Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold158
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: 1811518
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 13
Found at i:172609 original size:41 final size:41
Alignment explanation
Indices: 172562--172730 Score: 121
Period size: 41 Copynumber: 4.1 Consensus size: 41
172552 CTAAATAGGA
* *
172562 GGTTGACCAGGATGAAATCGATAAAGCCAACAAGTTAGAGG
1 GGTTGACCAGGATGAAATCAATAAAACCAACAAGTTAGAGG
* * ** * *
172603 GGTTGACTAAGG-TGAAAGCAATAAAATTAATAAGTTAAAGG
1 GGTTGAC-CAGGATGAAATCAATAAAACCAACAAGTTAGAGG
* * ** * *
172644 GGTTGACTAGGACGAAATTGATAAAACTAAC-AGATTTGAGG
1 GGTTGACCAGGATGAAATCAATAAAACCAACAAG-TTAGAGG
* **
172685 GATTGACCAGGATGAAA-CTAATAAAGTCAACCAA-TTAGAGG
1 GGTTGACCAGGATGAAATC-AATAAAACCAA-CAAGTTAGAGG
172726 GGTTG
1 GGTTG
172731 GCTAAGGCGA
Statistics
Matches: 95, Mismatches: 27, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
40 5 0.05
41 85 0.89
42 4 0.04
43 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.27, T:0.22
Consensus pattern (41 bp):
GGTTGACCAGGATGAAATCAATAAAACCAACAAGTTAGAGG
Found at i:172825 original size:40 final size:40
Alignment explanation
Indices: 172744--172852 Score: 112
Period size: 40 Copynumber: 2.7 Consensus size: 40
172734 AAGGCGAAAC
* * *
172744 CAATAAAGCCAACAAAGAGTAAAGATTGACTGGGACAAAAT
1 CAAT-AAGCCAACAAATAGTAAAGGTTGACTGAGACAAAAT
* * * **
172785 C-GTCAAGTCAATAAATAGTAAAGGTTGACTGAGATGAAAT
1 CAAT-AAGCCAACAAATAGTAAAGGTTGACTGAGACAAAAT
*
172825 CAATAAGCCAACAAATAGTAAAAGTTGA
1 CAATAAGCCAACAAATAGTAAAGGTTGA
172853 TCGAAGTAAA
Statistics
Matches: 54, Mismatches: 13, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
40 52 0.96
41 2 0.04
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (40 bp):
CAATAAGCCAACAAATAGTAAAGGTTGACTGAGACAAAAT
Found at i:173595 original size:77 final size:75
Alignment explanation
Indices: 173376--173595 Score: 210
Period size: 77 Copynumber: 2.9 Consensus size: 75
173366 GAAGATCATA
* * * **
173376 AGGGAATATGTGGTTTTTAAAATTTTTATCAACAGTCAAAGCAAAATGATAATAGGCTGAAGGA-
1 AGGGAATATGTGGTTTCTAAAATTTTTATCAACAGTCAAA-CAAACTGATAA-CGGCTGAAAAAG
173440 AAGGAACATAAT
64 AAGGAACATAAT
* ** * *
173452 AAGGAATATGTGGTTTCTAAAATTTTTATCAACAACCAAAACAAACTAATCACGGCCT-AAAGAA
1 AGGGAATATGTGGTTTCTAAAATTTTTATCAACAGTC-AAACAAACTGATAACGG-CTGAAA-AA
** *
173516 GAAGGCGCATGAT
63 GAAGGAACATAAT
* * * *
173529 AGGGAATATGTGATTTCTAAAAAATTTTATCAACTGTCAAACAAACTGATAACGACTTGAAAAAG
1 AGGGAATATGTGGTTTCT-AAAATTTTTATCAACAGTCAAACAAACTGATAACGGC-TGAAAAAG
173594 AA
64 AA
173596 ACTTGATAGG
Statistics
Matches: 115, Mismatches: 22, Indels: 13
0.77 0.15 0.09
Matches are distributed among these distances:
75 4 0.03
76 45 0.39
77 48 0.42
78 18 0.16
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (75 bp):
AGGGAATATGTGGTTTCTAAAATTTTTATCAACAGTCAAACAAACTGATAACGGCTGAAAAAGAA
GGAACATAAT
Found at i:174140 original size:30 final size:31
Alignment explanation
Indices: 174106--174188 Score: 73
Period size: 30 Copynumber: 2.7 Consensus size: 31
174096 TGGTCTAGAT
174106 AAAACCAAAAATAATGACTTGGGT-AAAACA
1 AAAACCAAAAATAATGACTTGGGTGAAAACA
* * * *
174136 AAAACTCAAGAA-AATGCCTTAGATGAAAACA
1 AAAAC-CAAAAATAATGACTTGGGTGAAAACA
* * *
174167 GAAACC-TAACTAATGACTTGGG
1 AAAACCAAAAATAATGACTTGGG
174189 ACATAACCAA
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
29 1 0.03
30 23 0.59
31 15 0.38
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.18
Consensus pattern (31 bp):
AAAACCAAAAATAATGACTTGGGTGAAAACA
Found at i:174286 original size:30 final size:30
Alignment explanation
Indices: 174239--174333 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
174229 AAGCCTAAAT
*
174239 AATGACTTAGGCT-AAACCAAGACTTAACAA
1 AATGACTT-GGGTGAAACCAAGACTTAACAA
* * *
174269 AATGACTTGGGTGAAACCCAAAACCTAA-AC
1 AATGACTTGGGTGAAA-CCAAGACTTAACAA
* *
174299 AATAACTTGGGTGAAACCAAGA-TTCAACGA
1 AATGACTTGGGTGAAACCAAGACTT-AACAA
174329 AATGA
1 AATGA
174334 TCTAGATAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
28 1 0.02
29 10 0.20
30 31 0.61
31 9 0.18
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (30 bp):
AATGACTTGGGTGAAACCAAGACTTAACAA
Found at i:174611 original size:30 final size:30
Alignment explanation
Indices: 174524--174613 Score: 87
Period size: 30 Copynumber: 3.0 Consensus size: 30
174514 ATAAGACTAG
174524 AAACCTAAATAATGACTTGGGTAAAACC-A
1 AAACCTAAATAATGACTTGGGTAAAACCAA
* * * *
174553 AGA-CTCAAGGA-AATGGCTTGAGTGAAACCAA
1 AAACCT-AA--ATAATGACTTGGGTAAAACCAA
*
174584 AAACCTAAATAATAACTTGGGTAAAACCAA
1 AAACCTAAATAATGACTTGGGTAAAACCAA
174614 GACTCAAGAA
Statistics
Matches: 46, Mismatches: 9, Indels: 11
0.70 0.14 0.17
Matches are distributed among these distances:
28 2 0.04
29 5 0.11
30 31 0.67
31 6 0.13
32 2 0.04
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.19
Consensus pattern (30 bp):
AAACCTAAATAATGACTTGGGTAAAACCAA
Found at i:174627 original size:60 final size:60
Alignment explanation
Indices: 174114--174659 Score: 337
Period size: 60 Copynumber: 9.2 Consensus size: 60
174104 ATAAAACCAA
* * * *
174114 AAATAATGACTTGGGTAAAACAAAAACTCAAGAAAATGCCTT-AGATGAAAACAGAAACCT
1 AAATAATGACTTGGGTAAAACCAAGACTCAAGAAAATGGCTTGAG-TGAAACCAGAAACCT
* * * * * * *
174174 AACTAATGACTTGGG-ACATAACCAAAACTCAATAAAATGGCTTGCGTGAAACTATAAGCCT
1 AAATAATGACTTGGGTA-A-AACCAAGACTCAAGAAAATGGCTTGAGTGAAACCAGAAACCT
* * * * *
174235 AAATAATGACTTAGGCT-AAACCAAGACTTAACAAAATGACTTGGGTGAAACCCA-AAACCT
1 AAATAATGACTT-GGGTAAAACCAAGACTCAAGAAAATGGCTTGAGTGAAA-CCAGAAACCT
* * * * * * * * *
174295 AAACAATAACTTGGGTGAAACCAAGATTCAACG-AAATGATCTAGA-TAAAATCAAAAACCT
1 AAATAATGACTTGGGTAAAACCAAGACTCAA-GAAAATG-GCTTGAGTGAAACCAGAAACCT
* * * *
174355 AAAT-AT---TAGGCG--AAACCAAGATTCAATG-AAATGGCCTTGA-T-AAGACTAGAATCCT
1 AAATAATGACTTGG-GTAAAACCAAGACTCAA-GAAAATGG-CTTGAGTGAA-ACCAGAAACCT
* * * * * * *
174410 AAACAATGACTTGGGCAAAACCAAGACT-AAAAGAAATAGCCTG-GAT-AAGACTAGAATCCT
1 AAATAATGACTTGGGTAAAACCAAGACTCAAGA-AAATGGCTTGAG-TGAA-ACCAGAAACCT
* * * * * * *
174470 AAACAATGACTTAGGCAAAAGCAAGACTCAA-AGAAATAGCCTG-GAT-AAGACTAGAAACCT
1 AAATAATGACTTGGGTAAAACCAAGACTCAAGA-AAATGGCTTGAG-TGAA-ACCAGAAACCT
* *
174530 AAATAATGACTTGGGTAAAACCAAGACTCAAGGAAATGGCTTGAGTGAAACCAAAAACCT
1 AAATAATGACTTGGGTAAAACCAAGACTCAAGAAAATGGCTTGAGTGAAACCAGAAACCT
* * *
174590 AAATAATAACTTGGGTAAAACCAAGACTCAAGAAAATGGCTAT-A-TAAAACCCGAAACCT
1 AAATAATGACTTGGGTAAAACCAAGACTCAAGAAAATGGCT-TGAGTGAAACCAGAAACCT
174649 AAATAATGACT
1 AAATAATGACT
174660 ATGTATGAAC
Statistics
Matches: 396, Mismatches: 62, Indels: 57
0.77 0.12 0.11
Matches are distributed among these distances:
54 2 0.01
55 35 0.09
56 5 0.01
57 1 0.00
58 1 0.00
59 38 0.10
60 256 0.65
61 55 0.14
62 3 0.01
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (60 bp):
AAATAATGACTTGGGTAAAACCAAGACTCAAGAAAATGGCTTGAGTGAAACCAGAAACCT
Found at i:174773 original size:35 final size:35
Alignment explanation
Indices: 174734--174802 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
174724 AAGAAATGAA
174734 ACATAGTTATTCACAAATGATGCAACTATTTGATT
1 ACATAGTTATTCACAAATGATGCAACTATTTGATT
*
174769 ACATAGTTATTCATAAATGATGCAACTATTTGAT
1 ACATAGTTATTCACAAATGATGCAACTATTTGAT
174803 ATCCTAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.38
Consensus pattern (35 bp):
ACATAGTTATTCACAAATGATGCAACTATTTGATT
Found at i:175166 original size:44 final size:43
Alignment explanation
Indices: 175112--175266 Score: 138
Period size: 44 Copynumber: 3.6 Consensus size: 43
175102 AATAATGTAG
* *
175112 ATGCACATGAAATGATGTAAATACAAGCATCAATAAAGTGGCAA
1 ATGCATATGAAATGATGCAAATACAAGCATCAATAAA-TGGCAA
* * *
175156 ATGCATATGAAATGATGCAAATACCAATGTCATTTAA-AAATAG-AT
1 ATGCATATGAAATGATGCAAATA-CAA-G-CA-TCAATAAATGGCAA
* * * *
175201 ATGC--GTGAAACGATGCAAATGCAAGGATCAATAAAATGGCAA
1 ATGCATATGAAATGATGCAAATACAAGCATCAAT-AAATGGCAA
*
175243 ATGCATATGAAATGATACAAATAC
1 ATGCATATGAAATGATGCAAATAC
175267 CAATGTCATT
Statistics
Matches: 86, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
39 3 0.03
40 1 0.01
41 6 0.07
42 8 0.09
43 14 0.16
44 35 0.41
45 8 0.09
46 3 0.03
47 5 0.06
48 3 0.03
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.23
Consensus pattern (43 bp):
ATGCATATGAAATGATGCAAATACAAGCATCAATAAATGGCAA
Found at i:175298 original size:44 final size:42
Alignment explanation
Indices: 175163--175306 Score: 130
Period size: 44 Copynumber: 3.3 Consensus size: 42
175153 CAAATGCATA
175163 TGAAATGATGCAAATACCAATGTCATTTAAAAATAGATATGCG
1 TGAAATGATGCAAATACCAATGTCATTT-AAAATAGATATGCG
* * * * * * *
175206 TGAAACGATGCAAAT-GCAAGGATCA-ATAAAATGGCAAATGCATA
1 TGAAATGATGCAAATACCAATG-TCATTTAAAATAG-ATATGC--G
*
175250 TGAAATGATACAAATACCAATGTCATTTAAAGTATAGATATGCG
1 TGAAATGATGCAAATACCAATGTCATTTAAA--ATAGATATGCG
*
175294 TGAAATAATGCAA
1 TGAAATGATGCAA
175307 CTATAAGTAT
Statistics
Matches: 76, Mismatches: 17, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
41 6 0.08
42 10 0.13
43 17 0.22
44 27 0.36
45 8 0.11
46 5 0.07
47 3 0.04
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (42 bp):
TGAAATGATGCAAATACCAATGTCATTTAAAATAGATATGCG
Found at i:175454 original size:88 final size:88
Alignment explanation
Indices: 175135--175458 Score: 402
Period size: 88 Copynumber: 3.7 Consensus size: 88
175125 GATGTAAATA
*
175135 CAAGCATCAATAAAGTGGCAAATGCATATGAAATGATGCAAATACCAATGTCATTTAAAA-ATAG
1 CAAGCATCAATAAAGTGGCAAATGCATATGAAATGATGCAAATACCAATGTCATCTAAAATATAG
* *
175199 ATATGCGTGAAACGATGCAAATG
66 ATATGCGTGAAAAGATGCAACTG
* * * * *
175222 CAAGGATCAATAAAATGGCAAATGCATATGAAATGATACAAATACCAATGTCATTTAAAGTATAG
1 CAAGCATCAATAAAGTGGCAAATGCATATGAAATGATGCAAATACCAATGTCATCTAAAATATAG
*
175287 ATATGCGTGAAATA-ATGCAACTA
66 ATATGCGTGAAA-AGATGCAACTG
* * * * * * ** *
175310 TAAGTATCAACAAAGTGACAAATACATATGAAATGATTCAAATGTCAATGTCATCTAAAATACAG
1 CAAGCATCAATAAAGTGGCAAATGCATATGAAATGATGCAAATACCAATGTCATCTAAAATATAG
*
175375 ATATGAGTGAAAAGATGCAACTG
66 ATATGCGTGAAAAGATGCAACTG
* * * *
175398 CAAGCATCAATGAAGAT-GCAAATGCACATGAAATGATGCAAATGCCAATGTTATCTAAAAT
1 CAAGCATCAATAAAG-TGGCAAATGCATATGAAATGATGCAAATACCAATGTCATCTAAAAT
175459 GCAAAATGCA
Statistics
Matches: 202, Mismatches: 31, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
87 57 0.28
88 144 0.71
89 1 0.00
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.24
Consensus pattern (88 bp):
CAAGCATCAATAAAGTGGCAAATGCATATGAAATGATGCAAATACCAATGTCATCTAAAATATAG
ATATGCGTGAAAAGATGCAACTG
Found at i:175691 original size:110 final size:110
Alignment explanation
Indices: 175498--175715 Score: 409
Period size: 110 Copynumber: 2.0 Consensus size: 110
175488 GATGTAAATA
* *
175498 CCAATGTCATCTAAAGGTGTAGATGCACATAAAATGATGCAAATACAGATGATAGCATTGTAGCA
1 CCAATGTCATCTAAAGGTGTAGATGCACATAAAATGATGCAAATACAGATGATAGAACTGTAGCA
175563 TATTCATAAATCAAAACTTTATTTGGCTATCTTTTAAGTCAAGTG
66 TATTCATAAATCAAAACTTTATTTGGCTATCTTTTAAGTCAAGTG
175608 CCAATGTCATCTAAAGGTGTAGATGCACATAAAATGATGCAAATACAGATGATAGAACTGTAGCA
1 CCAATGTCATCTAAAGGTGTAGATGCACATAAAATGATGCAAATACAGATGATAGAACTGTAGCA
*
175673 TATTCGTAAATCAAAACTTTATTTGGCTATCTTTTAAGTCAAG
66 TATTCATAAATCAAAACTTTATTTGGCTATCTTTTAAGTCAAG
175716 CTTAACCATT
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 105 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (110 bp):
CCAATGTCATCTAAAGGTGTAGATGCACATAAAATGATGCAAATACAGATGATAGAACTGTAGCA
TATTCATAAATCAAAACTTTATTTGGCTATCTTTTAAGTCAAGTG
Found at i:178956 original size:20 final size:20
Alignment explanation
Indices: 178932--178986 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
178922 CATGTTGAAG
*
178932 AATGTATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* * *
178952 CATGTATCGATACGTTGAAA
1 AATGTATCGATACATTCAAA
178972 AATGTATCGATACAT
1 AATGTATCGATACAT
178987 CTGAGTAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:182761 original size:3 final size:3
Alignment explanation
Indices: 182755--182808 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
182745 AAAAAAAGAA
182755 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
182803 AAT AAT
1 AAT AAT
182809 CATGGTGTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:183066 original size:23 final size:20
Alignment explanation
Indices: 183040--183082 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
183030 TACCTCTTTG
183040 TTTCTATTTCTTCTCTATTTTTT
1 TTTCT-TTT-TTCTCT-TTTTTT
*
183063 TTTCTTTTTTTTCTTTTTTT
1 TTTCTTTTTTCTCTTTTTTT
183083 AGTTGAACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 5 0.26
22 3 0.16
23 5 0.26
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTCTTTTTTCTCTTTTTTT
Found at i:183072 original size:8 final size:9
Alignment explanation
Indices: 183058--183082 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
183048 TCTTCTCTAT
183058 TTTTTTTTC
1 TTTTTTTTC
183067 TTTTTTTTC
1 TTTTTTTTC
183076 TTTTTTT
1 TTTTTTT
183083 AGTTGAACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:183412 original size:5 final size:5
Alignment explanation
Indices: 183397--183430 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
183387 CAAAATGAAC
183397 AAATAA AAATA AAATAA AAATA AAATA AAATA AA
1 AAAT-A AAATA AAAT-A AAATA AAATA AAATA AA
183431 TTCTAAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 18 0.67
6 9 0.33
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:183413 original size:11 final size:11
Alignment explanation
Indices: 183397--183430 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
183387 CAAAATGAAC
183397 AAATAAAAATA
1 AAATAAAAATA
183408 AAATAAAAATA
1 AAATAAAAATA
183419 AAAT-AAAATA
1 AAATAAAAATA
183429 AA
1 AA
183431 TTCTAAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:183423 original size:16 final size:17
Alignment explanation
Indices: 183397--183430 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
183387 CAAAATGAAC
183397 AAATAAAAATAAAATAA
1 AAATAAAAATAAAATAA
183414 AAAT-AAAATAAAATAA
1 AAATAAAAATAAAATAA
183430 A
1 A
183431 TTCTAAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATAAAAATAAAATAA
Found at i:183743 original size:16 final size:15
Alignment explanation
Indices: 183722--183754 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
183712 AAAACTCAGT
183722 TTTTTTTAAAAAAGAA
1 TTTTTTTAAAAAA-AA
183738 TTTTTTTAAAAAAAA
1 TTTTTTTAAAAAAAA
183753 TT
1 TT
183755 CAAAACTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
TTTTTTTAAAAAAAA
Found at i:184625 original size:31 final size:31
Alignment explanation
Indices: 184576--184913 Score: 127
Period size: 29 Copynumber: 11.5 Consensus size: 31
184566 ACTTGACTCG
*
184576 GACATAGG-TGCCACCAACTTGTGTGGGCTTT
1 GACA-AGGCTGCCACCAACTTGTATGGGCTTT
** * **
184607 GACTCGAGC-GTCACCAACTCATATGGGCTTT
1 GACAAG-GCTGCCACCAACTTGTATGGGCTTT
184638 GACAAGGCTGCCACCAACTTGTATGGGCTTT
1 GACAAGGCTGCCACCAACTTGTATGGGCTTT
* * **
184669 GAAAATGGTTGCCACTGACTTG--TGGGCTTT
1 GACAA-GGCTGCCACCAACTTGTATGGGCTTT
* * * ***
184699 GAAAATGATGCCATTGACTTG--TGGGCTTT
1 GACAAGGCTGCCACCAACTTGTATGGGCTTT
* * *
184728 GAAAAGGATGCCACGAACTTGTA--GGCTTTT
1 GACAAGGCTGCCACCAACTTGTATGGGC-TTT
* *
184758 GA-AAGGATGCCAGTC-ACTTGTA--GGCTTT
1 GACAAGGCTGCCA-CCAACTTGTATGGGCTTT
*
184786 GA-AAGGATGCCA-CAGACTTGTA--GGCTTTT
1 GACAAGGCTGCCACCA-ACTTGTATGGGC-TTT
* *
184815 GA-AAGGATGCCAGTC-ACTTG--TGGGCTTT
1 GACAAGGCTGCCA-CCAACTTGTATGGGCTTT
*
184843 GA-AAGGATGCCA-CAGACTTG--TGGGCTTTT
1 GACAAGGCTGCCACCA-ACTTGTATGGGC-TTT
* **
184872 GA-AAGGATGCCACTGACTTG--TGGGCTTT
1 GACAAGGCTGCCACCAACTTGTATGGGCTTT
* *
184900 GAAAAGGATGCCAC
1 GACAAGGCTGCCAC
184914 TGACTTGTGG
Statistics
Matches: 261, Mismatches: 26, Indels: 42
0.79 0.08 0.13
Matches are distributed among these distances:
26 2 0.01
28 55 0.21
29 120 0.46
30 21 0.08
31 50 0.19
32 13 0.05
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (31 bp):
GACAAGGCTGCCACCAACTTGTATGGGCTTT
Found at i:184720 original size:29 final size:29
Alignment explanation
Indices: 184630--185791 Score: 862
Period size: 28 Copynumber: 41.5 Consensus size: 29
184620 CCAACTCATA
* * **
184630 TGGGCTTTGACAAGGCTGCCACCAACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
*
184659 TATGGGCTTTGAAAATGGTTGCCACTGACTTG
1 --TGGGCTTTGAAAA-GGATGCCACTGACTTG
* *
184691 TGGGCTTTGAAAATGATGCCATTGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
184720 TGGGCTTTGAAAAGGATGCCAC-GAACTTG
1 TGGGCTTTGAAAAGGATGCCACTG-ACTTG
* * *
184749 TAGGCTTTTG-AAAGGATGCCAGTCACTTG
1 TGGGC-TTTGAAAAGGATGCCACTGACTTG
* *
184778 TAGGCTTTG-AAAGGATGCCACAGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* * *
184806 TAGGCTTTTG-AAAGGATGCCAGTCACTTG
1 TGGGC-TTTGAAAAGGATGCCACTGACTTG
*
184835 TGGGCTTTG-AAAGGATGCCACAGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
184863 TGGGCTTTTG-AAAGGATGCCACTGACTTG
1 TGGGC-TTTGAAAAGGATGCCACTGACTTG
184892 TGGGCTTTGAAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
*
184921 TGGGCTTTTG-AAAGGATGCTACTGACTTG
1 TGGGC-TTTGAAAAGGATGCCACTGACTTG
* * *
184950 T-GGCTTTGAAAATGATGCCACTCACTTA
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* *
184978 TGGGCTTTTG-AAAGAATGCCACTGACTTA
1 TGGGC-TTTGAAAAGGATGCCACTGACTTG
185007 TGGGCTTTTG-AAAGGATG-C-C--AC---
1 TGGGC-TTTGAAAAGGATGCCACTGACTTG
* *
185029 T-GGCTTTGAAAATGATGCCAATGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* * *
185057 TGAGCTTTTG-AAAGGATG-CACCTAACATG
1 TGGGC-TTTGAAAAGGATGCCA-CTGACTTG
* * *
185086 TGGGCCTTGAAAA-GATGTCACTGTCTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* *
185114 TGGGCTTTGAAAAGG-TGCCACTAATTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* * * *
185142 CGGAC-TTGAAAAAGG-TGCCACTTATTTG
1 TGGGCTTTG-AAAAGGATGCCACTGACTTG
*
185170 TGGACTTTG-AAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* * *
185198 TGGGC-TTCAAAAGGGTGCCACTGATTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* * * *
185226 TGGGCTTTCAAAAAGG-TACCACTAATTTG
1 TGGGCTTT-GAAAAGGATGCCACTGACTTG
* *
185255 TGGACTTTG-AAAGGATGTCACTGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
*
185283 TGGGCTTTG-AAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* * *
185311 TGGGCTTTAAAAAGG-TGCCAATAACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* ** *
185339 TGGGCCTT-AAAAATATGCCACTGTCTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* *
185367 TGGACTTTG-AAAGGATGCCACTAACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* *
185395 TGGGCTTT-AAAAGGGTGCCACTAACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* *
185423 TGGGCTTTG-AAAGGATGCTACTAACTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* *
185451 TGGGC-TT-AAAAGGATGCCACGGAGTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* ** *
185478 TGGAC-TT-AAAAGGATGGTAC-GAAATTG
1 TGGGCTTTGAAAAGGATGCCACTG-ACTTG
* * ** *
185505 TAGACTTT-AAAAGGATGCCACAAAGTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* * *
185533 TGGAC-TT-AAAAGGATGCCACGGAGTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* *
185560 TGGAC-TT-AAAAGGATGCCAC-GAAGTTG
1 TGGGCTTTGAAAAGGATGCCACTG-ACTTG
* * *
185587 TGGACTTT-AAAAGGATGCCACAGAGTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* *
185615 TGGAC-TT-AAAAGGATGCCAC-GAAGTTG
1 TGGGCTTTGAAAAGGATGCCACTG-ACTTG
* * *
185642 TGGACTTT-AAAAGGATGCCACAGAGTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* *
185670 TGGAC-TT-AAAAGGATGCCA-TGGAGTTG
1 TGGGCTTTGAAAAGGATGCCACT-GACTTG
* * *
185697 TGGAC-TT-AAAAGGATGCCA-TGAAGTTA
1 TGGGCTTTGAAAAGGATGCCACTG-ACTTG
* * *
185724 TGGAC-TT-AAAAGGATGCCACGGAGTTG
1 TGGGCTTTGAAAAGGATGCCACTGACTTG
* * *
185751 TGGAC-TT-AAAAGGATGGCA-TGGAGTTG
1 TGGGCTTTGAAAAGGATGCCACT-GACTTG
185778 TGGGCTTTGAAAAG
1 TGGGCTTTGAAAAG
185792 AAACACCACT
Statistics
Matches: 965, Mismatches: 113, Indels: 108
0.81 0.10 0.09
Matches are distributed among these distances:
20 4 0.00
21 10 0.01
22 2 0.00
25 4 0.00
26 4 0.00
27 236 0.24
28 393 0.41
29 252 0.26
30 35 0.04
31 12 0.01
32 13 0.01
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (29 bp):
TGGGCTTTGAAAAGGATGCCACTGACTTG
Found at i:184814 original size:57 final size:58
Alignment explanation
Indices: 184630--185791 Score: 811
Period size: 57 Copynumber: 20.7 Consensus size: 58
184620 CCAACTCATA
* ** *
184630 TGGGC-TTTGACAAGGCTGCCACCAACTTGTATGGGCTTTGAAAATGGTTGCCACTGACTTG
1 TGGGCTTTTGA-AAGGATGCCACTGACTTG--TGGGCTTTGAAAA-GGATGCCACTGACTTG
* *
184691 TGGGC-TTTGAAAATGATGCCATTGACTTGTGGGCTTTGAAAAGGATGCCAC-GAACTTG
1 TGGGCTTTTG-AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTG-ACTTG
* * * * *
184749 TAGGCTTTTGAAAGGATGCCAGTCACTTGTAGGCTTTG-AAAGGATGCCACAGACTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTG
* * * *
184806 TAGGCTTTTGAAAGGATGCCAGTCACTTGTGGGCTTTG-AAAGGATGCCACAGACTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTG
184863 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTG
* * * *
184921 TGGGCTTTTGAAAGGATGCTACTGACTTGT-GGCTTTGAAAATGATGCCACTCACTTA
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTG
* *
184978 TGGGCTTTTGAAAGAATGCCACTGACTTATGGGCTTTTG-AAAGGATG-C-C--AC---
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGC-TTTGAAAAGGATGCCACTGACTTG
* * * * *
185029 T-GGC-TTTGAAAATGATGCCAATGACTTGTGAGCTTTTG-AAAGGATG-CACCTAACATG
1 TGGGCTTTTG-AAAGGATGCCACTGACTTGTGGGC-TTTGAAAAGGATGCCA-CTGACTTG
* * * * * *
185086 TGGGC-CTTGAAAAGATGTCACTGTCTTGTGGGCTTTGAAAAGG-TGCCACTAATTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTG
* * *** * * *
185142 CGGACTTGAAAAAGG-TGCCACTTATTTGTGGACTTTG-AAAGGATGCCACTGACTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTG
** * * * * * *
185198 TGGGC-TTCAAAAGGGTGCCACTGATTTGTGGGCTTTCAAAAAGG-TACCACTAATTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTT-GAAAAGGATGCCACTGACTTG
* * *
185255 TGGAC-TTTGAAAGGATGTCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTG
** * * * ** *
185311 TGGGCTTTAAAAAGG-TGCCAATAACTTGTGGGCCTT-AAAAATATGCCACTGTCTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTG
* * * *
185367 TGGAC-TTTGAAAGGATGCCACTAACTTGTGGGCTTT-AAAAGGGTGCCACTAACTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTG
* * * *
185423 TGGGC-TTTGAAAGGATGCTACTAACTTGTGGGC-TT-AAAAGGATGCCACGGAGTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTG
* * ** * * * ** *
185478 TGGAC--TTAAAAGGATGGTAC-GAAATTGTAGACTTT-AAAAGGATGCCACAAAGTTG
1 TGGGCTTTTGAAAGGATGCCACTG-ACTTGTGGGCTTTGAAAAGGATGCCACTGACTTG
* * * * * *
185533 TGGAC--TTAAAAGGATGCCACGGAGTTGTGGAC-TT-AAAAGGATGCCAC-GAAGTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTG-ACTTG
* * * * * *
185587 TGGAC-TTTAAAAGGATGCCACAGAGTTGTGGAC-TT-AAAAGGATGCCAC-GAAGTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTG-ACTTG
* * * * * *
185642 TGGAC-TTTAAAAGGATGCCACAGAGTTGTGGAC-TT-AAAAGGATGCCA-TGGAGTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACT-GACTTG
* * * * * * *
185697 TGGAC--TTAAAAGGATGCCA-TGAAGTTATGGAC-TT-AAAAGGATGCCACGGAGTTG
1 TGGGCTTTTGAAAGGATGCCACTG-ACTTGTGGGCTTTGAAAAGGATGCCACTGACTTG
* * * *
185751 TGGAC--TTAAAAGGATGGCA-TGGAGTTGTGGGCTTTGAAAAG
1 TGGGCTTTTGAAAGGATGCCACT-GACTTGTGGGCTTTGAAAAG
185792 AAACACCACT
Statistics
Matches: 943, Mismatches: 119, Indels: 83
0.82 0.10 0.07
Matches are distributed among these distances:
49 4 0.00
50 36 0.04
51 1 0.00
52 1 0.00
53 1 0.00
54 119 0.13
55 200 0.21
56 188 0.20
57 239 0.25
58 110 0.12
59 21 0.02
61 22 0.02
62 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (58 bp):
TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTG
Found at i:185000 original size:25 final size:27
Alignment explanation
Indices: 184715--185028 Score: 165
Period size: 29 Copynumber: 11.0 Consensus size: 27
184705 GATGCCATTG
* *
184715 ACTTGTGGGC-TTTGAAAAGGATGCCAC
1 ACTTATGGGCTTTTG-AAAGAATGCCAC
* * *
184742 GAACTTGTAGGCTTTTGAAAGGATGCCAGTC
1 --ACTTATGGGCTTTTGAAAGAATGCCA--C
* * *
184773 ACTTGTAGGC-TTTGAAAGGATGCCAC
1 ACTTATGGGCTTTTGAAAGAATGCCAC
* * *
184799 AGACTTGTAGGCTTTTGAAAGGATGCCAGTC
1 --ACTTATGGGCTTTTGAAAGAATGCCA--C
* *
184830 ACTTGTGGGC-TTTGAAAGGATGCCAC
1 ACTTATGGGCTTTTGAAAGAATGCCAC
* *
184856 AGACTTGTGGGCTTTTGAAAGGATGCCAC
1 --ACTTATGGGCTTTTGAAAGAATGCCAC
* *
184885 TGACTTGTGGGC-TTTGAAAAGGATGCCAC
1 --ACTTATGGGCTTTTG-AAAGAATGCCAC
* * *
184914 TGACTTGTGGGCTTTTGAAAGGATGCTAC
1 --ACTTATGGGCTTTTGAAAGAATGCCAC
*
184943 TGACTTGT-GGC-TTTGAAA-ATGATGCCACTC
1 --ACTTATGGGCTTTTGAAAGA--ATGCCA--C
184973 ACTTATGGGCTTTTGAAAGAATGCCAC
1 ACTTATGGGCTTTTGAAAGAATGCCAC
*
185000 TGACTTATGGGCTTTTGAAAGGATGCCAC
1 --ACTTATGGGCTTTTGAAAGAATGCCAC
185029 TGGCTTTGAA
Statistics
Matches: 255, Mismatches: 8, Indels: 44
0.83 0.03 0.14
Matches are distributed among these distances:
26 2 0.01
27 8 0.03
28 67 0.26
29 159 0.62
30 16 0.06
31 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (27 bp):
ACTTATGGGCTTTTGAAAGAATGCCAC
Found at i:185090 original size:79 final size:78
Alignment explanation
Indices: 184950--185108 Score: 194
Period size: 79 Copynumber: 2.0 Consensus size: 78
184940 TACTGACTTG
* * * * *
184950 TGGCTTTGAAAATGATGCCACTCACTTATGGGCTTTTGAAAGAATGCCACTGACTTATGGGCTTT
1 TGGCTTTGAAAATGATGCCAATCACTTATGAGCTTTTGAAAGAATGCCACTAACATATGGGC-CT
*
185015 TGAAAGGATGCCAC
65 TGAAAAGATGCCAC
* * * *
185029 TGGCTTTGAAAATGATGCCAATGACTTGTGAGCTTTTGAAAGGATG-CACCTAACATGTGGGCCT
1 TGGCTTTGAAAATGATGCCAATCACTTATGAGCTTTTGAAAGAATGCCA-CTAACATATGGGCCT
*
185093 TGAAAAGATGTCAC
65 TGAAAAGATGCCAC
185107 TG
1 TG
185109 TCTTGTGGGC
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
78 17 0.25
79 51 0.75
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (78 bp):
TGGCTTTGAAAATGATGCCAATCACTTATGAGCTTTTGAAAGAATGCCACTAACATATGGGCCTT
GAAAAGATGCCAC
Found at i:185192 original size:84 final size:84
Alignment explanation
Indices: 185030--185791 Score: 492
Period size: 82 Copynumber: 9.1 Consensus size: 84
185020 GGATGCCACT
* * * * ** * * *
185030 GGCTTTGAAAATGATGCCAATGACTTGTGAGCTTTTGAAAGGATG-CACCTAACATGTGGGCCTT
1 GGCTTTGAAAA-GGTGCCACTAACTTGTGGGCTTTAAAAAGG-TGCCA-CTAACTTGTGGACTTT
* * *
185094 GAAAAGATGTCACTGTCTTGTG
63 GAAAGGATGCCACTGACTTGTG
* * * * * *
185116 GGCTTTGAAAAGGTGCCACTAATTTGCGGACTTGAAAAAGGTGCCACTTATTTGTGGACTTTGAA
1 GGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTTAAAAAGGTGCCACTAACTTGTGGACTTTGAA
185181 AGGATGCCACTGACTTGTG
66 AGGATGCCACTGACTTGTG
* * * * *
185200 GGC-TTCAAAAGGGTGCCACTGATTTGTGGGCTTTCAAAAAGGTACCACTAATTTGTGGACTTTG
1 GGCTTTGAAAA-GGTGCCACTAACTTGTGGGCTTT-AAAAAGGTGCCACTAACTTGTGGACTTTG
*
185264 AAAGGATGTCACTGACTTGTG
64 AAAGGATGCCACTGACTTGTG
* * * * * *
185285 GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAAGGTGCCAATAACTTGTGGGCCTTAAA
1 GGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTTAAAAAGGTGCCACTAACTTGTGGACTTTGAA
** *
185350 AATATGCCACTGTCTTGTG
66 AGGATGCCACTGACTTGTG
* * *
185369 GACTTTG-AAAGGATGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGTGGGCTTTGA
1 GGCTTTGAAAAGG-TGCCACTAACTTGTGGGCTTTAAAAAGGTGCCACTAACTTGTGGACTTTGA
* *
185433 AAGGATGCTACTAACTTGTG
65 AAGGATGCCACTGACTTGTG
** * * ** * * * *
185453 GGC-TT-AAAAGGATGCCACGGAGTTGTGGAC-TT-AAAAGGATGGTACGAAATTGTAGACTTTA
1 GGCTTTGAAAAGG-TGCCACTAACTTGTGGGCTTTAAAAAGG-TGCCACTAACTTGTGGACTTTG
** *
185514 AAAGGATGCCACAAAGTTGTG
64 AAAGGATGCCACTGACTTGTG
* ** * * * * *
185535 GAC-TT-AAAAGGATGCCACGGAGTTGTGGAC-TT-AAAAGGATGCCACGAAGTTGTGGACTTTA
1 GGCTTTGAAAAGG-TGCCACTAACTTGTGGGCTTTAAAAAGG-TGCCACTAACTTGTGGACTTTG
* *
185596 AAAGGATGCCACAGAGTTGTG
64 AAAGGATGCCACTGACTTGTG
* * * * *
185617 GAC-TT-AAAAGGATGCCACGAAGTTGTGGACTTT-AAAAGGATGCCAC-AGAGTTGTGGAC-TT
1 GGCTTTGAAAAGG-TGCCACTAACTTGTGGGCTTTAAAAAGG-TGCCACTA-ACTTGTGGACTTT
* *
185677 AAAAGGATGCCA-TGGAGTTGTG
63 GAAAGGATGCCACT-GACTTGTG
* * * * ** *
185699 GAC-TT-AAAAGGATGCCA-TGAAGTTATGGAC-TT-AAAAGGATGCCACGGAGTTGTGGAC-TT
1 GGCTTTGAAAAGG-TGCCACT-AACTTGTGGGCTTTAAAAAGG-TGCCACTAACTTGTGGACTTT
* * *
185758 AAAAGGATGGCA-TGGAGTTGTG
63 GAAAGGATGCCACT-GACTTGTG
185780 GGCTTTGAAAAG
1 GGCTTTGAAAAG
185792 AAACACCACT
Statistics
Matches: 582, Mismatches: 80, Indels: 31
0.84 0.12 0.04
Matches are distributed among these distances:
81 55 0.09
82 192 0.33
83 62 0.11
84 163 0.28
85 94 0.16
86 16 0.03
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (84 bp):
GGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTTAAAAAGGTGCCACTAACTTGTGGACTTTGAA
AGGATGCCACTGACTTGTG
Found at i:185515 original size:55 final size:54
Alignment explanation
Indices: 185364--185780 Score: 496
Period size: 55 Copynumber: 7.6 Consensus size: 54
185354 TGCCACTGTC
* * * * * * *
185364 TTGTGGACTTTGAAAGGATGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTAAC
1 TTGTGGAC-TTAAAAGGATGCCACGAAGTTGTGGAC-TTAAAAGGATGCCACGAAG
* * * * * * *
185420 TTGTGGGCTTTGAAAGGATGCTACTAACTTGTGGGCTTAAAAGGATGCCACGGAG
1 TTGTGGAC-TTAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGATGCCACGAAG
** * * *
185475 TTGTGGACTTAAAAGGATGGTACGAAATTGTAGACTTTAAAAGGATGCCACAAAG
1 TTGTGGACTTAAAAGGATGCCACGAAGTTGTGGAC-TTAAAAGGATGCCACGAAG
*
185530 TTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGAAG
1 TTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGATGCCACGAAG
185584 TTGTGGACTTTAAAAGGATGCCAC-AGAGTTGTGGACTTAAAAGGATGCCACGAAG
1 TTGTGGAC-TTAAAAGGATGCCACGA-AGTTGTGGACTTAAAAGGATGCCACGAAG
* *
185639 TTGTGGACTTTAAAAGGATGCCAC-AGAGTTGTGGACTTAAAAGGATGCCATGGAG
1 TTGTGGAC-TTAAAAGGATGCCACGA-AGTTGTGGACTTAAAAGGATGCCACGAAG
* * *
185694 TTGTGGACTTAAAAGGATGCCATGAAGTTATGGACTTAAAAGGATGCCACGGAG
1 TTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGATGCCACGAAG
* * *
185748 TTGTGGACTTAAAAGGATGGCATGGAGTTGTGG
1 TTGTGGACTTAAAAGGATGCCACGAAGTTGTGG
185781 GCTTTGAAAA
Statistics
Matches: 327, Mismatches: 30, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
54 118 0.36
55 175 0.54
56 34 0.10
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (54 bp):
TTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGATGCCACGAAG
Found at i:185534 original size:82 final size:82
Alignment explanation
Indices: 185123--185780 Score: 544
Period size: 82 Copynumber: 8.0 Consensus size: 82
185113 GTGGGCTTTG
* * * ** * *
185123 AAAAGG-TGCCACTAATTTGCGGACTTGAAAAAGG-TGCCACTTATTTGTGGACTTTGAAAGGAT
1 AAAAGGATGCCACGAAGTTGTGGACTT--AAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGAT
* * *
185186 GCCACTGACTTGTGGGCTT
64 GCCACAGAGTTGTGGACTT
* * * * * * *
185205 CAAAAGGGTGCCACTG-ATTTGTGGGCTTTCAAAAAGG-TACCACTAATTTGTGGACTTTGAAAG
1 -AAAAGGATGCCAC-GAAGTTGTGGAC-TT--AAAAGGATGCCACGAAGTTGTGGACTTTAAAAG
* * * *
185268 GATGTCACTGACTTGTGGGCTTT
61 GATGCCACAGAGTTGTGGAC-TT
* * * * ** * * * **
185291 GAAAGGGTGCCACTG-ACTTGTGGGCTTTAAAAAGG-TGCCAATAACTTGTGGGCCTTAAAAATA
1 AAAAGGATGCCAC-GAAGTTGTGGAC-TT-AAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGA
* **
185354 TGCCACTGTCTTGTGGACTTT
63 TGCCACAGAGTTGTGGAC-TT
* * * * * * * * *
185375 GAAAGGATGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGATG
1 AAAAGGATGCCACGAAGTTGTGGAC-TTAAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGATG
* * *
185440 CTACTA-ACTTGTGGGCTT
65 CCAC-AGAGTTGTGGACTT
* ** * *
185458 AAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGGTACGAAATTGTAGACTTTAAAAGGATGC
1 AAAAGGATGCCACGAAGTTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGATGC
*
185523 CACAAAGTTGTGGACTT
66 CACAGAGTTGTGGACTT
*
185540 AAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGATGC
1 AAAAGGATGCCACGAAGTTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGATGC
185605 CACAGAGTTGTGGACTT
66 CACAGAGTTGTGGACTT
185622 AAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGATGCCAC-AGAGTTGTGGAC-TTAAAAGGAT
1 AAAAGGATGCCACGAAGTTGTGGAC-TTAAAAGGATGCCACGA-AGTTGTGGACTTTAAAAGGAT
**
185685 GCCATGGAGTTGTGGACTT
64 GCCACAGAGTTGTGGACTT
* * * *
185704 AAAAGGATGCCATGAAGTTATGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGATGG
1 AAAAGGATGCCACGAAGTTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGATGC
**
185768 CATGGAGTTGTGG
66 CACAGAGTTGTGG
185781 GCTTTGAAAA
Statistics
Matches: 505, Mismatches: 59, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
81 50 0.10
82 196 0.39
83 59 0.12
84 120 0.24
85 78 0.15
86 2 0.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (82 bp):
AAAAGGATGCCACGAAGTTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGATGC
CACAGAGTTGTGGACTT
Found at i:187139 original size:23 final size:23
Alignment explanation
Indices: 187109--187172 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 23
187099 TTTTGTTCCC
187109 TTTTTTTATTTTGCTTTTGCATT
1 TTTTTTTATTTTGCTTTTGCATT
*
187132 TTTTTTTATTTTTCTTTT-CATT
1 TTTTTTTATTTTGCTTTTGCATT
* **
187154 TTTTGTGCTTTTGCTTTTG
1 TTTTTTTATTTTGCTTTTG
187173 ACTTTTTCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 18 0.51
23 17 0.49
ACGTcount: A:0.06, C:0.09, G:0.09, T:0.75
Consensus pattern (23 bp):
TTTTTTTATTTTGCTTTTGCATT
Found at i:187156 original size:12 final size:12
Alignment explanation
Indices: 187111--187156 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
187101 TTGTTCCCTT
* *
187111 TTTTTATTTTGC
1 TTTTCATTTTTC
187123 TTTTGCATTTTT-
1 TTTT-CATTTTTC
187135 TTTT-ATTTTTC
1 TTTTCATTTTTC
187146 TTTTCATTTTT
1 TTTTCATTTTT
187157 TGTGCTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 6 0.21
11 4 0.14
12 14 0.48
13 5 0.17
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTTCATTTTTC
Found at i:188908 original size:32 final size:33
Alignment explanation
Indices: 188848--188912 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
188838 CACACCCAGA
*
188848 TGTATCGATACATTATGCTTTGTATCGATATAT
1 TGTATCGATACATTATGCATTGTATCGATATAT
188881 TGTATCGATACATGT-T-CATTGTATCGATATAT
1 TGTATCGATACAT-TATGCATTGTATCGATATAT
188913 GGATAATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.50
33 14 0.47
34 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATTATGCATTGTATCGATATAT
Found at i:188923 original size:20 final size:19
Alignment explanation
Indices: 188874--188934 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
188864 GCTTTGTATC
188874 GATATATTGTATCGATACAT
1 GATA-ATTGTATCGATACAT
* * *
188894 GTTCATTGTATCGATATAT
1 GATAATTGTATCGATACAT
188913 GGATAATTGTATCGATACAT
1 -GATAATTGTATCGATACAT
188933 GA
1 GA
188935 GATTGGCAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (19 bp):
GATAATTGTATCGATACAT
Found at i:188988 original size:20 final size:20
Alignment explanation
Indices: 188963--189015 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
188953 TGCCACTGTT
188963 TGTATCGATACATGGTACAA
1 TGTATCGATACATGGTACAA
*
188983 TGTATCGATACAAGGTACAA
1 TGTATCGATACATGGTACAA
189003 TGTATCGATACAT
1 TGTATCGATACAT
189016 AACGAATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATGGTACAA
Found at i:191518 original size:21 final size:21
Alignment explanation
Indices: 191492--191545 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
191482 TTCAACAATT
191492 TGTATCGATACAAACAATAAA
1 TGTATCGATACAAACAATAAA
*
191513 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAACAATAAA
191534 TGTATCGATACA
1 TGTATCGATACA
191546 TAAGTGTTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (21 bp):
TGTATCGATACAAACAATAAA
Found at i:191571 original size:13 final size:13
Alignment explanation
Indices: 191553--191578 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
191543 ACATAAGTGT
191553 TGTATCGATACAA
1 TGTATCGATACAA
191566 TGTATCGATACAA
1 TGTATCGATACAA
191579 AGCTACCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:191628 original size:20 final size:22
Alignment explanation
Indices: 191603--191657 Score: 82
Period size: 20 Copynumber: 2.7 Consensus size: 22
191593 CTACCAAGGA
191603 AATGTATCGATACATT-AT-TT
1 AATGTATCGATACATTGATCTT
191623 AATGTATCGATACATTGATCTT
1 AATGTATCGATACATTGATCTT
191645 --TGTATCGATACAT
1 AATGTATCGATACAT
191658 CTAGAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 29 0.88
21 2 0.06
22 2 0.06
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (22 bp):
AATGTATCGATACATTGATCTT
Found at i:197750 original size:3 final size:3
Alignment explanation
Indices: 197744--197770 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
197734 AAAAAAAGAA
197744 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
197771 CATGGTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:202519 original size:52 final size:50
Alignment explanation
Indices: 202458--202557 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 50
202448 AGTATCCCCG
* * *
202458 ATTATGAAAAATCGATGTTTTGGAAAGAAAATTGGGATTGGAGTATTCCTA
1 ATTATG-AAAATCGATATTTTGAAAAGAAAATCGGGATTGGAGTATTCCTA
* * * *
202509 ATTATAGAAAATTGGTATTTTGAAAATAAAATCGGGGTTGGAGTATTCC
1 ATTAT-GAAAATCGATATTTTGAAAAGAAAATCGGGATTGGAGTATTCC
202558 CTCGAAAATA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 40 0.98
52 1 0.02
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (50 bp):
ATTATGAAAATCGATATTTTGAAAAGAAAATCGGGATTGGAGTATTCCTA
Found at i:202636 original size:51 final size:50
Alignment explanation
Indices: 202572--202678 Score: 153
Period size: 51 Copynumber: 2.1 Consensus size: 50
202562 AAAATAACGA
* *
202572 GGTTGGAATATCCCCGATTGTGAAAAATCGATGA-TTTAGAAATAAGGCTGG
1 GGTT-GAATATCCCCGATTGTGAAAAATCAAT-ATTTTAGAAATAAAGCTGG
*
202623 GGTTGAAGTATCCCCGATTGTGATAAATCAATATTTTAGAAATAAAGCTGG
1 GGTTGAA-TATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAGCTGG
202674 GGTTG
1 GGTTG
202679 GAGCATCTCC
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
50 4 0.08
51 47 0.92
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (50 bp):
GGTTGAATATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAGCTGG
Found at i:202705 original size:28 final size:27
Alignment explanation
Indices: 202671--202743 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 27
202661 GAAATAAAGC
202671 TGGGGTTGGAGCATCTCCTCG-GAAATAA
1 TGGGGTTGGAGCATC-CCT-GAGAAATAA
*
202699 TGGGGTTGGAGTATCCCTGATGAAATAA
1 TGGGGTTGGAGCATCCCTGA-GAAATAA
* *
202727 CGGGGTTGGAGTATCCC
1 TGGGGTTGGAGCATCCC
202744 CGATTGTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 1 0.02
27 3 0.07
28 37 0.90
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.26
Consensus pattern (27 bp):
TGGGGTTGGAGCATCCCTGAGAAATAA
Found at i:202791 original size:51 final size:51
Alignment explanation
Indices: 202730--202844 Score: 187
Period size: 51 Copynumber: 2.3 Consensus size: 51
202720 GAAATAACGG
* * *
202730 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCG-
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGA
202780 GAGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGA
1 G-GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGA
202832 GGTTGGAGTATCC
1 GGTTGGAGTATCC
202845 TCTCAAAAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
50 1 0.02
51 58 0.97
52 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGA
Found at i:202836 original size:158 final size:158
Alignment explanation
Indices: 202542--202839 Score: 395
Period size: 158 Copynumber: 1.9 Consensus size: 158
202532 AAATAAAATC
202542 GGGGTTGGAGTATTCCCTCGAAAATAACGAGGTTGGAATATCCCCGATTGTGAAAAATCGATGAT
1 GGGGTTGGAGTATTCCCTCGAAAATAACGAGGTTGGAATATCCCCGATTGTGAAAAATCGATGAT
* * * * *
202607 TTAGAAATAAGGCTGGGGTTGAAGTATCCCCGATTGTGATAAATCAATATTTTAGAAATAAAGCT
66 TTAGAAATAAAGCTGGAGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAACC
*
202672 GGGGTTGGAGCATCTCCTCGGAAATAAT
131 GAGGTTGGAGCATCTCCTCGGAAATAAT
* * * *
202700 GGGGTTGGAGTA-TCCCT-GATGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTG
1 GGGGTTGGAGTATTCCCTCGA--AAATAACGAGGTTGGAATATCCCCGATTGTGAAAAATCGATG
* * * * * * *
202763 TTTTGGAAATAAA-ATCGGAGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAA
64 ATTTAGAAATAAAGCT-GGAGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAA
202827 ACCGAGGTTGGAG
128 ACCGAGGTTGGAG
202840 TATCCTCTCA
Statistics
Matches: 120, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
156 2 0.02
157 6 0.05
158 112 0.93
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (158 bp):
GGGGTTGGAGTATTCCCTCGAAAATAACGAGGTTGGAATATCCCCGATTGTGAAAAATCGATGAT
TTAGAAATAAAGCTGGAGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAACC
GAGGTTGGAGCATCTCCTCGGAAATAAT
Found at i:202863 original size:158 final size:157
Alignment explanation
Indices: 202543--202873 Score: 380
Period size: 158 Copynumber: 2.1 Consensus size: 157
202533 AATAAAATCG
202543 GGGTTGGAGTATTCCCTCGAAAATAACGAGGTTGGAATATCCCCGATTGTGAAAAATCGATGATT
1 GGGTTGGAGTA-TCCCTCGAAAATAACGAGGTTGGAATATCCCCGATTGTGAAAAATCGATGATT
* * * * *
202608 TAGAAATAAGGCTGGGGTTGAAGTATCCCCGATTGTGATAAATCAATATTTTAGAAATAAAGCTG
65 TAGAAATAAAGCTGGAGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAACCG
* ** **
202673 GGGTTGGAGCATCTCCTCGGAAATAATG
130 AGGTTGGAGCATCTCCTCAAAAATAACA
* * * * *
202701 GGGTTGGAGTATCCCT-GATGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTT
1 GGGTTGGAGTATCCCTCGA--AAATAACGAGGTTGGAATATCCCCGATTGTGAAAAATCGATGAT
* * * * * *
202765 TTGGAAATAAA-ATCGGAGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAAC
64 TTAGAAATAAAGCT-GGAGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAAC
* *
202829 CGAGGTTGGAGTATC-CTCTCAAAAATGACA
128 CGAGGTTGGAGCATCTC-CTCAAAAATAACA
*
202859 GGGTTGAAGTATCCC
1 GGGTTGGAGTATCCC
202874 CAATTGTGAA
Statistics
Matches: 145, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
156 2 0.01
157 7 0.05
158 136 0.94
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (157 bp):
GGGTTGGAGTATCCCTCGAAAATAACGAGGTTGGAATATCCCCGATTGTGAAAAATCGATGATTT
AGAAATAAAGCTGGAGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAACCGA
GGTTGGAGCATCTCCTCAAAAATAACA
Found at i:202870 original size:79 final size:76
Alignment explanation
Indices: 202782--203004 Score: 230
Period size: 79 Copynumber: 2.8 Consensus size: 76
202772 TAAAATCGGA
* *
202782 GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGAGGTTGGAGTATCCTC
1 GTTGGAGTATCCCCGATTGTGAAAAATT-GTGTTTTAGAAATAAAATCG-GGTTGGAGTATCCCC
*
202847 TCAAAAATGACAGG
64 TCAAAAATAAC-GG
* * * * * *
202861 GTTGAAGTATCCCCAATTGTGAAAAACTGGTGTTTTAGGAATAAAATCGGGGTTAGAATATCCCC
1 GTTGGAGTATCCCCGATTGTGAAAAA-TTGTGTTTTAGAAATAAAATC-GGGTTGGAGTATCCCC
**
202926 TCGGAAATAACGG
64 TCAAAAATAACGG
* * * * *
202939 GATTGGAGTATTCTCGATTATGAAAAATTGATGTTTTGGAAATAAAATTGGGTTTGGAGTATCCC
1 G-TTGGAGTATCCCCGATTGTGAAAAATTG-TGTTTTAGAAATAAAATCGGG-TTGGAGTATCCC
203004 C
63 C
203005 GAGATGAAGA
Statistics
Matches: 117, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
78 8 0.07
79 107 0.91
80 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (76 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGTGTTTTAGAAATAAAATCGGGTTGGAGTATCCCCTC
AAAAATAACGG
Found at i:205327 original size:20 final size:19
Alignment explanation
Indices: 205302--205408 Score: 100
Period size: 20 Copynumber: 5.7 Consensus size: 19
205292 AAAATGCCTG
* *
205302 AATGTATCGATACATTGCAA
1 AATGTATCGATACAATG-AC
205322 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
205342 AATG--T--AT-CAAT-AC
1 AATGTATCGATACAATGAC
*
205355 AATATATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
*
205375 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AC
205395 AATGTATCGATACA
1 AATGTATCGATACA
205409 TCTGGGTAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
13 4 0.05
14 1 0.01
15 5 0.07
16 2 0.03
17 2 0.03
18 5 0.07
19 2 0.03
20 51 0.70
21 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (19 bp):
AATGTATCGATACAATGAC
Found at i:205368 original size:33 final size:33
Alignment explanation
Indices: 205326--205390 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
205316 TTGCAAAATG
205326 TATCGATACAATGAGCAATGTATCAATACAATA
1 TATCGATACAATGAGCAATGTATCAATACAATA
*
205359 TATCGATACAATGAGCAATGTATCGATACAAT
1 TATCGATACAATGAGCAATGTATCAATACAAT
205391 GCAAAATGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (33 bp):
TATCGATACAATGAGCAATGTATCAATACAATA
Found at i:205368 original size:53 final size:53
Alignment explanation
Indices: 205306--205408 Score: 138
Period size: 53 Copynumber: 1.9 Consensus size: 53
205296 TGCCTGAATG
* *
205306 TATCGATACATTGCA-AAATGTATCGATACAATG-AGCAATGTATCAATACAATA
1 TATCGATACAATG-AGAAATGTATCGATACAATGCA-AAATGTATCAATACAATA
* *
205359 TATCGATACAATGAGCAATGTATCGATACAATGCAAAATGTATCGATACA
1 TATCGATACAATGAGAAATGTATCGATACAATGCAAAATGTATCAATACA
205409 TCTGGGTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
52 1 0.02
53 42 0.95
54 1 0.02
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.27
Consensus pattern (53 bp):
TATCGATACAATGAGAAATGTATCGATACAATGCAAAATGTATCAATACAATA
Found at i:205437 original size:29 final size:29
Alignment explanation
Indices: 205395--205466 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
205385 TACAATGCAA
205395 AATGTATCGATACATCTGGGTAAACCCAG
1 AATGTATCGATACATCTGGGTAAACCCAG
205424 AATGTATCGATACATCTGGGTAAACCCAG
1 AATGTATCGATACATCTGGGTAAACCCAG
205453 AATGTATCGATACA
1 AATGTATCGATACA
205467 ATGAACAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.25
Consensus pattern (29 bp):
AATGTATCGATACATCTGGGTAAACCCAG
Found at i:209554 original size:28 final size:28
Alignment explanation
Indices: 209484--210187 Score: 545
Period size: 28 Copynumber: 24.8 Consensus size: 28
209474 CACTAACTTA
* * *
209484 TGTGGGCTTTAGAGAAAGTTGCCACCGACT
1 TGTGGGCTTT-GA-AAGGATGCCACTGACT
* *
209514 TGTGTAGGCTTTGAAAGGATGCCATTAACT
1 TGTG--GGCTTTGAAAGGATGCCACTGACT
* * *
209544 AGTGGACTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
209572 TGTGGGTTTTGAAAGAATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
209600 TGTGGGCTTTAAGAAGG-TGCCAATGACT
1 TGTGGGCTTTGA-AAGGATGCCACTGACT
*
209628 TGTGGGCTTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
*
209656 TGTGGGCTTTGAAAGGATGCCACTGACA
1 TGTGGGCTTTGAAAGGATGCCACTGACT
209684 TGTGGGCTTTGAGAAGG-TGCCACTGACT
1 TGTGGGCTTTGA-AAGGATGCCACTGACT
* * *
209712 TGTGAGCTTTGAAAAGG-TGTCATTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* * *
209740 TGTGGGTTTTGAAAAGG-TACTACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* * *
209768 TGTGGGCTCTGAAA-AAGTGCCAATGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
209796 TGTGGGCTTTGAAA-AAGTACCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * * * *
209824 TGTGAGCTTTGAAAAGATGCCATTGGCA
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
209852 TATGGGCTTTGAAA-AAGTGCCAATGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * *
209880 TGTGGGCTTTGAAAGGATGCCATTAACA
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
209908 TGTGGGTTTTGAGAAGG-TGCCACTAACT
1 TGTGGGCTTTGA-AAGGATGCCACTGACT
* * * *
209936 TGTAGGCCTTGAAAAGGGTTGCCACTAACT
1 TGTGGGCTTTG-AAA-GGATGCCACTGACT
* * *
209966 TGTGGGCTTTGAAA-AAGTGTCACTAACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * *
209994 TGTGGGCTTTAAAAGGGATACCATTGACT
1 TGTGGGCTTTGAAA-GGATGCCACTGACT
*
210023 TGTGTGCTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
210051 TGTGGGCTTTGAAATGG-TGCCACTGACT
1 TGTGGGCTTTGAAA-GGATGCCACTGACT
* ** *
210079 CGTGGGCTTCAAAAGGGTGCCACTGACTT
1 TGTGGGCTTTGAAAGGATGCCACTGAC-T
* *
210108 ATGTGGGCTTTGAAAAGGGTTGCCACCGACT
1 -TGTGGGCTTTG-AAA-GGATGCCACTGACT
* * * * *
210139 TGTGGAC-TTAAAAGGGTGCCACAGAAT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
210166 TGTGGAC-TTAAAAGGATGCCAC
1 TGTGGGCTTTGAAAGGATGCCAC
210188 AGAGTTGTAG
Statistics
Matches: 552, Mismatches: 96, Indels: 55
0.79 0.14 0.08
Matches are distributed among these distances:
27 46 0.08
28 385 0.70
29 42 0.08
30 56 0.10
31 6 0.01
32 17 0.03
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:210168 original size:27 final size:27
Alignment explanation
Indices: 210034--210367 Score: 255
Period size: 27 Copynumber: 12.1 Consensus size: 27
210024 GTGTGCTTTG
* *
210034 AAAA-GGTGCCACTGACTTGTGGGCTTT
1 AAAAGGGTGCCACTGAATTGTGGAC-TT
* * * * *
210061 GAAATGGTGCCACTGACTCGTGGGCTT
1 AAAAGGGTGCCACTGAATTGTGGACTT
* *
210088 CAAAAGGGTGCCACTGACTTATGTGGGCTTT
1 -AAAAGGGTGCCACTGA-AT-TGTGGAC-TT
* *
210119 GAAAAGGGTTGCCACCGACTTGTGGACTT
1 -AAAAGGG-TGCCACTGAATTGTGGACTT
*
210148 AAAAGGGTGCCACAGAATTGTGGACTT
1 AAAAGGGTGCCACTGAATTGTGGACTT
* * * *
210175 AAAAGGATGCCACAGAGTTGTAGACTT
1 AAAAGGGTGCCACTGAATTGTGGACTT
* * * * *
210202 AAAAGGTTACGACGGAGTTGTGGACTT
1 AAAAGGGTGCCACTGAATTGTGGACTT
* **
210229 AAAAAGGTGCCAC-GAAGTTGTAAACTT
1 AAAAGGGTGCCACTGAA-TTGTGGACTT
210256 AAAAGGGTGCCAC-GAAGTTGTGGACTT
1 AAAAGGGTGCCACTGAA-TTGTGGACTT
* *
210283 AAAAAGGTGCCA-TGAAGTTGTGGACTC
1 AAAAGGGTGCCACTGAA-TTGTGGACTT
* * * *
210310 AAAAGGTTGCTACGGAGTTGTGGACTT
1 AAAAGGGTGCCACTGAATTGTGGACTT
*
210337 AAAAAGGTGCCA-TGGAATTGTGGACTT
1 AAAAGGGTGCCACT-GAATTGTGGACTT
210364 AAAA
1 AAAA
210368 AGGAAAGGTG
Statistics
Matches: 254, Mismatches: 43, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
26 2 0.01
27 177 0.70
28 42 0.17
29 3 0.01
30 12 0.05
31 10 0.04
32 8 0.03
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (27 bp):
AAAAGGGTGCCACTGAATTGTGGACTT
Found at i:210423 original size:34 final size:33
Alignment explanation
Indices: 210337--210505 Score: 180
Period size: 32 Copynumber: 5.1 Consensus size: 33
210327 TTGTGGACTT
* *
210337 AAAAAGGTGCCATGGAATTGTGGACTTAAAAAG
1 AAAAAGGTGCCATGGAGTTGTGGACTTTAAAAG
* * * *
210370 -GAAAGGTGCCATAGTGTTGTGGACTTTAACAG
1 AAAAAGGTGCCATGGAGTTGTGGACTTTAAAAG
*
210402 AAAAAGGTTGCCATGGAGTTGTGGACTTAAAAAG
1 AAAAAGG-TGCCATGGAGTTGTGGACTTTAAAAG
** * *
210436 GGAAA-GTGCCACGGAGTTGTGGACTTTAACAG
1 AAAAAGGTGCCATGGAGTTGTGGACTTTAAAAG
* *
210468 AAAAAGGTTGTCACGGAGTTGTGGACTTTGAAAAG
1 AAAAAGG-TGCCATGGAGTTGTGGACTTT-AAAAG
210503 AAA
1 AAA
210506 TGCCACTGAA
Statistics
Matches: 111, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
32 52 0.47
33 7 0.06
34 45 0.41
35 7 0.06
ACGTcount: A:0.36, C:0.11, G:0.30, T:0.24
Consensus pattern (33 bp):
AAAAAGGTGCCATGGAGTTGTGGACTTTAAAAG
Found at i:210445 original size:66 final size:66
Alignment explanation
Indices: 210337--210495 Score: 241
Period size: 66 Copynumber: 2.4 Consensus size: 66
210327 TTGTGGACTT
* * *
210337 AAAAAGG-TGCCATGGAATTGTGGACTTAAAAAGGAAAGGTGCCATAGTGTTGTGGACTTTAACA
1 AAAAAGGTTGCCATGGAGTTGTGGACTTAAAAAGGAAAGGTGCCACAGAGTTGTGGACTTTAACA
210401 G
66 G
*
210402 AAAAAGGTTGCCATGGAGTTGTGGACTTAAAAAGGGAAA-GTGCCACGGAGTTGTGGACTTTAAC
1 AAAAAGGTTGCCATGGAGTTGTGGACTTAAAAA-GGAAAGGTGCCACAGAGTTGTGGACTTTAAC
210466 AG
65 AG
* *
210468 AAAAAGGTTGTCACGGAGTTGTGGACTT
1 AAAAAGGTTGCCATGGAGTTGTGGACTT
210496 TGAAAAGAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
65 7 0.08
66 74 0.86
67 5 0.06
ACGTcount: A:0.33, C:0.11, G:0.31, T:0.25
Consensus pattern (66 bp):
AAAAAGGTTGCCATGGAGTTGTGGACTTAAAAAGGAAAGGTGCCACAGAGTTGTGGACTTTAACA
G
Found at i:211857 original size:22 final size:22
Alignment explanation
Indices: 211832--211901 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
211822 TTGTTGTTTA
211832 TTTTTTTATTTTGCTTTTGCAC
1 TTTTTTTATTTTGCTTTTGCAC
* *
211854 TTTTTTTGTTTTTCTTTT-CA-
1 TTTTTTTATTTTGCTTTTGCAC
*
211874 TTTTTTGTGCTTTTGCTTTTG-AC
1 TTTTTT-T-ATTTTGCTTTTGCAC
211897 TTTTT
1 TTTTT
211902 CGTCATTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 6 0.15
21 3 0.08
22 26 0.65
23 5 0.12
ACGTcount: A:0.06, C:0.11, G:0.10, T:0.73
Consensus pattern (22 bp):
TTTTTTTATTTTGCTTTTGCAC
Found at i:211860 original size:44 final size:43
Alignment explanation
Indices: 211811--211901 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 43
211801 TATGTCCTTA
* *
211811 TTTTTTGATTTTTGTTGTTTATTTTTT-T-ATTTTGCTTTTGCACT
1 TTTTTTG-TTTTTCTT-TTCATTTTTTGTGATTTTGCTTTTG-ACT
*
211855 TTTTTTGTTTTTCTTTTCATTTTTTGTGCTTTTGCTTTTGACT
1 TTTTTTGTTTTTCTTTTCATTTTTTGTGATTTTGCTTTTGACT
211898 TTTT
1 TTTT
211902 CGTCATTTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
42 9 0.21
43 15 0.36
44 18 0.43
ACGTcount: A:0.07, C:0.09, G:0.11, T:0.74
Consensus pattern (43 bp):
TTTTTTGTTTTTCTTTTCATTTTTTGTGATTTTGCTTTTGACT
Found at i:218158 original size:20 final size:20
Alignment explanation
Indices: 218099--218166 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
218089 AGAATGTTTA
*
218099 GATACATTGAAAAATGTACC
1 GATACATTGAAAAATGTATC
* * * *
218119 AATACATTCATACATGTATC
1 GATACATTGAAAAATGTATC
*
218139 GATACATTGAAAAATATATC
1 GATACATTGAAAAATGTATC
218159 GATACATT
1 GATACATT
218167 TGTGTAAAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (20 bp):
GATACATTGAAAAATGTATC
Found at i:219998 original size:104 final size:104
Alignment explanation
Indices: 219818--220025 Score: 382
Period size: 104 Copynumber: 2.0 Consensus size: 104
219808 CTTCAGAACA
219818 CAATTTTTTGATATTTACGAATAAACCTTAAACTTTCTAAAATCGTAAAAAGACCCGGAAGAGGT
1 CAATTTTTTGATATTTACGAATAAACCTTAAACTTTCTAAAATCGTAAAAAGACCCGGAAGAGGT
*
219883 TAAAGACATGCAAATCATATTTAAACATTATAGATATAC
66 TAAAGACATGCAAATCATATTTAAACATGATAGATATAC
*
219922 CAATTTTTTGATATTTATGAATAAACCTTAAACTTTCTAAAATCGTAAAAAGACCTC-GAAGAGG
1 CAATTTTTTGATATTTACGAATAAACCTTAAACTTTCTAAAATCGTAAAAAGACC-CGGAAGAGG
219986 TTAAAGACATGCAAATCATATTTAAACATGATAGATATAC
65 TTAAAGACATGCAAATCATATTTAAACATGATAGATATAC
220026 ATGAAAGACA
Statistics
Matches: 101, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
104 100 0.99
105 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (104 bp):
CAATTTTTTGATATTTACGAATAAACCTTAAACTTTCTAAAATCGTAAAAAGACCCGGAAGAGGT
TAAAGACATGCAAATCATATTTAAACATGATAGATATAC
Found at i:221099 original size:25 final size:24
Alignment explanation
Indices: 221071--221137 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
221061 TGAAACTAGT
*
221071 TTAAAAATAAAATAAAAATCTAACA
1 TTAAAAATAAAATAAAAAT-TAAAA
* *
221096 TT-AAAAGAAAATTAAAATTAAAA
1 TTAAAAATAAAATAAAAATTAAAA
*
221119 TTAATAATCATAAATAAAA
1 TTAAAAAT-A-AAATAAAA
221138 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
23 6 0.18
24 17 0.52
25 3 0.09
26 7 0.21
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.27
Consensus pattern (24 bp):
TTAAAAATAAAATAAAAATTAAAA
Found at i:221114 original size:6 final size:6
Alignment explanation
Indices: 221071--221122 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
221061 TGAAACTAGT
* * * *
221071 TTAAAA ATAAAA TAAAAA TCTAACA TTAAAA -GAAAA TTAAAA TTAAAA
1 TTAAAA TTAAAA TTAAAA T-TAAAA TTAAAA TTAAAA TTAAAA TTAAAA
221119 TTAA
1 TTAA
221123 TAATCATAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
5 4 0.11
6 28 0.78
7 4 0.11
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (6 bp):
TTAAAA
Found at i:223305 original size:67 final size:67
Alignment explanation
Indices: 223234--223392 Score: 151
Period size: 67 Copynumber: 2.4 Consensus size: 67
223224 GTACTAAATG
* * * * *
223234 AGATTAAGGCGGAGCCTATGTCAAAAAAGGAGTTGACTAGAGCA-AAATCGATAAAGTTAACTAA
1 AGATTAAGGCAGAACCTAAGTCAAAAAAGGAGTTGACTA-AGCAGAAATCGATAAAGTCAACCAA
223298 AAA
65 AAA
* * * * * *
223301 AGATTAGGGCAGAACCTAAGTCGAATAGGGTGTTGACTAAGGAGAAATCGATAAAGTCAACCAAA
1 AGATTAAGGCAGAACCTAAGTCAAAAAAGGAGTTGACTAAGCAGAAATCGATAAAGTCAACCAAA
*
223366 AG
66 AA
* **
223368 AGACT-AGGGTGAAACCTAAGTCAAA
1 AGATTAAGGCAG-AACCTAAGTCAAA
223393 CAGGGTATAA
Statistics
Matches: 73, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
66 6 0.08
67 67 0.92
ACGTcount: A:0.44, C:0.13, G:0.25, T:0.18
Consensus pattern (67 bp):
AGATTAAGGCAGAACCTAAGTCAAAAAAGGAGTTGACTAAGCAGAAATCGATAAAGTCAACCAAA
AA
Found at i:223398 original size:67 final size:67
Alignment explanation
Indices: 223265--223398 Score: 164
Period size: 67 Copynumber: 2.0 Consensus size: 67
223255 CAAAAAAGGA
* * * * *
223265 GTTGACTAGAGCAAAATCGATAAAGTTAACTAAAAAAGATTAGGGCAGAACCTAAGTCGAATAGG
1 GTTGACTAGAGCAAAATCGATAAAGTCAACCAAAAAAGACTAGGGCAGAACCTAAGTCAAACAGG
223330 GT
66 GT
* * *
223332 GTTGACTA-AGGAGAAATCGATAAAGTCAACCAAAAGAGACTAGGG-TGAAACCTAAGTCAAACA
1 GTTGACTAGAGCA-AAATCGATAAAGTCAACCAAAAAAGACTAGGGCAG-AACCTAAGTCAAACA
223395 GGGT
64 GGGT
223399 ATAAACAAGG
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
66 4 0.07
67 53 0.93
ACGTcount: A:0.43, C:0.13, G:0.25, T:0.19
Consensus pattern (67 bp):
GTTGACTAGAGCAAAATCGATAAAGTCAACCAAAAAAGACTAGGGCAGAACCTAAGTCAAACAGG
GT
Found at i:223798 original size:68 final size:67
Alignment explanation
Indices: 223717--223915 Score: 258
Period size: 67 Copynumber: 3.0 Consensus size: 67
223707 GGCGGAGCCA
* * * *
223717 AAGTCGAAAAAGGTGTTGACTAGGGCAAAACTGATAAAGTTAACTAAAAAAATACTAGGGTGGAA
1 AAGTCGAAAAAGGTGTTAACTAGGGCAAAACTGATAAAGTCAACT-AAAAGAGACTAGGGTGGAA
223782 CCT
65 CCT
* * * * * *
223785 AAGTCAAAAAAGGTATTAATTATGGTG-AAAGC-GATAAAGTCAACTGAAAGAGACTAGGGTAGA
1 AAGTCGAAAAAGGTGTTAACTA-GG-GCAAAACTGATAAAGTCAACTAAAAGAGACTAGGGTGGA
*
223848 ACTT
64 ACCT
223852 AAGTCGAAAAAGGTGTTAACTAGGGCAAAACTGATAAAGTCAACTAAAAGAGACTAGGGTGGAA
1 AAGTCGAAAAAGGTGTTAACTAGGGCAAAACTGATAAAGTCAACTAAAAGAGACTAGGGTGGAA
223916 ATGAAATGGT
Statistics
Matches: 110, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
65 1 0.01
66 6 0.05
67 66 0.60
68 30 0.27
69 6 0.05
70 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.25, T:0.20
Consensus pattern (67 bp):
AAGTCGAAAAAGGTGTTAACTAGGGCAAAACTGATAAAGTCAACTAAAAGAGACTAGGGTGGAAC
CT
Found at i:224314 original size:40 final size:40
Alignment explanation
Indices: 224175--224314 Score: 138
Period size: 40 Copynumber: 3.5 Consensus size: 40
224165 CCAATAAAGC
* * ** * *
224175 CAACAAAAAGTAAAGATTGACCCAGACAAAATTGACAAGT
1 CAACAAATAGTAAAGGTTGACTAAGATAAAACTGACAAGT
* * * * *
224215 CAACAAATAGTAAAGGTCGATTAAGATGAAACTGATAAGC
1 CAACAAATAGTAAAGGTTGACTAAGATAAAACTGACAAGT
* **
224255 CAACAAATAGTAAAAGTTGACTGTGATAAAACTGACAAGT
1 CAACAAATAGTAAAGGTTGACTAAGATAAAACTGACAAGT
224295 CAACAAATGAG-AAAGGTTGA
1 CAACAAAT-AGTAAAGGTTGA
224315 GTAACATTTG
Statistics
Matches: 79, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 77 0.97
41 2 0.03
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.19
Consensus pattern (40 bp):
CAACAAATAGTAAAGGTTGACTAAGATAAAACTGACAAGT
Found at i:225405 original size:60 final size:60
Alignment explanation
Indices: 225341--226127 Score: 365
Period size: 60 Copynumber: 13.3 Consensus size: 60
225331 ACGAAACTAA
*
225341 AAACCTAAATAATGACTTAGGCAAAACCAAGACTCAGCAAAATGGCCTAGATGAAAGCAG
1 AAACCTAAATAATGACTTAGGCAAAACCAAGACTCAACAAAATGGCCTAGATGAAAGCAG
* * * * ** ** * *
225401 AAACCTAAACAATAACTT-GGCAAAACCAAGATTTAATGAAATGATCTAGATAAAATCAG
1 AAACCTAAATAATGACTTAGGCAAAACCAAGACTCAACAAAATGGCCTAGATGAAAGCAG
* * * * * * *
225460 AAACCTAAACAAAGA-TTCGAGTG-AAACCCAA-ATTCAACAAAATGGTCTGGAT-AAAACTAG
1 AAACCTAAATAATGACTT--AG-GCAAAACCAAGACTCAACAAAATGGCCTAGATGAAAGC-AG
* * * * * * *
225520 AACCCTAAATAATGACTTGGGGAAAACAAAGACGT-AA-AAAATGGTCT-GATAAAACCAG
1 AAACCTAAATAATGACTTAGGCAAAACCAAGAC-TCAACAAAATGGCCTAGATGAAAGCAG
* * * *
225578 AAA-C-----AATGACTT-GGTTAAAACCAAGACTCAAGAAAATGCCCTAGATGAAAACAG
1 AAACCTAAATAATGACTTAGG-CAAAACCAAGACTCAACAAAATGGCCTAGATGAAAGCAG
* * * * * * * *
225632 AAACCTAACTAATGAGTTAGGACATAACGAAAACTCAATAAAATGG-CTTGAGCGAAA-CTA-
1 AAACCTAAATAATGACTTAGG-CAAAACCAAGACTCAACAAAATGGCCTAGA-TGAAAGC-AG
* * * * * * * * **
225692 AAAGCCTAAATAATGACTTAGGCTAAATCAAGACTTAACAAAATGACTTGGGTG-AGGCTC
1 AAA-CCTAAATAATGACTTAGGCAAAACCAAGACTCAACAAAATGGCCTAGATGAAAGCAG
* * * * ** * * *** * * *
225752 TAACCTAAACAATAACTTTGGTGAAACCAAGATTCAACGAAATAATCTAGATTAAATCAA
1 AAACCTAAATAATGACTTAGGCAAAACCAAGACTCAACAAAATGGCCTAGATGAAAGCAG
* * * **
225812 AAACCTAAATAAAT-ATTTAGGCGAAACCAAGATTCAATGAAATGGCCTAGAT--AAGACTAG
1 AAACCTAAAT-AATGACTTAGGCAAAACCAAGACTCAACAAAATGGCCTAGATGAAAG-C-AG
* * * * *
225872 AATCCTAAACAATGACTTGGGCAAAACCAAGACT-AAAAGAAATAGCCTAGAT--AAGACTAG
1 AAACCTAAATAATGACTTAGGCAAAACCAAGACTCAACA-AAATGGCCTAGATGAAAG-C-AG
* * ** * * *
225932 AATCCTAAACAATGACTTTCGCAAAACCAAGACTCAA-AGAAATAGCTTGGAT--AAGACTAG
1 AAACCTAAATAATGACTTAGGCAAAACCAAGACTCAACA-AAATGGCCTAGATGAAAG-C-AG
* * * * * *
225992 AAACCTAAATAATGACTTGGGTAAAACCAAGACTCAAGAAAATGG-CTTGAGTGAAACCAA
1 AAACCTAAATAATGACTTAGGCAAAACCAAGACTCAACAAAATGGCCTAGA-TGAAAGCAG
* * * * * * *
226052 AAACCTAAATAATAACTTGGGTAAAACCAAGACTCAAGAAAATGG-CTACATAAAACCAG
1 AAACCTAAATAATGACTTAGGCAAAACCAAGACTCAACAAAATGGCCTAGATGAAAGCAG
226111 AAACCTAAATAATGACT
1 AAACCTAAATAATGACT
226128 ATATATGAAC
Statistics
Matches: 568, Mismatches: 121, Indels: 77
0.74 0.16 0.10
Matches are distributed among these distances:
51 3 0.01
52 20 0.04
53 8 0.01
54 12 0.02
55 1 0.00
57 1 0.00
58 12 0.02
59 138 0.24
60 309 0.54
61 61 0.11
62 3 0.01
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.19
Consensus pattern (60 bp):
AAACCTAAATAATGACTTAGGCAAAACCAAGACTCAACAAAATGGCCTAGATGAAAGCAG
Found at i:226051 original size:30 final size:30
Alignment explanation
Indices: 226002--226098 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
225992 AAACCTAAAT
* *
226002 AATGACTTGGGTAAAACCAAGACTCAAGAA
1 AATGGCTTGAGTAAAACCAAGACTCAAGAA
* * *
226032 AATGGCTTGAGTGAAACCAAAAAC-CTAA-AT
1 AATGGCTTGAGTAAAACC-AAGACTC-AAGAA
** *
226062 AATAACTTGGGTAAAACCAAGACTCAAGAA
1 AATGGCTTGAGTAAAACCAAGACTCAAGAA
226092 AATGGCT
1 AATGGCT
226099 ACATAAAACC
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
29 6 0.12
30 38 0.76
31 6 0.12
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.19
Consensus pattern (30 bp):
AATGGCTTGAGTAAAACCAAGACTCAAGAA
Found at i:229762 original size:52 final size:52
Alignment explanation
Indices: 229677--229801 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
229667 ATATGAAAAG
* * *
229677 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGTAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
229729 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
229781 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
229802 GAGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:229814 original size:52 final size:51
Alignment explanation
Indices: 229677--229821 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
229667 ATATGAAAAG
* *
229677 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGTAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
229729 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
229781 TTGCCTGCATGTATCGATACA-GAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
229822 ATGTATCAAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:229902 original size:20 final size:20
Alignment explanation
Indices: 229873--229930 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
229863 GCAGTAGCTT
229873 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
229892 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
229912 TTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
229931 TCATTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:230721 original size:14 final size:14
Alignment explanation
Indices: 230702--230729 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
230692 GTCATTGGGT
230702 TTTAGAGATGATGA
1 TTTAGAGATGATGA
230716 TTTAGAGATGATGA
1 TTTAGAGATGATGA
230730 AGGTGCCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.36
Consensus pattern (14 bp):
TTTAGAGATGATGA
Found at i:230917 original size:49 final size:49
Alignment explanation
Indices: 230862--231701 Score: 1089
Period size: 49 Copynumber: 17.6 Consensus size: 49
230852 GATGTCAACG
* * *
230862 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
230911 TGCTGATTCAAGGCCAGCGATATCGGGCTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* * *
230954 TGCTGATTCAAAGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* *
231003 TGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* * *
231046 TACTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* *
231095 TGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* * *
231138 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* *
231187 TGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
231230 TGCTGATTAAAGGCCAGCTACATTGGATTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
231279 TGCTGAGTCAAGGCCAGTTACATTGGACTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
*
231328 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
231377 TGCTGAGTCAAGGCCAGCTACATTGGACATAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* *
231426 TACTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* * *
231475 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* * *
231524 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGCTAAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* *
231573 TGCTGAGTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
*
231622 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
*
231671 TGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTA
231702 GAAGGGTTGC
Statistics
Matches: 690, Mismatches: 77, Indels: 48
0.85 0.09 0.06
Matches are distributed among these distances:
43 146 0.21
45 4 0.01
47 4 0.01
49 536 0.78
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
Found at i:231783 original size:34 final size:34
Alignment explanation
Indices: 231740--232028 Score: 334
Period size: 34 Copynumber: 8.8 Consensus size: 34
231730 TTAGGAAGGG
* * *
231740 AGAGTGCCACGGAGTTGTGCGCTTAGAAGGAAAA
1 AGAGTGCCACGGAGTTGTGGGCTTTGAAAGAAAA
* *
231774 AGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAA
1 AGAGTGCCACGGAGTTGTGGGCTTTGAAAGAAAA
*
231808 AGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGA
1 AGAGTGCCACGGAGTTGTGGGCTTTG-AAAGAAAA
231843 AGA-TGCCACGGAGTTGTGGGCTTT-----AAAA
1 AGAGTGCCACGGAGTTGTGGGCTTTGAAAGAAAA
*
231871 AGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGA
1 AGAGTGCCACGGAGTTGTGGGCTTTG-AAAGAAAA
*
231906 AG-GTGCCACGGAGTTGTGGGCTTTGAAAAGAAGA
1 AGAGTGCCACGGAGTTGTGGGCTTTG-AAAGAAAA
* *
231940 AG-GTGCCACAGAGTTGTGGGCTTT-AAAGGAAA
1 AGAGTGCCACGGAGTTGTGGGCTTTGAAAGAAAA
*
231972 AG-GTGCCACGGAGTTATGGGCTTTG-AAGAAAA
1 AGAGTGCCACGGAGTTGTGGGCTTTGAAAGAAAA
* * *
232004 A-A-TGCCACTGAGTCGTGGACTTTGA
1 AGAGTGCCACGGAGTTGTGGGCTTTGA
232029 GACAAAATGC
Statistics
Matches: 228, Mismatches: 16, Indels: 24
0.85 0.06 0.09
Matches are distributed among these distances:
28 6 0.03
29 21 0.09
31 18 0.08
32 35 0.15
34 134 0.59
35 14 0.06
ACGTcount: A:0.30, C:0.13, G:0.35, T:0.21
Consensus pattern (34 bp):
AGAGTGCCACGGAGTTGTGGGCTTTGAAAGAAAA
Found at i:231871 original size:97 final size:96
Alignment explanation
Indices: 231770--232028 Score: 362
Period size: 97 Copynumber: 2.7 Consensus size: 96
231760 GCTTAGAAGG
*
231770 AAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA-GAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA
*
231835 AAAGAAGAAGATGCCACGGAGTTGTGGGCTTT
65 AAAGAAGAAGATGCCACAGAGTTGTGGGCTTT
*
231867 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA-AAGAAGAAGGTGCCACGGAGTTGTGGGCTTTG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAGAAAAAG-A-GTGCCACGGAGTTGTGGGCTTTG
*
231931 AAAAGAAGAAGGTGCCACAGAGTTGTGGGCTTT
64 AAAAGAAGAAGATGCCACAGAGTTGTGGGCTTT
* * * * *
231964 AAAGGAAAAGGTGCCACGGAGTTATGGGCTTTGAAGAAAAA-A-TGCCACTGAGTCGTGGACTTT
1 AAA--AAGA-GTGCCACGGAGTTGTGGGCTTTGAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
232027 GA
63 GA
232029 GACAAAATGC
Statistics
Matches: 146, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
95 5 0.03
96 1 0.01
97 108 0.74
99 4 0.03
100 24 0.16
101 4 0.03
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (96 bp):
AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
AAGAAGAAGATGCCACAGAGTTGTGGGCTTT
Found at i:231928 original size:131 final size:132
Alignment explanation
Indices: 231740--232028 Score: 372
Period size: 131 Copynumber: 2.2 Consensus size: 132
231730 TTAGGAAGGG
* * * *
231740 AGAGTGCCACGGAGTTGTGCGCTTAG-AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAG-AAG
1 AGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAAA
* *
231803 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGATGCCACGGAGTTGTGGGCTTT-
66 GAAAAAG-GTGCCACAGAGTTGTGGGCTTT-AAAAGAA-AAGATGCCACGGAGTTATGGGCTTTG
231867 AA-AA
128 AAGAA
* *
231871 AGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAG-GTGCCACGGAGTTGTGGGCTTTGAAAA
1 AGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAAA
* * *
231935 GAAGAAGGTGCCACAGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTATGGGCTTTGAAG
66 GAAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAGATGCCACGGAGTTATGGGCTTTGAAG
232000 AA
131 AA
* * * * *
232002 AAAATGCCACTGAGTCGTGGACTTTGA
1 AGAGTGCCACGGAGTTGTGGGCTTTGA
232029 GACAAAATGC
Statistics
Matches: 138, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
129 23 0.17
130 8 0.06
131 91 0.66
132 16 0.12
ACGTcount: A:0.30, C:0.13, G:0.35, T:0.21
Consensus pattern (132 bp):
AGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAAA
GAAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAGATGCCACGGAGTTATGGGCTTTGAAG
AA
Found at i:232079 original size:62 final size:61
Alignment explanation
Indices: 231975--232152 Score: 207
Period size: 62 Copynumber: 2.9 Consensus size: 61
231965 AAGGAAAAGG
* * * * *
231975 TGCCACGGAGTTATGGGCTTTGAAGAAAAAATGCCACTGAGTCGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCATGGACTTT-AAGAAAAGATGCCACTGAGTCGTGGACTTTAAG-CAGAGAA
*
232036 TGCCACTGAGTCATGGACTTTAAAGAAAAGGATGCCACTGAGTCGTGGACTTTAAGCAGAGAT
1 TGCCACTGAGTCATGGACTTT-AAGAAAA-GATGCCACTGAGTCGTGGACTTTAAGCAGAGAA
* * * *
232099 TGCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTCGTAGACTTTAA
1 TGCCACTGAGTCATGGACTTTAAGAAAAGA-TGCCACTGAGTCGTGGACTTTAA
232153 AAAGGTATTT
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
61 29 0.28
62 52 0.51
63 21 0.21
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (61 bp):
TGCCACTGAGTCATGGACTTTAAGAAAAGATGCCACTGAGTCGTGGACTTTAAGCAGAGAA
Found at i:232106 original size:31 final size:31
Alignment explanation
Indices: 232006--232152 Score: 183
Period size: 31 Copynumber: 4.7 Consensus size: 31
231996 GAAGAAAAAA
* *
232006 TGCCACTGAGTCGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGACTTTAAGA-AGAGAT
* *
232036 TGCCACTGAGTCATGGACTTTAAAGAAAAGGA-
1 TGCCACTGAGTCGTGGACTTT-AAGAAGA-GAT
*
232068 TGCCACTGAGTCGTGGACTTTAAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTAAGAAGAGAT
*
232099 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTAAGAAGAGAT
*
232130 TGCCACTGAGTCGTAGACTTTAA
1 TGCCACTGAGTCGTGGACTTTAA
232153 AAAGGTATTT
Statistics
Matches: 103, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
30 23 0.22
31 59 0.57
32 20 0.19
33 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTAAGAAGAGAT
Found at i:234153 original size:13 final size:13
Alignment explanation
Indices: 234135--234160 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
234125 CAAGTTTTTG
234135 TGTATCGATACAT
1 TGTATCGATACAT
234148 TGTATCGATACAT
1 TGTATCGATACAT
234161 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:234185 original size:19 final size:18
Alignment explanation
Indices: 234115--234185 Score: 53
Period size: 19 Copynumber: 4.0 Consensus size: 18
234105 TACAAGCCAA
*
234115 TGTATCGATACAAGTTTTTG
1 TGTATCGATACAA--TTTGG
234135 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
234148 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
234167 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
234186 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:234239 original size:13 final size:13
Alignment explanation
Indices: 234221--234246 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
234211 ATCTTTTTCA
234221 TGTATCGATACAT
1 TGTATCGATACAT
234234 TGTATCGATACAT
1 TGTATCGATACAT
234247 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:234257 original size:86 final size:86
Alignment explanation
Indices: 234113--234321 Score: 384
Period size: 86 Copynumber: 2.4 Consensus size: 86
234103 GTTACAAGCC
** *
234113 AATGTATCGATACAAGTTTTT-GTGTATCGATACATTGTATCGATACATACTTGGTGTATCGATA
1 AATGTATCGATACATCTTTTTCATGTATCGATACATTGTATCGATACATACTTGGTGTATCGATA
234177 CAAGTTTGGCTACTGCCAAGA
66 CAAGTTTGGCTACTGCCAAGA
234198 AATGTATCGATACATCTTTTTCATGTATCGATACATTGTATCGATACATACTTGGTGTATCGATA
1 AATGTATCGATACATCTTTTTCATGTATCGATACATTGTATCGATACATACTTGGTGTATCGATA
234263 CAAGTTTGGCTACTGCCAAGA
66 CAAGTTTGGCTACTGCCAAGA
234284 AATGTATCGATACATCTTTTTCATGTATCGATACATTG
1 AATGTATCGATACATCTTTTTCATGTATCGATACATTG
234322 CAACATGTAT
Statistics
Matches: 120, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
85 19 0.16
86 101 0.84
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (86 bp):
AATGTATCGATACATCTTTTTCATGTATCGATACATTGTATCGATACATACTTGGTGTATCGATA
CAAGTTTGGCTACTGCCAAGA
Found at i:236642 original size:21 final size:21
Alignment explanation
Indices: 236618--236664 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
236608 TTTGATGCTG
236618 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
*
236638 AATTTGAAGTGAAAAACAAGT
1 ATTTTGAAGTGAAAAACAAGT
236659 ATTTTG
1 ATTTTG
236665 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:236803 original size:13 final size:13
Alignment explanation
Indices: 236785--236810 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
236775 ATAATCACCC
236785 TGTATCGATACAA
1 TGTATCGATACAA
236798 TGTATCGATACAA
1 TGTATCGATACAA
236811 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:238904 original size:15 final size:15
Alignment explanation
Indices: 238884--238913 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
238874 GTTCATCAAT
238884 TTCATTTGGAGCTTC
1 TTCATTTGGAGCTTC
*
238899 TTCATTTTGAGCTTC
1 TTCATTTGGAGCTTC
238914 CTCAATTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.50
Consensus pattern (15 bp):
TTCATTTGGAGCTTC
Found at i:243008 original size:13 final size:13
Alignment explanation
Indices: 242990--243015 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
242980 CAAGTTTTTG
242990 TGTATCGATACAT
1 TGTATCGATACAT
243003 TGTATCGATACAT
1 TGTATCGATACAT
243016 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:243040 original size:19 final size:18
Alignment explanation
Indices: 242970--243040 Score: 53
Period size: 19 Copynumber: 4.0 Consensus size: 18
242960 TACAAGCCAA
*
242970 TGTATCGATACAAGTTTTTG
1 TGTATCGATACAA--TTTGG
242990 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
243003 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
243022 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
243041 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:243094 original size:13 final size:13
Alignment explanation
Indices: 243076--243101 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
243066 ATCTTTTTCA
243076 TGTATCGATACAT
1 TGTATCGATACAT
243089 TGTATCGATACAT
1 TGTATCGATACAT
243102 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:243112 original size:86 final size:86
Alignment explanation
Indices: 242968--243176 Score: 384
Period size: 86 Copynumber: 2.4 Consensus size: 86
242958 GTTACAAGCC
** *
242968 AATGTATCGATACAAGTTTTT-GTGTATCGATACATTGTATCGATACATACTTGGTGTATCGATA
1 AATGTATCGATACATCTTTTTCATGTATCGATACATTGTATCGATACATACTTGGTGTATCGATA
243032 CAAGTTTGGCTACTGCCAAGA
66 CAAGTTTGGCTACTGCCAAGA
243053 AATGTATCGATACATCTTTTTCATGTATCGATACATTGTATCGATACATACTTGGTGTATCGATA
1 AATGTATCGATACATCTTTTTCATGTATCGATACATTGTATCGATACATACTTGGTGTATCGATA
243118 CAAGTTTGGCTACTGCCAAGA
66 CAAGTTTGGCTACTGCCAAGA
243139 AATGTATCGATACATCTTTTTCATGTATCGATACATTG
1 AATGTATCGATACATCTTTTTCATGTATCGATACATTG
243177 CAACATGTAT
Statistics
Matches: 120, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
85 19 0.16
86 101 0.84
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (86 bp):
AATGTATCGATACATCTTTTTCATGTATCGATACATTGTATCGATACATACTTGGTGTATCGATA
CAAGTTTGGCTACTGCCAAGA
Found at i:250414 original size:52 final size:52
Alignment explanation
Indices: 250329--250453 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
250319 ATATGAAAAG
* * *
250329 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGTAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
250381 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
250433 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
250454 GAGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:250466 original size:52 final size:51
Alignment explanation
Indices: 250329--250473 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
250319 ATATGAAAAG
* *
250329 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGTAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
250381 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
250433 TTGCCTGCATGTATCGATACA-GAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
250474 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:250480 original size:13 final size:13
Alignment explanation
Indices: 250462--250486 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
250452 CAGAGATCAG
250462 TGTATCGATACAA
1 TGTATCGATACAA
250475 TGTATCGATACA
1 TGTATCGATACA
250487 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:250554 original size:20 final size:20
Alignment explanation
Indices: 250525--250582 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
250515 GTAGTAGCTT
250525 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
250544 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
250564 TTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
250583 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:251372 original size:14 final size:14
Alignment explanation
Indices: 251353--251380 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
251343 GTCATTGGGT
251353 TTTAGAGATGATGA
1 TTTAGAGATGATGA
251367 TTTAGAGATGATGA
1 TTTAGAGATGATGA
251381 AGGTGCCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.36
Consensus pattern (14 bp):
TTTAGAGATGATGA
Found at i:251574 original size:49 final size:49
Alignment explanation
Indices: 251514--252255 Score: 940
Period size: 49 Copynumber: 15.6 Consensus size: 49
251504 GATGTCAACG
* * *
251514 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
251563 TGCTGATTCAAGGCCAGCGATATCGGGCTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* *
251606 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* *
251655 TGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
251698 TGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGAAGATGCTAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* *
251747 TGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
*
251790 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-AAGGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAA-GGTGCCAATA
* *
251839 TGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
251882 TGCTGATTAAAGGCCAGCTACATTGGGCTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* * *
251931 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* *
251980 TGCTGATTCAAGGCCAGCTAGATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* * *
252029 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
252078 TGTTGATTCAAGGCCAGCTATATTGGACTTAAAGCTAAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* *
252127 TGCTGAGTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
*
252176 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
*
252225 TGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTA
252256 GAAGGGTTGC
Statistics
Matches: 606, Mismatches: 63, Indels: 48
0.85 0.09 0.07
Matches are distributed among these distances:
43 145 0.24
44 2 0.00
45 4 0.01
47 4 0.01
48 2 0.00
49 449 0.74
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
Found at i:252011 original size:98 final size:92
Alignment explanation
Indices: 251513--252260 Score: 1012
Period size: 92 Copynumber: 7.9 Consensus size: 92
251503 AGATGTCAAC
* *
251513 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCC
* *
251578 AGCGATATCGGGCTTAAAGGTGCCAAT
66 AGCGATATTGGACTTAAAGGTGCCAAT
*
251605 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCC
251670 AGCGATATTGGACTTAAAGGTGCCAAT
66 AGCGATATTGGACTTAAAGGTGCCAAT
* * *
251697 GTGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGAAGATGCTAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCC
251762 AGCGATATTGGACTTAAAGGTGCCAAT
66 AGCGATATTGGACTTAAAGGTGCCAAT
251789 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-AAGGGTGCCAATATGCTGATTCAAGGC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA-GGTGCCAATATGCTGATTCAAGGC
251853 CAGCGATATTGGACTTAAAGGTGCCAAT
65 CAGCGATATTGGACTTAAAGGTGCCAAT
* * * *
251881 GTGCTGATTAAAGGCCAGCTACATTGGGCTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCC
* *
251946 AGCTACATTGGACTTAAAGATAAAGGTGCCAAT
66 AGCGATATTGGAC-T-----TAAAGGTGCCAAT
* * * *
251979 ATGCTGATTCAAGGCCAGCTAGATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCC
* *
252044 AGCTACATTGGACTTAAAGATAAAGGTGCCAAT
66 AGCGATATTGGAC-T-----TAAAGGTGCCAAT
* * * * * * *
252077 ATGTTGATTCAAGGCCAGCTATATTGGACTTAAAGCTAAAGGTGCCAATGTGCTGAGTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCC
*
252142 AGCTATATTGGACTTAAAGATAAAGGTGCCAAT
66 AGCGATATTGGAC-T-----TAAAGGTGCCAAT
* * *
252175 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCC
* *
252240 AGCTATATTGGGCTTAGAAGG
66 AGCGATATTGGACTTA-AAGG
252261 GTTGCCACCG
Statistics
Matches: 619, Mismatches: 28, Indels: 17
0.93 0.04 0.03
Matches are distributed among these distances:
91 2 0.00
92 336 0.54
93 7 0.01
97 1 0.00
98 273 0.44
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCC
AGCGATATTGGACTTAAAGGTGCCAAT
Found at i:252298 original size:33 final size:35
Alignment explanation
Indices: 252255--252324 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 35
252245 TATTGGGCTT
252255 AGAAGGGTTGCCACCGACTTATGTAGGCTTT-GGA
1 AGAAGGGTTGCCACCGACTTATGTAGGCTTTAGGA
* *
252289 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AGAAGGGTTGCCACCGACTTATGTAGGCTTTAGGA
252323 AG
1 AG
252325 GGAGAAAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 24 0.73
34 9 0.27
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (35 bp):
AGAAGGGTTGCCACCGACTTATGTAGGCTTTAGGA
Found at i:252360 original size:34 final size:34
Alignment explanation
Indices: 252322--252847 Score: 403
Period size: 34 Copynumber: 15.9 Consensus size: 34
252312 GGGCTTTAGG
* * *
252322 AAGGGAGAAAGATACCACGGAGTTGTGGACTTAA
1 AAGGGAAAAAGATGCCACGGAGTTGTGGGCTTAA
252356 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAGGGAAAAAGA-TGCCACGGAGTTGTGGGC-TTAA
*
252392 AA-GAAAAAAG-TGCCACGGAGTTGTGGGCTTTGAA
1 AAGGGAAAAAGATGCCACGGAGTTGTGGGC-TT-AA
*
252426 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AAGGGAAAAAGA-TGCCACGGAGTTGTGGGCTTAA
** *
252461 AACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAA
1 AAGGGAAAAAGATGCCACGGAGTTGTGGGC-TTAA
* * *
252496 AA-AGAAAAAGGTGCCACGGAGTTGTGGACTTAA
1 AAGGGAAAAAGATGCCACGGAGTTGTGGGCTTAA
* * *
252529 AGATGAAAAAAG-TGCCACGGAGTTTTGGGCTTAA
1 A-AGGGAAAAAGATGCCACGGAGTTGTGGGCTTAA
* * *
252563 AA-GG-----G-TGCCACAGAGTTATGGGCTTAG
1 AAGGGAAAAAGATGCCACGGAGTTGTGGGCTTAA
* * * *
252590 AA-GGAAAAAGAGTGCCACGAAGTTGTGCGCATAG
1 AAGGGAAAAAGA-TGCCACGGAGTTGTGGGCTTAA
*
252624 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTT-T
1 AAGGGAAAAAGA-TGCCACGGAGTTGTGGGCTTAA
*
252657 AA---AAAGAG-TGCCACGGAGTTGTGGGCTTTGAA
1 AAGGGAAAAAGATGCCACGGAGTTGTGGGC-TT-AA
* *
252689 AA--GAAGAAGATGCCACGGAGTTGTGGGCTT-T
1 AAGGGAAAAAGATGCCACGGAGTTGTGGGCTTAA
* *
252720 AA---AAAGAG-TGCCACGGAGTTATGGGCTTTGAA
1 AAGGGAAAAAGATGCCACGGAGTTGTGGGC-TT-AA
* *
252752 AA--GAAGAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGGAAAAAGATGCCACGGAGTTGTGGGC-TT-AA
* * *
252786 AA--GAAGAAGGTGCCACGGAGTTGTGGGCTTTA
1 AAGGGAAAAAGATGCCACGGAGTTGTGGGCTTAA
*
252818 AA-GG-AAAAGGTGCCACGGAGTTGTGGGCTT
1 AAGGGAAAAAGATGCCACGGAGTTGTGGGCTT
252848 TGAAGAAAAA
Statistics
Matches: 423, Mismatches: 42, Indels: 56
0.81 0.08 0.11
Matches are distributed among these distances:
27 24 0.06
29 35 0.08
30 8 0.02
31 7 0.02
32 34 0.08
33 42 0.10
34 196 0.46
35 51 0.12
36 8 0.02
37 18 0.04
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (34 bp):
AAGGGAAAAAGATGCCACGGAGTTGTGGGCTTAA
Found at i:252572 original size:27 final size:27
Alignment explanation
Indices: 252540--252593 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
252530 GATGAAAAAA
* *
252540 GTGCCACGGAGTTTTGGGCTTAAAAGG
1 GTGCCACAGAGTTATGGGCTTAAAAGG
*
252567 GTGCCACAGAGTTATGGGCTTAGAAGG
1 GTGCCACAGAGTTATGGGCTTAAAAGG
252594 AAAAAGAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.24, C:0.15, G:0.37, T:0.24
Consensus pattern (27 bp):
GTGCCACAGAGTTATGGGCTTAAAAGG
Found at i:252665 original size:63 final size:63
Alignment explanation
Indices: 252594--252848 Score: 327
Period size: 63 Copynumber: 4.0 Consensus size: 63
252584 GCTTAGAAGG
* * * *
252594 AAAAAGAGTGCCACGAAGTTGTGCGCATAG-AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTT
* * *
252657 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGATGCCACGGAGTTGTGGGCTTT
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
* * *
252720 AAAAAGAGTGCCACGGAGTTATGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
* *
252783 GAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTT--TAAAGGAAAAGGTGCCACGGAGTTGTGGGC
1 --AAA-AAG-A-GTGCCACGGAGTTGTGGGCTTAGAAAAGAAAAAGGTGCCACGGAGTTGTGGGC
252846 TTT
61 TTT
252849 GAAGAAAAAA
Statistics
Matches: 173, Mismatches: 13, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
63 108 0.62
64 8 0.05
65 3 0.02
66 33 0.19
67 1 0.01
68 20 0.12
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (63 bp):
AAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
Found at i:252703 original size:97 final size:97
Alignment explanation
Indices: 252361--252881 Score: 559
Period size: 97 Copynumber: 5.3 Consensus size: 97
252351 CTTAAAAGGG
252361 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAA-AGTGCCACGGAGTTGTGGGCTTTG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGA-TGCCACGGAGTTGTGGGC-TT-
252424 AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
63 -AAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-A
* * * *
252462 ACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
1 A-A-AAAGA-GTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGATGCCACGGAGTTGTGGGCTT
*
252527 AAAGATGAAAAA-AGTGCCACGGAGTTTTGGGC-TT-
63 AAAG--GAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
* * * * * * * *
252561 -AAAAGGGTGCCACAGAGTTATGGGCTTAG-AAGGAAAAAGAGTGCCACGAAGTTGTGCGCATAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGA-TGCCACGGAGTTGTGGGCTTA-
252624 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-
64 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
*
252657 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGATGCCACGGAGTTGTGGGCTT---
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGATGCCACGGAGTTGTGGGCTTAAA
* *
252719 -TAAAAAGAGTGCCACGGAGTTATGGGCTTTGA
66 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-A
* *
252751 AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTT
1 AAA-AAG-A-GTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGATGCCACGGAGTTGTGGGC-T
252816 TAAAGG-AAAAG-GTGCCACGGAGTTGTGGGCTTTGA
62 TAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-A
* * * *
252851 AGAAAA-AATGCCACTGAGTCGTGGACTTTGA
1 A-AAAAGAGTGCCACGGAGTTGTGGGCTTTGA
252882 GACAAAATGC
Statistics
Matches: 361, Mismatches: 35, Indels: 52
0.81 0.08 0.12
Matches are distributed among these distances:
92 28 0.08
94 18 0.05
95 58 0.16
96 9 0.02
97 115 0.32
98 12 0.03
100 26 0.07
101 11 0.03
102 23 0.06
103 10 0.03
104 24 0.07
105 27 0.07
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (97 bp):
AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGATGCCACGGAGTTGTGGGCTTAAA
GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
Found at i:252931 original size:32 final size:31
Alignment explanation
Indices: 252629--253006 Score: 232
Period size: 31 Copynumber: 12.0 Consensus size: 31
252619 CATAGAAGGA
* * *
252629 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-
1 AAAAGA-TGCCACTGAGTCGTGGACTTTAAAG
* * * *
252660 AAGAG-TGCCACGGAGTTGTGGGCTTTGAAAAG
1 AAAAGATGCCACTGAGTCGTGGACTTT--AAAG
* * *
252692 AAGAAGATGCCACGGAGTTGTGGGCTTTAAA-
1 AA-AAGATGCCACTGAGTCGTGGACTTTAAAG
* * ** *
252723 AAGAG-TGCCACGGAGTTATGGGCTTTGAAAAG
1 AAAAGATGCCACTGAGTCGTGGACTTT--AAAG
* * * *
252755 AAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG
1 AA-AAGATGCCACTGAGTCGTGGACTTT--AAAG
* * * *
252789 AAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGG
1 AA-AAGATGCCACTGAGTCGTGGACTTTAAA-G
* * * * *
252822 AAAAGGTGCCACGGAGTTGTGGGCTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTAAAG
* *
252853 AAAAAATGCCACTGAGTCGTGGACTTT-GAG
1 AAAAGATGCCACTGAGTCGTGGACTTTAAAG
252883 ACAAA-ATGCCACTGAGTCGTGGACTTTAAAG
1 A-AAAGATGCCACTGAGTCGTGGACTTTAAAG
* *
252914 AAAAGGATGCCATTGAGTCGTGGACTTT-GAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTAAAG
* * *
252945 CAGAGATTGCCACTGAGTCGTGGACTTT-GAG
1 AAAAGA-TGCCACTGAGTCGTGGACTTTAAAG
* *
252976 AAGAGATTGCCACTGAGTCGTAGACTTTAAA
1 AAAAGA-TGCCACTGAGTCGTGGACTTTAAA
253007 AAGGTATTTG
Statistics
Matches: 308, Mismatches: 22, Indels: 33
0.85 0.06 0.09
Matches are distributed among these distances:
29 41 0.13
30 32 0.10
31 94 0.31
32 59 0.19
33 7 0.02
34 75 0.24
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (31 bp):
AAAAGATGCCACTGAGTCGTGGACTTTAAAG
Found at i:252942 original size:93 final size:94
Alignment explanation
Indices: 252624--253006 Score: 266
Period size: 97 Copynumber: 4.0 Consensus size: 94
252614 GTGCGCATAG
* * * * * *
252624 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-A--AAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAGG-AAAAG-GTGCCACGGAGTCGTGGACTTTGAGCAAAA-AATGCCACTGAGTCGTGGACTTT
* * * *
252686 GAAAAGAAGAAGATGCCACGGAGTTGTGGGCTTTA
63 GAGAAG-AG-A-ATGCCACTGAGTCGTGGACTTTA
* ** * * * * *
252721 AA--AAGA-GTGCCACGGAGTTATGGGCTTTGA-AAAGAAGAAGGTGCCACGGAGTTGTGGGCTT
1 AAGGAAAAGGTGCCACGGAGTCGTGGACTTTGAGCAA-AA-AA--TGCCACTGAGTCGTGGACTT
* * * *
252782 TGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTA
62 TGAGAAG-AGAA--TGCCACTGAGTCGTGGACTTTA
* *
252818 AAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAG-AAAAAATGCCACTGAGTCGTGGACTTTGA
1 AAGGAAAAGGTGCCACGGAGTCGTGGACTTTG-AGCAAAAAATGCCACTGAGTCGTGGACTTTGA
252882 GACA-A-AATGCCACTGAGTCGTGGACTTTA
65 GA-AGAGAATGCCACTGAGTCGTGGACTTTA
** * * *
252911 AA-GAAAAGGATGCCATTGAGTCGTGGACTTTGAGCAGAGATTGCCACTGAGTCGTGGACTTTGA
1 AAGGAAAAGG-TGCCACGGAGTCGTGGACTTTGAGCAAAAAATGCCACTGAGTCGTGGACTTTGA
* *
252975 GAAGAGATTGCCACTGAGTCGTAGACTTTA
65 GAAGAGAATGCCACTGAGTCGTGGACTTTA
253005 AA
1 AA
253007 AAGGTATTTG
Statistics
Matches: 248, Mismatches: 21, Indels: 37
0.81 0.07 0.12
Matches are distributed among these distances:
92 31 0.12
93 69 0.28
94 29 0.12
95 7 0.03
96 2 0.01
97 77 0.31
98 1 0.00
99 5 0.02
100 24 0.10
101 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.33, T:0.23
Consensus pattern (94 bp):
AAGGAAAAGGTGCCACGGAGTCGTGGACTTTGAGCAAAAAATGCCACTGAGTCGTGGACTTTGAG
AAGAGAATGCCACTGAGTCGTGGACTTTA
Found at i:253585 original size:13 final size:13
Alignment explanation
Indices: 253567--253591 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
253557 CAAAGATCAG
253567 TGTATCGATACAA
1 TGTATCGATACAA
253580 TGTATCGATACA
1 TGTATCGATACA
253592 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:253659 original size:20 final size:20
Alignment explanation
Indices: 253630--253687 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
253620 GCAGTAGCTT
253630 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
253649 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
253669 TTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
253688 TTGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:254131 original size:87 final size:88
Alignment explanation
Indices: 253982--254291 Score: 250
Period size: 88 Copynumber: 3.5 Consensus size: 88
253972 TCTACAGATG
* * * * *
253982 CAAATACCAATGTCATGTAAAATATAGATGTGCGTGAAATTATGCAAATGCAAGCATTAATAAAA
1 CAAATACCAATGTCATCTAAAATATAGATATGCATGAAATAATGCAAATGCAAGCATCAATAAAA
* * *
254047 TGGCAAATGCCTATGAAATGATA
66 TGACAAATGCATATAAAATGATA
* * * * *
254070 CAAATACCAATGTCAT-TAAAGTATATATATGCATGAAATAATGCAACTGCATGCATCAATAAAG
1 CAAATACCAATGTCATCTAAAATATAGATATGCATGAAATAATGCAAATGCAAGCATCAATAAAA
*
254134 TGACAAATGCATATAAAATGATG
66 TGACAAATGCATATAAAATGATA
** * * * * ** * *
254157 CAAATGTCAATGTCATCTAAAATACAAATAT-AAGTGAAA-AGATGTAGTTACAAGCATTAATAA
1 CAAATACCAATGTCATCTAAAATATAGATATGCA-TGAAATA-ATGCAAATGCAAGCATCAATAA
* * *
254220 AGATG-CAAATGCACATGAAATGATG
64 A-ATGACAAATGCATATAAAATGATA
* * * ** * * *
254245 CAAATGCTAATGTTATCTAAAATGCAAATATGCATGAACTGATGCAA
1 CAAATACCAATGTCATCTAAAATATAGATATGCATGAAATAATGCAA
254292 TGAAATAATG
Statistics
Matches: 179, Mismatches: 37, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
87 74 0.41
88 102 0.57
89 3 0.02
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.26
Consensus pattern (88 bp):
CAAATACCAATGTCATCTAAAATATAGATATGCATGAAATAATGCAAATGCAAGCATCAATAAAA
TGACAAATGCATATAAAATGATA
Found at i:255019 original size:109 final size:107
Alignment explanation
Indices: 254893--255112 Score: 246
Period size: 108 Copynumber: 2.0 Consensus size: 107
254883 AATCTGACAT
* * * ** *
254893 TGTTGGCTCAAAATTTCAAAATTGATAAGATACATGCCTCACCTTCCTAGGTACGAATGAATCAG
1 TGTTGGCTCAAAATTTCAAAACTAATAAGATACAAGCC-CACCTTCCTAGACACAAATGAAT-AG
*
254958 -GTTGTATGAA-ACATGAATTTCTTTGAAAATTAGACAAATTTGA
64 TCTTGTAT-AAGACATGAATTTCTTTGAAAATTAGACAAATTTGA
** ** *** * *
255001 TGTTGGCTCAATTTTTTCAAAACTAATTGGATACAAGCCCTGTTTCCTAGACACAAATGGATTGT
1 TGTTGGCTCAA-AATTTCAAAACTAATAAGATACAAGCCCACCTTCCTAGACACAAATGAATAGT
255066 CTTGTATAAGACATGAATTTCTTTGAAAATTAGACAAATTTGA
65 CTTGTATAAGACATGAATTTCTTTGAAAATTAGACAAATTTGA
255109 TGTT
1 TGTT
255113 CTTCAAGTCC
Statistics
Matches: 93, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
107 3 0.03
108 70 0.75
109 20 0.22
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (107 bp):
TGTTGGCTCAAAATTTCAAAACTAATAAGATACAAGCCCACCTTCCTAGACACAAATGAATAGTC
TTGTATAAGACATGAATTTCTTTGAAAATTAGACAAATTTGA
Found at i:255397 original size:16 final size:15
Alignment explanation
Indices: 255372--255405 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
255362 AGCTTCATTC
255372 TTTTCATTTTTTTCTT
1 TTTTCATTTTTTT-TT
255388 TTTTC-TTTTTTTTT
1 TTTTCATTTTTTTTT
255402 TTTT
1 TTTT
255406 GATTGCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 7 0.39
16 5 0.28
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTCATTTTTTTTT
Found at i:258614 original size:161 final size:161
Alignment explanation
Indices: 258168--258626 Score: 482
Period size: 166 Copynumber: 2.8 Consensus size: 161
258158 ATTCCTCATA
* * * *
258168 TTTTTAAATTACAGG-GTTTTCTTCTCCGTAAATTTTTTTAG-GAGTATTTTTCTTAATTTTTAA
1 TTTTTAAAATA-AGGTGTTTTCTACTCCGTAAATTTTTTCAGAGAG-A--TTTCTTAGTTTTTAA
* * * *
258231 TTTTTAAAATTCATCAAACATTATCATTTATTTCATATTAATTTAGTTTTTAAAAATTCATTCAT
62 TTTTTAAAATTCATCAAATATCATTATTTA-TTCATATTAATTTAGTTTTCAAAAATTCATTCAT
*
258296 TTTCATGAGTTTTTTATTTTTTCCTTGAAATTCTCCTT
126 TTTCATGA--TATTTATTTTTTCCTTGAAATTCTCCTT
* * *
258334 TTTTTGAAATATGGTGTTTTCTACTCCGTAAATTTTTTCAGAGAGATTT-TTCCTGTTTTTCAAT
1 TTTTTAAAATAAGGTGTTTTCTACTCCGTAAATTTTTTCAGAGAGATTTCTT--AGTTTTT-AAT
*
258398 TTTTAAAATTCATCAAATGTCATTATTTGATTCATATTAATTTAGTTTTCAAAAATTCA-TCTAT
63 TTTTAAAATTCATCAAATATCATTATTT-ATTCATATTAATTTAGTTTTCAAAAATTCATTC-AT
* *
258462 TTTTATGA-ATTT-TTTTTTCCTTGAAACTTC-CTTT
126 TTTCATGATATTTATTTTTTCCTTGAAA-TTCTCCTT
* * * *
258496 TTTTTCAAAATAAGGTGTTTTCTACTCCGTGAATTTTTTCGGAGGGGTTTCTTAGTTTTTAATTT
1 TTTTT-AAAATAAGGTGTTTTCTACTCCGTAAATTTTTTCAGAGAGATTTCTTAGTTTTTAATTT
* * * * * * * * *
258561 TCAAAATTCATCAAATACCATTATTTATATCAGAGTAAATCAGTTTCCAAAAATTCCTTCGTTTT
65 TTAAAATTCATCAAATATCATTATTTAT-TCATATTAATTTAGTTTTCAAAAATTCATTCATTTT
258626 C
129 C
258627 TTAAATTTTT
Statistics
Matches: 248, Mismatches: 33, Indels: 29
0.80 0.11 0.09
Matches are distributed among these distances:
160 2 0.01
161 54 0.22
162 30 0.12
163 46 0.19
164 5 0.02
165 9 0.04
166 98 0.40
167 4 0.02
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (161 bp):
TTTTTAAAATAAGGTGTTTTCTACTCCGTAAATTTTTTCAGAGAGATTTCTTAGTTTTTAATTTT
TAAAATTCATCAAATATCATTATTTATTCATATTAATTTAGTTTTCAAAAATTCATTCATTTTCA
TGATATTTATTTTTTCCTTGAAATTCTCCTT
Found at i:258969 original size:5 final size:5
Alignment explanation
Indices: 258959--258983 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
258949 GAATTTTTGG
258959 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
258984 TTTATTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:259333 original size:25 final size:25
Alignment explanation
Indices: 259305--259354 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
259295 AAACTTAGCT
259305 GAAAAGAGAGAA-AAAAA-AGAAGAAA
1 GAAAAGAGA-AAGAAAAATAG-AGAAA
259330 GAAAAGAGAAAGAAAAATAGAGAAA
1 GAAAAGAGAAAGAAAAATAGAGAAA
259355 ATAGGTAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 2 0.09
25 19 0.83
26 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (25 bp):
GAAAAGAGAAAGAAAAATAGAGAAA
Found at i:259339 original size:14 final size:13
Alignment explanation
Indices: 259306--259353 Score: 55
Period size: 12 Copynumber: 3.7 Consensus size: 13
259296 AACTTAGCTG
259306 AAAAGAG-AGAAA
1 AAAAGAGAAGAAA
259318 AAAA-AGAAGAAA
1 AAAAGAGAAGAAA
259330 GAAAAGAGAAAGAAA
1 -AAAAGAG-AAGAAA
*
259345 AATAGAGAA
1 AAAAGAGAA
259354 AATAGGTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 2 0.06
12 9 0.29
13 6 0.19
14 8 0.26
15 6 0.19
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (13 bp):
AAAAGAGAAGAAA
Found at i:259354 original size:14 final size:14
Alignment explanation
Indices: 259306--259354 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 14
259296 AACTTAGCTG
259306 AAAAGAGAGAAA-A
1 AAAAGAGAGAAAGA
259319 AAAAGA-AGAAAG-
1 AAAAGAGAGAAAGA
259331 -AAA-AGAGAAAGA
1 AAAAGAGAGAAAGA
*
259343 AAAATAGAGAAA
1 AAAAGAGAGAAA
259355 ATAGGTAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
10 1 0.03
11 9 0.29
12 5 0.16
13 9 0.29
14 7 0.23
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (14 bp):
AAAAGAGAGAAAGA
Found at i:266966 original size:22 final size:20
Alignment explanation
Indices: 266932--266985 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
266922 TCTGGTGGCC
266932 TTTAGCTGCTGCCAGCAGCTCG
1 TTTAG-TGCTGCCAGCAGCT-G
*
266954 TTTCAGTGCTGCCAGCTGCTG
1 TTT-AGTGCTGCCAGCAGCTG
*
266975 TTTTGTGCTGC
1 TTTAGTGCTGC
266986 TGCCACCAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 7 0.24
21 4 0.14
22 16 0.55
23 2 0.07
ACGTcount: A:0.09, C:0.28, G:0.28, T:0.35
Consensus pattern (20 bp):
TTTAGTGCTGCCAGCAGCTG
Found at i:270552 original size:3 final size:3
Alignment explanation
Indices: 270538--270568 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
270528 ACCATCAATA
*
270538 ATG ATG AAG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
270569 AGTTGACTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:271520 original size:32 final size:32
Alignment explanation
Indices: 271482--271610 Score: 240
Period size: 32 Copynumber: 4.0 Consensus size: 32
271472 AATCTCATTT
271482 TCACTGTTCATGTATCGATACATCACTGTTCA
1 TCACTGTTCATGTATCGATACATCACTGTTCA
*
271514 TAACTGTTCATGTATCGATACATCACTGTTCA
1 TCACTGTTCATGTATCGATACATCACTGTTCA
271546 TCACTGTTCATGTATCGATACATCACTGTTCA
1 TCACTGTTCATGTATCGATACATCACTGTTCA
*
271578 TCACTATTCATGTATCGATACATCACTGTTCA
1 TCACTGTTCATGTATCGATACATCACTGTTCA
271610 T
1 T
271611 GTATCGATAA
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 94 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (32 bp):
TCACTGTTCATGTATCGATACATCACTGTTCA
Found at i:271604 original size:22 final size:22
Alignment explanation
Indices: 271576--271629 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
271566 CATCACTGTT
271576 CATCACTATTCATGTATCGATA
1 CATCACTATTCATGTATCGATA
*
271598 CATCACTGTTCATGTATCGATA
1 CATCACTATTCATGTATCGATA
*
271620 AATCACTATT
1 CATCACTATT
271630 TATCACTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.37
Consensus pattern (22 bp):
CATCACTATTCATGTATCGATA
Found at i:271604 original size:54 final size:54
Alignment explanation
Indices: 271544--271654 Score: 177
Period size: 54 Copynumber: 2.1 Consensus size: 54
271534 CATCACTGTT
* *
271544 CATCACTGTTCATGTATCGATACATCACTGTTCATCACTATTCATGTATCGATA
1 CATCACTGTTCATGTATCGATAAATCACTATTCATCACTATTCATGTATCGATA
* * *
271598 CATCACTGTTCATGTATCGATAAATCACTATTTATCACTGTTCATGTATTGATA
1 CATCACTGTTCATGTATCGATAAATCACTATTCATCACTATTCATGTATCGATA
271652 CAT
1 CAT
271655 TGTATCGATA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.39
Consensus pattern (54 bp):
CATCACTGTTCATGTATCGATAAATCACTATTCATCACTATTCATGTATCGATA
Found at i:276413 original size:13 final size:13
Alignment explanation
Indices: 276395--276419 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
276385 CATAAAGTGT
276395 TGTATCGATACAA
1 TGTATCGATACAA
276408 TGTATCGATACA
1 TGTATCGATACA
276420 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:276435 original size:32 final size:33
Alignment explanation
Indices: 276375--276443 Score: 122
Period size: 32 Copynumber: 2.1 Consensus size: 33
276365 TTCAACGATT
*
276375 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTATTGTATCGATACAA
276408 TGTATCGATACAT-AAGTATTGTATCGATACAA
1 TGTATCGATACATAAAGTATTGTATCGATACAA
276440 TGTA
1 TGTA
276444 AGCTACTGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 22 0.63
33 13 0.37
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATAAAGTATTGTATCGATACAA
Found at i:276499 original size:13 final size:13
Alignment explanation
Indices: 276481--276505 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
276471 ATTACTCAAA
276481 TGTATCGATACAT
1 TGTATCGATACAT
276494 TGTATCGATACA
1 TGTATCGATACA
276506 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:276556 original size:52 final size:52
Alignment explanation
Indices: 276514--276642 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
276504 CACTGATCTT
*
276514 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
276566 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
276618 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
276643 TCATATTTCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:290511 original size:11 final size:11
Alignment explanation
Indices: 290497--290566 Score: 81
Period size: 11 Copynumber: 6.2 Consensus size: 11
290487 AAAAAGAAGA
290497 AAAAACAAAAC
1 AAAAACAAAAC
290508 AAAAACAAAAAAC
1 AAAAAC--AAAAC
290521 AAAAACAAAAC
1 AAAAACAAAAC
*
290532 AAAAA-ACAAAG
1 AAAAACA-AAAC
290543 AAAAA-AAAAC
1 AAAAACAAAAC
290553 AAAAACAACAAC
1 AAAAACAA-AAC
290565 AA
1 AA
290567 CAAAAAGGGT
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
10 9 0.17
11 27 0.52
12 5 0.10
13 11 0.21
ACGTcount: A:0.83, C:0.16, G:0.01, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:290512 original size:6 final size:6
Alignment explanation
Indices: 290480--290566 Score: 72
Period size: 6 Copynumber: 14.0 Consensus size: 6
290470 AAAACCAAAT
*
290480 AAACAA AAA-AA AGAAGAA AAA-ACA AAACAA AAACAAA AAACAA AAAC-A
1 AAACAA AAACAA A-AACAA AAACA-A AAACAA AAAC-AA AAACAA AAACAA
* *
290528 AAACAAA AAACAAA GAAAAAA AAACAA AAACAA CAACAA
1 AAAC-AA AAAC-AA -AAACAA AAACAA AAACAA AAACAA
290567 CAAAAAGGGT
Statistics
Matches: 70, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
5 9 0.13
6 38 0.54
7 20 0.29
8 3 0.04
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (6 bp):
AAACAA
Done.