Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 114 of 344
Found at i:38692349 original size:24 final size:23
Alignment explanation
Indices: 38692313--38692432 Score: 81
Period size: 24 Copynumber: 5.2 Consensus size: 23
38692303 GACACAAACG
38692313 TAGCTCTTTATGAG-TGTCCTGATA
1 TAGCTC-TTATGAGCT-TCCTGATA
38692337 TAGGCTCTTATGAGCTTCCTGATA
1 TA-GCTCTTATGAGCTTCCTGATA
*
38692361 TAGCTCTCT-TGAACTTCCT-AT-
1 TAGCTCT-TATGAGCTTCCTGATA
* *
38692382 TAAGCTC-AATGAGCTTCCT-ATTT
1 T-AGCTCTTATGAGCTTCCTGA-TA
* * *
38692405 TAAACTCTTATGAGTTTCTTGATA
1 T-AGCTCTTATGAGCTTCCTGATA
38692429 TAGC
1 TAGC
38692433 CCAGATAAGA
Statistics
Matches: 78, Mismatches: 9, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
21 11 0.14
22 8 0.10
23 22 0.28
24 31 0.40
25 6 0.08
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (23 bp):
TAGCTCTTATGAGCTTCCTGATA
Found at i:38692377 original size:23 final size:24
Alignment explanation
Indices: 38692329--38692379 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
38692319 TTTATGAGTG
*
38692329 TCCTGATATAGGCTCTTATGAGCT
1 TCCTGATATAGGCTCTTATGAACT
38692353 TCCTGATATA-GCTCTCT-TGAACT
1 TCCTGATATAGGCTCT-TATGAACT
38692376 TCCT
1 TCCT
38692380 ATTAAGCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (24 bp):
TCCTGATATAGGCTCTTATGAACT
Found at i:38697272 original size:31 final size:31
Alignment explanation
Indices: 38697230--38697306 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 31
38697220 TAACGGTTAT
*
38697230 TGGGCCAAAGCCTTTTCATAAATCAAATCAC
1 TGGGCCGAAGCCTTTTCATAAATCAAATCAC
*
38697261 TGGGCCGAAGCCTTTTCATAAATCATATCAC
1 TGGGCCGAAGCCTTTTCATAAATCAAATCAC
38697292 TGGGCCGAAGCCTTT
1 TGGGCCGAAGCCTTT
38697307 ATTGTAAACG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (31 bp):
TGGGCCGAAGCCTTTTCATAAATCAAATCAC
Found at i:38697390 original size:42 final size:42
Alignment explanation
Indices: 38697330--38697421 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
38697320 TGGCCCATAG
*
38697330 GCCCATTTCAATAACACATGAAATATCAATGAATGTATGCAA
1 GCCCATTTCAATAACACATGAAATACCAATGAATGTATGCAA
*
38697372 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATAACACATGAAATACCAATGAATGTATGCAA
38697414 GCCCATTT
1 GCCCATTT
38697422 GGGGAGACTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (42 bp):
GCCCATTTCAATAACACATGAAATACCAATGAATGTATGCAA
Found at i:38697608 original size:26 final size:26
Alignment explanation
Indices: 38697566--38697714 Score: 221
Period size: 26 Copynumber: 5.8 Consensus size: 26
38697556 CCTCTTTAAT
*
38697566 AACTGGGGCA-AAGCCTTTTTTGGTA
1 AACTGGGGCATAAGCCCTTTTTGGTA
* *
38697591 AACTTGGG-AAAAGCCCTTTTTGGTA
1 AACTGGGGCATAAGCCCTTTTTGGTA
38697616 AACTGGGGCATAAGCCCTTTTTGGTA
1 AACTGGGGCATAAGCCCTTTTTGGTA
*
38697642 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTTGGTA
***
38697668 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTTGGTA
38697694 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
38697715 GCACTTCCTC
Statistics
Matches: 115, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
24 1 0.01
25 28 0.24
26 86 0.75
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTTGGTA
Found at i:38697789 original size:20 final size:20
Alignment explanation
Indices: 38697764--38697820 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
38697754 TTATGAATTC
*
38697764 ATCATGTGCATTTCATA-CA
1 ATCATGTGCATATCATATCA
38697783 TATCATGTGCATATCATATCA
1 -ATCATGTGCATATCATATCA
38697804 ATCATGT--ATATCATATC
1 ATCATGTGCATATCATATC
38697821 CCACGTATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 10 0.29
20 23 0.66
21 2 0.06
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (20 bp):
ATCATGTGCATATCATATCA
Found at i:38698552 original size:27 final size:26
Alignment explanation
Indices: 38698517--38698594 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 26
38698507 GGGCATATTC
38698517 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACC-TACAGGGGTATTACG
* *
38698544 GTCACTTTACCCTGCAGGGGCT-TTACG
1 GTCATTTTA-CCTACAGGGG-TATTACG
*
38698571 GTCATTTTACCTAATAGGGGTATT
1 GTCATTTTACCT-ACAGGGGTATT
38698595 TTAGTCATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
26 4 0.10
27 35 0.83
28 3 0.07
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (26 bp):
GTCATTTTACCTACAGGGGTATTACG
Found at i:38698665 original size:27 final size:27
Alignment explanation
Indices: 38698635--38698718 Score: 82
Period size: 27 Copynumber: 3.0 Consensus size: 27
38698625 GTAAATCTAC
38698635 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
*
38698662 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTC-AGTAATTTTGT
* * *
38698688 AGAAAGTCAAGGGTATTTCTGTAACTTTGT
1 --AAA-CCAAGGGTATTTCAGTAATTTTGT
38698718 A
1 A
38698719 GATCAGAGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
26 1 0.02
27 22 0.48
28 5 0.11
29 17 0.37
30 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:38698756 original size:27 final size:27
Alignment explanation
Indices: 38698726--38698848 Score: 167
Period size: 27 Copynumber: 4.6 Consensus size: 27
38698716 GTAGATCAGA
*
38698726 GGTATTTTGGTAATTTTACAAA-TTGAG
1 GGTATTTTGGTAATTTTACAAACTAG-G
* * * * *
38698753 GGTATTTCGATAATTTCACAAACCAGT
1 GGTATTTTGGTAATTTTACAAACTAGG
38698780 GGTATTTTGGTAATTTTACAAACTAGG
1 GGTATTTTGGTAATTTTACAAACTAGG
38698807 GGTATTTTGGTAATTTTACAAACTAGG
1 GGTATTTTGGTAATTTTACAAACTAGG
*
38698834 GGTAATTTGGTAATT
1 GGTATTTTGGTAATT
38698849 CTATCCTACA
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
27 82 0.99
28 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (27 bp):
GGTATTTTGGTAATTTTACAAACTAGG
Found at i:38698784 original size:54 final size:54
Alignment explanation
Indices: 38698726--38698881 Score: 181
Period size: 54 Copynumber: 2.9 Consensus size: 54
38698716 GTAGATCAGA
* *
38698726 GGTATTTTGGTAATTTTACAAA-TTGAGGGTATTTCGATAATTTCACAAACCAGT
1 GGTATTTTGGTAATTTTACAAACTAG-GGGTATTTCGATAATTTCACAAACCAGG
* * * *
38698780 GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAGG
1 GGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGATAATTTCACAAACCAGG
* * ** *
38698834 GGTAATTTGGTAATTCTATCCTAC-AGGGGTATTTCAATAATTTCACAA
1 GGTATTTTGGTAATTTTA-CAAACTAGGGGTATTTCGATAATTTCACAA
38698882 TCGAGGGTAA
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
54 81 0.94
55 5 0.06
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (54 bp):
GGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGATAATTTCACAAACCAGG
Found at i:38698914 original size:27 final size:27
Alignment explanation
Indices: 38698880--38699079 Score: 242
Period size: 27 Copynumber: 7.4 Consensus size: 27
38698870 ATAATTTCAC
*
38698880 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
*
38698907 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAACGGTAATTTTGTA
*
38698934 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * *
38698961 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* *
38698988 AATTGAGGGTAAAACGGTAATTTTCTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * *
38699015 AATCGAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* **
38699042 AATCGAGGGTAAAATC-GTAATTCTACA
1 AATCGAGGGTAAAA-CGGTAATTTTGTA
38699069 AATCGAGGGTA
1 AATCGAGGGTA
38699080 TTTTAGTAAT
Statistics
Matches: 156, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
26 1 0.01
27 153 0.98
28 2 0.01
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTTTGTA
Found at i:38698955 original size:54 final size:54
Alignment explanation
Indices: 38698880--38699079 Score: 269
Period size: 54 Copynumber: 3.7 Consensus size: 54
38698870 ATAATTTCAC
* * *
38698880 AATCGAGGGTAAAACGATAATTTTGTAAA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTAAATC-GAGGGTAAAATGGTAATTCTATA
*
38698934 AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
* * * *
38698988 AATTGAGGGTAAAACGGTAATTTTCTAAATCGAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
* **
38699042 AATCGAGGGTAAAATC-GTAATTCTACAAATCGAGGGTA
1 AATCGAGGGTAAAA-CGGTAATTTTGTAAATCGAGGGTA
38699080 TTTTAGTAAT
Statistics
Matches: 130, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
54 128 0.98
55 2 0.02
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (54 bp):
AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
Found at i:38698996 original size:81 final size:81
Alignment explanation
Indices: 38698880--38699079 Score: 274
Period size: 81 Copynumber: 2.5 Consensus size: 81
38698870 ATAATTTCAC
* * * * * * *
38698880 AATCGAGGGTAAAACGATAATTTTGTAAACTGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTA
1 AATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAACGGTAATTTTCTAAATCGAGGGTA
* * *
38698945 AAATGGTAATTTTGTA
66 AAACGGTAATTCTATA
*
38698961 AATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAACGGTAATTTTCTAAATCGAGGGTG
1 AATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAACGGTAATTTTCTAAATCGAGGGTA
38699026 AAACGGTAATTCTATA
66 AAACGGTAATTCTATA
* * *
38699042 AATCGAGGGTAAAATCGTAATTCTACAAATCGAGGGTA
1 AATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTA
38699080 TTTTAGTAAT
Statistics
Matches: 105, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 105 1.00
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (81 bp):
AATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAACGGTAATTTTCTAAATCGAGGGTA
AAACGGTAATTCTATA
Found at i:38707514 original size:27 final size:27
Alignment explanation
Indices: 38707484--38707661 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
38707474 ATATTGAGCC
* *
38707484 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
38707511 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
38707538 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
38707566 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* * **
38707593 CGTACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
38707620 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
38707647 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38707662 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:38715101 original size:27 final size:27
Alignment explanation
Indices: 38715071--38715248 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
38715061 ATATTGAGCC
* * * *
38715071 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
38715098 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38715125 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
38715153 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
38715180 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
38715207 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38715234 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38715249 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:38715210 original size:82 final size:81
Alignment explanation
Indices: 38715092--38715247 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
38715082 TGCTATATAA
* *
38715092 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
38715157 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
38715174 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
38715238 CACTTAGTGC
65 CACTTAGTGC
38715248 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:38719560 original size:38 final size:38
Alignment explanation
Indices: 38719509--38719585 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
38719499 TCCATAATCA
38719509 AATTTGATTTATTCTCCCTTTTTATTCTATTGAATTTT
1 AATTTGATTTATTCTCCCTTTTTATTCTATTGAATTTT
*
38719547 AATTTGATTTATTCTCCCTTTTTATTCTATTGGATTTT
1 AATTTGATTTATTCTCCCTTTTTATTCTATTGAATTTT
38719585 A
1 A
38719586 TCTTTTTATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.13, G:0.06, T:0.60
Consensus pattern (38 bp):
AATTTGATTTATTCTCCCTTTTTATTCTATTGAATTTT
Found at i:38734675 original size:8 final size:8
Alignment explanation
Indices: 38734662--38734708 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
38734652 ACACCCAGAT
38734662 TCACATAA
1 TCACATAA
38734670 TCACAT-A
1 TCACATAA
38734677 TACACATAA
1 T-CACATAA
* *
38734686 TCTCATGA
1 TCACATAA
*
38734694 GCACATAA
1 TCACATAA
38734702 TCACATA
1 TCACATA
38734709 GTTCCTAGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
7 2 0.06
8 27 0.87
9 2 0.06
ACGTcount: A:0.45, C:0.26, G:0.04, T:0.26
Consensus pattern (8 bp):
TCACATAA
Found at i:38740669 original size:20 final size:20
Alignment explanation
Indices: 38740644--38740684 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
38740634 GAATACGAAG
38740644 GAGTCTCAGTTGAAAATTGA
1 GAGTCTCAGTTGAAAATTGA
*
38740664 GAGTCTGAGTTGAAAATTGA
1 GAGTCTCAGTTGAAAATTGA
38740684 G
1 G
38740685 TTAGTACTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.29
Consensus pattern (20 bp):
GAGTCTCAGTTGAAAATTGA
Found at i:38745847 original size:46 final size:46
Alignment explanation
Indices: 38745797--38745951 Score: 138
Period size: 46 Copynumber: 3.3 Consensus size: 46
38745787 ACTCAGACGA
*
38745797 AACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGAACTC
1 AACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTC
* * * * *
38745843 AACTCAAGGAGCTCGAATGCCTAGTT-ACAT-C-TCA-CGAACTCGGACTC
1 AACTCAACGAGCTCG---GGC--GTTCGCATCCATAAGTGAACTCGGACTC
* * *
38745890 AACTCAATGAGTTCGGGCATTCGCATCCATAAGTGAACTCGGACTC
1 AACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTC
* *
38745936 AACTCTACGAGGTCGG
1 AACTCAACGAGCTCGG
38745952 ATGCCCAAAT
Statistics
Matches: 84, Mismatches: 16, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
42 2 0.02
43 3 0.04
44 3 0.04
45 2 0.02
46 39 0.46
47 24 0.29
48 2 0.02
49 3 0.04
50 3 0.04
51 3 0.04
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.21
Consensus pattern (46 bp):
AACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTC
Found at i:38746284 original size:18 final size:18
Alignment explanation
Indices: 38746261--38746306 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
38746251 CTTGGTATTT
38746261 TTTCGATTTTAGCCCGAA
1 TTTCGATTTTAGCCCGAA
38746279 TTTCGATTTTAGCCCGAA
1 TTTCGATTTTAGCCCGAA
38746297 TTTCGATTTT
1 TTTCGATTTT
38746307 CCTTTCTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (18 bp):
TTTCGATTTTAGCCCGAA
Found at i:38748747 original size:30 final size:29
Alignment explanation
Indices: 38748705--38748761 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
38748695 AAAGATAACA
* *
38748705 AGAAAACCGAATAAAGAAATCTAAGATTG
1 AGAAAACCGAATAAAAAAATCCAAGATTG
*
38748734 AGAAACCCAGAATAAAAAAATCCAAGAT
1 AGAAAACC-GAATAAAAAAATCCAAGAT
38748762 ACGATACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.58, C:0.14, G:0.14, T:0.14
Consensus pattern (29 bp):
AGAAAACCGAATAAAAAAATCCAAGATTG
Found at i:38751876 original size:46 final size:46
Alignment explanation
Indices: 38751701--38751869 Score: 157
Period size: 46 Copynumber: 3.7 Consensus size: 46
38751691 TGTAACCCGC
** * *
38751701 CCATAAGCGAACTCAGACGAAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACGTTCGCAT
* * * *
38751747 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAATGCCTAGTT-ACAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCG---GAC--GTTCGCAT
* * *
38751797 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACGTTCGCAT
*
38751840 CCATAAGTGAACTCAGACTCAACTCAACGA
1 CCATAAGCGAACTCAGACTCAACTCAACGA
38751870 CTTCGGATGC
Statistics
Matches: 99, Mismatches: 15, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 3 0.03
45 2 0.02
46 51 0.52
47 26 0.26
48 2 0.02
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:38752810 original size:13 final size:13
Alignment explanation
Indices: 38752792--38752816 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38752782 TAATGGTATA
38752792 TTGAATCCATGAT
1 TTGAATCCATGAT
38752805 TTGAATCCATGA
1 TTGAATCCATGA
38752817 AAATTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:38754562 original size:51 final size:49
Alignment explanation
Indices: 38754426--38755144 Score: 1071
Period size: 47 Copynumber: 14.5 Consensus size: 49
38754416 TTATTCATTG
* *
38754426 GAATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
38754473 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
38754522 GAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG--TATATATATGTGATAAGGCCTAATGGCCGATGTGAT
* *
38754573 GAATGTGAAAGTGTATATATATGTGATAAGACCTAATGGCCAATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
38754622 GAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG--TATATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
38754673 GAATGGGAAAGTGTATATATATATGTGATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG--------TA--T-ATATATGTGATAAGGCCTAATGGCCGATGTGAT
**
38754733 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCTAATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
* *
38754782 GAATCTGAAAGTGTATATATATATGTGATAAGGCCTAATGGCCAATGTGAT
1 GAATGTGAAAGTG--TATATATATGTGATAAGGCCTAATGGCCGATGTGAT
38754833 GAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG--TATATATATGTGATAAGGCCTAATGGCCGATGTGAT
38754884 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
* *
38754933 GAATGTGAAAGTG--TATATATGTGATAAGGCGTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
* *
38754980 GAATGTGAAAGTG--TATATATGTGATAAGGCTTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
38755027 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
38755074 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
38755121 GAATGTGAAAGTGTATATATATGT
1 GAATGTGAAAGTGTATATATATGT
38755145 TGTAACACCC
Statistics
Matches: 634, Mismatches: 19, Indels: 36
0.92 0.03 0.05
Matches are distributed among these distances:
47 196 0.31
49 193 0.30
50 1 0.00
51 192 0.30
52 2 0.00
57 4 0.01
59 1 0.00
60 45 0.07
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.31
Consensus pattern (49 bp):
GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
Found at i:38754595 original size:100 final size:100
Alignment explanation
Indices: 38754439--38755142 Score: 1067
Period size: 100 Copynumber: 7.0 Consensus size: 100
38754429 TGTGAAAGTG
* *
38754439 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
38754504 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
66 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
*
38754539 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
*
38754604 CCTAATGGCCAATGTGATGAATGTGAAAGTGTATA
66 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
*
38754639 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGGGAAAGTGTATATATATATGTGATAT
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--------TA--T-ATAT
38754704 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TA
55 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
** *
38754748 TATATATGTGATAAGGCCTAATGGCTAATGTGATGAATCTGAAAGTGTATATATATATGTGATAA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATATGTGATAA
*
38754813 GGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATA
64 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
38754850 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
38754915 CCTAATGGCCGATGTGATGAATGTGAAAGTG----
66 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* *
38754946 TATATATGTGATAAGGCGTAATAGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
* *
38755009 CTTAATAGCCGATGTGATGAATGTGAAAGTG----
66 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
*
38755040 TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
38755103 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
66 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
38755138 TATAT
1 TATAT
38755143 GTTGTAACAC
Statistics
Matches: 564, Mismatches: 23, Indels: 36
0.91 0.04 0.06
Matches are distributed among these distances:
94 136 0.24
96 45 0.08
98 5 0.01
100 235 0.42
101 1 0.00
102 46 0.08
103 4 0.01
108 2 0.00
109 45 0.08
110 1 0.00
111 44 0.08
ACGTcount: A:0.34, C:0.08, G:0.27, T:0.31
Consensus pattern (100 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
CCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
Found at i:38754739 original size:31 final size:31
Alignment explanation
Indices: 38754644--38754740 Score: 87
Period size: 31 Copynumber: 3.2 Consensus size: 31
38754634 GTATATATAT
38754644 ATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGATAAGGCCTAATGGCCGATGTGATGA
* ****
38754675 ATGGGA-AAGTG--TATAT-ATATATGTGAT-A
1 ATGTGATAAG-GCCTA-ATGGCCGATGTGATGA
38754703 TATGTGATAAGGCCTAATGGCCGATGTGATGA
1 -ATGTGATAAGGCCTAATGGCCGATGTGATGA
38754735 ATGTGA
1 ATGTGA
38754741 AAGTGTATAT
Statistics
Matches: 48, Mismatches: 10, Indels: 16
0.65 0.14 0.22
Matches are distributed among these distances:
28 1 0.02
29 15 0.31
30 10 0.21
31 21 0.44
32 1 0.02
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (31 bp):
ATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:38754851 original size:47 final size:47
Alignment explanation
Indices: 38754426--38755140 Score: 953
Period size: 51 Copynumber: 14.4 Consensus size: 47
38754416 TTATTCATTG
* *
38754426 GAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
38754473 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
38754522 GAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG----TATATATGTGATAAGGCCTAATGGCCGATGTGAT
* *
38754573 GAATGTGAAAGTGTATATATATGTGATAAGACCTAATGGCCAATGTGAT
1 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
38754622 GAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG----TATATATGTGATAAGGCCTAATGGCCGATGTGAT
* * *
38754673 GAATGGGAAAGTGTATATATATATGTGATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG----TATATATGTGATA-A---G----GCCT-AATGGCCGATGTGAT
**
38754733 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCTAATGTGAT
1 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
* *
38754782 GAATCTGAAAGTGTATATATATATGTGATAAGGCCTAATGGCCAATGTGAT
1 GAATGTGAAAGTG----TATATATGTGATAAGGCCTAATGGCCGATGTGAT
38754833 GAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG----TATATATGTGATAAGGCCTAATGGCCGATGTGAT
38754884 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
* *
38754933 GAATGTGAAAGTGTATATATGTGATAAGGCGTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
* *
38754980 GAATGTGAAAGTGTATATATGTGATAAGGCTTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
38755027 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
38755074 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
38755121 GAATGTGAAAGTGTATATAT
1 GAATGTGAAAGTGTATATAT
38755141 ATGTTGTAAC
Statistics
Matches: 628, Mismatches: 23, Indels: 34
0.92 0.03 0.05
Matches are distributed among these distances:
47 203 0.32
49 166 0.26
50 2 0.00
51 209 0.33
52 1 0.00
54 1 0.00
55 1 0.00
57 1 0.00
58 15 0.02
59 2 0.00
60 27 0.04
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.31
Consensus pattern (47 bp):
GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
Found at i:38756574 original size:39 final size:40
Alignment explanation
Indices: 38756529--38756700 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
38756519 GCTCCTCGTT
* * *
38756529 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
38756569 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
38756608 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
38756648 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
38756688 CAAATGCCTTCGG
1 CAAATGCCTTCGG
38756701 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:38756629 original size:40 final size:39
Alignment explanation
Indices: 38756531--38756753 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
38756521 TCCTCGTTCA
* * * *
38756531 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
38756570 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
38756609 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
38756649 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
38756689 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
38756730 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
38756754 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:38756713 original size:80 final size:79
Alignment explanation
Indices: 38756529--38756753 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
38756519 GCTCCTCGTT
* * * * *
38756529 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
38756593 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
38756608 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
38756673 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
38756688 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
38756752 GA
63 GA
38756754 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:38756762 original size:41 final size:41
Alignment explanation
Indices: 38756685--38756762 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
38756675 TTTGTATCTC
* * *
38756685 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
38756726 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
38756763 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:38764555 original size:40 final size:40
Alignment explanation
Indices: 38764455--38764626 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
38764445 GCTCCTCGTT
* * *
38764455 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* *
38764495 C-AATGCCTTCGGGACATAACCCAGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
38764534 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
38764574 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
38764614 CAAATGCCTTCGG
1 CAAATGCCTTCGG
38764627 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.29
40 79 0.68
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:38764639 original size:80 final size:79
Alignment explanation
Indices: 38764455--38764679 Score: 231
Period size: 80 Copynumber: 2.8 Consensus size: 79
38764445 GCTCCTCGTT
* * * * * *
38764455 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCAG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
38764519 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
38764534 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
38764599 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
38764614 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
38764678 GA
63 GA
38764680 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 68 0.56
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:38764688 original size:41 final size:41
Alignment explanation
Indices: 38764611--38764688 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
38764601 TTTGTATCTC
* * *
38764611 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
38764652 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
38764689 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:38780664 original size:40 final size:40
Alignment explanation
Indices: 38780569--38780819 Score: 314
Period size: 40 Copynumber: 6.3 Consensus size: 40
38780559 ACCCAAGTAT
*
38780569 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
38780608 C-TCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
38780647 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
38780687 CTTCGGGACATAGCCCGAATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
38780727 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
38780767 CTTCGGGACATAGCCTGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
*
38780807 CTTCGGATCTTAG
1 CTTCGGGTCTTAG
38780820 TCCGATTATC
Statistics
Matches: 180, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
37 1 0.01
38 9 0.05
39 31 0.17
40 135 0.75
41 4 0.02
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:38780710 original size:80 final size:80
Alignment explanation
Indices: 38780569--38780819 Score: 393
Period size: 80 Copynumber: 3.2 Consensus size: 80
38780559 ACCCAAGTAT
* * * *
38780569 CTTCGGGAT-TTAG-CCGGATATAA-CAACTCGCACAAATGCC-TCGGGTCTTAGCCCGGATATA
1 CTTCGGG-TCTTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGACATAGCCCGGATATA
38780630 GCAACTCGCACAAATGC
64 GCAACTCGCACAAATGC
*
38780647 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACATAGCCCGAATATAGC
1 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACATAGCCCGGATATAGC
38780712 AACTCGCACAAATGC
66 AACTCGCACAAATGC
*
38780727 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACATAGCCTGGATATAGC
1 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACATAGCCCGGATATAGC
38780792 AACTCGCACAAATGC
66 AACTCGCACAAATGC
*
38780807 CTTCGGATCTTAG
1 CTTCGGGTCTTAG
38780820 TCCGATTATC
Statistics
Matches: 161, Mismatches: 8, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
77 1 0.01
78 11 0.07
79 23 0.14
80 126 0.78
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACATAGCCCGGATATAGC
AACTCGCACAAATGC
Found at i:38786222 original size:40 final size:40
Alignment explanation
Indices: 38786164--38786385 Score: 313
Period size: 40 Copynumber: 5.6 Consensus size: 40
38786154 TATTCGAATG
*
38786164 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
38786204 ATGTCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
38786244 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
38786284 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * * *
38786324 ATATCTGGGCTTAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
* * *
38786364 ATAT-CTGGCTAAATCCTGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
38786386 TACTTGGGTT
Statistics
Matches: 162, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 12 0.07
40 148 0.91
41 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.30
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:38787911 original size:40 final size:40
Alignment explanation
Indices: 38787849--38787961 Score: 145
Period size: 40 Copynumber: 2.8 Consensus size: 40
38787839 TCACAGGCCG
* * *
38787849 GCTCACACAAGCTGACAATCAGGATGTAACTATACGGGCT
1 GCTCACACAAGCTGACAGTCAGGATGTAACTACAAGGGCT
* * *
38787889 GCTCACATAAGCTAACGGTCAGGATGTAACTACAAGGGCT
1 GCTCACACAAGCTGACAGTCAGGATGTAACTACAAGGGCT
* * *
38787929 GCTCATACAATCTGACAGTCAGGAAGTAACTAC
1 GCTCACACAAGCTGACAGTCAGGATGTAACTAC
38787962 TCAGGCTTGT
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (40 bp):
GCTCACACAAGCTGACAGTCAGGATGTAACTACAAGGGCT
Found at i:38799452 original size:32 final size:33
Alignment explanation
Indices: 38799373--38799453 Score: 105
Period size: 32 Copynumber: 2.5 Consensus size: 33
38799363 ACAGTCTCAA
**
38799373 TTGGGCCTAGCCCATCATAGAATCAATATCAGT
1 TTGGGCCTAGCCCATTTTAGAATCAATATCAGT
*
38799406 TTGGG-CTCGCCCATTTTAGAAT-AAGTATCAG-
1 TTGGGCCTAGCCCATTTTAGAATCAA-TATCAGT
38799437 TTGGGCCTAGCCCATTT
1 TTGGGCCTAGCCCATTT
38799454 CAATATCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 7 0.17
32 30 0.71
33 5 0.12
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (33 bp):
TTGGGCCTAGCCCATTTTAGAATCAATATCAGT
Found at i:38812016 original size:13 final size:13
Alignment explanation
Indices: 38811998--38812034 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
38811988 TTCGACAGGG
*
38811998 ACACGCCTGTGGC
1 ACACGCCCGTGGC
38812011 ACACGCCCGTGGC
1 ACACGCCCGTGGC
38812024 ACACGCCCGTG
1 ACACGCCCGTG
38812035 TTCGATTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.16, C:0.43, G:0.30, T:0.11
Consensus pattern (13 bp):
ACACGCCCGTGGC
Found at i:38813629 original size:39 final size:38
Alignment explanation
Indices: 38813547--38813646 Score: 119
Period size: 39 Copynumber: 2.6 Consensus size: 38
38813537 AAAATCCTTG
* *
38813547 TTATAATTATTGTAATTATAATTTACTATCAAATATTA
1 TTATAATTATTGTAATTGTAATTTACTATCAAACATTA
* ** *
38813585 TTATAATTATTGTAATTGTATTTTTTTGGTCAAACATTA
1 TTATAATTATTGTAATTGTAATTTACT-ATCAAACATTA
**
38813624 TTATAATTACAGTAATTGTAATT
1 TTATAATTATTGTAATTGTAATT
38813647 ATTATATTTG
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
38 23 0.44
39 29 0.56
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (38 bp):
TTATAATTATTGTAATTGTAATTTACTATCAAACATTA
Found at i:38822046 original size:52 final size:51
Alignment explanation
Indices: 38821925--38822101 Score: 225
Period size: 51 Copynumber: 3.5 Consensus size: 51
38821915 CGGATACCTG
* * ** * *
38821925 GTGGCCTGCACATAGTACCACCCTTGTGGTCAAAGCTACCTTCTTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTCTTCATAAA
*
38821976 GTGGCCTTCACATCGTACCACACTTGTGACCAAAGCTATCTTTCTTCATAAA
1 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATC-TTCTTCATAAA
* *
38822028 GTGGCCTTCATATGGTACCACACTTGTGACC-AAGCTATC-TCTTC-TCAAA
1 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTCTTCAT-AAA
*
38822077 GTGGCCTTCACATAGTACCCCACTT
1 GTGGCCTTCACATAGTACCACACTT
38822102 AAGTCACTAG
Statistics
Matches: 112, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
48 1 0.01
49 30 0.27
51 42 0.38
52 39 0.35
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.29
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTCTTCATAAA
Found at i:38824927 original size:47 final size:47
Alignment explanation
Indices: 38824857--38825156 Score: 447
Period size: 47 Copynumber: 6.4 Consensus size: 47
38824847 CCCTTCGGGA
* * * * *
38824857 CTTATCACATTTATACGCTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
38824904 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
38824951 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
38824998 CTTATCACATATATACACTTTCACATTAATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
38825045 CTTATCACATATACACACCTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38825092 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
38825139 CTTATCACATATACACAC
1 CTTATCACATATATACAC
38825157 CTTGTACATC
Statistics
Matches: 227, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 227 1.00
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:38825021 original size:94 final size:94
Alignment explanation
Indices: 38824857--38825156 Score: 501
Period size: 94 Copynumber: 3.2 Consensus size: 94
38824847 CCCTTCGGGA
* * * *
38824857 CTTATCACATTTATACGCTTTCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
* * *
38824922 CTTCACATCCATCACATCGGCCATTAGGT
66 TTTCACATTCATCACATCGGCCATTAGGC
* *
38824951 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
*
38825016 TTTCACATTAATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
*
38825045 CTTATCACATATACACACCTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
38825110 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
38825139 CTTATCACATATACACAC
1 CTTATCACATATACACAC
38825157 CTTGTACATC
Statistics
Matches: 194, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 194 1.00
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (94 bp):
CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:38825921 original size:12 final size:12
Alignment explanation
Indices: 38825893--38825921 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
38825883 TATATCTATA
38825893 TGGTAGAATTTT
1 TGGTAGAATTTT
38825905 T-GTAGAATTTT
1 TGGTAGAATTTT
38825916 TGGTAG
1 TGGTAG
38825922 GGCCAATTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (12 bp):
TGGTAGAATTTT
Found at i:38827201 original size:29 final size:27
Alignment explanation
Indices: 38827183--38827252 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
38827173 ATATTAAGTC
38827183 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
38827210 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
38827238 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
38827253 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:38827246 original size:28 final size:28
Alignment explanation
Indices: 38827183--38827280 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
38827173 ATATTAAGTC
*
38827183 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
38827210 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
38827238 CGCACACTTAGTGCTGTACAATTTAAACG
1 CGCACACTTAGTGCTATATAA-TCAAACT
38827267 CGCACACTTAGTGC
1 CGCACACTTAGTGC
38827281 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:38841615 original size:64 final size:64
Alignment explanation
Indices: 38841535--38841697 Score: 177
Period size: 67 Copynumber: 2.5 Consensus size: 64
38841525 AGACATTATG
* * * *
38841535 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACTAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
38841599 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
38841664 AA
63 AA
* *
38841666 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGT
1 A-TGTAGCTAGGTCGCATGGGTGGTACTATGTGT
38841698 TCACTGTAAT
Statistics
Matches: 79, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
63 1 0.01
64 25 0.32
66 21 0.27
67 30 0.38
68 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:38843011 original size:46 final size:46
Alignment explanation
Indices: 38842958--38843226 Score: 275
Period size: 46 Copynumber: 5.8 Consensus size: 46
38842948 TGGTTGAGCA
38842958 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
38843004 TCTGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
38843049 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * **
38843097 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GAT-TTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
38843142 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
38843190 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
38843227 GCGGGTTACA
Statistics
Matches: 183, Mismatches: 22, Indels: 36
0.76 0.09 0.15
Matches are distributed among these distances:
42 4 0.02
43 9 0.05
45 6 0.03
46 90 0.49
47 56 0.31
48 6 0.03
50 8 0.04
51 4 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:38843076 original size:47 final size:47
Alignment explanation
Indices: 38843007--38843172 Score: 216
Period size: 47 Copynumber: 3.6 Consensus size: 47
38842997 GCGAATGTCT
38843007 GAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCC
* * * *
38843054 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TTC
1 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCC
*
38843100 GAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATTTAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCC
38843147 GAACTCGTTGAGTTGAGTCCGAGTTC
1 GAACTCGTTGAGTTGAGTCCGAGTTC
38843173 ACTTATGGAT
Statistics
Matches: 101, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 28 0.28
47 54 0.53
48 3 0.03
50 5 0.05
51 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (47 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCC
Found at i:38843114 original size:93 final size:92
Alignment explanation
Indices: 38842955--38843219 Score: 467
Period size: 93 Copynumber: 2.8 Consensus size: 92
38842945 GGATGGTTGA
38842955 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC-GAACTCGTTGAGT
38843020 TGAGTCCGAGTTCGTGAGATGTAACTAG
65 TGAGTCCGAGTTCGTGAGATGTAACTAG
38843048 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-TCGAACTCGTTGAGT
*
38843113 TGAGTCCGAGTTCGTGAGATTTAACTAG
65 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
38843141 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-TCGAACTCGTTGAGT
38843206 TGAGTCCGAGTTCG
65 TGAGTCCGAGTTCG
38843220 CTTATGGGCG
Statistics
Matches: 166, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
93 164 0.99
94 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:38845431 original size:27 final size:27
Alignment explanation
Indices: 38845401--38845578 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
38845391 ATATTGAGTC
* * *
38845401 CGCACACTCAGTGCTATATAATCACCT
1 CGCACACTTAGTGCTACATAATCAACT
* *
38845428 CGCACACTTAGTGTTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
38845455 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
38845483 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
38845510 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
38845537 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
38845564 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38845579 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:38845540 original size:82 final size:81
Alignment explanation
Indices: 38845427--38845577 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 81
38845417 TATAATCACC
* *
38845427 TCGCACACTTAGTGTTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 TCGCACACTTAGTGATACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCACACTT
38845492 AGTGCCGCATGGTCAAT
65 AGTGCCGCATGGTCAAT
* **
38845509 TCGCACACTTAGTGCAT-CATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
1 TCGCACACTTAGTG-ATACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
38845573 AGTGC
65 AGTGC
38845578 TGTACAATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.24
82 47 0.75
83 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (81 bp):
TCGCACACTTAGTGATACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTTA
GTGCCGCATGGTCAAT
Found at i:38845550 original size:54 final size:55
Alignment explanation
Indices: 38845401--38845578 Score: 200
Period size: 54 Copynumber: 3.3 Consensus size: 55
38845391 ATATTGAGTC
* * * * ** *
38845401 CGCACACTCAGTGCTATATAATC-ACCTCGCACACTTAGTGTTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
** * *
38845455 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
* **
38845510 CGCACACTTAGTGC-ATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
38845564 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38845579 GTACAATTTA
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
54 60 0.58
55 44 0.42
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:38846077 original size:12 final size:12
Alignment explanation
Indices: 38846060--38846085 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
38846050 ATGGCATACT
38846060 TATGTATATATA
1 TATGTATATATA
38846072 TATGTATATATA
1 TATGTATATATA
38846084 TA
1 TA
38846086 CTTCGGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:38853540 original size:27 final size:27
Alignment explanation
Indices: 38853510--38853687 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
38853500 ATATTGAGTC
* * * *
38853510 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
38853537 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38853564 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
38853592 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
38853619 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
38853646 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38853673 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38853688 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:38853649 original size:82 final size:81
Alignment explanation
Indices: 38853531--38853686 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
38853521 TGCTATATAA
* *
38853531 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
38853596 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
38853613 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
38853677 CACTTAGTGC
65 CACTTAGTGC
38853687 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:38854186 original size:12 final size:12
Alignment explanation
Indices: 38854169--38854194 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
38854159 ATGGCATACT
38854169 TATGTATATATA
1 TATGTATATATA
38854181 TATGTATATATA
1 TATGTATATATA
38854193 TA
1 TA
38854195 CTTCGGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:38856800 original size:40 final size:40
Alignment explanation
Indices: 38856733--38856944 Score: 261
Period size: 40 Copynumber: 5.3 Consensus size: 40
38856723 ACCCAAGTAT
*
38856733 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
38856772 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
38856812 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
38856852 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * * *
38856892 CTTCGGGACATAGCCCGGATATAGAAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
*
38856932 CTTCGGATCTTAG
1 CTTCGGGTCTTAG
38856945 TCCAGTTATC
Statistics
Matches: 155, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
38 1 0.01
39 12 0.08
40 140 0.90
41 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:38862337 original size:21 final size:21
Alignment explanation
Indices: 38862313--38862366 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
38862303 TGCAGGGCTC
**
38862313 ACACACTCGTGTG-GTCTAGAG
1 ACACACTCGTGTGACCCTA-AG
*
38862334 ACACGCTCGTGTGACCCTAAG
1 ACACACTCGTGTGACCCTAAG
38862355 ACACACTCGTGT
1 ACACACTCGTGT
38862367 TGTAGGCTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (21 bp):
ACACACTCGTGTGACCCTAAG
Found at i:38863647 original size:57 final size:58
Alignment explanation
Indices: 38863548--38863689 Score: 162
Period size: 57 Copynumber: 2.5 Consensus size: 58
38863538 TAACATATAA
** * * *
38863548 TAGGATTACTAGTCCAGGCTAAATCCTTTTTGTAATATATGCTC-AGAAGAGCCCA-AT
1 TAGGATTACTAGTCCAGGCTAAATCCTAATTGTAACAAATGCTCGAG-AGAGACCATAT
* * **
38863605 TAGGATTACTAGTCCAGGCTAAATCCTAATTGTAGCAAATGCTCGAGAGGGATTATAT
1 TAGGATTACTAGTCCAGGCTAAATCCTAATTGTAACAAATGCTCGAGAGAGACCATAT
* *
38863663 CAGGATTACTAGTCTAGGCTAAATCCT
1 TAGGATTACTAGTCCAGGCTAAATCCT
38863690 GTCAACAACA
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
57 43 0.60
58 29 0.40
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (58 bp):
TAGGATTACTAGTCCAGGCTAAATCCTAATTGTAACAAATGCTCGAGAGAGACCATAT
Found at i:38884261 original size:20 final size:20
Alignment explanation
Indices: 38884238--38884303 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
38884228 GAAGTACAAA
*
38884238 CAGGGGCATGTAACTGCAAT
1 CAGGGGCATGTAAGTGCAAT
* * * *
38884258 CAGGGGTACCG-AAGTACAAA
1 CAGGGGCA-TGTAAGTGCAAT
*
38884278 CAGGGGCATTTAAGTGCAAT
1 CAGGGGCATGTAAGTGCAAT
38884298 CAGGGG
1 CAGGGG
38884304 TACTAAAGTA
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
20 33 0.97
21 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.33, T:0.17
Consensus pattern (20 bp):
CAGGGGCATGTAAGTGCAAT
Found at i:38884263 original size:40 final size:40
Alignment explanation
Indices: 38884219--38884337 Score: 175
Period size: 40 Copynumber: 3.0 Consensus size: 40
38884209 ATGTGCATTT
* *
38884219 AGGGGTGCCGAAGTACAAACAGGGGCATGTAACTGCAATC
1 AGGGGTACCGAAGTACAAACAGGGGCATGTAAGTGCAATC
*
38884259 AGGGGTACCGAAGTACAAACAGGGGCATTTAAGTGCAATC
1 AGGGGTACCGAAGTACAAACAGGGGCATGTAAGTGCAATC
** * *
38884299 AGGGGTACTAAAGTACAAACATGGGCACGTAAGTGCAAT
1 AGGGGTACCGAAGTACAAACAGGGGCATGTAAGTGCAAT
38884338 AATTCAATAA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.35, C:0.18, G:0.30, T:0.17
Consensus pattern (40 bp):
AGGGGTACCGAAGTACAAACAGGGGCATGTAAGTGCAATC
Found at i:38884312 original size:20 final size:20
Alignment explanation
Indices: 38884252--38884312 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
38884242 GGCATGTAAC
**
38884252 TGCAATCAGGGGTACCGAAG
1 TGCAATCAGGGGTACTAAAG
* * * * *
38884272 TACAAACAGGGGCATTTAAG
1 TGCAATCAGGGGTACTAAAG
38884292 TGCAATCAGGGGTACTAAAG
1 TGCAATCAGGGGTACTAAAG
38884312 T
1 T
38884313 ACAAACATGG
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (20 bp):
TGCAATCAGGGGTACTAAAG
Found at i:38887290 original size:27 final size:26
Alignment explanation
Indices: 38887246--38887297 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
38887236 GGACTACCGA
*
38887246 TTTACCCCTAGAGGGTAAAATGACTAT
1 TTTACCCCTAGAGCGT-AAATGACTAT
* *
38887273 TTTACCCCTCGTGCGTAAATGACTA
1 TTTACCCCTAGAGCGTAAATGACTA
38887298 ACTTGTGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (26 bp):
TTTACCCCTAGAGCGTAAATGACTAT
Found at i:38899102 original size:20 final size:21
Alignment explanation
Indices: 38899074--38899116 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
38899064 ACCCCTGCAG
* *
38899074 TTTTAAAAATTTTTAT-TGTT
1 TTTTAAAAAATTCTATATGTT
*
38899094 TTTTGAAAAATTCTATATGTT
1 TTTTAAAAAATTCTATATGTT
38899115 TT
1 TT
38899117 CGATTTAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.60
Consensus pattern (21 bp):
TTTTAAAAAATTCTATATGTT
Found at i:38899114 original size:21 final size:20
Alignment explanation
Indices: 38899074--38899116 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
38899064 ACCCCTGCAG
*
38899074 TTTTAAAAATTTTTATTGTT
1 TTTTAAAAATTTATATTGTT
38899094 TTTTGAAAAATTCTATA-TGTT
1 TTTT-AAAAATT-TATATTGTT
38899115 TT
1 TT
38899117 CGATTTAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 13 0.65
22 3 0.15
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.60
Consensus pattern (20 bp):
TTTTAAAAATTTATATTGTT
Found at i:38907561 original size:24 final size:25
Alignment explanation
Indices: 38907534--38907599 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
38907524 GATGGGAGGT
***
38907534 TGGAGTGATTTATGGAGTGTATC-A
1 TGGAGTGATTTATGGAGAAAATCAA
*
38907558 TGGAGAGATATTA-GGAGAAAATCAA
1 TGGAGTGAT-TTATGGAGAAAATCAA
38907583 T-GAGTGATTTATGGAGA
1 TGGAGTGATTTATGGAGA
38907600 GATTTAAGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 3 0.09
24 26 0.76
25 5 0.15
ACGTcount: A:0.35, C:0.03, G:0.32, T:0.30
Consensus pattern (25 bp):
TGGAGTGATTTATGGAGAAAATCAA
Found at i:38911386 original size:38 final size:39
Alignment explanation
Indices: 38911340--38911427 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 39
38911330 AAAATCCTTG
* *
38911340 TTATAATTATTGTAATTATAA-TTTACGATCAAATATTA
1 TTATAATTATTCTAATTATAATTTTACGATCAAACATTA
* * *
38911378 TTATAATTATTCTAATTGTAATTTTTCGGTCAAACATTA
1 TTATAATTATTCTAATTATAATTTTACGATCAAACATTA
38911417 TTATAATTATT
1 TTATAATTATT
38911428 ATATTCAGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 19 0.43
39 25 0.57
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.50
Consensus pattern (39 bp):
TTATAATTATTCTAATTATAATTTTACGATCAAACATTA
Found at i:38914166 original size:46 final size:46
Alignment explanation
Indices: 38914116--38914284 Score: 191
Period size: 46 Copynumber: 3.7 Consensus size: 46
38914106 TAGGCATCCG
*
38914116 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAGGCAAACGTCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCA
* * * * *
38914162 AACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CGTCCA
* * *
38914209 AACTCGTTGAATTGAGTCCGAGTTCACTTATGGATGCGAACGGCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCA
*
38914255 AGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTA
38914285 GGGGCGGGTT
Statistics
Matches: 100, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 5 0.05
45 3 0.03
46 56 0.56
47 28 0.28
48 3 0.03
50 5 0.05
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCA
Found at i:38914265 original size:93 final size:93
Alignment explanation
Indices: 38914106--38914279 Score: 303
Period size: 93 Copynumber: 1.9 Consensus size: 93
38914096 CTAGGATGTT
* *
38914106 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAGGCAAACGTCCAAACTCGTTG
1 TAGGCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGAGGCAAACGGCCAAACTCGTTG
38914171 AGTTGAGTCCGAGTTCGTGAGATGTAAC
66 AGTTGAGTCCGAGTTCGTGAGATGTAAC
* * *
38914199 TAGGCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGATGCGAACGGCCAAGCTCGTTG
1 TAGGCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGAGGCAAACGGCCAAACTCGTTG
38914264 AGTTGAGTCCGAGTTC
66 AGTTGAGTCCGAGTTC
38914280 ACTTAGGGGC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (93 bp):
TAGGCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGAGGCAAACGGCCAAACTCGTTG
AGTTGAGTCCGAGTTCGTGAGATGTAAC
Found at i:38925452 original size:37 final size:37
Alignment explanation
Indices: 38925402--38925481 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
38925392 CTTATTACGA
* *
38925402 AGTCTTACCCGGACATAA-TCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATTC-CCACACGAAGTCATCG
*
38925439 AGTCTTACCCGGACAAAATTCCCACACGCAGTCATCG
1 AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
*
38925476 GGTCTT
1 AGTCTT
38925482 TATAGCCCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
Found at i:38925671 original size:47 final size:47
Alignment explanation
Indices: 38925612--38926143 Score: 782
Period size: 47 Copynumber: 11.4 Consensus size: 47
38925602 TATCACATTT
* * *
38925612 ATACAC-T-TTCACATTCATCACATCGGCCATTAGGCCTTATCTCAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
* *
38925657 ATACACATGCTCACATTCATCACATTGGCCACTCGGCCTTATCACAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
* * *
38925704 ATACACCTGTTCACTTTCATCACATTGGCCATTCGGCTTTATCACAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
* *
38925751 ATATACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
* * *
38925798 ATATACGTGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
* *
38925845 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAT
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
** *
38925892 ATATGCATGTTCACATTCATCACATTGGCCATTCGGCCCTATCACAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
*
38925939 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
* * *
38925986 ATATACGTGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
* *
38926033 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAT
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
** *
38926080 ATATGCATGTTCACATTCATCACATTGGCCATTCGGCCCTATCACAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
*
38926127 ATATACACT-TTCACATT
1 ATACACA-TGTTCACATT
38926144 TATTCACTTA
Statistics
Matches: 443, Mismatches: 41, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
45 6 0.01
46 1 0.00
47 435 0.98
48 1 0.00
ACGTcount: A:0.26, C:0.31, G:0.11, T:0.32
Consensus pattern (47 bp):
ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
Found at i:38931353 original size:27 final size:27
Alignment explanation
Indices: 38931323--38931500 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
38931313 ATATTGAGTC
* * * *
38931323 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
38931350 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38931377 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
38931405 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
38931432 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
38931459 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38931486 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38931501 GTACAATTCA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:38931462 original size:82 final size:81
Alignment explanation
Indices: 38931344--38931499 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
38931334 TGCTATATAA
* *
38931344 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
38931409 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
38931426 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
38931490 CACTTAGTGC
65 CACTTAGTGC
38931500 TGTACAATTC
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:38931512 original size:82 final size:83
Alignment explanation
Indices: 38931323--38931512 Score: 221
Period size: 82 Copynumber: 2.3 Consensus size: 83
38931313 ATATTGAGTC
* * * * *
38931323 CGCACACTCAGTGCTATATAA-TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTA
1 CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
*
38931387 GTGCTACATAGTCAAACT
66 GTGCAACATAGTCAAACT
* * **
38931405 CGCACACTTAGTGCCG--C-ATGGTCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACAC
1 CGCACACTTAGTGCTGTACAAT--TCAATTCGCACACTTAGTGCTA-CATAATCAAATCGCACAC
38931466 TTAGTGCAACATAGTCAAA-T
63 TTAGTGCAACATAGTCAAACT
38931486 CGCACACTTAGTGCTGTACAATTCAAT
1 CGCACACTTAGTGCTGTACAATTCAAT
38931513 CCCGCGCACT
Statistics
Matches: 90, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
79 1 0.01
81 17 0.19
82 69 0.77
83 1 0.01
84 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (83 bp):
CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
GTGCAACATAGTCAAACT
Found at i:38954870 original size:40 final size:39
Alignment explanation
Indices: 38954815--38954990 Score: 239
Period size: 40 Copynumber: 4.5 Consensus size: 39
38954805 CGGATGATAA
*
38954815 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTATA-T
*
38954855 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAT
38954894 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
* * *
38954934 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTAGTTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTA-CTATAT
* *
38954974 TC-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAG
38954991 ATGCTTGGAT
Statistics
Matches: 125, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
39 51 0.41
40 74 0.59
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAT
Found at i:38954980 original size:79 final size:79
Alignment explanation
Indices: 38954815--38954990 Score: 250
Period size: 79 Copynumber: 2.2 Consensus size: 79
38954805 CGGATGATAA
*
38954815 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTG
* *
38954880 TGCGAGTTCTATAT
66 AGCAAGTTCTATAT
*
38954894 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-TCCGGGCTAAGTCCCGAAGGCATTT
38954958 GAGCAAGTAGT-TATAT
65 GAGCAAGT--TCTATAT
* *
38954974 TC-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAG
38954991 ATGCTTGGAT
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
78 2 0.02
79 79 0.90
80 6 0.07
81 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTG
AGCAAGTTCTATAT
Found at i:38955256 original size:22 final size:21
Alignment explanation
Indices: 38955215--38955258 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
38955205 GAATGTGCAT
38955215 ATATGAAGTTATCCATTTAGCC
1 ATATGAAGTTATCCA-TTAGCC
38955237 ATATGAATGTTATACC-TTAGCC
1 ATATGAA-GTTAT-CCATTAGCC
38955259 GAAACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 5 0.25
24 2 0.10
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
ATATGAAGTTATCCATTAGCC
Found at i:38962786 original size:40 final size:40
Alignment explanation
Indices: 38962731--38962947 Score: 307
Period size: 40 Copynumber: 5.5 Consensus size: 40
38962721 CGGATGATAA
* *
38962731 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGT-CTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-TACTATA-T
38962771 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
38962811 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
38962851 CCAGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
38962891 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TACTTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC-TATAT
* *
38962931 TC-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAG
38962948 ATGCTTGGGT
Statistics
Matches: 164, Mismatches: 10, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
39 18 0.11
40 145 0.88
41 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:38963215 original size:22 final size:21
Alignment explanation
Indices: 38963174--38963217 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
38963164 GAATATGCAT
38963174 ATATGAAGTTATCCATTTAGCC
1 ATATGAAGTTATCCA-TTAGCC
38963196 ATATGAATGTTATACC-TTAGCC
1 ATATGAA-GTTAT-CCATTAGCC
38963218 GAAACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 5 0.25
24 2 0.10
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
ATATGAAGTTATCCATTAGCC
Found at i:38965807 original size:13 final size:13
Alignment explanation
Indices: 38965789--38965817 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38965779 AATACATGAT
38965789 AATTTATATATAA
1 AATTTATATATAA
38965802 AATTTATATATAA
1 AATTTATATATAA
38965815 AAT
1 AAT
38965818 ACAATGGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTTATATATAA
Found at i:38967909 original size:37 final size:37
Alignment explanation
Indices: 38967859--38967937 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
38967849 TTATTACGAA
* *
38967859 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
38967896 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
38967933 GTCTT
1 GTCTT
38967938 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:38968134 original size:47 final size:47
Alignment explanation
Indices: 38968056--38968552 Score: 769
Period size: 47 Copynumber: 10.4 Consensus size: 47
38968046 CCCTTCGGGA
* * * * * * *
38968056 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
38968103 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
38968150 CTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
38968197 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG------C
*
38968250 ACATTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 -C-TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
38968299 CTTATCACATATATACACTCTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
38968346 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38968393 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
38968440 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38968487 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38968534 CTTATCACATATATACACT
1 CTTATCACATATATACACT
38968553 GTCTTGGCTG
Statistics
Matches: 419, Mismatches: 23, Indels: 16
0.91 0.05 0.03
Matches are distributed among these distances:
47 371 0.89
48 1 0.00
49 1 0.00
53 1 0.00
54 1 0.00
55 44 0.11
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:38971149 original size:27 final size:27
Alignment explanation
Indices: 38971107--38971164 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
38971097 TAAAATATGG
*
38971107 GTGGAGGGTACTCCACAGGCGGCACCA
1 GTGGAGGGTACCCCACAGGCGGCACCA
38971134 GTGGAGGGTACCCCACAGGCGGCACCA
1 GTGGAGGGTACCCCACAGGCGGCACCA
38971161 GTGG
1 GTGG
38971165 TGCCTTTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.21, C:0.29, G:0.40, T:0.10
Consensus pattern (27 bp):
GTGGAGGGTACCCCACAGGCGGCACCA
Found at i:38976204 original size:27 final size:27
Alignment explanation
Indices: 38976174--38976351 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
38976164 ATATTGAGTC
* * * *
38976174 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
38976201 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38976228 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
38976256 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
38976283 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
38976310 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38976337 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38976352 GTACAATTCA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:38976313 original size:82 final size:81
Alignment explanation
Indices: 38976195--38976350 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
38976185 TGCTATATAA
* *
38976195 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
38976260 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
38976277 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
38976341 CACTTAGTGC
65 CACTTAGTGC
38976351 TGTACAATTC
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:38976363 original size:82 final size:83
Alignment explanation
Indices: 38976174--38976363 Score: 221
Period size: 82 Copynumber: 2.3 Consensus size: 83
38976164 ATATTGAGTC
* * * * *
38976174 CGCACACTCAGTGCTATATAA-TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTA
1 CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
*
38976238 GTGCTACATAGTCAAACT
66 GTGCAACATAGTCAAACT
* * **
38976256 CGCACACTTAGTGCCG--C-ATGGTCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACAC
1 CGCACACTTAGTGCTGTACAAT--TCAATTCGCACACTTAGTGCTA-CATAATCAAATCGCACAC
38976317 TTAGTGCAACATAGTCAAA-T
63 TTAGTGCAACATAGTCAAACT
38976337 CGCACACTTAGTGCTGTACAATTCAAT
1 CGCACACTTAGTGCTGTACAATTCAAT
38976364 CCCGCGCACT
Statistics
Matches: 90, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
79 1 0.01
81 17 0.19
82 69 0.77
83 1 0.01
84 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (83 bp):
CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
GTGCAACATAGTCAAACT
Found at i:38984279 original size:27 final size:27
Alignment explanation
Indices: 38984249--38984425 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
38984239 ATATTGAGTC
* * * *
38984249 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
38984276 CGCACACTTAGTGCTACGTA-TCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38984302 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
38984330 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
38984357 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
38984384 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38984411 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38984426 GTACAATTCA
Statistics
Matches: 129, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
26 24 0.19
27 81 0.63
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:38984414 original size:81 final size:81
Alignment explanation
Indices: 38984270--38984424 Score: 233
Period size: 81 Copynumber: 1.9 Consensus size: 81
38984260 TGCTATATAA
* *
38984270 TCAACTCGCACACTTAGTGCTACGTATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCAC
1 TCAACTCGCACACTTAGTGCTACATATCAAATCGCACACTTAGTGCAACATAGTCAAACTCGCAC
38984335 ACTTAGTGCCGCATGG
66 ACTTAGTGCCGCATGG
* **
38984351 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAA-TCGC
1 TCAACTCGCACACTTAGTGCTA-CATA-TCAAATCGCACACTTAGTGCAACATAGTCAAACTCGC
38984414 ACACTTAGTGC
64 ACACTTAGTGC
38984425 TGTACAATTC
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
80 1 0.01
81 37 0.55
82 29 0.43
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATATCAAATCGCACACTTAGTGCAACATAGTCAAACTCGCAC
ACTTAGTGCCGCATGG
Found at i:38986227 original size:30 final size:31
Alignment explanation
Indices: 38986193--38986256 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
38986183 TTAGTCTTGA
38986193 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
38986223 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
38986254 CAT
1 CAT
38986257 TTCTCTGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:38986345 original size:42 final size:42
Alignment explanation
Indices: 38986298--38986389 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
38986288 ATGGCCATAG
* ** *
38986298 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
*
38986340 GCCCATTTCAATATCATATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
38986382 GCCCATTT
1 GCCCATTT
38986390 GGGAGACTAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:38986588 original size:50 final size:51
Alignment explanation
Indices: 38986521--38986654 Score: 197
Period size: 51 Copynumber: 2.7 Consensus size: 51
38986511 CTGGAGGCCT
*
38986521 AGCCTCTTTT-AAT-AACTGGGGCA-AAGCCCTTTCATGTAAACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATAAGCCCTTTC-GGTAAACTGGGGCATA
38986570 AGCCCTTTTCAATAAACT-GGGCATAAGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCC-TTTCGGTAAACTGGGGCATA
38986621 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTT
1 AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTT
38986655 TGCACTTCCT
Statistics
Matches: 78, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
48 5 0.06
49 12 0.15
50 23 0.29
51 26 0.33
52 12 0.15
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (51 bp):
AGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTCGGTAAACTGGGGCATA
Found at i:38986624 original size:26 final size:26
Alignment explanation
Indices: 38986521--38986655 Score: 183
Period size: 26 Copynumber: 5.3 Consensus size: 26
38986511 CTGGAGGCCT
38986521 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
*
38986545 AGCCC-TTTCATGTAAACTGGGGCA-A
1 AGCCCTTTTCA-ATAAACTGGGGCATA
38986570 AGCCCTTTTCAATAAACT-GGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
38986595 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
38986621 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
38986647 AGCCCTTTT
1 AGCCCTTTT
38986656 GCACTTCCTC
Statistics
Matches: 99, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.03
23 2 0.02
24 10 0.10
25 39 0.39
26 45 0.45
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:38986730 original size:20 final size:20
Alignment explanation
Indices: 38986705--38986771 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
38986695 TTATGAATAC
38986705 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
38986725 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
*
38986745 ATCATGTGCATATCATATCA-
1 ATCATGTGCATTTCATA-CAT
38986765 ATCATGT
1 ATCATGT
38986772 ATATCATATC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.39
Consensus pattern (20 bp):
ATCATGTGCATTTCATACAT
Found at i:38986835 original size:25 final size:25
Alignment explanation
Indices: 38986807--38986854 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
38986797 ATAATTAAAC
* * *
38986807 CCTAAGGGTATAATGGTCATTTTTA
1 CCTAAGGGCAAAATAGTCATTTTTA
*
38986832 CCTAGGGGCAAAATAGTCATTTT
1 CCTAAGGGCAAAATAGTCATTTT
38986855 CATACTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (25 bp):
CCTAAGGGCAAAATAGTCATTTTTA
Found at i:38987777 original size:81 final size:81
Alignment explanation
Indices: 38987660--38987815 Score: 199
Period size: 81 Copynumber: 1.9 Consensus size: 81
38987650 GAAAGTCAAG
** * * * *
38987660 GGTATTTCTGTAATTTTGTAAATTAGGGGTATTTTGGTAATTTTA-CAAATTGAGGGTATTTCGG
1 GGTATTTCTGTAATTTTACAAACTAGGGGTATTTTGGTAATTCTACCAAATAG-GGGTATTTCAG
38987724 TAATTTCACAAACCAGT
65 TAATTTCACAAACCAGT
* **
38987741 GGTATTT-TGGTAATTTTACAAACTAGGGGTGTTTTGGTAATTCTACCCTATAGGGGTATTTCAG
1 GGTATTTCT-GTAATTTTACAAACTAGGGGTATTTTGGTAATTCTACCAAATAGGGGTATTTCAG
38987805 TAATTTCACAA
65 TAATTTCACAA
38987816 TCGAGGGTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
80 1 0.02
81 59 0.92
82 4 0.06
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (81 bp):
GGTATTTCTGTAATTTTACAAACTAGGGGTATTTTGGTAATTCTACCAAATAGGGGTATTTCAGT
AATTTCACAAACCAGT
Found at i:38987844 original size:27 final size:27
Alignment explanation
Indices: 38987814--38988096 Score: 174
Period size: 27 Copynumber: 10.4 Consensus size: 27
38987804 GTAATTTCAC
*
38987814 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTATA
* ** * *
38987841 AATCAAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAATGGTAATTTTATA
* * ** *
38987868 AATCGAGGCTATAACAGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTATA
***
38987895 AATCGAGGGTACTTTGGTAATTTT-TA
1 AATCGAGGGTAAAATGGTAATTTTATA
*** * *
38987921 CAAGTCGAGGGTATTTTAGTAATTTTACA
1 -AA-TCGAGGGTAAAATGGTAATTTTATA
* *** * *
38987950 AATCAGGGGGTATTTTAGTAATTTTACA
1 AATC-GAGGGTAAAATGGTAATTTTATA
* *** * *
38987978 AA-CCAGGGGTATTTTAGTAATTTTGTA
1 AATCGA-GGGTAAAATGGTAATTTTATA
* *
38988005 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTATA
*
38988032 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTATA
* * *
38988059 AATCGAGGGTAGAACGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTATA
*
38988086 AATCGGGGGTA
1 AATCGAGGGTA
38988097 CTTTGGTAAT
Statistics
Matches: 215, Mismatches: 35, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
26 2 0.01
27 164 0.76
28 48 0.22
29 1 0.00
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.33
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTTTATA
Found at i:38987930 original size:28 final size:27
Alignment explanation
Indices: 38987883--38988015 Score: 151
Period size: 28 Copynumber: 4.9 Consensus size: 27
38987873 AGGCTATAAC
* * *
38987883 AGTAATTCTATAAATCGAGGGTACTTT
1 AGTAATTTTACAAATCGAGGGTATTTT
* *
38987910 GGTAATTTTTACAAGTCGAGGGTATTTT
1 AGTAA-TTTTACAAATCGAGGGTATTTT
*
38987938 AGTAATTTTACAAATCAGGGGGTATTTT
1 AGTAATTTTACAAATC-GAGGGTATTTT
*
38987966 AGTAATTTTACAAA-CCAGGGGTATTTT
1 AGTAATTTTACAAATCGA-GGGTATTTT
**
38987993 AGTAATTTTGTAAATCGAGGGTA
1 AGTAATTTTACAAATCGAGGGTA
38988016 AAACGGTAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
27 41 0.46
28 48 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (27 bp):
AGTAATTTTACAAATCGAGGGTATTTT
Found at i:38987953 original size:55 final size:54
Alignment explanation
Indices: 38987883--38988015 Score: 160
Period size: 55 Copynumber: 2.4 Consensus size: 54
38987873 AGGCTATAAC
* * **
38987883 AGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTTACAAGTC-GAGGGTATTTT
1 AGTAATTTTATAAATCGAGGGTACTTTAGTAA-TTTTACAAACCAG-GGGTATTTT
* * *
38987938 AGTAATTTTACAAATCAGGGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTT
1 AGTAATTTTATAAATC-GAGGGTACTTTAGTAATTTTACAAACCAGGGGTATTTT
*
38987993 AGTAATTTTGTAAATCGAGGGTA
1 AGTAATTTTATAAATCGAGGGTA
38988016 AAACGGTAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
54 6 0.09
55 46 0.70
56 14 0.21
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (54 bp):
AGTAATTTTATAAATCGAGGGTACTTTAGTAATTTTACAAACCAGGGGTATTTT
Found at i:38988042 original size:54 final size:54
Alignment explanation
Indices: 38987830--38988108 Score: 202
Period size: 54 Copynumber: 5.1 Consensus size: 54
38987820 GGGTAAAATG
* * * * * ***
38987830 GTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTGTAAATCGAGGCTATAACA
1 GTAATTTTATAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTATTTTA
* **** *
38987884 GTAATTCTATAAATCGAGGGTACTTTGGTAATT-TTTACAAGTCGAGGGTATTTTA
1 GTAATTTTATAAATCGAGGGTAAAACGGTAATTCTATA-AA-TCGAGGGTATTTTA
* * ***** * * *
38987939 GTAATTTTACAAATCAGGGGGTATTTTAGTAATTTTACAAA-CCAGGGGTATTTTA
1 GTAATTTTATAAATC-GAGGGTAAAACGGTAATTCTATAAATCGA-GGGTATTTTA
* *** *
38987994 GTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTTTATAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTATTTTA
* * * * *
38988048 GTAATTCTATAAATCGAGGGTAGAACGGTAATTCTATAAATCGGGGGTACTTTG
1 GTAATTTTATAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTATTTTA
38988102 GTAATTT
1 GTAATTT
38988109 GGTAAACTAA
Statistics
Matches: 175, Mismatches: 44, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
53 3 0.02
54 105 0.60
55 48 0.27
56 17 0.10
57 2 0.01
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.34
Consensus pattern (54 bp):
GTAATTTTATAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTATTTTA
Found at i:38988043 original size:191 final size:189
Alignment explanation
Indices: 38987741--38988108 Score: 490
Period size: 191 Copynumber: 1.9 Consensus size: 189
38987731 ACAAACCAGT
* * * ** *
38987741 GGTATTTTGGTAATTTTACAAACTAGGGGTGTTTTGGTAATTCTACCCTATAGGGGTATTTCAGT
1 GGTATTTTAGTAATTTTACAAACTAGGGGTATTTTAGTAATTCTACCAAACAGGGGTATTTCAGT
* * * *
38987806 AATTTCACAATCGAGGGTAAAATGGTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTGTAAAT
66 AATTTCACAATCGAGGGTAAAACGGTAATTCTATAAATCAAGGGTAAAACAGTAATTCTATAAAT
*
38987871 CGAGGCTATAACAGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTTACAAGTCGAG
131 CGAGGCTAGAACAGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTTACAAGTCGAG
* *
38987930 GGTATTTTAGTAATTTTACAAA-TCAGGGGGTATTTTAGTAATTTTA-CAAACCAGGGGTATTTT
1 GGTATTTTAGTAATTTTACAAACT-A-GGGGTATTTTAGTAATTCTACCAAA-CAGGGGTATTTC
* * **
38987993 AGTAATTTTGTA-AATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTA
63 AGTAA-TTT-CACAATCGAGGGTAAAACGGTAATTCTATAAATCAAGGGTAAAACAGTAATTCTA
* * *
38988057 TAAATCGAGGGTAGAACGGTAATTCTATAAATCGGGGGTACTTTGGTAATTT
126 TAAATCGAGGCTAGAACAGTAATTCTATAAATCGAGGGTACTTTGGTAATTT
38988109 GGTAAACTAA
Statistics
Matches: 154, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
188 1 0.01
189 24 0.16
190 32 0.21
191 96 0.62
192 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (189 bp):
GGTATTTTAGTAATTTTACAAACTAGGGGTATTTTAGTAATTCTACCAAACAGGGGTATTTCAGT
AATTTCACAATCGAGGGTAAAACGGTAATTCTATAAATCAAGGGTAAAACAGTAATTCTATAAAT
CGAGGCTAGAACAGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTTACAAGTCGAG
Found at i:38988104 original size:27 final size:27
Alignment explanation
Indices: 38987575--38988107 Score: 170
Period size: 27 Copynumber: 19.6 Consensus size: 27
38987565 TCATCCTACA
* * * *
38987575 AGGGTGTTTTGGTAAATCTATAAACCA
1 AGGGTATTTTGGTAATTCTATAAATCG
* * * * *
38987602 AGGGTATTTTAGTAATTTTGTAAACCA
1 AGGGTATTTTGGTAATTCTATAAATCG
* * * * *
38987629 ATGGTATTTCT-CTAATTTTTAGAAAGTCA
1 AGGGTATTT-TGGTAA-TTCTATAAA-TCG
* * *
38987658 AGGGTATTTCT-GTAATTTTGTAAAT-T
1 AGGGTATTT-TGGTAATTCTATAAATCG
* * *
38987684 AGGGGTATTTTGGTAATTTTACAAATTG
1 A-GGGTATTTTGGTAATTCTATAAATCG
* * *
38987712 AGGGTATTTCGGTAATT-TCACAAA-CC
1 AGGGTATTTTGGTAATTCT-ATAAATCG
* * *
38987738 AGTGGTATTTTGGTAATTTTACAAA-CT
1 AG-GGTATTTTGGTAATTCTATAAATCG
* *** *
38987765 AGGGGTGTTTTGGTAATTCTACCCTATAG
1 A-GGGTATTTTGGTAATTCTA-TAAATCG
** *
38987794 -GGGTATTTCAGTAATT-TCA-CAATCG
1 AGGGTATTTTGGTAATTCT-ATAAATCG
*** * * *
38987819 AGGGTAAAATGGTAATTTTGTAAATCA
1 AGGGTATTTTGGTAATTCTATAAATCG
***** *
38987846 AGGGTAAAACAGTAATTCTGTAAATCG
1 AGGGTATTTTGGTAATTCTATAAATCG
* ****
38987873 AGGCTATAACAGTAATTCTATAAATCG
1 AGGGTATTTTGGTAATTCTATAAATCG
* *
38987900 AGGGTACTTTGGTAATT-TTTACAAGTCG
1 AGGGTATTTTGGTAATTCTATA-AA-TCG
* * *
38987928 AGGGTATTTTAGTAATTTTACAAATCAG
1 AGGGTATTTTGGTAATTCTATAAATC-G
* * * * *
38987956 GGGGTATTTTAGTAATTTTACAAA-CC
1 AGGGTATTTTGGTAATTCTATAAATCG
* * *
38987982 AGGGGTATTTTAGTAATTTTGTAAATCG
1 A-GGGTATTTTGGTAATTCTATAAATCG
****
38988010 AGGGTAAAACGGTAATTCTATAAATCG
1 AGGGTATTTTGGTAATTCTATAAATCG
***
38988037 AGGGTAAAATGGTAATTCTATAAATCG
1 AGGGTATTTTGGTAATTCTATAAATCG
****
38988064 AGGGTAGAACGGTAATTCTATAAATCG
1 AGGGTATTTTGGTAATTCTATAAATCG
* *
38988091 GGGGTACTTTGGTAATT
1 AGGGTATTTTGGTAATT
38988108 TGGTAAACTA
Statistics
Matches: 403, Mismatches: 81, Indels: 44
0.76 0.15 0.08
Matches are distributed among these distances:
25 4 0.01
26 20 0.05
27 296 0.73
28 66 0.16
29 17 0.04
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.37
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTCTATAAATCG
Found at i:39001988 original size:28 final size:27
Alignment explanation
Indices: 39001937--39001989 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
39001927 ACAGGGGCTT
39001937 TCACACGGCCTGACACGCCAATGTCCC
1 TCACACGGCCTGACACGCCAATGTCCC
*
39001964 TCACACGGCCATGACACGCCCATGTC
1 TCACACGGCC-TGACACGCCAATGTC
39001990 TAAAAACCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.23, C:0.43, G:0.19, T:0.15
Consensus pattern (27 bp):
TCACACGGCCTGACACGCCAATGTCCC
Found at i:39003134 original size:49 final size:49
Alignment explanation
Indices: 39003024--39003151 Score: 143
Period size: 49 Copynumber: 2.6 Consensus size: 49
39003014 GCACATTAAA
* *
39003024 GTCGATGCCGTGTCCCAGACAGGTCTTACACTGACTTTAATATATCGAG
1 GTCGATGCCATGTCCCAGACAGGTCTTACACTGACTCTAATATATCGAG
* * * * * *
39003073 G-CTAATGTCATGTCCCAGACAAGTCTTACACTGGCTCTCATCTATCG-G
1 GTC-GATGCCATGTCCCAGACAGGTCTTACACTGACTCTAATATATCGAG
*
39003121 TGTCGATGCCATGTCCCAAACAGGTCTTACA
1 -GTCGATGCCATGTCCCAGACAGGTCTTACA
39003152 TTAACACACA
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
48 2 0.03
49 61 0.95
50 1 0.02
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.28
Consensus pattern (49 bp):
GTCGATGCCATGTCCCAGACAGGTCTTACACTGACTCTAATATATCGAG
Found at i:39005720 original size:49 final size:48
Alignment explanation
Indices: 39005566--39005739 Score: 153
Period size: 49 Copynumber: 3.6 Consensus size: 48
39005556 AAGATGCCGG
* * *
39005566 TGTCATGTCCCAGACATGGTCTTACACTGGCTAACACATC-A-A-AGTCGA
1 TGTCATGTCCCAGACA-GGTCTTACACTGG--ATCTCATCTATAGGGTCGA
* * * *
39005614 TGCCATGTCCCAGACAGGTCTTACACT-GACTTTCATATATCGAGGTC-A
1 TGTCATGTCCCAGACAGGTCTTACACTGGA-TCTCATCTATAG-GGTCGA
39005662 T-TGCTATGTCCCAGACAGGTCTTACACTGGATCTCATCTATAGGTGTCGA
1 TGT-C-ATGTCCCAGACAGGTCTTACACTGGATCTCATCTATAGG-GTCGA
**
39005712 TGTCATGTCCCAGACAAATCTTACACTG
1 TGTCATGTCCCAGACAGGTCTTACACTG
39005740 ACACACAACA
Statistics
Matches: 102, Mismatches: 13, Indels: 21
0.75 0.10 0.15
Matches are distributed among these distances:
44 1 0.01
45 3 0.03
46 2 0.02
47 11 0.11
48 19 0.19
49 60 0.59
50 5 0.05
51 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (48 bp):
TGTCATGTCCCAGACAGGTCTTACACTGGATCTCATCTATAGGGTCGA
Found at i:39005825 original size:48 final size:47
Alignment explanation
Indices: 39005760--39005925 Score: 185
Period size: 46 Copynumber: 3.6 Consensus size: 47
39005750 AGCTGACGCT
* *
39005760 ATGTCCCAAACAGGTCTTACACTAGCTTGTATATCTCGAGGCCGATGC
1 ATGTCCCAGACATGTCTTACACTAGCTT-TATATCTCGAGGCCGATGC
* ** * *
39005808 ATGTCCCAGACATGTCTTACACTAGCTCT-CGTCTCAATGCCGATGC
1 ATGTCCCAGACATGTCTTACACTAGCTTTATATCTCGAGGCCGATGC
* * * * *
39005854 ATTTCCCAGACATGTCTTACACTGGCTCTCATA-AT-GTGGCCGATGC
1 ATGTCCCAGACATGTCTTACACTAGCT-TTATATCTCGAGGCCGATGC
39005900 ATGTCCCAGACATGTCTTACACTAGC
1 ATGTCCCAGACATGTCTTACACTAGC
39005926 ACACATCTCA
Statistics
Matches: 97, Mismatches: 19, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
46 70 0.72
47 2 0.02
48 25 0.26
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (47 bp):
ATGTCCCAGACATGTCTTACACTAGCTTTATATCTCGAGGCCGATGC
Found at i:39009900 original size:51 final size:51
Alignment explanation
Indices: 39009815--39010008 Score: 284
Period size: 51 Copynumber: 3.8 Consensus size: 51
39009805 ACACGATGGC
* *
39009815 CTTT-ACATAGTACCACCCTTGTAG-CCAAATCTATTTTATTCACAAAGTGG
1 CTTTCACATAGTACCACACTTGT-GTCCAAAGCTATTTTATTCACAAAGTGG
39009865 CTTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAGTGG
1 CTTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAGTGG
* * * * *
39009916 CATTCACATAGTACCACACTTTTATCCAAAGCCATTATATTCACAAAGTGG
1 CTTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAGTGG
* *
39009967 CCTTCACATAGTACCACACTTGTGTCCAAAGTTATTTTATTC
1 CTTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
39010009 CTAAGGTTCA
Statistics
Matches: 129, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
50 5 0.04
51 124 0.96
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (51 bp):
CTTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAGTGG
Found at i:39010076 original size:28 final size:27
Alignment explanation
Indices: 39010032--39010123 Score: 118
Period size: 28 Copynumber: 3.4 Consensus size: 27
39010022 GGGAAATTTC
* *
39010032 TCACTTAGCACCGTGCCATGGACTTAAT
1 TCACTTAGCA-CATGCCATGGACTTATT
39010060 TCACTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
*
39010088 TCACTTAG---ATGCCATGGTCTTATT
1 TCACTTAGCACATGCCATGGACTTATT
39010112 TCACTTAGCACA
1 TCACTTAGCACA
39010124 ATGTCATATT
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
24 22 0.39
25 1 0.02
27 2 0.04
28 32 0.56
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (27 bp):
TCACTTAGCACATGCCATGGACTTATT
Found at i:39010109 original size:24 final size:26
Alignment explanation
Indices: 39010045--39010121 Score: 104
Period size: 24 Copynumber: 3.0 Consensus size: 26
39010035 CTTAGCACCG
*
39010045 TGCCATGGACTTAATTCACTTAGCACAT
1 TGCCATGGACTTATTTCACTTAG--CAT
39010073 TGCCATGGACTTATTTCACTTAG-A-
1 TGCCATGGACTTATTTCACTTAGCAT
*
39010097 TGCCATGGTCTTATTTCACTTAGCA
1 TGCCATGGACTTATTTCACTTAGCA
39010122 CAATGTCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
24 22 0.48
25 2 0.04
28 22 0.48
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (26 bp):
TGCCATGGACTTATTTCACTTAGCAT
Found at i:39013372 original size:18 final size:18
Alignment explanation
Indices: 39013342--39013376 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39013332 CTTCACAAGA
39013342 ATAAATCATTAACCAAAT
1 ATAAATCATTAACCAAAT
39013360 ATAAA-CATATAACCAAA
1 ATAAATCAT-TAACCAAA
39013377 ACAAAAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAAATCATTAACCAAAT
Found at i:39014516 original size:41 final size:44
Alignment explanation
Indices: 39014453--39014576 Score: 155
Period size: 41 Copynumber: 2.9 Consensus size: 44
39014443 ATGCTACCTC
* *
39014453 ATATCGATGCCACTGTCCCAGACATGGTCTTACACGAATCA-A-
1 ATATCGATGCCAATGTCCCAGACATGGTCTTACACGAACCATAT
* ** *
39014495 ATA-CGATGCCGATGTTTCAGACATGGTCTTACACGTACCCATAT
1 ATATCGATGCCAATGTCCCAGACATGGTCTTACACG-AACCATAT
*
39014539 ATATCGATGCCAATGTCCCAGACGTGGTCTTACACGAA
1 ATATCGATGCCAATGTCCCAGACATGGTCTTACACGAA
39014577 AACACATATC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 28 0.42
42 6 0.09
43 1 0.01
44 4 0.06
45 28 0.42
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.26
Consensus pattern (44 bp):
ATATCGATGCCAATGTCCCAGACATGGTCTTACACGAACCATAT
Found at i:39014567 original size:45 final size:43
Alignment explanation
Indices: 39014429--39014574 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 43
39014419 CCAACATCCT
* * * *
39014429 AGACGTGGTCTTACATGCTACC-TCATATCGATGCCACTGTCCC
1 AGACATGGTCTTACACG-TACCATAATATCGATGCCAATGTCCC
* * * **
39014472 AGACATGGTCTTACACGAATCA-AATA-CGATGCCGATGTTTC
1 AGACATGGTCTTACACGTACCATAATATCGATGCCAATGTCCC
39014513 AGACATGGTCTTACACGTACCCATATATATCGATGCCAATGTCCC
1 AGACATGGTCTTACACGTA-CCATA-ATATCGATGCCAATGTCCC
*
39014558 AGACGTGGTCTTACACG
1 AGACATGGTCTTACACG
39014575 AAAACACATA
Statistics
Matches: 83, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.35
42 7 0.08
43 16 0.19
44 3 0.04
45 28 0.34
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (43 bp):
AGACATGGTCTTACACGTACCATAATATCGATGCCAATGTCCC
Found at i:39015733 original size:14 final size:15
Alignment explanation
Indices: 39015716--39015744 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39015706 TCACAAAAAT
39015716 TTCACACAT-ATAAA
1 TTCACACATAATAAA
39015730 TTCACACATAATAAA
1 TTCACACATAATAAA
39015745 CACAGAAAAT
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:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:39017566 original size:55 final size:55
Alignment explanation
Indices: 39017482--39017647 Score: 314
Period size: 55 Copynumber: 3.0 Consensus size: 55
39017472 ATCACATTAG
39017482 TAAGGGGGTGAGGTCGTAAAGCCTCTAACTTGACTTCCATACATATACATATGGC
1 TAAGGGGGTGAGGTCGTAAAGCCTCTAACTTGACTTCCATACATATACATATGGC
39017537 TAAGGGGGTGAGGTCGTAAAGCCTCTAACTTGACTTCCATACATATACATATGGC
1 TAAGGGGGTGAGGTCGTAAAGCCTCTAACTTGACTTCCATACATATACATATGGC
* *
39017592 TAAGAGGGTGAGGTCGTAAAGCCTCTAACTTGACTTCCATACATACACATATGGC
1 TAAGGGGGTGAGGTCGTAAAGCCTCTAACTTGACTTCCATACATATACATATGGC
39017647 T
1 T
39017648 TAACATTCAT
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 109 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (55 bp):
TAAGGGGGTGAGGTCGTAAAGCCTCTAACTTGACTTCCATACATATACATATGGC
Found at i:39020828 original size:39 final size:39
Alignment explanation
Indices: 39020758--39021014 Score: 381
Period size: 39 Copynumber: 6.5 Consensus size: 39
39020748 ACAAAGCATG
* * * *
39020758 CGGGACTTTAAGCCCGGATATAATACTAGCAC-AAAGCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
39020798 CGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
39020838 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
39020877 CGGGACTTAGCTCGGATATAATACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
39020916 CGGGACTTAGCCCGGATATAACACCAGCACGAATACCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
39020955 TGGGACTTACCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
39020994 CGGGACTTAGGCAGGATATAA
1 CGGGACTTAGCCCGGATATAA
39021015 TTCTCCATTA
Statistics
Matches: 200, Mismatches: 16, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
39 179 0.89
40 21 0.10
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.20
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:39023831 original size:51 final size:51
Alignment explanation
Indices: 39023754--39023901 Score: 269
Period size: 51 Copynumber: 2.9 Consensus size: 51
39023744 CAGATACATG
* *
39023754 GTGGCCTTCACATAGTACCACCCTTGTGGCCAAAGCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
39023805 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
*
39023856 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGTTATTTTATTC
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
39023902 CTAAGGTTCA
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 94 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
Found at i:39023986 original size:28 final size:28
Alignment explanation
Indices: 39023925--39023987 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 28
39023915 GGGAAATTTC
*
39023925 TCACTAAGCACCATGCCATGGACTTATT
1 TCACTTAGCACCATGCCATGGACTTATT
39023953 TCACTTAGCA-CATTGCCATGGACTTATT
1 TCACTTAGCACCA-TGCCATGGACTTATT
39023981 TCACTTA
1 TCACTTA
39023988 ATGTAATGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
27 2 0.06
28 31 0.94
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (28 bp):
TCACTTAGCACCATGCCATGGACTTATT
Found at i:39027357 original size:23 final size:23
Alignment explanation
Indices: 39027321--39027364 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
39027311 CTTCCACCTG
39027321 AAGTTAGAGAGGCTCAAGAAAAA
1 AAGTTAGAGAGGCTCAAGAAAAA
*
39027344 AAGTTAG-GAGGGCTTAAGAAA
1 AAGTTAGAGA-GGCTCAAGAAA
39027365 CAACAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.48, C:0.07, G:0.30, T:0.16
Consensus pattern (23 bp):
AAGTTAGAGAGGCTCAAGAAAAA
Done.