Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 112 of 126
Found at i:34390313 original size:41 final size:42
Alignment explanation
Indices: 34390252--34390402 Score: 168
Period size: 41 Copynumber: 3.7 Consensus size: 42
34390242 CATAATTTAA
34390252 CATATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGA-TT
1 CATA-TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTT
* * *
34390294 CATATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTT
1 CATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTT
* * * **
34390336 C-GATCACCGGCACTTAGCCTGCTAGACTTATAGTCTGA-AA
1 CATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTT
*
34390376 AAT-TCACCGGCA-TTAAGCCTGCTAGGC
1 CATATCACCGGCACTT-AGCCTGCTAGGC
34390403 GCTTAGCCTG
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
39 2 0.02
40 20 0.22
41 63 0.68
42 7 0.08
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (42 bp):
CATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTT
Found at i:34390414 original size:40 final size:40
Alignment explanation
Indices: 34390255--34390421 Score: 115
Period size: 41 Copynumber: 4.1 Consensus size: 40
34390245 AATTTAACAT
* * ***
34390255 ATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTC
1 ATTCACCGGCACTTAGCCTGCTAGACCTATAGCCTGAAAA
* *** * ***
34390295 ATATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTTCG
1 AT-TCACCGGCACTTAGCCTGCTAGACCTATAGCCTGA--AAA
* *
34390338 A-TCACCGGCACTTAGCCTGCTAGACTTATAGTCTGAAAA
1 ATTCACCGGCACTTAGCCTGCTAGACCTATAGCCTGAAAA
*
34390377 ATTCACCGGCA-TTAAGCCTGCTAGGCGCT-TAGCCTGAAAA
1 ATTCACCGGCACTT-AGCCTGCTAGAC-CTATAGCCTGAAAA
*
34390417 TTTCA
1 ATTCA
34390422 ATTTCACAGA
Statistics
Matches: 104, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
39 3 0.03
40 36 0.35
41 63 0.61
43 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (40 bp):
ATTCACCGGCACTTAGCCTGCTAGACCTATAGCCTGAAAA
Found at i:34390871 original size:76 final size:66
Alignment explanation
Indices: 34390762--34390918 Score: 161
Period size: 70 Copynumber: 2.2 Consensus size: 66
34390752 TTATACCTAT
* *
34390762 ATATACATATATATATATTTAAACCTTATATATATAAATATATCGTCCATACCTTTAATTAAATT
1 ATATACATATATATATATTTAAACCTTATATATAT-AACAT-TC-T---TACCTTTAACTAAATT
34390827 CAAAATC
60 CAAAATC
* * * *
34390834 TTATACATATATATATACATTTTCGAATCTTATATATATAACATTCTTACCTTTAACTAAATTTA
1 ATATACATATATATAT--A-TTT-AAACCTTATATATATAACATTCTTACCTTTAACTAAATTCA
*
34390899 AGATC
62 AAATC
34390904 ATATACATATATATA
1 ATATACATATATATA
34390919 CATGTTCGAA
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
70 34 0.47
72 15 0.21
73 1 0.01
74 3 0.04
75 7 0.10
76 13 0.18
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.42
Consensus pattern (66 bp):
ATATACATATATATATATTTAAACCTTATATATATAACATTCTTACCTTTAACTAAATTCAAAAT
C
Found at i:34392222 original size:13 final size:13
Alignment explanation
Indices: 34392204--34392228 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34392194 CAATCAAATG
34392204 CACACAAAATAAA
1 CACACAAAATAAA
34392217 CACACAAAATAA
1 CACACAAAATAA
34392229 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:34396057 original size:72 final size:71
Alignment explanation
Indices: 34395936--34396082 Score: 249
Period size: 72 Copynumber: 2.1 Consensus size: 71
34395926 ACCAATGCAA
* * *
34395936 AAAGGTTGTGGAATATTACAAGGTTTGACCTTTACTTACCCCAAATAGCAGATATAATCACAATA
1 AAAGGTCGTGGAATATTACAAAGTTTGAACTTTACTTACCCCAAATAGCAGATATAATCACAATA
34396001 ATAACAT
66 ATAAC-T
*
34396008 AAAGGTCGTGGAATATTACAAAGTTTGAACTTTACTTACCCCAATTAGCAGATATAATCACAATA
1 AAAGGTCGTGGAATATTACAAAGTTTGAACTTTACTTACCCCAAATAGCAGATATAATCACAATA
34396073 ATAACT
66 ATAACT
34396079 AAAG
1 AAAG
34396083 CAAAAAAGTG
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
71 5 0.07
72 66 0.93
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (71 bp):
AAAGGTCGTGGAATATTACAAAGTTTGAACTTTACTTACCCCAAATAGCAGATATAATCACAATA
ATAACT
Found at i:34396899 original size:18 final size:18
Alignment explanation
Indices: 34396876--34396912 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
34396866 TGGAATTTTC
34396876 TTGCTAATCTAGGACAGG
1 TTGCTAATCTAGGACAGG
34396894 TTGCTAATCTAGGACAGG
1 TTGCTAATCTAGGACAGG
34396912 T
1 T
34396913 CGGATTTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (18 bp):
TTGCTAATCTAGGACAGG
Found at i:34409646 original size:51 final size:51
Alignment explanation
Indices: 34409587--34409690 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
34409577 AAATGAAAAT
34409587 GAGAAATAATTCATTTGCAAATGAACACGGATTTCTCAAAAGTGATCGGAA
1 GAGAAATAATTCATTTGCAAATGAACACGGATTTCTCAAAAGTGATCGGAA
*
34409638 GAGAAATAATTCATTTGCAAATGAACACGGATTTCTCAAAAGTGATCTGAA
1 GAGAAATAATTCATTTGCAAATGAACACGGATTTCTCAAAAGTGATCGGAA
34409689 GA
1 GA
34409691 ATGATTTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.26
Consensus pattern (51 bp):
GAGAAATAATTCATTTGCAAATGAACACGGATTTCTCAAAAGTGATCGGAA
Found at i:34412694 original size:36 final size:36
Alignment explanation
Indices: 34412654--34412729 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
34412644 CATTAACAGG
* * *
34412654 AAACCTAGAATCTAGAAGTTTCCTCCCTTACACCTC
1 AAACCTAAAATCTAGAACTTTCCTCCCTTACACCTA
34412690 AAACCTAAAATCTAGAACTTTCCTCCCTTACACCTA
1 AAACCTAAAATCTAGAACTTTCCTCCCTTACACCTA
34412726 AAAC
1 AAAC
34412730 TGACCCTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.33, G:0.05, T:0.26
Consensus pattern (36 bp):
AAACCTAAAATCTAGAACTTTCCTCCCTTACACCTA
Found at i:34420021 original size:31 final size:31
Alignment explanation
Indices: 34419983--34420045 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
34419973 ATGCATACAG
34419983 ATAATCAACAAAATTTAGTTAGATATAGTCT
1 ATAATCAACAAAATTTAGTTAGATATAGTCT
34420014 ATAATCAACAAAATTTAGTTAGATATAGTCT
1 ATAATCAACAAAATTTAGTTAGATATAGTCT
34420045 A
1 A
34420046 GCACCCGTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.35
Consensus pattern (31 bp):
ATAATCAACAAAATTTAGTTAGATATAGTCT
Found at i:34421961 original size:29 final size:31
Alignment explanation
Indices: 34421914--34421980 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
34421904 CTGCCCAAGA
* **
34421914 GTAAATACTCAAAATTTGAAGGGTCAA-AGT
1 GTAAATACTCAAAAGTTGAAGGACCAATAGT
*
34421944 GTAAATAC-GAAAAGTTGAAGGACCAATAGT
1 GTAAATACTCAAAAGTTGAAGGACCAATAGT
34421974 GTAAATA
1 GTAAATA
34421981 TTTTAAGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.24
Consensus pattern (31 bp):
GTAAATACTCAAAAGTTGAAGGACCAATAGT
Found at i:34425116 original size:5 final size:5
Alignment explanation
Indices: 34425106--34425212 Score: 57
Period size: 5 Copynumber: 22.4 Consensus size: 5
34425096 TGATCAAGTA
* * * * * *
34425106 AAATT AAATT -AATC AAATT -AATT TAATT TAATT TAATT TAATC AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT
* * * *
34425154 -AATT AAATT -AATC AAGTA AAATT AAATT -AATC AAATT -AATT AAAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT -AAATT
34425201 AAAATT -AATT AA
1 -AAATT AAATT AA
34425213 GTCAAACAAT
Statistics
Matches: 82, Mismatches: 12, Indels: 16
0.75 0.11 0.15
Matches are distributed among these distances:
4 25 0.30
5 47 0.57
6 10 0.12
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:34425125 original size:9 final size:9
Alignment explanation
Indices: 34425111--34425193 Score: 67
Period size: 9 Copynumber: 8.9 Consensus size: 9
34425101 AAGTAAAATT
34425111 AAATTAATC
1 AAATTAATC
*
34425120 AAATTAATTT
1 AAATTAA-TC
* *
34425130 AATTTAATTT
1 AAATTAA-TC
*
34425140 AATTTAATC
1 AAATTAATC
*
34425149 AAATTAATT
1 AAATTAATC
34425158 AAATTAATC
1 AAATTAATC
* * *
34425167 AAGTAAAATT
1 AAAT-TAATC
34425177 AAATTAATC
1 AAATTAATC
34425186 AAATTAAT
1 AAATTAAT
34425194 TAAAATTAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
9 37 0.62
10 23 0.38
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (9 bp):
AAATTAATC
Found at i:34425131 original size:19 final size:18
Alignment explanation
Indices: 34425111--34425202 Score: 94
Period size: 19 Copynumber: 4.9 Consensus size: 18
34425101 AAGTAAAATT
* *
34425111 AAATTAATCAAATTAATTT
1 AAATTAATTAAATTAA-TC
* *
34425130 AATTTAATTTAATTTAATC
1 AAATTAA-TTAAATTAATC
34425149 AAATTAATTAAATTAATC
1 AAATTAATTAAATTAATC
* *
34425167 AAGTAAAATTAAATTAATC
1 AAAT-TAATTAAATTAATC
34425186 AAATTAATTAAAATTAA
1 AAATTAATT-AAATTAA
34425203 AATTAATTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
18 17 0.28
19 36 0.60
20 7 0.12
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (18 bp):
AAATTAATTAAATTAATC
Found at i:34425136 original size:24 final size:23
Alignment explanation
Indices: 34425107--34425209 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 23
34425097 GATCAAGTAA
34425107 AATTAAATTAATCAAATTAATTT
1 AATTAAATTAATCAAATTAATTT
* ** * *
34425130 AATTTAATTTAATTTAATCAAATT
1 AA-TTAAATTAATCAAATTAATTT
*
34425154 AATTAAATTAATC-AAGTAA---
1 AATTAAATTAATCAAATTAATTT
*
34425173 AATTAAATTAATCAAATTAATTAA
1 AATTAAATTAATCAAATTAATT-T
34425197 AATTAAAATTAAT
1 AATT-AAATTAAT
34425210 TAAGTCAAAC
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
19 13 0.21
20 5 0.08
22 4 0.06
23 11 0.17
24 22 0.35
25 8 0.13
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (23 bp):
AATTAAATTAATCAAATTAATTT
Found at i:34430957 original size:25 final size:26
Alignment explanation
Indices: 34430897--34430973 Score: 67
Period size: 25 Copynumber: 3.1 Consensus size: 26
34430887 AGTTCAAGCA
*
34430897 AGCCA-ATAT-GGAGAAGCTCTAGAG
1 AGCCATATATCGGAGAAGCTCTAAAG
*
34430921 AGCCAT-TAATCGG-GAAGTTCTAAAG
1 AGCCATAT-ATCGGAGAAGCTCTAAAG
*
34430946 AGCCATATATC-GAGACGCTC-ATAAG
1 AGCCATATATCGGAGAAGCTCTA-AAG
34430971 AGC
1 AGC
34430974 TGTGGTGTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
24 8 0.19
25 32 0.74
26 3 0.07
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.19
Consensus pattern (26 bp):
AGCCATATATCGGAGAAGCTCTAAAG
Found at i:34434353 original size:31 final size:31
Alignment explanation
Indices: 34434318--34434377 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
34434308 GATCATATTG
34434318 ACAAGGAAAATATTAAAGGTTCAGAGGTCAC
1 ACAAGGAAAATATTAAAGGTTCAGAGGTCAC
34434349 ACAAGGAAAATATTAAAGGTTCAGAGGTC
1 ACAAGGAAAATATTAAAGGTTCAGAGGTC
34434378 TTTGAGGCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.45, C:0.12, G:0.23, T:0.20
Consensus pattern (31 bp):
ACAAGGAAAATATTAAAGGTTCAGAGGTCAC
Found at i:34442650 original size:32 final size:30
Alignment explanation
Indices: 34442573--34442652 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 30
34442563 TGTTTAAGAG
* * *
34442573 TTAATAGAGGTATTTTAAGTAGTATAAATAA
1 TTAATAG-GGTATTTTAAATAATATAAAAAA
34442604 TTAATAAGGGTATTTTAAATAATATAAAAAAA
1 TTAAT-AGGGTATTTTAAATAATAT-AAAAAA
34442636 TTAATAGGGATATTTTA
1 TTAATAGGG-TATTTTA
34442653 GGTTAGTTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
31 24 0.56
32 19 0.44
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (30 bp):
TTAATAGGGTATTTTAAATAATATAAAAAA
Found at i:34447400 original size:14 final size:14
Alignment explanation
Indices: 34447378--34447407 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
34447368 TTCGCGTATA
34447378 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
*
34447392 AAAAGTAAAAAAAT
1 AAAAATAAAAAAAT
34447406 AA
1 AA
34447408 TGAAACGAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:34449720 original size:6 final size:6
Alignment explanation
Indices: 34449709--34449736 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
34449699 TTTTATGCCC
34449709 ATGATA ATGATA ATGATA ATGATA ATGA
1 ATGATA ATGATA ATGATA ATGATA ATGA
34449737 ATTTCATGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (6 bp):
ATGATA
Found at i:34454193 original size:7 final size:7
Alignment explanation
Indices: 34454176--34454214 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
34454166 TTCAATGGAT
34454176 TGATG-C
1 TGATGAC
34454182 TGATGAC
1 TGATGAC
34454189 TGATGAC
1 TGATGAC
34454196 TGATGAC
1 TGATGAC
*
34454203 TGATGAA
1 TGATGAC
34454210 TGATG
1 TGATG
34454215 TATTACTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.28, C:0.10, G:0.31, T:0.31
Consensus pattern (7 bp):
TGATGAC
Found at i:34456708 original size:16 final size:16
Alignment explanation
Indices: 34456687--34456717 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
34456677 TGACCATATT
34456687 TGCTGCTTCTTTGTTC
1 TGCTGCTTCTTTGTTC
34456703 TGCTGCTTCTTTGTT
1 TGCTGCTTCTTTGTT
34456718 TTGCAATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.23, G:0.19, T:0.58
Consensus pattern (16 bp):
TGCTGCTTCTTTGTTC
Found at i:34457649 original size:13 final size:13
Alignment explanation
Indices: 34457631--34457658 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
34457621 CAAGGCTAGA
34457631 CATAACTAATTAT
1 CATAACTAATTAT
34457644 CATAACTAATTAT
1 CATAACTAATTAT
34457657 CA
1 CA
34457659 CTAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (13 bp):
CATAACTAATTAT
Found at i:34462580 original size:28 final size:29
Alignment explanation
Indices: 34462549--34462622 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 29
34462539 AGAATTTTTT
*
34462549 TATTATATTTAATGTAATTTAATTTAA-A
1 TATTATATTTAATATAATTTAATTTAATA
* * *
34462577 TATTTTA-TTGATATATTTTAATTTAATA
1 TATTATATTTAATATAATTTAATTTAATA
34462605 TATTATATTATATATATA
1 TATTATATT-TA-ATATA
34462623 TAGGCGGATA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
27 16 0.44
28 13 0.36
29 1 0.03
30 1 0.03
31 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (29 bp):
TATTATATTTAATATAATTTAATTTAATA
Found at i:34462601 original size:27 final size:27
Alignment explanation
Indices: 34462566--34462619 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
34462556 TTTAATGTAA
*
34462566 TTTAATTTAA-ATATTTTATTGATATAT
1 TTTAATTTAATATATTATATT-ATATAT
34462593 TTTAATTTAATATATTATATTATATAT
1 TTTAATTTAATATATTATATTATATAT
34462620 ATATAGGCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTAATTTAATATATTATATTATATAT
Found at i:34462607 original size:15 final size:15
Alignment explanation
Indices: 34462555--34462608 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
34462545 TTTTTATTAT
* *
34462555 ATTTAATGTAATTTA
1 ATTTAATATATTTTA
34462570 ATTTAA-ATATTTT-
1 ATTTAATATATTTTA
*
34462583 A-TTGATATATTTTA
1 ATTTAATATATTTTA
34462597 ATTTAATATATT
1 ATTTAATATATT
34462609 ATATTATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
12 3 0.09
13 8 0.25
14 6 0.19
15 15 0.47
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (15 bp):
ATTTAATATATTTTA
Found at i:34463491 original size:18 final size:18
Alignment explanation
Indices: 34463468--34463505 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
34463458 TCGAGATATG
34463468 CGGCTTCTGTTAGACCAA
1 CGGCTTCTGTTAGACCAA
34463486 CGGCTTCTGTTAGACCAA
1 CGGCTTCTGTTAGACCAA
34463504 CG
1 CG
34463506 ATCGGAAGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (18 bp):
CGGCTTCTGTTAGACCAA
Found at i:34472579 original size:34 final size:34
Alignment explanation
Indices: 34472505--34472591 Score: 79
Period size: 34 Copynumber: 2.6 Consensus size: 34
34472495 AAGTTTTTAC
* * * * * *
34472505 AAATTTTATAACAATATTGTTTTATAAAATTTTTA
1 AAATTTT-TAATAATTTTTTTTTAGAAAATATATA
*
34472540 TAATTTTTAATAATTTTTTTTTAGAAAATATATA
1 AAATTTTTAATAATTTTTTTTTAGAAAATATATA
*
34472574 AAA--TTTAATAAATTTTTT
1 AAATTTTTAATAATTTTTTT
34472592 ATTAATAATT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
32 14 0.33
34 23 0.53
35 6 0.14
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (34 bp):
AAATTTTTAATAATTTTTTTTTAGAAAATATATA
Found at i:34482382 original size:30 final size:29
Alignment explanation
Indices: 34482348--34482425 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 29
34482338 TCAATATTCA
34482348 TATTTTCACTATCATACC-TGTAATCACTCT
1 TATTTTCACTATCATACCTTGTAATCA-T-T
* * *
34482378 TATTTGCATTTTCATACCTTGTAATCATT
1 TATTTTCACTATCATACCTTGTAATCATT
34482407 TACATTTTC-CTATCATACC
1 T--ATTTTCACTATCATACC
34482426 CTGTGTTCGT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 2 0.05
30 24 0.62
31 13 0.33
ACGTcount: A:0.26, C:0.24, G:0.04, T:0.46
Consensus pattern (29 bp):
TATTTTCACTATCATACCTTGTAATCATT
Found at i:34486743 original size:28 final size:28
Alignment explanation
Indices: 34486711--34486766 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
34486701 ACAAAAGAAA
34486711 AGAAAAAGATGTCATCTTCTTTAATTTT
1 AGAAAAAGATGTCATCTTCTTTAATTTT
34486739 AGAAAAAGATGTCATCTTCTTTAATTTT
1 AGAAAAAGATGTCATCTTCTTTAATTTT
34486767 CTTTCTCCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (28 bp):
AGAAAAAGATGTCATCTTCTTTAATTTT
Found at i:34489599 original size:5 final size:5
Alignment explanation
Indices: 34489589--34489659 Score: 62
Period size: 5 Copynumber: 14.6 Consensus size: 5
34489579 AAAAAAATAT
* *
34489589 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TATTA TTATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA -TATTA
34489635 -A-TA TATTA TATTA TATTA TA-TA TAT
1 TATTA TATTA TATTA TATTA TATTA TAT
34489660 ACATAAAACA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
3 4 0.07
4 8 0.15
5 31 0.56
6 11 0.20
7 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:34489641 original size:19 final size:19
Alignment explanation
Indices: 34489617--34489659 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
34489607 ATTATGTTTT
34489617 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
34489636 TATATTATATTATATTATA
1 TATATTATATTATATTATA
34489655 TATAT
1 TATAT
34489660 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:34490330 original size:29 final size:30
Alignment explanation
Indices: 34490271--34490328 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
34490261 TCCGAGCCTT
*
34490271 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
34490301 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
34490329 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:34490720 original size:46 final size:44
Alignment explanation
Indices: 34490661--34490775 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
34490651 ACAGGACAGA
* *
34490661 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
34490707 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
34490751 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
34490776 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:34490756 original size:44 final size:45
Alignment explanation
Indices: 34490661--34490794 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
34490651 ACAGGACAGA
* *
34490661 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
34490707 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
34490751 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
34490795 CAGGGTATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:34493192 original size:13 final size:13
Alignment explanation
Indices: 34493174--34493201 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
34493164 TGATCTCTTC
34493174 TGGGTATTCTATA
1 TGGGTATTCTATA
34493187 TGGGTATTCTATA
1 TGGGTATTCTATA
34493200 TG
1 TG
34493202 CTCTTTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.25, T:0.46
Consensus pattern (13 bp):
TGGGTATTCTATA
Found at i:34495094 original size:5 final size:5
Alignment explanation
Indices: 34495084--34495155 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
34495074 TGTTAAAAAA
* *
34495084 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATCATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT AT-ATT
34495130 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
34495156 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 33 0.59
6 10 0.18
7 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:34495137 original size:19 final size:19
Alignment explanation
Indices: 34495113--34495155 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
34495103 ATTATGTTTT
34495113 TATATTATATTATCATTA-A
1 TATATTATATTAT-ATTATA
34495132 TATATTATATTATATTATA
1 TATATTATATTATATTATA
34495151 TATAT
1 TATAT
34495156 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:34495827 original size:29 final size:30
Alignment explanation
Indices: 34495768--34495825 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
34495758 TCCGAGCCTT
*
34495768 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
34495798 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
34495826 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:34496055 original size:13 final size:13
Alignment explanation
Indices: 34496037--34496068 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
34496027 TTTCCAGCAA
34496037 TTATGAATTTATT
1 TTATGAATTTATT
34496050 TTATGAATTTATT
1 TTATGAATTTATT
*
34496063 TGATGA
1 TTATGA
34496069 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:34496276 original size:50 final size:50
Alignment explanation
Indices: 34496163--34496404 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
34496153 ATTTGGGTAA
* * *
34496163 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
34496219 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
34496269 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
34496319 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
34496369 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
34496405 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:34496352 original size:100 final size:103
Alignment explanation
Indices: 34496163--34496412 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
34496153 ATTTGGGTAA
34496163 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
34496228 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
34496269 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
34496331 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
34496369 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
34496413 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:34501509 original size:15 final size:14
Alignment explanation
Indices: 34501489--34501524 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
34501479 GTGTTGTATT
34501489 AATAAAATAAATAAA
1 AATAAAATAAAT-AA
34501504 AATAAAATAAATAA
1 AATAAAATAAATAA
34501518 AATAAAA
1 AATAAAA
34501525 CATATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AATAAAATAAATAA
Found at i:34513361 original size:60 final size:60
Alignment explanation
Indices: 34513288--34513409 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
34513278 GAGAAAAATC
34513288 AACTCAATTGAGAGGTTAATTGAGCAGGGATGAAATTATCATTTATTGAAAGCTTAGGGA
1 AACTCAATTGAGAGGTTAATTGAGCAGGGATGAAATTATCATTTATTGAAAGCTTAGGGA
34513348 AACTCAATTGAGAGGTTAATTGAGCAGGGATGAAATTATCATTTATTGAAAGCTTAGGGA
1 AACTCAATTGAGAGGTTAATTGAGCAGGGATGAAATTATCATTTATTGAAAGCTTAGGGA
34513408 AA
1 AA
34513410 GAATGGTAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.30
Consensus pattern (60 bp):
AACTCAATTGAGAGGTTAATTGAGCAGGGATGAAATTATCATTTATTGAAAGCTTAGGGA
Found at i:34517072 original size:21 final size:21
Alignment explanation
Indices: 34517014--34517072 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
34517004 TGAGGCTAAT
34517014 TTCAAAATGATTTAAAAATCCA
1 TTCAAAAT-ATTTAAAAATCCA
**
34517036 TTCAAAATATAGAAAAATACC-
1 TTCAAAATATTTAAAAAT-CCA
34517057 TT-AAGAATATTTAAAA
1 TTCAA-AATATTTAAAA
34517073 TTCCCCTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 2 0.06
21 19 0.61
22 10 0.32
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (21 bp):
TTCAAAATATTTAAAAATCCA
Found at i:34522730 original size:41 final size:41
Alignment explanation
Indices: 34522668--34522783 Score: 151
Period size: 41 Copynumber: 2.8 Consensus size: 41
34522658 TTTTGTAAGT
* *
34522668 TCAGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAAATATA
* * * *
34522709 TCAGACTTTATGTCTAGCAGGCTTTGTGACGGTGAAATGTA
1 TCAGGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAAATATA
* * *
34522750 TCGGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 TCAGGCTTTATGCCTAGCAGGCTTTGTGCCGGTG
34522784 TTTTATAAAG
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAAATATA
Found at i:34523701 original size:68 final size:69
Alignment explanation
Indices: 34523591--34523800 Score: 264
Period size: 68 Copynumber: 3.0 Consensus size: 69
34523581 TATGATGTAT
* * * *
34523591 TATGTATATGCTT-CCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATACTGCTCAA
1 TATGTATATG-TTGCCCATTTGTTGTATATATGATGTTAAATTTTGGTGTAAAAATGCTGTTAAA
34523655 TTTGG
65 TTTGG
* *
34523660 TATGTATA-GTTGCCCATTTGTTGTATATATGATGTTAAATTTTGGTGTAAAAGTGCTATTAAAT
1 TATGTATATGTTGCCCATTTGTTGTATATATGATGTTAAATTTTGGTGTAAAAATGCTGTTAAAT
34523724 TTGG
66 TTGG
** * * * *
34523728 TATGTATATGCGGCCCATTTGTTGTATATA-AACTGTCCAAATTTTGGTGTATAAATGCTGTTTA
1 TATGTATATGTTGCCCATTTGTTGTATATATGA-TGT-TAAATTTTGGTGTAAAAATGCTGTTAA
34523792 ATTTGG
64 ATTTGG
34523798 TAT
1 TAT
34523801 ATAAATGATG
Statistics
Matches: 123, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
67 2 0.02
68 60 0.49
69 30 0.24
70 31 0.25
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.45
Consensus pattern (69 bp):
TATGTATATGTTGCCCATTTGTTGTATATATGATGTTAAATTTTGGTGTAAAAATGCTGTTAAAT
TTGG
Found at i:34526835 original size:27 final size:32
Alignment explanation
Indices: 34526739--34526876 Score: 164
Period size: 32 Copynumber: 4.5 Consensus size: 32
34526729 TGTCAATCAT
34526739 TTCAATAT-TCAACAAGCTTAAAACATAATAAA
1 TTCAATATCT-AACAAGCTTAAAACATAATAAA
*
34526771 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCTAACAAGCTTAAAACATAATAAA
34526803 TTCAATATCTAACAAGCTT-AAA-AT-AT-AA
1 TTCAATATCTAACAAGCTTAAAACATAATAAA
* * *
34526831 -TCAATATCTAACAA-ATTCAAGACATAATAAT
1 TTCAATATCTAACAAGCTT-AAAACATAATAAA
*
34526862 TTCAAAATCTAACAA
1 TTCAATATCTAACAA
34526877 ACTAAAATTT
Statistics
Matches: 93, Mismatches: 6, Indels: 14
0.82 0.05 0.12
Matches are distributed among these distances:
26 2 0.02
27 14 0.15
28 4 0.04
29 4 0.04
30 4 0.04
31 4 0.04
32 61 0.66
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (32 bp):
TTCAATATCTAACAAGCTTAAAACATAATAAA
Found at i:34526866 original size:59 final size:62
Alignment explanation
Indices: 34526737--34526884 Score: 164
Period size: 59 Copynumber: 2.4 Consensus size: 62
34526727 ATTGTCAATC
*
34526737 ATTTCAATAT-TCAACAAGCTTAAAACATAATAAATTCAATATCCAACAAGCTTAAAACATAATA
1 ATTTCAATATCT-AACAAGCTT-AAA-ATAATAAATTCAATATCCAACAAGATTAAAACATAATA
* * *
34526801 AATTCAATATCTAACAAGCTTAAAAT-AT-AA-TCAATATCTAACAA-ATTCAAGACATAATA
1 ATTTCAATATCTAACAAGCTTAAAATAATAAATTCAATATCCAACAAGATT-AAAACATAATA
* *
34526860 ATTTCAAAATCTAACAAAC-TAAAAT
1 ATTTCAATATCTAACAAGCTTAAAAT
34526885 TTCAATATTA
Statistics
Matches: 75, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
58 8 0.11
59 39 0.52
60 2 0.03
61 2 0.03
62 2 0.03
63 3 0.04
64 18 0.24
65 1 0.01
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.28
Consensus pattern (62 bp):
ATTTCAATATCTAACAAGCTTAAAATAATAAATTCAATATCCAACAAGATTAAAACATAATA
Found at i:34530116 original size:17 final size:17
Alignment explanation
Indices: 34530067--34530116 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
34530057 TCTTCAACAG
34530067 ACAGATGCAAAATCCAA
1 ACAGATGCAAAATCCAA
* *
34530084 ATAGAT--TAAA--CAA
1 ACAGATGCAAAATCCAA
34530097 ACAGATGCAAAATCCAA
1 ACAGATGCAAAATCCAA
34530114 ACA
1 ACA
34530117 TATTCTTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
13 8 0.32
15 6 0.24
17 11 0.44
ACGTcount: A:0.56, C:0.20, G:0.10, T:0.14
Consensus pattern (17 bp):
ACAGATGCAAAATCCAA
Found at i:34534033 original size:24 final size:24
Alignment explanation
Indices: 34533989--34534040 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
34533979 ATTCTAGAAG
**
34533989 ATTTAGTATTTATTATTATAATAT
1 ATTTAGTATTTATTAGCATAATAT
*
34534013 ATTTAGTATTTATTAGCATAATTT
1 ATTTAGTATTTATTAGCATAATAT
34534037 ATTT
1 ATTT
34534041 GATCTATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (24 bp):
ATTTAGTATTTATTAGCATAATAT
Found at i:34535747 original size:1 final size:1
Alignment explanation
Indices: 34535743--34535777 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
34535733 GGTGGGGGGG
34535743 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
34535778 GGGGGGGGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:34543083 original size:11 final size:13
Alignment explanation
Indices: 34543063--34543094 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
34543053 AATAAAATAA
34543063 TAAAATATC-AAT
1 TAAAATATCAAAT
34543075 TAAAA-ATCAAAT
1 TAAAATATCAAAT
34543087 TAAAATAT
1 TAAAATAT
34543095 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 13 0.72
13 2 0.11
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAAATATCAAAT
Found at i:34543389 original size:30 final size:31
Alignment explanation
Indices: 34543333--34543390 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
34543323 CACCCTTAAA
** *
34543333 ATATTTACACTATTGGTCCTTCAAATTTTTC
1 ATATTTACACTATTAATCCATCAAATTTTTC
34543364 ATATTTACACT-TTAATCCATCAAATTT
1 ATATTTACACTATTAATCCATCAAATTT
34543391 CAAGTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.31, C:0.19, G:0.03, T:0.47
Consensus pattern (31 bp):
ATATTTACACTATTAATCCATCAAATTTTTC
Found at i:34550821 original size:66 final size:66
Alignment explanation
Indices: 34550685--34550868 Score: 228
Period size: 66 Copynumber: 2.8 Consensus size: 66
34550675 CTCTACATGC
* * * *
34550685 TGCCATAGCTGAGCTATGGTCTTACATACAT-AACCCCATGTTTAATGTCTTAGTAGACTCCACA
1 TGCCATAGCTGAGCTAAGGTCTTAC--ACATGTACCCCATGTTTAATGTCCTAGGAGACTCCACA
34550749 CAT
64 CAT
* * *
34550752 TGCCATAG-TCGAGCTAAGGTCTTACACATGTACCTCATGTTTAATGTCCTAGGGGACTCCATAC
1 TGCCATAGCT-GAGCTAAGGTCTTACACATGTACCCCATGTTTAATGTCCTAGGAGACTCCACAC
*
34550816 GT
65 AT
* * *
34550818 TGCCATAGCTGAGTTAAGGGCTTACACATGTACCCCATATTTAATGTCCTA
1 TGCCATAGCTGAGCTAAGGTCTTACACATGTACCCCATGTTTAATGTCCTA
34550869 ACGAACACCA
Statistics
Matches: 102, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
65 4 0.04
66 75 0.74
67 23 0.23
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (66 bp):
TGCCATAGCTGAGCTAAGGTCTTACACATGTACCCCATGTTTAATGTCCTAGGAGACTCCACACA
T
Found at i:34550886 original size:66 final size:66
Alignment explanation
Indices: 34550744--34550898 Score: 186
Period size: 66 Copynumber: 2.3 Consensus size: 66
34550734 TTAGTAGACT
* * * * * ** *
34550744 CCACACATTGCCATAG-TCGAGCTAAGGTCTTACACATGTACCTCATGTTTAATGTCCTAGGGGA
1 CCACACGTTGCCATAGCT-GAGTTAAGGGCTTACACATGTACCCCATATTTAATGTCCTAACGAA
*
34550808 CT
65 CA
*
34550810 CCATACGTTGCCATAGCTGAGTTAAGGGCTTACACATGTACCCCATATTTAATGTCCTAACGAAC
1 CCACACGTTGCCATAGCTGAGTTAAGGGCTTACACATGTACCCCATATTTAATGTCCTAACGAAC
34550875 A
66 A
* *
34550876 CCACATGTTGCCCTAGCTGAGTT
1 CCACACGTTGCCATAGCTGAGTT
34550899 CAGGTATTAA
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
66 74 0.99
67 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (66 bp):
CCACACGTTGCCATAGCTGAGTTAAGGGCTTACACATGTACCCCATATTTAATGTCCTAACGAAC
A
Found at i:34554701 original size:17 final size:16
Alignment explanation
Indices: 34554657--34554704 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
34554647 CATTCCAATG
*
34554657 TAACATATAAATGAAA
1 TAACATAAAAATGAAA
*
34554673 TAGA-ACAAAAATGAACA
1 TA-ACATAAAAATGAA-A
34554690 TAACATAAAAATGAA
1 TAACATAAAAATGAA
34554705 TAGTAAGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (16 bp):
TAACATAAAAATGAAA
Found at i:34556473 original size:19 final size:18
Alignment explanation
Indices: 34556437--34556483 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
34556427 GTAAATTATC
* *
34556437 TTAATTAACTAAATTAAA
1 TTAATTAATTAAACTAAA
34556455 TTAATTAAGTTAAACTAAA
1 TTAATTAA-TTAAACTAAA
*
34556474 TTAATAAATT
1 TTAATTAATT
34556484 TAATCTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (18 bp):
TTAATTAATTAAACTAAA
Found at i:34556486 original size:19 final size:19
Alignment explanation
Indices: 34556446--34556492 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
34556436 CTTAATTAAC
* *
34556446 TAAATTAAATTAATTAAGT
1 TAAACTAAATTAATAAAGT
*
34556465 TAAACTAAATTAATAAATT
1 TAAACTAAATTAATAAAGT
*
34556484 TAATCTAAA
1 TAAACTAAA
34556493 GTATAAAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (19 bp):
TAAACTAAATTAATAAAGT
Found at i:34559053 original size:21 final size:21
Alignment explanation
Indices: 34559027--34559067 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
34559017 CACCTACAAT
*
34559027 GGTATCGTTATATCCACCTTG
1 GGTATCGTGATATCCACCTTG
34559048 GGTATCGTGATATCCACCTT
1 GGTATCGTGATATCCACCTT
34559068 CTAAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.37
Consensus pattern (21 bp):
GGTATCGTGATATCCACCTTG
Found at i:34560553 original size:17 final size:18
Alignment explanation
Indices: 34560522--34560555 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
34560512 TAGATATGAA
*
34560522 TTTGATTTGAGTTTTTTT
1 TTTGATTTGAATTTTTTT
34560540 TTTG-TTTGAATTTTTT
1 TTTGATTTGAATTTTTT
34560556 ACTAATTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.74
Consensus pattern (18 bp):
TTTGATTTGAATTTTTTT
Found at i:34568738 original size:37 final size:37
Alignment explanation
Indices: 34568646--34568748 Score: 107
Period size: 38 Copynumber: 2.6 Consensus size: 37
34568636 GACCTCGAGT
*
34568646 CGATGAGACACTGGGTGTCACTATTTTACTTCGGATAGAT
1 CGATGAGACACTGGGTGTCAC---TTTACTTCGGATAGAC
* * * * *
34568686 TGTATGAGATACTGGGTATCACTTTACTTCGGCTAGGC
1 CG-ATGAGACACTGGGTGTCACTTTACTTCGGATAGAC
34568724 CGATGAGACACTGGGTGTCAACTTT
1 CGATGAGACACTGGGTGTC-ACTTT
34568749 GCTTTGAACT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
37 15 0.29
38 19 0.37
40 1 0.02
41 17 0.33
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (37 bp):
CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAC
Found at i:34569141 original size:33 final size:33
Alignment explanation
Indices: 34569025--34569167 Score: 110
Period size: 33 Copynumber: 4.3 Consensus size: 33
34569015 AATTGATGGA
* *
34569025 TAAGACCATAACTGGGTTATGGCA-TTATGAATG
1 TAAGACCATAACTGGGCTATGGCACTTCT-AATG
*** * * * *
34569058 TAAGACCATGGTTGGACCATGGCAGTGTTTATATG
1 TAAGACCATAACTGGGCTATGGCACT-TCTA-ATG
* *
34569093 TAAGATCATAGCTGGGCTATGGCA-TTCTAATG
1 TAAGACCATAACTGGGCTATGGCACTTCTAATG
* * *
34569125 ATAAGACCATAACTGGGTTATGGCACTACAAATG
1 -TAAGACCATAACTGGGCTATGGCACTTCTAATG
34569159 TAAGACCAT
1 TAAGACCAT
34569168 GGCAGGGCCA
Statistics
Matches: 87, Mismatches: 18, Indels: 10
0.76 0.16 0.09
Matches are distributed among these distances:
32 3 0.03
33 51 0.59
34 9 0.10
35 24 0.28
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (33 bp):
TAAGACCATAACTGGGCTATGGCACTTCTAATG
Found at i:34570371 original size:21 final size:21
Alignment explanation
Indices: 34570345--34570385 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
34570335 TCCCTCTTGG
34570345 AAGGTGGATATCGCGATACCC
1 AAGGTGGATATCGCGATACCC
* *
34570366 AAGGTGGGTCTCGCGATACC
1 AAGGTGGATATCGCGATACC
34570386 ACTGTAGGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.20
Consensus pattern (21 bp):
AAGGTGGATATCGCGATACCC
Found at i:34580606 original size:19 final size:20
Alignment explanation
Indices: 34580582--34580619 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
34580572 TACATTGATC
34580582 AAACATACCAAC-AACAAAA
1 AAACATACCAACAAACAAAA
34580601 AAACATACCAACAAACAAA
1 AAACATACCAACAAACAAA
34580620 GCAAGTTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.68, C:0.26, G:0.00, T:0.05
Consensus pattern (20 bp):
AAACATACCAACAAACAAAA
Found at i:34582712 original size:16 final size:15
Alignment explanation
Indices: 34582686--34582734 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
34582676 ATACTTTGGG
34582686 TTTATTTTTTAGTAACT
1 TTTA-TTTTTAGTAA-T
34582703 TTTATTTTTAGATAAT
1 TTTATTTTTAG-TAAT
**
34582719 TCAATTTTTAGTAAT
1 TTTATTTTTAGTAAT
34582734 T
1 T
34582735 ATATGCAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 5 0.17
16 17 0.59
17 7 0.24
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTATTTTTAGTAAT
Found at i:34584198 original size:10 final size:9
Alignment explanation
Indices: 34584128--34584212 Score: 73
Period size: 10 Copynumber: 8.9 Consensus size: 9
34584118 CATGTGGTAA
34584128 AAAAATTAT
1 AAAAATTAT
*
34584137 AAAAA-AAT
1 AAAAATTAT
*
34584145 AAAAATCAAT
1 AAAAAT-TAT
34584155 AAAAATTATT
1 AAAAATTA-T
*
34584165 AAAATTTAAT
1 AAAAATT-AT
34584175 AAAAATTAT
1 AAAAATTAT
34584184 AAAAATTATTT
1 AAAAATTA--T
*
34584195 AAAATTTACT
1 AAAAATTA-T
34584205 AAAAATTA
1 AAAAATTA
34584213 GAGAATATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
8 7 0.11
9 16 0.25
10 31 0.49
11 9 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:34584211 original size:30 final size:29
Alignment explanation
Indices: 34584142--34584212 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 29
34584132 ATTATAAAAA
*
34584142 AATAAAAATCAATAAAAATTATTAAAATTT
1 AATAAAAAT-TATAAAAATTATTAAAATTT
34584172 AATAAAAATTATAAAAATTATTTAAAATTT
1 AATAAAAATTATAAAAATTA-TTAAAATTT
*
34584202 ACTAAAAATTA
1 AATAAAAATTA
34584213 GAGAATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 10 0.26
30 28 0.74
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (29 bp):
AATAAAAATTATAAAAATTATTAAAATTT
Found at i:34584520 original size:19 final size:19
Alignment explanation
Indices: 34584475--34584517 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
34584465 CGATACGATA
*
34584475 ATTTTTATAATTCTTTATG
1 ATTTTTATAATTCTTTATC
*
34584494 AATTTTATAATTCTTTA-C
1 ATTTTTATAATTCTTTATC
34584512 ATTTTT
1 ATTTTT
34584518 TATCATTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTTTTATAATTCTTTATC
Found at i:34585708 original size:18 final size:17
Alignment explanation
Indices: 34585687--34585721 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
34585677 TTATTATTAA
*
34585687 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
34585705 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
34585722 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:34585775 original size:157 final size:157
Alignment explanation
Indices: 34585581--34585889 Score: 582
Period size: 157 Copynumber: 2.0 Consensus size: 157
34585571 CCCTTAGCAT
*
34585581 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* *
34585646 TAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
34585711 TTTAATAAAATTCTTAATAATTACCAG
131 TTTAATAAAATTCTTAATAATTACCAG
*
34585738 AAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
34585803 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
34585868 TTTAATAAAATTCTTAATAATT
131 TTTAATAAAATTCTTAATAATT
34585890 CATATTCTTA
Statistics
Matches: 148, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 148 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
TTTAATAAAATTCTTAATAATTACCAG
Found at i:34585861 original size:16 final size:16
Alignment explanation
Indices: 34585824--34585865 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
34585814 TTAATCATAT
*
34585824 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
34585840 TT-AAATATATTATAA
1 TTAAAATATATTATAA
34585855 TTAAAATATAT
1 TTAAAATATAT
34585866 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:34585872 original size:14 final size:15
Alignment explanation
Indices: 34585833--34585874 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
34585823 TTTAAACATA
*
34585833 ATTATTATTAAATAT
1 ATTATAATTAAATAT
34585848 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
34585862 A-TATAATTTAATA
1 ATTATAATTAAATA
34585875 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:34592738 original size:45 final size:44
Alignment explanation
Indices: 34592652--34592744 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
34592642 ATTACAACAT
*
34592652 CATTCCATTCAACCAAACACAATAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAATAATACTATTACAGCTCTATTC
* *
34592696 CATTTCATTCAACCAAACA-ATTGAATTACTATTAC-GCCTCTATTC
1 CATTCCATTCAACCAAACACAAT-AA-TACTATTACAG-CTCTATTC
34592741 CATT
1 CATT
34592745 ACAGCGAACC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 2 0.05
44 21 0.49
45 20 0.47
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.34
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAATAATACTATTACAGCTCTATTC
Found at i:34599437 original size:17 final size:17
Alignment explanation
Indices: 34599415--34599468 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 17
34599405 ATATAGGTAA
34599415 AAATATAATGATATTTG
1 AAATATAATGATATTTG
* * * *
34599432 AAATAT-TTCACATAT-
1 AAATATAATGATATTTG
34599447 AAA-ATAATGATATTTG
1 AAATATAATGATATTTG
34599463 AAATAT
1 AAATAT
34599469 TTTTTATATA
Statistics
Matches: 26, Mismatches: 8, Indels: 6
0.65 0.20 0.15
Matches are distributed among these distances:
14 2 0.08
15 8 0.31
16 8 0.31
17 8 0.31
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (17 bp):
AAATATAATGATATTTG
Found at i:34599498 original size:32 final size:32
Alignment explanation
Indices: 34599414--34599499 Score: 111
Period size: 31 Copynumber: 2.7 Consensus size: 32
34599404 AATATAGGTA
34599414 AAAATATAATGATATTTGAAATATTTCACATAT
1 AAAA-ATAATGATATTTGAAATATTTCACATAT
***
34599447 -AAAATAATGATATTTGAAATATTTTTTATAT
1 AAAAATAATGATATTTGAAATATTTCACATAT
* *
34599478 AAAAATAATGTTATTAGAAATA
1 AAAAATAATGATATTTGAAATA
34599500 ATGATTTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
31 25 0.53
32 22 0.47
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (32 bp):
AAAAATAATGATATTTGAAATATTTCACATAT
Found at i:34599596 original size:17 final size:16
Alignment explanation
Indices: 34599570--34599606 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
34599560 TATTTGACAT
*
34599570 AAAAATTATATATAAA
1 AAAAAATATATATAAA
34599586 CAAAAAATATATATAAA
1 -AAAAAATATATATAAA
34599603 AAAA
1 AAAA
34599607 TTAGTTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAAATATATATAAA
Found at i:34599973 original size:42 final size:42
Alignment explanation
Indices: 34599909--34599993 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
34599899 AATAGATGAT
** *
34599909 ATTTTTTAATGTAATTCGGATTCACTAATTCTACATCTACGG
1 ATTTTTTAACATAATTCAGATTCACTAATTCTACATCTACGG
34599951 ATTTTTTAACATAATTCAGATTCACTAATTCTACATCTACGG
1 ATTTTTTAACATAATTCAGATTCACTAATTCTACATCTACGG
34599993 A
1 A
34599994 GCCTTACTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (42 bp):
ATTTTTTAACATAATTCAGATTCACTAATTCTACATCTACGG
Found at i:34613002 original size:41 final size:40
Alignment explanation
Indices: 34612945--34613105 Score: 162
Period size: 41 Copynumber: 3.9 Consensus size: 40
34612935 TAAACAGATT
* * *
34612945 CACCGGCATTTTGCCTGCTAGGCTTAAAGCCTGATTCAGTA
1 CACCGGCATTTAGCCTGCTAGACTTAAAGTCTGATT-AGTA
* * * *
34612986 CACCGGCACTTAGCCTGCTAGACATATAGTCTGA-AATGTA
1 CACCGGCATTTAGCCTGCTAGACTTAAAGTCTGATTA-GTA
* *
34613026 TCACCGGCATTTAGCCTGCTAGACTTAAAGTCTGAATTACTT
1 -CACCGGCATTTAGCCTGCTAGACTTAAAGTCTG-ATTAGTA
* * *
34613068 CACCGGCATTAAGCCTGCTAGACGTAACGTCTGTATTA
1 CACCGGCATTTAGCCTGCTAGACTTAAAGTCTG-ATTA
34613106 CATTCAATCA
Statistics
Matches: 99, Mismatches: 17, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.01
40 3 0.03
41 92 0.93
42 2 0.02
43 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (40 bp):
CACCGGCATTTAGCCTGCTAGACTTAAAGTCTGATTAGTA
Found at i:34614868 original size:25 final size:24
Alignment explanation
Indices: 34614782--34614872 Score: 83
Period size: 25 Copynumber: 3.7 Consensus size: 24
34614772 TTCAAGCTAA
* **
34614782 ATAATGGGAAGCTCATGTGAGCCAT
1 ATAACGGGAAGCTCAT-TGAGCTGT
* *
34614807 GTAACGGGAAGCTCATTTGAGTTGT
1 ATAACGGGAAGCTCA-TTGAGCTGT
* **
34614832 ATAATGAAAAGCTCATTCGAGCTGT
1 ATAACGGGAAGCTCATT-GAGCTGT
34614857 ATAACGGGAAGCTCAT
1 ATAACGGGAAGCTCAT
34614873 AAGAGCCGCA
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
24 2 0.04
25 48 0.94
26 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26
Consensus pattern (24 bp):
ATAACGGGAAGCTCATTGAGCTGT
Found at i:34614965 original size:25 final size:24
Alignment explanation
Indices: 34614861--34615001 Score: 85
Period size: 25 Copynumber: 5.8 Consensus size: 24
34614851 AGCTGTATAA
*
34614861 CGGGAAGCTCATAAGAGCCGCA-AT
1 CGGGAAGCTCATAAGAGCC-AATAT
*
34614885 CGGGAAGTTC--AAGCAAGCCAATAT
1 CGGGAAGCTCATAAG--AGCCAATAT
* * *
34614909 TGGGAAGCTC-TGGAGAGCCATTAAT
1 CGGGAAGCTCAT-AAGAGCCAAT-AT
** *
34614934 CAAGAAGCTCATAAGAGCCAGCTAT
1 CGGGAAGCTCATAAGAGCCA-ATAT
**
34614959 CGGGAAGCTCCGAAGAGCCATATAT
1 CGGGAAGCTCATAAGAGCCA-ATAT
34614984 CGGGACA-CTCATAAGAGC
1 CGGGA-AGCTCATAAGAGC
34615002 TACGGTGTGT
Statistics
Matches: 89, Mismatches: 19, Indels: 17
0.71 0.15 0.14
Matches are distributed among these distances:
22 3 0.03
23 1 0.01
24 29 0.33
25 51 0.57
26 5 0.06
ACGTcount: A:0.34, C:0.23, G:0.27, T:0.16
Consensus pattern (24 bp):
CGGGAAGCTCATAAGAGCCAATAT
Found at i:34618676 original size:9 final size:9
Alignment explanation
Indices: 34618643--34618686 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
34618633 TTAAGTGGGA
34618643 AATTAATTT
1 AATTAATTT
*
34618652 -AGTAATTTT
1 AATTAA-TTT
*
34618661 GATTAATTT
1 AATTAATTT
34618670 AATTAATTT
1 AATTAATTT
34618679 AATTAATT
1 AATTAATT
34618687 AATACTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 4 0.13
9 22 0.73
10 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (9 bp):
AATTAATTT
Found at i:34629447 original size:2 final size:2
Alignment explanation
Indices: 34629442--34629469 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
34629432 ATATATATAT
34629442 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
34629470 TTAAATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:34659347 original size:39 final size:39
Alignment explanation
Indices: 34659304--34659378 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
34659294 TGAATGAAAA
* *
34659304 GATGAAGAGCTCGTTGGCCCCCAGGATACTAACGCTGAG
1 GATGAAGAGCTCGTTGGCCCCCAAGATACCAACGCTGAG
34659343 GATGAAGAGCTCGTTGGCCCCCAAGATACCAACGCT
1 GATGAAGAGCTCGTTGGCCCCCAAGATACCAACGCT
34659379 AATTCATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.17
Consensus pattern (39 bp):
GATGAAGAGCTCGTTGGCCCCCAAGATACCAACGCTGAG
Found at i:34659454 original size:13 final size:13
Alignment explanation
Indices: 34659436--34659460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34659426 CCAAGCTTTA
34659436 TTTGATAAAATAT
1 TTTGATAAAATAT
34659449 TTTGATAAAATA
1 TTTGATAAAATA
34659461 AATTGAAGTG
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTGATAAAATAT
Found at i:34659599 original size:22 final size:22
Alignment explanation
Indices: 34659573--34659621 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
34659563 TTTCGAAACA
* *
34659573 ATTTTAAAATCAAGTGAAAATG
1 ATTTTAAAACCAAGTCAAAATG
34659595 ATTTT--AACCAAGTCAAAATG
1 ATTTTAAAACCAAGTCAAAATG
34659615 ATTTTAA
1 ATTTTAA
34659622 TTAATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 18 0.78
22 5 0.22
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (22 bp):
ATTTTAAAACCAAGTCAAAATG
Found at i:34659633 original size:20 final size:20
Alignment explanation
Indices: 34659583--34659621 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
34659573 ATTTTAAAAT
*
34659583 CAAGTGAAAATGATTTTAAC
1 CAAGTCAAAATGATTTTAAC
34659603 CAAGTCAAAATGATTTTAA
1 CAAGTCAAAATGATTTTAA
34659622 TTAATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (20 bp):
CAAGTCAAAATGATTTTAAC
Found at i:34660992 original size:131 final size:131
Alignment explanation
Indices: 34660758--34661315 Score: 632
Period size: 131 Copynumber: 4.3 Consensus size: 131
34660748 AGTGTTTGGA
* * * *
34660758 AAATCAGCTAACACAAATGAGATTGTTCATGATATTAGATCTAATAAACTTAGGTTGTGATCTTA
1 AAATCAGCTAACTCAAATAAGATTGTTCATGATATTAAATCTAATAAACTTAGGTTGTAATCTTA
* * * * * ** *
34660823 AATCAATGAACTTTAATGATGTCAACTGCGATCTTAAATCAATAAGCTGTTTGGAGTAGCGATAG
66 AATCAACGAACCTTAACGATATCAACTGCAATCTTAAATCAACGAGCTGTTTGGAGTAGCGATAT
34660888 T
131 T
* * * * *
34660889 AAATCAGCTAACTCAGATATGATTGTTGATGATATTAAATCTAATAAACTTCGGTTGCAATCTTA
1 AAATCAGCTAACTCAAATAAGATTGTTCATGATATTAAATCTAATAAACTTAGGTTGTAATCTTA
** * * * * *
34660954 AATCAGTGAACCTTAACGATATTAGCTGTAATCTTAAATCAACGAGTTGTTTGGAGTAGCAATAT
66 AATCAACGAACCTTAACGATATCAACTGCAATCTTAAATCAACGAGCTGTTTGGAGTAGCGATAT
34661019 T
131 T
* * * * * * *
34661020 AAATTAGCTAACTTAAATAATATTGTTCATGATTTTAAATCAAATTAACTTAGGTTGTGATCTTA
1 AAATCAGCTAACTCAAATAAGATTGTTCATGATATTAAATCTAATAAACTTAGGTTGTAATCTTA
* * * * *
34661085 AATCAACGAACCTTAATGACATTAGCTGCAATCTTAAATCAACGAGCTGTTTGAAGTAGCGATAT
66 AATCAACGAACCTTAACGATATCAACTGCAATCTTAAATCAACGAGCTGTTTGGAGTAGCGATAT
34661150 T
131 T
* * ** * * *
34661151 AAATCAACTAACTCAAATAAGATTGTTCATGATATTAAAT-TGAATGAACTTAAATAGAAATATT
1 AAATCAGCTAACTCAAATAAGATTGTTCATGATATTAAATCT-AATAAACTTAGGTTGTAATCTT
* * * * ** *
34661215 AAATTAGCGAACCTTAACGATATCAACTGTAATATTAAATCAGTGAGTTGTTTGGAGTAGCGATA
65 AAATCAACGAACCTTAACGATATCAACTGCAATCTTAAATCAACGAGCTGTTTGGAGTAGCGATA
34661280 TT
130 TT
* *
34661282 AAATTAGCTAACTCAAATAAGATTATTCATGATA
1 AAATCAGCTAACTCAAATAAGATTGTTCATGATA
34661316 GATAAAGTAA
Statistics
Matches: 356, Mismatches: 70, Indels: 2
0.83 0.16 0.00
Matches are distributed among these distances:
131 356 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (131 bp):
AAATCAGCTAACTCAAATAAGATTGTTCATGATATTAAATCTAATAAACTTAGGTTGTAATCTTA
AATCAACGAACCTTAACGATATCAACTGCAATCTTAAATCAACGAGCTGTTTGGAGTAGCGATAT
T
Found at i:34661229 original size:262 final size:262
Alignment explanation
Indices: 34660758--34661315 Score: 740
Period size: 262 Copynumber: 2.1 Consensus size: 262
34660748 AGTGTTTGGA
* * * * *
34660758 AAATCAGCTAACACAAATGAGATTGTTCATGATATTAGATCTAATAAACTTAGGTTGTGATCTTA
1 AAATTAGCTAACTCAAATAAGATTGTTCATGATATTAAATCAAATAAACTTAGGTTGTGATCTTA
* * ** * * *
34660823 AATCAATGAACTTTAATGATGTCAACTGCGATCTTAAATCAATAAGCTGTTTGGAGTAGCGATAG
66 AATCAACGAACCTTAATGACATCAACTGCAATCTTAAATCAACAAGCTGTTTGAAGTAGCGATAG
* * * * *** * * *
34660888 TAAATCAGCTAACTCAGATATGATTGTTGATGATATTAAATCTAATAAACTTCGGTTGCAATCTT
131 TAAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCTAATAAACTTAAATAGAAATATT
* * * *
34660953 AAATCAGTGAACCTTAACGATATTAGCTGTAATCTTAAATCAACGAGTTGTTTGGAGTAGCAATA
196 AAATCAGCGAACCTTAACGATATCAACTGTAATATTAAATCAACGAGTTGTTTGGAGTAGCAATA
34661018 TT
261 TT
* * * *
34661020 AAATTAGCTAACTTAAATAATATTGTTCATGATTTTAAATCAAATTAACTTAGGTTGTGATCTTA
1 AAATTAGCTAACTCAAATAAGATTGTTCATGATATTAAATCAAATAAACTTAGGTTGTGATCTTA
* * * *
34661085 AATCAACGAACCTTAATGACATTAGCTGCAATCTTAAATCAACGAGCTGTTTGAAGTAGCGATAT
66 AATCAACGAACCTTAATGACATCAACTGCAATCTTAAATCAACAAGCTGTTTGAAGTAGCGATAG
*
34661150 TAAATCAACTAACTCAAATAAGATTGTTCATGATATTAAAT-TGAATGAACTTAAATAGAAATAT
131 TAAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCT-AATAAACTTAAATAGAAATAT
* ** *
34661214 TAAATTAGCGAACCTTAACGATATCAACTGTAATATTAAATCAGTGAGTTGTTTGGAGTAGCGAT
195 TAAATCAGCGAACCTTAACGATATCAACTGTAATATTAAATCAACGAGTTGTTTGGAGTAGCAAT
34661279 ATT
260 ATT
*
34661282 AAATTAGCTAACTCAAATAAGATTATTCATGATA
1 AAATTAGCTAACTCAAATAAGATTGTTCATGATA
34661316 GATAAAGTAA
Statistics
Matches: 252, Mismatches: 43, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
261 1 0.00
262 251 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (262 bp):
AAATTAGCTAACTCAAATAAGATTGTTCATGATATTAAATCAAATAAACTTAGGTTGTGATCTTA
AATCAACGAACCTTAATGACATCAACTGCAATCTTAAATCAACAAGCTGTTTGAAGTAGCGATAG
TAAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCTAATAAACTTAAATAGAAATATT
AAATCAGCGAACCTTAACGATATCAACTGTAATATTAAATCAACGAGTTGTTTGGAGTAGCAATA
TT
Found at i:34665824 original size:41 final size:41
Alignment explanation
Indices: 34665678--34665829 Score: 137
Period size: 41 Copynumber: 3.7 Consensus size: 41
34665668 CAACATTCAC
* * *
34665678 TACACTGGCACGAAGCCTACTAGGCTCAAGGCCTGATTTC-A
1 TACACCGGCACGAAGCCTACTAGGCTCAAGGCCTGA-ATCGT
* * * * *
34665719 TACACCGACATGAAGCTTGA-TAGGCCCAGGGCCTGAATCGT
1 TACACCGGCACGAAGCCT-ACTAGGCTCAAGGCCTGAATCGT
* * ** *
34665760 TACACCAGTACGGGGCCTGCTAGGCTCAAGGCCTGAATCGT
1 TACACCGGCACGAAGCCTACTAGGCTCAAGGCCTGAATCGT
* *
34665801 TACACCGGCATGAAGCCTACTAGGTTCAA
1 TACACCGGCACGAAGCCTACTAGGCTCAA
34665830 AACCCAATAC
Statistics
Matches: 83, Mismatches: 25, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
40 2 0.02
41 80 0.96
42 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.20
Consensus pattern (41 bp):
TACACCGGCACGAAGCCTACTAGGCTCAAGGCCTGAATCGT
Found at i:34668674 original size:17 final size:17
Alignment explanation
Indices: 34668652--34668716 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
34668642 GACTATAACA
34668652 TCCATTTCATTTCCATT
1 TCCATTTCATTTCCATT
* *
34668669 TCCATTTCCATTTTCATA
1 TCCATTT-CATTTCCATT
34668687 T-CATTCTCA-TTCTCATT
1 TCCATT-TCATTTC-CATT
*
34668704 TCAATTTCATTTC
1 TCCATTTCATTTC
34668717 ATATTCAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
16 2 0.05
17 20 0.53
18 16 0.42
ACGTcount: A:0.20, C:0.28, G:0.00, T:0.52
Consensus pattern (17 bp):
TCCATTTCATTTCCATT
Found at i:34668723 original size:6 final size:5
Alignment explanation
Indices: 34668654--34668723 Score: 59
Period size: 6 Copynumber: 12.4 Consensus size: 5
34668644 CTATAACATC
*
34668654 CATTT CATTT CCATTT CCATTT CCATTTT CATAT CATTCT CATTCT CATTT
1 CATTT CATTT -CATTT -CATTT -CA-TTT CATTT CATT-T CATT-T CATTT
34668705 CAATTT CATTT CATATT CA
1 C-ATTT CATTT CAT-TT CA
34668724 AATCATAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
5 19 0.33
6 36 0.62
7 3 0.05
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (5 bp):
CATTT
Found at i:34668723 original size:11 final size:10
Alignment explanation
Indices: 34668654--34668723 Score: 59
Period size: 11 Copynumber: 6.2 Consensus size: 10
34668644 CTATAACATC
34668654 CATTTCATTT
1 CATTTCATTT
34668664 CCATTTCCATTT
1 -CATTT-CATTT
*
34668676 CCATTTTCATAT
1 -CA-TTTCATTT
34668688 CATTCTCATTCT
1 CATT-TCATT-T
34668700 CATTTCAATTT
1 CATTTC-ATTT
34668711 CATTTCATATT
1 CATTTCAT-TT
34668722 CA
1 CA
34668724 AATCATAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
10 4 0.08
11 24 0.47
12 20 0.39
13 3 0.06
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (10 bp):
CATTTCATTT
Found at i:34668723 original size:17 final size:16
Alignment explanation
Indices: 34668655--34668724 Score: 61
Period size: 17 Copynumber: 4.1 Consensus size: 16
34668645 TATAACATCC
*
34668655 ATTTCATTTCCATTTCC
1 ATTTCATTT-CATTTCA
*
34668672 ATTTCCATTTTCATATC-
1 ATTT-CA-TTTCATTTCA
34668689 ATTCTCATTCTCATTTCA
1 ATT-TCATT-TCATTTCA
34668707 ATTTCATTTCATATTCA
1 ATTTCATTTCAT-TTCA
34668724 A
1 A
34668725 ATCATAAATC
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
16 6 0.13
17 25 0.56
18 11 0.24
19 3 0.07
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTCATTTCATTTCA
Found at i:34678580 original size:27 final size:27
Alignment explanation
Indices: 34678542--34678595 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
34678532 TGGAAGAAAG
* *
34678542 ATAGAACGTGAGAAAGGTTCCTTATGC
1 ATAGAACATGAGAAAGGTTCCCTATGC
34678569 ATAGAACATGAGAAAGGTTCCCTATGC
1 ATAGAACATGAGAAAGGTTCCCTATGC
34678596 TTCAGCAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (27 bp):
ATAGAACATGAGAAAGGTTCCCTATGC
Found at i:34694413 original size:41 final size:41
Alignment explanation
Indices: 34694356--34694485 Score: 197
Period size: 41 Copynumber: 3.2 Consensus size: 41
34694346 GAGCTTTCGA
* * *
34694356 GGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAG
1 GGATTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAG
*
34694397 GGATTTAGCGGTGTTTTTGAGAAAGTGCCGCTAATGCTCAG
1 GGATTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAG
* * *
34694438 GGCTTTAGCTGTGTTTTTGAGAAAACGCCGCTAATGCTCAG
1 GGATTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAG
34694479 GGATTTA
1 GGATTTA
34694486 AAGTAATTTA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 80 1.00
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (41 bp):
GGATTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAG
Found at i:34694674 original size:14 final size:14
Alignment explanation
Indices: 34694655--34694688 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
34694645 TATCACTATA
* *
34694655 GTTTAGGGTTTTTG
1 GTTTAGGGTATATG
34694669 GTTTAGGGTATATG
1 GTTTAGGGTATATG
34694683 GTTTAG
1 GTTTAG
34694689 ATAGGTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
GTTTAGGGTATATG
Found at i:34694745 original size:75 final size:75
Alignment explanation
Indices: 34694655--34694823 Score: 284
Period size: 75 Copynumber: 2.3 Consensus size: 75
34694645 TATCACTATA
**
34694655 GTTTAGGGTTTTTGGTTTAGGGTATATGGTTTAGATAGGTTTATGTGTTACCATTTTAAGGTTTA
1 GTTTAGGGTTTTTGGTTTAGGGTATATGGTTTAGATAGGTTTAAATGTTACCATTTTAAGGTTTA
34694720 TGGATTATGG
66 TGGATTATGG
* *
34694730 GTTTAAGGTTTTTGGTTTAGGGTATATGTTTTAGATAGGTTTAAATGTTACCATTTTAAGGTTTA
1 GTTTAGGGTTTTTGGTTTAGGGTATATGGTTTAGATAGGTTTAAATGTTACCATTTTAAGGTTTA
34694795 TGGATTATGG
66 TGGATTATGG
* *
34694805 GTTTAGGGATTATGGTTTA
1 GTTTAGGGTTTTTGGTTTA
34694824 TGGTTTAAAG
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 87 1.00
ACGTcount: A:0.22, C:0.02, G:0.28, T:0.48
Consensus pattern (75 bp):
GTTTAGGGTTTTTGGTTTAGGGTATATGGTTTAGATAGGTTTAAATGTTACCATTTTAAGGTTTA
TGGATTATGG
Found at i:34694807 original size:15 final size:14
Alignment explanation
Indices: 34694789--34694826 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
34694779 ACCATTTTAA
34694789 GGTTTATGGATTAT
1 GGTTTATGGATTAT
*
34694803 GGGTTTAGGGATTAT
1 -GGTTTATGGATTAT
34694818 GGTTTATGG
1 GGTTTATGG
34694827 TTTAAAGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (14 bp):
GGTTTATGGATTAT
Found at i:34694809 original size:22 final size:21
Alignment explanation
Indices: 34694784--34694831 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
34694774 ATGTTACCAT
*
34694784 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGATTATGGATTAT-GG
* *
34694806 TTTAGGGATTATGGTTTATGG
1 TTTAAGGATTATGGATTATGG
34694827 TTTAA
1 TTTAA
34694832 AGGCTGGGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (21 bp):
TTTAAGGATTATGGATTATGG
Found at i:34694827 original size:7 final size:7
Alignment explanation
Indices: 34694784--34694915 Score: 63
Period size: 7 Copynumber: 18.6 Consensus size: 7
34694774 ATGTTACCAT
*
34694784 TTTAAGG
1 TTTATGG
34694791 TTTATGG
1 TTTATGG
*
34694798 ATTATGGG
1 TTTAT-GG
*
34694806 TTTAGGG
1 TTTATGG
*
34694813 ATTATGG
1 TTTATGG
34694820 TTTATGG
1 TTTATGG
*
34694827 TTTAAAGG
1 TTT-ATGG
* **
34694835 -CTGGGG
1 TTTATGG
*
34694841 TTTAAGG
1 TTTATGG
34694848 TTTA-GAG
1 TTTATG-G
*
34694855 GTTATGTG
1 TTTATG-G
* *
34694863 TTAAGGG
1 TTTATGG
34694870 TTTATGG
1 TTTATGG
34694877 TTTATGG
1 TTTATGG
*
34694884 TTTTAGGG
1 -TTTATGG
*
34694892 TTTA-GA
1 TTTATGG
34694898 TTTATGG
1 TTTATGG
*
34694905 TTTAGGG
1 TTTATGG
34694912 TTTA
1 TTTA
34694916 GATTAACTAG
Statistics
Matches: 93, Mismatches: 25, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
6 8 0.09
7 66 0.71
8 19 0.20
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.46
Consensus pattern (7 bp):
TTTATGG
Found at i:34694830 original size:21 final size:20
Alignment explanation
Indices: 34694792--34694916 Score: 88
Period size: 22 Copynumber: 5.9 Consensus size: 20
34694782 ATTTTAAGGT
*
34694792 TTATGGATTATGGGTTTAGGG
1 TTATGGTTTA-GGGTTTAGGG
* *
34694813 ATTATGGTTTATGGTTTAAAGG
1 -TTATGGTTTAGGGTTT-AGGG
* ** *
34694835 CTGGGGTTTAAGGTTTAGAGG
1 TTATGGTTTAGGGTTTAG-GG
* *
34694856 TTATGTGTTAAGGGTTTATGGT
1 TTATG-GTTTAGGGTTTA-GGG
**
34694878 TTATGGTTTTAGGGTTTAGAT
1 TTATGG-TTTAGGGTTTAGGG
34694899 TTATGGTTTAGGGTTTAG
1 TTATGGTTTAGGGTTTAG
34694917 ATTAACTAGT
Statistics
Matches: 82, Mismatches: 16, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
20 13 0.16
21 30 0.37
22 38 0.46
23 1 0.01
ACGTcount: A:0.20, C:0.01, G:0.34, T:0.46
Consensus pattern (20 bp):
TTATGGTTTAGGGTTTAGGG
Found at i:34694907 original size:57 final size:56
Alignment explanation
Indices: 34694784--34694913 Score: 143
Period size: 57 Copynumber: 2.3 Consensus size: 56
34694774 ATGTTACCAT
* * * *
34694784 TTTAAGGTTTATGGATTATGGGTTTAGGGATTATGGTTTATGGTTTAAAGGCTGGGG
1 TTTAAGGTTTA-GGGTTATGGGTTAAGGGATTATGGTTTATGGTTTAAAGGCTGAGA
* * * * * *
34694841 TTTAAGGTTTAGAGGTTATGTGTTAAGGGTTTATGGTTTATGGTTTTAGGGTTTAGA
1 TTTAAGGTTTAG-GGTTATGGGTTAAGGGATTATGGTTTATGGTTTAAAGGCTGAGA
*
34694898 TTTATGGTTTAGGGTT
1 TTTAAGGTTTAGGGTT
34694914 TAGATTAACT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
56 5 0.08
57 56 0.92
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.46
Consensus pattern (56 bp):
TTTAAGGTTTAGGGTTATGGGTTAAGGGATTATGGTTTATGGTTTAAAGGCTGAGA
Found at i:34702703 original size:43 final size:43
Alignment explanation
Indices: 34702642--34702732 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
34702632 CTTTGACTTC
** * * *
34702642 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTAATTGATTAAGAAAATGCATTACATCTTTT
* *
34702684 ATTACCAAGATTTAATTGATTAAGAAAATGCATTGCATTTTTT
1 ATTACCAAGATTTAATTGATTAAGAAAATGCATTACATCTTTT
34702727 ATTACC
1 ATTACC
34702733 TTGCAATGTG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 4 0.10
43 37 0.90
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTAATTGATTAAGAAAATGCATTACATCTTTT
Found at i:34703212 original size:87 final size:87
Alignment explanation
Indices: 34703092--34703272 Score: 256
Period size: 87 Copynumber: 2.1 Consensus size: 87
34703082 GTTTGTTCTA
* ** * *
34703092 TAGCGGCATTTGTGATAAAAAGTGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAG
1 TAGCGGCATTTATGATAAAAAGCACCGCTAAAGGTCATGATCTGTAGCGGCGTTTGTGATAAAAG
*
34703157 CACCGCTAAAAGGCCATGACCTT
66 CACCGCT-AAAGACCATGACCTT
* *
34703180 TAGCGGCATTTATGA-CAAAAGCACCGCTAAAGGTCGTGATCTGTAGCGGCGTTTGTGATAAAAG
1 TAGCGGCATTTATGATAAAAAGCACCGCTAAAGGTCATGATCTGTAGCGGCGTTTGTGATAAAAG
* *
34703244 CGCCGCTAAAGACCATGATCTT
66 CACCGCTAAAGACCATGACCTT
34703266 TAGCGGC
1 TAGCGGC
34703273 GTTTTTTCAC
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
86 20 0.24
87 49 0.59
88 14 0.17
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.25
Consensus pattern (87 bp):
TAGCGGCATTTATGATAAAAAGCACCGCTAAAGGTCATGATCTGTAGCGGCGTTTGTGATAAAAG
CACCGCTAAAGACCATGACCTT
Found at i:34703273 original size:43 final size:43
Alignment explanation
Indices: 34703092--34703276 Score: 226
Period size: 43 Copynumber: 4.3 Consensus size: 43
34703082 GTTTGTTCTA
* ** * *
34703092 TAGCGGCATTTGTGATAAAAAGTGCCGCTAAAGGTCATGTTCTT
1 TAGCGGCGTTTGTGAT-AAAAGCACCGCTAAAGGCCATGATCTT
*
34703136 TAGCGGCGTTTGTGATAAAAGCACCGCTAAAAGGCCATGACCTT
1 TAGCGGCGTTTGTGATAAAAGCACCGCT-AAAGGCCATGATCTT
* * * * * *
34703180 TAGCGGCATTTATGACAAAAGCACCGCTAAAGGTCGTGATCTG
1 TAGCGGCGTTTGTGATAAAAGCACCGCTAAAGGCCATGATCTT
* *
34703223 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGACCATGATCTT
1 TAGCGGCGTTTGTGATAAAAGCACCGCTAAAGGCCATGATCTT
34703266 TAGCGGCGTTT
1 TAGCGGCGTTT
34703277 TTTCACATAA
Statistics
Matches: 119, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
43 67 0.56
44 52 0.44
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGATAAAAGCACCGCTAAAGGCCATGATCTT
Found at i:34712768 original size:3 final size:3
Alignment explanation
Indices: 34712760--34712784 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
34712750 GTATTAACCC
34712760 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
34712785 ATTTTTGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:34715188 original size:18 final size:16
Alignment explanation
Indices: 34715165--34715202 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 16
34715155 AAATTAGAGT
34715165 ATAATGTGCAACAAACAA
1 ATAAT-TGCAA-AAACAA
34715183 ATAA-TGCAAAAACAA
1 ATAATTGCAAAAACAA
34715198 ATAAT
1 ATAAT
34715203 AAAATTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 10 0.53
16 5 0.26
18 4 0.21
ACGTcount: A:0.61, C:0.13, G:0.08, T:0.18
Consensus pattern (16 bp):
ATAATTGCAAAAACAA
Found at i:34715197 original size:15 final size:16
Alignment explanation
Indices: 34715171--34715202 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
34715161 GAGTATAATG
34715171 TGCAACAAACAAATAA
1 TGCAACAAACAAATAA
34715187 TGCAA-AAACAAATAA
1 TGCAACAAACAAATAA
34715202 T
1 T
34715203 AAAATTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.62, C:0.16, G:0.06, T:0.16
Consensus pattern (16 bp):
TGCAACAAACAAATAA
Found at i:34722206 original size:35 final size:35
Alignment explanation
Indices: 34722167--34722237 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
34722157 CTTATAGTTT
34722167 TCTCAATGCCTTCCATAACAATTAAGAAAATGACC
1 TCTCAATGCCTTCCATAACAATTAAGAAAATGACC
34722202 TCTCAATGCCTTCCATAACAATTAAGAAAATGACC
1 TCTCAATGCCTTCCATAACAATTAAGAAAATGACC
34722237 T
1 T
34722238 GGCTAGAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.25, G:0.08, T:0.27
Consensus pattern (35 bp):
TCTCAATGCCTTCCATAACAATTAAGAAAATGACC
Found at i:34726233 original size:24 final size:25
Alignment explanation
Indices: 34726206--34726253 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
34726196 AAAATAATTT
34726206 TAAAATCTGAA-AATAAAAAAAAAC
1 TAAAATCTGAAGAATAAAAAAAAAC
* *
34726230 TAAATTGTGAAGAATAAAAAAAAA
1 TAAAATCTGAAGAATAAAAAAAAA
34726254 TAGAAGAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.69, C:0.04, G:0.08, T:0.19
Consensus pattern (25 bp):
TAAAATCTGAAGAATAAAAAAAAAC
Found at i:34727181 original size:22 final size:22
Alignment explanation
Indices: 34727147--34727188 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
34727137 ACTTCTCTTT
*
34727147 TTTTTATCATAAATATTTTAAG
1 TTTTTATCATAAATAATTTAAG
**
34727169 TTTTTATTTTAAATAATTTA
1 TTTTTATCATAAATAATTTA
34727189 TATTTACATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTTATCATAAATAATTTAAG
Found at i:34728126 original size:31 final size:29
Alignment explanation
Indices: 34728088--34728161 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 29
34728078 TATATTAGTA
* * *
34728088 GTCACCCAACTATGGTCATTTTCATTTTTGG
1 GTCACCCAACTATAGTAAATTTC--TTTTGG
*
34728119 GTCACCCAACTATTAGTAAATTTCTTTTGT
1 GTCACCCAACTA-TAGTAAATTTCTTTTGG
34728149 GTCACCCAACTAT
1 GTCACCCAACTAT
34728162 CTTGGATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 1 0.03
30 17 0.45
31 12 0.32
32 8 0.21
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (29 bp):
GTCACCCAACTATAGTAAATTTCTTTTGG
Found at i:34733019 original size:28 final size:28
Alignment explanation
Indices: 34732930--34733026 Score: 88
Period size: 28 Copynumber: 3.5 Consensus size: 28
34732920 AAATTAACGC
* *
34732930 GCTTATCG-TATTATTTTGCACTTGAAT
1 GCTTATCGTTATTATTTTGCACTTCAGT
* * * * * *
34732957 GCTTATTGTTGTAAAATTTGCAATTCGGT
1 GCTTATCGTTAT-TATTTTGCACTTCAGT
* *
34732986 GTTTATCGATATTATTTTGCACTTCAGT
1 GCTTATCGTTATTATTTTGCACTTCAGT
34733014 GCTTATCGTTATT
1 GCTTATCGTTATT
34733027 TGCACCATGT
Statistics
Matches: 50, Mismatches: 18, Indels: 3
0.70 0.25 0.04
Matches are distributed among these distances:
27 7 0.14
28 25 0.50
29 18 0.36
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.48
Consensus pattern (28 bp):
GCTTATCGTTATTATTTTGCACTTCAGT
Found at i:34735393 original size:31 final size:31
Alignment explanation
Indices: 34735355--34735425 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
34735345 AAAAAGTAAG
34735355 ATAAATGGATTTTGGATGGATTATTATGTAT
1 ATAAATGGATTTTGGATGGATTATTATGTAT
34735386 ATAAATGGATTTTGGATGGATTATTATGTAT
1 ATAAATGGATTTTGGATGGATTATTATGTAT
*
34735417 A-ACATGGAT
1 ATAAATGGAT
34735426 GATGATATTG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 7 0.18
31 32 0.82
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.42
Consensus pattern (31 bp):
ATAAATGGATTTTGGATGGATTATTATGTAT
Found at i:34739673 original size:43 final size:42
Alignment explanation
Indices: 34739625--34739730 Score: 117
Period size: 43 Copynumber: 2.5 Consensus size: 42
34739615 AAGATACTGA
* * * *
34739625 CACACATAGTACATCATCGA-GCAACACAAAGTAATTATATTGG
1 CACACATAGTGCATCATCGATG-AAC-CAAAGAAATTATACTAG
*
34739668 CACACA-AGGTGCATCATAGGATGAACCAAAGAAATTATACTAG
1 CACACATA-GTGCATCAT-CGATGAACCAAAGAAATTATACTAG
34739711 CACACATAGTGCATCATCGA
1 CACACATAGTGCATCATCGA
34739731 ATAAACTGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
42 3 0.06
43 43 0.81
44 6 0.11
45 1 0.02
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.21
Consensus pattern (42 bp):
CACACATAGTGCATCATCGATGAACCAAAGAAATTATACTAG
Found at i:34739751 original size:43 final size:42
Alignment explanation
Indices: 34739653--34739827 Score: 143
Period size: 42 Copynumber: 4.1 Consensus size: 42
34739643 GAGCAACACA
* * * * * *
34739653 AAGTAATTATATTGGCACACAAGGTGCATCATAGGATGAACCA
1 AAGTAATTATACTAGCACACAA-GTGCATCATCGAATAAACCG
* *
34739696 AAGAAATTATACTAGCACACATAGTGCATCATCGAATAAACTG
1 AAGTAATTATACTAGCACACA-AGTGCATCATCGAATAAACCG
* ** * * * *
34739739 AAGTAATCATACTAGCACGTAAGTGCATTATCGGATAAGCTG
1 AAGTAATTATACTAGCACACAAGTGCATCATCGAATAAACCG
* * ** * *
34739781 AAGAAAATATACTAGCACGTAAATGCATCATCGAATATACCG
1 AAGTAATTATACTAGCACACAAGTGCATCATCGAATAAACCG
34739823 AAGTA
1 AAGTA
34739828 TAAACCTATA
Statistics
Matches: 106, Mismatches: 25, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
42 55 0.52
43 50 0.47
44 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (42 bp):
AAGTAATTATACTAGCACACAAGTGCATCATCGAATAAACCG
Found at i:34739782 original size:42 final size:42
Alignment explanation
Indices: 34739696--34739817 Score: 147
Period size: 42 Copynumber: 2.9 Consensus size: 42
34739686 GGATGAACCA
* **
34739696 AAGAAATTATACTAGCACACATAGTGCATCATCGAATAAACTG
1 AAGAAAATATACTAGCACGTA-AGTGCATCATCGAATAAACTG
* * * *
34739739 AAG-TAATCATACTAGCACGTAAGTGCATTATCGGATAAGCTG
1 AAGAAAAT-ATACTAGCACGTAAGTGCATCATCGAATAAACTG
*
34739781 AAGAAAATATACTAGCACGTAAATGCATCATCGAATA
1 AAGAAAATATACTAGCACGTAAGTGCATCATCGAATA
34739818 TACCGAAGTA
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
42 49 0.74
43 17 0.26
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (42 bp):
AAGAAAATATACTAGCACGTAAGTGCATCATCGAATAAACTG
Found at i:34740254 original size:17 final size:17
Alignment explanation
Indices: 34740242--34740276 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
34740232 ATAATACAAT
34740242 ATCAAATTCAATATCAA
1 ATCAAATTCAATATCAA
* *
34740259 ATCATATTCAATTTCAA
1 ATCAAATTCAATATCAA
34740276 A
1 A
34740277 GTCATACATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (17 bp):
ATCAAATTCAATATCAA
Found at i:34741104 original size:23 final size:23
Alignment explanation
Indices: 34741064--34741135 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
34741054 TGGGGATAGG
*
34741064 ATCTAAATCTGTATCTGTTATGC
1 ATCTGAATCTGTATCTGTTATGC
* * *
34741087 ATTTGAATCTATAACTGTTATGC
1 ATCTGAATCTGTATCTGTTATGC
*
34741110 ATCTGAATCTGTATCTGCTATGC
1 ATCTGAATCTGTATCTGTTATGC
34741133 ATC
1 ATC
34741136 GATGTCTGTA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (23 bp):
ATCTGAATCTGTATCTGTTATGC
Found at i:34741374 original size:19 final size:20
Alignment explanation
Indices: 34741352--34741399 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
34741342 CGTTTTGTTT
34741352 GACTGTTTTGGA-CTTTTAG
1 GACTGTTTTGGATCTTTTAG
* *
34741371 GACTGTTTTGGATTTTTTTG
1 GACTGTTTTGGATCTTTTAG
34741391 GACTGTTTT
1 GACTGTTTT
34741400 AAATATGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.12, C:0.08, G:0.25, T:0.54
Consensus pattern (20 bp):
GACTGTTTTGGATCTTTTAG
Done.