Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 143 of 163
Found at i:38818150 original size:16 final size:16
Alignment explanation
Indices: 38818111--38818158 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
38818101 GAATGATATT
*
38818111 TTAGGTTTAAATTTTA
1 TTAGATTTAAATTTTA
*
38818127 TTATATTTAAATTTTCA
1 TTAGATTTAAATTTT-A
*
38818144 TT-GATTTATATTTTA
1 TTAGATTTAAATTTTA
38818159 AAATATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 1 0.04
16 23 0.85
17 3 0.11
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.60
Consensus pattern (16 bp):
TTAGATTTAAATTTTA
Found at i:38818849 original size:22 final size:21
Alignment explanation
Indices: 38818818--38818859 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
38818808 AATAAAGAAA
*
38818818 TGACGTGGGATGGAGTAGATAC
1 TGACGAGGGA-GGAGTAGATAC
*
38818840 TGACGAGGGAGTAGTAGATA
1 TGACGAGGGAGGAGTAGATA
38818860 ATTAAAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.31, C:0.07, G:0.40, T:0.21
Consensus pattern (21 bp):
TGACGAGGGAGGAGTAGATAC
Found at i:38837383 original size:12 final size:13
Alignment explanation
Indices: 38837368--38837396 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
38837358 GTTTTTCCTT
38837368 TTTTTATTTT-AA
1 TTTTTATTTTGAA
38837380 TTTTTATTTTGAA
1 TTTTTATTTTGAA
38837393 TTTT
1 TTTT
38837397 CCAATAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTTTATTTTGAA
Found at i:38839591 original size:26 final size:26
Alignment explanation
Indices: 38839537--38839593 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
38839527 CGCTTTTTTT
*
38839537 ATTTTAATATTTTTGAATTTTTATGA
1 ATTTTAATATTTTTGAATTTATATGA
*
38839563 ATTTTAATTTATTTTT-CATTTATAT-A
1 ATTTTAA--TATTTTTGAATTTATATGA
38839589 ATTTT
1 ATTTT
38839594 TAACGTAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 13 0.48
27 7 0.26
28 7 0.26
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (26 bp):
ATTTTAATATTTTTGAATTTATATGA
Found at i:38840522 original size:18 final size:18
Alignment explanation
Indices: 38840489--38840535 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
38840479 TTTTATAAGA
38840489 ATAATTTTTAAAATT-ATAC
1 ATAA-TTTT-AAATTAATAC
*
38840508 ATGAATTTTAAATTAATAT
1 AT-AATTTTAAATTAATAC
38840527 ATAATTTTA
1 ATAATTTTA
38840536 TACATGAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 12 0.48
19 11 0.44
20 2 0.08
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
ATAATTTTAAATTAATAC
Found at i:38848114 original size:6 final size:6
Alignment explanation
Indices: 38848105--38848131 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
38848095 GGGAGGAAAG
38848105 GGAAGC GGAAGC GGAAGC GGAAGC GGA
1 GGAAGC GGAAGC GGAAGC GGAAGC GGA
38848132 TGAGGAGCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.52, T:0.00
Consensus pattern (6 bp):
GGAAGC
Found at i:38849719 original size:30 final size:30
Alignment explanation
Indices: 38849685--38849749 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
38849675 ACTTATTTTA
* * * *
38849685 TTGTTAATTTTGTTATTATCTTATAGGTAT
1 TTGTTAATTTTATTACTATCTTAAAGGCAT
*
38849715 TTGTTAATTTTATTACTATTTTAAAGGCAT
1 TTGTTAATTTTATTACTATCTTAAAGGCAT
38849745 TTGTT
1 TTGTT
38849750 TGTTAAGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.05, G:0.12, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTATTACTATCTTAAAGGCAT
Found at i:38849916 original size:13 final size:12
Alignment explanation
Indices: 38849860--38849917 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 12
38849850 ATGTATTATA
*
38849860 TATATTAAAAAT
1 TATATAAAAAAT
*
38849872 TATTTAAAAAAAT
1 TATAT-AAAAAAT
*
38849885 TTTGATCAAAAAAT
1 TAT-AT-AAAAAAT
38849899 TATATAAAAAAT
1 TATATAAAAAAT
38849911 TAATATA
1 T-ATATA
38849918 GGCGGGTCGG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
12 12 0.32
13 15 0.41
14 10 0.27
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (12 bp):
TATATAAAAAAT
Found at i:38850087 original size:56 final size:56
Alignment explanation
Indices: 38850021--38850139 Score: 193
Period size: 56 Copynumber: 2.1 Consensus size: 56
38850011 ATGTTATTTT
* * * * *
38850021 TTGGTAACTTAATTATGAAAAGTTAGAAAATTATCACCCAACTATTAGTAAAATTA
1 TTGGTCACTTAATTAAGAAAAGTTACAAAATGATCACCCAACCATTAGTAAAATTA
38850077 TTGGTCACTTAATTAAGAAAAGTTACAAAATGATCACCCAACCATTAGTAAAATTA
1 TTGGTCACTTAATTAAGAAAAGTTACAAAATGATCACCCAACCATTAGTAAAATTA
38850133 TTGGTCA
1 TTGGTCA
38850140 TCCGACTATG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (56 bp):
TTGGTCACTTAATTAAGAAAAGTTACAAAATGATCACCCAACCATTAGTAAAATTA
Found at i:38850153 original size:56 final size:56
Alignment explanation
Indices: 38850034--38850168 Score: 182
Period size: 56 Copynumber: 2.4 Consensus size: 56
38850024 GTAACTTAAT
* * * * *
38850034 TATGAAAAGTTAGAAAATTATCACCCAACTATTAGTAAAATTATTGGTCACTTAAT
1 TATGAAAAGTTACAAAATGATCACCCAACCATTAGTAAAATTATTGGTCACTCAAC
* *
38850090 TAAGAAAAGTTACAAAATGATCACCCAACCATTAGTAAAATTATTGGTCA-TCCGAC
1 TATGAAAAGTTACAAAATGATCACCCAACCATTAGTAAAATTATTGGTCACT-CAAC
*
38850146 TATGAAAAATTACAAAATGATCA
1 TATGAAAAGTTACAAAATGATCA
38850169 TTCAATTATT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
55 1 0.01
56 68 0.99
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (56 bp):
TATGAAAAGTTACAAAATGATCACCCAACCATTAGTAAAATTATTGGTCACTCAAC
Found at i:38851066 original size:30 final size:30
Alignment explanation
Indices: 38851000--38851063 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
38850990 TTTTTGTATT
* * *
38851000 TAAAAAT-AAATAAATTAAATTCTTAAAGA
1 TAAAAATAAAAAAAACTAAATTCTTAAACA
38851029 TAAAAATAAAAAAAACTAAATTC-TAAACA
1 TAAAAATAAAAAAAACTAAATTCTTAAACA
38851058 TAAAAA
1 TAAAAA
38851064 ATATGTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (30 bp):
TAAAAATAAAAAAAACTAAATTCTTAAACA
Found at i:38852512 original size:11 final size:11
Alignment explanation
Indices: 38852481--38852522 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
38852471 CCCAACTTGG
38852481 ATTTTAAATTA
1 ATTTTAAATTA
* *
38852492 AGTTTGAATTA
1 ATTTTAAATTA
*
38852503 ATTTTAAATTT
1 ATTTTAAATTA
38852514 A-TTTAAATT
1 ATTTTAAATT
38852523 TAAATTTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (11 bp):
ATTTTAAATTA
Found at i:38852522 original size:17 final size:17
Alignment explanation
Indices: 38852483--38852544 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
38852473 CAACTTGGAT
*
38852483 TTTAAA-TTAAGTTTGA
1 TTTAAATTTAAATTTGA
* *
38852499 ATTAATTTTAAATTT-A
1 TTTAAATTTAAATTTGA
*
38852515 TTTAAATTTAAATTTGT
1 TTTAAATTTAAATTTGA
38852532 TTTAAATTTAAAT
1 TTTAAATTTAAAT
38852545 ACATTTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
16 18 0.47
17 20 0.53
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAATTTAAATTTGA
Found at i:38852525 original size:22 final size:22
Alignment explanation
Indices: 38852481--38852522 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
38852471 CCCAACTTGG
*
38852481 ATTTTAAATTAAGTTTGAATTA
1 ATTTTAAATTAAGTTTAAATTA
*
38852503 ATTTTAAATTTA-TTTAAATT
1 ATTTTAAATTAAGTTTAAATT
38852523 TAAATTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTTTAAATTAAGTTTAAATTA
Found at i:38852528 original size:27 final size:27
Alignment explanation
Indices: 38852487--38852569 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 27
38852477 TTGGATTTTA
* *
38852487 AATTAAGTTTGAATTAATTTTAAATTT
1 AATTAAATTTAAATTAATTTTAAATTT
* **
38852514 ATTTAAATTTAAATTTGTTTTAAATTT
1 AATTAAATTTAAATTAATTTTAAATTT
* * * * *
38852541 AAATACATTTAAAATAATTTGAAACTT
1 AATTAAATTTAAATTAATTTTAAATTT
38852568 AA
1 AA
38852570 ACTTAAAATT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (27 bp):
AATTAAATTTAAATTAATTTTAAATTT
Found at i:38852553 original size:16 final size:16
Alignment explanation
Indices: 38852500--38852553 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
38852490 TAAGTTTGAA
* *
38852500 TTAATTTTAAATTTAT
1 TTAAATTTAAATTCAT
**
38852516 TTAAATTTAAATTTGTT
1 TTAAATTTAAA-TTCAT
*
38852533 TTAAATTTAAATACAT
1 TTAAATTTAAATTCAT
38852549 TTAAA
1 TTAAA
38852554 ATAATTTGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
TTAAATTTAAATTCAT
Found at i:38853031 original size:24 final size:25
Alignment explanation
Indices: 38852953--38853031 Score: 74
Period size: 24 Copynumber: 3.2 Consensus size: 25
38852943 AAGGGTTACG
* * *
38852953 AACCCAATTC-TGAAAATCAACACA
1 AACCCGATTCTTGAAAATAAAAACA
*
38852977 AACCCTATTCTTGATAAATAAAAA-A
1 AACCCGATTCTTGA-AAATAAAAACA
*
38853002 AGACCCGGTTCTTG-AAATAAAAACA
1 A-ACCCGATTCTTGAAAATAAAAACA
38853027 AACCC
1 AACCC
38853032 TTTTCATTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
24 22 0.48
25 7 0.15
26 17 0.37
ACGTcount: A:0.48, C:0.24, G:0.08, T:0.20
Consensus pattern (25 bp):
AACCCGATTCTTGAAAATAAAAACA
Found at i:38853301 original size:3 final size:3
Alignment explanation
Indices: 38853295--38853376 Score: 65
Period size: 3 Copynumber: 26.3 Consensus size: 3
38853285 TAAATATTAT
* * * * *
38853295 TAA TAA TAT TAC TAA TAA TCA TAA TAA TAA TTAA TAG TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
* * *
38853341 TCAA TAA TAA TTAT TAA TAA TAG TAA TAA TAT TAA T
1 T-AA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA T
38853377 GACCATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 6
0.74 0.18 0.07
Matches are distributed among these distances:
3 54 0.89
4 7 0.11
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:38853335 original size:16 final size:15
Alignment explanation
Indices: 38853316--38853376 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 15
38853306 CTAATAATCA
38853316 TAATAATAATTAATAG
1 TAATAAT-ATTAATAG
*
38853332 TAATAATATTCAATAA
1 TAATAATATT-AATAG
* *
38853348 TAATTATTAATAATAG
1 TAA-TAATATTAATAG
38853364 TAATAATATTAAT
1 TAATAATATTAAT
38853377 GACCATAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
15 11 0.30
16 21 0.57
17 5 0.14
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (15 bp):
TAATAATATTAATAG
Found at i:38853348 original size:13 final size:12
Alignment explanation
Indices: 38853287--38853376 Score: 74
Period size: 12 Copynumber: 7.2 Consensus size: 12
38853277 TAACCTTTTA
*
38853287 AATATTATTAAT
1 AATATTAATAAT
*
38853299 AATATTACTAAT
1 AATATTAATAAT
38853311 AATCA-TAATAAT
1 AAT-ATTAATAAT
* *
38853323 AATTAATAGTAAT
1 AA-TATTAATAAT
38853336 AATATTCAATAAT
1 AATATT-AATAAT
38853349 AATTATTAATAAT
1 AA-TATTAATAAT
* * *
38853362 AGTAATAATATT
1 AATATTAATAAT
38853374 AAT
1 AAT
38853377 GACCATAAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
12 36 0.56
13 24 0.38
14 4 0.06
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (12 bp):
AATATTAATAAT
Found at i:38854444 original size:29 final size:29
Alignment explanation
Indices: 38854406--38854558 Score: 179
Period size: 29 Copynumber: 5.3 Consensus size: 29
38854396 AAAATTCTAT
38854406 TTTTGACCCCAAAACTTCCAAAAATTACCA
1 TTTT-ACCCCAAAACTTCCAAAAATTACCA
* * *
38854436 TTTTACCCCTAAACTTTCTAAAATT-CCA
1 TTTTACCCCAAAACTTCCAAAAATTACCA
*
38854464 TTTTAACCCAAAAACTTCCAAAAATTACCA
1 TTTT-ACCCCAAAACTTCCAAAAATTACCA
* *
38854494 TTTTACCCCTAAACTTCC-TAAATT-CCA
1 TTTTACCCCAAAACTTCCAAAAATTACCA
*
38854521 TTTTA-ACCATGAAACTTCCAAAAATTACCA
1 TTTTACCCCA--AAACTTCCAAAAATTACCA
38854551 TTTTACCC
1 TTTTACCC
38854559 TCGAACTTTC
Statistics
Matches: 102, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
26 2 0.02
27 8 0.08
28 20 0.20
29 52 0.51
30 19 0.19
31 1 0.01
ACGTcount: A:0.37, C:0.29, G:0.01, T:0.33
Consensus pattern (29 bp):
TTTTACCCCAAAACTTCCAAAAATTACCA
Found at i:38854485 original size:58 final size:57
Alignment explanation
Indices: 38854391--38854705 Score: 295
Period size: 59 Copynumber: 5.4 Consensus size: 57
38854381 TCCTCGAACT
* * *
38854391 TTTCAAAAATTCTATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCCTAAAC
1 TTTCTAAAATTCCATTTTT-AACCC-AAACTTCCAAAAATTACCATTTTACCCCTAAAC
38854450 TTTCTAAAATTCCA-TTTTAACCCAAAAACTTCCAAAAATTACCATTTTACCCCTAAAC
1 TTTCTAAAATTCCATTTTTAACCC--AAACTTCCAAAAATTACCATTTTACCCCTAAAC
* * *
38854508 TTCCT-AAATTCCA-TTTTAACCATGAAACTTCCAAAAATTACCATTTTA-CCCTCGAAC
1 TTTCTAAAATTCCATTTTTAACC--CAAACTTCCAAAAATTACCATTTTACCCCT-AAAC
* * * * *
38854565 TTTCTAAAATTTCATTTTTAACCCCAATTTCACCAAAAATTACCATTTT-GCCCTCGAAC
1 TTTCTAAAATTCCATTTTTAACCCAAACTT--CCAAAAATTACCATTTTACCCCT-AAAC
* ** * *
38854624 TTTCTAAAA-TCCTATTTTTAATCCTGATTTCACCAAAAATTACCATTTTACCCTTAAAC
1 TTTCTAAAATTCC-ATTTTTAACCCAAACTT--CCAAAAATTACCATTTTACCCCTAAAC
38854683 TTT-TCAAAA-TCTCATTTTTAACC
1 TTTCT-AAAATTC-CATTTTTAACC
38854706 TCGATTTCAC
Statistics
Matches: 224, Mismatches: 19, Indels: 26
0.83 0.07 0.10
Matches are distributed among these distances:
56 4 0.02
57 55 0.25
58 52 0.23
59 109 0.49
60 4 0.02
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (57 bp):
TTTCTAAAATTCCATTTTTAACCCAAACTTCCAAAAATTACCATTTTACCCCTAAAC
Found at i:38854523 original size:57 final size:58
Alignment explanation
Indices: 38854396--38854613 Score: 257
Period size: 58 Copynumber: 3.7 Consensus size: 58
38854386 GAACTTTTCA
* * * *
38854396 AAAATTCTATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCCTAAACTTTCT
1 AAAATTCCA-TTTTAACCCAAAAACTTCCAAAAATTACCATTTTACCCCTAAACTTCCT
38854455 AAAATTCCATTTTAACCCAAAAACTTCCAAAAATTACCATTTTACCCCTAAACTTCCT
1 AAAATTCCATTTTAACCCAAAAACTTCCAAAAATTACCATTTTACCCCTAAACTTCCT
* * *
38854513 -AAATTCCATTTTAA-CCATGAAACTTCCAAAAATTACCATTTTA-CCCTCGAACTTTCT
1 AAAATTCCATTTTAACCCA-AAAACTTCCAAAAATTACCATTTTACCCCT-AAACTTCCT
* * *
38854570 AAAATTTCATTTTTAACCC--CAATTTCACCAAAAATTACCATTTT
1 AAAATTCCA-TTTTAACCCAAAAACTT--CCAAAAATTACCATTTT
38854614 GCCCTCGAAC
Statistics
Matches: 142, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
56 7 0.05
57 49 0.35
58 53 0.37
59 31 0.22
60 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.01, T:0.35
Consensus pattern (58 bp):
AAAATTCCATTTTAACCCAAAAACTTCCAAAAATTACCATTTTACCCCTAAACTTCCT
Found at i:38854565 original size:29 final size:28
Alignment explanation
Indices: 38854406--38854613 Score: 165
Period size: 29 Copynumber: 7.1 Consensus size: 28
38854396 AAAATTCTAT
38854406 TTTTGACCCCAAAACTTCCAAAAATTACCA
1 TTTT-ACCCC-AAACTTCCAAAAATTACCA
* *
38854436 TTTTACCCCTAAACTTTCTAAAATT-CCA
1 TTTTACCCC-AAACTTCCAAAAATTACCA
*
38854464 TTTTAACCCAAAAACTTCCAAAAATTACCA
1 TTTT-ACCC-CAAACTTCCAAAAATTACCA
*
38854494 TTTTACCCCTAAACTTCC-TAAATT-CCA
1 TTTTACCCC-AAACTTCCAAAAATTACCA
**
38854521 TTTTAACCATGAAACTTCCAAAAATTACCA
1 TTTT-ACC-CCAAACTTCCAAAAATTACCA
* * * *
38854551 TTTTACCCTCGAACTTTCTAAAATT-TCA
1 TTTTACCC-CAAACTTCCAAAAATTACCA
*
38854579 TTTTTAACCCC-AATTTCACCAAAAATTACCA
1 -TTTT-ACCCCAAACTT--CCAAAAATTACCA
38854610 TTTT
1 TTTT
38854614 GCCCTCGAAC
Statistics
Matches: 143, Mismatches: 21, Indels: 28
0.74 0.11 0.15
Matches are distributed among these distances:
27 7 0.05
28 29 0.20
29 72 0.50
30 33 0.23
31 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.01, T:0.35
Consensus pattern (28 bp):
TTTTACCCCAAACTTCCAAAAATTACCA
Found at i:38854613 original size:59 final size:59
Alignment explanation
Indices: 38854423--38854740 Score: 304
Period size: 59 Copynumber: 5.4 Consensus size: 59
38854413 CCCAAAACTT
*
38854423 CCAAAAATTACCATTTTACCC-CTAAACTTTCTAAAATTCCA-TTTTAACCCAAAAACTT--
1 CCAAAAATTACCATTTTACCCTC-AAACTTTCTAAAATTCCATTTTTAACCC--AAATTTCA
* * *
38854481 CCAAAAATTACCATTTTACCC-CTAAACTTCCT-AAATTCCA-TTTTAACCATGAAACTT--
1 CCAAAAATTACCATTTTACCCTC-AAACTTTCTAAAATTCCATTTTTAACC--CAAATTTCA
* * *
38854538 CCAAAAATTACCATTTTACCCTCGAACTTTCTAAAATTTCATTTTTAACCCCAATTTCA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCTAAAATTCCATTTTTAACCCAAATTTCA
* * * **
38854597 CCAAAAATTACCATTTTGCCCTCGAACTTTCTAAAA-TCCTATTTTTAATCCTGATTTCA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCTAAAATTCC-ATTTTTAACCCAAATTTCA
* *
38854656 CCAAAAATTACCATTTTACCCTTAAACTTT-TCAAAA-TCTCATTTTTAACCTC-GATTTCA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCT-AAAATTC-CATTTTTAACC-CAAATTTCA
*
38854715 CCAAAAATCA-CATTTTTACCCTCAAA
1 CCAAAAATTACCA-TTTTACCCTCAAA
38854741 AGTCAAAATT
Statistics
Matches: 229, Mismatches: 19, Indels: 23
0.85 0.07 0.08
Matches are distributed among these distances:
57 54 0.24
58 44 0.19
59 129 0.56
60 2 0.01
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.36
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCTCAAACTTTCTAAAATTCCATTTTTAACCCAAATTTCA
Found at i:38866720 original size:199 final size:198
Alignment explanation
Indices: 38866330--38866974 Score: 828
Period size: 199 Copynumber: 3.2 Consensus size: 198
38866320 AGAGTAGTTC
* * * *
38866330 AACAAGCGAGGCAGTCATCTTTCTGATGAGACACAGAGAAGAACACCAACTCAGCGCTCAAAACA
1 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAGCGCTC--AATA
* * * * * *
38866395 CGAGCAAATCTTCGAACCTAGCTTCCTGATGAGACACTAAGAAGTAGGTTGAAGCAATAAAAAGG
64 CGAGCAAATCTTCGAACCCAGCTTCCT-ATGAGGCACTGAGAAGCAGG-TCAAGCAATAAAAAAG
* *
38866460 TTAGCTTCTTGATGAGACACAGAGAAGTGGACTAGATTTGTCTTCCTGAGGAGATCCAGAGAAGC
127 TTAGCTTCCTGATGAGACACAGAGAAGTGGACTAGATTCGTCTTCCTGAGGAGATCCAGAGAAGC
38866525 GAATCAA
192 GAATCAA
*
38866532 AACAAGC-ATGGCGGTCATCTTCCTGATGAGATATAGAGAAGAACACCAACTCAGCGCTCAATAC
1 AACAAGCGA-GGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAGCGCTCAATAC
* *
38866596 GAGCAAATCTTCGAACCCAGCTTCCTATGAGGCACTGAGAAGCAGGTCAAGGCAACAAAAAAGTC
65 GAGCAAATCTTCGAACCCAGCTTCCTATGAGGCACTGAGAAGCAGGTCAA-GCAATAAAAAAGTT
*
38866661 AGCTTCCTGATGAGACACAAAGAAGTGGACTAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGA
129 AGCTTCCTGATGAGACACAGAGAAGTGGACTAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGA
*
38866726 ATGAA
194 ATCAA
** * * * *
38866731 AACAAGCGAGATGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAATTCAACGCTCAATGCG
1 AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAGCGCTCAATACG
* * **
38866796 AGCAAACCTTCGAACCCAGCTTCCCGATGAGGTGCTGAGAAGCAGGTCGAAGCAATAAAAAAGTT
66 AGCAAATCTTCGAACCCAGCTT-CCTATGAGGCACTGAGAAGCAGGTC-AAGCAATAAAAAAGTT
** * * *
38866861 AGCTTCCTGATGAGACATGGAGAAGTGGACCAAATTCGTCTTCCTG-GGAAGATTCAGAGAAGCG
129 AGCTTCCTGATGAGACACAGAGAAGTGGACTAGATTCGTCTTCCTGAGG-AGATCCAGAGAAGCG
*
38866925 AATTAA
193 AATCAA
* * * * *
38866931 AAC-AGATGATTGCGGTCATCCTCCTGATGAGACACGGAGAAGAA
1 AACAAG-CGA-GGCGGTCATCTTCCTGATGAGATACAGAGAAGAA
38866975 GGCCAGGTCA
Statistics
Matches: 391, Mismatches: 44, Indels: 17
0.87 0.10 0.04
Matches are distributed among these distances:
198 3 0.01
199 175 0.45
200 129 0.33
201 31 0.08
202 53 0.14
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (198 bp):
AACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAGCGCTCAATACG
AGCAAATCTTCGAACCCAGCTTCCTATGAGGCACTGAGAAGCAGGTCAAGCAATAAAAAAGTTAG
CTTCCTGATGAGACACAGAGAAGTGGACTAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAAT
CAA
Found at i:38867343 original size:11 final size:11
Alignment explanation
Indices: 38867312--38867353 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
38867302 CCCAACTTGG
38867312 ATTTTAAATTA
1 ATTTTAAATTA
* *
38867323 AGTTTGAATTA
1 ATTTTAAATTA
*
38867334 ATTTTAAATTT
1 ATTTTAAATTA
38867345 A-TTTAAATT
1 ATTTTAAATT
38867354 TAAATTTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (11 bp):
ATTTTAAATTA
Found at i:38867353 original size:17 final size:17
Alignment explanation
Indices: 38867314--38867375 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
38867304 CAACTTGGAT
*
38867314 TTTAAA-TTAAGTTTGA
1 TTTAAATTTAAATTTGA
* *
38867330 ATTAATTTTAAATTT-A
1 TTTAAATTTAAATTTGA
*
38867346 TTTAAATTTAAATTTGT
1 TTTAAATTTAAATTTGA
38867363 TTTAAATTTAAAT
1 TTTAAATTTAAAT
38867376 ACATTTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
16 18 0.47
17 20 0.53
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAATTTAAATTTGA
Found at i:38867356 original size:22 final size:22
Alignment explanation
Indices: 38867312--38867353 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
38867302 CCCAACTTGG
*
38867312 ATTTTAAATTAAGTTTGAATTA
1 ATTTTAAATTAAGTTTAAATTA
*
38867334 ATTTTAAATTTA-TTTAAATT
1 ATTTTAAATTAAGTTTAAATT
38867354 TAAATTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTTTAAATTAAGTTTAAATTA
Found at i:38867359 original size:27 final size:27
Alignment explanation
Indices: 38867318--38867391 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
38867308 TTGGATTTTA
* *
38867318 AATTAAGTTTGAATTAATTTTAAATTT
1 AATTAAATTTAAATTAATTTTAAATTT
* **
38867345 ATTTAAATTTAAATTTGTTTTAAATTT
1 AATTAAATTTAAATTAATTTTAAATTT
* * *
38867372 AAATACATTTAAAATAATTT
1 AATTAAATTTAAATTAATTT
38867392 GAAGCTTAAA
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (27 bp):
AATTAAATTTAAATTAATTTTAAATTT
Found at i:38867384 original size:16 final size:16
Alignment explanation
Indices: 38867331--38867384 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
38867321 TAAGTTTGAA
* *
38867331 TTAATTTTAAATTTAT
1 TTAAATTTAAATTCAT
**
38867347 TTAAATTTAAATTTGTT
1 TTAAATTTAAA-TTCAT
*
38867364 TTAAATTTAAATACAT
1 TTAAATTTAAATTCAT
38867380 TTAAA
1 TTAAA
38867385 ATAATTTGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
TTAAATTTAAATTCAT
Found at i:38867836 original size:26 final size:25
Alignment explanation
Indices: 38867805--38867862 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
38867795 TAAAATTAAC
*
38867805 ACAAACCCTATTCTTGATAAATAAAAA
1 ACAAACCCGATTCTTG--AAATAAAAA
*
38867832 A-AAACCCGGTTCTTGAAATAAAAA
1 ACAAACCCGATTCTTGAAATAAAAA
38867856 ACAAACC
1 ACAAACC
38867863 ATTTTCATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 10 0.36
25 5 0.18
26 12 0.43
27 1 0.04
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.21
Consensus pattern (25 bp):
ACAAACCCGATTCTTGAAATAAAAA
Found at i:38868133 original size:3 final size:3
Alignment explanation
Indices: 38868127--38868204 Score: 75
Period size: 3 Copynumber: 25.0 Consensus size: 3
38868117 TAAATATTAT
* * * *
38868127 TAA TAA TAT TAC TAC TAA TAA TAA TAA TAA TAA TGAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
* *
38868173 TAT TCAA TAA TAA TTAA TAA TAA TAG TAA TAA
1 TAA T-AA TAA TAA -TAA TAA TAA TAA TAA TAA
38868205 ATATTAATGA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
3 55 0.87
4 8 0.13
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:38868181 original size:10 final size:9
Alignment explanation
Indices: 38868119--38868194 Score: 62
Period size: 9 Copynumber: 7.8 Consensus size: 9
38868109 TAACCTTTTA
*
38868119 AATATTATT
1 AATAATATT
38868128 AATAATATT
1 AATAATATT
*
38868137 ACTACTAATAAT
1 A--A-TAATATT
*
38868149 AATAATAAT
1 AATAATATT
*
38868158 AATGAATAGT
1 AAT-AATATT
38868168 AATAATATT
1 AATAATATT
38868177 CAATAATAATT
1 -AATAAT-ATT
38868188 AATAATA
1 AATAATA
38868195 ATAGTAATAA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
9 25 0.44
10 21 0.37
11 4 0.07
12 7 0.12
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (9 bp):
AATAATATT
Found at i:38868183 original size:13 final size:12
Alignment explanation
Indices: 38868119--38868212 Score: 70
Period size: 12 Copynumber: 8.0 Consensus size: 12
38868109 TAACCTTTTA
*
38868119 AATATTATTAAT
1 AATAATATTAAT
* * *
38868131 AATATTACTACT
1 AATAATATTAAT
*
38868143 AATAATAATAAT
1 AATAATATTAAT
* *
38868155 AATAATGAATAGT
1 AATAAT-ATTAAT
38868168 AATAATATTCAAT
1 AATAATATT-AAT
38868181 AAT-A-ATTAAT
1 AATAATATTAAT
*
38868191 AATAATAGTAAT
1 AATAATATTAAT
38868203 -A-AATATTAAT
1 AATAATATTAAT
38868213 GACCATAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
10 14 0.21
11 5 0.07
12 33 0.49
13 16 0.24
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:38868207 original size:16 final size:15
Alignment explanation
Indices: 38868127--38868204 Score: 75
Period size: 16 Copynumber: 5.0 Consensus size: 15
38868117 TAAATATTAT
* * *
38868127 TAATAATATTACTAC
1 TAATAATAATAATAA
38868142 TAATAATAATAATAA
1 TAATAATAATAATAA
*
38868157 TAATGAATAGTAATAA
1 TAAT-AATAATAATAA
*
38868173 TATTCAATAATAATTAA
1 TAAT-AATAATAA-TAA
*
38868190 TAATAATAGTAATAA
1 TAATAATAATAATAA
38868205 ATATTAATGA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
15 19 0.37
16 27 0.52
17 6 0.12
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (15 bp):
TAATAATAATAATAA
Found at i:38868212 original size:16 final size:15
Alignment explanation
Indices: 38868145--38868212 Score: 64
Period size: 16 Copynumber: 4.3 Consensus size: 15
38868135 TTACTACTAA
*
38868145 TAATAATAATAATAAT
1 TAATAGTAATAAT-AT
*
38868161 GAATAGTAATAATAT
1 TAATAGTAATAATAT
* *
38868176 TCAATAATAATTAATAA
1 T-AATAGTAA-TAATAT
38868193 TAATAGTAATAAATAT
1 TAATAGTAAT-AATAT
38868209 TAAT
1 TAAT
38868213 GACCATAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
15 3 0.07
16 33 0.79
17 6 0.14
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (15 bp):
TAATAGTAATAATAT
Found at i:38869247 original size:29 final size:29
Alignment explanation
Indices: 38869210--38869356 Score: 115
Period size: 30 Copynumber: 5.0 Consensus size: 29
38869200 TCTAGTCCTC
*
38869210 AAACTTTCCAAAATTCCATTTTTGACCTCG
1 AAACTTTCCAAAATTCCATTTTT-ACCCCG
* *
38869240 AAAC-TTCCAAAAATTAC-TATTTTACCCCT
1 AAACTTTCC-AAAATTCCAT-TTTTACCCCG
* * * *
38869269 AAACTTTCTAAATTTTCATTTTTAACCCCA
1 AAACTTTCCAAAATTCCATTTTT-ACCCCG
38869299 AAAC-TTCCAAAAATTACCA-TTTTACTCCCG
1 AAACTTTCC-AAAATT-CCATTTTTAC-CCCG
*
38869329 -AACTTTCCAAAATCCCATTTTTAACCCC
1 AAACTTTCCAAAATTCCATTTTT-ACCCC
38869357 CATTTCACCA
Statistics
Matches: 94, Mismatches: 12, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
28 3 0.03
29 43 0.46
30 46 0.49
31 2 0.02
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (29 bp):
AAACTTTCCAAAATTCCATTTTTACCCCG
Found at i:38869303 original size:59 final size:58
Alignment explanation
Indices: 38869210--38869447 Score: 225
Period size: 59 Copynumber: 4.1 Consensus size: 58
38869200 TCTAGTCCTC
* * * *
38869210 AAACTTTCCAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTACTATTTTACCCCT
1 AAACTTTCCAAAATCCCATTTTTAACC-CCAAACTTCCAAAAATTACCATTTTACCCCT
* * **
38869269 AAACTTTCTAAATTTTCATTTTTAACCCCAAAACTTCCAAAAATTACCATTTTACTCCC-
1 AAACTTTCCAAAATCCCATTTTTAACCCC-AAACTTCCAAAAATTACCATTTTAC-CCCT
* * *
38869328 GAACTTTCCAAAATCCCATTTTTAACCCC-CATTTCACCAAAAATTACCATTTTACCCCT
1 AAACTTTCCAAAATCCCATTTTTAACCCCAAACTT--CCAAAAATTACCATTTTACCCCT
* * * * *
38869387 AAACTTTCTAAAATCTCA-TTTTAA-CCCTAATTTCACCAAAAATCA-CATTTTTACCCCT
1 AAACTTTCCAAAATCCCATTTTTAACCCCAAACTT--CCAAAAATTACCA-TTTTACCCCT
38869445 AAA
1 AAA
38869448 AGTCAAAATT
Statistics
Matches: 154, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
57 8 0.05
58 38 0.25
59 105 0.68
60 3 0.02
ACGTcount: A:0.35, C:0.29, G:0.01, T:0.35
Consensus pattern (58 bp):
AAACTTTCCAAAATCCCATTTTTAACCCCAAACTTCCAAAAATTACCATTTTACCCCT
Found at i:38869400 original size:29 final size:29
Alignment explanation
Indices: 38869210--38869416 Score: 108
Period size: 30 Copynumber: 7.1 Consensus size: 29
38869200 TCTAGTCCTC
* * *
38869210 AAACTTTCCAAAATT-CCATTTTTGACCTCG
1 AAACTTTCAAAAATTACCA-TTTT-ACCCCT
* *
38869240 AAACTTCCAAAAATTACTATTTTACCCCT
1 AAACTTTCAAAAATTACCATTTTACCCCT
* ** *
38869269 AAACTTTC-TAAATTTTCATTTTTAACCCCA
1 AAACTTTCAAAAATTACCA-TTTT-ACCCCT
*
38869299 AAACTTCCAAAAATTACCATTTTACTCCC-
1 AAACTTTCAAAAATTACCATTTTAC-CCCT
* * *
38869328 GAACTTTCCAAAA-TCCCATTTTTAACCCC-
1 AAACTTTCAAAAATTACCA-TTTT-ACCCCT
*
38869357 -CA-TTTCACCAAAAATTACCATTTTACCCCT
1 AAACTTT---CAAAAATTACCATTTTACCCCT
* *
38869387 AAACTTTCTAAAA-T-CTCATTTTAACCCT
1 AAACTTTCAAAAATTAC-CATTTTACCCCT
38869415 AA
1 AA
38869417 TTTCACCAAA
Statistics
Matches: 137, Mismatches: 25, Indels: 32
0.71 0.13 0.16
Matches are distributed among these distances:
27 4 0.03
28 25 0.18
29 44 0.32
30 47 0.34
31 14 0.10
32 3 0.02
ACGTcount: A:0.35, C:0.29, G:0.01, T:0.35
Consensus pattern (29 bp):
AAACTTTCAAAAATTACCATTTTACCCCT
Found at i:38869428 original size:29 final size:29
Alignment explanation
Indices: 38869337--38869442 Score: 76
Period size: 29 Copynumber: 3.6 Consensus size: 29
38869327 CGAACTTTCC
* **
38869337 AAAATCCCATTTTTAACCCCCATTTCACCA
1 AAAATCTCA-TTTTAACCCTAATTTCACCA
* *
38869367 AAAAT-TACCATTTTACCCCTAAACTTT---CT
1 AAAATCT--CATTTTAACCCT-AA-TTTCACCA
38869396 AAAATCTCATTTTAACCCTAATTTCACCA
1 AAAATCTCATTTTAACCCTAATTTCACCA
* *
38869425 AAAATCACATTTTTACCC
1 AAAATCTCATTTTAACCC
38869443 CTAAAAGTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
26 3 0.05
27 2 0.03
28 11 0.19
29 23 0.39
30 14 0.24
31 3 0.05
32 3 0.05
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.34
Consensus pattern (29 bp):
AAAATCTCATTTTAACCCTAATTTCACCA
Found at i:38872687 original size:28 final size:28
Alignment explanation
Indices: 38872655--38872785 Score: 97
Period size: 28 Copynumber: 4.6 Consensus size: 28
38872645 GTAGTCAGGA
*
38872655 TAAAATGCAATTTTTGGATACTCGGGGG
1 TAAAATGTAATTTTTGGATACTCGGGGG
*
38872683 TAAAACGGTAA-TTTTGGATACTTC-GGGG
1 TAAAA-TGTAATTTTTGGATAC-TCGGGGG
* *** *
38872711 -CAAATAGTAATTTTTGGAGGTTCGGGGT
1 TAAAAT-GTAATTTTTGGATACTCGGGGG
* * *
38872739 TAAAAATGTAATTTTTGGGACATTCGAGGG
1 T-AAAATGTAATTTTT-GGATACTCGGGGG
38872769 TAAAATGGTAATTTTTG
1 TAAAAT-GTAATTTTTG
38872786 AAAATTTAAG
Statistics
Matches: 81, Mismatches: 13, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
27 9 0.11
28 29 0.36
29 20 0.25
30 23 0.28
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (28 bp):
TAAAATGTAATTTTTGGATACTCGGGGG
Found at i:38872797 original size:29 final size:29
Alignment explanation
Indices: 38872765--38873107 Score: 168
Period size: 29 Copynumber: 11.7 Consensus size: 29
38872755 GGGACATTCG
38872765 AGGGTAAAATGGTAATTTTTGAAAATTTA
1 AGGGTAAAATGGTAATTTTTGAAAATTTA
* * *
38872794 AGGGTAATATGGTAATTTTTGAAAGGTTCGGA
1 AGGGTAAAATGGTAATTTTTGAAA-ATT--TA
*** * * **
38872826 A-CCAAAAAT-G-AATTTTTTGGAAGTTCG
1 AGGGTAAAATGGTAA-TTTTTGAAAATTTA
* * *
38872853 AGGGTAATATGGTAAGTTTTGAAGAGTTT-
1 AGGGTAAAATGGTAATTTTTGAA-AATTTA
* *
38872882 GGGGTCAAAAATAG-AATTTTTGAAAATTTA
1 AGGGT--AAAATGGTAATTTTTGAAAATTTA
* * * * * *
38872912 GGGGTAATACGGTAATTTTTAAAAAGTTC
1 AGGGTAAAATGGTAATTTTTGAAAATTTA
* * * *
38872941 GGGGTAAAAAAT-GAAATTTTTGGAAATCTA
1 AGGGT--AAAATGGTAATTTTTGAAAATTTA
* * *
38872971 AGGGTAATATGGTAATTTTTGGAAAGTT-
1 AGGGTAAAATGGTAATTTTTGAAAATTTA
* **
38872999 CGGGTCAAAAATGG-AATTTTT-AGAAATTCG
1 AGGGT--AAAATGGTAATTTTTGA-AAATTTA
38873029 AGGGTAAAATGGTAATTTTTTGAAAATTTA
1 AGGGTAAAATGGTAA-TTTTTGAAAATTTA
* *
38873059 AGGGTTAAAT-GTAATTTTTAGAAAGTTTA
1 AGGGTAAAATGGTAATTTTT-GAAAATTTA
*
38873088 GGGGTTAAAAT-GTAATTTTT
1 AGGG-TAAAATGGTAATTTTT
38873108 AGAGAGTTTG
Statistics
Matches: 237, Mismatches: 53, Indels: 47
0.70 0.16 0.14
Matches are distributed among these distances:
27 1 0.00
28 28 0.12
29 103 0.43
30 90 0.38
31 13 0.05
32 2 0.01
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (29 bp):
AGGGTAAAATGGTAATTTTTGAAAATTTA
Found at i:38872809 original size:59 final size:57
Alignment explanation
Indices: 38872746--38873107 Score: 241
Period size: 59 Copynumber: 6.2 Consensus size: 57
38872736 GGTTAAAAAT
** *
38872746 GTAATTTTTGGGACATTCGAGGGT-AAAATGGTAATTTTTGAAAATTTAAGGGTAATATG
1 GTAATTTTTGAAAAATTCG-GGGTAAAAAT-G-AATTTTTGAAAATTTAAGGGTAATATG
** *** * * **
38872805 GTAATTTTTGAAAGGTTCGGAACCAAAAATGAATTTTTTGGAAGTTCGAGGGTAATATG
1 GTAATTTTTGAAAAATTCGG-GGTAAAAATGAA-TTTTTGAAAATTTAAGGGTAATATG
* * * * * *
38872864 GTAAGTTTTGAAGAGTTTGGGGTCAAAAATAGAATTTTTGAAAATTTAGGGGTAATACG
1 GTAATTTTTGAAAAATTCGGGGT-AAAAAT-GAATTTTTGAAAATTTAAGGGTAATATG
* *
38872923 GTAATTTTT-AAAAAGTTCGGGGTAAAAAATGAAATTTTTGGAAATCTAAGGGTAATATG
1 GTAATTTTTGAAAAA-TTCGGGGT-AAAAATG-AATTTTTGAAAATTTAAGGGTAATATG
* * ** *
38872982 GTAATTTTTGGAAAGTTC-GGGTCAAAAATGGAATTTTT-AGAAATTCGAGGGTAAAATG
1 GTAATTTTTGAAAAATTCGGGGT-AAAAAT-GAATTTTTGA-AAATTTAAGGGTAATATG
* ** * * * *
38873040 GTAATTTTTTGAAAATTTAAGGGT-TAAATGTAATTTTTAGAAAGTTTAGGGGTTAAAAT-
1 GTAA-TTTTTGAAAAATTCGGGGTAAAAATG-AATTTTT-GAAAATTTAAGGG-TAATATG
38873099 GTAATTTTT
1 GTAATTTTT
38873108 AGAGAGTTTG
Statistics
Matches: 238, Mismatches: 49, Indels: 33
0.74 0.15 0.10
Matches are distributed among these distances:
57 1 0.00
58 58 0.24
59 157 0.66
60 22 0.09
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (57 bp):
GTAATTTTTGAAAAATTCGGGGTAAAAATGAATTTTTGAAAATTTAAGGGTAATATG
Found at i:38872900 original size:118 final size:117
Alignment explanation
Indices: 38872778--38873054 Score: 335
Period size: 118 Copynumber: 2.4 Consensus size: 117
38872768 GTAAAATGGT
* * *
38872778 AATTTTTGAAAATTTAAGGGTAATATGGTAATTTTTGAAAGGTTCGGAACCAAAAATGAATTTTT
1 AATTTTTGAAAATTTAAGGGTAATATGGTAATTTTTGAAAAGTTCGGAACAAAAAATGAAATTTT
* * *
38872843 TGGAAGT-TCGAGGGTAATATGGTAAGTTTT-GAAGAGTTTGGGGTCAAAAATAG
66 TGGAAATCT-AAGGGTAATATGGTAAGTTTTGGAA-AG-TTCGGGTCAAAAATAG
* * * ***
38872896 AATTTTTGAAAATTTAGGGGTAATACGGTAATTTTTAAAAAGTTCGGGGTAAAAAATGAAATTTT
1 AATTTTTGAAAATTTAAGGGTAATATGGTAATTTTTGAAAAGTTCGGAACAAAAAATGAAATTTT
* *
38872961 TGGAAATCTAAGGGTAATATGGTAATTTTTGGAAAGTTCGGGTCAAAAATGG
66 TGGAAATCTAAGGGTAATATGGTAAGTTTTGGAAAGTTCGGGTCAAAAATAG
** *
38873013 AATTTTT-AGAAATTCGAGGGTAAAATGGTAATTTTTTGAAAA
1 AATTTTTGA-AAATTTAAGGGTAATATGGTAA-TTTTTGAAAA
38873055 TTTAAGGGTT
Statistics
Matches: 135, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
116 1 0.01
117 38 0.28
118 92 0.68
119 4 0.03
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (117 bp):
AATTTTTGAAAATTTAAGGGTAATATGGTAATTTTTGAAAAGTTCGGAACAAAAAATGAAATTTT
TGGAAATCTAAGGGTAATATGGTAAGTTTTGGAAAGTTCGGGTCAAAAATAG
Found at i:38873108 original size:30 final size:30
Alignment explanation
Indices: 38872896--38873150 Score: 156
Period size: 30 Copynumber: 8.7 Consensus size: 30
38872886 TCAAAAATAG
* **
38872896 AATTTTT-GAAAATTTAGGGG-TAATACGGT
1 AATTTTTAGAAAGTTTAGGGGTTAA-AATGT
* * * *
38872925 AATTTTTAAAAAG-TTCGGGGTAAAAAATGA
1 AATTTTTAGAAAGTTTAGGGGT-TAAAATGT
* * * *
38872955 AATTTTTGGAAA-TCTAAGGG-TAATATGGT
1 AATTTTTAGAAAGTTTAGGGGTTAAAAT-GT
* * * *
38872984 AATTTTTGGAAAG-TT-CGGGTCAAAAATGG
1 AATTTTTAGAAAGTTTAGGGGT-TAAAATGT
*
38873013 AATTTTTAGAAA--TTCGAGGG-TAAAATGGT
1 AATTTTTAGAAAGTTTAG-GGGTTAAAAT-GT
* * *
38873042 AATTTTTTGAAAATTTAAGGGTT-AAATGT
1 AATTTTTAGAAAGTTTAGGGGTTAAAATGT
38873071 AATTTTTAGAAAGTTTAGGGGTTAAAATGT
1 AATTTTTAGAAAGTTTAGGGGTTAAAATGT
* *
38873101 AATTTTTAGAGAGTTT-GAGGGTTAAAATAT
1 AATTTTTAGAAAGTTTAG-GGGTTAAAATGT
* *
38873131 GATTTTTAGACAGTTTAGGG
1 AATTTTTAGAAAGTTTAGGG
38873151 ACCTTCTGGG
Statistics
Matches: 175, Mismatches: 34, Indels: 33
0.72 0.14 0.14
Matches are distributed among these distances:
28 14 0.08
29 74 0.42
30 81 0.46
31 6 0.03
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
AATTTTTAGAAAGTTTAGGGGTTAAAATGT
Found at i:38874338 original size:3 final size:3
Alignment explanation
Indices: 38874285--38874355 Score: 63
Period size: 3 Copynumber: 23.0 Consensus size: 3
38874275 CTCACTTTCT
* * * * *
38874285 TTA TT- TTA TTT TTA TTA ATA TGTA TTA ATG TTA TTTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA -TTA TTA TTA TTA
38874331 TTTA TTA TTA TTA TTA TTA TTA TTA
1 -TTA TTA TTA TTA TTA TTA TTA TTA
38874356 ATTGTTTTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
2 2 0.04
3 43 0.80
4 9 0.17
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:38875550 original size:41 final size:41
Alignment explanation
Indices: 38875493--38875690 Score: 206
Period size: 41 Copynumber: 4.8 Consensus size: 41
38875483 TGCTTTTTTT
*
38875493 ACAAGCGCCGCTAATGCTCTGACCTTTAACGACGCCTTCTC
1 ACAAGCGTCGCTAATGCTCTGACCTTTAACGACGCCTTCTC
*
38875534 ACAAGCGTCACTAATGCTCTGACCTTTAACGACG-CTT-TAC
1 ACAAGCGTCGCTAATGCTCTGACCTTTAACGACGCCTTCT-C
* * *
38875574 AACAAGCGTCGCTAATGCTCTGACCTTTAGCGGCGCTTTCTC
1 -ACAAGCGTCGCTAATGCTCTGACCTTTAACGACGCCTTCTC
* * ** *
38875616 ACAAGCG-CTGCTAATGTTCTGACCTTTAGCGGTGCTTTAC-C
1 ACAAGCGTC-GCTAATGCTCTGACCTTTAACGACGCCTT-CTC
* * * *
38875657 ATAAGCGCCGTTAATGCTCTGACCTTTAGCGACG
1 ACAAGCGTCGCTAATGCTCTGACCTTTAACGACG
38875691 TTTTTTCTAT
Statistics
Matches: 137, Mismatches: 13, Indels: 14
0.84 0.08 0.09
Matches are distributed among these distances:
39 1 0.01
40 5 0.04
41 125 0.91
42 5 0.04
43 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (41 bp):
ACAAGCGTCGCTAATGCTCTGACCTTTAACGACGCCTTCTC
Found at i:38875594 original size:82 final size:82
Alignment explanation
Indices: 38875493--38875690 Score: 272
Period size: 82 Copynumber: 2.4 Consensus size: 82
38875483 TGCTTTTTTT
*
38875493 ACAAGCGCCGCTAATGCTCTGACCTTTAACGACGCCTTCTCACAAGCG-TCACTAATGCTCTGAC
1 ACAAGCGCCGCTAATGCTCTGACCTTTAGCGACGCCTTCTCACAAGCGCT-ACTAATGCTCTGAC
38875557 CTTTAACGACGCTTTACA
65 CTTTAACGACGCTTTACA
* * * * *
38875575 ACAAGCGTCGCTAATGCTCTGACCTTTAGCGGCGCTTTCTCACAAGCGCTGCTAATGTTCTGACC
1 ACAAGCGCCGCTAATGCTCTGACCTTTAGCGACGCCTTCTCACAAGCGCTACTAATGCTCTGACC
* ** *
38875640 TTTAGCGGTGCTTTACC
66 TTTAACGACGCTTTACA
* *
38875657 ATAAGCGCCGTTAATGCTCTGACCTTTAGCGACG
1 ACAAGCGCCGCTAATGCTCTGACCTTTAGCGACG
38875691 TTTTTTCTAT
Statistics
Matches: 101, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
82 100 0.99
83 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (82 bp):
ACAAGCGCCGCTAATGCTCTGACCTTTAGCGACGCCTTCTCACAAGCGCTACTAATGCTCTGACC
TTTAACGACGCTTTACA
Found at i:38875794 original size:40 final size:40
Alignment explanation
Indices: 38875708--38875794 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 40
38875698 TATAAAAGCA
* * * *
38875708 GCTATTGTTTTACTTTTTGAGACGTTTACGGAAAATCGCC
1 GCTATTGCTTTACCTTTTGAGACATTTACGGAAAAACGCC
** * *
38875748 ATTATTGCTTTACCTTTTGAGGCATTTATGGAAAAACGCC
1 GCTATTGCTTTACCTTTTGAGACATTTACGGAAAAACGCC
38875788 GCTATTG
1 GCTATTG
38875795 TTTTGTCTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (40 bp):
GCTATTGCTTTACCTTTTGAGACATTTACGGAAAAACGCC
Found at i:38876559 original size:31 final size:32
Alignment explanation
Indices: 38876492--38876560 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
38876482 ATTTGATTAT
*
38876492 TTTTAGTCCAGGCACTTTTTGAATTGGTCAAA
1 TTTTAGTCCAGGCACTTTTTGAATTGGTAAAA
* * *
38876524 -TTTAGTCCATGTACTTTTTGAATT-TTAAAA
1 TTTTAGTCCAGGCACTTTTTGAATTGGTAAAA
38876554 TTTTAGT
1 TTTTAGT
38876561 TATGACCCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (32 bp):
TTTTAGTCCAGGCACTTTTTGAATTGGTAAAA
Found at i:38881275 original size:5 final size:5
Alignment explanation
Indices: 38881243--38881272 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
38881233 AGACACCACC
*
38881243 TGCTG TGCTG TGCTG TGCTG TGCTG AGCTG
1 TGCTG TGCTG TGCTG TGCTG TGCTG TGCTG
38881273 AGCCTGGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.03, C:0.20, G:0.40, T:0.37
Consensus pattern (5 bp):
TGCTG
Found at i:38883889 original size:2 final size:2
Alignment explanation
Indices: 38883882--38883907 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38883872 TCTTAGTTTC
38883882 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
38883908 TTTTTTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38897411 original size:31 final size:31
Alignment explanation
Indices: 38897371--38897449 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
38897361 TATTTTGACT
*
38897371 TAAATAATCAATTAAGCT-TGGTAAAATAATAA
1 TAAA-AATCAATTAAGCTCTAGTAAAATAAT-A
*
38897403 TAAAAATCAATTAAACTCTAGTAAAATAATA
1 TAAAAATCAATTAAGCTCTAGTAAAATAATA
*
38897434 GAAAAATCAATTAAGC
1 TAAAAATCAATTAAGC
38897450 CTTCCATATC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
31 27 0.64
32 15 0.36
ACGTcount: A:0.56, C:0.09, G:0.08, T:0.28
Consensus pattern (31 bp):
TAAAAATCAATTAAGCTCTAGTAAAATAATA
Found at i:38900318 original size:3 final size:3
Alignment explanation
Indices: 38900310--38900338 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
38900300 TAGAGAAATC
38900310 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
38900339 CTACTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:38907550 original size:11 final size:10
Alignment explanation
Indices: 38907533--38907582 Score: 59
Period size: 11 Copynumber: 5.0 Consensus size: 10
38907523 TCGGTATTAT
38907533 TATTTTTTAA
1 TATTTTTTAA
38907543 TCATTTTTTAA
1 T-ATTTTTTAA
38907554 TGATTTTTT-A
1 T-ATTTTTTAA
*
38907564 TAGTTTTT-A
1 TATTTTTTAA
38907573 TATTTTTTAA
1 TATTTTTTAA
38907583 ATAAATTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 14 0.40
10 4 0.11
11 17 0.49
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (10 bp):
TATTTTTTAA
Found at i:38909371 original size:72 final size:74
Alignment explanation
Indices: 38909243--38909445 Score: 220
Period size: 72 Copynumber: 2.8 Consensus size: 74
38909233 TCGTGTGTCA
* * * * *
38909243 TGGAAACCAAAAATAGTGAGTTACACGGTCTGGGCACACAGGCGTGT-TTTGAACCGTGTGGATA
1 TGGAAATCAAAAATAGTGAGTTACACGGTCTGGGCACACGGGCGTGTGCTAG-ACCGTGTGGACA
* *
38909307 TTCTGTG--T
65 CTCTGCGATT
* *
38909315 TGTG-AATCAAAAATAGTGAGTTACACGGTCTGGGCACACGGGCATGTGCTAGACCGTGTGGCCA
1 TG-GAAATCAAAAATAGTGAGTTACACGGTCTGGGCACACGGGCGTGTGCTAGACCGTGTGGACA
38909379 CTCTGCGATT
65 CTCTGCGATT
* * * *
38909389 TGGAAATC-GAAACAGTGAGTTACACGGTCTAGACACACGGGCGTGTGC-ATGACCGTG
1 TGGAAATCAAAAATAGTGAGTTACACGGTCTGGGCACACGGGCGTGTGCTA-GACCGTG
38909446 AAGTGTAAAT
Statistics
Matches: 111, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
72 58 0.52
73 46 0.41
74 7 0.06
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (74 bp):
TGGAAATCAAAAATAGTGAGTTACACGGTCTGGGCACACGGGCGTGTGCTAGACCGTGTGGACAC
TCTGCGATT
Found at i:38910383 original size:33 final size:33
Alignment explanation
Indices: 38910333--38910397 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
38910323 GTGAAATGAA
38910333 AGCAAAATAGTAAAAAAACAATAAG-AAAACAAT
1 AGCAAAATAGTAAAAAAACAAT-AGTAAAACAAT
** *
38910366 AGCAAAATAGTGGAAAAATAATAGTAAAACAA
1 AGCAAAATAGTAAAAAAACAATAGTAAAACAA
38910398 CAGTTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.66, C:0.08, G:0.12, T:0.14
Consensus pattern (33 bp):
AGCAAAATAGTAAAAAAACAATAGTAAAACAAT
Found at i:38916359 original size:17 final size:18
Alignment explanation
Indices: 38916327--38916360 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38916317 AAAAAATATG
38916327 ATATTTACACATTTAAAA
1 ATATTTACACATTTAAAA
*
38916345 ATATTTAGA-ATTTAAA
1 ATATTTACACATTTAAA
38916361 TTACAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (18 bp):
ATATTTACACATTTAAAA
Found at i:38921906 original size:20 final size:21
Alignment explanation
Indices: 38921873--38921920 Score: 60
Period size: 25 Copynumber: 2.1 Consensus size: 21
38921863 ATTCGTTAAC
38921873 TCGACTCGATTCGACTTGAAAATTT
1 TCGACTCGATTCGA----AAAATTT
38921898 TCGACTCGATTCGAAAAATTT
1 TCGACTCGATTCGAAAAATTT
38921919 TC
1 TC
38921921 AAATTGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 9 0.39
25 14 0.61
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (21 bp):
TCGACTCGATTCGAAAAATTT
Found at i:38956154 original size:2 final size:2
Alignment explanation
Indices: 38956145--38956184 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
38956135 AATTAAAAAT
38956145 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38956185 TAAAAATTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38971694 original size:22 final size:24
Alignment explanation
Indices: 38971651--38971704 Score: 76
Period size: 22 Copynumber: 2.3 Consensus size: 24
38971641 CCCTATTTTC
*
38971651 TATTTCTTTCAATTCTGTTTTCTTT
1 TATTT-TTTCAATTATGTTTTCTTT
38971676 TATTTTTT-AATTATG-TTTCTTT
1 TATTTTTTCAATTATGTTTTCTTT
38971698 TATTTTT
1 TATTTTT
38971705 CCTTAGATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 14 0.50
23 6 0.21
24 3 0.11
25 5 0.18
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.72
Consensus pattern (24 bp):
TATTTTTTCAATTATGTTTTCTTT
Found at i:38974450 original size:24 final size:23
Alignment explanation
Indices: 38974422--38974467 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
38974412 AAAATAATAT
* *
38974422 AATTTTATTCGAATTCTAAAATTA
1 AATTTGATTCGAACTC-AAAATTA
38974446 AATTTGATTCGAACTCAAAATT
1 AATTTGATTCGAACTCAAAATT
38974468 CGAAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (23 bp):
AATTTGATTCGAACTCAAAATTA
Found at i:38976122 original size:27 final size:28
Alignment explanation
Indices: 38976082--38976136 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
38976072 ATTTTAAAAA
38976082 ATTTAAAAATATATATA-AATACATAAAT
1 ATTTAAAAATATATATATAATA-ATAAAT
*
38976110 ATTTTAAAA-ATATATATAATAATAAAT
1 ATTTAAAAATATATATATAATAATAAAT
38976137 TTAAATTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (28 bp):
ATTTAAAAATATATATATAATAATAAAT
Found at i:38976145 original size:31 final size:29
Alignment explanation
Indices: 38976083--38976136 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
38976073 TTTTAAAAAA
38976083 TTTAAAAATATATATAAATACATAAATAT
1 TTTAAAAATATATATAAATACATAAATAT
38976112 TTTAAAAATATATAT-AATA-ATAAAT
1 TTTAAAAATATATATAAATACATAAAT
38976137 TTAAATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 6 0.24
28 4 0.16
29 15 0.60
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (29 bp):
TTTAAAAATATATATAAATACATAAATAT
Found at i:38983461 original size:18 final size:18
Alignment explanation
Indices: 38983429--38983488 Score: 81
Period size: 18 Copynumber: 3.4 Consensus size: 18
38983419 AACAAATAAT
38983429 TTAAAATATAAAAAAATTC
1 TTAAAATA-AAAAAAATTC
38983448 TTAAAATAAAAAAAATTC
1 TTAAAATAAAAAAAATTC
38983466 --AAAATTAAAAAAAATT-
1 TTAAAA-TAAAAAAAATTC
38983482 TTAAAAT
1 TTAAAAT
38983489 TTTAAAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.11
17 12 0.32
18 14 0.37
19 8 0.21
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
TTAAAATAAAAAAAATTC
Found at i:38983487 original size:27 final size:28
Alignment explanation
Indices: 38983457--38983518 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 28
38983447 CTTAAAATAA
38983457 AAAAAATTCAAAA-TTAAAAAAAAT-TT
1 AAAAAATTCAAAATTTAAAAAAAATATT
* * * *
38983483 TAAAATTTTAAAATTTTAAAAAAATATT
1 AAAAAATTCAAAATTTAAAAAAAATATT
38983511 AAAAAATT
1 AAAAAATT
38983519 AACATGAAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
26 10 0.36
27 10 0.36
28 8 0.29
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (28 bp):
AAAAAATTCAAAATTTAAAAAAAATATT
Found at i:38983514 original size:8 final size:8
Alignment explanation
Indices: 38983476--38983503 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
38983466 AAAATTAAAA
38983476 AAAATTTT
1 AAAATTTT
38983484 AAAATTTT
1 AAAATTTT
38983492 AAAATTTT
1 AAAATTTT
38983500 AAAA
1 AAAA
38983504 AAATATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
AAAATTTT
Found at i:38983520 original size:27 final size:26
Alignment explanation
Indices: 38983457--38983520 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
38983447 CTTAAAATAA
*
38983457 AAAAAATTCAAAATTAAAAAAAATTTT
1 AAAAAATT-AAAATTAAAAAAAATATT
** *
38983484 AAAATTTTAAAATTTTAAAAAAATATT
1 AAAAAATTAAAA-TTAAAAAAAATATT
38983511 AAAAAATTAA
1 AAAAAATTAA
38983521 CATGAAGTAC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAAAATTAAAATTAAAAAAAATATT
Found at i:38988402 original size:16 final size:16
Alignment explanation
Indices: 38988378--38988411 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
38988368 TTCTAATAAT
*
38988378 AAATATATAGATATTA
1 AAATATATAAATATTA
*
38988394 AAATTTATAAATATTA
1 AAATATATAAATATTA
38988410 AA
1 AA
38988412 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAATATATAAATATTA
Found at i:38989016 original size:13 final size:13
Alignment explanation
Indices: 38988998--38989023 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38988988 CAACAGTTTT
38988998 AAATTCTATAAGG
1 AAATTCTATAAGG
38989011 AAATTCTATAAGG
1 AAATTCTATAAGG
38989024 TTAAATAAAA
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:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
AAATTCTATAAGG
Found at i:39011461 original size:19 final size:20
Alignment explanation
Indices: 39011437--39011474 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
39011427 ATTTTTATCT
39011437 TAAAAAAATT-AAATTTAAA
1 TAAAAAAATTAAAATTTAAA
*
39011456 TAAAAATATTAAAATTTAA
1 TAAAAAAATTAAAATTTAA
39011475 GATTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAAAATTAAAATTTAAA
Found at i:39013857 original size:124 final size:126
Alignment explanation
Indices: 39013630--39013859 Score: 320
Period size: 124 Copynumber: 1.8 Consensus size: 126
39013620 ATATTAGTGC
* * * * * * * *
39013630 TTCCATATGTCGCAAATTTCCAATGCATAGTAAGAGCTTTGTGGTCTCTTTTTCTCAAATTGTTA
1 TTCCATATGTCCCAAATTCCCAATGCATAGTAAGAGCGTTCTAGACTCTTTTGCTCAAATTGATA
*
39013695 ACATGGTTAAAGTATCCAGAGATTGCATAGTTAGATGGCTTCGCTATGTCACTTTTAGTAT
66 ACATGGTTAAAGTATCCAGAGATTGCATAGTCAGATGGCTTCGCTATGTCACTTTTAGTAT
* *
39013756 TTCCA-ATGTCCCAAATTCCCAATGCATGGTAAGAGCGTTCTAGACTC-TTTGCTCAGATTGATA
1 TTCCATATGTCCCAAATTCCCAATGCATAGTAAGAGCGTTCTAGACTCTTTTGCTCAAATTGATA
* * *
39013819 ATATGGTTATAGTATCCAGAGGTTGCATAGTCAGATGGCTT
66 ACATGGTTAAAGTATCCAGAGATTGCATAGTCAGATGGCTT
39013860 TTATAAGTCC
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
124 50 0.56
125 35 0.39
126 5 0.06
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (126 bp):
TTCCATATGTCCCAAATTCCCAATGCATAGTAAGAGCGTTCTAGACTCTTTTGCTCAAATTGATA
ACATGGTTAAAGTATCCAGAGATTGCATAGTCAGATGGCTTCGCTATGTCACTTTTAGTAT
Found at i:39021612 original size:174 final size:175
Alignment explanation
Indices: 39021142--39021808 Score: 1099
Period size: 175 Copynumber: 3.8 Consensus size: 175
39021132 AATTTGCATA
** * *
39021142 TTTGTTGCTGTGATGATTATATTA-AACTTTATGAAAATTTTGTGAATCATCGACAACTATGTCG
1 TTTGTTGCTGTGATGATTATATTAGAA-TTTATGAAAATTTAATGAAACATCGACAACCATGTCG
* * * *
39021206 ATCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCTATATCTTTGTTGATTTGTTACATT
65 ATCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATT
* ** * *
39021271 GTTTTAGTCGTCTTACAATTA-ATCTTATTGTATGTGAATCTGTGGT
130 GCTTTAGTCGTCTTATGA-TACATCTTATTGTATGTGAATTTGTGAT
39021317 TTTGTTGCTGTGATGATTATATTAGAATTTATGAAAAATTT-ATGAAACATCGACAACCATGTCG
1 TTTGTTGCTGTGATGATTATATTAGAATTTATG-AAAATTTAATGAAACATCGACAACCATGTCG
39021381 ATCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATT
65 ATCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATT
39021446 GCTTTAGTCGTCTTATGATACATCTTATTGTATGTGAATTTGTGAT
130 GCTTTAGTCGTCTTATGATACATCTTATTGTATGTGAATTTGTGAT
39021492 TTTGTTGCTGTGATGATTATATTAGAATTTATG-AAATTTAATGAAACATCGACAACCATGTCGA
1 TTTGTTGCTGTGATGATTATATTAGAATTTATGAAAATTTAATGAAACATCGACAACCATGTCGA
39021556 TCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATTG
66 TCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATTG
39021621 CTTTAGTCGTCTTATGATACATCTTATTGTATGTGAATTTGTGAT
131 CTTTAGTCGTCTTATGATACATCTTATTGTATGTGAATTTGTGAT
* *
39021666 TTTGTTGCTGTGATGATTATACTAGAATTTATGAAAATTTAATGAAACATTGACAACCATGTCGA
1 TTTGTTGCTGTGATGATTATATTAGAATTTATGAAAATTTAATGAAACATCGACAACCATGTCGA
* * *
39021731 TCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAATTTCTTTGTTGATTTGTTACTTTG
66 TCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATTG
* *
39021796 TTTTAGTTGTCTT
131 CTTTAGTCGTCTT
39021809 GTAATATCTA
Statistics
Matches: 468, Mismatches: 19, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
173 6 0.01
174 168 0.36
175 285 0.61
176 9 0.02
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (175 bp):
TTTGTTGCTGTGATGATTATATTAGAATTTATGAAAATTTAATGAAACATCGACAACCATGTCGA
TCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATTG
CTTTAGTCGTCTTATGATACATCTTATTGTATGTGAATTTGTGAT
Found at i:39021770 original size:349 final size:350
Alignment explanation
Indices: 39021142--39021808 Score: 1099
Period size: 349 Copynumber: 1.9 Consensus size: 350
39021132 AATTTGCATA
** * *
39021142 TTTGTTGCTGTGATGATTATATTAAACTTTATGAAAATTTTGTGAATCATCGACAACTATGTCGA
1 TTTGTTGCTGTGATGATTATATTAAACTTTATGAAAATTTAATGAAACATCGACAACCATGTCGA
* * *
39021207 TCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCTATATCTTTGTTGATTTGTTACATTG
66 TCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAATATCCTTGTTGATTTATTACATTG
* *
39021272 TTTTAGTCGTCTTACAATTAATCTTATTGTATGTGAATCTGTGGTTTTGTTGCTGTGATGATTAT
131 CTTTAGTCGTCTTACAATTAATCTTATTGTATGTGAATCTGTGATTTTGTTGCTGTGATGATTAT
*
39021337 ATTAGAATTTATGAAAAATTTATGAAACATCGACAACCATGTCGATCTGAGCGGTTACCTGAGCA
196 ACTAGAATTTATGAAAAATTTATGAAACATCGACAACCATGTCGATCTGAGCGGTTACCTGAGCA
39021402 ACAAAATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATTGCTTTAGTCGTCTTATGATAC
261 ACAAAATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATTGCTTTAGTCGTCTTATGATAC
39021467 ATCTTATTGTATGTGAATTTGTGAT
326 ATCTTATTGTATGTGAATTTGTGAT
39021492 TTTGTTGCTGTGATGATTATATTAGAA-TTTATG-AAATTTAATGAAACATCGACAACCATGTCG
1 TTTGTTGCTGTGATGATTATATTA-AACTTTATGAAAATTTAATGAAACATCGACAACCATGTCG
*
39021555 ATCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATT
65 ATCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAATATCCTTGTTGATTTATTACATT
** *
39021620 GCTTTAGTCGTCTTATGA-TACATCTTATTGTATGTGAATTTGTGATTTTGTTGCTGTGATGATT
130 GCTTTAGTCGTCTTACAATTA-ATCTTATTGTATGTGAATCTGTGATTTTGTTGCTGTGATGATT
*
39021684 ATACTAGAATTTATG-AAAATTTAATGAAACATTGACAACCATGTCGATCTGAGCGGTTACCTGA
194 ATACTAGAATTTATGAAAAATTT-ATGAAACATCGACAACCATGTCGATCTGAGCGGTTACCTGA
* * * * *
39021748 GCAACAAAATTTGTTCAAATTCAATTTCTTTGTTGATTTGTTACTTTGTTTTAGTTGTCTT
258 GCAACAAAATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATTGCTTTAGTCGTCTT
39021809 GTAATATCTA
Statistics
Matches: 294, Mismatches: 20, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
348 9 0.03
349 253 0.86
350 30 0.10
351 2 0.01
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (350 bp):
TTTGTTGCTGTGATGATTATATTAAACTTTATGAAAATTTAATGAAACATCGACAACCATGTCGA
TCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAATATCCTTGTTGATTTATTACATTG
CTTTAGTCGTCTTACAATTAATCTTATTGTATGTGAATCTGTGATTTTGTTGCTGTGATGATTAT
ACTAGAATTTATGAAAAATTTATGAAACATCGACAACCATGTCGATCTGAGCGGTTACCTGAGCA
ACAAAATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATTGCTTTAGTCGTCTTATGATAC
ATCTTATTGTATGTGAATTTGTGAT
Found at i:39023265 original size:36 final size:36
Alignment explanation
Indices: 39023224--39023326 Score: 111
Period size: 36 Copynumber: 2.9 Consensus size: 36
39023214 ATAAAAAAAT
* *
39023224 TAATTTTTAATAAAAATTACAAAAATTTT-AAAT-TT
1 TAATTTTTAA-AAAAATTATAAAAATTTTAAAATATA
* ***
39023259 TAAATTTTAAAATGTTTATAAAAATTTTAAAATATA
1 TAATTTTTAAAAAAATTATAAAAATTTTAAAATATA
* *
39023295 TAATTTTTTAAAAAATTATAAAATTTTTAAAA
1 TAATTTTTAAAAAAATTATAAAAATTTTAAAA
39023327 GAAATTCTAA
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
34 14 0.26
35 13 0.24
36 27 0.50
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (36 bp):
TAATTTTTAAAAAAATTATAAAAATTTTAAAATATA
Found at i:39023268 original size:35 final size:35
Alignment explanation
Indices: 39023218--39023326 Score: 96
Period size: 34 Copynumber: 3.1 Consensus size: 35
39023208 TTGAAAATAA
* * *
39023218 AAAAATTAATTTTTAATAAAAATTACAAAAATTTT
1 AAAATTTAAATTTTAATAAAAATTATAAAAATTTT
* ***
39023253 AAATTTTAAATTTTAA-AATGTTTATAAAAATTTT
1 AAAATTTAAATTTTAATAAAAATTATAAAAATTTT
* * *
39023287 AAAATATATAATTTT-TTAAAAAATTATAAAATTTTT
1 AAAATTTA-AATTTTAAT-AAAAATTATAAAAATTTT
39023323 AAAA
1 AAAA
39023327 GAAATTCTAA
Statistics
Matches: 57, Mismatches: 14, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
34 20 0.35
35 19 0.33
36 18 0.32
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (35 bp):
AAAATTTAAATTTTAATAAAAATTATAAAAATTTT
Found at i:39023331 original size:21 final size:20
Alignment explanation
Indices: 39023287--39023337 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
39023277 TAAAAATTTT
* *
39023287 AAAA-TATATAATTTTTTAA
1 AAAATTATAAAATTTTTAAA
39023306 AAAATTATAAAATTTTTAAA
1 AAAATTATAAAATTTTTAAA
*
39023326 AGAAATTCTAAA
1 A-AAATTATAAA
39023338 GAATATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 4 0.15
20 14 0.52
21 9 0.33
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
AAAATTATAAAATTTTTAAA
Found at i:39029302 original size:14 final size:14
Alignment explanation
Indices: 39029271--39029301 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
39029261 AGAGCTAAAC
39029271 AAAACAGGGGAAGG
1 AAAACAGGGGAAGG
39029285 AAAACA-GGGAAGG
1 AAAACAGGGGAAGG
39029298 AAAA
1 AAAA
39029302 AGAAAATGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.58, C:0.06, G:0.35, T:0.00
Consensus pattern (14 bp):
AAAACAGGGGAAGG
Found at i:39032947 original size:58 final size:56
Alignment explanation
Indices: 39032885--39033050 Score: 164
Period size: 58 Copynumber: 2.9 Consensus size: 56
39032875 GTTTTTCTAA
* *
39032885 TATTATATATTATCATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATGT
1 TATTA-ATATTATCATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAAATAT
* * *
39032943 TATTAA-ATTAT-ATATTTATTAAATTGTATTTAATAATAATTATGTT-AAAATAT
1 TATTAATATTATCATTTTTATTAAATTATATTTAATAATAATTATATTAAAAATAT
*
39032996 AATTAA-ATTATTTCTTATTTTTATTAAATTATATTTAATAATAATCT-TATTAAAA
1 TATTAATATTA--TC--ATTTTTATTAAATTATATTTAATAATAAT-TATATTAAAA
39033051 TTTAATAACA
Statistics
Matches: 91, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
53 15 0.16
54 17 0.19
55 10 0.11
56 9 0.10
57 1 0.01
58 35 0.38
59 4 0.04
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (56 bp):
TATTAATATTATCATTTTTATTAAATTATATTTAATAATAATTATATTAAAAATAT
Found at i:39032990 original size:26 final size:27
Alignment explanation
Indices: 39032917--39032993 Score: 86
Period size: 26 Copynumber: 2.9 Consensus size: 27
39032907 TAATTCATAT
39032917 TTTAATAATAATTATATTAAAAATGTTA
1 TTTAATAATAATTATATT-AAAATGTTA
* * *
39032945 TTAAATTATATATT-TATTAAATTG-TA
1 TTTAATAATA-ATTATATTAAAATGTTA
*
39032971 TTTAATAATAATTATGTTAAAAT
1 TTTAATAATAATTATATTAAAAT
39032994 ATAATTAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
25 3 0.08
26 17 0.43
27 5 0.12
28 12 0.30
29 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (27 bp):
TTTAATAATAATTATATTAAAATGTTA
Found at i:39033233 original size:16 final size:16
Alignment explanation
Indices: 39033212--39033250 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
39033202 TGAATTATTG
*
39033212 ATTACAGCCCTATTCC
1 ATTACAGCCCAATTCC
*
39033228 ATTACAGCTCAATTCC
1 ATTACAGCCCAATTCC
39033244 ATTACAG
1 ATTACAG
39033251 AGAACCCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (16 bp):
ATTACAGCCCAATTCC
Found at i:39035021 original size:27 final size:27
Alignment explanation
Indices: 39034944--39035022 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
39034934 TGACAGGAAG
* *
39034944 GAATAGCCTTTGTGGTAAACTCTAAAA
1 GAATAGCCTTTGTGGCAAACTCTGAAA
* * * *
39034971 GAATAACCTTTGTGACGACCTCTGAAA
1 GAATAGCCTTTGTGGCAAACTCTGAAA
*
39034998 GAATAGCCTTTGTGGCAAATTCTGA
1 GAATAGCCTTTGTGGCAAACTCTGA
39035023 TATCATAGTC
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (27 bp):
GAATAGCCTTTGTGGCAAACTCTGAAA
Found at i:39035431 original size:26 final size:26
Alignment explanation
Indices: 39035395--39035445 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
39035385 AATTAAGTAT
39035395 GAAAAGTAATTTTGAACACATTGGTG
1 GAAAAGTAATTTTGAACACATTGGTG
*
39035421 GAAAAGTAATTTTTAACACATTGGT
1 GAAAAGTAATTTTGAACACATTGGT
39035446 TTGCAAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (26 bp):
GAAAAGTAATTTTGAACACATTGGTG
Found at i:39040480 original size:14 final size:14
Alignment explanation
Indices: 39040461--39040488 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39040451 AAATTAAATA
39040461 AAAAATATTTTTTT
1 AAAAATATTTTTTT
39040475 AAAAATATTTTTTT
1 AAAAATATTTTTTT
39040489 TTTAATTTTA
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AAAAATATTTTTTT
Found at i:39044431 original size:48 final size:48
Alignment explanation
Indices: 39044360--39044511 Score: 250
Period size: 48 Copynumber: 3.2 Consensus size: 48
39044350 CAGGATCTAT
39044360 AGAGGAAGCCGATGAATCGAAAGCAGTAAGTTCTGTTCCGAAATCTGC
1 AGAGGAAGCCGATGAATCGAAAGCAGTAAGTTCTGTTCCGAAATCTGC
* * * *
39044408 AGAGGAAACCGACGAATCGAAAGCAGCAAGTTCTGTTTCGAAATCTGC
1 AGAGGAAGCCGATGAATCGAAAGCAGTAAGTTCTGTTCCGAAATCTGC
* *
39044456 GGAGGAAGCCGATGAATCGAAAGCAGTAAGTTTTGTTCCGAAATCTGC
1 AGAGGAAGCCGATGAATCGAAAGCAGTAAGTTCTGTTCCGAAATCTGC
39044504 AGAGGAAG
1 AGAGGAAG
39044512 GAAGCGTTAG
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 93 1.00
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (48 bp):
AGAGGAAGCCGATGAATCGAAAGCAGTAAGTTCTGTTCCGAAATCTGC
Found at i:39044925 original size:9 final size:9
Alignment explanation
Indices: 39044903--39044951 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
39044893 CAATTCCGGC
*
39044903 AGAAGAGAA
1 AGAAGTGAA
39044912 AGAAGTGAA
1 AGAAGTGAA
* *
39044921 GGAAGTAAA
1 AGAAGTGAA
39044930 AGAAGTGAA
1 AGAAGTGAA
* *
39044939 ACAAGAGAA
1 AGAAGTGAA
39044948 AGAA
1 AGAA
39044952 AAGAAAGAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.61, C:0.02, G:0.31, T:0.06
Consensus pattern (9 bp):
AGAAGTGAA
Found at i:39044949 original size:18 final size:18
Alignment explanation
Indices: 39044905--39044951 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
39044895 ATTCCGGCAG
**
39044905 AAGAGAAAGAAGTGAAGG
1 AAGAGAAAGAAGTGAAAC
39044923 AAGTA-AAAGAAGTGAAAC
1 AAG-AGAAAGAAGTGAAAC
39044941 AAGAGAAAGAA
1 AAGAGAAAGAA
39044952 AAGAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 1 0.04
18 23 0.92
19 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.30, T:0.06
Consensus pattern (18 bp):
AAGAGAAAGAAGTGAAAC
Found at i:39047152 original size:21 final size:21
Alignment explanation
Indices: 39047117--39047164 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
39047107 TGATAACAAA
*
39047117 GAGGATGTTGGGAACGAAGAGG
1 GAGGA-GTTGAGAACGAAGAGG
39047139 GAGGAGTTGAGAACGAAGAGG
1 GAGGAGTTGAGAACGAAGAGG
39047160 G-GGAG
1 GAGGAG
39047165 CTAAGAATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 4 0.16
21 16 0.64
22 5 0.20
ACGTcount: A:0.33, C:0.04, G:0.52, T:0.10
Consensus pattern (21 bp):
GAGGAGTTGAGAACGAAGAGG
Found at i:39047171 original size:20 final size:21
Alignment explanation
Indices: 39047128--39047181 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
39047118 AGGATGTTGG
* *
39047128 GAACGAAGAGGGAGGAGTTGA
1 GAACGAAGAGGGAGGAGCTAA
39047149 GAACGAAGAGGG-GGAGCTAA
1 GAACGAAGAGGGAGGAGCTAA
* *
39047169 GAATGAATAGGGA
1 GAACGAAGAGGGA
39047182 TCTAAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.41, C:0.06, G:0.44, T:0.09
Consensus pattern (21 bp):
GAACGAAGAGGGAGGAGCTAA
Found at i:39048047 original size:2 final size:2
Alignment explanation
Indices: 39048040--39048069 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39048030 TTATCTTTCA
39048040 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
39048070 TCTTCTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:39052825 original size:2 final size:2
Alignment explanation
Indices: 39052818--39052862 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
39052808 TTATTTCTAA
39052818 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
39052860 TG T
1 TG T
39052863 TTAGAGGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:39062467 original size:67 final size:67
Alignment explanation
Indices: 39062359--39062490 Score: 255
Period size: 67 Copynumber: 2.0 Consensus size: 67
39062349 TGAGCACTCA
*
39062359 TTGGTGAGGTTATAAATAAAGCGTTTGAACCATGGTTGTTAGATCATTAGTAACACAATGAGCAA
1 TTGGTGAGGTTATAAATAAAGCATTTGAACCATGGTTGTTAGATCATTAGTAACACAATGAGCAA
39062424 CT
66 CT
39062426 TTGGTGAGGTTATAAATAAAGCATTTGAACCATGGTTGTTAGATCATTAGTAACACAATGAGCAA
1 TTGGTGAGGTTATAAATAAAGCATTTGAACCATGGTTGTTAGATCATTAGTAACACAATGAGCAA
39062491 TGTCTGCCAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (67 bp):
TTGGTGAGGTTATAAATAAAGCATTTGAACCATGGTTGTTAGATCATTAGTAACACAATGAGCAA
CT
Found at i:39087471 original size:25 final size:23
Alignment explanation
Indices: 39087443--39087488 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
39087433 GTTGGATCCA
39087443 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAATT-TAAAAA-ATAATTAG
*
39087468 AATTAAATTTAAATAATAATT
1 AATTAAATTTAAAAAATAATT
39087489 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (23 bp):
AATTAAATTTAAAAAATAATTAG
Found at i:39091433 original size:19 final size:18
Alignment explanation
Indices: 39091393--39091453 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
39091383 ATTTTAATAA
* *
39091393 AAAAATATAAAAAATATTT
1 AAAATTATAAAAAAT-TGT
39091412 AAACATTATAAAAAATTGT
1 AAA-ATTATAAAAAATTGT
* *
39091431 AAAATTTTATAAAAATCGT
1 AAAATTATA-AAAAATTGT
39091450 AAAA
1 AAAA
39091454 AATATTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 5 0.14
19 20 0.56
20 11 0.31
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAATTATAAAAAATTGT
Found at i:39091454 original size:20 final size:20
Alignment explanation
Indices: 39091416--39091465 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
39091406 ATATTTAAAC
*
39091416 ATTATAAAAAATTGT-AAAAT
1 ATTAT-AAAAATCGTAAAAAT
*
39091436 TTTATAAAAATCGTAAAAAAT
1 ATTATAAAAATCGT-AAAAAT
39091457 ATTATAAAA
1 ATTATAAAA
39091466 TATATAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 8 0.32
20 4 0.16
21 13 0.52
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (20 bp):
ATTATAAAAATCGTAAAAAT
Found at i:39091476 original size:10 final size:10
Alignment explanation
Indices: 39091394--39091468 Score: 50
Period size: 10 Copynumber: 7.7 Consensus size: 10
39091384 TTTTAATAAA
*
39091394 AAAATA-TAA
1 AAAATATTAT
39091403 AAAATATT-T
1 AAAATATTAT
*
39091412 -AAACATTAT
1 AAAATATTAT
* *
39091421 AAAAAATTGT
1 AAAATATTAT
*
39091431 AAAATTTTAT
1 AAAATATTAT
*
39091441 AAAA-ATCGTAA
1 AAAATAT--TAT
39091452 AAAATATTAT
1 AAAATATTAT
39091462 AAAATAT
1 AAAATAT
39091469 ATAGAAATGT
Statistics
Matches: 50, Mismatches: 10, Indels: 11
0.70 0.14 0.15
Matches are distributed among these distances:
8 6 0.12
9 8 0.16
10 28 0.56
11 6 0.12
12 2 0.04
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (10 bp):
AAAATATTAT
Found at i:39091521 original size:19 final size:19
Alignment explanation
Indices: 39091499--39091565 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
39091489 CTATAAAATT
39091499 TTATAAAATTGT-AAGAAGA
1 TTATAAAATTGTAAAGAA-A
*
39091518 TTATAAAAAATGTAAAGAAA
1 TTAT-AAAATTGTAAAGAAA
*
39091538 -TATAAAATTCATAAA-AAA
1 TTATAAAATT-GTAAAGAAA
*
39091556 ATATAAAATT
1 TTATAAAATT
39091566 TATGATACTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
18 8 0.20
19 20 0.49
20 8 0.20
21 5 0.12
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.30
Consensus pattern (19 bp):
TTATAAAATTGTAAAGAAA
Found at i:39091528 original size:62 final size:62
Alignment explanation
Indices: 39091421--39091538 Score: 141
Period size: 62 Copynumber: 1.9 Consensus size: 62
39091411 TAAACATTAT
* * * *
39091421 AAAAAATTGTAAAATTTTATAAAAATCGTAAAAAATATTATAAAATATATAGAAATGTAGAA
1 AAAAAACTATAAAATTTTATAAAAATCGTAAAAAATATTAAAAAATATAAAGAAATGTAGAA
* * *
39091483 AAAAAACTATAAAATTTTAT-AAAATTGTAAGAAGAT-TATAAAAAATGTAAAGAAAT
1 AAAAAACTATAAAATTTTATAAAAATCGTAA-AAAATAT-TAAAAAATATAAAGAAAT
39091539 ATAAAATTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
61 10 0.21
62 37 0.79
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (62 bp):
AAAAAACTATAAAATTTTATAAAAATCGTAAAAAATATTAAAAAATATAAAGAAATGTAGAA
Found at i:39092189 original size:24 final size:24
Alignment explanation
Indices: 39092140--39092189 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
39092130 TTTAAATATT
*
39092140 TTATATAATAAAAAATAAAATTAA
1 TTATATAATAAAAAATAAAATGAA
* *
39092164 TTATATATTAAACAA-AAAATAGAA
1 TTATATAATAAAAAATAAAAT-GAA
39092188 TT
1 TT
39092190 GGGAATTTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
TTATATAATAAAAAATAAAATGAA
Found at i:39100457 original size:5 final size:5
Alignment explanation
Indices: 39100447--39100476 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
39100437 TCCTGTAAGC
39100447 TCTTT TCTTT TCTTT TCTTT TCTTT T-TTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
39100477 AAATTTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TCTTT
Found at i:39107955 original size:6 final size:6
Alignment explanation
Indices: 39107946--39107971 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
39107936 AAAGGCAATC
39107946 GAAACA GAAACA GAAACA GAAACA GA
1 GAAACA GAAACA GAAACA GAAACA GA
39107972 TCAATCTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.15, G:0.19, T:0.00
Consensus pattern (6 bp):
GAAACA
Found at i:39110229 original size:17 final size:17
Alignment explanation
Indices: 39110204--39110252 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
39110194 GTTTGGAGGG
*
39110204 ATTTGATTTAATTAAAA
1 ATTTAATTTAATTAAAA
* *
39110221 ATTTAATTTAATTTAAG
1 ATTTAATTTAATTAAAA
* *
39110238 ATCTAATGTAATTAA
1 ATTTAATTTAATTAA
39110253 TCGAATATCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (17 bp):
ATTTAATTTAATTAAAA
Found at i:39114288 original size:28 final size:29
Alignment explanation
Indices: 39114251--39114324 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
39114241 TTGTAAAATT
* *
39114251 TTTAATAATGATAAAATTCT-ATTTTA-TC
1 TTTAAAAATGATAAAATT-TAATTTGACTC
39114279 TTTAAAAATGATAAAAATTTAATTTGACTC
1 TTTAAAAATGAT-AAAATTTAATTTGACTC
*
39114309 TTTAAAAATTATAAAA
1 TTTAAAAATGATAAAA
39114325 ATATAAATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
28 12 0.30
29 15 0.38
30 13 0.32
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (29 bp):
TTTAAAAATGATAAAATTTAATTTGACTC
Found at i:39114315 original size:29 final size:29
Alignment explanation
Indices: 39114251--39114326 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 29
39114241 TTGTAAAATT
* *
39114251 TTTAATAATGAT-AAAATTCTATTTTATC
1 TTTAAAAATGATAAAAATTCTATTTGATC
39114279 TTTAAAAATGATAAAAATT-TAATTTGACTC
1 TTTAAAAATGATAAAAATTCT-ATTTGA-TC
*
39114309 TTTAAAAATTATAAAAAT
1 TTTAAAAATGATAAAAAT
39114327 ATAAATTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 12 0.29
29 11 0.26
30 19 0.45
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (29 bp):
TTTAAAAATGATAAAAATTCTATTTGATC
Found at i:39114381 original size:23 final size:24
Alignment explanation
Indices: 39114315--39114381 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 24
39114305 ACTCTTTAAA
39114315 AATTATAAAAATATA-AA-TTATT
1 AATTATAAAAATATATAATTTATT
* * *
39114337 AAATGATAAAATTATAT-TTTTATT
1 -AATTATAAAAATATATAATTTATT
39114361 -ATTATAAAAATATATAATTTA
1 AATTATAAAAATATATAATTTA
39114382 ATTTTGACGA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
22 13 0.37
23 17 0.49
24 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (24 bp):
AATTATAAAAATATATAATTTATT
Found at i:39120916 original size:17 final size:19
Alignment explanation
Indices: 39120895--39120930 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39120885 ACTTTTTTCA
39120895 TTTTTGT-TAAATTATAAT
1 TTTTTGTATAAATTATAAT
*
39120913 TTTTTTTATAAATTATAA
1 TTTTTGTATAAATTATAA
39120931 ATTGATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTTTGTATAAATTATAAT
Found at i:39122214 original size:32 final size:29
Alignment explanation
Indices: 39122174--39122244 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 29
39122164 TTAAATCAAT
39122174 AAATATAAAATTGT-ATTTTAACTTTTTTTAA
1 AAATATAAAATTGTGA-TTTAA--TTTTTTAA
*
39122205 AAATAATAAAATTTTGATTTAATTTTTTAA
1 AAAT-ATAAAATTGTGATTTAATTTTTTAA
39122235 AAATTATAAA
1 AAA-TATAAA
39122245 GATATAAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
30 16 0.44
31 5 0.14
32 14 0.39
33 1 0.03
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (29 bp):
AAATATAAAATTGTGATTTAATTTTTTAA
Found at i:39122587 original size:20 final size:22
Alignment explanation
Indices: 39122559--39122603 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
39122549 GAATTTTATA
*
39122559 TTTCTTTAC-ACTTTTTAAAAT
1 TTTCTTTACTACTTTATAAAAT
39122580 TTTC-TTACTACTTTATAAAAT
1 TTTCTTTACTACTTTATAAAAT
39122601 TTT
1 TTT
39122604 ATAATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTCTTTACTACTTTATAAAAT
Found at i:39122623 original size:21 final size:21
Alignment explanation
Indices: 39122599--39122670 Score: 78
Period size: 20 Copynumber: 3.5 Consensus size: 21
39122589 ACTTTATAAA
39122599 ATTTTATAATTTTTTTTCTAT
1 ATTTTATAATTTTTTTTCTAT
* *
39122620 ATTTCTATATATTTTTTTACAAT
1 ATTT-TATA-ATTTTTTTTCTAT
*
39122643 -TTTTATAAGTTTTTTTCTA-
1 ATTTTATAATTTTTTTTCTAT
39122662 ATTTT-TAAT
1 ATTTTATAAT
39122671 AAAATTTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 3 0.07
20 13 0.31
21 8 0.19
22 7 0.17
23 11 0.26
ACGTcount: A:0.26, C:0.06, G:0.01, T:0.67
Consensus pattern (21 bp):
ATTTTATAATTTTTTTTCTAT
Found at i:39122678 original size:22 final size:21
Alignment explanation
Indices: 39122600--39122678 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 21
39122590 CTTTATAAAA
*
39122600 TTTTATAATTTTTTTTCTATAT
1 TTTTATAAATTTTTTTCTA-AT
* *
39122622 TTCTATATATTTTTTTAC-AAT
1 TTTTATAAATTTTTTT-CTAAT
*
39122643 TTTTATAAGTTTTTTTCTAAT
1 TTTTATAAATTTTTTTCTAAT
*
39122664 TTTTAATAAAATTTT
1 TTTT-ATAAATTTTT
39122679 AATATTTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.02
21 22 0.48
22 22 0.48
23 1 0.02
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.66
Consensus pattern (21 bp):
TTTTATAAATTTTTTTCTAAT
Found at i:39122918 original size:21 final size:20
Alignment explanation
Indices: 39122894--39122932 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
39122884 GTGAAAAAAC
*
39122894 AAAAGCTTAATTATTTTTTCG
1 AAAAGCTTAAAT-TTTTTTCG
*
39122915 AAAAGTTTAAATTTTTTT
1 AAAAGCTTAAATTTTTTT
39122933 ATGTATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (20 bp):
AAAAGCTTAAATTTTTTTCG
Found at i:39123218 original size:6 final size:6
Alignment explanation
Indices: 39123209--39123238 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
39123199 ACAAGTACAA
39123209 GCATGG GCATGG GCATGG GCATGG GCATGG
1 GCATGG GCATGG GCATGG GCATGG GCATGG
39123239 CTGAGATGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.17
Consensus pattern (6 bp):
GCATGG
Found at i:39124332 original size:90 final size:90
Alignment explanation
Indices: 39124179--39124360 Score: 355
Period size: 90 Copynumber: 2.0 Consensus size: 90
39124169 TACATCACTT
39124179 CTAATGTGGAAGTGCCTTCCAATTTGCTCAACCCTCTCAAGAAGTCACTTTATCCTTATGGCTTC
1 CTAATGTGGAAGTGCCTTCCAATTTGCTCAACCCTCTCAAGAAGTCACTTTATCCTTATGGCTTC
39124244 ACCAGCTCTCCTGCTGGATCTTTGC
66 ACCAGCTCTCCTGCTGGATCTTTGC
*
39124269 CTAATGTGGAAGTGCCTTCCAATTTGCTCAACCCTTTCAAGAAGTCACTTTATCCTTATGGCTTC
1 CTAATGTGGAAGTGCCTTCCAATTTGCTCAACCCTCTCAAGAAGTCACTTTATCCTTATGGCTTC
39124334 ACCAGCTCTCCTGCTGGATCTTTGC
66 ACCAGCTCTCCTGCTGGATCTTTGC
39124359 CT
1 CT
39124361 CCCAATTCAT
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (90 bp):
CTAATGTGGAAGTGCCTTCCAATTTGCTCAACCCTCTCAAGAAGTCACTTTATCCTTATGGCTTC
ACCAGCTCTCCTGCTGGATCTTTGC
Found at i:39129847 original size:37 final size:37
Alignment explanation
Indices: 39129806--39129909 Score: 118
Period size: 37 Copynumber: 2.8 Consensus size: 37
39129796 AAAAGTATGG
* *
39129806 AGCTTGAAGGGTTGAAGGAATAAGGAAGAAACTAGAA
1 AGCTTGAAGGGTTGAAGCAAGAAGGAAGAAACTAGAA
* * **
39129843 AGCTTGAAGGGTTGAAGCAAGAGGGAAGAAAGTAGGG
1 AGCTTGAAGGGTTGAAGCAAGAAGGAAGAAACTAGAA
* * * *
39129880 AGTTTGAATGGTTGAAGAAAGAGGGAAGAA
1 AGCTTGAAGGGTTGAAGCAAGAAGGAAGAA
39129910 CGTAAAGATT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.04, G:0.38, T:0.16
Consensus pattern (37 bp):
AGCTTGAAGGGTTGAAGCAAGAAGGAAGAAACTAGAA
Found at i:39129964 original size:37 final size:37
Alignment explanation
Indices: 39129934--39130079 Score: 150
Period size: 37 Copynumber: 4.0 Consensus size: 37
39129924 TGAATGAATC
* * *
39129934 GGGAAGAAAGTATGGATCTTCAAGGGTTGAAAGAA-A
1 GGGAAGAAAGTAGGGAGCTTGAAGGGTTGAAAGAAGA
* * * *
39129970 AGGAAGAATGTAGGGAGCTTGAAGCGTTGAAGGAAGA
1 GGGAAGAAAGTAGGGAGCTTGAAGGGTTGAAAGAAGA
* * * * *
39130007 GGGAAGAACGTAAGGTGCTTGATGGGTTGAAAGAAGC
1 GGGAAGAAAGTAGGGAGCTTGAAGGGTTGAAAGAAGA
* * *
39130044 GAGAAGAAAGTAGGGAGCTTTAAGGGTTGAAGGAAG
1 GGGAAGAAAGTAGGGAGCTTGAAGGGTTGAAAGAAG
39130080 GTGTGCGATT
Statistics
Matches: 87, Mismatches: 22, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
36 28 0.32
37 59 0.68
ACGTcount: A:0.38, C:0.05, G:0.39, T:0.18
Consensus pattern (37 bp):
GGGAAGAAAGTAGGGAGCTTGAAGGGTTGAAAGAAGA
Found at i:39130050 original size:142 final size:143
Alignment explanation
Indices: 39129791--39130051 Score: 339
Period size: 142 Copynumber: 1.8 Consensus size: 143
39129781 TGAAGAAAGA
* * *
39129791 GGGAAAAAAGTATGGAGCTTGAAGGGTTGAAGGAATAAGGAAGAAACTAGAAAGCTTGAAGGGTT
1 GGGAAAAAAGTATGGAGCTTCAAGGGTTGAAAGAATAAGGAAGAAACTAGAAAGCTTGAAGCGTT
* * *
39129856 GAAGCAAGAGGGAAGAAAGTAGGGAGTTTGAATGGTTGAAGAAAGAGGGAAGAACGTAAAGATTT
66 GAAGCAAGAGGGAAGAAAGTAAGGAGCTTGAATGGTTGAAGAAAGAGAGAAGAACGTAAAGATTT
39129921 GGTTGAATGAATC
131 GGTTGAATGAATC
* * ** **
39129934 GGGAAGAAAGTATGGATCTTCAAGGGTTGAAAGAA-AAGGAAGAATGTAGGGAGCTTGAAGCGTT
1 GGGAAAAAAGTATGGAGCTTCAAGGGTTGAAAGAATAAGGAAGAAACTAGAAAGCTTGAAGCGTT
* * * *
39129998 GAAGGAAGAGGGAAGAACGTAAGGTGCTTG-ATGGGTTGAA-AGAAGCGAGAAGAA
66 GAAGCAAGAGGGAAGAAAGTAAGGAGCTTGAAT-GGTTGAAGA-AAGAGAGAAGAA
39130052 AGTAGGGAGC
Statistics
Matches: 100, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
141 3 0.03
142 66 0.66
143 31 0.31
ACGTcount: A:0.40, C:0.05, G:0.37, T:0.18
Consensus pattern (143 bp):
GGGAAAAAAGTATGGAGCTTCAAGGGTTGAAAGAATAAGGAAGAAACTAGAAAGCTTGAAGCGTT
GAAGCAAGAGGGAAGAAAGTAAGGAGCTTGAATGGTTGAAGAAAGAGAGAAGAACGTAAAGATTT
GGTTGAATGAATC
Found at i:39131194 original size:42 final size:42
Alignment explanation
Indices: 39131147--39131231 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
39131137 ATAAGAAGAA
39131147 TATCTCGACCCATTTGTGCACAAATAGGAAATCTAAGCCTAT
1 TATCTCGACCCATTTGTGCACAAATAGGAAATCTAAGCCTAT
*
39131189 TATCTCGACCCATTTGTGCACAAATAGGGAATCTAAGCCTAT
1 TATCTCGACCCATTTGTGCACAAATAGGAAATCTAAGCCTAT
39131231 T
1 T
39131232 CATTTTCTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (42 bp):
TATCTCGACCCATTTGTGCACAAATAGGAAATCTAAGCCTAT
Found at i:39133170 original size:36 final size:37
Alignment explanation
Indices: 39133103--39133172 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
39133093 AAAAAGAAAA
* *
39133103 TAGGGAGTTTGAAGGGTTGAAGGAAAGGGGAAGAAGG
1 TAGGGAGTTTGAAGGGTTAAAAGAAAGGGGAAGAAGG
39133140 TAGGG-GTTTGAAGGGTTAAAAG-AAGAGGGAAGA
1 TAGGGAGTTTGAAGGGTTAAAAGAAAG-GGGAAGA
39133173 GCGTAGAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 3 0.10
36 22 0.73
37 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.46, T:0.17
Consensus pattern (37 bp):
TAGGGAGTTTGAAGGGTTAAAAGAAAGGGGAAGAAGG
Found at i:39133259 original size:37 final size:37
Alignment explanation
Indices: 39133051--39133260 Score: 181
Period size: 37 Copynumber: 5.7 Consensus size: 37
39133041 GAAATAGGAT
*
39133051 GAAAAGGGAAGAAAGTAGGGAGCTTGAAGGGTTGAAG
1 GAAACGGGAAGAAAGTAGGGAGCTTGAAGGGTTGAAG
* *** * *
39133088 GAATCAAAAAGAAAATAGGGAGTTTGAAGGGTTGAAG
1 GAAACGGGAAGAAAGTAGGGAGCTTGAAGGGTTGAAG
* * * * *
39133125 GAAAGGGGAAGAAGGTAGGG-GTTTGAAGGGTTAAAA
1 GAAACGGGAAGAAAGTAGGGAGCTTGAAGGGTTGAAG
** * * * * *
39133161 GAAGA-GGGAAGAGCGTAGAGATCTTTAAGGGATGAAT
1 GAA-ACGGGAAGAAAGTAGGGAGCTTGAAGGGTTGAAG
* * * *
39133198 GAATCGGGATGAAATTAGGAAGCTTGAAGGGTTGAAG
1 GAAACGGGAAGAAAGTAGGGAGCTTGAAGGGTTGAAG
*
39133235 GAAACGGGAAGAAATTAGGGAGCTTG
1 GAAACGGGAAGAAAGTAGGGAGCTTG
39133261 GAATATTGAA
Statistics
Matches: 131, Mismatches: 39, Indels: 6
0.74 0.22 0.03
Matches are distributed among these distances:
36 29 0.22
37 102 0.78
ACGTcount: A:0.40, C:0.04, G:0.39, T:0.18
Consensus pattern (37 bp):
GAAACGGGAAGAAAGTAGGGAGCTTGAAGGGTTGAAG
Done.