Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 55 of 276
Found at i:17227848 original size:20 final size:21
Alignment explanation
Indices: 17227823--17227876 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
17227813 TTCAATTAAC
*
17227823 TAACGAAGCTTTAAAA-TTCT
1 TAACGAAACTTTAAAATTTCT
17227843 TAACGAAACTTTAAAATTTCT
1 TAACGAAACTTTAAAATTTCT
*
17227864 TGACGAAACTTTA
1 TAACGAAACTTTA
17227877 CAACTATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (21 bp):
TAACGAAACTTTAAAATTTCT
Found at i:17228441 original size:28 final size:28
Alignment explanation
Indices: 17228402--17228460 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
17228392 ATTTTTGACA
* *
17228402 AAAAGGTCAATT-AGGGGTTATATTGAG
1 AAAAGGTAAATTGAGGGGTTAAATTGAG
*
17228429 AAAAGTGTAAATTGAGGGGTTAAATTGTG
1 AAAAG-GTAAATTGAGGGGTTAAATTGAG
17228458 AAA
1 AAA
17228461 TAAATGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 6 0.22
29 16 0.59
ACGTcount: A:0.41, C:0.02, G:0.29, T:0.29
Consensus pattern (28 bp):
AAAAGGTAAATTGAGGGGTTAAATTGAG
Found at i:17233466 original size:32 final size:33
Alignment explanation
Indices: 17233368--17233480 Score: 108
Period size: 33 Copynumber: 3.5 Consensus size: 33
17233358 GGTGTACATT
* * **
17233368 CCTTTCCAAGTGGTACACACAAAATATACCTTT
1 CCTTTCCAAGTGGTACACACAAAGTATACATAA
* *
17233401 CCTTTTCATA-TGGTATACACAAAGTATAC-TAA
1 CCTTTCCA-AGTGGTACACACAAAGTATACATAA
*
17233433 CCTTTCCAAGT-GTACACACAAAGTGTACATAA
1 CCTTTCCAAGTGGTACACACAAAGTATACATAA
*
17233465 CCCTTT-CAAGTTGTAC
1 -CCTTTCCAAGTGGTAC
17233481 CATTTGGGTA
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
31 16 0.24
32 17 0.25
33 33 0.49
34 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (33 bp):
CCTTTCCAAGTGGTACACACAAAGTATACATAA
Found at i:17238596 original size:28 final size:29
Alignment explanation
Indices: 17238560--17238624 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
17238550 AAAGTGATTT
* * *
17238560 TTGACAAAAATGTCAATT-AGGGGTTAAA
1 TTGAGAAAAATGTAAATTGAGGGATTAAA
*
17238588 TTGAGAAAAGTGTAAATTGAGGGATTAAA
1 TTGAGAAAAATGTAAATTGAGGGATTAAA
*
17238617 TTGTGAAA
1 TTGAGAAA
17238625 TAAATGAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 15 0.48
29 16 0.52
ACGTcount: A:0.43, C:0.03, G:0.25, T:0.29
Consensus pattern (29 bp):
TTGAGAAAAATGTAAATTGAGGGATTAAA
Found at i:17240749 original size:31 final size:31
Alignment explanation
Indices: 17240708--17240771 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
17240698 CCTTTTCATA
*
17240708 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
17240739 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
17240770 TT
1 TT
17240772 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:17241017 original size:24 final size:24
Alignment explanation
Indices: 17240965--17241130 Score: 239
Period size: 24 Copynumber: 7.0 Consensus size: 24
17240955 GCTTTATCAT
*
17240965 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
17240990 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
17241014 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
17241037 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
17241061 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
17241085 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
17241108 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
17241131 TCACTTCCTC
Statistics
Matches: 129, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
23 43 0.33
24 74 0.57
25 12 0.09
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:17241041 original size:47 final size:48
Alignment explanation
Indices: 17240964--17241130 Score: 241
Period size: 47 Copynumber: 3.5 Consensus size: 48
17240954 TGCTTTATCA
* *
17240964 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTT
1 TATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTT
*
17241013 TATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCGTAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
* *
17241060 GATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC-TTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
*
17241107 AATAACTGGGGCATAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTT
17241131 TCACTTCCTC
Statistics
Matches: 109, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
47 70 0.64
48 26 0.24
49 13 0.12
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (48 bp):
TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
Found at i:17241065 original size:71 final size:71
Alignment explanation
Indices: 17240965--17241130 Score: 262
Period size: 71 Copynumber: 2.3 Consensus size: 71
17240955 GCTTTATCAT
* *
17240965 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAA
17241029 GCCCTTTA
64 GCCCTTTA
* * *
17241037 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC
17241102 CCTTTA
66 CCTTTA
17241108 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
17241131 TCACTTCCTC
Statistics
Matches: 88, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
71 76 0.86
72 12 0.14
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (71 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC
CCTTTA
Found at i:17241246 original size:20 final size:20
Alignment explanation
Indices: 17241180--17241237 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
17241170 TTATGATTAC
*
17241180 ATCACGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
17241200 ATCAGGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
17241220 GTCATGTGTATATCATAC
1 ATCATGTGCATATCATAC
17241238 GTACCATGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:17241315 original size:25 final size:25
Alignment explanation
Indices: 17241283--17241330 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
17241273 ATACATAAAC
* * *
17241283 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
17241308 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
17241331 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:17243006 original size:482 final size:482
Alignment explanation
Indices: 17242101--17243064 Score: 1867
Period size: 482 Copynumber: 2.0 Consensus size: 482
17242091 AAGGCCTATA
17242101 CCCATATTCGGCCACCTCCCTAAACTAGAGGGGTTTCGGCTTTTGGCCAAAAGTTACTCTAGGAA
1 CCCATATTCGGCCACCTCCCTAAACTAGAGGGGTTTCGGCTTTTGGCCAAAAGTTACTCTAGGAA
17242166 TTGTTTAGAGTTCGAGTACTTACCACAGTCTTACTCCTCTTGAATCCGGATGCCTAAAAGGTAAA
66 TTGTTTAGAGTTCGAGTACTTACCACAGTCTTACTCCTCTTGAATCCGGATGCCTAAAAGGTAAA
*
17242231 GGAATTGAACGCCAACAATTGAAAAGGAAGGAAAAGGTTGCTGGTCACAAAGAATCGGCACCCCC
131 GGAATTGAACGCCAACAATTGAAAAGGAAGGAAAAGGCTGCTGGTCACAAAGAATCGGCACCCCC
*
17242296 TATCTTCACTGATTTCGGCTTTTGCGGTATTTCGGTAGAAGTAGAGATTAAGGAAAGAAATAATA
196 TATCTTCACTGATTTCGGCTTTTGCGGTATTTCGGCAGAAGTAGAGATTAAGGAAAGAAATAATA
17242361 AATGAGTAGAGGAAAGTAATGGGCTGGTTTTTGAAAAAGAAAAGGGAGAAAAGATGAGAGGAAGG
261 AATGAGTAGAGGAAAGTAATGGGCTGGTTTTTGAAAAAGAAAAGGGAGAAAAGATGAGAGGAAGG
17242426 ATGGAAGATTCGGCTAGGGAAGAAGAAAGAAGAGAAAAACTAAACCAAAAGAGAAAACGGCACAG
326 ATGGAAGATTCGGCTAGGGAAGAAGAAAGAAGAGAAAAACTAAACCAAAAGAGAAAACGGCACAG
17242491 CTAAGACCCTAATGCCGAAATTGCTAACCTAATACCCCTCTACCGAAATCCCCTCTCTAATACCT
391 CTAAGACCCTAATGCCGAAATTGCTAACCTAATACCCCTCTACCGAAATCCCCTCTCTAATACCT
17242556 TCAAATCGGCTAAGCTCTATCCCTTTT
456 TCAAATCGGCTAAGCTCTATCCCTTTT
17242583 CCCATATTCGGCCACCTCCCTAAACTAGAGGGGTTTCGGCTTTTGGCCAAAAGTTACTCTAGGAA
1 CCCATATTCGGCCACCTCCCTAAACTAGAGGGGTTTCGGCTTTTGGCCAAAAGTTACTCTAGGAA
17242648 TTGTTTAGAGTTCGAGTACTTACCACAGTCTTACTCCTCTTGAATCCGGATGCCTAAAAGGTAAA
66 TTGTTTAGAGTTCGAGTACTTACCACAGTCTTACTCCTCTTGAATCCGGATGCCTAAAAGGTAAA
* * *
17242713 GGAATTGAACGCCCATAATTGAAAAGTTAA-GAAAAGGCTGCTGGTCACAAAGAATCGGCACCCC
131 GGAATTGAACGCCAACAATTGAAAAG-GAAGGAAAAGGCTGCTGGTCACAAAGAATCGGCACCCC
17242777 CTATCTTCACTGATTTCGGCTTTTGCGGTATTTCGGCAGAAGTAGAGATTAAGGAAAGAAATAAT
195 CTATCTTCACTGATTTCGGCTTTTGCGGTATTTCGGCAGAAGTAGAGATTAAGGAAAGAAATAAT
17242842 AAATGAGTAGAGGAAAGTAATGGGCTGGTTTTTGAAAAAGAAAAGGGAGAAAAGATGAGAGGAAG
260 AAATGAGTAGAGGAAAGTAATGGGCTGGTTTTTGAAAAAGAAAAGGGAGAAAAGATGAGAGGAAG
17242907 GATGGAAGATTCGGCTAGGGAAGAAGAAAGAAGAGAAAAACTAAACCAAAAGAGAAAACGGCACA
325 GATGGAAGATTCGGCTAGGGAAGAAGAAAGAAGAGAAAAACTAAACCAAAAGAGAAAACGGCACA
17242972 GCTAAGACCCTAATGCCGAAATTGCTAACCTAATACCCCTCTACCGAAATCCCCTCTCTAATACC
390 GCTAAGACCCTAATGCCGAAATTGCTAACCTAATACCCCTCTACCGAAATCCCCTCTCTAATACC
17243037 TTCAAATCGGCTAAGCTCTATCCCTTTT
455 TTCAAATCGGCTAAGCTCTATCCCTTTT
17243065 TCAAATCCCT
Statistics
Matches: 476, Mismatches: 5, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
482 474 1.00
483 2 0.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (482 bp):
CCCATATTCGGCCACCTCCCTAAACTAGAGGGGTTTCGGCTTTTGGCCAAAAGTTACTCTAGGAA
TTGTTTAGAGTTCGAGTACTTACCACAGTCTTACTCCTCTTGAATCCGGATGCCTAAAAGGTAAA
GGAATTGAACGCCAACAATTGAAAAGGAAGGAAAAGGCTGCTGGTCACAAAGAATCGGCACCCCC
TATCTTCACTGATTTCGGCTTTTGCGGTATTTCGGCAGAAGTAGAGATTAAGGAAAGAAATAATA
AATGAGTAGAGGAAAGTAATGGGCTGGTTTTTGAAAAAGAAAAGGGAGAAAAGATGAGAGGAAGG
ATGGAAGATTCGGCTAGGGAAGAAGAAAGAAGAGAAAAACTAAACCAAAAGAGAAAACGGCACAG
CTAAGACCCTAATGCCGAAATTGCTAACCTAATACCCCTCTACCGAAATCCCCTCTCTAATACCT
TCAAATCGGCTAAGCTCTATCCCTTTT
Found at i:17244476 original size:19 final size:19
Alignment explanation
Indices: 17244454--17244501 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
17244444 GCACATACGA
17244454 TTCCACTAATCACACACAG
1 TTCCACTAATCACACACAG
* * * *
17244473 TTCCATTACTCAGACATAG
1 TTCCACTAATCACACACAG
*
17244492 TTCTACTAAT
1 TTCCACTAAT
17244502 AAAACACCAT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.31
Consensus pattern (19 bp):
TTCCACTAATCACACACAG
Found at i:17246506 original size:30 final size:32
Alignment explanation
Indices: 17246457--17246516 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
17246447 TAATAGCCTA
*
17246457 GTGACTTAAATAAAAAATTTT-GAATAGTTCG
1 GTGACTTAAATAAAAAATTTTCAAATAGTTCG
*
17246488 GTGACTTAAAT-GAAAATTTTCAAATAGTT
1 GTGACTTAAATAAAAAATTTTCAAATAGTT
17246517 TAGTGGCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.37
Consensus pattern (32 bp):
GTGACTTAAATAAAAAATTTTCAAATAGTTCG
Found at i:17247328 original size:20 final size:20
Alignment explanation
Indices: 17247303--17247341 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17247293 TGATTAAATA
17247303 AATTTTATAAAAAAAATTAT
1 AATTTTATAAAAAAAATTAT
**
17247323 AATTTTATTTAAAAAATTA
1 AATTTTATAAAAAAAATTA
17247342 GTTCAACCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTTTATAAAAAAAATTAT
Found at i:17255182 original size:49 final size:50
Alignment explanation
Indices: 17255066--17255197 Score: 187
Period size: 49 Copynumber: 2.7 Consensus size: 50
17255056 TAACTTCGAC
* **
17255066 GTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCAAGTGTGTA
1 GTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCAAGTGTGTA
*
17255116 GTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCTCA-TGTGTA
1 GTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTC-AAGTGTGTA
* *
17255165 GTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 GTACTAAGTGCAGGCTACTACGTGTACCAGATA
17255198 GCTTTGGCTA
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
49 41 0.55
50 34 0.45
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (50 bp):
GTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCAAGTGTGTA
Found at i:17257330 original size:15 final size:16
Alignment explanation
Indices: 17257312--17257345 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
17257302 TCTCGTATCA
17257312 TGGATTTCTTTATT-T
1 TGGATTTCTTTATTCT
17257327 TGGATTTCTTTATTCT
1 TGGATTTCTTTATTCT
17257343 TGG
1 TGG
17257346 CTTCTCTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.12, C:0.09, G:0.18, T:0.62
Consensus pattern (16 bp):
TGGATTTCTTTATTCT
Found at i:17262616 original size:12 final size:12
Alignment explanation
Indices: 17262599--17262625 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17262589 GTTAAAGGAG
17262599 TAATGTTTGAAA
1 TAATGTTTGAAA
17262611 TAATGTTTGAAA
1 TAATGTTTGAAA
17262623 TAA
1 TAA
17262626 GGAAATAGAC
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:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (12 bp):
TAATGTTTGAAA
Found at i:17262865 original size:19 final size:19
Alignment explanation
Indices: 17262841--17262877 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
17262831 TTTGGAATGA
17262841 TGTTATTCTGGATTTTTTT
1 TGTTATTCTGGATTTTTTT
17262860 TGTTATTCTGGATTTTTT
1 TGTTATTCTGGATTTTTT
17262878 CTTTGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.05, G:0.16, T:0.68
Consensus pattern (19 bp):
TGTTATTCTGGATTTTTTT
Found at i:17262999 original size:16 final size:15
Alignment explanation
Indices: 17262966--17262996 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
17262956 TCTCGTATCA
17262966 TGGATTTCTTTATTT
1 TGGATTTCTTTATTT
17262981 TGGATTTCTTTATTT
1 TGGATTTCTTTATTT
17262996 T
1 T
17262997 TGGCTTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.06, G:0.13, T:0.68
Consensus pattern (15 bp):
TGGATTTCTTTATTT
Found at i:17264810 original size:23 final size:21
Alignment explanation
Indices: 17264748--17264801 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 21
17264738 AATACCATGG
*
17264748 ATATATTTTTTATATTT-A-T
1 ATATATTATTTATATTTCATT
*
17264767 -TGTATTATTTATATTTCATT
1 ATATATTATTTATATTTCATT
17264787 ATATATTATTTATAT
1 ATATATTATTTATAT
17264802 ATTTTATTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 14 0.48
19 1 0.03
20 1 0.03
21 13 0.45
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
ATATATTATTTATATTTCATT
Found at i:17264834 original size:10 final size:10
Alignment explanation
Indices: 17264769--17264836 Score: 61
Period size: 10 Copynumber: 6.7 Consensus size: 10
17264759 ATATTTATTG
17264769 TATTATT-TA
1 TATTATTATA
17264778 TATTTCATTATA
1 TA-TT-ATTATA
17264790 TATTATTTATA
1 TATTA-TTATA
17264801 TATT-TTAT-
1 TATTATTATA
*
17264809 TACTTATCATA
1 TA-TTATTATA
*
17264820 GATTATTATA
1 TATTATTATA
17264830 TATTATT
1 TATTATT
17264837 CCCTATATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
8 2 0.04
9 8 0.17
10 19 0.40
11 15 0.31
12 4 0.08
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (10 bp):
TATTATTATA
Found at i:17265125 original size:21 final size:21
Alignment explanation
Indices: 17265083--17265132 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
17265073 TATATTTCAT
*
17265083 TTTTTATTTTTTTATTTATTG
1 TTTTTATTTTTTCATTTATTG
*
17265104 TTTTTATTTTTATCCTTT-TTG
1 TTTTTATTTTT-TCATTTATTG
*
17265125 TATTTATT
1 TTTTTATT
17265133 AGATATTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.78
Consensus pattern (21 bp):
TTTTTATTTTTTCATTTATTG
Found at i:17266738 original size:9 final size:9
Alignment explanation
Indices: 17266696--17266822 Score: 130
Period size: 9 Copynumber: 14.1 Consensus size: 9
17266686 ACCATTTCCT
*
17266696 CAAATTCCA
1 CAAATCCCA
*
17266705 GAAATCCCA
1 CAAATCCCA
*
17266714 -AGAATTCCA
1 CA-AATCCCA
*
17266723 GAAATCCCA
1 CAAATCCCA
17266732 CAAATCCCA
1 CAAATCCCA
*
17266741 CAGATCCCA
1 CAAATCCCA
17266750 CAAATCCCA
1 CAAATCCCA
*
17266759 CAAATTCCA
1 CAAATCCCA
*
17266768 CTAATCCCA
1 CAAATCCCA
*
17266777 CAGATCCCA
1 CAAATCCCA
*
17266786 CAAGTCCCA
1 CAAATCCCA
*
17266795 CAGATCCCA
1 CAAATCCCA
*
17266804 CAAGTCCCA
1 CAAATCCCA
*
17266813 AAAATCCCA
1 CAAATCCCA
17266822 C
1 C
17266823 TAATGCCAGG
Statistics
Matches: 95, Mismatches: 21, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
8 1 0.01
9 93 0.98
10 1 0.01
ACGTcount: A:0.40, C:0.39, G:0.06, T:0.14
Consensus pattern (9 bp):
CAAATCCCA
Found at i:17268744 original size:18 final size:18
Alignment explanation
Indices: 17268717--17268752 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17268707 TAAGATTAAA
*
17268717 ATTTTTAAAATCAATAAT
1 ATTTTAAAAATCAATAAT
17268735 ATTTTAAAAATCAATAAT
1 ATTTTAAAAATCAATAAT
17268753 TACTTTTATC
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:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTTAAAAATCAATAAT
Found at i:17270334 original size:19 final size:19
Alignment explanation
Indices: 17270310--17270352 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
17270300 AACCTGCTAG
17270310 ATTTAAAAGTTGAATATAT
1 ATTTAAAAGTTGAATATAT
*
17270329 ATTT--AAGTTTAATATAT
1 ATTTAAAAGTTGAATATAT
*
17270346 ATATAAA
1 ATTTAAA
17270353 GGTGAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
17 15 0.75
19 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (19 bp):
ATTTAAAAGTTGAATATAT
Found at i:17270430 original size:26 final size:23
Alignment explanation
Indices: 17270401--17270449 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 23
17270391 TTGTTATTTT
*
17270401 TTATTTATATTTATATATATACAATA
1 TTATTTAT-TTCAT-TATATA-AATA
17270427 TTATTTATTTCATTATATAAATA
1 TTATTTATTTCATTATATAAATA
17270450 CCTTCAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 6 0.27
25 4 0.18
26 8 0.36
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (23 bp):
TTATTTATTTCATTATATAAATA
Found at i:17271173 original size:3 final size:3
Alignment explanation
Indices: 17271165--17271200 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
17271155 TGATTTCCTT
17271165 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17271201 CTATAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17283780 original size:21 final size:21
Alignment explanation
Indices: 17283754--17283794 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17283744 AGACGAGCAA
* *
17283754 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
17283775 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
17283795 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:17285733 original size:16 final size:16
Alignment explanation
Indices: 17285700--17285733 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17285690 GGAGATTGTT
* *
17285700 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
17285716 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
17285732 AA
1 AA
17285734 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:17287543 original size:17 final size:17
Alignment explanation
Indices: 17287521--17287554 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17287511 AATAATATAA
*
17287521 GATAATTTTTTATTATT
1 GATAATTTATTATTATT
17287538 GATAATTTATTATTATT
1 GATAATTTATTATTATT
17287555 AAATAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
GATAATTTATTATTATT
Found at i:17306705 original size:7 final size:8
Alignment explanation
Indices: 17306690--17306715 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
17306680 AACATTTAAG
17306690 AGAAAAAA
1 AGAAAAAA
17306698 AGAAAAAA
1 AGAAAAAA
17306706 AGAAAAAA
1 AGAAAAAA
17306714 AG
1 AG
17306716 GAAAGGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:17320567 original size:33 final size:33
Alignment explanation
Indices: 17320520--17320606 Score: 122
Period size: 33 Copynumber: 2.7 Consensus size: 33
17320510 GTTTAGGCCG
* * *
17320520 TAGCCTTATTCAGTAACAGAGTAGTCTGGGCTT
1 TAGCCCTATACAGTAACAGAGTAGTCTAGGCTT
*
17320553 TAGCCCTATACAGTAACAGAGCAGTCTAGGCTT
1 TAGCCCTATACAGTAACAGAGTAGTCTAGGCTT
*
17320586 TAGCCCTATA-AGTAGCAGAGT
1 TAGCCCTATACAGTAACAGAGT
17320607 GGGTCCAAGC
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 9 0.19
33 39 0.81
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (33 bp):
TAGCCCTATACAGTAACAGAGTAGTCTAGGCTT
Found at i:17321013 original size:27 final size:27
Alignment explanation
Indices: 17320983--17321052 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
17320973 GGGCATAATC
*
17320983 GTCATTTTA-CCATACAGGGGTATTACG
1 GTCATTTTATCC-TACAGGGGCATTACG
17321010 GTCATTTTATCCTACAGGGGCATTACG
1 GTCATTTTATCCTACAGGGGCATTACG
17321037 GTCATTTTTATCCTAC
1 GTCA-TTTTATCCTAC
17321053 TAGGTTTCAG
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 27 0.68
28 13 0.32
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (27 bp):
GTCATTTTATCCTACAGGGGCATTACG
Found at i:17326897 original size:25 final size:25
Alignment explanation
Indices: 17326868--17326933 Score: 123
Period size: 25 Copynumber: 2.6 Consensus size: 25
17326858 TTAGCCCTCT
17326868 CGAGCTTCCCGTTATATGGTTCTTG
1 CGAGCTTCCCGTTATATGGTTCTTG
17326893 CGAGCTTCCCGTTATATGGTTCTTG
1 CGAGCTTCCCGTTATATGGTTCTTG
*
17326918 CGAGCTTTCCGTTATA
1 CGAGCTTCCCGTTATA
17326934 GCTCTTCGGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.14, C:0.24, G:0.23, T:0.39
Consensus pattern (25 bp):
CGAGCTTCCCGTTATATGGTTCTTG
Found at i:17327047 original size:23 final size:23
Alignment explanation
Indices: 17327013--17327129 Score: 85
Period size: 23 Copynumber: 5.0 Consensus size: 23
17327003 CTCGATATAT
*
17327013 GGCTCTTCGTGAGCTTCCTGATA
1 GGCTCTTCGTGAGCTTCCCGATA
*
17327036 GGCTCTTTGTGAGCTTCCCGATA
1 GGCTCTTCGTGAGCTTCCCGATA
* * *
17327059 GTGCTC-GCTTGAACTTCCCGATATA
1 G-GCTCTTCGTGAGCTTCCCG--ATA
* * * * *
17327084 TAGCTATCCG-GAGCTTCTCGGTA
1 -GGCTCTTCGTGAGCTTCCCGATA
*
17327107 GGCTCTTCGTGAGCTTCTCGATA
1 GGCTCTTCGTGAGCTTCCCGATA
17327130 TGGTTCTTTG
Statistics
Matches: 71, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
22 6 0.08
23 46 0.65
24 4 0.06
25 14 0.20
26 1 0.01
ACGTcount: A:0.15, C:0.26, G:0.25, T:0.33
Consensus pattern (23 bp):
GGCTCTTCGTGAGCTTCCCGATA
Found at i:17336055 original size:44 final size:44
Alignment explanation
Indices: 17336005--17336089 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
17335995 GTATGGGTTT
* ** *
17336005 AGCACTTCTGTGCTTTCTATTTAGTACTTCGGTACTCTTTGATC
1 AGCACTTCTGTGCTATCTATTTAACACTACGGTACTCTTTGATC
* * *
17336049 AGCACTTTTGTGCTATCTGTTTAACACTACGGTGCTCTTTG
1 AGCACTTCTGTGCTATCTATTTAACACTACGGTACTCTTTG
17336090 GTGTGATGTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (44 bp):
AGCACTTCTGTGCTATCTATTTAACACTACGGTACTCTTTGATC
Found at i:17344328 original size:35 final size:35
Alignment explanation
Indices: 17344282--17344352 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
17344272 ATTATCTTGT
*
17344282 ATGTGGAATAATTCATTGAGAAATGACATACCAAC
1 ATGTGGAATAATTCATTGAGAAACGACATACCAAC
17344317 ATGTGGAATAATTCATTGAGAAACGACATACCAAC
1 ATGTGGAATAATTCATTGAGAAACGACATACCAAC
17344352 A
1 A
17344353 AAGGAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (35 bp):
ATGTGGAATAATTCATTGAGAAACGACATACCAAC
Found at i:17344365 original size:35 final size:35
Alignment explanation
Indices: 17344291--17344365 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
17344281 TATGTGGAAT
* * * *
17344291 AATTCATTGAGAAATGACATACCAACATGTGGAAT
1 AATTCATTGAGAAACGACATACCAACAAGTGAAAA
17344326 AATTCATTGAGAAACGACATACCAACAAAG-GAAAA
1 AATTCATTGAGAAACGACATACCAAC-AAGTGAAAA
17344361 AATTC
1 AATTC
17344366 CTTCATATAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 33 0.94
36 2 0.06
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.21
Consensus pattern (35 bp):
AATTCATTGAGAAACGACATACCAACAAGTGAAAA
Found at i:17352036 original size:42 final size:43
Alignment explanation
Indices: 17351933--17352048 Score: 162
Period size: 43 Copynumber: 2.7 Consensus size: 43
17351923 GGAATTAAAA
* **
17351933 AATCCGAGCTCGTTGAGTGGTCTGAGTTTGTGATATATGTGAG
1 AATCCGAGCTCGTTGAGTGGTCCGAGTTCATGATATATGTGAG
* * *
17351976 AATCCGAACTTGTTGAGTGGTCCAAGTTCATGATATATGT-AG
1 AATCCGAGCTCGTTGAGTGGTCCGAGTTCATGATATATGTGAG
*
17352018 CATCCGAGCTCGTTGAGTGGTCCGAGTTCAT
1 AATCCGAGCTCGTTGAGTGGTCCGAGTTCAT
17352049 CATGGATACA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 29 0.46
43 34 0.54
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.33
Consensus pattern (43 bp):
AATCCGAGCTCGTTGAGTGGTCCGAGTTCATGATATATGTGAG
Found at i:17362359 original size:24 final size:24
Alignment explanation
Indices: 17362330--17362425 Score: 62
Period size: 24 Copynumber: 4.3 Consensus size: 24
17362320 ATTTCTTTAG
17362330 TAATTTTATTTTATTTTATCACCT
1 TAATTTTATTTTATTTTATCACCT
* * * * *
17362354 TAATTTT-TATTA-TTAATTATCG
1 TAATTTTATTTTATTTTATCACCT
* *
17362376 TAA---TA--TTATTTTGTCCCCT
1 TAATTTTATTTTATTTTATCACCT
*
17362395 TGATTTTATTTTATTTTATCACCT
1 TAATTTTATTTTATTTTATCACCT
*
17362419 TAGTTTT
1 TAATTTT
17362426 CAAGAAAAAG
Statistics
Matches: 49, Mismatches: 16, Indels: 14
0.62 0.20 0.18
Matches are distributed among these distances:
18 3 0.06
19 7 0.14
22 11 0.22
23 4 0.08
24 24 0.49
ACGTcount: A:0.24, C:0.11, G:0.04, T:0.60
Consensus pattern (24 bp):
TAATTTTATTTTATTTTATCACCT
Found at i:17364075 original size:3 final size:3
Alignment explanation
Indices: 17364067--17364103 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
17364057 ACTTATTACT
*
17364067 ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
17364104 CTTTGGATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:17364571 original size:19 final size:19
Alignment explanation
Indices: 17364529--17364571 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17364519 TTATATTTTT
17364529 AATTTTTCATAAATTATCA
1 AATTTTTCATAAATTATCA
* *
17364548 TATTTTT-ATAATATTATTA
1 AATTTTTCATAA-ATTATCA
17364567 AATTT
1 AATTT
17364572 AAAATACATA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
AATTTTTCATAAATTATCA
Found at i:17365929 original size:20 final size:20
Alignment explanation
Indices: 17365906--17365946 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
17365896 TTGATCATTC
17365906 ATTTTATCTTTTTAAAAATT
1 ATTTTATCTTTTTAAAAATT
17365926 ATTTTATCTTTTTAAAAATT
1 ATTTTATCTTTTTAAAAATT
17365946 A
1 A
17365947 ATATTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTATCTTTTTAAAAATT
Found at i:17365958 original size:21 final size:20
Alignment explanation
Indices: 17365906--17365959 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
17365896 TTGATCATTC
*
17365906 ATTTTATCTTTTTAAAAATT
1 ATTTAATCTTTTTAAAAATT
*
17365926 ATTTTATCTTTTTAAAAATT
1 ATTTAATCTTTTTAAAAATT
17365946 AATATTAAT-TTTTT
1 -AT-TTAATCTTTTT
17365960 TCTAGTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 20 0.65
21 7 0.23
22 4 0.13
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTAATCTTTTTAAAAATT
Found at i:17370233 original size:13 final size:12
Alignment explanation
Indices: 17370203--17370235 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
17370193 TTATTCGCTA
17370203 TATTT-AATATT
1 TATTTAAATATT
17370214 TATTTAAATATT
1 TATTTAAATATT
17370226 TGATTTAAAT
1 T-ATTTAAAT
17370236 GAATCAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 7 0.35
13 8 0.40
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (12 bp):
TATTTAAATATT
Found at i:17370685 original size:17 final size:17
Alignment explanation
Indices: 17370665--17370697 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17370655 AATATCGATA
17370665 TTAACATAA-AAAATATT
1 TTAA-ATAACAAAATATT
17370682 TTAAATAACAAAATAT
1 TTAAATAACAAAATAT
17370698 ATTTTTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAATAACAAAATATT
Found at i:17373493 original size:34 final size:32
Alignment explanation
Indices: 17373452--17373529 Score: 86
Period size: 34 Copynumber: 2.4 Consensus size: 32
17373442 GGGCCCTGCC
* * *
17373452 ATGGTCTTACATTCATAGTGCCATAAACCCAGTT
1 ATGGTCTTACATTCAGAATGCCAT--ACCCAGCT
*
17373486 ATGGTCTTATCA-TCAGAATGCCATAGCCAGCT
1 ATGGTCTTA-CATTCAGAATGCCATACCCAGCT
17373518 ATGGTCTTACAT
1 ATGGTCTTACAT
17373530 ATAAATACCG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
31 2 0.05
32 15 0.39
34 19 0.50
35 2 0.05
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (32 bp):
ATGGTCTTACATTCAGAATGCCATACCCAGCT
Found at i:17373561 original size:101 final size:101
Alignment explanation
Indices: 17373450--17373669 Score: 309
Period size: 101 Copynumber: 2.2 Consensus size: 101
17373440 TAGGGCCCTG
* *
17373450 CCATGGTCTTACATTCATA-GTGCCATAAACCCAGTTATGGTCTTATCATCAGAATGCCATAG-C
1 CCATGGTCTTACGTTCA-AGGTGCCAT-AACCCAGTTATGGTCTTATCATCAAAATGCCATAGCC
*
17373513 CAGCTATGGTCTTACATATAAATACCGCCATGGTCCAA
64 CAGCTATGGTCTTACATATAAATACCACCATGGTCCAA
* * * * * *
17373551 CCATGATCTTACGTTTAAGGTGCCATAACCTAGTTATGGTCTTTTCATTAAAATGTCATAGCCCA
1 CCATGGTCTTACGTTCAAGGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCA
* *
17373616 GCTATGGTCTTACATATAAATACTACCATGGTTCAA
66 GCTATGGTCTTACATATAAATACCACCATGGTCCAA
17373652 CCATGGTCTTACGTTCAA
1 CCATGGTCTTACGTTCAA
17373670 TTCACCTTTT
Statistics
Matches: 104, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
100 31 0.30
101 73 0.70
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (101 bp):
CCATGGTCTTACGTTCAAGGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCA
GCTATGGTCTTACATATAAATACCACCATGGTCCAA
Found at i:17374190 original size:29 final size:29
Alignment explanation
Indices: 17374124--17374191 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
17374114 TCCCTATCAG
* *
17374124 CCCAATTTTTCATTTATTTCACATTTTAAC
1 CCCAATTTTCCA-TTATTTCACAATTTAAC
*
17374154 CACAAATTTTCCA-TATTTCACAATTTAATC
1 C-CCAATTTTCCATTATTTCACAATTTAA-C
17374184 CCCAATTT
1 CCCAATTT
17374192 ACATTTTCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
29 20 0.62
30 3 0.09
31 9 0.28
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (29 bp):
CCCAATTTTCCATTATTTCACAATTTAAC
Found at i:17374254 original size:21 final size:20
Alignment explanation
Indices: 17374226--17374264 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
17374216 CAAAACTTGT
17374226 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
*
17374246 ATAATCTATCATTAAACAT
1 ATAA-CTATCATCAAACAT
17374265 CAAAATAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:17375671 original size:32 final size:32
Alignment explanation
Indices: 17375630--17375693 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
17375620 TTGGTTGAAA
*
17375630 GACATTTTAGTTTTAGTTTAATTTATTTCAAT
1 GACATTTTAGTTTTAGTTTAATGTATTTCAAT
17375662 GACATTTTAGTTTTAGTTTAATGTATTTCAAT
1 GACATTTTAGTTTTAGTTTAATGTATTTCAAT
17375694 TTCTTCGACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.55
Consensus pattern (32 bp):
GACATTTTAGTTTTAGTTTAATGTATTTCAAT
Found at i:17376043 original size:15 final size:15
Alignment explanation
Indices: 17376023--17376052 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17376013 GTCACATCCC
17376023 AAAAATTGGGTTAGT
1 AAAAATTGGGTTAGT
*
17376038 AAAAATTGTGTTAGT
1 AAAAATTGGGTTAGT
17376053 GAACCAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (15 bp):
AAAAATTGGGTTAGT
Found at i:17380290 original size:63 final size:63
Alignment explanation
Indices: 17380115--17380290 Score: 189
Period size: 63 Copynumber: 2.8 Consensus size: 63
17380105 CCCTCATATG
* * ** *
17380115 GCTTGGAAACACGC-CTATGTCCTTCGCCCATGTGACCTTAAATC-CAAATAGTGAGTTACACA
1 GCTTGGAAACACGCTC-ATGTCCCTAGCCCATGTGACCCCAAATCACAAATAATGAGTTACACA
* * * *
17380177 GCCTGGACACACGCTCATATCCCTAGCCCGTGTGACCCCAAAAT-ACAAATAATGAGTTACAC-
1 GCTTGGAAACACGCTCATGTCCCTAGCCCATGTGACCCC-AAATCACAAATAATGAGTTACACA
* * *
17380239 GACTTGGAAACACGCTCATGTCCCTAGCCTATGTGACCCCAATTCATAAATA
1 G-CTTGGAAACACGCTCATGTCCCTAGCCCATGTGACCCCAAATCACAAATA
17380291 GTAACTTACA
Statistics
Matches: 93, Mismatches: 16, Indels: 9
0.79 0.14 0.08
Matches are distributed among these distances:
62 33 0.35
63 60 0.65
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (63 bp):
GCTTGGAAACACGCTCATGTCCCTAGCCCATGTGACCCCAAATCACAAATAATGAGTTACACA
Found at i:17380964 original size:22 final size:23
Alignment explanation
Indices: 17380932--17380975 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
17380922 TTTAACTAAG
* *
17380932 TAAAAATAGAAAGTAAA-TAAAA
1 TAAAAAAAGAAAGAAAACTAAAA
17380954 TAAAAAAAGAAAGAAAACTAAA
1 TAAAAAAAGAAAGAAAACTAAA
17380976 TGATTTACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.14
Consensus pattern (23 bp):
TAAAAAAAGAAAGAAAACTAAAA
Found at i:17380976 original size:22 final size:22
Alignment explanation
Indices: 17380925--17380976 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
17380915 GTCAACATTT
* * *
17380925 AACTAAGTAAAAATAGAAAGTA
1 AACTAAATAAAAAAAGAAAGAA
17380947 AA-TAAAATAAAAAAAGAAAGAA
1 AACT-AAATAAAAAAAGAAAGAA
17380969 AACTAAAT
1 AACTAAAT
17380977 GATTTACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.71, C:0.04, G:0.10, T:0.15
Consensus pattern (22 bp):
AACTAAATAAAAAAAGAAAGAA
Found at i:17383134 original size:34 final size:34
Alignment explanation
Indices: 17383096--17383206 Score: 150
Period size: 34 Copynumber: 3.3 Consensus size: 34
17383086 AAATAAATGT
* * *
17383096 ATATATATTCACCTTCGGTTATATCAAACCATAC
1 ATATATATTCACCTTCGATTATACCAAGCCATAC
* *
17383130 ATATATATTCACTTTCGATTATACCAAGCTATAC
1 ATATATATTCACCTTCGATTATACCAAGCCATAC
* * *
17383164 ATATATAATCACCTTTGATTATGCCAAGCCATAC
1 ATATATATTCACCTTCGATTATACCAAGCCATAC
17383198 ATATATATT
1 ATATATATT
17383207 TATGTACTTC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 66 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.37
Consensus pattern (34 bp):
ATATATATTCACCTTCGATTATACCAAGCCATAC
Found at i:17390310 original size:34 final size:34
Alignment explanation
Indices: 17390267--17390377 Score: 141
Period size: 34 Copynumber: 3.3 Consensus size: 34
17390257 AAAAATGTAT
* * *
17390267 ATATATATTCACCTTCGGTTATATCAAACCATAC
1 ATATATATTCACCTTCGATTATACCAAGCCATAC
* * *
17390301 ATATATATTCACTTTCGATTATACCAAGCTATGC
1 ATATATATTCACCTTCGATTATACCAAGCCATAC
* *
17390335 ATATATAATCACCTTCGATTATGCCAAGCCATAC
1 ATATATATTCACCTTCGATTATACCAAGCCATAC
*
17390369 TTATATATT
1 ATATATATT
17390378 TATTTACTTC
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (34 bp):
ATATATATTCACCTTCGATTATACCAAGCCATAC
Found at i:17395848 original size:27 final size:27
Alignment explanation
Indices: 17395807--17395870 Score: 110
Period size: 27 Copynumber: 2.3 Consensus size: 27
17395797 GTCATTCATT
*
17395807 ATGCAAGTAAGAAACTCAATATAGTGTA
1 ATGCAA-TTAGAAACTCAATATAGTGTA
17395835 ATGCAATTAGAAACTCAATATAGTGTA
1 ATGCAATTAGAAACTCAATATAGTGTA
17395862 ATGCAATTA
1 ATGCAATTA
17395871 CACTACAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 29 0.83
28 6 0.17
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.28
Consensus pattern (27 bp):
ATGCAATTAGAAACTCAATATAGTGTA
Found at i:17398240 original size:6 final size:6
Alignment explanation
Indices: 17398167--17398239 Score: 110
Period size: 6 Copynumber: 12.0 Consensus size: 6
17398157 ATGTACACAG
17398167 ACAGAT ACAGAT ACAGAT ACAGAT ACAGAT ACAGAT ACAGAT ACAGAT
1 ACAGAT ACAGAT ACAGAT ACAGAT ACAGAT ACAGAT ACAGAT ACAGAT
* * *
17398215 CCAGAT TCAGAT AACAGAT TCAGAT
1 ACAGAT ACAGAT -ACAGAT ACAGAT
17398240 TTACGATATG
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
6 57 0.92
7 5 0.08
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (6 bp):
ACAGAT
Found at i:17401017 original size:36 final size:36
Alignment explanation
Indices: 17400922--17401040 Score: 125
Period size: 36 Copynumber: 3.2 Consensus size: 36
17400912 CTTTGTTTTG
* * *
17400922 GTGTGTTTTCGGTTAGACTAGCTC-TTTGGAGCCAT-TA
1 GTGTG-TTTCGGATGGACTAGCTCGTAT-GAG-CATCTA
*
17400959 GTGTGTTATCGGATGGACTAGCTCGTATGAGCATCTG
1 GTGTGTT-TCGGATGGACTAGCTCGTATGAGCATCTA
* * *
17400996 GTGTGTTTTGGATGGATTAGCTCTTATGAGCATCTA
1 GTGTGTTTCGGATGGACTAGCTCGTATGAGCATCTA
17401032 GTGTGTTTC
1 GTGTGTTTC
17401041 AGTTGGAATA
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
36 38 0.54
37 30 0.43
38 2 0.03
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.39
Consensus pattern (36 bp):
GTGTGTTTCGGATGGACTAGCTCGTATGAGCATCTA
Found at i:17403620 original size:39 final size:39
Alignment explanation
Indices: 17403481--17403608 Score: 238
Period size: 39 Copynumber: 3.3 Consensus size: 39
17403471 GCTTTGATGA
17403481 GCTTCAGTTAGCCTCCGGGCTTCCATTTAGCACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTTCCATTTAGCACTTATGT
17403520 GCTTCAGTTAGCCTCCGGGCTTCCATTTAGCACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTTCCATTTAGCACTTATGT
**
17403559 GCTTCAGTTAGCCTCCAAGCTTCCATTTAGCACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTTCCATTTAGCACTTATGT
17403598 GCTTCAGTTAG
1 GCTTCAGTTAG
17403609 ATTTCGGGCT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 87 1.00
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.36
Consensus pattern (39 bp):
GCTTCAGTTAGCCTCCGGGCTTCCATTTAGCACTTATGT
Found at i:17408051 original size:42 final size:43
Alignment explanation
Indices: 17407988--17408095 Score: 130
Period size: 42 Copynumber: 2.5 Consensus size: 43
17407978 GCAAGCCTCG
* **
17407988 ATTGAGATTTACATATAAGACCATGTCTGGGACATCGGCATCG-T
1 ATTGA-ATTT-CATGTAAGACCATGTCTGGGACAGAGGCATCGAT
*
17408032 ATCT-AATTTCATGTAAGACCCTGTCTGGGACAGAGGCATCGAT
1 AT-TGAATTTCATGTAAGACCATGTCTGGGACAGAGGCATCGAT
*
17408075 ATTGAATTACATGTAAGACCA
1 ATTGAATTTCATGTAAGACCA
17408096 CGTTCAGGAC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
42 29 0.53
43 22 0.40
44 3 0.05
45 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (43 bp):
ATTGAATTTCATGTAAGACCATGTCTGGGACAGAGGCATCGAT
Found at i:17411583 original size:13 final size:13
Alignment explanation
Indices: 17411565--17411591 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17411555 AAAGCCGCAC
17411565 TTATAAAATTGTT
1 TTATAAAATTGTT
17411578 TTATAAAATTGTT
1 TTATAAAATTGTT
17411591 T
1 T
17411592 GTTTTATGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (13 bp):
TTATAAAATTGTT
Found at i:17417371 original size:48 final size:48
Alignment explanation
Indices: 17417226--17417408 Score: 139
Period size: 48 Copynumber: 3.9 Consensus size: 48
17417216 TAGGGTTATG
* * *
17417226 TATGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATCGATA
1 TATGATCCCATGTAAGACCATGTATGAGACATGGCATTGGCATCGATA
* * ** * * *
17417274 TGTAATTTCGTATAAGACC----AT-AG-C-TGGGCTATCGGCA-CTGATA
1 TATGATCCCATGTAAGACCATGTATGAGACAT-GGC-ATTGGCATC-GATA
*
17417317 TGTGATCCCATGTAAGACCATGTATGAGACATGGCATTGGCATCGATA
1 TATGATCCCATGTAAGACCATGTATGAGACATGGCATTGGCATCGATA
* * ** *
17417365 TATGATCCTATGTAAGACCATATCCGAGATATGGCATTGGCATC
1 TATGATCCCATGTAAGACCATGTATGAGACATGGCATTGGCATC
17417409 TTACTATGTG
Statistics
Matches: 102, Mismatches: 22, Indels: 22
0.70 0.15 0.15
Matches are distributed among these distances:
41 1 0.01
42 5 0.05
43 24 0.24
44 1 0.01
47 2 0.02
48 63 0.62
49 5 0.05
50 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (48 bp):
TATGATCCCATGTAAGACCATGTATGAGACATGGCATTGGCATCGATA
Found at i:17419352 original size:29 final size:31
Alignment explanation
Indices: 17419272--17419353 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 31
17419262 TAATTTTTTA
* *
17419272 ATTTTAAAAATTCAAAAAAATTAGAAAAATT
1 ATTTTAAAAGTTTAAAAAAATTAGAAAAATT
*
17419303 ATTTTAAAAGTTT--AAAGATTA-AAAAA-T
1 ATTTTAAAAGTTTAAAAAAATTAGAAAAATT
** *
17419330 ATTTTTTAATTTTAAAAAAATTAG
1 ATTTTAAAAGTTTAAAAAAATTAG
17419354 TTAATTGTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
27 11 0.27
28 5 0.12
29 14 0.34
31 11 0.27
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (31 bp):
ATTTTAAAAGTTTAAAAAAATTAGAAAAATT
Found at i:17419357 original size:19 final size:21
Alignment explanation
Indices: 17419321--17419364 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
17419311 AGTTTAAAGA
**
17419321 TTAAAAAATATTTTTTAATT-
1 TTAAAAAATATTAGTTAATTG
17419341 TTAAAAAA-ATTAGTTAATTG
1 TTAAAAAATATTAGTTAATTG
17419361 TTAA
1 TTAA
17419365 CATAACATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
TTAAAAAATATTAGTTAATTG
Found at i:17422862 original size:22 final size:22
Alignment explanation
Indices: 17422834--17422883 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
17422824 TAATTGGGAA
17422834 TGAATTGATTC-TTTATTATTTT
1 TGAATTGATTCGTTT-TTATTTT
*
17422856 TGAATTGATTCGTTTTTCTTTT
1 TGAATTGATTCGTTTTTATTTT
*
17422878 TTAATT
1 TGAATT
17422884 TTATAGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.20, C:0.06, G:0.10, T:0.64
Consensus pattern (22 bp):
TGAATTGATTCGTTTTTATTTT
Found at i:17443179 original size:9 final size:9
Alignment explanation
Indices: 17443153--17443182 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
17443143 TTCTTTAAGT
17443153 TTATTTTTA
1 TTATTTTTA
17443162 TTATGTTTTA
1 TTAT-TTTTA
17443172 TTATTTTTA
1 TTATTTTTA
17443181 TT
1 TT
17443183 TAACAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (9 bp):
TTATTTTTA
Found at i:17443856 original size:30 final size:30
Alignment explanation
Indices: 17443820--17443878 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
17443810 GTTGTTTCCC
*
17443820 CAAGTTTAGGTATTATCTTGAGTTGAAATT
1 CAAGTTTAGGTATTATCTTGAATTGAAATT
17443850 CAAGTTTAGGTATTATCTTGAATTGAAAT
1 CAAGTTTAGGTATTATCTTGAATTGAAAT
17443879 CCACAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.42
Consensus pattern (30 bp):
CAAGTTTAGGTATTATCTTGAATTGAAATT
Found at i:17455115 original size:43 final size:43
Alignment explanation
Indices: 17455045--17455147 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 43
17455035 AATGCTATAT
* * *
17455045 CCCAGATATGGTCTTATATGAAATCTCGTATTGATGCCAATAG
1 CCCAGATATGGTCTTACACGAAATCTCGTATCGATGCCAATAG
* * *
17455088 CCCAGCTATGGTCTTACACGAAGTCTCGTATCGATGCC-ATAT
1 CCCAGATATGGTCTTACACGAAATCTCGTATCGATGCCAATAG
* *
17455130 CTCAGATATGATCTTACA
1 CCCAGATATGGTCTTACA
17455148 TATAATCTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
42 18 0.35
43 33 0.65
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (43 bp):
CCCAGATATGGTCTTACACGAAATCTCGTATCGATGCCAATAG
Found at i:17458080 original size:30 final size:30
Alignment explanation
Indices: 17458046--17458142 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
17458036 TAAACTAAAA
* *
17458046 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * *
17458076 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
*
17458106 TGAGCTAAGGTTTAGCTCGTGAGCTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGCT-AAAGT
17458136 TGAGCTA
1 TGAGCTA
17458143 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
30 48 0.94
31 3 0.06
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:17460455 original size:157 final size:157
Alignment explanation
Indices: 17460169--17460483 Score: 614
Period size: 157 Copynumber: 2.0 Consensus size: 157
17460159 ACGTCACAGC
17460169 ATAATGTGCAAGCGTACACTATCGATGCAAGTATAGTAGATAGATATGAGTCTATCCGATATCGA
1 ATAATGTGCAAGCGTACACTATCGATGCAAGTATAGTAGATAGATATGAGTCTATCCGATATCGA
17460234 TCCCACAAGGATGGTTGTCTTTTATCTATGAATGTCAGTGTAATAAACAGATAGAAACGAGATAA
66 TCCCACAAGGATGGTTGTCTTTTATCTATGAATGTCAGTGTAATAAACAGATAGAAACGAGATAA
17460299 ATTGTGAGAGTAGTTGCCGAAGCAATA
131 ATTGTGAGAGTAGTTGCCGAAGCAATA
17460326 ATAATGTGCAAGCGTACACTATCGATGCAAGTATAGTAGATAGATATGAGTCTAT-CGAATATCG
1 ATAATGTGCAAGCGTACACTATCGATGCAAGTATAGTAGATAGATATGAGTCTATCCG-ATATCG
17460390 ATCCCACAAGGATGGTTGTCTTTTATCTATGAATGTCAGTGTAATAAACAGATAGAAACGAGATA
65 ATCCCACAAGGATGGTTGTCTTTTATCTATGAATGTCAGTGTAATAAACAGATAGAAACGAGATA
17460455 AATTGTGAGAGTAGTTGCCGAAGCAATA
130 AATTGTGAGAGTAGTTGCCGAAGCAATA
17460483 A
1 A
17460484 CTTTAAAACA
Statistics
Matches: 157, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
156 2 0.01
157 155 0.99
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (157 bp):
ATAATGTGCAAGCGTACACTATCGATGCAAGTATAGTAGATAGATATGAGTCTATCCGATATCGA
TCCCACAAGGATGGTTGTCTTTTATCTATGAATGTCAGTGTAATAAACAGATAGAAACGAGATAA
ATTGTGAGAGTAGTTGCCGAAGCAATA
Found at i:17465375 original size:13 final size:14
Alignment explanation
Indices: 17465353--17465384 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
17465343 TACATCCTGA
17465353 TTTATAATTTTAAT
1 TTTATAATTTTAAT
17465367 TTTAT-ATTTTAAT
1 TTTATAATTTTAAT
17465380 TTTAT
1 TTTAT
17465385 TCTTGATTTA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTATAATTTTAAT
Found at i:17465419 original size:72 final size:72
Alignment explanation
Indices: 17465302--17465446 Score: 218
Period size: 72 Copynumber: 2.0 Consensus size: 72
17465292 TGTTTCCGCA
* * * * *
17465302 TTTAATTTTGTTCTTAATTTATTCTTGATTATTTGACATGATACATCCTGATTTATAATTTTAAT
1 TTTAATTTTATTCTTAATTTATTCTTAATAATTTGACATGATACATCCTAATTTATAATTCTAAT
17465367 TTTATAT
66 TTTATAT
* * *
17465374 TTTAATTTTATTCTTGATTTATTCTTAATAATTTGATATGATACATCCTAATTTATAGTTCTAAT
1 TTTAATTTTATTCTTAATTTATTCTTAATAATTTGACATGATACATCCTAATTTATAATTCTAAT
17465439 TTTATAT
66 TTTATAT
17465446 T
1 T
17465447 AAATATTATT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (72 bp):
TTTAATTTTATTCTTAATTTATTCTTAATAATTTGACATGATACATCCTAATTTATAATTCTAAT
TTTATAT
Found at i:17467884 original size:22 final size:23
Alignment explanation
Indices: 17467859--17467903 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
17467849 TATTGCATAG
17467859 TTGAAATGA-AAAAAAATCAGAA
1 TTGAAATGACAAAAAAATCAGAA
**
17467881 TTGAGGTGACCAAAAAAATCAGA
1 TTGAAATGA-CAAAAAAATCAGA
17467904 TCTTGGTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
24 12 0.63
ACGTcount: A:0.56, C:0.09, G:0.18, T:0.18
Consensus pattern (23 bp):
TTGAAATGACAAAAAAATCAGAA
Found at i:17468726 original size:44 final size:44
Alignment explanation
Indices: 17468665--17468752 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
17468655 TTATGTTAGC
* *
17468665 TTGATAGCTAGAGTGTTTATTATCCTAAGTGTCGTCTAGATGTT
1 TTGATAGCTAGAATGTTTATTATCCTAAGTGTCGCCTAGATGTT
*
17468709 TTGATAGTTAGAATGTTTATTATCCTAAGTGTCGCCTAGATGTT
1 TTGATAGCTAGAATGTTTATTATCCTAAGTGTCGCCTAGATGTT
17468753 ACTGTTAAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (44 bp):
TTGATAGCTAGAATGTTTATTATCCTAAGTGTCGCCTAGATGTT
Found at i:17469430 original size:15 final size:16
Alignment explanation
Indices: 17469410--17469442 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17469400 CAAAACCATG
*
17469410 TAAAAAGGGGGTTCTT
1 TAAAAGGGGGGTTCTT
17469426 TAAAAGGGGGGTTCTT
1 TAAAAGGGGGGTTCTT
17469442 T
1 T
17469443 TTGGAGAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.33, T:0.33
Consensus pattern (16 bp):
TAAAAGGGGGGTTCTT
Found at i:17470328 original size:27 final size:27
Alignment explanation
Indices: 17470287--17470346 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
17470277 TTTATTTAGC
17470287 TATTTGTTTTATTTATT-TAATTTTTT
1 TATTTGTTTTATTTATTATAATTTTTT
*
17470313 TATTTCGTTTTCTTTATTATAATTTTTT
1 TATTT-GTTTTATTTATTATAATTTTTT
17470341 T-TTTGT
1 TATTTGT
17470347 ATATATTGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 7 0.23
27 14 0.45
28 10 0.32
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (27 bp):
TATTTGTTTTATTTATTATAATTTTTT
Found at i:17470373 original size:27 final size:25
Alignment explanation
Indices: 17470343--17470392 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
17470333 AATTTTTTTT
* *
17470343 TTGTATATATTGTCTTTTATTTTATCG
1 TTGTACATATT-TATTTT-TTTTATCG
17470370 TTGTACATATTTATTTTTTTTAT
1 TTGTACATATTTATTTTTTTTAT
17470393 TAGTATTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 5 0.24
27 10 0.48
ACGTcount: A:0.20, C:0.06, G:0.08, T:0.66
Consensus pattern (25 bp):
TTGTACATATTTATTTTTTTTATCG
Found at i:17470555 original size:3 final size:3
Alignment explanation
Indices: 17470547--17470581 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
17470537 AAAATTTATG
*
17470547 TTA TTA TTA TTA TTA TTA TTA TTA TCA TTCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA T
17470582 CGTCGTCGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:17470779 original size:16 final size:16
Alignment explanation
Indices: 17470758--17470788 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17470748 CTAATCTATC
*
17470758 TTGTTTATTTATTTAT
1 TTGTTTATTCATTTAT
17470774 TTGTTTATTCATTTA
1 TTGTTTATTCATTTA
17470789 AAAAAAACTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.71
Consensus pattern (16 bp):
TTGTTTATTCATTTAT
Found at i:17472046 original size:130 final size:129
Alignment explanation
Indices: 17471902--17472196 Score: 357
Period size: 130 Copynumber: 2.3 Consensus size: 129
17471892 GATGTTTGAT
* * * * * **
17471902 GTTTAGAAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTGTAATTTCTCGTTTGTTCAAAATGG
1 GTTTAGAAATTCGAGAAATCGTGCCCTATCATGCTGGGTCGCAATTTCCCGTTTGTTC-AAATAA
* *
17471967 TCAAATATTCTTTTGGAATTTCACTCATGTTTTAAAAATTCTTTAAAACGAAGGCAACGTTCGAA
65 TCAAATATTCCTTTAGAATTTCACTCATGTTTTAAAAATTCTTTAAAACGAAGGCAACGTTCGAA
*
17472032 GTTTAGAAATTCGAGAAATCGTGCCCTATCATGTTGGGTCGCAATTTCCCGTTTGTTCAAATAAT
1 GTTTAGAAATTCGAGAAATCGTGCCCTATCATGCTGGGTCGCAATTTCCCGTTTGTTCAAATAAT
* ** * ** *
17472097 CGAATATTCCTTTAGAATTTCACTCATGTTTTCTAAATTC--TAAAA-TAAGGCAATATTTCG-T
66 CAAATATTCCTTTAGAATTTCACTCATGTTTTAAAAATTCTTTAAAACGAAGGCAA-CGTTCGAA
* *
17472158 GTTTGGAAATTTCGAGAAATTGTGCCCTA-CATGCTGGGT
1 GTTTAGAAA-TTCGAGAAATCGTGCCCTATCATGCTGGGT
17472197 TTCGATTTAT
Statistics
Matches: 143, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
126 24 0.17
127 27 0.19
129 40 0.28
130 52 0.36
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (129 bp):
GTTTAGAAATTCGAGAAATCGTGCCCTATCATGCTGGGTCGCAATTTCCCGTTTGTTCAAATAAT
CAAATATTCCTTTAGAATTTCACTCATGTTTTAAAAATTCTTTAAAACGAAGGCAACGTTCGAA
Found at i:17473724 original size:17 final size:19
Alignment explanation
Indices: 17473687--17473730 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
17473677 TTCTATAAAA
17473687 AATTATTAATACAATT-TTT
1 AATT-TTAATACAATTATTT
*
17473706 TATTTTAATA-AATTATTT
1 AATTTTAATACAATTATTT
17473724 AATTTTA
1 AATTTTA
17473731 CAATTTCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 15 0.68
19 3 0.14
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTTTAATACAATTATTT
Found at i:17474237 original size:19 final size:20
Alignment explanation
Indices: 17474195--17474237 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
17474185 TCAAAATATT
17474195 AAAAAATATCAATTTTTCCA
1 AAAAAATATCAATTTTTCCA
** *
17474215 AAAAAATATTTATTTTTCGA
1 AAAAAATATCAATTTTTCCA
17474235 AAA
1 AAA
17474238 CTGTTATCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAAAATATCAATTTTTCCA
Found at i:17476334 original size:26 final size:26
Alignment explanation
Indices: 17476305--17476356 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
17476295 AAGAAATATT
17476305 GAAAGAAAAAGTAGTTTTCAACATTC
1 GAAAGAAAAAGTAGTTTTCAACATTC
17476331 GAAAGAAAAAGTAGTTTTCAACATTC
1 GAAAGAAAAAGTAGTTTTCAACATTC
17476357 CAACTCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (26 bp):
GAAAGAAAAAGTAGTTTTCAACATTC
Found at i:17477309 original size:25 final size:26
Alignment explanation
Indices: 17477281--17477329 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
17477271 AGAGAATGGA
17477281 AAATAA-AGAAAA-AAAAAGAAATTTC
1 AAATAACAGAAAAGAAAAA-AAATTTC
*
17477306 AAATAACATAAAAGAAAAAAAATT
1 AAATAACAGAAAAGAAAAAAAATT
17477330 AAATTACTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 6 0.29
26 10 0.48
27 5 0.24
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.16
Consensus pattern (26 bp):
AAATAACAGAAAAGAAAAAAAATTTC
Found at i:17490747 original size:21 final size:21
Alignment explanation
Indices: 17490721--17490789 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
17490711 TTTGAGCTTC
17490721 TGTTTAACCCTTATGGGTTTT
1 TGTTTAACCCTTATGGGTTTT
* * * *
17490742 TGTTTAGCTCTTATGAGCTTT
1 TGTTTAACCCTTATGGGTTTT
* * * *
17490763 CGATCAACCCTTATGGGTTTC
1 TGTTTAACCCTTATGGGTTTT
17490784 TGTTTA
1 TGTTTA
17490790 GCTCTCATGA
Statistics
Matches: 33, Mismatches: 15, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.16, C:0.17, G:0.19, T:0.48
Consensus pattern (21 bp):
TGTTTAACCCTTATGGGTTTT
Found at i:17490753 original size:42 final size:42
Alignment explanation
Indices: 17490707--17490809 Score: 145
Period size: 42 Copynumber: 2.5 Consensus size: 42
17490697 TTACGTTCAA
* * *
17490707 CTCTTTTGAGCTTCTGTTTAACCCTTATGGGTTTTTGTTTAG
1 CTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTCTGTTTAG
*
17490749 CTCTTATGAGCTT-TCGATCAACCCTTATGGGTTTCTGTTTAG
1 CTCTTATGAGCTTCT-GTTCAACCCTTATGGGTTTCTGTTTAG
*
17490791 CTCTCATGAGCTTCTGTTC
1 CTCTTATGAGCTTCTGTTC
17490810 GGGCTTCTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
41 1 0.02
42 51 0.96
43 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (42 bp):
CTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTCTGTTTAG
Found at i:17498861 original size:21 final size:21
Alignment explanation
Indices: 17498837--17498957 Score: 73
Period size: 21 Copynumber: 5.8 Consensus size: 21
17498827 TCTCACAAGC
*
17498837 TTCTGTTTAACTCATATGAGT
1 TTCTGTTTAACTCTTATGAGT
* * * *
17498858 TTCTGTTCAGCTCTTTTGAGC
1 TTCTGTTTAACTCTTATGAGT
* *
17498879 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTTAACTCTTATGAGT
* * * * *
17498900 TTCTATTCAGCTCTTACGAGC
1 TTCTGTTTAACTCTTATGAGT
* * *
17498921 TTCTATTCAACCCTTAT-AGGT
1 TTCTGTTTAACTCTTATGA-GT
* *
17498942 TTCTGTTCAGCTCTTA
1 TTCTGTTTAACTCTTA
17498958 CAAGCTTCCA
Statistics
Matches: 74, Mismatches: 25, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
20 1 0.01
21 73 0.99
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.45
Consensus pattern (21 bp):
TTCTGTTTAACTCTTATGAGT
Found at i:17498883 original size:42 final size:42
Alignment explanation
Indices: 17498815--17499011 Score: 173
Period size: 42 Copynumber: 4.7 Consensus size: 42
17498805 TCGTGTTTAC
* * * * * *
17498815 TTTCCGTTTAGCTCTCACAAGCTTCTGTTTAACTCATATGAG
1 TTTCTGTTCAGCTCTTACGAGCTTCTGTTTAACCCTTATGAG
** *
17498857 TTTCTGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGG
1 TTTCTGTTCAGCTCTTACGAGCTTCTGTTTAACCCTTATGAG
* * *
17498899 TTTCTATTCAGCTCTTACGAGCTTCTATTCAACCCTTAT-AGG
1 TTTCTGTTCAGCTCTTACGAGCTTCTGTTTAACCCTTATGA-G
* ** *
17498941 TTTCTGTTCAGCTCTTACAAGCTTCCATTCAACCCTTAT-AGG
1 TTTCTGTTCAGCTCTTACGAGCTTCTGTTTAACCCTTATGA-G
* * * * *
17498983 TTTTTGTTTAGCTCTCATGAGCTTTTGTT
1 TTTCTGTTCAGCTCTTACGAGCTTCTGTT
17499012 CAGCCTTCGG
Statistics
Matches: 128, Mismatches: 26, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
42 128 1.00
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.44
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTTACGAGCTTCTGTTTAACCCTTATGAG
Found at i:17498971 original size:21 final size:21
Alignment explanation
Indices: 17498900--17498971 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
17498890 CCTTATGGGT
*
17498900 TTCTATTCAGCTCTTACGAGC
1 TTCTATTCAGCTCTTACAAGC
* * * * *
17498921 TTCTATTCAACCCTTATAGGT
1 TTCTATTCAGCTCTTACAAGC
*
17498942 TTCTGTTCAGCTCTTACAAGC
1 TTCTATTCAGCTCTTACAAGC
*
17498963 TTCCATTCA
1 TTCTATTCA
17498972 ACCCTTATAG
Statistics
Matches: 37, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.21, C:0.28, G:0.11, T:0.40
Consensus pattern (21 bp):
TTCTATTCAGCTCTTACAAGC
Found at i:17498996 original size:84 final size:84
Alignment explanation
Indices: 17498815--17499006 Score: 206
Period size: 84 Copynumber: 2.3 Consensus size: 84
17498805 TCGTGTTTAC
* * * * * ***
17498815 TTTCCGTTTAGCTCTCACAAGCTTCTGTTTAACTCATATGAGTTTCTGTTCAGCTCTTTTGAGCT
1 TTTCTGTTTAGCTCTCACGAGCTTCTATTCAACCCATATGAGTTTCTGTTCAGCTCTTACAAGCT
** * *
17498880 TCTGTTTAACCCTTATGGG
66 TCCATTCAACCCTTATAGG
* * * *
17498899 TTTCTATTCAGCTCTTACGAGCTTCTATTCAACCCTTAT-AGGTTTCTGTTCAGCTCTTACAAGC
1 TTTCTGTTTAGCTCTCACGAGCTTCTATTCAACCCATATGA-GTTTCTGTTCAGCTCTTACAAGC
17498963 TTCCATTCAACCCTTATAGG
65 TTCCATTCAACCCTTATAGG
* *
17498983 TTTTTGTTTAGCTCTCATGAGCTT
1 TTTCTGTTTAGCTCTCACGAGCTT
17499007 TTGTTCAGCC
Statistics
Matches: 86, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
83 1 0.01
84 85 0.99
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.43
Consensus pattern (84 bp):
TTTCTGTTTAGCTCTCACGAGCTTCTATTCAACCCATATGAGTTTCTGTTCAGCTCTTACAAGCT
TCCATTCAACCCTTATAGG
Found at i:17501643 original size:63 final size:63
Alignment explanation
Indices: 17501506--17501630 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 63
17501496 AATACGAAAA
* * *
17501506 CAGTGAGTTACACGGCCTGGACACACGCCCATGTCTCTGGCCTGTGTATCTCTAAGTCATGAT
1 CAGTGAGTTACACGGCCTGGACACACGCCCATGTCCCTAGCCTGCGTATCTCTAAGTCATGAT
* * * *
17501569 CAGTGAGTTACACGGCCTGGACACACGTCCGTGTCCCTAGCCTGCGTGTCTCTAATTCATGA
1 CAGTGAGTTACACGGCCTGGACACACGCCCATGTCCCTAGCCTGCGTATCTCTAAGTCATGA
17501631 ATAGTAGGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (63 bp):
CAGTGAGTTACACGGCCTGGACACACGCCCATGTCCCTAGCCTGCGTATCTCTAAGTCATGAT
Found at i:17504209 original size:3 final size:3
Alignment explanation
Indices: 17504201--17504225 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17504191 CAACTAATCT
17504201 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
17504226 CAAAAAATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:17505179 original size:30 final size:31
Alignment explanation
Indices: 17505116--17505191 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
17505106 AAATTTTAAA
* *
17505116 TTAATAAA-GATAAAATTGTATTTTAATTCTT
1 TTAA-AAATGATAAAATTGTAATTTAAGTCTT
*
17505147 TTAAAAATGATAAAATTTTAATTT-AGTCTT
1 TTAAAAATGATAAAATTGTAATTTAAGTCTT
*
17505177 TTAAAAATTATAAAA
1 TTAAAAATGATAAAA
17505192 ATATAAACTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
30 22 0.55
31 18 0.45
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (31 bp):
TTAAAAATGATAAAATTGTAATTTAAGTCTT
Found at i:17509956 original size:30 final size:30
Alignment explanation
Indices: 17509917--17509976 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
17509907 TCCCAAACCG
* *
17509917 TTTTTACTTTTCC-CTCCAAACTTTTACTCC
1 TTTTCACTTTTCCCCT-AAAACTTTTACTCC
17509947 TTTTCACTTTTCCCCTAAAACTTTTACTCC
1 TTTTCACTTTTCCCCTAAAACTTTTACTCC
17509977 CCTCCCATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.48
Consensus pattern (30 bp):
TTTTCACTTTTCCCCTAAAACTTTTACTCC
Found at i:17511128 original size:554 final size:555
Alignment explanation
Indices: 17510074--17511186 Score: 2219
Period size: 554 Copynumber: 2.0 Consensus size: 555
17510064 AAAAACCCTC
17510074 AAAACTTTTTATTTTCCCCCAAAATTTTTACTCCCTCCCACTTTTCCCCTAAAACTTTTACTCCA
1 AAAACTTTTTATTTTCCCCCAAAATTTTTACTCCCTCCCACTTTTCCCCTAAAACTTTTACTCCA
17510139 TTCTCATCCTACCCCCTATCTACCCCAAACCCATCCCCTCCCTCCAATTTCTTTTTAATATTTTC
66 TTCTCATCCTACCCCCTATCTACCCCAAACCCATCCCCTCCCTCCAATTTCTTTTTAATATTTTC
17510204 CCTCCAAAATTTTACTCCCCCTATTTACTTTCCCTCAAACTTTCACTCCCCAAAACTTTTTATTT
131 CCTCCAAAATTTTACTCCCCCTATTTACTTTCCCTCAAACTTTCACTCCCCAAAACTTTTTATTT
17510269 TTCCCCTAAACTTTTACTTCTCACCCTTTACTTCCAAATAAAAAATCAAAATTATCCAAAAAAAA
196 TTCCCCTAAACTTTTACTTCTCACCCTTTACTTCCAAATAAAAAATCAAAATTATCCAAAAAAAA
17510334 TCCCTAAACATAAATAGTAATAATTTTATTTATATCTACTATTTATATTATTAAATTAAATTTCA
261 TCCCTAAACATAAATAGTAATAATTTTATTTATATCTACTATTTATATTATTAAATTAAATTTCA
17510399 CATTTCATATTATTTATATTATTAAATTGTTTAGTCATATTGAATATTTATATTAAAATTGAATT
326 CATTTCATATTATTTATATTATTAAATTGTTTAGTCATATTGAATATTTATATTAAAATTGAATT
17510464 ATTAATGATGCCATAAAATATTCGTCTGAAAAATTTTATATTGGTATCAATTCCATATTGTATCT
391 ATTAATGATGCCATAAAATATTCGTCTGAAAAATTTTATATTGGTATCAATTCCATATTGTATCT
17510529 TTAAAATAACTTTTATTAAAAAATCACATTTTTACATTTAATATATTTTTTTAATTTTAAAATAC
456 TTAAAATAACTTTTATTAAAAAATCACATTTTTACATTTAATATATTTTTTTAATTTTAAAATAC
17510594 ATAATGACAAGAATCTGAAGATAATTGAAACAACT
521 ATAATGACAAGAATCTGAAGATAATTGAAACAACT
17510629 AAAA-TTTTTATTTTCCCCCAAAATTTTTACTCCCTCCCACTTTTCCCCTAAAACTTTTACTCCA
1 AAAACTTTTTATTTTCCCCCAAAATTTTTACTCCCTCCCACTTTTCCCCTAAAACTTTTACTCCA
17510693 TTCTCATCCTACCCCCTATCTACCCCAAACCCATCCCCTCCCTCCAATTTCTTTTTAATATTTTC
66 TTCTCATCCTACCCCCTATCTACCCCAAACCCATCCCCTCCCTCCAATTTCTTTTTAATATTTTC
17510758 CCTCCAAAATTTTACTCCCCCTATTTACTTTCCCTCAAACTTTCACTCCCCAAAACTTTTTATTT
131 CCTCCAAAATTTTACTCCCCCTATTTACTTTCCCTCAAACTTTCACTCCCCAAAACTTTTTATTT
17510823 TTCCCCTAAACTTTTACTTCTCACCCTTTACTTCCAAATAAAAAATCAAAATTATCCAAAAAAAA
196 TTCCCCTAAACTTTTACTTCTCACCCTTTACTTCCAAATAAAAAATCAAAATTATCCAAAAAAAA
17510888 TCCCTAAACATAAATAGTAATAATTTTATTTATATCTACTATTTATATTATTAAATTAAATTTCA
261 TCCCTAAACATAAATAGTAATAATTTTATTTATATCTACTATTTATATTATTAAATTAAATTTCA
17510953 CATTTCATATTATTTATATTATTAAATTGTTTAGTCATATTGAATATTTATATTAAAATTGAATT
326 CATTTCATATTATTTATATTATTAAATTGTTTAGTCATATTGAATATTTATATTAAAATTGAATT
17511018 ATTAATGATGCCATAAAATATTCGTCTGAAAAATTTTATATTGGTATCAATTCCATATTGTATCT
391 ATTAATGATGCCATAAAATATTCGTCTGAAAAATTTTATATTGGTATCAATTCCATATTGTATCT
17511083 TTAAAATAACTTTTATTAAAAAATCACATTTTTACATTTAATATATTTTTTTAATTTTAAAATAC
456 TTAAAATAACTTTTATTAAAAAATCACATTTTTACATTTAATATATTTTTTTAATTTTAAAATAC
17511148 ATAATGACAAGAATCTGAAGATAATTGAAACAACT
521 ATAATGACAAGAATCTGAAGATAATTGAAACAACT
17511183 AAAA
1 AAAA
17511187 AAGCAAAGAA
Statistics
Matches: 558, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
554 554 0.99
555 4 0.01
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (555 bp):
AAAACTTTTTATTTTCCCCCAAAATTTTTACTCCCTCCCACTTTTCCCCTAAAACTTTTACTCCA
TTCTCATCCTACCCCCTATCTACCCCAAACCCATCCCCTCCCTCCAATTTCTTTTTAATATTTTC
CCTCCAAAATTTTACTCCCCCTATTTACTTTCCCTCAAACTTTCACTCCCCAAAACTTTTTATTT
TTCCCCTAAACTTTTACTTCTCACCCTTTACTTCCAAATAAAAAATCAAAATTATCCAAAAAAAA
TCCCTAAACATAAATAGTAATAATTTTATTTATATCTACTATTTATATTATTAAATTAAATTTCA
CATTTCATATTATTTATATTATTAAATTGTTTAGTCATATTGAATATTTATATTAAAATTGAATT
ATTAATGATGCCATAAAATATTCGTCTGAAAAATTTTATATTGGTATCAATTCCATATTGTATCT
TTAAAATAACTTTTATTAAAAAATCACATTTTTACATTTAATATATTTTTTTAATTTTAAAATAC
ATAATGACAAGAATCTGAAGATAATTGAAACAACT
Found at i:17513515 original size:27 final size:27
Alignment explanation
Indices: 17513485--17513552 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
17513475 ACTACCTTAT
* *
17513485 TTTTATTGTCTCAGTGGACTACCCCGC
1 TTTTATTGTCCCAATGGACTACCCCGC
* *
17513512 TTTTATTATCCCAATGGGCTACCCCGC
1 TTTTATTGTCCCAATGGACTACCCCGC
* *
17513539 ATTTAATGTCCCAA
1 TTTTATTGTCCCAA
17513553 CAAAATACAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (27 bp):
TTTTATTGTCCCAATGGACTACCCCGC
Found at i:17513760 original size:67 final size:67
Alignment explanation
Indices: 17513587--17513922 Score: 350
Period size: 67 Copynumber: 5.1 Consensus size: 67
17513577 CGGAAAACTA
* * * *
17513587 CCCAGTGTTTAATGTCCTGAAAGG-CTCTCTATGTTGTCATAGCCGAGCCAAGGTCTTACACA-C
1 CCCA-TGTTTAATGTCCTG-ACGGACTCTCTATGTTGTCATAGCCGAGCTATGGTCTTACACATT
17513650 ATA-
64 ATAC
* * ** *
17513653 -CCATATGT-AT-TCCCTGGA-GGACTCTCCTA-GTTACCATAGCCGAGCTATGGTCTTACACGT
1 CCCATGTTTAATGT-CCT-GACGGACTCT-CTATGTTGTCATAGCCGAGCTATGGTCTTACACAT
17513713 TATAC
63 TATAC
*
17513718 CCCATGTTTAATGTCCTGACGGACTCTCTATGTTGTCATAGCCAAGCTATGGTCTTACACATTAT
1 CCCATGTTTAATGTCCTGACGGACTCTCTATGTTGTCATAGCCGAGCTATGGTCTTACACATTAT
17513783 AC
66 AC
* * * * * * * *
17513785 CACATGTTTAATGTTCTGACAGACTCTCTATGTTGCCATAGTCGAGTTATAGTCTTATACATTAT
1 CCCATGTTTAATGTCCTGACGGACTCTCTATGTTGTCATAGCCGAGCTATGGTCTTACACATTAT
17513850 AC
66 AC
* * * *
17513852 CCCATGTTTAATGTCCTG-CAGACTCTCTATGTT-TCCATAGCCGGGCTATGGTTTTACAAATTA
1 CCCATGTTTAATGTCCTGACGGACTCTCTATGTTGT-CATAGCCGAGCTATGGTCTTACACATTA
17513915 TAC
65 TAC
17513918 CCCAT
1 CCCAT
17513923 TATAGTCCAT
Statistics
Matches: 225, Mismatches: 33, Indels: 24
0.80 0.12 0.09
Matches are distributed among these distances:
62 3 0.01
63 35 0.16
64 10 0.04
65 3 0.01
66 55 0.24
67 118 0.52
68 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (67 bp):
CCCATGTTTAATGTCCTGACGGACTCTCTATGTTGTCATAGCCGAGCTATGGTCTTACACATTAT
AC
Found at i:17531314 original size:18 final size:19
Alignment explanation
Indices: 17531274--17531314 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
17531264 TGCTTCTGTA
*
17531274 ATCTGAATCTGAATCTGAT
1 ATCTGAATCTGAAACTGAT
*
17531293 -TCTGCATCTGAAACT-AT
1 ATCTGAATCTGAAACTGAT
17531310 ATCTG
1 ATCTG
17531315 TTTTCGACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (19 bp):
ATCTGAATCTGAAACTGAT
Found at i:17543309 original size:26 final size:26
Alignment explanation
Indices: 17543267--17543322 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
17543257 CTCTTATAAA
*
17543267 CTTCCCGATATATGGCT-TTTCATGAG
1 CTTCCCGATATAAGGCTCTTT-ATGAG
*
17543293 CTTCCCGAT-TAAAGGCTCTTTGTGAG
1 CTTCCCGATAT-AAGGCTCTTTATGAG
17543319 CTTC
1 CTTC
17543323 TTGATTAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 1 0.04
26 22 0.85
27 3 0.12
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.38
Consensus pattern (26 bp):
CTTCCCGATATAAGGCTCTTTATGAG
Found at i:17543361 original size:24 final size:24
Alignment explanation
Indices: 17543331--17543397 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
17543321 TCTTGATTAA
*
17543331 TGGCTCTCCGGAGCTTCCCGATAT
1 TGGCTCTCCGGAACTTCCCGATAT
** *
17543355 TGGCTCTCTTGAACTTCCCGATTT
1 TGGCTCTCCGGAACTTCCCGATAT
* *
17543379 GTGGCTATTCGGAACTTCC
1 -TGGCTCTCCGGAACTTCC
17543398 TAATTAATGG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
24 20 0.59
25 14 0.41
ACGTcount: A:0.13, C:0.30, G:0.22, T:0.34
Consensus pattern (24 bp):
TGGCTCTCCGGAACTTCCCGATAT
Found at i:17553533 original size:6 final size:6
Alignment explanation
Indices: 17553510--17553553 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
17553500 TACAAATAAA
* * *
17553510 TCATTT CTCATTT CCATTT TCATTT TCATTT CCATTT CCATTT T
1 TCATTT -TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT T
17553554 TTTGAGAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.16, C:0.25, G:0.00, T:0.59
Consensus pattern (6 bp):
TCATTT
Found at i:17553534 original size:12 final size:12
Alignment explanation
Indices: 17553511--17553553 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
17553501 ACAAATAAAT
17553511 CATTTCTCATTTC
1 CATTT-TCATTTC
*
17553524 CATTTTCATTTT
1 CATTTTCATTTC
*
17553536 CATTTCCATTTC
1 CATTTTCATTTC
17553548 CATTTT
1 CATTTT
17553554 TTTGAGAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 21 0.81
13 5 0.19
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (12 bp):
CATTTTCATTTC
Found at i:17553540 original size:18 final size:18
Alignment explanation
Indices: 17553510--17553553 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
17553500 TACAAATAAA
17553510 TCATTTCTCATTTCCATTT
1 TCATTT-TCATTTCCATTT
17553529 TCATTTTCATTTCCATTT
1 TCATTTTCATTTCCATTT
*
17553547 CCATTTT
1 TCATTTT
17553554 TTTGAGAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.16, C:0.25, G:0.00, T:0.59
Consensus pattern (18 bp):
TCATTTTCATTTCCATTT
Found at i:17555846 original size:46 final size:44
Alignment explanation
Indices: 17555756--17555858 Score: 109
Period size: 46 Copynumber: 2.3 Consensus size: 44
17555746 TAACATTTAA
*
17555756 TTAATTTTTAAAATTTTAAAAAAATATATAATTTTTAAATATTT
1 TTAAATTTTAAAATTTTAAAAAAATATATAATTTTTAAATATTT
* * * * **
17555800 TTAATGATTTTAAAATTTTAAAAATAGTTTTTATTTTTTTGA-ATTT
1 TTAA--ATTTTAAAATTTTAAAAA-AATATATAATTTTTAAATATTT
17555846 TTAAATTTTAAAA
1 TTAAATTTTAAAA
17555859 AATAGTCTCG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
44 13 0.27
46 25 0.51
47 11 0.22
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (44 bp):
TTAAATTTTAAAATTTTAAAAAAATATATAATTTTTAAATATTT
Found at i:17560961 original size:43 final size:43
Alignment explanation
Indices: 17560903--17561092 Score: 299
Period size: 43 Copynumber: 4.4 Consensus size: 43
17560893 GCTTTTTTCT
* * *
17560903 CAAAAACGCCACTAAAGATCGTGACCTTTAGCGGCGCTTTCCC
1 CAAAAACGCCGCTAAAGATCGTGACCTATAGCGACGCTTTCCC
* * *
17560946 CAAAAATGCCGCTAAAGATCGTGGCCTATAGCGACGCTTTCCT
1 CAAAAACGCCGCTAAAGATCGTGACCTATAGCGACGCTTTCCC
* * *
17560989 CAAAAACGCCACTAAAAATCGTGACCTATAGCGGCGCTTTCCC
1 CAAAAACGCCGCTAAAGATCGTGACCTATAGCGACGCTTTCCC
17561032 CAAAAACGCCGCTAAAGATCGTGACCTATAGCGACGCTTTCCC
1 CAAAAACGCCGCTAAAGATCGTGACCTATAGCGACGCTTTCCC
17561075 CAAAAACGCCGCTAAAGA
1 CAAAAACGCCGCTAAAGA
17561093 CCATATATAT
Statistics
Matches: 132, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 132 1.00
ACGTcount: A:0.32, C:0.31, G:0.18, T:0.19
Consensus pattern (43 bp):
CAAAAACGCCGCTAAAGATCGTGACCTATAGCGACGCTTTCCC
Found at i:17561587 original size:23 final size:23
Alignment explanation
Indices: 17561561--17561662 Score: 168
Period size: 23 Copynumber: 4.4 Consensus size: 23
17561551 ACACAAAGAA
17561561 CATTTAAACACTTCAATTTACAG
1 CATTTAAACACTTCAATTTACAG
** * *
17561584 CATTTAAATTCTTCAGTTTACAA
1 CATTTAAACACTTCAATTTACAG
17561607 CATTTAAACACTTCAATTTACAG
1 CATTTAAACACTTCAATTTACAG
17561630 CATTTAAACACTTCAATTTACAG
1 CATTTAAACACTTCAATTTACAG
17561653 CATTTAAACA
1 CATTTAAACA
17561663 GCAGCAACCA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (23 bp):
CATTTAAACACTTCAATTTACAG
Found at i:17564544 original size:62 final size:63
Alignment explanation
Indices: 17564417--17564592 Score: 198
Period size: 63 Copynumber: 2.8 Consensus size: 63
17564407 CAGGAAACTA
17564417 GAAAACTAATATAATAGAAATAAGAAACCCAAACAAAAAAAATCAAAAAATTTTAAGACGATT
1 GAAAACTAATATAATAGAAATAAGAAACCCAAACAAAAAAAATCAAAAAATTTTAAGACGATT
** ** *
17564480 GAAAACTAATATAATAGAAAATAAGAAACCCAAA-TTAAAATTTC-TAAAATTTTAAGACGATT
1 GAAAACTAATATAATAG-AAATAAGAAACCCAAACAAAAAAAATCAAAAAATTTTAAGACGATT
* * * *
17564542 GAAAATTAA-AGGAAGTA-AATTTCAACAAACCCAAACAAAAAAAATCAAAAA
1 GAAAACTAATA-TAA-TAGAA-AT-AAGAAACCCAAACAAAAAAAATCAAAAA
17564593 CCTCACATAC
Statistics
Matches: 92, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
61 3 0.03
62 28 0.30
63 36 0.39
64 22 0.24
65 3 0.03
ACGTcount: A:0.60, C:0.11, G:0.08, T:0.20
Consensus pattern (63 bp):
GAAAACTAATATAATAGAAATAAGAAACCCAAACAAAAAAAATCAAAAAATTTTAAGACGATT
Found at i:17565569 original size:21 final size:21
Alignment explanation
Indices: 17565526--17565569 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
17565516 CCTAACACTT
* * *
17565526 AACCCCTACCCCTAAGCCTTA
1 AACCCCAACCCCTAAACCATA
*
17565547 AACCCCAACCCTTAAACCATA
1 AACCCCAACCCCTAAACCATA
17565568 AA
1 AA
17565570 TCATAATCCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.43, G:0.02, T:0.16
Consensus pattern (21 bp):
AACCCCAACCCCTAAACCATA
Found at i:17565591 original size:15 final size:15
Alignment explanation
Indices: 17565553--17565604 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
17565543 CTTAAACCCC
* *
17565553 AACCCTTAAACCATA
1 AACCCATAATCCATA
*
17565568 AA-TCATAATCCATA
1 AACCCATAATCCATA
17565582 AACCCATAATCCATA
1 AACCCATAATCCATA
17565597 AACCCATA
1 AACCCATA
17565605 TTTCATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 11 0.34
15 21 0.66
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (15 bp):
AACCCATAATCCATA
Found at i:17565651 original size:19 final size:19
Alignment explanation
Indices: 17565629--17565671 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
17565619 TTGTACTTCA
*
17565629 TTTTTATTTGTTATCAATG
1 TTTTTATTTATTATCAATG
17565648 TTTTTATTTATTATCAATG
1 TTTTTATTTATTATCAATG
17565667 TTTTT
1 TTTTT
17565672 TTAAATCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (19 bp):
TTTTTATTTATTATCAATG
Found at i:17566082 original size:22 final size:21
Alignment explanation
Indices: 17566047--17566096 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
17566037 AAGCCCCAAC
*
17566047 CCTTAAACTATAATACATAAA
1 CCTTAAAATATAATACATAAA
*
17566068 CCTTAAAATAGTAATTCATAAA
1 CCTTAAAATA-TAATACATAAA
17566090 CCTTAAA
1 CCTTAAA
17566097 CCCTTAACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.30
Consensus pattern (21 bp):
CCTTAAAATATAATACATAAA
Found at i:17566127 original size:14 final size:14
Alignment explanation
Indices: 17566093--17566137 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
17566083 TCATAAACCT
* *
17566093 TAAACCCTTAACCA
1 TAAACCCTAAACTA
* *
17566107 TATACCCTAAATTA
1 TAAACCCTAAACTA
17566121 TAAACCCTAAACTA
1 TAAACCCTAAACTA
17566135 TAA
1 TAA
17566138 TGATTAATTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:17566251 original size:14 final size:13
Alignment explanation
Indices: 17566232--17566274 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
17566222 TAATTAACTA
17566232 AACCCTAAACTCCT
1 AACCCTAAAC-CCT
*
17566246 AACCCTTAACCCT
1 AACCCTAAACCCT
*
17566259 AACTCATAAACCCT
1 AAC-CCTAAACCCT
17566273 AA
1 AA
17566275 ATCTTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 6 0.24
14 19 0.76
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.21
Consensus pattern (13 bp):
AACCCTAAACCCT
Found at i:17566270 original size:21 final size:21
Alignment explanation
Indices: 17566232--17566272 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17566222 TAATTAACTA
*
17566232 AACCCTAAACTCCTAACCCTT
1 AACCCTAAACTCATAACCCTT
17566253 AACCCT-AACTCATAAACCCT
1 AACCCTAAACTCAT-AACCCT
17566273 AAATCTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.37, C:0.41, G:0.00, T:0.22
Consensus pattern (21 bp):
AACCCTAAACTCATAACCCTT
Found at i:17566593 original size:23 final size:21
Alignment explanation
Indices: 17566551--17566600 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 21
17566541 TTAGAGGTTA
17566551 TATTTTAGTGTTTAGGGATTTAG
1 TATTTTAGTGTTTA-GGA-TTAG
17566574 TATTTTAGGTGTTATA-GATTAG
1 TATTTTA-GTGTT-TAGGATTAG
17566596 TATTT
1 TATTT
17566601 ATGATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 9 0.36
23 9 0.36
24 5 0.20
25 2 0.08
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (21 bp):
TATTTTAGTGTTTAGGATTAG
Found at i:17566667 original size:35 final size:35
Alignment explanation
Indices: 17566628--17566694 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
17566618 AGGGTTTTAG
17566628 GGGTTATATGACTTTTAGCGGCGTTTTATCGATAT
1 GGGTTATATGACTTTTAGCGGCGTTTTATCGATAT
17566663 GGGTTATATGACTTTTAGCGGCGTTTTATCGA
1 GGGTTATATGACTTTTAGCGGCGTTTTATCGA
17566695 AAGCACCGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.19, C:0.12, G:0.27, T:0.42
Consensus pattern (35 bp):
GGGTTATATGACTTTTAGCGGCGTTTTATCGATAT
Found at i:17566737 original size:41 final size:41
Alignment explanation
Indices: 17566675--17566992 Score: 336
Period size: 41 Copynumber: 7.8 Consensus size: 41
17566665 GTTATATGAC
* * *
17566675 TTTTAGCGGCGTTTTATCGAAAGCACCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCCGGT
* * * *
17566716 TTTTAGCTGTGTTTTACCGAAAGCGCCGCTAATGCTTCGAT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCCGGT
*
17566757 TTTTAGCAGCGTTTTACCGAAAGCGCCGC-AAGTGCTCCGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAA-TGCTCCGGT
*
17566798 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAGTGCTCCGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCCGGT
* * * * *
17566839 TTTTAGAGGCGTTTTACCGAAAACGCCGCTAGTGTTCCGAT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCCGGT
* ** * **
17566880 TTTTAGCTGCGTTTTACCGAAAGCGCAACTATTGCT-ATGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCCGGT
*** * * *
17566920 TTTTAGCGGCGTTTTAATAAAAAACGCCGCTATTGCT-CTGT
1 TTTTAGCGGCGTTTT-ACCGAAAGCGCCGCTAATGCTCCGGT
* * *
17566961 TTTTAGCAGCGTTTTACCAAAAACGCCGCTAA
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAA
17566993 AGCCCTATTT
Statistics
Matches: 235, Mismatches: 39, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
40 31 0.13
41 203 0.86
42 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCCGGT
Found at i:17566894 original size:123 final size:121
Alignment explanation
Indices: 17566675--17566992 Score: 379
Period size: 123 Copynumber: 2.6 Consensus size: 121
17566665 GTTATATGAC
* * * * *
17566675 TTTTAGCGGCGTTTTATCGAAAGCACCGCTAATGCTCTGGTTTTTAGCTGTGTTTTACCGAAAGC
1 TTTTAGCGGCGTTTTATCGAAAGCGCCGCTAATGCTCCGGTTTTTAG-AGCGTTTTACCGAAAAC
** *
17566740 GCCGCTAATGCTTCGATTTTTAGCAGCGTTTTACCGAAAGCGCCGCAAGTGCTCCGGT
65 GCCGCTAATGCTTCGATTTTTAGCAGCGTTTTACCGAAAGCGCAACAAGTGCT-AGGT
* *
17566798 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAGTGCTCCGGTTTTTAGAGGCGTTTTACCGAAAAC
1 TTTTAGCGGCGTTTTATCGAAAGCGCCGCTAATGCTCCGGTTTTTAGA-GCGTTTTACCGAAAAC
* * * * *
17566863 GCCGCTAGTG-TTCCGATTTTTAGCTGCGTTTTACCGAAAGCGCAACTATTGCTATGT
65 GCCGCTAATGCTT-CGATTTTTAGCAGCGTTTTACCGAAAGCGCAACAAGTGCTAGGT
** * * * *
17566920 TTTTAGCGGCGTTTTAATAAAAAACGCCGCTATTGCT-CTGTTTTTAGCAGCGTTTTACCAAAAA
1 TTTTAGCGGCGTTTT-ATCGAAAGCGCCGCTAATGCTCCGGTTTTTAG-AGCGTTTTACCGAAAA
17566984 CGCCGCTAA
64 CGCCGCTAA
17566993 AGCCCTATTT
Statistics
Matches: 168, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
122 50 0.30
123 118 0.70
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (121 bp):
TTTTAGCGGCGTTTTATCGAAAGCGCCGCTAATGCTCCGGTTTTTAGAGCGTTTTACCGAAAACG
CCGCTAATGCTTCGATTTTTAGCAGCGTTTTACCGAAAGCGCAACAAGTGCTAGGT
Done.