 bp):
GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGCAGATGA
Found at i:58599900 original size:17 final size:15
Alignment explanation
Indices: 58599882--58599923 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
58599872 TGAACCTTCT
58599882 TTTCTTCTTTCTTTTC
1 TTTCTTCTTT-TTTTC
*
58599898 TTTCTT-TCTTTTTC
1 TTTCTTCTTTTTTTC
58599912 TTTCTTCTTTTT
1 TTTCTTCTTTTT
58599924 ACTATATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 11 0.48
15 6 0.26
16 6 0.26
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTTCTTTTTTTC
Found at i:58599904 original size:13 final size:13
Alignment explanation
Indices: 58599878--58599922 Score: 67
Period size: 12 Copynumber: 3.5 Consensus size: 13
58599868 GCGTTGAACC
58599878 TTCTTTTC-TTCT
1 TTCTTTTCTTTCT
58599890 TTCTTTTCTTTCT
1 TTCTTTTCTTTCT
58599903 TTCTTTTTCTTTC-
1 TTC-TTTTCTTTCT
58599916 TTCTTTT
1 TTCTTTT
58599923 TACTATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.39
13 10 0.32
14 9 0.29
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TTCTTTTCTTTCT
Found at i:58599923 original size:13 final size:13
Alignment explanation
Indices: 58599877--58599923 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
58599867 TGCGTTGAAC
58599877 CTTC-TTTTC-TT
1 CTTCTTTTTCTTT
58599888 CTT-TCTTTTCTTT
1 CTTCT-TTTTCTTT
58599901 CTTTCTTTTTCTTT
1 C-TTCTTTTTCTTT
58599915 CTTCTTTTT
1 CTTCTTTTT
58599924 ACTATATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 3 0.10
12 5 0.16
13 11 0.35
14 11 0.35
15 1 0.03
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
CTTCTTTTTCTTT
Found at i:58600772 original size:2 final size:2
Alignment explanation
Indices: 58600765--58600798 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
58600755 CCTTATGTAC
58600765 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
58600799 ATGAACCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:58603801 original size:14 final size:14
Alignment explanation
Indices: 58603782--58603808 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
58603772 TAATAATGTA
58603782 ACAATAACAATAAT
1 ACAATAACAATAAT
58603796 ACAATAACAATAA
1 ACAATAACAATAA
58603809 ACATAATTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.19
Consensus pattern (14 bp):
ACAATAACAATAAT
Found at i:58604684 original size:15 final size:17
Alignment explanation
Indices: 58604658--58604691 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
58604648 AATAGGGAAG
58604658 AAAAATAGAAAAAC-AA
1 AAAAATAGAAAAACGAA
58604674 AAAAATA-AAAAACGAA
1 AAAAATAGAAAAACGAA
58604690 AA
1 AA
58604692 TAGATCTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.82, C:0.06, G:0.06, T:0.06
Consensus pattern (17 bp):
AAAAATAGAAAAACGAA
Found at i:58605103 original size:22 final size:22
Alignment explanation
Indices: 58605034--58605109 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 22
58605024 ATTGGGTTAT
*
58605034 TTGGGTAGGTTTAGTTGGGGTA
1 TTGGGTAGGTTTAGTTAGGGTA
* *
58605056 TTGGGCCCATAATGGGTTA-TTTGGGTA
1 TTGGG----T-A-GGTTTAGTTAGGGTA
58605083 TTGGGTAGGTTTAGTTAGGGTA
1 TTGGGTAGGTTTAGTTAGGGTA
58605105 TTGGG
1 TTGGG
58605110 CCCCGGGTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
21 5 0.12
22 18 0.42
23 1 0.02
26 1 0.02
27 13 0.30
28 5 0.12
ACGTcount: A:0.16, C:0.04, G:0.41, T:0.39
Consensus pattern (22 bp):
TTGGGTAGGTTTAGTTAGGGTA
Found at i:58605842 original size:38 final size:38
Alignment explanation
Indices: 58605791--58605866 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
58605781 TGAATCCTCA
58605791 ACTGTTTGCTGGTTAGGTTGACTTGGCATGTTTACATC
1 ACTGTTTGCTGGTTAGGTTGACTTGGCATGTTTACATC
58605829 ACTGTTTGCTGGTTAGGTTGACTTGGCATGTTTACATC
1 ACTGTTTGCTGGTTAGGTTGACTTGGCATGTTTACATC
58605867 GAAATGATCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.42
Consensus pattern (38 bp):
ACTGTTTGCTGGTTAGGTTGACTTGGCATGTTTACATC
Found at i:58606141 original size:18 final size:19
Alignment explanation
Indices: 58606099--58606149 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
58606089 TCATGAATAC
*
58606099 AATTTTATTTATTATGAGAT
1 AATTTTA-TTGTTATGAGAT
*
58606119 CATTTTATTGTTAT-AGAT
1 AATTTTATTGTTATGAGAT
*
58606137 AATTTTGTTGTTA
1 AATTTTATTGTTA
58606150 AGTATGTGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 15 0.56
19 6 0.22
20 6 0.22
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (19 bp):
AATTTTATTGTTATGAGAT
Found at i:58609494 original size:2 final size:2
Alignment explanation
Indices: 58609487--58609537 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
58609477 GGAGAAAAAG
58609487 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
58609529 TA TA TA TA T
1 TA TA TA TA T
58609538 TGCCATTCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58609848 original size:21 final size:21
Alignment explanation
Indices: 58609823--58609863 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
58609813 AAAATTGCAA
58609823 CAAAACAACAACAAACAACAT
1 CAAAACAACAACAAACAACAT
** *
58609844 CAAAACTTCAGCAAACAACA
1 CAAAACAACAACAAACAACA
58609864 GTAGAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.61, C:0.29, G:0.02, T:0.07
Consensus pattern (21 bp):
CAAAACAACAACAAACAACAT
Found at i:58612986 original size:21 final size:22
Alignment explanation
Indices: 58612946--58612986 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
58612936 AAGTTGTAAT
*
58612946 AAATTTTACTATGCAAGTTTCA
1 AAATTTTACCATGCAAGTTTCA
*
58612968 AAATTTT-CCATGGAAGTTT
1 AAATTTTACCATGCAAGTTT
58612987 TACTATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (22 bp):
AAATTTTACCATGCAAGTTTCA
Found at i:58614979 original size:18 final size:18
Alignment explanation
Indices: 58614956--58614990 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
58614946 TATATTTAAT
58614956 AATTAAAAAGTTGAAAAA
1 AATTAAAAAGTTGAAAAA
58614974 AATTAAAAAGTTGAAAA
1 AATTAAAAAGTTGAAAA
58614991 GTTTGAGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (18 bp):
AATTAAAAAGTTGAAAAA
Found at i:58627307 original size:91 final size:90
Alignment explanation
Indices: 58627150--58627331 Score: 249
Period size: 91 Copynumber: 2.0 Consensus size: 90
58627140 GCTGACTGTA
* * *
58627150 AAGAAAAAGAACAAAGAAGGATAGAAGCAAGTAACTTCGAGTAAGATGAATAAATATCTAGTTAT
1 AAGAAAAAGAACAAAGAAGGATAAAAGCAAGGAACTTAGAGTAAGATGAATAAATATCTAG-TAT
* *
58627215 CCTCTGGAGAATAAATTAGAAATTCT
65 CCTCTAGAAAATAAATTAGAAATTCT
* * * *
58627241 AAGAAAAAGCACAAAGAACGTATAAAAGCAAGGAACTTAGAGTGAAGCTGAATACATATCTA-TA
1 AAGAAAAAGAACAAAGAA-GGATAAAAGCAAGGAACTTAGAGT-AAGATGAATAAATATCTAGTA
58627305 TCCTCTAGAAAATAAATTAGAAATTCT
64 TCCTCTAGAAAATAAATTAGAAATTCT
58627332 TAGTCAATAA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
91 44 0.55
92 20 0.25
93 16 0.20
ACGTcount: A:0.49, C:0.12, G:0.17, T:0.23
Consensus pattern (90 bp):
AAGAAAAAGAACAAAGAAGGATAAAAGCAAGGAACTTAGAGTAAGATGAATAAATATCTAGTATC
CTCTAGAAAATAAATTAGAAATTCT
Found at i:58644404 original size:6 final size:6
Alignment explanation
Indices: 58644393--58644418 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
58644383 AGCAACCATT
58644393 GGCATG GGCATG GGCATG GGCATG GG
1 GGCATG GGCATG GGCATG GGCATG GG
58644419 ATTTTTGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.54, T:0.15
Consensus pattern (6 bp):
GGCATG
Found at i:58646054 original size:15 final size:15
Alignment explanation
Indices: 58646034--58646064 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
58646024 ACCCAAAATA
58646034 TCAATCCTTCAACCT
1 TCAATCCTTCAACCT
58646049 TCAATCCTTCAACCT
1 TCAATCCTTCAACCT
58646064 T
1 T
58646065 ACCTTTACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.39, G:0.00, T:0.35
Consensus pattern (15 bp):
TCAATCCTTCAACCT
Found at i:58646642 original size:43 final size:43
Alignment explanation
Indices: 58646560--58646743 Score: 257
Period size: 43 Copynumber: 4.3 Consensus size: 43
58646550 ACGTCGCTAA
* * *
58646560 CTTTTGCGGCGCTTAAG-AAAAAACGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTT
*
58646602 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAATGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTT
* * *
58646645 CTTTAGCGGCGCTT-GGGAAAAAACGTCGTTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTT
* *
58646687 CTTTAGCGGTGCTTAGGAAAAAAACGCCGCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGA-TCATGTT
58646730 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
58646744 CATCTACAAA
Statistics
Matches: 125, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
42 53 0.42
43 72 0.58
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (43 bp):
CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:58646708 original size:85 final size:85
Alignment explanation
Indices: 58646560--58646743 Score: 271
Period size: 85 Copynumber: 2.2 Consensus size: 85
58646550 ACGTCGCTAA
* *
58646560 CTTTTGCGGCGCTTAAGAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTAGGAAAAAA
1 CTTTAGCGGCGCTTAAGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
* *
58646625 ACGCCGCT-AATGATCATGTT
66 ACGCCGCTAAAAG-TAATGTT
** * * *
58646645 CTTTAGCGGCGCTTGGGAAAAAACGTCGTTAAAGATCATGTTCTTTAGCGGTGCTTAGGAAAAAA
1 CTTTAGCGGCGCTTAAGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
58646710 ACGCCGCTAAAAGTAATGTT
66 ACGCCGCTAAAAGTAATGTT
58646730 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
58646744 CATCTACAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
85 86 0.97
86 3 0.03
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (85 bp):
CTTTAGCGGCGCTTAAGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
ACGCCGCTAAAAGTAATGTT
Done.