Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_pilon, whole genome shotgun sequence
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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 73
Found at i:2413712 original size:135 final size:134
Alignment explanation
Indices: 2413571--2413986 Score: 432
Period size: 134 Copynumber: 3.1 Consensus size: 134
2413561 ATTTCCAATA
* * **
2413571 AAATAAATTCAATGATTTATTTTCTTTTACAAACGAGGAAAATAAATCCAACAACATATTTTCTT
1 AAATAAATTCAACGATTTATTTTCTTTTACAAAC-AGGAAAATAAATCCAATAATTTATTTTCTT
* *
2413636 TTACAAAATA-GAAAATAAATCCAATAATTTACTTTCTTTTACAACTCAGAATCATATAAGATTA
65 TTACAAAATAGGAAAATAAATCTAACAATTTA-TTTCTTTTACAACTCAGAATCATATAAGATTA
2413700 TCAAGG
129 TCAAGG
* * * ** *
2413706 AAATAAATTCAACGAGTTATTTGCTTTTACAAACA-AAAGAATAAATCCAATGGTTTATTTACTT
1 AAATAAATTCAACGATTTATTTTCTTTTACAAACAGGAA-AATAAATCCAATAATTTATTTTCTT
* * * *
2413770 TTGCAAAATAGGAAAATAAATCTAACGATTTATTTCTTTTTACAA-ACAGAATCATATAAGATTC
65 TTACAAAATAGGAAAATAAATCTAACAATTTATTTC-TTTTACAACTCAGAATCATATAAGATTA
*
2413834 T-TAGG
129 TCAAGG
* * * * ** *
2413839 AAAATAAATTCAACAATTTATTTTATTTTATAAAATAGGAAAATAAATATAATAATTTA-TTTCC
1 -AAATAAATTCAACGATTTATTTTCTTTTA-CAAACAGGAAAATAAATCCAATAATTTATTTTCT
* * * * *
2413903 TTTACAAAATAGGAAAATAAATCTACCAATTTATTTCCTTTTATAAACT-TGAATCATTTAAGAC
64 TTTACAAAATAGGAAAATAAATCTAACAATTTATTT-CTTTTA-CAACTCAGAATCATATAAGAT
*
2413967 TA-CTAAGA
127 TATC-AAGG
2413975 AAATAAATTCAA
1 AAATAAATTCAA
2413987 TAACGTATTT
Statistics
Matches: 229, Mismatches: 41, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
133 5 0.02
134 117 0.51
135 103 0.45
136 4 0.02
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (134 bp):
AAATAAATTCAACGATTTATTTTCTTTTACAAACAGGAAAATAAATCCAATAATTTATTTTCTTT
TACAAAATAGGAAAATAAATCTAACAATTTATTTCTTTTACAACTCAGAATCATATAAGATTATC
AAGG
Found at i:2413882 original size:39 final size:39
Alignment explanation
Indices: 2413835--2413949 Score: 137
Period size: 39 Copynumber: 3.0 Consensus size: 39
2413825 ATAAGATTCT
*
2413835 TAGGAAAATAAATTCAACAATTTATTTTATTTTATAAAA
1 TAGGAAAATAAATTCAACAATTTATTTTCTTTTATAAAA
* * *
2413874 TAGGAAAATAAATAT-AATAATTTA-TTTCCTTTACAAAA
1 TAGGAAAATAAAT-TCAACAATTTATTTTCTTTTATAAAA
* *
2413912 TAGGAAAATAAA-TCTACCAATTTATTTCCTTTTATAAA
1 TAGGAAAATAAATTC-AACAATTTATTTTCTTTTATAAA
2413950 CTTGAATCAT
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
36 1 0.02
38 30 0.48
39 31 0.49
40 1 0.02
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (39 bp):
TAGGAAAATAAATTCAACAATTTATTTTCTTTTATAAAA
Found at i:2413921 original size:38 final size:37
Alignment explanation
Indices: 2413835--2413943 Score: 137
Period size: 38 Copynumber: 2.8 Consensus size: 37
2413825 ATAAGATTCT
** *
2413835 TAGGAAAATAAATTCAACAATTTATTTTATTTTATAAAA
1 TAGGAAAATAAATT-AACAATTTA-TTTCCTTTACAAAA
*
2413874 TAGGAAAATAAATATAATAATTTATTTCCTTTACAAAA
1 TAGGAAAATAAAT-TAACAATTTATTTCCTTTACAAAA
*
2413912 TAGGAAAATAAATCTACCAATTTATTTCCTTT
1 TAGGAAAATAAAT-TAACAATTTATTTCCTTT
2413944 TATAAACTTG
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
38 40 0.65
39 21 0.34
40 1 0.02
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (37 bp):
TAGGAAAATAAATTAACAATTTATTTCCTTTACAAAA
Found at i:2414134 original size:58 final size:56
Alignment explanation
Indices: 2414001--2414388 Score: 354
Period size: 58 Copynumber: 6.7 Consensus size: 56
2413991 GTATTTCTTT
* *
2414001 ATTCAAGATTCTCAAGAAAATAAATTTAATAATTTA-TTTCCTTTTA-AAATATAGAATC
1 ATTCAAGATTCTCAAGAAAATAAATTCAAT-ATTTATTTTCC--TTACAAGT-TAGAATC
* * * * *
2414059 ATTCAATATTCTCAAGAAAATAACTTCACTATTTATTTTTCTTACATGTTTAGAATC
1 ATTCAAGATTCTCAAGAAAATAAATTCAATATTTATTTTCCTTACAAG-TTAGAATC
*
2414116 ATTCAAGATTCTCAA-AGAAATAAA-TCAAATAATTTGTTTTCCTTACAAAGTTAGAATC
1 ATTCAAGATTCTCAAGA-AAATAAATTC-AAT-ATTTATTTTCCTTAC-AAGTTAGAATC
* * *
2414174 ATTCAAGATTCTCAAGGAAATAAATTAAACTATTTATTTTCCTTATAATGTTAGAATC
1 ATTCAAGATTCTCAAGAAAATAAATTCAA-TATTTATTTTCCTTACAA-GTTAGAATC
* * *
2414232 ATTTAAGATTCTCAAGGAAATAAATTCAATTATTTATTTTCCTTACAAAGTTAGAATA
1 ATTCAAGATTCTCAAGAAAATAAATTCAA-TATTTATTTTCCTTAC-AAGTTAGAATC
* * * * * *
2414290 ATCCAAAATTCTTAAGGAAATAAATTCAACGATTTATTTTCCTTATGAAGTTAGAATC
1 ATTCAAGATTCTCAAGAAAATAAATTCAA-TATTTATTTTCCTTA-CAAGTTAGAATC
** *
2414348 AACGCAAGATTCT-AATGATGAAATAAATCCAATGATTTATT
1 -ATTCAAGATTCTCAA-GA--AAATAAATTCAAT-ATTTATT
2414389 CATCTCTCCT
Statistics
Matches: 276, Mismatches: 36, Indels: 33
0.80 0.10 0.10
Matches are distributed among these distances:
56 6 0.02
57 37 0.13
58 199 0.72
59 16 0.06
61 18 0.07
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (56 bp):
ATTCAAGATTCTCAAGAAAATAAATTCAATATTTATTTTCCTTACAAGTTAGAATC
Found at i:2414246 original size:116 final size:113
Alignment explanation
Indices: 2414001--2414348 Score: 405
Period size: 116 Copynumber: 3.0 Consensus size: 113
2413991 GTATTTCTTT
* * ** *
2414001 ATTCAAGATTCTC-AAGAAAATAAATTTAATAATTTATTTCCTTTTAAAATATAGAATCATTCAA
1 ATTCAAGATTCTCAAAG-AAATAAA-TCAATAATTTTTTTCCTTACAAAGT-TAGAATCATTCAA
* * * * * *
2414065 TATTCTCAAGAAAATAACTTCACTATTTATTTTTCTTA-CATGTTTAGAATC
63 AATTCTCAAGGAAATAAATTAACTATTTATTTTCCTTATAATG-TTAGAATC
*
2414116 ATTCAAGATTCTCAAAGAAATAAATCAAATAATTTGTTTTCCTTACAAAGTTAGAATCATTCAAG
1 ATTCAAGATTCTCAAAGAAATAAATC-AATAATTT-TTTTCCTTACAAAGTTAGAATCATTCAAA
2414181 ATTCTCAAGGAAATAAATTAAACTATTTATTTTCCTTATAATGTTAGAATC
64 ATTCTCAAGGAAATAAATT-AACTATTTATTTTCCTTATAATGTTAGAATC
* * * * *
2414232 ATTTAAGATTCTCAAGGAAATAAATTCAATTATTTATTTTCCTTACAAAGTTAGAATAATCCAAA
1 ATTCAAGATTCTCAAAGAAATAAA-TCAATAATTT-TTTTCCTTACAAAGTTAGAATCATTCAAA
* *
2414297 ATTCTTAAGGAAATAAATTCAACGATTTATTTTCCTTATGAA-GTTAGAATC
64 ATTCTCAAGGAAATAAATT-AACTATTTATTTTCCTTAT-AATGTTAGAATC
2414348 A
1 A
2414349 ACGCAAGATT
Statistics
Matches: 205, Mismatches: 21, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
114 1 0.00
115 58 0.28
116 139 0.68
117 7 0.03
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.39
Consensus pattern (113 bp):
ATTCAAGATTCTCAAAGAAATAAATCAATAATTTTTTTCCTTACAAAGTTAGAATCATTCAAAAT
TCTCAAGGAAATAAATTAACTATTTATTTTCCTTATAATGTTAGAATC
Found at i:2414343 original size:174 final size:173
Alignment explanation
Indices: 2414001--2414348 Score: 425
Period size: 174 Copynumber: 2.0 Consensus size: 173
2413991 GTATTTCTTT
* * *
2414001 ATTCAAGATTCTCAAGAAAATAAATTTAATAATTTATTTCCTTTTAAAATATAGAATCATTCAAT
1 ATTCAAGATTCTCAAGAAAATAAATTAAATAATTTATTTCCTTATAAAATATAGAATCATTCAAG
* * * * * *
2414066 ATTCTCAAGAAAATAACTTCACTATTTATTTTTCTTACATGTTTAGAATCATTCAAGATTCTCAA
66 ATTCTCAAGAAAATAAATTCACTATTTATTTTCCTTACAAGTTTAGAATAATCCAAAATTCTCAA
* *
2414131 AGAAATAAATCAAATAATTTGTTTTCCTTACAAAGTTAGAATC
131 AGAAATAAATCAAACAATTTATTTTCCTTACAAAGTTAGAATC
* ** *
2414174 ATTCAAGATTCTCAAGGAAATAAATTAAACT-ATTTATTTTCCTTATAATGT-TAGAATCATTTA
1 ATTCAAGATTCTCAAGAAAATAAATTAAA-TAATTTA-TTTCCTTATAAAATATAGAATCATTCA
* *
2414237 AGATTCTCAAGGAAATAAATTCAATTATTTATTTTCCTTACAAAG-TTAGAATAATCCAAAATTC
64 AGATTCTCAAGAAAATAAATTC-ACTATTTATTTTCCTTAC-AAGTTTAGAATAATCCAAAATTC
* * * **
2414301 TTAAGGAAATAAATTC-AACGATTTATTTTCCTTATGAAGTTAGAATC
127 TCAAAGAAATAAA-TCAAACAATTTATTTTCCTTACAAAGTTAGAATC
2414348 A
1 A
2414349 ACGCAAGATT
Statistics
Matches: 148, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
173 62 0.42
174 82 0.55
175 4 0.03
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.39
Consensus pattern (173 bp):
ATTCAAGATTCTCAAGAAAATAAATTAAATAATTTATTTCCTTATAAAATATAGAATCATTCAAG
ATTCTCAAGAAAATAAATTCACTATTTATTTTCCTTACAAGTTTAGAATAATCCAAAATTCTCAA
AGAAATAAATCAAACAATTTATTTTCCTTACAAAGTTAGAATC
Found at i:2423304 original size:32 final size:31
Alignment explanation
Indices: 2423232--2423315 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 31
2423222 CTAATGCGAC
* *
2423232 TCTTAGGTAGGCTCTGTGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGTGGCCCTAAGATCAT
** *
2423263 TCTCGGGTAGGCCCTGTGGCCCTAAGATGTAT
1 TCTTAGGTAGGCCCTGTGGCCCTAAGAT-CAT
*
2423295 TCTTAGGTAGGCCCCGTGGCC
1 TCTTAGGTAGGCCCTGTGGCC
2423316 TCGAAACTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.55
32 20 0.45
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGTGGCCCTAAGATCAT
Found at i:2427968 original size:22 final size:22
Alignment explanation
Indices: 2427942--2427985 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2427932 TTCTAAAAAT
2427942 ATTTACA-AAACTAACACCCAAA
1 ATTTACACAAA-TAACACCCAAA
*
2427964 ATTTACACAAATAGCACCCAAA
1 ATTTACACAAATAACACCCAAA
2427986 CAGAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.52, C:0.27, G:0.02, T:0.18
Consensus pattern (22 bp):
ATTTACACAAATAACACCCAAA
Found at i:2430529 original size:2 final size:2
Alignment explanation
Indices: 2430522--2430570 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2430512 AACCCTTAAT
2430522 AC AC AC AC AC AC AC AC AC AC AC 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
2430564 AC AC AC A
1 AC AC AC A
2430571 TATACAAACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2431428 original size:21 final size:22
Alignment explanation
Indices: 2431392--2431433 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2431382 TATAAATATA
2431392 TTAAAGGATGTACCGATACTCG
1 TTAAAGGATGTACCGATACTCG
*
2431414 TTAATGGAT-TACCGATACTC
1 TTAAAGGATGTACCGATACTC
2431434 CCTGTCCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (22 bp):
TTAAAGGATGTACCGATACTCG
Found at i:2433267 original size:20 final size:20
Alignment explanation
Indices: 2433242--2433284 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2433232 TTTTCTCTTG
**
2433242 AAAGCAAAATTGGATTTTGA
1 AAAGCAAAATTAAATTTTGA
2433262 AAAGCAAAATTAAATTTTGA
1 AAAGCAAAATTAAATTTTGA
2433282 AAA
1 AAA
2433285 ATGATTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (20 bp):
AAAGCAAAATTAAATTTTGA
Found at i:2437736 original size:17 final size:17
Alignment explanation
Indices: 2437711--2437752 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
2437701 TGGAAATATT
*
2437711 TTATAATTATAATTATA
1 TTATTATTATAATTATA
*
2437728 TTATTATTATTATTATA
1 TTATTATTATAATTATA
2437745 TTAATTAT
1 TT-ATTAT
2437753 GGAAATATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTATTATAATTATA
Found at i:2438903 original size:31 final size:31
Alignment explanation
Indices: 2438865--2439005 Score: 255
Period size: 31 Copynumber: 4.5 Consensus size: 31
2438855 AGGGTCGAGG
2438865 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2438896 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2438927 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
2438958 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
2438989 GATTACCTAAGTTCTTC
1 GTTTACCTATGTTCTTC
2439006 AGAATCTATG
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 107 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2439526 original size:21 final size:21
Alignment explanation
Indices: 2439501--2439543 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2439491 AAAGAATATA
2439501 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
2439522 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
2439543 T
1 T
2439544 AAATGCTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:2440410 original size:608 final size:608
Alignment explanation
Indices: 2439256--2440482 Score: 2278
Period size: 608 Copynumber: 2.0 Consensus size: 608
2439246 TGATATAGAT
2439256 TATGATAATGATGGTATATGTTTATGTATGCTTTATGTTATATGAAATATTATATGTTTTATATG
1 TATGATAATGATGGTATATGTTTATGTATGCTTTATGTTATATGAAATATTATATGTTTTATATG
2439321 CCTCACTAAGTCATCGACTTAGCGTGTGATATTTTCACACGTAGGTTTGGAAAACGAAAAGAAAA
66 CCTCACTAAGTCATCGACTTAGCGTGTGATATTTTCACACGTAGGTTTGGAAAACGAAAAGAAAA
*
2439386 GTAAAGAGGAACAAGACAGGTTAGTTCTCCTTACCGAATGTCAGATCAGAAGAGAGGTGAATAAT
131 GTAAAGAGGAACAAGACAGGTCAGTTCTCCTTACCGAATGTCAGATCAGAAGAGAGGTGAATAAT
*
2439451 ATGTATTTTTGTATATAAAGTTCAAGTTGGCATGTAATCAAAAGAATATATTGTATAAGCTCTGA
196 ATGTATTTTTGTATATAAAGTTCAAGTTGACATGTAATCAAAAGAATATATTGTATAAGCTCTGA
*
2439516 ATAATTTTGTAAATGTTTTGAATAATTTAAATGCTATAAAAGTTTTTAAATTACTCACTATTTTA
261 ATAATTTTGTAAATGTTTTGAATAATTTAAATACTATAAAAGTTTTTAAATTACTCACTATTTTA
*
2439581 TACAAATAAATTTTTGAAAAGTCAATGTGACACTTCAGACTCGTATCCTGGTCGGATACGGGATG
326 TACAAATAAATTTTTGAAAAGTCAATATGACACTTCAGACTCGTATCCTGGTCGGATACGGGATG
2439646 GGGGTATTACATTTAATGGTATCAGAGCTACGGTTTAGCCGATTCTAGGCTAAAAACGAAGTCGA
391 GGGGTATTACATTTAATGGTATCAGAGCTACGGTTTAGCCGATTCTAGGCTAAAAACGAAGTCGA
* *
2439711 AAGTGTTTTAAAAAGTGTACTTGCCAACACAAAGTGAAAAATTTTCTGATCTGATAGGGCAAGGA
456 AAGTGTTTTAAAAAGTGTACATGCCAACACAAAGTAAAAAATTTTCTGATCTGATAGGGCAAGGA
2439776 GTGTGAAGTCTTGTTAATAGAGTTAAATTGTTATGTTATATAAGATAAGTGAATACTGAGAATGA
521 GTGTGAAGTCTTGTTAATAGAGTTAAATTGTTATGTTATATAAGATAAGTGAATACTGAGAATGA
2439841 TTTATGAGATATATATATGTTTA
586 TTTATGAGATATATATATGTTTA
2439864 TATGATAATGATGGTATATGTTTATGTATGCTTTATGTTATATGAAATATTATATGTTTTATATG
1 TATGATAATGATGGTATATGTTTATGTATGCTTTATGTTATATGAAATATTATATGTTTTATATG
*
2439929 CCTCACTAAGTCATCGACTTAGCGTGTGAT-TGTTTCACACGTAGGTTTGGAAAGCGAAAAGAAA
66 CCTCACTAAGTCATCGACTTAGCGTGTGATAT-TTTCACACGTAGGTTTGGAAAACGAAAAGAAA
2439993 AGTAAAGAGGAACAAGACAGGTCAGTTCTCCTTACCGAATGTCAGATCAGAAGAGAGGTGAATAA
130 AGTAAAGAGGAACAAGACAGGTCAGTTCTCCTTACCGAATGTCAGATCAGAAGAGAGGTGAATAA
* *
2440058 TATGTATTTTTGTATATAAAGTTCTAGTTGACATGTAATCAAAATAATATATTGTATAAGCTCTG
195 TATGTATTTTTGTATATAAAGTTCAAGTTGACATGTAATCAAAAGAATATATTGTATAAGCTCTG
*
2440123 AATAATTTTGTAAATGTTTTGAATAATTTAAATATTATAAAAGTTTTTAAATTACTCACTATTTT
260 AATAATTTTGTAAATGTTTTGAATAATTTAAATACTATAAAAGTTTTTAAATTACTCACTATTTT
*
2440188 ATACAAATAAATTTTTGAAAAGTCAATATGACACTTCAGACTCGTATCCTGGTCGGATACGGGTT
325 ATACAAATAAATTTTTGAAAAGTCAATATGACACTTCAGACTCGTATCCTGGTCGGATACGGGAT
* *
2440253 GGGGGTGTTATATTTAATGGTATCAGAGCTACGGTTTAGCCGATTCTAGGCTAAAAACGAAGTCG
390 GGGGGTATTACATTTAATGGTATCAGAGCTACGGTTTAGCCGATTCTAGGCTAAAAACGAAGTCG
*
2440318 AAAGTGTTTTAAAAAGTGTACATGCCAACACAAAGTAAAAAATTTTCTGATCTGATAGGGTAAGG
455 AAAGTGTTTTAAAAAGTGTACATGCCAACACAAAGTAAAAAATTTTCTGATCTGATAGGGCAAGG
**
2440383 AGTGTGTTGTCTTGTTAATAGAGTTAAATTGTTATGTTATATAAGATAAGTGAATACTGAGAATG
520 AGTGTGAAGTCTTGTTAATAGAGTTAAATTGTTATGTTATATAAGATAAGTGAATACTGAGAATG
2440448 ATTTATGAGATATATATATGTTTA
585 ATTTATGAGATATATATATGTTTA
*
2440472 TATTAT-ATGAT
1 TATGATAATGAT
2440483 AGATGATATG
Statistics
Matches: 601, Mismatches: 17, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
607 6 0.01
608 595 0.99
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (608 bp):
TATGATAATGATGGTATATGTTTATGTATGCTTTATGTTATATGAAATATTATATGTTTTATATG
CCTCACTAAGTCATCGACTTAGCGTGTGATATTTTCACACGTAGGTTTGGAAAACGAAAAGAAAA
GTAAAGAGGAACAAGACAGGTCAGTTCTCCTTACCGAATGTCAGATCAGAAGAGAGGTGAATAAT
ATGTATTTTTGTATATAAAGTTCAAGTTGACATGTAATCAAAAGAATATATTGTATAAGCTCTGA
ATAATTTTGTAAATGTTTTGAATAATTTAAATACTATAAAAGTTTTTAAATTACTCACTATTTTA
TACAAATAAATTTTTGAAAAGTCAATATGACACTTCAGACTCGTATCCTGGTCGGATACGGGATG
GGGGTATTACATTTAATGGTATCAGAGCTACGGTTTAGCCGATTCTAGGCTAAAAACGAAGTCGA
AAGTGTTTTAAAAAGTGTACATGCCAACACAAAGTAAAAAATTTTCTGATCTGATAGGGCAAGGA
GTGTGAAGTCTTGTTAATAGAGTTAAATTGTTATGTTATATAAGATAAGTGAATACTGAGAATGA
TTTATGAGATATATATATGTTTA
Found at i:2443898 original size:31 final size:31
Alignment explanation
Indices: 2443860--2443969 Score: 175
Period size: 31 Copynumber: 3.5 Consensus size: 31
2443850 AGGGTCGAGG
2443860 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
**
2443891 GTTTACCTATGTTCTTTAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
2443922 GTTTACCTATGTTCTTTGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
2443953 GTTTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
2443970 AGAATCTATG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 73 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2443980 original size:62 final size:62
Alignment explanation
Indices: 2443860--2443984 Score: 189
Period size: 62 Copynumber: 2.0 Consensus size: 62
2443850 AGGGTCGAGG
* * * *
2443860 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTTAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATAGACTGTTTACCTAGGTTCTTCAGAACATATGGACT
*
2443922 GTTTACCTATGTTCTTTGGGACATATAGACTGTTTACCTAGGTTCTTCAGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGACATATAGACTGTTTACCTAGGTTCTTCAGAA-CATATGGACT
2443984 G
1 G
2443985 GTCCTTCGGG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 56 0.98
63 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATAGACTGTTTACCTAGGTTCTTCAGAACATATGGACT
Found at i:2443984 original size:31 final size:31
Alignment explanation
Indices: 2443860--2443984 Score: 171
Period size: 31 Copynumber: 4.0 Consensus size: 31
2443850 AGGGTCGAGG
*
2443860 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
*
2443891 GTTTACCTATGTTCTTTAGGACATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
** *
2443922 GTTTACCTATGTTCTTTGGGACATATAGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
* *
2443953 GTTTACCTAGGTTCTTCAGAATC-TATGGACT
1 GTTTACCTATGTTCTTCAGGA-CATATGGACT
2443984 G
1 G
2443985 GTCCTTCGGG
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
31 83 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCAGGACATATGGACT
Found at i:2451288 original size:24 final size:24
Alignment explanation
Indices: 2451261--2451309 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2451251 TATATCAAAA
*
2451261 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* *
2451285 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
2451309 A
1 A
2451310 ATAGATCAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAAATCAGGTCAAGT
Found at i:2451317 original size:24 final size:24
Alignment explanation
Indices: 2451271--2451393 Score: 123
Period size: 24 Copynumber: 5.2 Consensus size: 24
2451261 ATCAAAACAT
*
2451271 AAATCAGGTCAAGTATCATATCAG
1 AAATCAGGTCAAGTATCAGATCAG
2451295 AAATCAGGTCAAGTAAT-AGATCAG
1 AAATCAGGTCAAGT-ATCAGATCAG
*
2451319 -AATCCAAGTCAAGTATCAGATCAG
1 AAAT-CAGGTCAAGTATCAGATCAG
*
2451343 -AATCCATGTC-AGATATCAGATCAG
1 AAAT-CAGGTCAAG-TATCAGATCAG
*
2451367 -AATCCATGTCAAGTATCAGATCA-
1 AAAT-CAGGTCAAGTATCAGATCAG
2451390 AAAT
1 AAAT
2451394 TCAAATCGAA
Statistics
Matches: 90, Mismatches: 3, Indels: 12
0.86 0.03 0.11
Matches are distributed among these distances:
23 7 0.08
24 79 0.88
25 4 0.04
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (24 bp):
AAATCAGGTCAAGTATCAGATCAG
Found at i:2451364 original size:48 final size:48
Alignment explanation
Indices: 2451278--2451393 Score: 150
Period size: 48 Copynumber: 2.4 Consensus size: 48
2451268 CATAAATCAG
*
2451278 GTCAAGTATCATATCAGAAATCAGGTCAAGTAATAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAAATCAGGTCAAGTAATAGATCAGAATCCAA
* *
2451326 GTCAAGTATCAGATCAG-AATCCATGTC-AG-ATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAAT-CAGGTCAAGTA-AT-AGATCAGAATCCAA
2451374 GTCAAGTATCAGATCA-AAAT
1 GTCAAGTATCAGATCAGAAAT
2451394 TCAAATCGAA
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
46 1 0.02
47 7 0.11
48 53 0.87
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAAATCAGGTCAAGTAATAGATCAGAATCCAA
Found at i:2451463 original size:24 final size:24
Alignment explanation
Indices: 2451436--2451545 Score: 145
Period size: 24 Copynumber: 4.6 Consensus size: 24
2451426 GTAGGGAACA
* *
2451436 CAAGTATCATATCAGAAAT-CAGGT
1 CAAGTATCAGATCAG-AATCCATGT
*
2451460 CAAGTAAT-AGATCAGAATCCAAGT
1 CAAGT-ATCAGATCAGAATCCATGT
2451484 CAAGTATCAGATCAGAATCCATGT
1 CAAGTATCAGATCAGAATCCATGT
2451508 C-AGATATCAGATCAGAATCCATGT
1 CAAG-TATCAGATCAGAATCCATGT
2451532 CAAGTATCAGATCA
1 CAAGTATCAGATCA
2451546 AAATTCAAAT
Statistics
Matches: 78, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
23 7 0.09
24 67 0.86
25 4 0.05
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (24 bp):
CAAGTATCAGATCAGAATCCATGT
Found at i:2451564 original size:156 final size:156
Alignment explanation
Indices: 2451280--2451593 Score: 628
Period size: 156 Copynumber: 2.0 Consensus size: 156
2451270 TAAATCAGGT
2451280 CAAGTATCATATCAGAAATCAGGTCAAGTAATAGATCAGAATCCAAGTCAAGTATCAGATCAGAA
1 CAAGTATCATATCAGAAATCAGGTCAAGTAATAGATCAGAATCCAAGTCAAGTATCAGATCAGAA
2451345 TCCATGTCAGATATCAGATCAGAATCCATGTCAAGTATCAGATCAAAATTCAAATCGAAAATCGA
66 TCCATGTCAGATATCAGATCAGAATCCATGTCAAGTATCAGATCAAAATTCAAATCGAAAATCGA
2451410 TAAAATATTCATGTGAGTAGGGAACA
131 TAAAATATTCATGTGAGTAGGGAACA
2451436 CAAGTATCATATCAGAAATCAGGTCAAGTAATAGATCAGAATCCAAGTCAAGTATCAGATCAGAA
1 CAAGTATCATATCAGAAATCAGGTCAAGTAATAGATCAGAATCCAAGTCAAGTATCAGATCAGAA
2451501 TCCATGTCAGATATCAGATCAGAATCCATGTCAAGTATCAGATCAAAATTCAAATCGAAAATCGA
66 TCCATGTCAGATATCAGATCAGAATCCATGTCAAGTATCAGATCAAAATTCAAATCGAAAATCGA
2451566 TAAAATATTCATGTGAGTAGGGAACA
131 TAAAATATTCATGTGAGTAGGGAACA
2451592 CA
1 CA
2451594 CCAGAGTTTA
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
156 158 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (156 bp):
CAAGTATCATATCAGAAATCAGGTCAAGTAATAGATCAGAATCCAAGTCAAGTATCAGATCAGAA
TCCATGTCAGATATCAGATCAGAATCCATGTCAAGTATCAGATCAAAATTCAAATCGAAAATCGA
TAAAATATTCATGTGAGTAGGGAACA
Found at i:2454058 original size:8 final size:8
Alignment explanation
Indices: 2454034--2454074 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
2454024 GGTCAATGCC
2454034 GGTCAACG
1 GGTCAACG
*
2454042 AGTCAACG
1 GGTCAACG
2454050 GGTCAACG
1 GGTCAACG
2454058 GGT---CG
1 GGTCAACG
2454063 GGTCAACG
1 GGTCAACG
2454071 GGTC
1 GGTC
2454075 GGGTCGGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
5 5 0.18
8 23 0.82
ACGTcount: A:0.22, C:0.24, G:0.39, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:2454066 original size:13 final size:13
Alignment explanation
Indices: 2454048--2454079 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
2454038 AACGAGTCAA
2454048 CGGGTCAACGGGT
1 CGGGTCAACGGGT
2454061 CGGGTCAACGGGT
1 CGGGTCAACGGGT
2454074 CGGGTC
1 CGGGTC
2454080 GGGTAAACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:2454079 original size:18 final size:18
Alignment explanation
Indices: 2454056--2454102 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
2454046 AACGGGTCAA
2454056 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
2454074 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
2454092 CGGGTCGGGTC
1 CGGGTCGGGTC
2454103 GGGTTATGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.11, C:0.21, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:2456213 original size:24 final size:24
Alignment explanation
Indices: 2456186--2456266 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
2456176 TATATCAAAA
*
2456186 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAATCATAAATCAGGTCAAGT
* *
2456210 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAATCATAAATCAGGTCAAGT
* * *
2456234 AACAGATCAT-AATCCAAGTCAAGT
1 ATCAAATCATAAAT-CAGGTCAAGT
*
2456258 ATCAGATCA
1 ATCAAATCA
2456267 GAATCCATGT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 3 0.06
24 45 0.94
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAATCATAAATCAGGTCAAGT
Found at i:2456314 original size:29 final size:24
Alignment explanation
Indices: 2456203--2456342 Score: 203
Period size: 24 Copynumber: 5.8 Consensus size: 24
2456193 CATAAATCAG
* *
2456203 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
* * *
2456227 GTCAAGTAACAGATCATAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
2456251 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
2456275 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
2456299 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
2456323 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
2456343 TCAAATCGAA
Statistics
Matches: 106, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
23 5 0.05
24 99 0.93
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:2458763 original size:16 final size:15
Alignment explanation
Indices: 2458737--2458766 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2458727 GTCAACGCCG
2458737 GTCAACGGTCAACGA
1 GTCAACGGTCAACGA
2458752 GTCAACCGGTCAACG
1 GTCAA-CGGTCAACG
2458767 GGTCGGGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.30, G:0.27, T:0.13
Consensus pattern (15 bp):
GTCAACGGTCAACGA
Found at i:2458777 original size:13 final size:13
Alignment explanation
Indices: 2458759--2458789 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2458749 CGAGTCAACC
2458759 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
2458772 GGTCAACGGTTCG
1 GGTCAACGGGTCG
2458785 GGTCA
1 GGTCA
2458790 GGTAAACGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.23, G:0.42, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2458788 original size:18 final size:18
Alignment explanation
Indices: 2458765--2458810 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2458755 AACCGGTCAA
* *
2458765 CGGGTCGGGTCAACGGTT
1 CGGGTCGGGTAAACGGGT
*
2458783 CGGGTCAGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
2458801 CGGGTCGGGT
1 CGGGTCGGGT
2458811 TGGGTTATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.20, G:0.48, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:2460924 original size:24 final size:24
Alignment explanation
Indices: 2460897--2460972 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
2460887 TATATCAAAA
*
2460897 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* *
2460921 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* * * *
2460945 AACAGATCAG-AATCCAAGTCAAGT
1 ATCAAAACAGAAAT-CAGGTCAAGT
2460969 ATCA
1 ATCA
2460973 GATCAGAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAAAACAGAAATCAGGTCAAGT
Found at i:2460974 original size:24 final size:24
Alignment explanation
Indices: 2460914--2461049 Score: 186
Period size: 24 Copynumber: 5.7 Consensus size: 24
2460904 CATAAATCAG
* *
2460914 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
* *
2460938 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
2460962 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
2460986 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
*
2461010 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
2461034 GTCAAGTATCATATCA
1 GTCAAGTATCAGATCA
2461050 TAATTCAAAT
Statistics
Matches: 103, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
23 5 0.05
24 96 0.93
25 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:2463557 original size:15 final size:17
Alignment explanation
Indices: 2463527--2463567 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
2463517 GGTCAACAGT
2463527 GGTCAACGCCAGTCAAC-
1 GGTCAACG-CAGTCAACG
2463544 GGTCAACG-AGTCAACG
1 GGTCAACGCAGTCAACG
2463560 GGTCAACG
1 GGTCAACG
2463568 GGTCGGGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.30
16 8 0.35
17 8 0.35
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.12
Consensus pattern (17 bp):
GGTCAACGCAGTCAACG
Found at i:2463568 original size:8 final size:8
Alignment explanation
Indices: 2463538--2463571 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
2463528 GTCAACGCCA
2463538 GTCAAC-G
1 GTCAACGG
*
2463545 GTCAACGA
1 GTCAACGG
2463553 GTCAACGG
1 GTCAACGG
2463561 GTCAACGG
1 GTCAACGG
2463569 GTC
1 GTC
2463572 GGGTAAACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.15
Consensus pattern (8 bp):
GTCAACGG
Found at i:2463580 original size:13 final size:13
Alignment explanation
Indices: 2463558--2463588 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2463548 AACGAGTCAA
*
2463558 CGGGTCAACGGGT
1 CGGGTAAACGGGT
2463571 CGGGTAAACGGGT
1 CGGGTAAACGGGT
2463584 CGGGT
1 CGGGT
2463589 CGGATCGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTAAACGGGT
Found at i:2465689 original size:24 final size:24
Alignment explanation
Indices: 2465662--2465809 Score: 81
Period size: 24 Copynumber: 6.2 Consensus size: 24
2465652 TATATCAAAA
*
2465662 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* *
2465686 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* * * *
2465710 AACAGATCAG-AATCCAAGTCAAGT
1 ATCAAAACAGAAAT-CAGGTCAAGT
* * *
2465734 ATCAGATCAG-AATCCATGTC-AGAT
1 ATCAAAACAGAAAT-CAGGTCAAG-T
* *
2465758 ATCAAATCAG-AATCCATGTCAAGT
1 ATCAAAACAGAAAT-CAGGTCAAGT
* * *
2465782 ATCATATCAG-AATCCATGTCAAGT
1 ATCAAAACAGAAAT-CAGGTCAAGT
2465806 ATCA
1 ATCA
2465810 TATCAGAATT
Statistics
Matches: 111, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
23 5 0.05
24 104 0.94
25 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.24
Consensus pattern (24 bp):
ATCAAAACAGAAATCAGGTCAAGT
Found at i:2465767 original size:48 final size:48
Alignment explanation
Indices: 2465679--2465836 Score: 185
Period size: 48 Copynumber: 3.3 Consensus size: 48
2465669 CATAAATCAG
* * * *
2465679 GTCAAGTATCATATCAGAAAT-CAGGTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAG-AATCCATGTCAAGTATCAAATCAGAATCCAA
*
2465727 GTCAAGTATCAGATCAGAATCCATGTC-AGATATCAAATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCATGTCAAG-TATCAAATCAGAATCCAA
* * *
2465775 GTCAAGTATCATATCAGAATCCATGTCAAGTATCATATCAGAATTCAA
1 GTCAAGTATCAGATCAGAATCCATGTCAAGTATCAAATCAGAATCCAA
* **
2465823 ATCAAAAATCAGAT
1 GTCAAGTATCAGAT
2465837 AAAATATTCA
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
47 5 0.05
48 87 0.93
49 2 0.02
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCATGTCAAGTATCAAATCAGAATCCAA
Found at i:2465827 original size:24 final size:24
Alignment explanation
Indices: 2465679--2465818 Score: 194
Period size: 24 Copynumber: 5.8 Consensus size: 24
2465669 CATAAATCAG
*
2465679 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCATATCAG-AATCCAT
* * *
2465703 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAT
*
2465727 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAT
*
2465751 GTC-AGATATCAAATCAGAATCCAT
1 GTCAAG-TATCATATCAGAATCCAT
2465775 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAT
2465799 GTCAAGTATCATATCAGAAT
1 GTCAAGTATCATATCAGAAT
2465819 TCAAATCAAA
Statistics
Matches: 106, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
23 5 0.05
24 99 0.93
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAT
Found at i:2465833 original size:24 final size:24
Alignment explanation
Indices: 2465715--2465833 Score: 76
Period size: 24 Copynumber: 5.0 Consensus size: 24
2465705 CAAGTAACAG
* ** *
2465715 ATCAGAATCCAAGTCAAGTATCAG
1 ATCAGAATCCAAATCAAAAATCAT
** * * *
2465739 ATCAGAATCCATGTCAGATATCAA
1 ATCAGAATCCAAATCAAAAATCAT
** **
2465763 ATCAGAATCCATGTCAAGTATCAT
1 ATCAGAATCCAAATCAAAAATCAT
** **
2465787 ATCAGAATCCATGTCAAGTATCAT
1 ATCAGAATCCAAATCAAAAATCAT
*
2465811 ATCAGAATTCAAATCAAAAATCA
1 ATCAGAATCCAAATCAAAAATCA
2465834 GATAAAATAT
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 83 1.00
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (24 bp):
ATCAGAATCCAAATCAAAAATCAT
Found at i:2468316 original size:15 final size:16
Alignment explanation
Indices: 2468286--2468319 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
2468276 GGTCAACAAT
2468286 GGTCAACGCCGGTCAAC
1 GGTCAACG-CGGTCAAC
2468303 GGTCAACG-GGTCAAC
1 GGTCAACGCGGTCAAC
2468318 GG
1 GG
2468320 GTCGGGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.29, G:0.35, T:0.12
Consensus pattern (16 bp):
GGTCAACGCGGTCAAC
Found at i:2468336 original size:12 final size:13
Alignment explanation
Indices: 2468309--2468351 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
2468299 CAACGGTCAA
2468309 CGGGTCAACGGGT
1 CGGGTCAACGGGT
2468322 CGGGTCAAC-GGT
1 CGGGTCAACGGGT
*
2468334 CGGGTAAACGGGT
1 CGGGTCAACGGGT
2468347 CGGGT
1 CGGGT
2468352 TATGACCGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.16, C:0.21, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:2470428 original size:24 final size:24
Alignment explanation
Indices: 2470405--2470523 Score: 159
Period size: 24 Copynumber: 5.0 Consensus size: 24
2470395 AAACATAAAT
*
2470405 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
2470429 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* *
2470453 CAAGTCAAGTATCATATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* *
2470477 CATGTCAAGTATCAGATCAGAATA
1 CAGGTCAAGTATCAGATCAGAATC
*
2470501 CATGTCAAGTATCAGATCAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
2470524 TCAAATCGAA
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
23 3 0.03
24 83 0.97
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:2470539 original size:48 final size:48
Alignment explanation
Indices: 2470408--2470541 Score: 130
Period size: 48 Copynumber: 2.8 Consensus size: 48
2470398 CATAAATCAG
* ** *
2470408 GTCAAGTATCATATCAGAAAT-CAGGTCAAGTAA-CAGATCAGAATCCAA
1 GTCAAGTATCAGATCAG-AATCCAAATCAAG-AATCAGATCAGAATACAA
* ** * *
2470456 GTCAAGTATCATATCAGAATCCATGTCAAGTATCAGATCAGAATACAT
1 GTCAAGTATCAGATCAGAATCCAAATCAAGAATCAGATCAGAATACAA
*
2470504 GTCAAGTATCAGATCAGAATTCAAATCGAA-AATCAGAT
1 GTCAAGTATCAGATCAGAATCCAAATC-AAGAATCAGAT
2470542 AAAATATTCA
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
47 4 0.05
48 68 0.92
49 2 0.03
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.24
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAAATCAAGAATCAGATCAGAATACAA
Found at i:2473071 original size:13 final size:13
Alignment explanation
Indices: 2473031--2473088 Score: 89
Period size: 13 Copynumber: 4.5 Consensus size: 13
2473021 AATGAGTCAA
2473031 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
2473044 CAGGTCAACGGGT
1 CGGGTCAACGGGT
2473057 CGGGTCAACGGGT
1 CGGGTCAACGGGT
* *
2473070 CGGGTAAATGGGT
1 CGGGTCAACGGGT
2473083 CGGGTC
1 CGGGTC
2473089 GGGTCGGGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:2475035 original size:2 final size:2
Alignment explanation
Indices: 2475024--2475072 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
2475014 TTCATTCTCA
2475024 AT AT AT -T AT AT AT AT 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 AT AT AT AT AT AT AT AT
2475065 AT AT AT AT
1 AT AT AT AT
2475073 CCGAACTGTC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2475529 original size:2 final size:2
Alignment explanation
Indices: 2475522--2475555 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2475512 ATCATCATCA
2475522 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2475556 TATTTAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2477494 original size:24 final size:24
Alignment explanation
Indices: 2477464--2477525 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
2477454 TAATAGAATC
2477464 CAAATCAGAAATCAGAACATAATT
1 CAAATCAGAAATCAGAACATAATT
* *
2477488 CAGATCAGAAATCAGAACGTAATT
1 CAAATCAGAAATCAGAACATAATT
* *
2477512 TAAATCGGAAATCA
1 CAAATCAGAAATCA
2477526 AATAAAGCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.50, C:0.16, G:0.13, T:0.21
Consensus pattern (24 bp):
CAAATCAGAAATCAGAACATAATT
Found at i:2486783 original size:24 final size:28
Alignment explanation
Indices: 2486736--2486788 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 28
2486726 TACATCTGCT
*
2486736 TTTATAATAAATAAACTCTGGTAC-ATA
1 TTTATAATAAATAAACCCTGGTACTATA
2486763 TTTATAA-AAAT-AACCCT-GTACTATA
1 TTTATAATAAATAAACCCTGGTACTATA
2486788 T
1 T
2486789 CGCGGGGCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 4 0.17
25 9 0.38
26 4 0.17
27 7 0.29
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (28 bp):
TTTATAATAAATAAACCCTGGTACTATA
Found at i:2489140 original size:18 final size:18
Alignment explanation
Indices: 2489117--2489172 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
2489107 AGAGGACAAT
* *
2489117 AATAAGGAGGATGAGAAG
1 AATAAGAAGAATGAGAAG
*
2489135 AATAAGAAGAATGAGAAT
1 AATAAGAAGAATGAGAAG
*
2489153 AATAA-ATAGAAGGAGAAG
1 AATAAGA-AGAATGAGAAG
2489171 AA
1 AA
2489173 GGACAAAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 1 0.03
18 31 0.97
ACGTcount: A:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (18 bp):
AATAAGAAGAATGAGAAG
Found at i:2489195 original size:6 final size:6
Alignment explanation
Indices: 2489181--2489368 Score: 96
Period size: 6 Copynumber: 30.8 Consensus size: 6
2489171 AAGGACAAAA
* * * * *
2489181 AGAATG AGAAGG AGAAGG AGAAGA AGAAGA AGAAAGG -GAAGG AGCATG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AG-AAGG AGAAGG AGAAGG
* * * * * * *
2489229 AGAAGG AGAAGAAG AAGAAGC ATAAGA ATAAGG AGAAAG AGAATG AGAAGA
1 AGAAGG AGAAG--G -AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * *
2489280 AGAAGG AGGAA-G AGGAA-G AGGAGG AGAAGA AGAAGA AGGAGG AGGAA-G
1 AGAAGG A-GAAGG A-GAAGG AGAAGG AGAAGG AGAAGG AGAAGG A-GAAGG
* * * * *
2489328 AGGATG AGAAGA AGAAGA AGAAGA AGAAGG AGAAGG AGAAG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAG
2489369 AAGGAATATA
Statistics
Matches: 145, Mismatches: 28, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
5 8 0.06
6 123 0.85
7 8 0.06
8 1 0.01
9 5 0.03
ACGTcount: A:0.54, C:0.01, G:0.41, T:0.03
Consensus pattern (6 bp):
AGAAGG
Found at i:2489206 original size:36 final size:36
Alignment explanation
Indices: 2489166--2489361 Score: 151
Period size: 36 Copynumber: 5.4 Consensus size: 36
2489156 AAATAGAAGG
* *
2489166 AGAAGAAGGACAAAAAGAATGAGAAGGAGAAGGAGA
1 AGAAGAAGGAGAAAAAGAAGGAGAAGGAGAAGGAGA
* ** * *
2489202 AGAAGAAGAAGAAAGGGAAGGAGCATGAGAAGGAGA
1 AGAAGAAGGAGAAAAAGAAGGAGAAGGAGAAGGAGA
* * * *
2489238 AGAAGAAGAAGCATAAGAATAAGGAGAAAGAGAATGAGA
1 AGAAGAAGGAG-A-AA-AAGAAGGAGAAGGAGAAGGAGA
* * * *
2489277 AGAAGAAGGAGGAAGAGGAA-GAGGAGGAGAAGAAGA
1 AGAAGAAGGA-GAAAAAGAAGGAGAAGGAGAAGGAGA
* * * * * * *
2489313 AGAAGGAGGAGGAAGAGGATGAGAAGAAGAAGAAGA
1 AGAAGAAGGAGAAAAAGAAGGAGAAGGAGAAGGAGA
2489349 AGAAGAAGGAGAA
1 AGAAGAAGGAGAA
2489362 GGAGAAGAAG
Statistics
Matches: 124, Mismatches: 31, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
35 4 0.03
36 86 0.69
37 4 0.03
38 3 0.02
39 26 0.21
40 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.40, T:0.03
Consensus pattern (36 bp):
AGAAGAAGGAGAAAAAGAAGGAGAAGGAGAAGGAGA
Found at i:2489214 original size:30 final size:29
Alignment explanation
Indices: 2489160--2489368 Score: 119
Period size: 30 Copynumber: 7.2 Consensus size: 29
2489150 AATAATAAAT
*
2489160 AGAAGGAGAAGAAGGACAAAAAGAATGAGAAGG
1 AGAAGGAGAAGAA-G--AAGAAGAA-GAGAAGG
*
2489193 AGAAGGAGAAGAAGAAGAAGAAAGGGAAGG
1 AGAAGGAGAAGAAGAAGAAG-AAGAGAAGG
* * * *
2489223 AGCATGAGAAGGAGAAGAAG-A-AGAAGC
1 AGAAGGAGAAGAAGAAGAAGAAGAGAAGG
* * * * *
2489250 ATAAGAATAAGGAGAA-AGAGAATGAGAAGA
1 AGAAGGAGAAGAAGAAGA-AGAA-GAGAAGG
*
2489280 AGAAGGAG--GAAG-AG--GAAGAGGAGG
1 AGAAGGAGAAGAAGAAGAAGAAGAGAAGG
* * * * *
2489304 AGAAGAAGAAGAAGGAGGAGGAAGAGGATG
1 AGAAGGAGAAGAA-GAAGAAGAAGAGAAGG
*
2489334 AGAAGAAGAAGAAGAAGAAGAAGGAGAAGG
1 AGAAGGAGAAGAAGAAGAAGAA-GAGAAGG
2489364 AGAAG
1 AGAAG
2489369 AAGGAATATA
Statistics
Matches: 137, Mismatches: 26, Indels: 29
0.71 0.14 0.15
Matches are distributed among these distances:
24 12 0.09
25 3 0.02
26 4 0.03
27 19 0.14
28 6 0.04
29 7 0.05
30 70 0.51
31 2 0.01
32 1 0.01
33 13 0.09
ACGTcount: A:0.55, C:0.01, G:0.41, T:0.03
Consensus pattern (29 bp):
AGAAGGAGAAGAAGAAGAAGAAGAGAAGG
Found at i:2489369 original size:30 final size:30
Alignment explanation
Indices: 2489161--2489371 Score: 126
Period size: 33 Copynumber: 6.6 Consensus size: 30
2489151 ATAATAAATA
*
2489161 GAAGGAGAAGAAGGACAAAAAGAATG-AGAAGGA
1 GAAGGAGAAGAA-G--AAGAAGAA-GAAGAAGGA
*
2489194 GAAGGAGAAGAAGAAGAAGAA-AGGGAAGGA
1 GAAGGAGAAGAAGAAGAAGAAGA-AGAAGGA
* * * *
2489224 GCATGAGAAGGAGAAGAAGAAGAAGCATAAGAA
1 GAAGGAGAAGAAGAAGAAGAAGAAG---AAGGA
*
2489257 TAAGGAGAA-AGAGAATG-AGAAGAAGAAGGA
1 GAAGGAGAAGA-AGAA-GAAGAAGAAGAAGGA
*
2489287 GGAA-GAGGAAGAGGAGGAGAAGAAGAAGAAGGA
1 -GAAGGA-GAAGA--AGAAGAAGAAGAAGAAGGA
* * *
2489320 GGAGGAAGAGGATGAGAAGAAGAAGAAGAAGAA
1 GAAGG-AGAAGA--AGAAGAAGAAGAAGAAGGA
*
2489353 GAAGGAGAAGGAGAAGAAG
1 GAAGGAGAAGAAGAAGAAG
2489372 GAATATAAGA
Statistics
Matches: 141, Mismatches: 22, Indels: 33
0.72 0.11 0.17
Matches are distributed among these distances:
30 46 0.33
31 6 0.04
32 9 0.06
33 78 0.55
34 2 0.01
ACGTcount: A:0.55, C:0.01, G:0.41, T:0.03
Consensus pattern (30 bp):
GAAGGAGAAGAAGAAGAAGAAGAAGAAGGA
Found at i:2489388 original size:9 final size:9
Alignment explanation
Indices: 2489130--2489371 Score: 97
Period size: 9 Copynumber: 26.9 Consensus size: 9
2489120 AAGGAGGATG
*
2489130 AGAAGAATA
1 AGAAGAAGA
2489139 AGAAGAATG-
1 AGAAGAA-GA
* *
2489148 AGAATAATA
1 AGAAGAAGA
*
2489157 A-ATAGAAGG
1 AGA-AGAAGA
*
2489166 AGAAGAAGG
1 AGAAGAAGA
* *
2489175 ACAAAAAGA
1 AGAAGAAGA
*
2489184 ATG-AGAAGG
1 A-GAAGAAGA
*
2489193 AGAAGGAGA
1 AGAAGAAGA
2489202 AGAAGAAGA
1 AGAAGAAGA
*
2489211 AGAA-AGGGA
1 AGAAGA-AGA
* *
2489220 AGGAGCATG-
1 AGAAG-AAGA
*
2489229 AGAAGGAGA
1 AGAAGAAGA
2489238 AGAAGAAGA
1 AGAAGAAGA
* *
2489247 AGCATAAGA
1 AGAAGAAGA
* *
2489256 ATAAGGAGA
1 AGAAGAAGA
2489265 A-AGAGAATG-
1 AGA-AGAA-GA
2489274 AGAAGAAGA
1 AGAAGAAGA
*
2489283 AGGAGGAAGA
1 A-GAAGAAGA
* *
2489293 GGAAG-AGG
1 AGAAGAAGA
*
2489301 AGGAGAAGA
1 AGAAGAAGA
2489310 AGAAGAAGGA
1 AGAAGAA-GA
* *
2489320 GGAGGAAGA
1 AGAAGAAGA
* *
2489329 GGATG-AGA
1 AGAAGAAGA
2489337 AGAAGAAGA
1 AGAAGAAGA
2489346 AGAAGAAGA
1 AGAAGAAGA
* *
2489355 AGGAGAAGG
1 AGAAGAAGA
2489364 AGAAGAAG
1 AGAAGAAG
2489372 GAATATAAGA
Statistics
Matches: 170, Mismatches: 45, Indels: 36
0.68 0.18 0.14
Matches are distributed among these distances:
8 17 0.10
9 134 0.79
10 18 0.11
11 1 0.01
ACGTcount: A:0.56, C:0.01, G:0.38, T:0.05
Consensus pattern (9 bp):
AGAAGAAGA
Found at i:2489456 original size:12 final size:12
Alignment explanation
Indices: 2489441--2489467 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2489431 GGAGAAGGAG
2489441 AAGAAAAATGAT
1 AAGAAAAATGAT
2489453 AAGAAAAATGAT
1 AAGAAAAATGAT
2489465 AAG
1 AAG
2489468 GAGGGGGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.15
Consensus pattern (12 bp):
AAGAAAAATGAT
Found at i:2489481 original size:3 final size:3
Alignment explanation
Indices: 2489466--2489503 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2489456 AAAAATGATA
* *
2489466 AGG AGG GGG AGG AGG ATG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
2489504 CCATGAACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.66, T:0.03
Consensus pattern (3 bp):
AGG
Found at i:2490015 original size:2 final size:2
Alignment explanation
Indices: 2490008--2490044 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2489998 TACACGTTAT
2490008 TA 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 T
2490045 TTAAAAAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2490446 original size:25 final size:27
Alignment explanation
Indices: 2490418--2490472 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
2490408 GCATACATAA
2490418 ACTCCC-A-GGCTCTGCAAAATCAGAT
1 ACTCCCAATGGCTCTGCAAAATCAGAT
2490443 ACTCCCAATGGCTCTGCAAAATCAGAT
1 ACTCCCAATGGCTCTGCAAAATCAGAT
2490470 ACT
1 ACT
2490473 ATATCTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.21
26 1 0.04
27 21 0.75
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.22
Consensus pattern (27 bp):
ACTCCCAATGGCTCTGCAAAATCAGAT
Found at i:2495573 original size:14 final size:14
Alignment explanation
Indices: 2495554--2495623 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 14
2495544 GGGTTCTTTG
2495554 CATAATTCAATAAA
1 CATAATTCAATAAA
2495568 CATAATTCAAATTTAATTA
1 CATAATTC-AA--TAA--A
* * * *
2495587 AATAGATTTAATTAG
1 CATA-ATTCAATAAA
2495602 CATAATTCAATAAA
1 CATAATTCAATAAA
2495616 CATAATTC
1 CATAATTC
2495624 TAATTTAATC
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
14 23 0.55
15 5 0.12
17 5 0.12
19 6 0.14
20 3 0.07
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.36
Consensus pattern (14 bp):
CATAATTCAATAAA
Found at i:2495629 original size:48 final size:48
Alignment explanation
Indices: 2495553--2495645 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
2495543 AGGGTTCTTT
* *
2495553 GCATAATTCAATAAACATAATTCAAATTTAATTAAATAGATTTAATTA
1 GCATAATTCAATAAACATAATTCAAATTTAATCAAATAAATTTAATTA
*
2495601 GCATAATTCAATAAACATAATTCTAATTTAATCAAATAAATTTAA
1 GCATAATTCAATAAACATAATTCAAATTTAATCAAATAAATTTAA
2495646 ATCTCTAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.37
Consensus pattern (48 bp):
GCATAATTCAATAAACATAATTCAAATTTAATCAAATAAATTTAATTA
Found at i:2500661 original size:17 final size:18
Alignment explanation
Indices: 2500639--2500715 Score: 58
Period size: 17 Copynumber: 4.4 Consensus size: 18
2500629 AAAAAATATG
2500639 AAATAAAGAGAAAAAA-T
1 AAATAAAGAGAAAAAACT
2500656 AAATAAAGA-ATATAAAGACT
1 AAATAAAGAGA-A-AAA-ACT
2500676 AAAATAAAG-G-AAAAA-T
1 -AAATAAAGAGAAAAAACT
* *
2500692 -AATAAAAATAAAAAACT
1 AAATAAAGAGAAAAAACT
2500709 AAATAAA
1 AAATAAA
2500716 TAAAAAATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 19
0.70 0.03 0.28
Matches are distributed among these distances:
14 6 0.12
16 7 0.15
17 12 0.25
18 12 0.25
19 2 0.04
20 1 0.02
21 8 0.17
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.16
Consensus pattern (18 bp):
AAATAAAGAGAAAAAACT
Found at i:2500703 original size:32 final size:35
Alignment explanation
Indices: 2500639--2500725 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 35
2500629 AAAAAATATG
*
2500639 AAATAAAGAGAAAAAATAAATAAAGAATAT-AAAGACT
1 AAATAAAG-G-AAAAAT-AATAAAGAATATAAAAAACT
2500676 AAAATAAAGGAAAAATAAT-AA-AA-ATAAAAAACT
1 -AAATAAAGGAAAAATAATAAAGAATATAAAAAACT
**
2500709 AAATAAATAAAAAATAA
1 AAATAAAGGAAAAATAA
2500726 CATCAAATGA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
32 17 0.38
33 8 0.18
34 2 0.04
35 3 0.07
36 6 0.13
37 1 0.02
38 8 0.18
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (35 bp):
AAATAAAGGAAAAATAATAAAGAATATAAAAAACT
Found at i:2520114 original size:178 final size:178
Alignment explanation
Indices: 2519815--2520170 Score: 613
Period size: 178 Copynumber: 2.0 Consensus size: 178
2519805 GGTAACGCGA
2519815 GAGAGAATTATTTTAAAGAGATATAATTCTTTTTGGGATCTCCGCAACATTTGAGTTTATTTTAC
1 GAGAGAATTATTTTAAAGAGATATAATTCTTTTTGGGATCTCCGCAACATTTGAGTTTATTTTAC
2519880 AGAGATGATTTTATAGGGAAGTTGGTAGAGTGTTTTGATATATACCGAGTTTTGGTATCTATATT
66 AGAGATGATTTTATAGGGAAGTTGGTAGAGTGTTTTGATATATACCGAGTTTTGGTATCTATATT
*
2519945 GAGTTTTGAGATACATGTGATATCAAATATTTTTACTCTTTATGTTTT
131 GAGTTTTGAGATACATGTGATATCAAATATTTTTACTCTTCATGTTTT
* * *
2519993 GAGAGAATTATTTTAAAGAGATGTAGTTCTTTTTGGGATCTTCGCAACATTTGAGTTTATTTTAC
1 GAGAGAATTATTTTAAAGAGATATAATTCTTTTTGGGATCTCCGCAACATTTGAGTTTATTTTAC
* * ** *
2520058 ATAGATGATTTTATAGGGATGTTGGTAGAGTGTTTTGATATATTTCGGGTTTTGGTATCTATATT
66 AGAGATGATTTTATAGGGAAGTTGGTAGAGTGTTTTGATATATACCGAGTTTTGGTATCTATATT
* *
2520123 GAGTTTTGAGATACATGTGATGTCAAGTATTTTTACTCTTCATGTTTT
131 GAGTTTTGAGATACATGTGATATCAAATATTTTTACTCTTCATGTTTT
2520171 CTATGTTTAT
Statistics
Matches: 167, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
178 167 1.00
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.45
Consensus pattern (178 bp):
GAGAGAATTATTTTAAAGAGATATAATTCTTTTTGGGATCTCCGCAACATTTGAGTTTATTTTAC
AGAGATGATTTTATAGGGAAGTTGGTAGAGTGTTTTGATATATACCGAGTTTTGGTATCTATATT
GAGTTTTGAGATACATGTGATATCAAATATTTTTACTCTTCATGTTTT
Found at i:2523386 original size:20 final size:20
Alignment explanation
Indices: 2523361--2523401 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2523351 GATCCATTTG
2523361 TGAAAAAAGGATCAATCCCT
1 TGAAAAAAGGATCAATCCCT
* *
2523381 TGAAAAATGGATCCATCCCT
1 TGAAAAAAGGATCAATCCCT
2523401 T
1 T
2523402 TTGAAAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (20 bp):
TGAAAAAAGGATCAATCCCT
Found at i:2535086 original size:15 final size:17
Alignment explanation
Indices: 2535068--2535108 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
2535058 TCAAAGTTAC
2535068 AAATTTCA-AT-AAACT
1 AAATTTCACATCAAACT
2535083 AAATTTCACATCAAACT
1 AAATTTCACATCAAACT
2535100 AAATTTCAC
1 AAATTTCAC
2535109 GTTTATACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.33
16 2 0.08
17 14 0.58
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATTTCACATCAAACT
Found at i:2541345 original size:19 final size:19
Alignment explanation
Indices: 2541323--2541363 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2541313 TGACCTTCGG
2541323 GACTCTGATAGTACTTCAT
1 GACTCTGATAGTACTTCAT
2541342 GACTCTGATAGTACTTCAT
1 GACTCTGATAGTACTTCAT
2541361 GAC
1 GAC
2541364 AGACTGGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (19 bp):
GACTCTGATAGTACTTCAT
Found at i:2542077 original size:22 final size:23
Alignment explanation
Indices: 2542051--2542095 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2542041 ACTGAACTAC
2542051 AAAATTTTAAGAATAC-AAATTA
1 AAAATTTTAAGAATACGAAATTA
* *
2542073 AAAATTTTAGGGATACGAAATTA
1 AAAATTTTAAGAATACGAAATTA
2542096 GATTATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.31
Consensus pattern (23 bp):
AAAATTTTAAGAATACGAAATTA
Found at i:2543914 original size:12 final size:12
Alignment explanation
Indices: 2543897--2543921 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2543887 CTAGAATACC
2543897 TATTTTTCTTTA
1 TATTTTTCTTTA
2543909 TATTTTTCTTTA
1 TATTTTTCTTTA
2543921 T
1 T
2543922 CTCTTTAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTTTCTTTA
Found at i:2544062 original size:45 final size:45
Alignment explanation
Indices: 2543963--2544224 Score: 409
Period size: 45 Copynumber: 5.8 Consensus size: 45
2543953 TCCATTGATA
* * * * *
2543963 GCATCCATTCATACCTATAATGCA-CCATTATACATTTTCAATTATA
1 GCATCCTTTCATGCCAATAATGCACCCA-TATGCA-TTTCAATTATG
*
2544009 TCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
*
2544054 GCATCCTTTCATGCCATTAATGCACCCATATGCATTTCAATTATG
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
2544099 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
* *
2544144 GCATCCTTTCATGCCAATAATGCACTCATATGCATTTCAGTTATG
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
*
2544189 GCATCCTTTCATGCAAATAATGCACCCATATGCATT
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATT
2544225 ATTTTATTCA
Statistics
Matches: 202, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
45 174 0.86
46 25 0.12
47 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (45 bp):
GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
Found at i:2549097 original size:19 final size:20
Alignment explanation
Indices: 2549067--2549138 Score: 83
Period size: 19 Copynumber: 3.5 Consensus size: 20
2549057 ATACAAAAAT
*
2549067 GGTATTGATACCATAATA-G
1 GGTATCGATACCATAATAGG
*
2549086 GGTATCGGTACCATAATATGG
1 GGTATCGATACCATAATA-GG
* *
2549107 TAGTATCGATACCATGATAGG
1 -GGTATCGATACCATAATAGG
2549128 GGTATCGATAC
1 GGTATCGATAC
2549139 TGAGGAGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.36
20 10 0.23
21 3 0.07
22 15 0.34
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (20 bp):
GGTATCGATACCATAATAGG
Found at i:2549119 original size:22 final size:19
Alignment explanation
Indices: 2549067--2549138 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 19
2549057 ATACAAAAAT
*
2549067 GGTATTGATACCATAATAG
1 GGTATCGATACCATAATAG
*
2549086 GGTATCGGTACCATAATATG
1 GGTATCGATACCATAATA-G
*
2549106 GTAGTATCGATACCATGATAGG
1 G--GTATCGATACCATAATA-G
2549128 GGTATCGATAC
1 GGTATCGATAC
2549139 TGAGGAGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 16 0.36
20 12 0.27
22 17 0.38
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (19 bp):
GGTATCGATACCATAATAG
Found at i:2549660 original size:20 final size:20
Alignment explanation
Indices: 2549635--2549834 Score: 85
Period size: 20 Copynumber: 8.8 Consensus size: 20
2549625 AATTTAAAAT
2549635 GCATGAAAGGATCCATTAAG
1 GCATGAAAGGATCCATTAAG
*
2549655 GCATGAAAGGATGCCATAATTTAAAAT
1 GCATGAAAGGAT-CC---A-TT--AAG
*
2549682 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATCCATTAAG
*
2549702 GCATGAAAGGATGCCAAAATTTTAAAAT
1 GCATGAAAGGAT-CC---A--TT--AAG
* *
2549730 GCATGAAAGAATGCATTAAG
1 GCATGAAAGGATCCATTAAG
*
2549750 GCATGAAAGGATGCCAAAATTTTAAAAT
1 GCATGAAAGGAT-CC---A--TT--AAG
* *
2549778 CCATGAAAGGATGCATTAAG
1 GCATGAAAGGATCCATTAAG
* *
2549798 GCATGAAAAGATGCATTAAG
1 GCATGAAAGGATCCATTAAG
*
2549818 GAATGAAAGGATGCCAT
1 GCATGAAAGGAT-CCAT
2549835 AATTAAAATG
Statistics
Matches: 137, Mismatches: 19, Indels: 47
0.67 0.09 0.23
Matches are distributed among these distances:
20 69 0.50
21 7 0.05
22 6 0.04
23 1 0.01
24 5 0.04
25 2 0.01
26 5 0.04
27 16 0.12
28 26 0.19
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATCCATTAAG
Found at i:2549735 original size:28 final size:28
Alignment explanation
Indices: 2549702--2549791 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 28
2549692 ATGCATTAAG
2549702 GCATGAAAGGATGCCAAAATTTTAAAAT
1 GCATGAAAGGATGCCAAAATTTTAAAAT
* *
2549730 GCATGAAAGAATG-C---A--TT--AAG
1 GCATGAAAGGATGCCAAAATTTTAAAAT
2549750 GCATGAAAGGATGCCAAAATTTTAAAAT
1 GCATGAAAGGATGCCAAAATTTTAAAAT
*
2549778 CCATGAAAGGATGC
1 GCATGAAAGGATGC
2549792 ATTAAGGCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
20 14 0.29
21 1 0.02
22 2 0.04
24 2 0.04
26 2 0.04
27 1 0.02
28 27 0.55
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.22
Consensus pattern (28 bp):
GCATGAAAGGATGCCAAAATTTTAAAAT
Found at i:2549745 original size:48 final size:47
Alignment explanation
Indices: 2549527--2549811 Score: 435
Period size: 47 Copynumber: 6.0 Consensus size: 47
2549517 AAAATCGAAT
* * *
2549527 CCATAATTTAGAATGCATAAAAGGATGCATTAAGGGATGAAAGGATG
1 CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* ** *
2549574 CCATAATTAAAAATGCATGAAAGGATGCATTAATACATGAAATGATG
1 CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
2549621 CCATAATTTAAAATGCATGAAAGGATCCATTAAGGCATGAAAGGATG
1 CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
2549668 CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
2549715 CCAAAATTTTAAAATGCATGAAAGAATGCATTAAGGCATGAAAGGATG
1 CCATAA-TTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
2549763 CCAAAATTTTAAAATCCATGAAAGGATGCATTAAGGCATGAAAAGATG
1 CCATAA-TTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
2549811 C
1 C
2549812 ATTAAGGAAT
Statistics
Matches: 219, Mismatches: 18, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
47 133 0.61
48 86 0.39
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (47 bp):
CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:2551310 original size:18 final size:18
Alignment explanation
Indices: 2551287--2551322 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2551277 AAAATACCTG
*
2551287 TTATGATTTTAGGGTCAT
1 TTATGATTTCAGGGTCAT
2551305 TTATGATTTCAGGGTCAT
1 TTATGATTTCAGGGTCAT
2551323 CTCAATCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.47
Consensus pattern (18 bp):
TTATGATTTCAGGGTCAT
Found at i:2553321 original size:45 final size:45
Alignment explanation
Indices: 2553248--2553438 Score: 269
Period size: 45 Copynumber: 4.2 Consensus size: 45
2553238 TAATGAACCA
* * *
2553248 ATATGCATGTTCAATTATAGCATCCTTTCATACCAATAATCTATCC
1 ATATGCAT-TTCAATTATGGCATCCTTTCATGCCAATAATCTACCC
*
2553294 ATATGCATTTCAATTATGGCATCCTTTCATGCCAATAATGTACCC
1 ATATGCATTTCAATTATGGCATCCTTTCATGCCAATAATCTACCC
** *
2553339 ATATGCATTTTGATTATGACATCCTTTCATGCCAATAATGC-ACCC
1 ATATGCATTTCAATTATGGCATCCTTTCATGCCAATAAT-CTACCC
2553384 ATATGCATTTCAATTATGGCATCCTTTCATGCCAATAATGC-ACCC
1 ATATGCATTTCAATTATGGCATCCTTTCATGCCAATAAT-CTACCC
*
2553429 ATATGAATTT
1 ATATGCATTT
2553439 TTTTATTCAT
Statistics
Matches: 132, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
45 124 0.94
46 8 0.06
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (45 bp):
ATATGCATTTCAATTATGGCATCCTTTCATGCCAATAATCTACCC
Found at i:2557930 original size:24 final size:24
Alignment explanation
Indices: 2557898--2557954 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
2557888 TTTCTTTTCT
* *
2557898 TTGATTTTTCTTGTTTTGGAGTGC
1 TTGACTTTTCTTCTTTTGGAGTGC
*
2557922 TTGACTTTTCTTCTTTTGGATTGC
1 TTGACTTTTCTTCTTTTGGAGTGC
2557946 TTGACTTTT
1 TTGACTTTT
2557955 TCTTTTCTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.09, C:0.12, G:0.19, T:0.60
Consensus pattern (24 bp):
TTGACTTTTCTTCTTTTGGAGTGC
Found at i:2559296 original size:84 final size:84
Alignment explanation
Indices: 2559155--2559322 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
2559145 ATTGAGCTTT
2559155 CCTTAGTGTTCCATGAGCTGCCATGTTCCTTGTGAGCTGAATTTGATGTCCAAATAATCCACCAA
1 CCTTAGTGTTCCATGAGCTGCCATGTTCCTTGTGAGCTGAATTTGATGTCCAAATAATCCACCAA
2559220 GCTACCCCAACGTGTGCCA
66 GCTACCCCAACGTGTGCCA
2559239 CCTTAGTGTTCCATGAGCTGCCATGTTCCTTGTGAGCTGAATTTGATGTCCAAATAATCCACCAA
1 CCTTAGTGTTCCATGAGCTGCCATGTTCCTTGTGAGCTGAATTTGATGTCCAAATAATCCACCAA
2559304 GCTACCCCAACGTGTGCCA
66 GCTACCCCAACGTGTGCCA
2559323 TGATCCAATG
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (84 bp):
CCTTAGTGTTCCATGAGCTGCCATGTTCCTTGTGAGCTGAATTTGATGTCCAAATAATCCACCAA
GCTACCCCAACGTGTGCCA
Found at i:2561907 original size:17 final size:17
Alignment explanation
Indices: 2561885--2561917 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2561875 AAGATCAAAG
2561885 GACTAAAGTATTACACA
1 GACTAAAGTATTACACA
2561902 GACTAAAGTATTACAC
1 GACTAAAGTATTACAC
2561918 GGACCACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.24
Consensus pattern (17 bp):
GACTAAAGTATTACACA
Found at i:2570492 original size:158 final size:158
Alignment explanation
Indices: 2570261--2570578 Score: 611
Period size: 158 Copynumber: 2.0 Consensus size: 158
2570251 TTCAAATCAA
2570261 TATACTTATAAAAAATAGTGGAAACTTTAACTTATATTAAATATACTGAATAATTTACAGAAATC
1 TATACTTATAAAAAATAGTGGAAACTTTAACTTATATTAAATATACTGAATAATTTACAGAAATC
2570326 CAATAAAAAAGGTTTACAAAATGATAAAAGCATATACAACTTAAACCTTTATTTACACGC-ACAG
66 CAATAAAAAAGGTTTACAAAATGATAAAAGCATATACAACTTAAACCTTTATTTACACGCAACAG
2570390 TGTTTAATATAAAAAAAAAGAACCTACTG
131 TGTTTAATAT-AAAAAAAAGAACCTACTG
2570419 TATACTTATAAAAAATAGTGGAAACTTTAACTTATATTAAATATACTGAATAATTTACAGAAATC
1 TATACTTATAAAAAATAGTGGAAACTTTAACTTATATTAAATATACTGAATAATTTACAGAAATC
2570484 CAATAAAAAAGGTTTACAAAATGATAAAAGCATATACAACTTAAACCTTTATTTACACGCAAACA
66 CAATAAAAAAGGTTTACAAAATGATAAAAGCATATACAACTTAAACCTTTATTTACACGC-AACA
2570549 GTGTTTAATATAAAAAAAAGAACCTACTG
130 GTGTTTAATATAAAAAAAAGAACCTACTG
2570578 T
1 T
2570579 TTAAATTGTT
Statistics
Matches: 158, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
158 125 0.79
159 19 0.12
160 14 0.09
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.30
Consensus pattern (158 bp):
TATACTTATAAAAAATAGTGGAAACTTTAACTTATATTAAATATACTGAATAATTTACAGAAATC
CAATAAAAAAGGTTTACAAAATGATAAAAGCATATACAACTTAAACCTTTATTTACACGCAACAG
TGTTTAATATAAAAAAAAGAACCTACTG
Found at i:2570905 original size:23 final size:22
Alignment explanation
Indices: 2570879--2570932 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
2570869 GTCCCTCAGG
**
2570879 ACCAAATATAATTGTTCTTAAGA
1 ACCAAATATAA-TGTTCCAAAGA
*
2570902 ACCACATAT-ATGTTCCAAAGA
1 ACCAAATATAATGTTCCAAAGA
2570923 ACCAAATATA
1 ACCAAATATA
2570933 TGTCTCGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 17 0.65
22 1 0.04
23 8 0.31
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.28
Consensus pattern (22 bp):
ACCAAATATAATGTTCCAAAGA
Found at i:2570922 original size:21 final size:21
Alignment explanation
Indices: 2570898--2570977 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
2570888 AATTGTTCTT
2570898 AAGAACCACATATATGTTCCA
1 AAGAACCACATATATGTTCCA
* *
2570919 AAGAACCAAATATATG-TCTCG
1 AAGAACCACATATATGTTC-CA
* * **
2570940 AAGGACCTCATATATGTTAAA
1 AAGAACCACATATATGTTCCA
* *
2570961 AAGGATCACATATATGT
1 AAGAACCACATATATGT
2570978 CCCGAAGGGC
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.94
22 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.26
Consensus pattern (21 bp):
AAGAACCACATATATGTTCCA
Found at i:2570957 original size:42 final size:42
Alignment explanation
Indices: 2570906--2570985 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
2570896 TTAAGAACCA
** *
2570906 CATATATGTTCCAAAGAACCAAATATATGTCTCGAAGGACCT
1 CATATATGTTAAAAAGAACCAAATATATGTCCCGAAGGACCT
* * *
2570948 CATATATGTTAAAAAGGATCACATATATGTCCCGAAGG
1 CATATATGTTAAAAAGAACCAAATATATGTCCCGAAGG
2570986 GCAACATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (42 bp):
CATATATGTTAAAAAGAACCAAATATATGTCCCGAAGGACCT
Found at i:2584993 original size:134 final size:133
Alignment explanation
Indices: 2584758--2585192 Score: 351
Period size: 134 Copynumber: 3.3 Consensus size: 133
2584748 CATATCCATC
* * * * * * * * *
2584758 TTTTACAAGATTTGATATT-CCTAAGTGACAGCGGAACAAATCTACCCCAATTCAGTCTTCTCTT
1 TTTTCCAAGATTTGATATTCCCTGAGTGACAGTGAAACAAATCAACCCCGATTCAATCTTCGCTG
**** *
2584822 A-GTAACGGGGGAATGGATCAACTCCCTCAAATTTGATATTCCTTTCAGAAAAAGTAGAACATGT
66 AGGTAA-AACAGAATGGATCAACTCCCT-AAATCTGATATTCCTTTCAGAAAAAGTAGAACATGT
* *
2584886 TCCTC
129 ACCTA
* * * **
2584891 TTTTCCAAGATTTGATATTCCTTGAGTGACAGTGAAATAAGTTTACCCCGATTCAATCTTCGCTG
1 TTTTCCAAGATTTGATATTCCCTGAGTGACAGTGAAACAAATCAACCCCGATTCAATCTTCGCTG
* ** * * **
2584956 A-GTGAAAATAGAATGGATCAACTTCCCTGGATCTGATATTCCCTTCAGAAGAAGCT-GAACAAA
66 AGGT-AAAACAGAATGGATCAAC-TCCCTAAATCTGATATTCCTTTCAGAAAAAG-TAGAACATG
*
2585019 TACCTT
128 TACCTA
* * * * * * **
2585025 TTTTCCAAGATTTGAGATTCCCTGAGTGATAGCGGAACAAATCAACCCCGTTTGAATCTTTTCTG
1 TTTTCCAAGATTTGATATTCCCTGAGTGACAGTGAAACAAATCAACCCCGATTCAATCTTCGCTG
** * * * * *
2585090 AGGTTCAGCGGAATGGATTAACATCCCTATACCTGATATTCCCTTT-AGAAAAAG-AGAAACATG
66 AGGTAAAACAGAATGGATCAAC-TCCCTAAATCTGATATT-CCTTTCAGAAAAAGTAG-AACATG
2585153 TACCTA
128 TACCTA
*
2585159 TTTTTCAAGATTTGATATTCCCTGAGTGACAGTG
1 TTTTCCAAGATTTGATATTCCCTGAGTGACAGTG
2585193 GAGGATCTGA
Statistics
Matches: 237, Mismatches: 57, Indels: 15
0.77 0.18 0.05
Matches are distributed among these distances:
133 19 0.08
134 204 0.86
135 14 0.06
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (133 bp):
TTTTCCAAGATTTGATATTCCCTGAGTGACAGTGAAACAAATCAACCCCGATTCAATCTTCGCTG
AGGTAAAACAGAATGGATCAACTCCCTAAATCTGATATTCCTTTCAGAAAAAGTAGAACATGTAC
CTA
Found at i:2585240 original size:77 final size:78
Alignment explanation
Indices: 2585122--2585272 Score: 225
Period size: 78 Copynumber: 1.9 Consensus size: 78
2585112 ATCCCTATAC
* *
2585122 CTGATATTCCCTTTAGAAAAAGAGAAACATGTACC-TATTTTTCAAGATTTGATATTCCCTGAGT
1 CTGATATTCCCTTCAGAAAAAGAGAAACAAGTACCTTATTTTTCAAGATTTGATATTCCCTGAGT
2585186 GACAGTGGAGGAT
66 GACAGTGGAGGAT
* * *
2585199 CTGATATTCCCTTCAGAAGAAGTGAAACAAGT-CCTTTTTTTTTCAAGATTTGATATTCCCTGAG
1 CTGATATTCCCTTCAGAAAAAGAGAAACAAGTACC-TTATTTTTCAAGATTTGATATTCCCTGAG
*
2585263 TGATAGTGGA
65 TGACAGTGGA
2585273 ACAAGTCTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
76 2 0.03
77 28 0.42
78 36 0.55
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (78 bp):
CTGATATTCCCTTCAGAAAAAGAGAAACAAGTACCTTATTTTTCAAGATTTGATATTCCCTGAGT
GACAGTGGAGGAT
Found at i:2585382 original size:212 final size:211
Alignment explanation
Indices: 2584984--2585401 Score: 475
Period size: 212 Copynumber: 2.0 Consensus size: 211
2584974 CAACTTCCCT
2584984 GGATCTGATATTCCCTTCAGAAGAAGCTGAACAAATACCTTTTTTCCAAGATTTGAGATTCCCTG
1 GGATCTGATATTCCCTTCAGAAGAAGCTGAACAAATACCTTTTTTCCAAGATTTGAGATTCCCTG
* * ** * * * * * *
2585049 AGTGATAGCGGAACAAATCAACCCCGTTTGAATCTTTTCTGAGGTTCAGCGGAATGGATTAACAT
66 AGTGATAGCGGAACAAATCAACCCCGATTCAATCTTCCCTCAGGTACAACGAAATAGATCAACAT
* * * * *
2585114 CCCTATACCTGATATTCCCTTTAGAAAAAGAGAAACATGTACCTATTTTTCAAGATTTGATATTC
131 CCCCATACATGATATTCCATTCAGAAAAAGAGAAACATATACCTATTTTTCAAGATTTGATATTC
*
2585179 CCTGAGTGACAGTGGA
196 CCTAAGTGACAGTGGA
* * *
2585195 GGATCTGATATTCCCTTCAGAAGAAG-TGAAACAAGT-CCTTTTTTTTTCAAGATTTGATATTCC
1 GGATCTGATATTCCCTTCAGAAGAAGCTG-AACAAATACC--TTTTTTCCAAGATTTGAGATTCC
* * ** *
2585258 CTGAGTGATAGTGGAACAAGTCTTCCCCGATTCAATCTTCCCTCAGGTACAACGAAATATATCAA
63 CTGAGTGATAGCGGAACAAATCAACCCCGATTCAATCTTCCCTCAGGTACAACGAAATAGATCAA
* * * * ** * *
2585323 C-TCCCCCATATATGATATTCCATTCAGAAGAAGCGGAATTTATCCCT-TTTTTCCAAGATTTGT
128 CAT-CCCCATACATGATATTCCATTCAGAAAAAGAGAAACATATACCTATTTTT-CAAGATTTGA
2585386 TATTCCCTAAGTGACA
191 TATTCCCTAAGTGACA
2585402 CTGAACAAGT
Statistics
Matches: 170, Mismatches: 32, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
210 4 0.02
211 38 0.22
212 128 0.75
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (211 bp):
GGATCTGATATTCCCTTCAGAAGAAGCTGAACAAATACCTTTTTTCCAAGATTTGAGATTCCCTG
AGTGATAGCGGAACAAATCAACCCCGATTCAATCTTCCCTCAGGTACAACGAAATAGATCAACAT
CCCCATACATGATATTCCATTCAGAAAAAGAGAAACATATACCTATTTTTCAAGATTTGATATTC
CCTAAGTGACAGTGGA
Found at i:2585561 original size:263 final size:266
Alignment explanation
Indices: 2585196--2585839 Score: 673
Period size: 263 Copynumber: 2.4 Consensus size: 266
2585186 GACAGTGGAG
* ** *
2585196 GATCTGATATTCCCTTCAGAAGAAGTGAAACAAGTCCTTTTTTTTTCAAGATTTGATATTCCCTG
1 GATCTGATATTCCCTTCAGAAGAAGTGAAACAAGTCCTCTCCTTTCCAAGATTTGATATTCCC--
* * * *
2585261 AGTGATAGTGGAACAAGTCTTCCCCGATTCAATCTTCCCTC-AG-GTACAACGAAAT-ATATCAA
64 -GTGACAGTAGAACAAGTATACCCCGATTCAATCTTCCC-CGAGTG-ACAACGAAATGA-ATCAA
* ** * * *
2585323 CTCCCCCATATATGATATTCCATTCAGAAGAAGCGGAATTTATCCCTTTTTTCCAAGATTTGTTA
125 CTCCCCCAAATATGATATTCCATTCAGAAGAAGCGGAACATATACCTCTTTTCCAAGATTTGATA
* * * ***
2585388 TTCCCTAAGTGACA-CTGAACAAGTCTACCCTGATTCAATCTTCCCTGAGTGATAGTGGAATGGA
190 TTCCCTAAGTGACAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAACAGAATGGA
2585452 TCAACTC-CTCAA
255 TCAACTCTCT-AA
***
2585464 GATCTGATATTCCCTTCAGAAGAAGCTG-AATGGGTCC-CTCCTTTCCAAGATTTGATATTCCC-
1 GATCTGATATTCCCTTCAGAAGAAG-TGAAACAAGTCCTCTCCTTTCCAAGATTTGATATTCCCG
* *
2585526 TGACAGTAGAACAAGTATACCCCGATTCAATCTTCCCCGAGTGACAACGGAATGAATCAACTCCT
65 TGACAGTAGAACAAGTATACCCCGATTCAATCTTCCCCGAGTGACAACGAAATGAATCAACTCCC
* * * * *
2585591 CTAAATCTGATATTCCCTTCAGAAGAAGCGGGACATATACCTCTTTTCCAAGATTTGATATTCTC
130 CCAAATATGATATTCCATTCAGAAGAAGCGGAACATATACCTCTTTTCCAAGATTTGATATTCCC
* * * * *
2585656 TGAGTGATAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGGGTGACAACAGAATGTATCAAC
195 TAAGTGACAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAACAGAATGGATCAAC
**
2585721 TCTCTTG
260 TCTCTAA
* * *
2585728 GATATGATATTCCCTTCAGAAAAAAT-AGAACATA-TACCTCT-CTTT-CAAGATTTGATATTCC
1 GATCTGATATTCCCTTCAGAAGAAGTGA-AACA-AGT-CCTCTCCTTTCCAAGATTTGATATTCC
* * * * *
2585789 CTGAGTGATAGTGGAAGAAGTCTACCCCGATTCAATCTTCCCTGAGTGACA
63 C---GTGACAGTAGAACAAGTATACCCCGATTCAATCTTCCCCGAGTGACA
2585840 GCATAATGGA
Statistics
Matches: 313, Mismatches: 48, Indels: 30
0.80 0.12 0.08
Matches are distributed among these distances:
262 1 0.00
263 115 0.37
264 92 0.29
265 8 0.03
266 2 0.01
267 21 0.07
268 72 0.23
269 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (266 bp):
GATCTGATATTCCCTTCAGAAGAAGTGAAACAAGTCCTCTCCTTTCCAAGATTTGATATTCCCGT
GACAGTAGAACAAGTATACCCCGATTCAATCTTCCCCGAGTGACAACGAAATGAATCAACTCCCC
CAAATATGATATTCCATTCAGAAGAAGCGGAACATATACCTCTTTTCCAAGATTTGATATTCCCT
AAGTGACAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAACAGAATGGATCAACT
CTCTAA
Found at i:2585721 original size:134 final size:133
Alignment explanation
Indices: 2585197--2585875 Score: 669
Period size: 134 Copynumber: 5.1 Consensus size: 133
2585187 ACAGTGGAGG
* * * *
2585197 ATCTGATATTCCCTTCAGAAGAAGTGAAACA-AGT-CCTTTTTTTTTCAAGATTTGATATTCCCT
1 ATCTGATATTCCCTTCAGAAGAAGCGGAACATA-TACC--TCTTTTCCAAGATTTGATATTCCCT
* * * **
2585260 GAGTGATAGTGGAACAAGTCTTCCCCGATTCAATCTTCCCTCAG-GTACAAC-GAAATATATCAA
63 GAGTGATAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTG-ACAACAG-AATGGATCAA
* *
2585323 CTCCCCCAT
126 CT-CCTCAA
* * ** * * * *
2585332 ATATGATATTCCATTCAGAAGAAGCGGAATTTATCCCTTTTTTCCAAGATTTGTTATTCCCTAAG
1 ATCTGATATTCCCTTCAGAAGAAGCGGAACATATACCTCTTTTCCAAGATTTGATATTCCCTGAG
* * * * ***
2585397 TGACA-CTGAACAAGTCTACCCTGATTCAATCTTCCCTGAGTGATAGTGGAATGGATCAACTCCT
66 TGATAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAACAGAATGGATCAACTCCT
2585461 CAA
131 CAA
* **** * *
2585464 GATCTGATATTCCCTTCAGAAGAAGCTGAATGGGTCCCTCCTTTCCAAGATTTGATATTCCCTGA
1 -ATCTGATATTCCCTTCAGAAGAAGCGGAACATATACCTCTTTTCCAAGATTTGATATTCCCTGA
** * * * *
2585529 CAG-TA---GAACAAGTATACCCCGATTCAATCTTCCCCGAGTGACAACGGAATGAATCAACTCC
65 GTGATAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAACAGAATGGATCAACTCC
2585590 TCTAA
130 TC-AA
* *
2585595 ATCTGATATTCCCTTCAGAAGAAGCGGGACATATACCTCTTTTCCAAGATTTGATATTCTCTGAG
1 ATCTGATATTCCCTTCAGAAGAAGCGGAACATATACCTCTTTTCCAAGATTTGATATTCCCTGAG
* * *
2585660 TGATAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGGGTGACAACAGAATGTATCAACTCTC
66 TGATAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAACAGAATGGATCAACTC-C
***
2585725 TTGG
130 TCAA
* * ***
2585729 ATATGATATTCCCTTCAGAAAAAATAGAACATATACCTCTCTTT-CAAGATTTGATATTCCCTGA
1 ATCTGATATTCCCTTCAGAAGAAGCGGAACATATACCTCT-TTTCCAAGATTTGATATTCCCTGA
* * * *
2585793 GTGATAGTGGAAGAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCATAATGGATCAACATC
65 GTGATAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAACAGAATGGATCAAC-TC
*
2585858 C-CAG
129 CTCAA
2585862 ATCTGATATTCCCT
1 ATCTGATATTCCCT
2585876 GAGTGACAGC
Statistics
Matches: 452, Mismatches: 79, Indels: 28
0.81 0.14 0.05
Matches are distributed among these distances:
130 107 0.24
131 4 0.01
132 5 0.01
133 111 0.25
134 189 0.42
135 33 0.07
136 3 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (133 bp):
ATCTGATATTCCCTTCAGAAGAAGCGGAACATATACCTCTTTTCCAAGATTTGATATTCCCTGAG
TGATAGCGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAACAGAATGGATCAACTCCT
CAA
Found at i:2586137 original size:23 final size:23
Alignment explanation
Indices: 2586107--2586152 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2586097 TACAAAGGGT
*
2586107 CATCTGA-CCGAAACCCGGAGCC
1 CATCTGACCCAAAACCCGGAGCC
*
2586129 CATCATGACCCAAAACCTGGAGCC
1 CATC-TGACCCAAAACCCGGAGCC
2586153 TAGAGACAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 3 0.15
24 13 0.65
ACGTcount: A:0.30, C:0.39, G:0.20, T:0.11
Consensus pattern (23 bp):
CATCTGACCCAAAACCCGGAGCC
Found at i:2586849 original size:20 final size:20
Alignment explanation
Indices: 2586824--2586868 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
2586814 TTTTAGGTCC
*
2586824 AGATCTAGTTCTAGGGTGTT
1 AGATCTAGTGCTAGGGTGTT
2586844 AGATCTAGTGCTAGGGTGTT
1 AGATCTAGTGCTAGGGTGTT
2586864 AGATC
1 AGATC
2586869 GAGGTGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.11, G:0.31, T:0.36
Consensus pattern (20 bp):
AGATCTAGTGCTAGGGTGTT
Found at i:2590724 original size:16 final size:16
Alignment explanation
Indices: 2590703--2590752 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
2590693 AACAACTAGG
*
2590703 ATGCAATAAAATAAAA
1 ATGCAATAACATAAAA
* *
2590719 ATGCAATGACA-AAAT
1 ATGCAATAACATAAAA
*
2590734 ATGCAACAACATAAAA
1 ATGCAATAACATAAAA
2590750 ATG
1 ATG
2590753 ATCATGCTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.18
Consensus pattern (16 bp):
ATGCAATAACATAAAA
Found at i:2590951 original size:30 final size:31
Alignment explanation
Indices: 2590917--2590978 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 31
2590907 TTCCTCTTAT
2590917 TTTTC-TTTTTTCACTAGCCTCTCTAGTAGG
1 TTTTCTTTTTTTCACTAGCCTCTCTAGTAGG
2590947 TTTTCTTTTTTTTCACTAGCCTCTCTAGTAGG
1 TTTTC-TTTTTTTCACTAGCCTCTCTAGTAGG
2590979 CTCAGTGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 5 0.17
32 25 0.83
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.52
Consensus pattern (31 bp):
TTTTCTTTTTTTCACTAGCCTCTCTAGTAGG
Found at i:2591253 original size:24 final size:24
Alignment explanation
Indices: 2591221--2591267 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2591211 TGACTACATT
2591221 TGTAGTAGTCACAATTGGCTCATC
1 TGTAGTAGTCACAATTGGCTCATC
2591245 TGTAGTAGTCACAATTGGCTCAT
1 TGTAGTAGTCACAATTGGCTCAT
2591268 TCTCATGCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (24 bp):
TGTAGTAGTCACAATTGGCTCATC
Found at i:2592660 original size:21 final size:21
Alignment explanation
Indices: 2592635--2592681 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
2592625 CACCCATGCA
*
2592635 ATGAGTGCTCATTTTCTCTCG
1 ATGAGTGCTCATTTTCCCTCG
*
2592656 ATGAGTGCTCCTTTTCCCTCG
1 ATGAGTGCTCATTTTCCCTCG
2592677 ATGAG
1 ATGAG
2592682 AGCTTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (21 bp):
ATGAGTGCTCATTTTCCCTCG
Found at i:2592690 original size:21 final size:21
Alignment explanation
Indices: 2592635--2592691 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
2592625 CACCCATGCA
* * *
2592635 ATGAGTGCTCATTTTCTCTCG
1 ATGAGAGCTCCTTTTCCCTCG
*
2592656 ATGAGTGCTCCTTTTCCCTCG
1 ATGAGAGCTCCTTTTCCCTCG
*
2592677 ATGAGAGCTTCTTTT
1 ATGAGAGCTCCTTTT
2592692 TCTTCTCCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (21 bp):
ATGAGAGCTCCTTTTCCCTCG
Found at i:2607548 original size:13 final size:14
Alignment explanation
Indices: 2607526--2607557 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
2607516 CCTTTTTTCT
2607526 TTTTTATTATTTTA
1 TTTTTATTATTTTA
2607540 TTTTT-TTATTTTA
1 TTTTTATTATTTTA
2607553 TTTTT
1 TTTTT
2607558 GATGAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTATTATTTTA
Found at i:2613746 original size:20 final size:20
Alignment explanation
Indices: 2613710--2613758 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2613700 TCAAAATAAT
*
2613710 TTTTCAAAATTTCA-TTTTG
1 TTTTCAAAATTCCATTTTTG
2613729 CTTTTCAAAA-TCCAATTTTTG
1 -TTTTCAAAATTCC-ATTTTTG
2613750 TTTTCAAAA
1 TTTTCAAAA
2613759 GAAAATCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 2 0.08
20 19 0.73
21 5 0.19
ACGTcount: A:0.31, C:0.14, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTTG
Found at i:2615132 original size:131 final size:131
Alignment explanation
Indices: 2614961--2615272 Score: 310
Period size: 131 Copynumber: 2.4 Consensus size: 131
2614951 TCGTGCATTA
* * ** * *** *
2614961 TTAAAACATTCATTTA-TGACCCCAATTTAAATAAAGAGATATTACTATTTTGTCTTAA-AATTC
1 TTAAAACAGTCATTTATTG-CTCCAATCAAAATGAAGAGATATTACTATTCCATCCTAAGAA-TC
* * * * * * *
2615024 AATATCGATTCGAGTA-AGAACGATAATATCTAATGACTTCCAATCAAGAATAAATGACATCTTA
64 AATATCAATTCGAG-AGAAAACAAAAATATCAAATGACTTCAAATCAAGAATAAATGACATCTCA
2615088 TACC
128 TACC
*
2615092 TTAAAACAGTCATTTATTGCTCCAATCAAAATGAAGAGATATCACTATTCCATCCTAAGAATCAA
1 TTAAAACAGTCATTTATTGCTCCAATCAAAATGAAGAGATATTACTATTCCATCCTAAGAATCAA
* * * * *
2615157 TATTAATTCGAGAGAAAACAAAAATATCAAATTATTTCAAATCGAGAATAAATGACCTCTCATAC
66 TATCAATTCGAGAGAAAACAAAAATATCAAATGACTTCAAATCAAGAATAAATGACATCTCATAC
2615222 C
131 C
* ** *
2615223 TTAAAGCAGTCATTTATCACT-CAGA-CTAAAATGAAAAGATATTACTATTC
1 TTAAAACAGTCATTTATTGCTCCA-ATC-AAAATGAAGAGATATTACTATTC
2615273 TCAATATCGA
Statistics
Matches: 149, Mismatches: 27, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
130 4 0.03
131 141 0.95
132 4 0.03
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (131 bp):
TTAAAACAGTCATTTATTGCTCCAATCAAAATGAAGAGATATTACTATTCCATCCTAAGAATCAA
TATCAATTCGAGAGAAAACAAAAATATCAAATGACTTCAAATCAAGAATAAATGACATCTCATAC
C
Found at i:2616302 original size:108 final size:108
Alignment explanation
Indices: 2616083--2616284 Score: 248
Period size: 108 Copynumber: 1.9 Consensus size: 108
2616073 TCGAAATGTA
* * * * *
2616083 AAAACATGCTAAAGATACGAGGACTAAATAGAAATTAAACCATAAAAATATAGCATGCATAAGAA
1 AAAACATGCTAAAGATACGAGAACTAAACAGAAATTAAAACATAAAAACATAACATGCATAAGAA
* *
2616148 ATGAGTAAATTACAGAAAGGTCCCTACCGGTAACTAACATACC
66 ATGAGTAAATTACAGAAAGGTCCCTACAGGTAACCAACATACC
* *
2616191 AAAACATGCTAAAGTTAGCG-GAACTAAACA-ACAATTAAAACATAAATACATAACATGCATAAG
1 AAAACATGCTAAAGATA-CGAGAACTAAACAGA-AATTAAAACATAAAAACATAACATGCATAAG
* *
2616254 AAATGGGTAAATTATA-AAACTGGTCCCTACA
64 AAATGAGTAAATTACAGAAA--GGTCCCTACA
2616285 TGTGACCATT
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
107 4 0.05
108 65 0.81
109 11 0.14
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (108 bp):
AAAACATGCTAAAGATACGAGAACTAAACAGAAATTAAAACATAAAAACATAACATGCATAAGAA
ATGAGTAAATTACAGAAAGGTCCCTACAGGTAACCAACATACC
Found at i:2617312 original size:3 final size:3
Alignment explanation
Indices: 2617306--2617361 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
2617296 AACAACGATG
2617306 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2617354 ATA A-A ATA
1 ATA ATA ATA
2617362 TTGGGATGAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2618010 original size:134 final size:134
Alignment explanation
Indices: 2617785--2618044 Score: 405
Period size: 134 Copynumber: 1.9 Consensus size: 134
2617775 AGACATATGC
* * *
2617785 GTTCCACTGTTACTCATGAAATATCAAATCTTGAAAGAGAGGGATCTATTCCACTTTTTCTTGAG
1 GTTCCACTGTTACTCAGGAAATATCAAATCTTAAAAGAGAGGGATCTATTCCACTTCTTCTTGAG
* * * *
2617850 GGAAAATCATATATGTGGACGTTGATTCATTCCACTGTTACTTAGGGAAGATTTAATCGAGGCAG
66 GGAAAATCAGATATGGGGACGTTGATTCATTCAACTGTTACTCAGGGAAGATTTAATCGAGGCAG
2617915 ACTT
131 ACTT
* * *
2617919 GTTCCA-TCGTTACTCAGGGAATATCAAATCTTAAAAGAGAGGGATTTGTTCCACTTCTTCTTGA
1 GTTCCACT-GTTACTCAGGAAATATCAAATCTTAAAAGAGAGGGATCTATTCCACTTCTTCTTGA
*
2617983 GGGAAAATCAGATCTGGGGACGTTGATTCATTCAACTGTTACTCAGGGAAGATTTAATCGAG
65 GGGAAAATCAGATATGGGGACGTTGATTCATTCAACTGTTACTCAGGGAAGATTTAATCGAG
2618045 TTCGATTTGC
Statistics
Matches: 114, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
133 1 0.01
134 113 0.99
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (134 bp):
GTTCCACTGTTACTCAGGAAATATCAAATCTTAAAAGAGAGGGATCTATTCCACTTCTTCTTGAG
GGAAAATCAGATATGGGGACGTTGATTCATTCAACTGTTACTCAGGGAAGATTTAATCGAGGCAG
ACTT
Found at i:2621491 original size:22 final size:22
Alignment explanation
Indices: 2621430--2621492 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
2621420 CATTTATTTT
2621430 ATTTTTC-CTTTT-TCTTTCTC
1 ATTTTTCTCTTTTCTCTTTCTC
2621450 ATTTTT-TCTTATTCGT-TTTCT-
1 ATTTTTCTCTT-TTC-TCTTTCTC
2621471 ATATTTTCTCTTTTCTCTTTCT
1 AT-TTTTCTCTTTTCTCTTTCT
2621493 TTTTCCCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
20 9 0.25
21 5 0.14
22 17 0.47
23 5 0.14
ACGTcount: A:0.08, C:0.21, G:0.02, T:0.70
Consensus pattern (22 bp):
ATTTTTCTCTTTTCTCTTTCTC
Found at i:2621512 original size:43 final size:42
Alignment explanation
Indices: 2621457--2621567 Score: 114
Period size: 43 Copynumber: 2.6 Consensus size: 42
2621447 CTCATTTTTT
* **
2621457 CTTATTCGTTTTCTATATTTTCTCTTTTCTCTTTCTTTTTCC
1 CTTATTCTTTTTCTATATTTTCTCTTTTCTCCCTCTTTTTCC
* * * * * *
2621499 CATTCTTCTTTTTCTATCCTTTTTTATTTTTTCCCTCTTTTTTC
1 C-TTATTCTTTTTCTAT-ATTTTCTCTTTTCTCCCTCTTTTTCC
*
2621543 CTTATTCTTTTTCAATATTTTCTCT
1 CTTATTCTTTTTCTATATTTTCTCT
2621568 CTCTCTCTCT
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
42 7 0.13
43 26 0.49
44 20 0.38
ACGTcount: A:0.09, C:0.23, G:0.01, T:0.67
Consensus pattern (42 bp):
CTTATTCTTTTTCTATATTTTCTCTTTTCTCCCTCTTTTTCC
Found at i:2627081 original size:42 final size:42
Alignment explanation
Indices: 2627022--2627107 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
2627012 GCGAACAAGT
2627022 AATATAATGATAACTGAGTATTGTCTCCACTGGGATTGGTGG
1 AATATAATGATAACTGAGTATTGTCTCCACTGGGATTGGTGG
2627064 AATATAATGATAACTGAGTATTGTCTCCACTGGGATTGGTGG
1 AATATAATGATAACTGAGTATTGTCTCCACTGGGATTGGTGG
2627106 AA
1 AA
2627108 ATTTATGAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.33
Consensus pattern (42 bp):
AATATAATGATAACTGAGTATTGTCTCCACTGGGATTGGTGG
Found at i:2627666 original size:18 final size:19
Alignment explanation
Indices: 2627631--2627667 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2627621 CACGGAATGT
2627631 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
2627651 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
2627668 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:2627886 original size:37 final size:37
Alignment explanation
Indices: 2627813--2627887 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
2627803 GTTTGAAAAT
*
2627813 ATTTATATATTTTCTTTAAAAAATTCAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTCAAAATCATAAA
* * *
2627850 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTCAAAATCATAAA
2627887 A
1 A
2627888 AAGGTTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTCAAAATCATAAA
Found at i:2633495 original size:48 final size:45
Alignment explanation
Indices: 2633431--2633529 Score: 117
Period size: 48 Copynumber: 2.1 Consensus size: 45
2633421 ATATTAAGAC
* * *
2633431 TATTATTTTATAAATTATATTAATTAATTAATTTAATAATAATAATAA
1 TATTATGTTATAAATTATATGAATTAATT-A-TTAA-AATAAAAATAA
* * *
2633479 TATTATGTTATTAATTATATGAATTAGTTATTAAAATAAAAATAT
1 TATTATGTTATAAATTATATGAATTAATTATTAAAATAAAAATAA
2633524 TATTAT
1 TATTAT
2633530 AACATTAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
45 15 0.33
46 4 0.09
47 1 0.02
48 25 0.56
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (45 bp):
TATTATGTTATAAATTATATGAATTAATTATTAAAATAAAAATAA
Found at i:2633678 original size:47 final size:51
Alignment explanation
Indices: 2633601--2633710 Score: 115
Period size: 47 Copynumber: 2.2 Consensus size: 51
2633591 TTTAATAGTT
* *
2633601 TAATAGTATTAT-TTTATGAAATTGATAAATAAAAT-TAAT-TA-TATTA-A
1 TAATA-TATTATATTTATGAAAATGAAAAATAAAATGTAATATATTATTATA
* *
2633648 TAATATATTATATATTATGAAAAT-AAAAATATAATGTCATATATTATTATA
1 TAATATATTATAT-TTATGAAAATGAAAAATAAAATGTAATATATTATTATA
*
2633699 TAATTTATTATA
1 TAATATATTATA
2633711 ACTTATTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
46 6 0.12
47 15 0.29
48 12 0.23
49 2 0.04
50 5 0.10
51 12 0.23
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (51 bp):
TAATATATTATATTTATGAAAATGAAAAATAAAATGTAATATATTATTATA
Found at i:2636205 original size:21 final size:21
Alignment explanation
Indices: 2636171--2636328 Score: 77
Period size: 24 Copynumber: 7.0 Consensus size: 21
2636161 AAACTATATA
* * *
2636171 ATATATTATATTTTCAAAATC
1 ATATAATATGTTTTCAAAAAC
* *
2636192 ATATAATATGTTTTCAAATTTAT
1 ATATAATATGTTTTCAAA--AAC
* *
2636215 ATAACAATATGTTTTTAAAAAC
1 AT-ATAATATGTTTTCAAAAAC
*
2636237 -TATACTATATATTTT-AAAAAC
1 ATATA--ATATGTTTTCAAAAAC
*
2636258 TATATATTATGTTTTCAAAAAC
1 -ATATAATATGTTTTCAAAAAC
* *
2636280 TATACTATATATTTTTTAAAAAAC
1 -ATA-TA-ATATGTTTTCAAAAAC
*
2636304 TATATTATATATGCTTTCCAAAAAC
1 -ATA-TA-ATATG-TTTTCAAAAAC
2636329 CATTTTTTAA
Statistics
Matches: 106, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.02
21 30 0.28
22 19 0.18
23 8 0.08
24 38 0.36
25 9 0.08
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (21 bp):
ATATAATATGTTTTCAAAAAC
Found at i:2636326 original size:24 final size:24
Alignment explanation
Indices: 2636221--2636328 Score: 127
Period size: 24 Copynumber: 4.7 Consensus size: 24
2636211 TTATATAACA
*
2636221 ATATGTTTTTAAAAACTATACTAT
1 ATATGTTTTCAAAAACTATACTAT
2636245 ATA--TTTT-AAAAACTATA-TAT
1 ATATGTTTTCAAAAACTATACTAT
2636265 -TATGTTTTCAAAAACTATACTAT
1 ATATGTTTTCAAAAACTATACTAT
* * *
2636288 ATATTTTTTAAAAAACTATATTAT
1 ATATGTTTTCAAAAACTATACTAT
*
2636312 ATATGCTTTCCAAAAAC
1 ATATG-TTTTCAAAAAC
2636329 CATTTTTTAA
Statistics
Matches: 72, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
19 2 0.03
20 3 0.04
21 14 0.19
22 14 0.19
23 3 0.04
24 27 0.38
25 9 0.12
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (24 bp):
ATATGTTTTCAAAAACTATACTAT
Found at i:2637395 original size:14 final size:15
Alignment explanation
Indices: 2637378--2637406 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2637368 ACAATCTTGA
2637378 TTTGATTCT-TAATT
1 TTTGATTCTCTAATT
2637392 TTTGATTCTCTAATT
1 TTTGATTCTCTAATT
2637407 CCTCAATGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.10, G:0.07, T:0.62
Consensus pattern (15 bp):
TTTGATTCTCTAATT
Found at i:2638806 original size:96 final size:96
Alignment explanation
Indices: 2638642--2638833 Score: 384
Period size: 96 Copynumber: 2.0 Consensus size: 96
2638632 CTAATGAAAA
2638642 TGAGGTTGCCACAGTCGAAGTCAACCCTCAAGTTCGATAAGCTAACAAGGCAAAAGGTAACTTAT
1 TGAGGTTGCCACAGTCGAAGTCAACCCTCAAGTTCGATAAGCTAACAAGGCAAAAGGTAACTTAT
2638707 TATGCCAATCTTTGTATGTCTCATCCGTTTT
66 TATGCCAATCTTTGTATGTCTCATCCGTTTT
2638738 TGAGGTTGCCACAGTCGAAGTCAACCCTCAAGTTCGATAAGCTAACAAGGCAAAAGGTAACTTAT
1 TGAGGTTGCCACAGTCGAAGTCAACCCTCAAGTTCGATAAGCTAACAAGGCAAAAGGTAACTTAT
2638803 TATGCCAATCTTTGTATGTCTCATCCGTTTT
66 TATGCCAATCTTTGTATGTCTCATCCGTTTT
2638834 CTCAACTATT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (96 bp):
TGAGGTTGCCACAGTCGAAGTCAACCCTCAAGTTCGATAAGCTAACAAGGCAAAAGGTAACTTAT
TATGCCAATCTTTGTATGTCTCATCCGTTTT
Found at i:2653664 original size:21 final size:21
Alignment explanation
Indices: 2653637--2653687 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
2653627 AATTAGGGTT
*
2653637 AAAATAAAAT-AGAATTTAAA
1 AAAATAAAATAAAAATTTAAA
*
2653657 AAAGATAAGATAAAAATTTAAA
1 AAA-ATAAAATAAAAATTTAAA
2653679 AAAATAAAA
1 AAAATAAAA
2653688 AATTTAAGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 3 0.12
21 11 0.42
22 12 0.46
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.22
Consensus pattern (21 bp):
AAAATAAAATAAAAATTTAAA
Found at i:2654956 original size:22 final size:22
Alignment explanation
Indices: 2654931--2655123 Score: 81
Period size: 22 Copynumber: 8.4 Consensus size: 22
2654921 ATAATAAGCT
2654931 TAATATATATTTAAAAACTATA
1 TAATATATATTTAAAAACTATA
* *
2654953 TAATAAATTATATTCTCAAAA-TCGTA
1 TAAT--A-TATATT-TAAAAACT-ATA
* * *
2654979 TAATATGT-TTTCAAAATTATA
1 TAATATATATTTAAAAACTATA
* *
2655000 TAACAATATGTTTTTAAAAA--ATA
1 T---AATATATATTTAAAAACTATA
*
2655023 TACTATATATTTTCAAAAACTATA
1 TAATATATA-TTT-AAAAACTATA
* * *
2655047 TATATTATATGTTTTCAAAATTATA
1 TA-A-TATAT-ATTTAAAAACTATA
* * *
2655072 TAACATGTTTTTAAAAACTATA
1 TAATATATATTTAAAAACTATA
*
2655094 TTATATAT-TTTCAAAAACTATA
1 TAATATATATTT-AAAAACTATA
*
2655116 TTATATAT
1 TAATATAT
2655124 GTTTTCCAAA
Statistics
Matches: 134, Mismatches: 19, Indels: 36
0.71 0.10 0.19
Matches are distributed among these distances:
20 5 0.04
21 15 0.11
22 47 0.35
23 9 0.07
24 15 0.11
25 24 0.18
26 19 0.14
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (22 bp):
TAATATATATTTAAAAACTATA
Found at i:2655012 original size:24 final size:24
Alignment explanation
Indices: 2654980--2655076 Score: 99
Period size: 24 Copynumber: 4.0 Consensus size: 24
2654970 AAAATCGTAT
2654980 AATATGTTTTCAAAATTATATAAC
1 AATATGTTTTCAAAATTATATAAC
* *
2655004 AATATGTTTTTAAAA-AATAT-AC
1 AATATGTTTTCAAAATTATATAAC
* * * *
2655026 TATATATTTTCAAAAACTATATATAT
1 AATATGTTTTC-AAAATTATATA-AC
*
2655052 TATATGTTTTCAAAATTATATAAC
1 AATATGTTTTCAAAATTATATAAC
2655076 A
1 A
2655077 TGTTTTTAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
22 10 0.17
23 8 0.14
24 19 0.33
25 10 0.17
26 11 0.19
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (24 bp):
AATATGTTTTCAAAATTATATAAC
Found at i:2655105 original size:69 final size:68
Alignment explanation
Indices: 2654981--2655134 Score: 238
Period size: 69 Copynumber: 2.2 Consensus size: 68
2654971 AAATCGTATA
2654981 ATATGTTTTCAAAATTATATAACAATATGTTTTTAAAAAATATACTATATATTTTCAAAAACTAT
1 ATATGTTTTCAAAATTATATAAC-A-ATGTTTTTAAAAAATATACTATATATTTTCAAAAACTAT
2655046 ATATATT
64 AT-TA-T
* *
2655053 ATATGTTTTCAAAATTATATAAC-ATGTTTTTAAAAACTATATTATATATTTTCAAAAACTATAT
1 ATATGTTTTCAAAATTATATAACAATGTTTTTAAAAAATATACTATATATTTTCAAAAACTATAT
2655117 TAT
66 TAT
2655120 ATATGTTTTCCAAAA
1 ATATGTTTT-CAAAA
2655135 ACCATTTTTA
Statistics
Matches: 79, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
67 10 0.13
68 7 0.09
69 39 0.49
72 23 0.29
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (68 bp):
ATATGTTTTCAAAATTATATAACAATGTTTTTAAAAAATATACTATATATTTTCAAAAACTATAT
TAT
Found at i:2655151 original size:38 final size:37
Alignment explanation
Indices: 2655100--2655171 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 37
2655090 TATATTATAT
2655100 ATTTTCAAAAACTATAT-TATATATGTTTTCCAAAAACC
1 ATTTTCAAAAACTATATAT-TATAT-TTTTCCAAAAACC
*
2655138 ATTTTTAAAAACTATATATTATATTTTTCCAAAA
1 ATTTTCAAAAACTATATATTATATTTTTCCAAAA
2655172 TTGTTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 10 0.31
38 21 0.66
39 1 0.03
ACGTcount: A:0.43, C:0.12, G:0.01, T:0.43
Consensus pattern (37 bp):
ATTTTCAAAAACTATATATTATATTTTTCCAAAAACC
Found at i:2655197 original size:36 final size:35
Alignment explanation
Indices: 2655100--2655207 Score: 107
Period size: 38 Copynumber: 3.0 Consensus size: 35
2655090 TATATTATAT
*
2655100 ATTTTCAAAAACTATATTATATATGTTTTCCAAAAACC
1 ATTTTTAAAAACTATA-TATATAT-TTTTCCAAAAA-C
2655138 ATTTTTAAAAACTATATATTATATTTTTCC-AAAA-
1 ATTTTTAAAAACTATATA-TATATTTTTCCAAAAAC
*
2655172 TTGTTTTAAAATACTATACTATATA-TTTT-CAAAAAC
1 AT-TTTTAAAA-ACTATA-TATATATTTTTCCAAAAAC
2655208 TATATATATT
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
34 2 0.03
35 16 0.26
36 14 0.23
37 10 0.16
38 20 0.32
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.44
Consensus pattern (35 bp):
ATTTTTAAAAACTATATATATATTTTTCCAAAAAC
Found at i:2655205 original size:34 final size:35
Alignment explanation
Indices: 2655101--2655200 Score: 98
Period size: 36 Copynumber: 2.7 Consensus size: 35
2655091 ATATTATATA
*
2655101 TTTTCAAAAACTATAT-TATATATGTTTTCCAAAAACCAT-
1 TTTT-AAAAACTATATAT-TATAT-TTTTCC-AAAA--TTG
2655140 TTTTAAAAACTATATATTATATTTTTCCAAAATTG
1 TTTTAAAAACTATATATTATATTTTTCCAAAATTG
2655175 TTTTAAAATACTATACTA-TATATTTT
1 TTTTAAAA-ACTATA-TATTATATTTT
2655201 CAAAAACTAT
Statistics
Matches: 56, Mismatches: 1, Indels: 11
0.82 0.01 0.16
Matches are distributed among these distances:
34 1 0.02
35 8 0.14
36 18 0.32
37 8 0.14
38 16 0.29
39 5 0.09
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (35 bp):
TTTTAAAAACTATATATTATATTTTTCCAAAATTG
Done.