Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 142 of 228
Found at i:42774023 original size:18 final size:19
Alignment explanation
Indices: 42773982--42774026 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
42773972 TAAAAAAAAC
42773982 ATTTTGAAATTGAATAATG
1 ATTTTGAAATTGAATAATG
42774001 A-TTTGTAAA-TGAATAAT-
1 ATTTTG-AAATTGAATAATG
42774018 ATTTTGAAA
1 ATTTTGAAA
42774027 ACGAACGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 4 0.17
18 16 0.67
19 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (19 bp):
ATTTTGAAATTGAATAATG
Found at i:42778170 original size:9 final size:9
Alignment explanation
Indices: 42778156--42778217 Score: 61
Period size: 9 Copynumber: 6.7 Consensus size: 9
42778146 TTCACATCCT
42778156 TCTCTCAAC
1 TCTCTCAAC
*
42778165 TCTCTCAAT
1 TCTCTCAAC
* *
42778174 TCTTTCAAAT
1 TCTCTC-AAC
42778184 TCTCTCAAAC
1 TCTCTC-AAC
* *
42778194 ACTCTCAAG
1 TCTCTCAAC
42778203 TCTCTCAAC
1 TCTCTCAAC
42778212 TCTCTC
1 TCTCTC
42778218 GCTTTTAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
9 28 0.64
10 16 0.36
ACGTcount: A:0.24, C:0.37, G:0.02, T:0.37
Consensus pattern (9 bp):
TCTCTCAAC
Found at i:42786264 original size:27 final size:28
Alignment explanation
Indices: 42786227--42786283 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
42786217 TCAAATATTG
*
42786227 TAATATCATCA-TAT-ACATATCATTCAA
1 TAATATAATCATTATCACAT-TCATTCAA
*
42786254 TAATATAATCATTTTCACATTCATTCAA
1 TAATATAATCATTATCACATTCATTCAA
42786282 TA
1 TA
42786284 CATTGTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 12 0.46
29 4 0.15
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (28 bp):
TAATATAATCATTATCACATTCATTCAA
Found at i:42790881 original size:346 final size:348
Alignment explanation
Indices: 42790232--42790930 Score: 1267
Period size: 346 Copynumber: 2.0 Consensus size: 348
42790222 ACACACAAAT
42790232 TTAACGTGGAAAAAACCCTCCAAAGAGGATAAAAAAACCACGGGCAAAGATAATTTTACTATAAT
1 TTAACGTGGAAAAAACCCTCCAAAGAGGATAAAAAAACCACGGGCAAAGATAATTTTACTATAAT
* * *
42790297 GGCAAAAGAATGAAGAGTACAAAAGATGGAGATAAAACTAAACCCCCAAAAACTCAAAAAATAAA
66 GGAAAAAGAATGAAGAGTACAAAAGATGGAGATAAAACTAAACCCCCAAAAACCCAAAAAACAAA
*
42790362 GAACCCTCAAAACGTAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAATGGGTGTTT
131 GAACCCTCAAAACGTAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAATGGATGTTT
*
42790427 TTTCTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTCATATGTCAAATAATAATAAAATAAT
196 TTACTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTCATATGTCAAATAATAATAAAATAAT
* * * *
42790492 CTAAACTAATCAGTGTTTGACTGAAATAAATAAATAGAGTTTAACTAAAAGATTATTTTTCAAAT
261 CTAAACTAATCAGTGTTTGACTGAAACAAATAAACAAAGTTTAACTAAAAGATTATTTCTCAAAT
42790557 TTGACTGAAAATAGGAGTCATAC
326 TTGACTGAAAATAGGAGTCATAC
*
42790580 TTAACGTGGAAAAACCCCTCCAAAGAGGAT-AAAAAACCACGGGCAAAGATAATTTTACTATAAT
1 TTAACGTGGAAAAAACCCTCCAAAGAGGATAAAAAAACCACGGGCAAAGATAATTTTACTATAAT
* *
42790644 GGAAAAAGAATGAAGAGTACAAAAGATGGAGATAAAACTAAA-CCCCGAAAACCCGAAAAACAAA
66 GGAAAAAGAATGAAGAGTACAAAAGATGGAGATAAAACTAAACCCCCAAAAACCCAAAAAACAAA
42790708 GAACCCTCAAAACGTAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAATGGATGTTT
131 GAACCCTCAAAACGTAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAATGGATGTTT
42790773 TTACTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTCATATGTCAAATAATAATAAAATAAT
196 TTACTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTCATATGTCAAATAATAATAAAATAAT
*
42790838 CTAAACTAATCAGTGTTTGACTGAAACAAATAAACAAAGTTTAATTAAAAGATTATTTCTCAAAT
261 CTAAACTAATCAGTGTTTGACTGAAACAAATAAACAAAGTTTAACTAAAAGATTATTTCTCAAAT
42790903 TTGACTGAAAATAGGAGTCATAC
326 TTGACTGAAAATAGGAGTCATAC
42790926 TTAAC
1 TTAAC
42790931 AAATCTCCAC
Statistics
Matches: 338, Mismatches: 13, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
346 234 0.69
347 75 0.22
348 29 0.09
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (348 bp):
TTAACGTGGAAAAAACCCTCCAAAGAGGATAAAAAAACCACGGGCAAAGATAATTTTACTATAAT
GGAAAAAGAATGAAGAGTACAAAAGATGGAGATAAAACTAAACCCCCAAAAACCCAAAAAACAAA
GAACCCTCAAAACGTAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAATGGATGTTT
TTACTAAGGTTGTAAAAGAGCCTATTTATAGGCTAAATTCATATGTCAAATAATAATAAAATAAT
CTAAACTAATCAGTGTTTGACTGAAACAAATAAACAAAGTTTAACTAAAAGATTATTTCTCAAAT
TTGACTGAAAATAGGAGTCATAC
Found at i:42796853 original size:30 final size:30
Alignment explanation
Indices: 42796817--42796876 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
42796807 GGTCTCTTTC
42796817 ATGTTTTCTAATTAAGTGATTAGAGTTTAT
1 ATGTTTTCTAATTAAGTGATTAGAGTTTAT
42796847 ATGTTTTCTAATTAAGTGATTAGAGTTTAT
1 ATGTTTTCTAATTAAGTGATTAGAGTTTAT
42796877 TTAAGTTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.50
Consensus pattern (30 bp):
ATGTTTTCTAATTAAGTGATTAGAGTTTAT
Found at i:42799497 original size:28 final size:28
Alignment explanation
Indices: 42799466--42800005 Score: 184
Period size: 28 Copynumber: 19.4 Consensus size: 28
42799456 AGTCGTTTCA
* *
42799466 TGGATAGGTATCATTAGGAGTCGTACCG
1 TGGATAGGTACCATTAGGAGTCATACCG
* *
42799494 TGGATGGGTACCATTATGAGTCATACCG
1 TGGATAGGTACCATTAGGAGTCATACCG
* * * ** ***
42799522 T--AAAGAATACCAGTAGGAGTTGTATAA
1 TGGATAG-GTACCATTAGGAGTCATACCG
* * * * * *
42799549 TAGATAGATACCTTTAAGAGTCGTATCG
1 TGGATAGGTACCATTAGGAGTCATACCG
* ** *
42799577 TGGAT-GAGTACCAATAGGAGTTGTATCG
1 TGGATAG-GTACCATTAGGAGTCATACCG
** * *
42799605 TGGAGGGGTACTATTAGGAGTCATACCA
1 TGGATAGGTACCATTAGGAGTCATACCG
* * * ** ***
42799633 TGGAT-GATACCTTTAAGAGTTGTGTAG
1 TGGATAGGTACCATTAGGAGTCATACCG
**
42799660 TGGATAGGTACCATTAGGAGTTTTACCG
1 TGGATAGGTACCATTAGGAGTCATACCG
* *
42799688 TAGAT-GCGTACCTTTAGGAGTCATACCG
1 TGGATAG-GTACCATTAGGAGTCATACCG
* * *
42799716 TGGGTAGGTACC-TATAGGAGTCATGCCA
1 TGGATAGGTACCAT-TAGGAGTCATACCG
* * * *
42799744 TGGAT-GAATACTATTATGAGTCATACCA
1 TGGATAG-GTACCATTAGGAGTCATACCG
* * **
42799772 TGGATAGGTACCTTTAAGAGTCATGTCG
1 TGGATAGGTACCATTAGGAGTCATACCG
* * * ** *
42799800 TAGAT-GGATACCACTAGAAGTTGTACCA
1 TGGATAGG-TACCATTAGGAGTCATACCG
** * * ** **
42799828 TGGAGGGGAACCATTAGGAATTTTATTG
1 TGGATAGGTACCATTAGGAGTCATACCG
* **
42799856 TGGAT-GGCTACTATTAGGAGTCATGTCG
1 TGGATAGG-TACCATTAGGAGTCATACCG
* * *
42799884 TGGAT-GGTACCGTTAGAAGTCATACCA
1 TGGATAGGTACCATTAGGAGTCATACCG
* ** *
42799911 TGGATAGGTACCTTTCA-GAGTTGTATCG
1 TGGATAGGTACCATT-AGGAGTCATACCG
* ** *
42799939 TGGATGGGTACCATTAGGAGTTGTACCA
1 TGGATAGGTACCATTAGGAGTCATACCG
* * ** *
42799967 TGGATGGGTACCTTTAGGAGTTGTATCG
1 TGGATAGGTACCATTAGGAGTCATACCG
*
42799995 TGGATGGGTAC
1 TGGATAGGTAC
42800006 TGTAACACCC
Statistics
Matches: 375, Mismatches: 119, Indels: 36
0.71 0.22 0.07
Matches are distributed among these distances:
26 2 0.01
27 59 0.16
28 304 0.81
29 10 0.03
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
TGGATAGGTACCATTAGGAGTCATACCG
Found at i:42799642 original size:83 final size:83
Alignment explanation
Indices: 42799555--42799714 Score: 207
Period size: 83 Copynumber: 1.9 Consensus size: 83
42799545 ATAATAGATA
* * * *
42799555 GATACCTTTAAGAGTCGTATCGTGGAT-GAGTACCAATAGGAGTTGTATCGTGGAGGGGTA-CTA
1 GATACCTTTAAGAGTCGTATAGTGGATAG-GTACCAATAGGAGTTGTACCGTAGAGGCGTACCT-
42799618 TTAGGAGTCATACCATGGAT
64 TTAGGAGTCATACCATGGAT
* * * * *
42799638 GATACCTTTAAGAGTTGTGTAGTGGATAGGTACCATTAGGAGTTTTACCGTAGATGCGTACCTTT
1 GATACCTTTAAGAGTCGTATAGTGGATAGGTACCAATAGGAGTTGTACCGTAGAGGCGTACCTTT
42799703 AGGAGTCATACC
66 AGGAGTCATACC
42799715 GTGGGTAGGT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
83 63 0.95
84 3 0.05
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (83 bp):
GATACCTTTAAGAGTCGTATAGTGGATAGGTACCAATAGGAGTTGTACCGTAGAGGCGTACCTTT
AGGAGTCATACCATGGAT
Found at i:42799653 original size:111 final size:111
Alignment explanation
Indices: 42799480--42799846 Score: 303
Period size: 111 Copynumber: 3.3 Consensus size: 111
42799470 TAGGTATCAT
* * * * * ** *
42799480 TAGGAGTCGTACCGTGGATGGGTACCATTATGAGTCATACCGT-AAAGAATACCAGTAGGAGTTG
1 TAGGAGTCGTACCGTGGAGGGGTACCATTAGGAGTCATACCATGGATGAATACCTTTAAGAGTTG
* * * *
42799544 TATAATAGATAGATACCTTTAAGAGTCGTATCGTGGATGAGTACCAA
66 TATAATGGATAGGTACCTTTAAGAGTCATATCGTAGATG-GTACCAA
* * *
42799591 TAGGAGTTGTATCGTGGAGGGGTACTATTAGGAGTCATACCATGGATG-ATACCTTTAAGAGTTG
1 TAGGAGTCGTACCGTGGAGGGGTACCATTAGGAGTCATACCATGGATGAATACCTTTAAGAGTTG
* * * * ** * **
42799655 TGTAGTGGATAGGTACCATTAGGAGTTTTACCGTAGATGCGTACCTT
66 TATAATGGATAGGTACCTTTAAGAGTCATATCGTAGATG-GTACCAA
* * * *
42799702 TAGGAGTCATACCGTGG-GTAGGTACC-TATAGGAGTCATGCCATGGATGAATA-CTATTATGAG
1 TAGGAGTCGTACCGTGGAG-GGGTACCAT-TAGGAGTCATACCATGGATGAATACCT-TTAAGAG
** ** * *
42799764 TCATACCATGGATAGGTACCTTTAAGAGTCATGTCGTAGATGGATACCAC
63 TTGTATAATGGATAGGTACCTTTAAGAGTCATATCGTAGATGG-TACCAA
* * * *
42799814 TAGAAGTTGTACCATGGAGGGGAACCATTAGGA
1 TAGGAGTCGTACCGTGGAGGGGTACCATTAGGA
42799847 ATTTTATTGT
Statistics
Matches: 197, Mismatches: 51, Indels: 15
0.75 0.19 0.06
Matches are distributed among these distances:
110 2 0.01
111 125 0.63
112 68 0.35
113 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.28
Consensus pattern (111 bp):
TAGGAGTCGTACCGTGGAGGGGTACCATTAGGAGTCATACCATGGATGAATACCTTTAAGAGTTG
TATAATGGATAGGTACCTTTAAGAGTCATATCGTAGATGGTACCAA
Found at i:42799709 original size:139 final size:138
Alignment explanation
Indices: 42799529--42800005 Score: 447
Period size: 139 Copynumber: 3.4 Consensus size: 138
42799519 CCGTAAAGAA
* ** * * * *
42799529 TACCAGTAGGAGTTGTATAATAGATAGATACCTTTAAGAGTCGTATCGTGGATGAGTACCAATAG
1 TACCATTAGGAGTTGTACCATGGATGGGTACCTTTAGGAGTCGTATCGTGGATGAGTACCAATAG
** * *
42799594 GAGTTGTATCGTGGAGGGGTACTATTAGGAGTCATACCATGGAT-GATACCTTTAAGAGTTGTGT
66 GAGTCATGTCGTGGA-GGGTACTATTAGGAGTCATACCATGGATAGGTACCTTTAAGAGTTGTGT
*
42799658 AGTGGATAGG
130 CGTGGAT-GG
* * * * * * * *
42799668 TACCATTAGGAGTTTTACCGTAGATGCGTACCTTTAGGAGTCATACCGTGGGT-AGGTACCTATA
1 TACCATTAGGAGTTGTACCATGGATGGGTACCTTTAGGAGTCGTATCGTGGATGA-GTACCAATA
* * ** * **
42799732 GGAGTCATGCCATGGATGAATACTATTATGAGTCATACCATGGATAGGTACCTTTAAGAGTCATG
65 GGAGTCATGTCGTGGA-GGGTACTATTAGGAGTCATACCATGGATAGGTACCTTTAAGAGTTGTG
*
42799797 TCGTAGATGG
129 TCGTGGATGG
* * * * * * ** * * *
42799807 ATACCACTAGAAGTTGTACCATGGAGGGGAACCATTAGGAATTTTATTGTGGATG-GCTACTATT
1 -TACCATTAGGAGTTGTACCATGGATGGGTACCTTTAGGAGTCGTATCGTGGATGAG-TACCAAT
* ** * * *
42799871 AGGAGTCATGTCGTGGATGGTACCGTTAGAAGTCATACCATGGATAGGTACCTTTCAGAGTTGTA
64 AGGAGTCATGTCGTGGAGGGTACTATTAGGAGTCATACCATGGATAGGTACCTTTAAGAGTTGTG
42799936 TCGTGGATGGG
129 TCGTGGAT-GG
* *
42799947 TACCATTAGGAGTTGTACCATGGATGGGTACCTTTAGGAGTTGTATCGTGGATGGGTAC
1 TACCATTAGGAGTTGTACCATGGATGGGTACCTTTAGGAGTCGTATCGTGGATGAGTAC
42800006 TGTAACACCC
Statistics
Matches: 264, Mismatches: 67, Indels: 14
0.77 0.19 0.04
Matches are distributed among these distances:
138 1 0.00
139 181 0.69
140 82 0.31
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (138 bp):
TACCATTAGGAGTTGTACCATGGATGGGTACCTTTAGGAGTCGTATCGTGGATGAGTACCAATAG
GAGTCATGTCGTGGAGGGTACTATTAGGAGTCATACCATGGATAGGTACCTTTAAGAGTTGTGTC
GTGGATGG
Found at i:42799970 original size:56 final size:56
Alignment explanation
Indices: 42799419--42800005 Score: 206
Period size: 56 Copynumber: 10.6 Consensus size: 56
42799409 TTAGTAGAAG
* * * * **
42799419 GGTACCTTTAGGAG-T-TATTGT-GATAGGTACCACTAGAAGTCGTTTCATGGATA
1 GGTACCTTTAGGAGTTGTATCGTGGATGGGTACCATTAGAAGTCATACCATGGATA
* * * * * *
42799472 GGTATCATTAGGAGTCGTACCGTGGATGGGTACCATTATG-AGTCATACC--GTAAA
1 GGTACCTTTAGGAGTTGTATCGTGGATGGGTACCATTA-GAAGTCATACCATGGATA
* ** ** * * * * * * *
42799526 GAATACCAGTAGGAGTTGTATAATAGATAGATACCTTTA-AGAGTCGTATCGTGGAT-
1 G-GTACCTTTAGGAGTTGTATCGTGGATGGGTACCATTAGA-AGTCATACCATGGATA
** * * *
42799582 GAGTACCAATAGGAGTTGTATCGTGGAGGGGTACTATTAGGAGTCATACCATGGAT-
1 G-GTACCTTTAGGAGTTGTATCGTGGATGGGTACCATTAGAAGTCATACCATGGATA
* * * * * * ** * *
42799638 GATACCTTTAAGAGTTGTGTAGTGGATAGGTACCATTAGGAGTTTTACCGTAGAT-
1 GGTACCTTTAGGAGTTGTATCGTGGATGGGTACCATTAGAAGTCATACCATGGATA
** * * * * *
42799693 GCGTACCTTTAGGAGTCATACCGTGGGTAGGTACC-TATAGGAGTCATGCCATGGAT-
1 G-GTACCTTTAGGAGTTGTATCGTGGATGGGTACCAT-TAGAAGTCATACCATGGATA
* * ** * * * * ** * *
42799749 GAATA-CTATTATGAGTCATACCATGGATAGGTACCTTTA-AGAGTCATGTCGTAGAT-
1 G-GTACCT-TTAGGAGTTGTATCGTGGATGGGTACCATTAGA-AGTCATACCATGGATA
** * * * * * ** ***
42799805 GGATACCACTAGAAGTTGTACCATGGAGGGGAACCATTAGGAA-TTTTATTGTGGAT-
1 GG-TACCTTTAGGAGTTGTATCGTGGATGGGTACCATTA-GAAGTCATACCATGGATA
** * *
42799861 GGCTA-CTATTAGGAGTCATGTCGTGGAT-GGTACCGTTAGAAGTCATACCATGGATA
1 GG-TACCT-TTAGGAGTTGTATCGTGGATGGGTACCATTAGAAGTCATACCATGGATA
* ** *
42799917 GGTACCTTTCA-GAGTTGTATCGTGGATGGGTACCATTAGGAGTTGTACCATGGATG
1 GGTACCTTT-AGGAGTTGTATCGTGGATGGGTACCATTAGAAGTCATACCATGGATA
42799973 GGTACCTTTAGGAGTTGTATCGTGGATGGGTAC
1 GGTACCTTTAGGAGTTGTATCGTGGATGGGTAC
42800006 TGTAACACCC
Statistics
Matches: 391, Mismatches: 117, Indels: 49
0.70 0.21 0.09
Matches are distributed among these distances:
53 12 0.03
54 7 0.02
55 117 0.30
56 248 0.63
57 6 0.02
58 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.30
Consensus pattern (56 bp):
GGTACCTTTAGGAGTTGTATCGTGGATGGGTACCATTAGAAGTCATACCATGGATA
Found at i:42803031 original size:18 final size:18
Alignment explanation
Indices: 42803008--42803052 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
42802998 CATGTGTAAA
42803008 GTTTTATTTCAG-GTTAGG
1 GTTTTATTT-AGAGTTAGG
*
42803026 GTTTTATTTTGAGTTAGG
1 GTTTTATTTAGAGTTAGG
42803044 GTTTTATTT
1 GTTTTATTT
42803053 TTTAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.16, C:0.02, G:0.24, T:0.58
Consensus pattern (18 bp):
GTTTTATTTAGAGTTAGG
Found at i:42803169 original size:23 final size:23
Alignment explanation
Indices: 42803124--42803169 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
42803114 TGCTATATAT
* * *
42803124 ATTTTTAATTTTTTATATATAAA
1 ATTTATAATTTTTGAGATATAAA
*
42803147 ATTTATAATTTTTGAGATGTAAA
1 ATTTATAATTTTTGAGATATAAA
42803170 GTTAACAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (23 bp):
ATTTATAATTTTTGAGATATAAA
Found at i:42806619 original size:18 final size:18
Alignment explanation
Indices: 42806576--42806620 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
42806566 GTGGTGGGAC
*
42806576 CATCGGTATCGATTCTTG
1 CATCGGTGTCGATTCTTG
42806594 CATCGGTGTCGATTCTTG
1 CATCGGTGTCGATTCTTG
42806612 CATCGGTGT
1 CATCGGTGT
42806621 AGATGATGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.13, C:0.22, G:0.27, T:0.38
Consensus pattern (18 bp):
CATCGGTGTCGATTCTTG
Found at i:42809139 original size:20 final size:20
Alignment explanation
Indices: 42809092--42809144 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
42809082 AAAATTGACT
* *
42809092 ATTTTTAGAATTCTTTTTGA
1 ATTTTTATAATTCTTGTTGA
* * *
42809112 AATCTTATAATTCTTGTTGG
1 ATTTTTATAATTCTTGTTGA
*
42809132 ATTTTTATGATTC
1 ATTTTTATAATTC
42809145 CAAAAGTTAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.08, G:0.11, T:0.57
Consensus pattern (20 bp):
ATTTTTATAATTCTTGTTGA
Found at i:42812124 original size:50 final size:50
Alignment explanation
Indices: 42812013--42812208 Score: 194
Period size: 50 Copynumber: 3.8 Consensus size: 50
42812003 ATTTGGGTAA
* * *
42812013 AGAGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCATTGAGGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATG
*
42812069 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*** * *
42812119 AGAGGTCCCCCATAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** ** * * *
42812169 AGAACTATCGTGTAAGACCATATCTGGGATATGGCATTGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
42812209 TAGTACAAGA
Statistics
Matches: 120, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 77 0.64
52 1 0.01
53 2 0.02
55 1 0.01
56 39 0.32
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:42814366 original size:3 final size:3
Alignment explanation
Indices: 42814358--42814402 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
42814348 ATTGCAGATA
42814358 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42814403 GAGGTAACCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:42814838 original size:31 final size:31
Alignment explanation
Indices: 42814803--42814868 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
42814793 TAATAGTTTG
*
42814803 GTGACATGAATAAAAATTTTCAAATAATTCA
1 GTGACATAAATAAAAATTTTCAAATAATTCA
* * *
42814834 GTGACTTAAATGAAAATTTTCAAATAATTTA
1 GTGACATAAATAAAAATTTTCAAATAATTCA
42814865 GTGA
1 GTGA
42814869 TGATTTTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (31 bp):
GTGACATAAATAAAAATTTTCAAATAATTCA
Found at i:42815530 original size:20 final size:20
Alignment explanation
Indices: 42815503--42815547 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
42815493 TTTATACAAT
42815503 AATA-ATATTTTAATTTTTA
1 AATATATATTTTAATTTTTA
42815522 AATATATATTTTAATTTTTA
1 AATATATATTTTAATTTTTA
42815542 AATATA
1 AATATA
42815548 ATTATATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AATATATATTTTAATTTTTA
Found at i:42815825 original size:33 final size:33
Alignment explanation
Indices: 42815788--42815853 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
42815778 GAAATGTTAG
42815788 AGTAATAAAATAAAATTACTCAAGATTTTAATT
1 AGTAATAAAATAAAATTACTCAAGATTTTAATT
42815821 AGTAATAAAATAAAATTACTCAAGATTTTAATT
1 AGTAATAAAATAAAATTACTCAAGATTTTAATT
42815854 TTCTCTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (33 bp):
AGTAATAAAATAAAATTACTCAAGATTTTAATT
Found at i:42816937 original size:15 final size:15
Alignment explanation
Indices: 42816917--42816945 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42816907 CCAGTCACAC
42816917 AGGCGTGTCTTACAT
1 AGGCGTGTCTTACAT
42816932 AGGCGTGTCTTACA
1 AGGCGTGTCTTACA
42816946 AACACGCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (15 bp):
AGGCGTGTCTTACAT
Found at i:42819130 original size:35 final size:35
Alignment explanation
Indices: 42819084--42819153 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
42819074 ATGGCATGAC
*
42819084 TTTACTAGCAACAGTGGAATTCATAGCTCAATTAA
1 TTTACTAGCAACAGTGGAATTCATAGCCCAATTAA
42819119 TTTACTAGCAACAGTGGAATTCATAGCCCAATTAA
1 TTTACTAGCAACAGTGGAATTCATAGCCCAATTAA
42819154 AGAGTTAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (35 bp):
TTTACTAGCAACAGTGGAATTCATAGCCCAATTAA
Found at i:42822770 original size:19 final size:18
Alignment explanation
Indices: 42822724--42822771 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
42822714 GATAGAATTT
*
42822724 TTGTCATAAAATAATTAAT
1 TTGT-ATAAAATAATTAAA
*
42822743 TTTTATAAAATAATTAAA
1 TTGTATAAAATAATTAAA
42822761 TTGTATTAAAA
1 TTGTA-TAAAA
42822772 ATTTGAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (18 bp):
TTGTATAAAATAATTAAA
Found at i:42825490 original size:27 final size:28
Alignment explanation
Indices: 42825427--42825494 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
42825417 TTCTTCGAAG
* *
42825427 TTTTCTTTTTCTTTTTCCTCTTTCTGGG
1 TTTTCTTTTTCTTTTTCCTCTTGCTGGA
** *
42825455 TTTTC-TTTTCTTTTTGTTCTTGCT-TA
1 TTTTCTTTTTCTTTTTCCTCTTGCTGGA
42825481 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
42825495 GAAAACTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 5 0.15
27 24 0.71
28 5 0.15
ACGTcount: A:0.01, C:0.18, G:0.07, T:0.74
Consensus pattern (28 bp):
TTTTCTTTTTCTTTTTCCTCTTGCTGGA
Found at i:42826165 original size:21 final size:22
Alignment explanation
Indices: 42826140--42826197 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
42826130 ATGTCCTTGG
*
42826140 CCCACACGGGCGTGTGCCTCAT
1 CCCACACAGGCGTGTGCCTCAT
* * *
42826162 -CCACATAGTCGTGTGCCTCCT
1 CCCACACAGGCGTGTGCCTCAT
*
42826183 CCCACACAAGCGTGT
1 CCCACACAGGCGTGT
42826198 TGACCCCTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.17, C:0.40, G:0.22, T:0.21
Consensus pattern (22 bp):
CCCACACAGGCGTGTGCCTCAT
Found at i:42834572 original size:22 final size:22
Alignment explanation
Indices: 42834546--42834589 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
42834536 ATTATGTGTA
42834546 TAATTCATAATATAA-TTAATTT
1 TAATT-ATAATATAATTTAATTT
* *
42834568 TAATTTTAATCTAATTTAATTT
1 TAATTATAATATAATTTAATTT
42834590 GGGTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATTATAATATAATTTAATTT
Found at i:42840131 original size:12 final size:13
Alignment explanation
Indices: 42840114--42840142 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
42840104 CTCATACATG
42840114 AATAAATAAA-GC
1 AATAAATAAATGC
42840126 AATAAATAAATGC
1 AATAAATAAATGC
42840139 AATA
1 AATA
42840143 GTTATAGCTC
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:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:42842075 original size:25 final size:26
Alignment explanation
Indices: 42842041--42842089 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
42842031 TTGTAAAGAG
*
42842041 AAATTCTCTAAAGAGATTATTCTAGA
1 AAATTCTCTAAAGACATTATTCTAGA
* *
42842067 AAATT-TCTAGAGACATTTTTCTA
1 AAATTCTCTAAAGACATTATTCTA
42842090 ATTTACAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (26 bp):
AAATTCTCTAAAGACATTATTCTAGA
Found at i:42845578 original size:66 final size:66
Alignment explanation
Indices: 42845454--42845583 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 66
42845444 ATTTAAGATC
* * ** * *
42845454 ACCAAAATCCTTTTCAAAATCACAATATGAATTAACAAAATTCACATGCATAAGAACAAAAAAAT
1 ACCAAAAACCTATTCAAAATCACAATACAAATTAACAAAATTCACATACATAAAAACAAAAAAAT
42845519 T
66 T
* * * * *
42845520 ACCAAAAACCTATTCAAATTCATAATACAAATTAACGAAATTCACATATATAAAAACAACAAAA
1 ACCAAAAACCTATTCAAAATCACAATACAAATTAACAAAATTCACATACATAAAAACAAAAAAA
42845584 CATCTATTCA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.55, C:0.18, G:0.03, T:0.23
Consensus pattern (66 bp):
ACCAAAAACCTATTCAAAATCACAATACAAATTAACAAAATTCACATACATAAAAACAAAAAAAT
T
Found at i:42851445 original size:48 final size:48
Alignment explanation
Indices: 42851387--42851478 Score: 175
Period size: 48 Copynumber: 1.9 Consensus size: 48
42851377 TATCAATACC
42851387 AATCTCATAATAATAATACTCAAATTCATGCTTATAATATTTTATAAT
1 AATCTCATAATAATAATACTCAAATTCATGCTTATAATATTTTATAAT
*
42851435 AATCTCATAATAATAATACTCAAATTCATGCTTATAATCTTTTA
1 AATCTCATAATAATAATACTCAAATTCATGCTTATAATATTTTA
42851479 ATTTTATTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.41
Consensus pattern (48 bp):
AATCTCATAATAATAATACTCAAATTCATGCTTATAATATTTTATAAT
Found at i:42853466 original size:19 final size:19
Alignment explanation
Indices: 42853450--42853496 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
42853440 GTGTGCCCTG
42853450 GCCGTGTAGAAGTGCCCAA
1 GCCGTGTAGAAGTGCCCAA
* *
42853469 GTCGTGTGGAAGTGCCCAA
1 GCCGTGTAGAAGTGCCCAA
*
42853488 GCCATGTAG
1 GCCGTGTAG
42853497 GGGTCTACAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.34, T:0.19
Consensus pattern (19 bp):
GCCGTGTAGAAGTGCCCAA
Found at i:42857113 original size:47 final size:47
Alignment explanation
Indices: 42857055--42857242 Score: 349
Period size: 47 Copynumber: 4.0 Consensus size: 47
42857045 TATTTGAATA
* *
42857055 AATGTGTAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
42857102 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
*
42857149 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
42857196 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
42857243 TGTAACACCC
Statistics
Matches: 137, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 137 1.00
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
Found at i:42858726 original size:40 final size:40
Alignment explanation
Indices: 42858628--42858890 Score: 307
Period size: 40 Copynumber: 6.6 Consensus size: 40
42858618 TCCTCGTTCA
* * * * *
42858628 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
42858667 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
42858707 AATGCCTTCGGGACTTAACCCGGATTTAATAACTGGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
42858747 AATGCCTTCGGGGCTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
42858787 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
42858827 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
42858867 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
42858891 CAGCATTCAA
Statistics
Matches: 196, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
39 37 0.19
40 151 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:42860454 original size:47 final size:47
Alignment explanation
Indices: 42860385--42860648 Score: 447
Period size: 47 Copynumber: 5.6 Consensus size: 47
42860375 GGCTGTCACA
42860385 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATG
1 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATG
*
42860432 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATG
1 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATG
42860479 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATG
1 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATG
42860526 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATG
1 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATG
* * * * * *
42860573 TGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACG
1 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATG
* *
42860620 TGATGGATGTGAAAGTGTATAAATGTGAT
1 TGATGAATGTGAAAGTGTATATATGTGAT
42860649 GAGTCCCGAA
Statistics
Matches: 206, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 206 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATG
Found at i:42866082 original size:18 final size:18
Alignment explanation
Indices: 42865985--42866088 Score: 66
Period size: 18 Copynumber: 5.6 Consensus size: 18
42865975 CATGTTGTAA
*
42865985 TGAAAAAGAAAAAGAGAT
1 TGAAAAAGAAAAAGAAAT
*
42866003 TGAAAAAGAGGAAAAAAAAAT
1 TG-AAAA-A-GAAAAAGAAAT
*
42866024 TGAAAGAGAGAAAAG-AAT
1 TGAAAAAGA-AAAAGAAAT
* ***** *
42866042 CGAAAAAGATTGTTAAAA
1 TGAAAAAGAAAAAGAAAT
*
42866060 AGAAAAAGAAAAAGAAAT
1 TGAAAAAGAAAAAGAAAT
42866078 TGAAAAAGAAA
1 TGAAAAAGAAA
42866089 GTGAAAGTGA
Statistics
Matches: 61, Mismatches: 20, Indels: 10
0.67 0.22 0.11
Matches are distributed among these distances:
18 37 0.61
19 9 0.15
20 4 0.07
21 11 0.18
ACGTcount: A:0.67, C:0.01, G:0.20, T:0.12
Consensus pattern (18 bp):
TGAAAAAGAAAAAGAAAT
Found at i:42866093 original size:12 final size:12
Alignment explanation
Indices: 42866056--42866094 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
42866046 AAAGATTGTT
*
42866056 AAAAAGAAAAAG
1 AAAAAGAAAATG
*
42866068 AAAAAGAAATTG
1 AAAAAGAAAATG
*
42866080 AAAAAGAAAGTG
1 AAAAAGAAAATG
42866092 AAA
1 AAA
42866095 GTGAGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:42866094 original size:18 final size:20
Alignment explanation
Indices: 42866060--42866110 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
42866050 ATTGTTAAAA
*
42866060 AGAAAAAGAAAAAGAAA-T-
1 AGAAAAAGAAAGAGAAAGTG
* *
42866078 TGAAAAAGAAAGTGAAAGTG
1 AGAAAAAGAAAGAGAAAGTG
42866098 AGAAAAAGAAAGA
1 AGAAAAAGAAAGA
42866111 CAAAATTGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 14 0.54
19 1 0.04
20 11 0.42
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.08
Consensus pattern (20 bp):
AGAAAAAGAAAGAGAAAGTG
Found at i:42872651 original size:30 final size:30
Alignment explanation
Indices: 42872615--42872676 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
42872605 GCTAGGATTC
*
42872615 TTCAACTCTTTAACCGGTCATATTGAGAAG
1 TTCAACTCTTTAAACGGTCATATTGAGAAG
*
42872645 TTCAACTCTTTAAATGGTCATATTGAGAAG
1 TTCAACTCTTTAAACGGTCATATTGAGAAG
42872675 TT
1 TT
42872677 TAAAGTAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (30 bp):
TTCAACTCTTTAAACGGTCATATTGAGAAG
Found at i:42873971 original size:14 final size:14
Alignment explanation
Indices: 42873954--42873993 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
42873944 CTTTATTAAT
*
42873954 ATATTTTATTTGGG
1 ATATTTTATTTAGG
42873968 ATATTTTATTTAGG
1 ATATTTTATTTAGG
42873982 ATATTTTATTTA
1 ATATTTTATTTA
42873994 TCTTTGAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (14 bp):
ATATTTTATTTAGG
Found at i:42877188 original size:25 final size:25
Alignment explanation
Indices: 42877159--42877207 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
42877149 AAGGAGTCAA
42877159 CTTACCCTTTGGTATAATGTTTGAC
1 CTTACCCTTTGGTATAATGTTTGAC
42877184 CTTACCCTTTGGTATAATGTTTGA
1 CTTACCCTTTGGTATAATGTTTGA
42877208 ATCCCTACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.45
Consensus pattern (25 bp):
CTTACCCTTTGGTATAATGTTTGAC
Found at i:42884504 original size:25 final size:25
Alignment explanation
Indices: 42884476--42884534 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
42884466 AGCTGTAAAC
* *
42884476 GGTAAGCTCCTCCGAGATGATTAAT
1 GGTAAGCTCCTCCAAGATGAATAAT
* *
42884501 GGTAAGCTCCTCTAAGCTGAATAAT
1 GGTAAGCTCCTCCAAGATGAATAAT
42884526 GGTAAGCTC
1 GGTAAGCTC
42884535 ATATGAGCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (25 bp):
GGTAAGCTCCTCCAAGATGAATAAT
Found at i:42884543 original size:25 final size:25
Alignment explanation
Indices: 42884497--42884571 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
42884487 CCGAGATGAT
* * *
42884497 TAATGGTAAGCTCCTCTAAGCTGAA
1 TAATGGTAAGCTCATATGAGCTGAA
*
42884522 TAATGGTAAGCTCATATGAGCTGAG
1 TAATGGTAAGCTCATATGAGCTGAA
*
42884547 T-ATCGGTAAGCTCATAAGAGCTGAA
1 TAAT-GGTAAGCTCATATGAGCTGAA
42884572 ATCAATAACC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 2 0.05
25 41 0.95
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (25 bp):
TAATGGTAAGCTCATATGAGCTGAA
Found at i:42887155 original size:27 final size:27
Alignment explanation
Indices: 42887125--42887227 Score: 136
Period size: 27 Copynumber: 3.8 Consensus size: 27
42887115 TAAATGATCG
*
42887125 AAATACCCTCGAAGGGTAAAATTATCA
1 AAATACCCTCGAAGGGTAAAATTACCA
*
42887152 AAATACCCTCGAAGGGTAAATTTACCA
1 AAATACCCTCGAAGGGTAAAATTACCA
* * *
42887179 CAATACCCTCGATGGGTAAAATTACCG
1 AAATACCCTCGAAGGGTAAAATTACCA
*
42887206 AATTACCCTC-ATAGGGTAAAAT
1 AAATACCCTCGA-AGGGTAAAAT
42887228 GACTGTTATA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
26 1 0.02
27 65 0.98
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (27 bp):
AAATACCCTCGAAGGGTAAAATTACCA
Found at i:42895474 original size:17 final size:18
Alignment explanation
Indices: 42895444--42895480 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
42895434 GCAACTAAAC
42895444 AAAACAAGGTTTTTC-TA
1 AAAACAAGGTTTTTCGTA
42895461 AAAACTAAGG-TTTTCGTA
1 AAAAC-AAGGTTTTTCGTA
42895479 AA
1 AA
42895481 TAGAAATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (18 bp):
AAAACAAGGTTTTTCGTA
Found at i:42905669 original size:13 final size:13
Alignment explanation
Indices: 42905651--42905680 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
42905641 GTTAGCACTT
42905651 TGAAATGACTATA
1 TGAAATGACTATA
*
42905664 TGAAATGGCTATA
1 TGAAATGACTATA
42905677 TGAA
1 TGAA
42905681 TCAGTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (13 bp):
TGAAATGACTATA
Found at i:42905689 original size:26 final size:25
Alignment explanation
Indices: 42905660--42905723 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 25
42905650 TTGAAATGAC
*
42905660 TATATGAAATGGCTATATGAA-TCAGT
1 TATATGAAATGACTATATGAAGT--GT
* *
42905686 TATATGGAAATAATTATATGAAGTGT
1 TATAT-GAAATGACTATATGAAGTGT
42905712 TATATGAAATGA
1 TATATGAAATGA
42905724 TTACATGGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
25 6 0.19
26 12 0.38
27 13 0.41
28 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (25 bp):
TATATGAAATGACTATATGAAGTGT
Found at i:42909339 original size:27 final size:27
Alignment explanation
Indices: 42909309--42909366 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
42909299 TTCATCTCCT
*
42909309 AGGGGTA-TAAAGATCATTTTACCCTTA
1 AGGGGTATTAAAG-TAATTTTACCCTTA
* *
42909336 AGGGGTATTACAGTAATTTTACTCTTA
1 AGGGGTATTAAAGTAATTTTACCCTTA
42909363 AGGG
1 AGGG
42909367 TTTTTGGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (27 bp):
AGGGGTATTAAAGTAATTTTACCCTTA
Found at i:42909444 original size:28 final size:27
Alignment explanation
Indices: 42909324--42909544 Score: 193
Period size: 27 Copynumber: 8.3 Consensus size: 27
42909314 TATAAAGATC
* *
42909324 ATTTTACCCTT-AAGGGGTATTAC-AGTA
1 ATTTTACCCTTCGA-GGGTATTTCGA-TA
* * * *
42909351 ATTTTACTCTT-AAGGGT-TTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
*
42909376 ATTTTACCCTTCGAGGGTATTTTGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
42909403 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
*
42909430 ATTTTTACCCTTCGAGGGTATTTCGGTA
1 A-TTTTACCCTTCGAGGGTATTTCGATA
* * *
42909458 ATTTAACCCTTTGAGGGTATTT-TAGTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
* * * *
42909485 ATTTTACCCTT-GGGGGTAATTCGGTC
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * * *
42909511 ATTTTACCCTTCGGGGGTAATTCGGTC
1 ATTTTACCCTTCGAGGGTATTTCGATA
42909538 ATTTTAC
1 ATTTTAC
42909545 TTTTAGGGGG
Statistics
Matches: 168, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
25 14 0.08
26 29 0.17
27 99 0.59
28 26 0.15
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATA
Found at i:42909447 original size:55 final size:55
Alignment explanation
Indices: 42909324--42909544 Score: 215
Period size: 55 Copynumber: 4.1 Consensus size: 55
42909314 TATAAAGATC
* * * * * *
42909324 ATTTTACCCTT-AAGGGGTATTACAGTAATTTTACTCTT-AAGGGT-TTTTG-GTA
1 ATTTTACCCTTCGA-GGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGAGTA
* *
42909376 ATTTTACCCTTCGAGGGTATTTTGATAATTTTACCCTTCGAGGGTATTTCGA-TA
1 ATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGAGTA
* * *
42909430 ATTTTTACCCTTCGAGGGTATTTCGGTAATTTAACCCTTTGAGGGTATTT-TAGTA
1 A-TTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGAGTA
* * * * * *
42909485 ATTTTACCCTT-GGGGGTAATTCGGTCATTTTACCCTTCGGGGGTAATTCG-GTC
1 ATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGAGTA
42909538 ATTTTAC
1 ATTTTAC
42909545 TTTTAGGGGG
Statistics
Matches: 140, Mismatches: 22, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
52 30 0.21
53 45 0.32
54 18 0.13
55 47 0.34
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (55 bp):
ATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGAGTA
Found at i:42909553 original size:27 final size:27
Alignment explanation
Indices: 42909322--42909571 Score: 148
Period size: 27 Copynumber: 9.3 Consensus size: 27
42909312 GGTATAAAGA
* *
42909322 TCATTTTACCCTTAAGGGGT-ATTACAG
1 TCATTTTACCCTTAGGGGGTAATT-CGG
* * * * *
42909349 TAATTTTACTCTTA-AGGGT-TTTTGG
1 TCATTTTACCCTTAGGGGGTAATTCGG
* * * * * *
42909374 TAATTTTACCCTTCGAGGGTATTTTGA
1 TCATTTTACCCTTAGGGGGTAATTCGG
* * * * *
42909401 TAATTTTACCCTTCGAGGGTATTTCGA
1 TCATTTTACCCTTAGGGGGTAATTCGG
* * * *
42909428 TAATTTTTACCCTTCGAGGGTATTTCGG
1 TCA-TTTTACCCTTAGGGGGTAATTCGG
* * * * * **
42909456 TAATTTAACCCTTTGAGGGTATTTTAG
1 TCATTTTACCCTTAGGGGGTAATTCGG
*
42909483 TAATTTTACCCTT-GGGGGTAATTCGG
1 TCATTTTACCCTTAGGGGGTAATTCGG
*
42909509 TCATTTTACCCTTCGGGGGTAATTCGG
1 TCATTTTACCCTTAGGGGGTAATTCGG
** *
42909536 TCATTTTACTTTTAGGGGGTAATACGG
1 TCATTTTACCCTTAGGGGGTAATTCGG
42909563 TCATTTTAC
1 TCATTTTAC
42909572 GCACGATTCG
Statistics
Matches: 194, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
25 13 0.07
26 32 0.16
27 123 0.63
28 26 0.13
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTTAGGGGGTAATTCGG
Found at i:42925013 original size:20 final size:20
Alignment explanation
Indices: 42924990--42925032 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
42924980 CCCCTGTATA
* *
42924990 CACTTCGGTGTCCCTATTCG
1 CACTACGGTGCCCCTATTCG
*
42925010 CACTACGGTGCCCCTATTTG
1 CACTACGGTGCCCCTATTCG
42925030 CAC
1 CAC
42925033 ATTTGTGCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.37, G:0.19, T:0.30
Consensus pattern (20 bp):
CACTACGGTGCCCCTATTCG
Found at i:42946654 original size:20 final size:20
Alignment explanation
Indices: 42946631--42946674 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
42946621 AATTTTGATA
42946631 TTTTATTTCAATT-TTTTTAT
1 TTTTATTT-AATTATTTTTAT
*
42946651 TTTTCTTTAATTATTTTTAT
1 TTTTATTTAATTATTTTTAT
42946671 TTTT
1 TTTT
42946675 TATAACTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTATTTAATTATTTTTAT
Found at i:42956700 original size:14 final size:13
Alignment explanation
Indices: 42956679--42956718 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
42956669 AGTATCTTAG
42956679 AAATTAAATTATA
1 AAATTAAATTATA
*
42956692 AATATTAAATTTTA
1 AA-ATTAAATTATA
*
42956706 AAATTAAAATATA
1 AAATTAAATTATA
42956719 TTAGAGGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTAAATTATA
Found at i:42958454 original size:28 final size:28
Alignment explanation
Indices: 42958412--42958561 Score: 173
Period size: 28 Copynumber: 5.4 Consensus size: 28
42958402 AAACAGCATG
* *
42958412 CAGTAACAGTCTGGGCCTTAGCCCAATA
1 CAGTAACAATGTGGGCCTTAGCCCAATA
42958440 CAGTAACAATGTGGGCCTTAGCCCAATA
1 CAGTAACAATGTGGGCCTTAGCCCAATA
* *
42958468 GAGTAAC-A-GATGGGACTTAGCCCAATA
1 CAGTAACAATG-TGGGCCTTAGCCCAATA
* * *
42958495 CAG-AATTAGTGTGGGCCTTAGCCCAGTA
1 CAGTAA-CAATGTGGGCCTTAGCCCAATA
*
42958523 CAG-AATCAGTGTGGGCCTTAGCCCAATA
1 CAGTAA-CAATGTGGGCCTTAGCCCAATA
42958551 CAGTAACAATG
1 CAGTAACAATG
42958562 CAGTGCAATA
Statistics
Matches: 105, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
26 3 0.03
27 19 0.18
28 80 0.76
29 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.21
Consensus pattern (28 bp):
CAGTAACAATGTGGGCCTTAGCCCAATA
Found at i:42958508 original size:55 final size:56
Alignment explanation
Indices: 42958412--42958561 Score: 198
Period size: 55 Copynumber: 2.7 Consensus size: 56
42958402 AAACAGCATG
*
42958412 CAGTAACAGTCTGGGCCTTAGCCCAATACAGTAACAATGTGGGCCTTAGCCCAATA
1 CAGTAACAGTATGGGCCTTAGCCCAATACAGTAACAATGTGGGCCTTAGCCCAATA
* * * * *
42958468 GAGTAACAG-ATGGGACTTAGCCCAATACAG-AATTAGTGTGGGCCTTAGCCCAGTA
1 CAGTAACAGTATGGGCCTTAGCCCAATACAGTAA-CAATGTGGGCCTTAGCCCAATA
*
42958523 CAG-AATCAGTGTGGGCCTTAGCCCAATACAGTAACAATG
1 CAGTAA-CAGTATGGGCCTTAGCCCAATACAGTAACAATG
42958562 CAGTGCAATA
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
54 4 0.05
55 43 0.54
56 30 0.38
57 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.21
Consensus pattern (56 bp):
CAGTAACAGTATGGGCCTTAGCCCAATACAGTAACAATGTGGGCCTTAGCCCAATA
Found at i:42958957 original size:27 final size:26
Alignment explanation
Indices: 42958927--42959149 Score: 248
Period size: 27 Copynumber: 8.2 Consensus size: 26
42958917 GGTATAAAAA
* *
42958927 TCATTTTACCTTATGGGGTTATTTTGG
1 TCATTTTACCCTATGGGG-TATTTCGG
*
42958954 TCATTTTACCCTATGAGGGTATTTCGA
1 TCATTTTACCCTATG-GGGTATTTCGG
*
42958981 TCATTTTACCCTATTAGGGGTATTTTGG
1 TCATTTTACCCTA-T-GGGGTATTTCGG
* *
42959009 TTATTCTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTAT-GGGGTATTTCGG
* *
42959036 TCATTCTACCCTATGAGGGTATTTTGG
1 TCATTTTACCCTATG-GGGTATTTCGG
* **
42959063 TCATTTTACACTATGGGGGTATTTCAA
1 TCATTTTACCCTAT-GGGGTATTTCGG
42959090 TCATTTTACCCTATGGAGGTATTTCGG
1 TCATTTTACCCTATGG-GGTATTTCGG
* *
42959117 TCATTTTACCTTATGGGGGTATTTCGA
1 TCATTTTACCCTAT-GGGGTATTTCGG
42959144 TCATTT
1 TCATTT
42959150 ATCGACCTCT
Statistics
Matches: 168, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
26 3 0.02
27 137 0.82
28 27 0.16
29 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (26 bp):
TCATTTTACCCTATGGGGTATTTCGG
Found at i:42959022 original size:55 final size:53
Alignment explanation
Indices: 42958926--42959149 Score: 313
Period size: 54 Copynumber: 4.1 Consensus size: 53
42958916 GGGTATAAAA
* *
42958926 ATCATTTTACCTTATGGGGTTATTTTGGTCATTTTACCCTATGAGGGTATTTCG
1 ATCATTTTACCCTATGGGG-TATTTTGGTCATTTTACCCTATGGGGGTATTTCG
* *
42958980 ATCATTTTACCCTATTAGGGGTATTTTGGTTATTCTACCCTATGGGGGTATTTCG
1 ATCATTTTACCCTA-T-GGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCG
* * * *
42959035 GTCATTCTACCCTATGAGGGTATTTTGGTCATTTTACACTATGGGGGTATTTCA
1 ATCATTTTACCCTATG-GGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCG
* *
42959089 ATCATTTTACCCTATGGAGGTATTTCGGTCATTTTACCTTATGGGGGTATTTCG
1 ATCATTTTACCCTATGG-GGTATTTTGGTCATTTTACCCTATGGGGGTATTTCG
42959143 ATCATTT
1 ATCATTT
42959150 ATCGACCTCT
Statistics
Matches: 150, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
53 2 0.01
54 100 0.67
55 44 0.29
56 4 0.03
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (53 bp):
ATCATTTTACCCTATGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCG
Found at i:42961560 original size:40 final size:39
Alignment explanation
Indices: 42961485--42961715 Score: 293
Period size: 40 Copynumber: 5.8 Consensus size: 39
42961475 CCAGCATGAT
* * *
42961485 TGCTCTTCGGG-CCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAG-CCGGATATATCACTAGCACGAA
* **
42961524 TGCTCTTTGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGC-CGGATATATCACTAGCACGAA
* *
42961564 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAG-CCGGATATATCACTAGCACGAA
* *
42961604 TGCTCTTCGGGATTTAACCTGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCC-GGATATATCACTAGCACGAA
* *
42961644 TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCATGAA
1 TGCTCTTCGGGACTTAG-CCGGATATATCACTAGCACGAA
42961684 TGCTCTTCGGGACTTAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAG-CCGGATATATCACT
42961716 CTCAATTCTC
Statistics
Matches: 167, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
39 13 0.08
40 151 0.90
41 3 0.02
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (39 bp):
TGCTCTTCGGGACTTAGCCGGATATATCACTAGCACGAA
Found at i:42961600 original size:80 final size:79
Alignment explanation
Indices: 42961485--42961715 Score: 329
Period size: 80 Copynumber: 2.9 Consensus size: 79
42961475 CCAGCATGAT
* * * * * * *
42961485 TGCTCTTCGG-GCCTAGCCCGGATATAACACCAGCACGAATGCTCTTTGGGGTTTAGCACGGATA
1 TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAATGCTCTTCGGGATTTAGC-CGGATA
42961549 TATCACTAGCACGAA
65 TATCACTAGCACGAA
* *
42961564 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTCTTCGGGATTTAACCTGGATA
1 TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAATGCTCTTCGGGATTTAGCC-GGATA
42961629 TATCACTAGCACGAA
65 TATCACTAGCACGAA
* *
42961644 TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATA
1 TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAATGCTCTTCGGGATTTAG-CCGGATA
42961709 TATCACT
65 TATCACT
42961716 CTCAATTCTC
Statistics
Matches: 136, Mismatches: 13, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
79 11 0.08
80 123 0.90
81 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (79 bp):
TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAATGCTCTTCGGGATTTAGCCGGATAT
ATCACTAGCACGAA
Found at i:42962991 original size:37 final size:37
Alignment explanation
Indices: 42962934--42963008 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
42962924 TACGAAGTCC
* * *
42962934 TACCCGGACATAATCTCCACACGAAGTTATCGGGTCT
1 TACCCGGACAAAATCCCCACACGAAGTCATCGGGTCT
* *
42962971 TACCCGGATAAAATCCCCACACGTAGTCATCGGGTCT
1 TACCCGGACAAAATCCCCACACGAAGTCATCGGGTCT
42963008 T
1 T
42963009 TAGAGCTCGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
TACCCGGACAAAATCCCCACACGAAGTCATCGGGTCT
Found at i:42963205 original size:47 final size:47
Alignment explanation
Indices: 42963127--42963349 Score: 306
Period size: 47 Copynumber: 4.7 Consensus size: 47
42963117 CCCTTCGGGA
* * * * *
42963127 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGC
* * *
42963174 CCTGTCACATATATACACTTTCACATTCATCATATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42963221 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42963268 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
42963315 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
42963350 AGAATCCTAA
Statistics
Matches: 158, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
46 3 0.02
47 155 0.98
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:42967223 original size:40 final size:40
Alignment explanation
Indices: 42967191--42967422 Score: 320
Period size: 40 Copynumber: 5.8 Consensus size: 40
42967181 CCAGCATGAT
* * *
42967191 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
** * *
42967231 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGGACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
42967271 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
42967311 TGCTCTTCGGGATTTAACCTGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
42967351 TGCTCTTCGGAACATAGTCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
42967391 TGCTCTTCGGGACTTAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATATATCACT
42967423 CTCAATTCTC
Statistics
Matches: 163, Mismatches: 29, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 163 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:42968698 original size:37 final size:37
Alignment explanation
Indices: 42968637--42968715 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
42968627 TTATTACGAA
* * *
42968637 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
* *
42968674 GTCTTACCCGGATAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
42968711 GTCTT
1 GTCTT
42968716 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:42968912 original size:47 final size:47
Alignment explanation
Indices: 42968834--42969150 Score: 535
Period size: 47 Copynumber: 6.7 Consensus size: 47
42968824 CCCTTCGGGA
* * * * * *
42968834 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42968881 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42968928 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42968975 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42969022 CTTATCACATATATCCACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42969069 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42969116 CTTATCACATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
42969151 AGAATCCTAA
Statistics
Matches: 255, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 255 1.00
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:42969078 original size:22 final size:22
Alignment explanation
Indices: 42969003--42969078 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
42968993 TTTCACATTC
*
42969003 ATCACATCGGCCATTAGGCCTT
1 ATCACATTGGCCATTAGGCCTT
** *** *
42969025 ATCACATATATCCACTTTCACATT
1 ATCACAT-TGGCCA-TTAGGCCTT
42969049 CATCACATTGGCCATTAGGCCTT
1 -ATCACATTGGCCATTAGGCCTT
42969072 ATCACAT
1 ATCACAT
42969079 ATATACACTT
Statistics
Matches: 38, Mismatches: 13, Indels: 6
0.67 0.23 0.11
Matches are distributed among these distances:
22 14 0.37
23 8 0.21
24 9 0.24
25 7 0.18
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTAGGCCTT
Found at i:42971950 original size:12 final size:12
Alignment explanation
Indices: 42971933--42971974 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
42971923 ATCCCAATAT
42971933 TCTCTCCTCAAA
1 TCTCTCCTCAAA
*
42971945 TCTCTCC-AAATA
1 TCTCTCCTCAA-A
*
42971957 TCCCTCCTCAAA
1 TCTCTCCTCAAA
42971969 TCTCTC
1 TCTCTC
42971975 TATGACCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.24, C:0.43, G:0.00, T:0.33
Consensus pattern (12 bp):
TCTCTCCTCAAA
Found at i:42974038 original size:18 final size:18
Alignment explanation
Indices: 42974012--42974051 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42974002 GACAGATGTT
* * *
42974012 CAAATATAGGAGTTTGGA
1 CAAAGATAGGAGATAGGA
42974030 CAAAGATAGGAGATAGGA
1 CAAAGATAGGAGATAGGA
42974048 CAAA
1 CAAA
42974052 AGCACACATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.07, G:0.28, T:0.17
Consensus pattern (18 bp):
CAAAGATAGGAGATAGGA
Found at i:42976079 original size:21 final size:22
Alignment explanation
Indices: 42976050--42976090 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
42976040 AATTATATTT
**
42976050 TTAATAGAATTATAAAAAATAA
1 TTAATAGAAAAATAAAAAATAA
42976072 TTAA-AGAAAAATAAAAAAT
1 TTAATAGAAAAATAAAAAAT
42976091 TTGACATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (22 bp):
TTAATAGAAAAATAAAAAATAA
Found at i:42978122 original size:27 final size:27
Alignment explanation
Indices: 42978091--42978268 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42978081 TAAATTGTAC
42978091 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42978118 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42978144 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42978172 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42978200 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42978227 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42978254 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42978269 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42978205 original size:82 final size:81
Alignment explanation
Indices: 42978092--42978247 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42978082 AAATTGTACA
* *
42978092 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42978156 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42978173 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
42978238 TGCGAGTTGA
65 TGCGAATTGA
42978248 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42978259 original size:82 final size:81
Alignment explanation
Indices: 42978088--42978268 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
42978078 GATTAAATTG
* *
42978088 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42978153 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42978169 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
42978233 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42978251 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42978269 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42988539 original size:30 final size:31
Alignment explanation
Indices: 42988500--42988559 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
42988490 GGAGATGGGA
*
42988500 TGGGAAGGGAATAAAAGTTTTAAGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAAGGGAAAAG
* **
42988531 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAAGGGAAAA
42988560 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAAGGGAAAAG
Found at i:42988786 original size:9 final size:9
Alignment explanation
Indices: 42988772--42988808 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42988762 TATAGTTTGA
42988772 TATTCGAAT
1 TATTCGAAT
42988781 TATTCGAAT
1 TATTCGAAT
*
42988790 TATTCGAGT
1 TATTCGAAT
42988799 TATTCGAAT
1 TATTCGAAT
42988808 T
1 T
42988809 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:42993119 original size:27 final size:27
Alignment explanation
Indices: 42993086--42993200 Score: 115
Period size: 27 Copynumber: 4.3 Consensus size: 27
42993076 CGAAAAGGTT
42993086 GTAAAATTACTAAAATACCCTTAAAGG
1 GTAAAATTACTAAAATACCCTTAAAGG
* * * *
42993113 GTAAAATTACAAAAATACCCCTGATGG
1 GTAAAATTACTAAAATACCCTTAAAGG
* * * *
42993140 GTAAGATTACTGAAATACCCTCACTA-G
1 GTAAAATTACTAAAATACCCTTA-AAGG
* * *
42993167 GTAAAATTACTGAAATGCCCTTATAGG
1 GTAAAATTACTAAAATACCCTTAAAGG
42993194 GTAAAAT
1 GTAAAAT
42993201 GATCGTAATG
Statistics
Matches: 71, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
26 2 0.03
27 69 0.97
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.26
Consensus pattern (27 bp):
GTAAAATTACTAAAATACCCTTAAAGG
Found at i:42993221 original size:27 final size:27
Alignment explanation
Indices: 42993191--42993256 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
42993181 ATGCCCTTAT
* *
42993191 AGGGTAAAATGATCGTAATGCCTCTGG
1 AGGGTAAAATGATCGTAATGCCCCTGA
* * *
42993218 AGGGTAAATTAACCGTAATGCCCCTGA
1 AGGGTAAAATGATCGTAATGCCCCTGA
42993245 AGGGT-AAATGAT
1 AGGGTAAAATGAT
42993257 TGATTTTTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.24
Consensus pattern (27 bp):
AGGGTAAAATGATCGTAATGCCCCTGA
Found at i:42993420 original size:27 final size:27
Alignment explanation
Indices: 42993377--42993442 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
42993367 GGAAGTACTA
* *
42993377 TACTGGTGGTTTTGCCACA-ATCACTGT
1 TACTGGTGGCTTGGCCACATAT-ACTGT
42993404 TACTGGTGGCTTGGCCACATATACTGT
1 TACTGGTGGCTTGGCCACATATACTGT
*
42993431 TACTGGTAGCTT
1 TACTGGTGGCTT
42993443 TATTGCGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 33 0.94
28 2 0.06
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.36
Consensus pattern (27 bp):
TACTGGTGGCTTGGCCACATATACTGT
Found at i:42993477 original size:26 final size:26
Alignment explanation
Indices: 42993424--42993477 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
42993414 TTGGCCACAT
* *
42993424 ATACTGTTACTGGTAGCTTTATTGCG
1 ATACTGTTACTGGCAGCTTTATTACG
** *
42993450 ATACTGTTGTTGGCAGCTTTGTTACG
1 ATACTGTTACTGGCAGCTTTATTACG
42993476 AT
1 AT
42993478 GCTACTGAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.43
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTATTACG
Found at i:42993603 original size:22 final size:22
Alignment explanation
Indices: 42993578--42993641 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 22
42993568 ATTACTGAAC
*
42993578 TTATGGCTCGTAGCCATTCTAT
1 TTATGGCTCATAGCCATTCTAT
* * * * *
42993600 TTATAGCTTATAGCTATCCTGT
1 TTATGGCTCATAGCCATTCTAT
* *
42993622 TTACGGCTCTTAGCCATTCT
1 TTATGGCTCATAGCCATTCT
42993642 GGTTACTGGC
Statistics
Matches: 30, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (22 bp):
TTATGGCTCATAGCCATTCTAT
Found at i:42996713 original size:12 final size:13
Alignment explanation
Indices: 42996681--42996723 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
42996671 AATTAGAGAT
*
42996681 AAAAATAATTATCA
1 AAAAAT-ATTAACA
42996695 GAAAAATATTAA-A
1 -AAAAATATTAACA
42996708 AAAAATATTAACA
1 AAAAATATTAACA
42996721 AAA
1 AAA
42996724 GATGTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 11 0.42
13 5 0.19
14 4 0.15
15 6 0.23
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (13 bp):
AAAAATATTAACA
Found at i:43017370 original size:41 final size:41
Alignment explanation
Indices: 43017316--43017591 Score: 329
Period size: 41 Copynumber: 6.8 Consensus size: 41
43017306 CATTAGTGGA
* * * * * *
43017316 ATTTTTCCTATAAATGCCGCAAAAGGTAAAGCAATAGTGGT
1 ATTTTGCCCATAAACGCCACAAAAGGTAAAGCAATAGCGGC
* * * *
43017357 ATATTGCCCATAAACACCGCAAAAGGTAAAGCAATAGCGGT
1 ATTTTGCCCATAAACGCCACAAAAGGTAAAGCAATAGCGGC
*
43017398 ATTTTGCCCATAAATGCCACAAAAGGTAAAGCAATAGCGGC
1 ATTTTGCCCATAAACGCCACAAAAGGTAAAGCAATAGCGGC
* *
43017439 ATTTTGCCCATAAATGCCACAAAAGGTAAAGCAATAGCGGT
1 ATTTTGCCCATAAACGCCACAAAAGGTAAAGCAATAGCGGC
* * * ***
43017480 GTTTTTCCCATACACGCTGTAAAAGGT-AAGCAATAGCGGC
1 ATTTTGCCCATAAACGCCACAAAAGGTAAAGCAATAGCGGC
* *
43017520 ATTTTTCCCATAAACGCCACAAAAGGTAAAGCAATAGTGGC
1 ATTTTGCCCATAAACGCCACAAAAGGTAAAGCAATAGCGGC
* * *
43017561 GTTTTTCCCATAAACGCCATAAAAGGTAAAG
1 ATTTTGCCCATAAACGCCACAAAAGGTAAAG
43017592 TTGTTGAATA
Statistics
Matches: 206, Mismatches: 28, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
40 34 0.17
41 172 0.83
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (41 bp):
ATTTTGCCCATAAACGCCACAAAAGGTAAAGCAATAGCGGC
Found at i:43017545 original size:81 final size:82
Alignment explanation
Indices: 43017317--43017591 Score: 363
Period size: 82 Copynumber: 3.4 Consensus size: 82
43017307 ATTAGTGGAA
* * ** * * * * *
43017317 TTTTTCCTATAAATGCCGCAAAAGGTAAAGCAATAGTGGTATATTGCCCATAAACACCGCAAAAG
1 TTTTTCCCATAAACGCCATAAAAGGTAAAGCAATAGCGGCATTTTGCCCATAAACGCCACAAAAG
*
43017382 GTAAAGCAATAGCGGTA
66 GTAAAGCAATAGCGGTG
* * * *
43017399 TTTTGCCCATAAATGCCACAAAAGGTAAAGCAATAGCGGCATTTTGCCCATAAATGCCACAAAAG
1 TTTTTCCCATAAACGCCATAAAAGGTAAAGCAATAGCGGCATTTTGCCCATAAACGCCACAAAAG
43017464 GTAAAGCAATAGCGGTG
66 GTAAAGCAATAGCGGTG
* ** *
43017481 TTTTTCCCATACACGCTGTAAAAGGT-AAGCAATAGCGGCATTTTTCCCATAAACGCCACAAAAG
1 TTTTTCCCATAAACGCCATAAAAGGTAAAGCAATAGCGGCATTTTGCCCATAAACGCCACAAAAG
* *
43017545 GTAAAGCAATAGTGGCG
66 GTAAAGCAATAGCGGTG
43017562 TTTTTCCCATAAACGCCATAAAAGGTAAAG
1 TTTTTCCCATAAACGCCATAAAAGGTAAAG
43017592 TTGTTGAATA
Statistics
Matches: 169, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
81 74 0.44
82 95 0.56
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.23
Consensus pattern (82 bp):
TTTTTCCCATAAACGCCATAAAAGGTAAAGCAATAGCGGCATTTTGCCCATAAACGCCACAAAAG
GTAAAGCAATAGCGGTG
Found at i:43020361 original size:21 final size:22
Alignment explanation
Indices: 43020332--43020378 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
43020322 CAGAAGGAGT
*
43020332 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
43020354 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
43020375 GAGT
1 GAGT
43020379 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:43024783 original size:25 final size:25
Alignment explanation
Indices: 43024697--43024780 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 25
43024687 CAGCTCTTAT
* * *
43024697 GAGCTTACCATTACTCAACTCGTAT
1 GAGCTTACCATTATTCAACTCGAAG
**
43024722 GAGCTTACCATTATTCCTCTCGAAG
1 GAGCTTACCATTATTCAACTCGAAG
*
43024747 GAGCTTACCGTTATTCAACTC-AGAG
1 GAGCTTACCATTATTCAACTCGA-AG
43024772 GAGCTTACC
1 GAGCTTACC
43024781 GTTTACAGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
24 1 0.02
25 49 0.98
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (25 bp):
GAGCTTACCATTATTCAACTCGAAG
Found at i:43024799 original size:24 final size:25
Alignment explanation
Indices: 43024745--43024792 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
43024735 TTCCTCTCGA
*
43024745 AGGAGCTTACCGTTATTCAACTCAG
1 AGGAGCTTACCGTTATACAACTCAG
*
43024770 AGGAGCTTACCGTT-TACAGCTCA
1 AGGAGCTTACCGTTATACAACTCA
43024793 TATGAGCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (25 bp):
AGGAGCTTACCGTTATACAACTCAG
Found at i:43034706 original size:27 final size:27
Alignment explanation
Indices: 43034667--43034742 Score: 136
Period size: 27 Copynumber: 2.9 Consensus size: 27
43034657 GAAAAGAAAT
43034667 TAAAAAAA-TGAAGTATTTAAGAATAA
1 TAAAAAAATTGAAGTATTTAAGAATAA
*
43034693 TAAAAAAATTGAAGTATTTAAAAATAA
1 TAAAAAAATTGAAGTATTTAAGAATAA
43034720 TAAAAAAATTGAAGTATTTAAGA
1 TAAAAAAATTGAAGTATTTAAGA
43034743 CCATGGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 8 0.17
27 39 0.83
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (27 bp):
TAAAAAAATTGAAGTATTTAAGAATAA
Found at i:43034918 original size:101 final size:101
Alignment explanation
Indices: 43034738--43034950 Score: 309
Period size: 101 Copynumber: 2.1 Consensus size: 101
43034728 TTGAAGTATT
* * * *
43034738 TAAGACCATGGTTGGACCATGGCAGTGTATATATGTAAGACCATTGCTGGGTTATGGCATTTTGA
1 TAAGACCATGGTTAGACCATGGCAGTGTATATATGTAAGACCATAGCTGGGCTATGGCATTCTGA
* *
43034803 TGGTAAGACCATAACTGAGTTATAACACTATGGACG
66 TGGTAAGACCATAACTGAGTTATAACACTATGAACA
* * *
43034839 TAAGACAATGGTTAGACCATGGTAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGA
1 TAAGACCATGGTTAGACCATGGCAGTGTATATATGTAAGACCATAGCTGGGCTATGGCATTCTGA
* * **
43034904 TGGTAAGACTATAACTGGGTTATGGCACTATGAACA
66 TGGTAAGACCATAACTGAGTTATAACACTATGAACA
43034940 TAAGACCATGG
1 TAAGACCATGG
43034951 CAAGGCTATG
Statistics
Matches: 98, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 98 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.29
Consensus pattern (101 bp):
TAAGACCATGGTTAGACCATGGCAGTGTATATATGTAAGACCATAGCTGGGCTATGGCATTCTGA
TGGTAAGACCATAACTGAGTTATAACACTATGAACA
Found at i:43036196 original size:49 final size:49
Alignment explanation
Indices: 43036124--43036222 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
43036114 CCGCAGAAAC
43036124 ATAGTCATTTTCCAAAAAATCATTTTATCGAATCTCATGCCAAAACTCA
1 ATAGTCATTTTCCAAAAAATCATTTTATCGAATCTCATGCCAAAACTCA
*
43036173 ATAGTCATTTTCCGAAAAATCATTTTATCGAATCTCATGCCAAAACTCA
1 ATAGTCATTTTCCAAAAAATCATTTTATCGAATCTCATGCCAAAACTCA
43036222 A
1 A
43036223 ATTAAAAGGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.32
Consensus pattern (49 bp):
ATAGTCATTTTCCAAAAAATCATTTTATCGAATCTCATGCCAAAACTCA
Found at i:43039871 original size:31 final size:32
Alignment explanation
Indices: 43039822--43039884 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
43039812 ATGAGATAGC
43039822 AAAAAGAAAGATTAAAAATTACCCACTTCCAA
1 AAAAAGAAAGATTAAAAATTACCCACTTCCAA
43039854 AAAAAGAAAGATT-AAAATTACCCACTTCCAA
1 AAAAAGAAAGATTAAAAATTACCCACTTCCAA
43039885 CATGAAAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 18 0.58
32 13 0.42
ACGTcount: A:0.56, C:0.19, G:0.06, T:0.19
Consensus pattern (32 bp):
AAAAAGAAAGATTAAAAATTACCCACTTCCAA
Found at i:43044628 original size:15 final size:15
Alignment explanation
Indices: 43044608--43044637 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
43044598 AAAAAAAAGA
43044608 AAAATAAACAATAAT
1 AAAATAAACAATAAT
43044623 AAAATAAACAATAAT
1 AAAATAAACAATAAT
43044638 TAAAGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAATAAACAATAAT
Found at i:43046169 original size:24 final size:24
Alignment explanation
Indices: 43046121--43046167 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
43046111 ACTGGTCATA
*
43046121 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
43046145 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
43046168 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:43046799 original size:27 final size:27
Alignment explanation
Indices: 43046769--43047096 Score: 404
Period size: 27 Copynumber: 12.1 Consensus size: 27
43046759 TTACACTTTT
* * *
43046769 ATGACCGATATGCCCCCATAGGATAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
43046796 ATGACTGAAATACCCTCATAAGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
43046823 ATGACTGAAATACCCCCATATGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
43046850 ATAACCGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
43046877 ATGACCGAAATACCTCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
** * *
43046904 ATGACTAAAATACCCCTAGAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
43046931 ATAACCGAAATACCCCCATAGCGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
** *
43046958 ATGACTAAAATACTCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* **
43046985 ATGACCAAAATACCCCCATAATGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
43047012 ATGATCGAAATAGCCCTATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
43047039 ATGATCGAAATACCCCTATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
43047066 ATGACCGAAATGCCCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
43047093 ATGA
1 ATGA
43047097 GTGTTATACC
Statistics
Matches: 258, Mismatches: 43, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 258 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.19
Consensus pattern (27 bp):
ATGACCGAAATACCCCCATAGGGTAAA
Found at i:43047374 original size:18 final size:18
Alignment explanation
Indices: 43047348--43047393 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
43047338 ACTAGCAGTT
*
43047348 GTGCTGCAATATTGTTTA
1 GTGCCGCAATATTGTTTA
43047366 GTGCCGCAATATTGTTTA
1 GTGCCGCAATATTGTTTA
*
43047384 GTGTCGCAAT
1 GTGCCGCAAT
43047394 CGGTGCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (18 bp):
GTGCCGCAATATTGTTTA
Found at i:43049364 original size:24 final size:24
Alignment explanation
Indices: 43049316--43049362 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
43049306 ACAAGTAATA
*
43049316 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
43049340 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
43049363 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:43050528 original size:24 final size:26
Alignment explanation
Indices: 43050470--43050528 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 26
43050460 TATTCCTTAT
43050470 TTTAGTTA-CTCAACTGTATATATTTA
1 TTTA-TTAGCTCAACTGTATATATTTA
**
43050496 TTT-CGAGCTCAACT-TATATA-TTA
1 TTTATTAGCTCAACTGTATATATTTA
43050519 TTTATTAGCT
1 TTTATTAGCT
43050529 TACACATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
23 6 0.22
24 11 0.41
25 7 0.26
26 3 0.11
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (26 bp):
TTTATTAGCTCAACTGTATATATTTA
Found at i:43057829 original size:19 final size:19
Alignment explanation
Indices: 43057805--43057853 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
43057795 TGGTCTATGT
*
43057805 AGGGTCCAATTTTTGACCC
1 AGGGTCCAATTTTTGACCA
43057824 AGGGTCCAATTTTTGACCA
1 AGGGTCCAATTTTTGACCA
*
43057843 AGGGCCCAATT
1 AGGGTCCAATT
43057854 ACAAAAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (19 bp):
AGGGTCCAATTTTTGACCA
Found at i:43058997 original size:3 final size:3
Alignment explanation
Indices: 43058989--43059033 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
43058979 GTGCTATCAT
** * *
43058989 TTA TTA TTA TTA TTA TTA TTA TTA GCA TCA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43059034 AATACTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:43082141 original size:27 final size:27
Alignment explanation
Indices: 43082111--43082288 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
43082101 ATATTGAGTC
* * * *
43082111 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
43082138 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43082165 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
43082193 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
43082220 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
43082247 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43082274 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43082289 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:43082250 original size:82 final size:81
Alignment explanation
Indices: 43082132--43082287 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
43082122 TGCTATATAA
* *
43082132 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
43082197 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
43082214 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
43082278 CACTTAGTGC
65 CACTTAGTGC
43082288 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:43092264 original size:27 final size:27
Alignment explanation
Indices: 43092233--43092323 Score: 87
Period size: 27 Copynumber: 3.3 Consensus size: 27
43092223 TATTACGAGA
*
43092233 GTAAAACAATAAGTATTTTTATGGTTT
1 GTAAAATAATAAGTATTTTTATGGTTT
** * *
43092260 GTAAAATAATGAACAATTATATTACGAG--A
1 GTAAAATAAT-AAGTATT-T-TTATG-GTTT
43092289 GTAAAATAATAAGTATTTTTATGGTTT
1 GTAAAATAATAAGTATTTTTATGGTTT
43092316 GTAAAATA
1 GTAAAATA
43092324 TTGAAATAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
25 1 0.02
26 4 0.08
27 18 0.37
28 10 0.20
29 11 0.22
30 4 0.08
31 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.14, T:0.38
Consensus pattern (27 bp):
GTAAAATAATAAGTATTTTTATGGTTT
Found at i:43092282 original size:56 final size:56
Alignment explanation
Indices: 43092217--43092328 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
43092207 TACTTTAAGT
43092217 CAATTATATTACGAGAGTAAAACAATAAGTATTTTTATGGTTTGTAAAATAATGAA
1 CAATTATATTACGAGAGTAAAACAATAAGTATTTTTATGGTTTGTAAAATAATGAA
* *
43092273 CAATTATATTACGAGAGTAAAATAATAAGTATTTTTATGGTTTGTAAAATATTGAA
1 CAATTATATTACGAGAGTAAAACAATAAGTATTTTTATGGTTTGTAAAATAATGAA
43092329 ATAAAATATC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.38
Consensus pattern (56 bp):
CAATTATATTACGAGAGTAAAACAATAAGTATTTTTATGGTTTGTAAAATAATGAA
Found at i:43098604 original size:50 final size:50
Alignment explanation
Indices: 43098515--43098611 Score: 115
Period size: 50 Copynumber: 1.9 Consensus size: 50
43098505 AATCGAGCCA
* * * *
43098515 ATCCAACCAAGAACACGCTTGGGCACCAAATTCCTAGCCCGTTGGCTAAC
1 ATCCAACCAACAACACGCATAGGCACCAAATTCCTAGCCCGTAGGCTAAC
* * *
43098565 ATCCATCCAACAACACGCATAGGCACCCAGTT-CTAAGCCCGTAGGCT
1 ATCCAACCAACAACACGCATAGGCACCAAATTCCT-AGCCCGTAGGCT
43098612 TTACATCCGC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
49 2 0.05
50 37 0.95
ACGTcount: A:0.30, C:0.35, G:0.18, T:0.18
Consensus pattern (50 bp):
ATCCAACCAACAACACGCATAGGCACCAAATTCCTAGCCCGTAGGCTAAC
Found at i:43112493 original size:20 final size:20
Alignment explanation
Indices: 43112468--43112507 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
43112458 AGCTGGGAGA
43112468 TAGCTTCCCATAGATGATTT
1 TAGCTTCCCATAGATGATTT
43112488 TAGCTTCCCATAGATGATTT
1 TAGCTTCCCATAGATGATTT
43112508 CATTCCCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (20 bp):
TAGCTTCCCATAGATGATTT
Found at i:43113547 original size:26 final size:28
Alignment explanation
Indices: 43113517--43113586 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
43113507 AGTAAACACA
* *
43113517 AAACATAGATAG-TTC-ACTGAGACAGT
1 AAACATAGATAGAGTCTACCGAGACAGT
* *
43113543 AAACACAAATAGAGTCTACCGAGACAGT
1 AAACATAGATAGAGTCTACCGAGACAGT
43113571 AAACATAGGATA-AGTC
1 AAACATA-GATAGAGTC
43113587 CGATGGGATG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 10 0.29
27 2 0.06
28 20 0.57
29 3 0.09
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.19
Consensus pattern (28 bp):
AAACATAGATAGAGTCTACCGAGACAGT
Found at i:43117095 original size:19 final size:18
Alignment explanation
Indices: 43117047--43117098 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 18
43117037 CTTATAGAGT
*
43117047 TTCAATTTTTTATATTAT
1 TTCAATTTTTTATATTAA
*
43117065 TTTAATAGTTTTATATATTAA
1 TTCAAT--TTTT-TATATTAA
43117086 TTCAATTTTTTAT
1 TTCAATTTTTTAT
43117099 TAATTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 8 0.29
19 4 0.14
20 4 0.14
21 12 0.43
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (18 bp):
TTCAATTTTTTATATTAA
Found at i:43118037 original size:2 final size:2
Alignment explanation
Indices: 43118030--43118088 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
43118020 CCTACAATAA
* *
43118030 AC AC AC AC AC AC AC AT AC AC AT AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
43118072 AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC A
43118089 TAATAACATA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:43120519 original size:73 final size:73
Alignment explanation
Indices: 43120442--43120578 Score: 195
Period size: 73 Copynumber: 1.9 Consensus size: 73
43120432 GCCAAGCTAT
* * * * *
43120442 TTGATGTGTTGACATAAAGGTTTAGCCCAGACGGGTAA-CTTGACATGATTGTATGTTCAGCTTG
1 TTGATGTATCGACATAAAGGTTTAGCCCAGACAGGTAATCTT-ACATGATTATATGATCAGCTTG
43120506 AACGAGGAA
65 AACGAGGAA
**
43120515 TTGATGTATCGGTATAAAGGTTTAGCCCAGACAGGTAATCTTACATGATTATATGATCAGCTTG
1 TTGATGTATCGACATAAAGGTTTAGCCCAGACAGGTAATCTTACATGATTATATGATCAGCTTG
43120579 GACAAACCTT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 53 0.95
74 3 0.05
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (73 bp):
TTGATGTATCGACATAAAGGTTTAGCCCAGACAGGTAATCTTACATGATTATATGATCAGCTTGA
ACGAGGAA
Found at i:43122819 original size:17 final size:17
Alignment explanation
Indices: 43122767--43122830 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 17
43122757 AACAATTTAA
43122767 TTTTTTTCTTTTATGTTT-
1 TTTTTTTC-TTTAT-TTTC
* *
43122785 TTTTTTCACTTTCCTTTTC
1 TTTTTT-TCTTT-ATTTTC
43122804 TTTTTTTCTTTATTTTC
1 TTTTTTTCTTTATTTTC
*
43122821 -TATTTTCTTT
1 TTTTTTTCTTT
43122831 TACTTCTCCC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 9 0.24
17 5 0.13
18 16 0.42
19 8 0.21
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTTTTCTTTATTTTC
Found at i:43125294 original size:21 final size:18
Alignment explanation
Indices: 43125260--43125313 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 18
43125250 ACACCACATA
43125260 GTGGATAAAACCACTCATCGTT
1 GTGGAT-AAACCACTCA---TT
*
43125282 GTGGATGAACCACTCATT
1 GTGGATAAACCACTCATT
43125300 GTGGATAAACCACT
1 GTGGATAAACCACT
43125314 AGTAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 15 0.50
21 9 0.30
22 6 0.20
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (18 bp):
GTGGATAAACCACTCATT
Found at i:43125596 original size:34 final size:35
Alignment explanation
Indices: 43125539--43125634 Score: 110
Period size: 34 Copynumber: 2.8 Consensus size: 35
43125529 ATCATTTAAT
* * *
43125539 TATGCTTTTAACAGAAC-AGTACAGTAGC-AATCAA
1 TATGCTTATAACAGATCAACTACAGTAGCAAAT-AA
* *
43125573 TATGCTTATAATAGTTCAA-TACAGTAGCAAATAA
1 TATGCTTATAACAGATCAACTACAGTAGCAAATAA
43125607 TATGCTTATAACAGATCAACT-CAGTAGC
1 TATGCTTATAACAGATCAACTACAGTAGC
43125635 CAAAAGTCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
34 48 0.91
35 5 0.09
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.29
Consensus pattern (35 bp):
TATGCTTATAACAGATCAACTACAGTAGCAAATAA
Found at i:43125939 original size:27 final size:27
Alignment explanation
Indices: 43125890--43125984 Score: 99
Period size: 27 Copynumber: 3.6 Consensus size: 27
43125880 GGTAAAACTA
43125890 TAAAATCT--AAAA-AAGGGAAAATTG
1 TAAAATCTGAAAAATAAGGGAAAATTG
*
43125914 TAAAATTTGAAAAATAAGGGAAAATTAG
1 TAAAATCTGAAAAATAAGGGAAAATT-G
* ***
43125942 -AAAATCTAAAAAATAAGGGTAAAACCA
1 TAAAATCTGAAAAATAAGGG-AAAATTG
43125969 TAAAATCTGAAAAATA
1 TAAAATCTGAAAAATA
43125985 GGAGACGCAC
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
24 7 0.12
26 4 0.07
27 28 0.48
28 19 0.33
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (27 bp):
TAAAATCTGAAAAATAAGGGAAAATTG
Found at i:43131699 original size:44 final size:44
Alignment explanation
Indices: 43131641--43131727 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
43131631 TGAACTAAAA
* * * *
43131641 TAGAAGTTGTGATAATTATACATTTAAAAATAACTATAATTTAG
1 TAGAAGTTATGATAATTACAAATTTAAAAATAAATATAATTTAG
43131685 TAGAAGTTATGATAATTACAAATTTAAAAATAAATATAATTTA
1 TAGAAGTTATGATAATTACAAATTTAAAAATAAATATAATTTA
43131728 AAATACAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.38
Consensus pattern (44 bp):
TAGAAGTTATGATAATTACAAATTTAAAAATAAATATAATTTAG
Found at i:43132903 original size:8 final size:8
Alignment explanation
Indices: 43132890--43132916 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
43132880 CAAGTTCGAG
43132890 TATTTTAA
1 TATTTTAA
43132898 TATTTTAA
1 TATTTTAA
43132906 TATTTTAA
1 TATTTTAA
43132914 TAT
1 TAT
43132917 AAGATGGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATTTTAA
Found at i:43133127 original size:31 final size:31
Alignment explanation
Indices: 43133092--43133150 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
43133082 CATTAATTTT
*
43133092 GTTCAATTATAAACATGAAAA-TTTGATTATA
1 GTTCAAATATAAACAT-AAAATTTTGATTATA
*
43133123 GTTCAAATGTAAACATAAAATTTTGATT
1 GTTCAAATATAAACATAAAATTTTGATT
43133151 TTAATTCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (31 bp):
GTTCAAATATAAACATAAAATTTTGATTATA
Found at i:43144416 original size:18 final size:18
Alignment explanation
Indices: 43144382--43144416 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43144372 AATAAATGGA
*
43144382 AGGGCAAGAACATGAGGC
1 AGGGCAAGAACAGGAGGC
*
43144400 AGGGCAAGAGCAGGAGG
1 AGGGCAAGAACAGGAGG
43144417 AGTGATGGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.14, G:0.46, T:0.03
Consensus pattern (18 bp):
AGGGCAAGAACAGGAGGC
Found at i:43148905 original size:13 final size:13
Alignment explanation
Indices: 43148887--43148911 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43148877 ATTTACAAGA
43148887 TTACATAATCAAT
1 TTACATAATCAAT
43148900 TTACATAATCAA
1 TTACATAATCAA
43148912 ATTCAATCTA
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:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
TTACATAATCAAT
Found at i:43149813 original size:215 final size:215
Alignment explanation
Indices: 43149435--43149863 Score: 777
Period size: 215 Copynumber: 2.0 Consensus size: 215
43149425 TCCTTTCTTC
*
43149435 AAAACTTTAAAAGGGCCTCTACATTCTTGTCAAGCTAAATAGGATGCAAAACACTACCAAAGTGT
1 AAAACTTTAAAAGGGCCTCTACATTCTTGCCAAGCTAAATAGGATGCAAAACACTACCAAAGTGT
* * *
43149500 TCAGAATGTACCTTTATCGCAACATTTACTCAGGTCAACTGTCCAACTTACATTACCACTTTCTT
66 TCAGAATGTACCTTTATCGCAACATTTACTCAGGTCAACTATCCAACTTACATCACCACTTTCCT
* *
43149565 GGAGTTTGATGCACAACCCACCTCTCCCATAGGTGGTAGCTCATTCGATGTGTTAATAGAAGTGA
131 GAAGTTTGATGCACAACCCACCTCTCCCATAGGTGGTAGCTCATCCGATGTGTTAATAGAAGTGA
43149630 GCCTAATTGATCCTAGCTTA
196 GCCTAATTGATCCTAGCTTA
43149650 AAAACTTTAAAAGGGCCTCTACATTCTTGCCAAGCTAAATAGGATGCAAAACACTACCAAAGTGT
1 AAAACTTTAAAAGGGCCTCTACATTCTTGCCAAGCTAAATAGGATGCAAAACACTACCAAAGTGT
43149715 TCAGAATGTACCTTTATCGCAACATTTACTCAGGTCAACTATCCAACTTACATCACCACTTTCCT
66 TCAGAATGTACCTTTATCGCAACATTTACTCAGGTCAACTATCCAACTTACATCACCACTTTCCT
* *
43149780 GAAGTTTGATGCACAACCCACCTCTCTCATAGGTGGTAGCTCCTCCGATGTGTTAATAGAAGTGA
131 GAAGTTTGATGCACAACCCACCTCTCCCATAGGTGGTAGCTCATCCGATGTGTTAATAGAAGTGA
*
43149845 GCCTCATTGATCCTAGCTT
196 GCCTAATTGATCCTAGCTT
43149864 CAAAGTTTGT
Statistics
Matches: 205, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
215 205 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (215 bp):
AAAACTTTAAAAGGGCCTCTACATTCTTGCCAAGCTAAATAGGATGCAAAACACTACCAAAGTGT
TCAGAATGTACCTTTATCGCAACATTTACTCAGGTCAACTATCCAACTTACATCACCACTTTCCT
GAAGTTTGATGCACAACCCACCTCTCCCATAGGTGGTAGCTCATCCGATGTGTTAATAGAAGTGA
GCCTAATTGATCCTAGCTTA
Found at i:43158848 original size:12 final size:10
Alignment explanation
Indices: 43158818--43158860 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
43158808 AATATGAACA
*
43158818 TGATGAATTT
1 TGATTAATTT
*
43158828 TAATTAATTT
1 TGATTAATTT
43158838 TGTAGTTAATTT
1 TG-A-TTAATTT
43158850 TGATTAATTT
1 TGATTAATTT
43158860 T
1 T
43158861 TACTATTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 17 0.61
11 2 0.07
12 9 0.32
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (10 bp):
TGATTAATTT
Found at i:43162874 original size:80 final size:80
Alignment explanation
Indices: 43162722--43162914 Score: 221
Period size: 80 Copynumber: 2.4 Consensus size: 80
43162712 CGGTTTTAGT
* * * *
43162722 AACTCACACAATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTT
1 AACTCGCACAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTT
*
43162787 AACCCGGATTTA-AC
66 AACCCGGATATATAC
* *
43162801 AACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCACAAAGGCCTTC-GGATC
1 AACTCGCAC-AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGA-C
** *
43162865 TTAGTCCGGATATATTC
64 TTAACCCGGATATATAC
* * *
43162882 -ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AAC-TCGCACAATGCCTTCGGGACTTAACCCGGA
43162915 CAGCATTCAA
Statistics
Matches: 97, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
79 11 0.11
80 80 0.82
81 6 0.06
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (80 bp):
AACTCGCACAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTT
AACCCGGATATATAC
Found at i:43162875 original size:40 final size:40
Alignment explanation
Indices: 43162692--43162861 Score: 234
Period size: 40 Copynumber: 4.3 Consensus size: 40
43162682 TCCTCGTTCA
* * * ** *
43162692 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
43162731 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
43162771 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * *
43162811 AATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
43162851 AAGGCCTTCGG
1 AATGCCTTCGG
43162862 ATCTTAGTCC
Statistics
Matches: 120, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
39 34 0.28
40 86 0.72
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:43162923 original size:41 final size:41
Alignment explanation
Indices: 43162846--43162923 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
43162836 TTAATATCTC
* * *
43162846 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
43162887 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
43162924 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:43168552 original size:23 final size:23
Alignment explanation
Indices: 43168525--43168600 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
43168515 AGTGTTATTG
*
43168525 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
43168548 TTCAGTGGTAGCTAT-GGCTACGT
1 ATCAGTGGTAGCT-TCGGCTACAT
43168571 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
43168594 ATCAGTG
1 ATCAGTG
43168601 TGGCACTCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 1 0.02
23 44 0.96
24 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Done.