Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 96 of 120
Found at i:28368449 original size:156 final size:156
Alignment explanation
Indices: 28368162--28368457 Score: 427
Period size: 156 Copynumber: 1.9 Consensus size: 156
28368152 TTTTTGAAAA
* *
28368162 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGCTTGTGGGAAAAGCGCCGCTAAAAGTCAAGAT
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCACTTGTGGGAAAAGCGCCGCTAAAAGTCAAGAC
*
28368227 CTATAGCGGCAATTGTGGGATAAGCGCCGCTAAAGAACATGACATTTAGCGGCGTTTGTGGAATA
66 CTATAGCGGCAATTGTGGGATAACCGCCGCTAAAGAACATGACATTTAGCGGCGTTTGTGGAATA
*
28368292 AGCGCCGCTAGCGGCGCTTATGGGAT
131 AGCACCGCTAGCGGCGCTTATGGGAT
* * * *
28368318 AAGCGTCGCTAAAGAACATGAGCTTTAGCGGCATTTGT-GGAATAAGCGCCGCTAAAGAG-CATG
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCACTTGTGGGAA-AAGCGCCGCTAAA-AGTCAAG
* ** * *
28368381 ACCTTTAGCGGCGTTTGTGGGATAACCGCCGCTAAAGAACATGAGC-TTTTGCGGCGTTTGTGGG
64 ACCTATAGCGGCAATTGTGGGATAACCGCCGCTAAAGAACATGA-CATTTAGCGGCGTTTGTGGA
28368445 ATAAGCACCGCTA
128 ATAAGCACCGCTA
28368458 AAGGTCATGA
Statistics
Matches: 124, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
155 4 0.03
156 117 0.94
157 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (156 bp):
AAGCGCCGCTAAAGAACATGACCTTTAGCGGCACTTGTGGGAAAAGCGCCGCTAAAAGTCAAGAC
CTATAGCGGCAATTGTGGGATAACCGCCGCTAAAGAACATGACATTTAGCGGCGTTTGTGGAATA
AGCACCGCTAGCGGCGCTTATGGGAT
Found at i:28373180 original size:12 final size:11
Alignment explanation
Indices: 28373144--28373177 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
28373134 TGTAAAAAAG
*
28373144 TAAAGAAATAA
1 TAAATAAATAA
28373155 TAAATAAATGAA
1 TAAATAAAT-AA
28373167 TAAATAAATAA
1 TAAATAAATAA
28373178 ATATAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:28378077 original size:20 final size:20
Alignment explanation
Indices: 28378048--28378094 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
28378038 ACTAAATATT
* *
28378048 GATACGTGCAATTTTGTGTC
1 GATACCTGCAATTTTGTATC
28378068 GATACCTGCAATTTTGTATC
1 GATACCTGCAATTTTGTATC
28378088 GATACCT
1 GATACCT
28378095 ACTTTGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (20 bp):
GATACCTGCAATTTTGTATC
Found at i:28380445 original size:51 final size:51
Alignment explanation
Indices: 28380385--28380492 Score: 171
Period size: 51 Copynumber: 2.1 Consensus size: 51
28380375 TTCTTTTTAG
28380385 ATATTGATATATTAACTCTTCTAGAGCTTTCAACTAATTTTGTACGACCAA
1 ATATTGATATATTAACTCTTCTAGAGCTTTCAACTAATTTTGTACGACCAA
* * ** *
28380436 ATATTGATATATTAACTTTTCTGGAGCTTTTGACTAATTTTGTACTACCAA
1 ATATTGATATATTAACTCTTCTAGAGCTTTCAACTAATTTTGTACGACCAA
28380487 ATATTG
1 ATATTG
28380493 GAATAATATT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (51 bp):
ATATTGATATATTAACTCTTCTAGAGCTTTCAACTAATTTTGTACGACCAA
Found at i:28391826 original size:17 final size:18
Alignment explanation
Indices: 28391796--28391838 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
28391786 TATATTCTTT
28391796 TAATTTTTTAAAAAAATA
1 TAATTTTTTAAAAAAATA
28391814 TAATTTTTT-AAAAAATA
1 TAATTTTTTAAAAAAATA
28391831 TAAATTTT
1 T-AATTTT
28391839 AGAATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTTTTTAAAAAAATA
Found at i:28393265 original size:23 final size:23
Alignment explanation
Indices: 28393234--28393289 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
28393224 TTTTCACGTT
28393234 TTTTA-AAATTA-T-TATATATATA
1 TTTTATAAATTACTCTAT-TAT-TA
28393256 TTTTATAAATTACTCTATTATTA
1 TTTTATAAATTACTCTATTATTA
*
28393279 TTTTATCAATT
1 TTTTATAAATT
28393290 TTTTCATCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.17
23 18 0.60
24 4 0.13
25 3 0.10
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTATAAATTACTCTATTATTA
Found at i:28393444 original size:18 final size:18
Alignment explanation
Indices: 28393421--28393463 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
28393411 TCTTTATATT
28393421 TATGGGTTG-GGAAGAGGC
1 TATGGGTTGAGG-AGAGGC
28393439 TATGGGTTGAGGAGAGGC
1 TATGGGTTGAGGAGAGGC
28393457 TATGGGT
1 TATGGGT
28393464 AGTTTTAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.21, C:0.05, G:0.49, T:0.26
Consensus pattern (18 bp):
TATGGGTTGAGGAGAGGC
Found at i:28394158 original size:24 final size:23
Alignment explanation
Indices: 28394127--28394207 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
28394117 ATATTTTTCG
*
28394127 TGAACATGTTCAATTATATGTTCA
1 TGAACATGTTCAATTA-ATGTTAA
* **
28394151 TGAACATGTTCATTTAATGTTTG
1 TGAACATGTTCAATTAATGTTAA
*
28394174 TGAACATGTTCGATTAA-GTTAAA
1 TGAACATGTTCAATTAATGTT-AA
28394197 TGAACATGTTC
1 TGAACATGTTC
28394208 GTGGATATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 3 0.06
23 31 0.63
24 15 0.31
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (23 bp):
TGAACATGTTCAATTAATGTTAA
Found at i:28421358 original size:20 final size:20
Alignment explanation
Indices: 28421329--28421366 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28421319 GACTCGTTAA
*
28421329 TTTTATATAATTATTTTTAT
1 TTTTACATAATTATTTTTAT
*
28421349 TTTTACATAATTCTTTTT
1 TTTTACATAATTATTTTT
28421367 TCAATCATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTACATAATTATTTTTAT
Found at i:28424751 original size:40 final size:40
Alignment explanation
Indices: 28424662--28424752 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
28424652 CCTGTAAATA
* *
28424662 TTTTGGTGTCCCTGATTGCACATTCGTGCCCCTGAATGCAC
1 TTTT-GTGCCCCTGATTGCACACTCGTGCCCCTGAATGCAC
** ** * *
28424703 TTCGGTGCCCCTGATTGCACACTCGTGTTCTTGATTGCAC
1 TTTTGTGCCCCTGATTGCACACTCGTGCCCCTGAATGCAC
28424743 TTTTGTGCCC
1 TTTTGTGCCC
28424753 TTGTTTTGCA
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
40 38 0.95
41 2 0.05
ACGTcount: A:0.12, C:0.30, G:0.22, T:0.36
Consensus pattern (40 bp):
TTTTGTGCCCCTGATTGCACACTCGTGCCCCTGAATGCAC
Found at i:28424755 original size:20 final size:20
Alignment explanation
Indices: 28424671--28424752 Score: 85
Period size: 20 Copynumber: 4.1 Consensus size: 20
28424661 ATTTTGGTGT
28424671 CCCTGATTGCACATTCGTGC
1 CCCTGATTGCACATTCGTGC
*
28424691 CCCTGAATGCAC-TTCGGTGC
1 CCCTGATTGCACATTC-GTGC
* *
28424711 CCCTGATTGCACACTCGTGT
1 CCCTGATTGCACATTCGTGC
* * * *
28424731 TCTTGATTGCACTTTTGTGC
1 CCCTGATTGCACATTCGTGC
28424751 CC
1 CC
28424753 TTGTTTTGCA
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 3 0.06
20 44 0.90
21 2 0.04
ACGTcount: A:0.13, C:0.33, G:0.21, T:0.33
Consensus pattern (20 bp):
CCCTGATTGCACATTCGTGC
Found at i:28425934 original size:22 final size:21
Alignment explanation
Indices: 28425908--28425952 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
28425898 TTATTCTATG
28425908 AATTG-ATATATGTTTATAAATT
1 AATTGAATAT-TG-TTATAAATT
*
28425930 AATTGAATATTGTTCTAAATT
1 AATTGAATATTGTTATAAATT
28425951 AA
1 AA
28425953 GATAAATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 7 0.33
23 4 0.19
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (21 bp):
AATTGAATATTGTTATAAATT
Found at i:28427955 original size:42 final size:41
Alignment explanation
Indices: 28427908--28428049 Score: 121
Period size: 42 Copynumber: 3.4 Consensus size: 41
28427898 CTCGGTGGAT
* *
28427908 TCAGCACTTAGCAATCACCTTTATATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAATCACCTTTAAATTCAAT-ATACGGGGAA
* **
28427950 TCAGCACATAGCAA-C-CCATTTTACAATGAAATATACGGTGGAA
1 TCAGCACTTAGCAATCACC--TTTA-AATTCAATATACGG-GGAA
* *
28427993 T-AGCACTTAGCAACCACCTTTAGAA-TCAATAATTCGGGGAA
1 TCAGCACTTAGCAATCACCTTTA-AATTCAAT-ATACGGGGAA
*
28428034 TCAACACTTAGCAATC
1 TCAGCACTTAGCAATC
28428050 CCTCGGGGAA
Statistics
Matches: 80, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
40 2 0.03
41 9 0.11
42 57 0.71
43 10 0.12
44 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (41 bp):
TCAGCACTTAGCAATCACCTTTAAATTCAATATACGGGGAA
Found at i:28441675 original size:20 final size:20
Alignment explanation
Indices: 28441650--28441696 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
28441640 CTCGTAATTT
*
28441650 TTTTTTGTACTTTCTTA-TAA
1 TTTTTTGTACTTT-TTAGAAA
*
28441670 TTTTTTATACTTTTTAGAAA
1 TTTTTTGTACTTTTTAGAAA
28441690 TTTTTTG
1 TTTTTTG
28441697 GTATACCCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.66
Consensus pattern (20 bp):
TTTTTTGTACTTTTTAGAAA
Found at i:28442592 original size:20 final size:19
Alignment explanation
Indices: 28442544--28442716 Score: 109
Period size: 20 Copynumber: 8.7 Consensus size: 19
28442534 TAGTGCTTCC
*
28442544 TAATTTTTGGTATCCCCTCA
1 TAATTTTTGGTAT-TCCTCA
*
28442564 T-GTTATTTGGTATTCTCTCA
1 TAATT-TTTGGTATTC-CTCA
**
28442584 TAATTTTTGACACTTCCTCA
1 TAATTTTTGGTA-TTCCTCA
* *
28442604 TATTTTTTGGTATTCACTTA
1 TAATTTTTGGTATTC-CTCA
*
28442624 TAATTTTTTGTATTCCCTCA
1 TAATTTTTGGTATT-CCTCA
* *
28442644 T-GTTTTCTGGTATTCCCTTA
1 TAATTTT-TGGTATT-CCTCA
* *
28442664 AAAATTTTGGTACTTCCTCA
1 TAATTTTTGGTA-TTCCTCA
* *
28442684 -ACAATTTTGATACTTCCTCA
1 TA-ATTTTTGGTA-TTCCTCA
28442704 TAATTTTTGGTAT
1 TAATTTTTGGTAT
28442717 GGTCTCAGAA
Statistics
Matches: 120, Mismatches: 22, Indels: 23
0.73 0.13 0.14
Matches are distributed among these distances:
19 12 0.10
20 96 0.80
21 12 0.10
ACGTcount: A:0.21, C:0.18, G:0.10, T:0.50
Consensus pattern (19 bp):
TAATTTTTGGTATTCCTCA
Found at i:28442683 original size:40 final size:39
Alignment explanation
Indices: 28442544--28442683 Score: 131
Period size: 40 Copynumber: 3.5 Consensus size: 39
28442534 TAGTGCTTCC
* * *
28442544 TAATTTTTGGTA-TCCCCTCATGTTATTTGGTATTCTCTCA
1 TAATTTTTGGTACT-TCCTCATGTT-TTTGGTATTCACTTA
** *
28442584 TAATTTTTGACACTTCCTCATATTTTTTGGTATTCACTTA
1 TAATTTTTGGTACTTCCTCAT-GTTTTTGGTATTCACTTA
* *
28442624 TAATTTTTTGTA-TTCCCTCATGTTTTCTGGTATTCCCTTA
1 TAATTTTTGGTACTT-CCTCATGTTTT-TGGTATTCACTTA
* *
28442664 AAAATTTTGGTACTTCCTCA
1 TAATTTTTGGTACTTCCTCA
28442684 ACAATTTTGA
Statistics
Matches: 81, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
39 6 0.07
40 70 0.86
41 5 0.06
ACGTcount: A:0.20, C:0.19, G:0.10, T:0.51
Consensus pattern (39 bp):
TAATTTTTGGTACTTCCTCATGTTTTTGGTATTCACTTA
Found at i:28442692 original size:80 final size:80
Alignment explanation
Indices: 28442544--28442716 Score: 190
Period size: 80 Copynumber: 2.2 Consensus size: 80
28442534 TAGTGCTTCC
* * * **
28442544 TAATTTTTGGTATCCCCTCATGTTATTTGGTATTCTCTCATAATTTTTGACACTTCCTCATATTT
1 TAATTTTTGGTATCCCCTCATGTTATTTGGTATTCCCTCAAAAATTTTGACACTTCCTCATAAAT
* *
28442609 TTTGGTA-TTCACTTA
66 TTTGATACTTC-CTCA
* * * **
28442624 TAATTTTTTGTATTCCCTCATGTT-TTCTGGTATTCCCTTAAAAATTTTGGTACTTCCTCA-ACA
1 TAATTTTTGGTATCCCCTCATGTTATT-TGGTATTCCCTCAAAAATTTTGACACTTCCTCATA-A
28442687 ATTTTGATACTTCCTCA
64 ATTTTGATACTTCCTCA
28442704 TAATTTTTGGTAT
1 TAATTTTTGGTAT
28442717 GGTCTCAGAA
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
79 3 0.04
80 71 0.92
81 3 0.04
ACGTcount: A:0.21, C:0.18, G:0.10, T:0.50
Consensus pattern (80 bp):
TAATTTTTGGTATCCCCTCATGTTATTTGGTATTCCCTCAAAAATTTTGACACTTCCTCATAAAT
TTTGATACTTCCTCA
Found at i:28442894 original size:22 final size:22
Alignment explanation
Indices: 28442866--28442928 Score: 117
Period size: 22 Copynumber: 2.9 Consensus size: 22
28442856 ATTTGGTACG
*
28442866 ACATGAGAGCTTAGTACGTTAA
1 ACATGAGAGCTTAGTACGTGAA
28442888 ACATGAGAGCTTAGTACGTGAA
1 ACATGAGAGCTTAGTACGTGAA
28442910 ACATGAGAGCTTAGTACGT
1 ACATGAGAGCTTAGTACGT
28442929 ACTATCAACA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.25
Consensus pattern (22 bp):
ACATGAGAGCTTAGTACGTGAA
Found at i:28444767 original size:27 final size:27
Alignment explanation
Indices: 28444732--28444904 Score: 114
Period size: 28 Copynumber: 6.3 Consensus size: 27
28444722 TTAAAATTTG
* * *
28444732 TAAAGAATAGGACAAAATTGTAATATA
1 TAAAAAATAGGACAAAATTGTAAAATC
* * *
28444759 TAAAAAATAAGAGCAAAACTATAAAAT-
1 TAAAAAATAGGA-CAAAATTGTAAAATC
** **
28444786 TTGAAAATAGGGGAAAATTGTAAAATC
1 TAAAAAATAGGACAAAATTGTAAAATC
*
28444813 TAAAAAACATGGACAAAATTGTAAAAATC
1 TAAAAAATA-GGACAAAATTGT-AAAATC
** * * *
28444842 TAAAAAATAGGGGTAAAACTATAAAATT
1 TAAAAAATA-GGACAAAATTGTAAAATC
* * *
28444870 TAAAAAATATGGGCAAAACTATAAAATC
1 TAAAAAATA-GGACAAAATTGTAAAATC
*
28444898 TAGAAAA
1 TAAAAAA
28444905 CATGGGCCAA
Statistics
Matches: 114, Mismatches: 28, Indels: 7
0.77 0.19 0.05
Matches are distributed among these distances:
26 11 0.10
27 24 0.21
28 57 0.50
29 22 0.19
ACGTcount: A:0.58, C:0.06, G:0.13, T:0.23
Consensus pattern (27 bp):
TAAAAAATAGGACAAAATTGTAAAATC
Found at i:28444859 original size:29 final size:28
Alignment explanation
Indices: 28444759--28444924 Score: 147
Period size: 28 Copynumber: 6.0 Consensus size: 28
28444749 TTGTAATATA
* *
28444759 TAAAAAATAAGAGCAAAACTATAAAAT-
1 TAAAAAATAGGGGCAAAACTATAAAATC
** * *
28444786 TTGAAAATAGGGG-AAAATTGTAAAATC
1 TAAAAAATAGGGGCAAAACTATAAAATC
* * * * *
28444813 TAAAAAACATGGACAAAATTGTAAAAATC
1 TAAAAAATAGGGGCAAAACTAT-AAAATC
* *
28444842 TAAAAAATAGGGGTAAAACTATAAAATT
1 TAAAAAATAGGGGCAAAACTATAAAATC
*
28444870 TAAAAAATATGGGCAAAACTATAAAATC
1 TAAAAAATAGGGGCAAAACTATAAAATC
* * * *
28444898 TAGAAAACATGGGCCAAACTATAAAAT
1 TAAAAAATAGGGGCAAAACTATAAAAT
28444925 ATGGAAAATA
Statistics
Matches: 112, Mismatches: 24, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
26 11 0.10
27 17 0.15
28 62 0.55
29 22 0.20
ACGTcount: A:0.57, C:0.08, G:0.13, T:0.22
Consensus pattern (28 bp):
TAAAAAATAGGGGCAAAACTATAAAATC
Found at i:28444875 original size:56 final size:56
Alignment explanation
Indices: 28444772--28444924 Score: 143
Period size: 57 Copynumber: 2.7 Consensus size: 56
28444762 AAAATAAGAG
** * *
28444772 CAAAACTATAAAAT-TTGAAAATAGGGGAAAATTGTAAAATCT-AAAAAACATGGA
1 CAAAACTATAAAATCTAAAAAATAGGGGAAAACTATAAAATCTAAAAAAACATGGA
* * * * *
28444826 CAAAATTGTAAAAATCTAAAAAATAGGGGTAAAACTATAAAAT-TTAAAAAATATGGG
1 CAAAACTAT-AAAATCTAAAAAATAGGGG-AAAACTATAAAATCTAAAAAAACATGGA
**
28444883 CAAAACTATAAAATCTAGAAAACAT-GGGCCAAACTATAAAAT
1 CAAAACTATAAAATCTA-AAAA-ATAGGGGAAAACTATAAAAT
28444925 ATGGAAAATA
Statistics
Matches: 81, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
54 7 0.09
55 5 0.06
56 32 0.40
57 35 0.43
58 2 0.02
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (56 bp):
CAAAACTATAAAATCTAAAAAATAGGGGAAAACTATAAAATCTAAAAAAACATGGA
Found at i:28447783 original size:5 final size:6
Alignment explanation
Indices: 28447767--28447822 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 6
28447757 AGGAAAATGC
* *
28447767 ATCTGT ATCTG- ATCTG- ATCTGT -TCTGC ATCTGT ATCTGC A-CTGT
1 ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT
*
28447811 -TCTGT AACTGT A
1 ATCTGT ATCTGT A
28447823 ACAAATATCC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
5 21 0.51
6 20 0.49
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (6 bp):
ATCTGT
Found at i:28447821 original size:22 final size:22
Alignment explanation
Indices: 28447768--28447822 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
28447758 GGAAAATGCA
28447768 TCTGTATCTG-ATCTGATCTGT
1 TCTGTATCTGTATCTGATCTGT
*
28447789 TCTGCATCTGTATCTGCA-CTGT
1 TCTGTATCTGTATCTG-ATCTGT
*
28447811 TCTGTAACTGTA
1 TCTGTATCTGTA
28447823 ACAAATATCC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.31
22 19 0.66
23 1 0.03
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (22 bp):
TCTGTATCTGTATCTGATCTGT
Found at i:28448653 original size:31 final size:31
Alignment explanation
Indices: 28448618--28448678 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
28448608 ATGTGTATGA
28448618 TTAAATCAAAATTAAAGTTTCAAGTATATAT
1 TTAAATCAAAATTAAAGTTTCAAGTATATAT
* **
28448649 TTAAATCACAATTAGTGTTTCAAGTATATA
1 TTAAATCAAAATTAAAGTTTCAAGTATATA
28448679 ATTACACCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (31 bp):
TTAAATCAAAATTAAAGTTTCAAGTATATAT
Found at i:28449200 original size:21 final size:21
Alignment explanation
Indices: 28449176--28449226 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
28449166 CGAATCCAGA
28449176 CTATATCCAAGTGATGAATAC
1 CTATATCCAAGTGATGAATAC
28449197 CTATATCCAAGTGATGAATAC
1 CTATATCCAAGTGATGAATAC
28449218 CTATATCCA
1 CTATATCCA
28449227 TTAAGCCGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (21 bp):
CTATATCCAAGTGATGAATAC
Found at i:28456198 original size:7 final size:7
Alignment explanation
Indices: 28456190--28456221 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
28456180 TATTAAAAAA
*
28456190 AACAAAA
1 AACAAAT
28456197 AACAAAT
1 AACAAAT
28456204 AACAAAT
1 AACAAAT
28456211 AACAAAT
1 AACAAAT
28456218 AACA
1 AACA
28456222 CAAATAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.75, C:0.16, G:0.00, T:0.09
Consensus pattern (7 bp):
AACAAAT
Found at i:28458742 original size:20 final size:20
Alignment explanation
Indices: 28458717--28458763 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
28458707 TAGTAAAATG
*
28458717 TTTTCTAGAAAATGATTTAT
1 TTTTCTAGAAAATGATTTAC
*
28458737 TTTTCT-GGAAATGATTTAC
1 TTTTCTAGAAAATGATTTAC
28458756 TTTTCTAG
1 TTTTCTAG
28458764 TATTTGGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.51
Consensus pattern (20 bp):
TTTTCTAGAAAATGATTTAC
Found at i:28460160 original size:32 final size:32
Alignment explanation
Indices: 28460114--28460193 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
28460104 TGTCAATCAC
*
28460114 TTCAATATCCAACAAGCTT-AAAACATAATAAA
1 TTCAATATCCAACAA-ATTCAAAACATAATAAA
* * *
28460146 TTCAATATCTAACAAATTCAAGACATAATAAT
1 TTCAATATCCAACAAATTCAAAACATAATAAA
*
28460178 TTCAAAATCCAACAAA
1 TTCAATATCCAACAAA
28460194 CTAAAATTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 2 0.05
32 39 0.95
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.26
Consensus pattern (32 bp):
TTCAATATCCAACAAATTCAAAACATAATAAA
Found at i:28486633 original size:25 final size:25
Alignment explanation
Indices: 28486605--28486674 Score: 83
Period size: 24 Copynumber: 2.8 Consensus size: 25
28486595 GCTGAATAAC
28486605 GGTAAGCTTATACGAGCTGTGAATT
1 GGTAAGCTTATACGAGCTGTGAATT
*
28486630 GGTAAGCTCTCAT--GAGCTG-AAATT
1 GGTAAGCT-T-ATACGAGCTGTGAATT
*
28486654 GGTAAGCTCATACGAGCTGTG
1 GGTAAGCTTATACGAGCTGTG
28486675 GTGTGCCCGA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
22 2 0.05
24 18 0.49
25 14 0.38
26 1 0.03
27 2 0.05
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (25 bp):
GGTAAGCTTATACGAGCTGTGAATT
Found at i:28486659 original size:49 final size:50
Alignment explanation
Indices: 28486561--28486674 Score: 137
Period size: 49 Copynumber: 2.3 Consensus size: 50
28486551 GTACATGTAT
* *
28486561 GCTCATACGAGC-GAT-AAATGGTAAGTTCCTCTGAGCTGAATAACGGTAA
1 GCTCATACGAGCTG-TGAATTGGTAAGCTCCTCTGAGCTGAATAACGGTAA
* **
28486610 GCTTATACGAGCTGTGAATTGGTAAGCT-CTCATGAGCTGAA-ATTGGTAA
1 GCTCATACGAGCTGTGAATTGGTAAGCTCCTC-TGAGCTGAATAACGGTAA
28486659 GCTCATACGAGCTGTG
1 GCTCATACGAGCTGTG
28486675 GTGTGCCCGA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
49 36 0.64
50 20 0.36
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (50 bp):
GCTCATACGAGCTGTGAATTGGTAAGCTCCTCTGAGCTGAATAACGGTAA
Found at i:28486670 original size:24 final size:24
Alignment explanation
Indices: 28486561--28486672 Score: 86
Period size: 25 Copynumber: 4.6 Consensus size: 24
28486551 GTACATGTAT
28486561 GCTCATACGAGC-GATAAATGGTAA
1 GCTCATACGAGCTGA-AAATGGTAA
* * *
28486585 GTTCCT-CTGAGCTGAATAACGGTAA
1 GCTCATAC-GAGCTGAA-AATGGTAA
* * *
28486610 GCTTATACGAGCTGTGAATTGGTAA
1 GCTCATACGAGCTG-AAAATGGTAA
* *
28486635 GCTC-TCATGAGCTGAAATTGGTAA
1 GCTCAT-ACGAGCTGAAAATGGTAA
28486659 GCTCATACGAGCTG
1 GCTCATACGAGCTG
28486673 TGGTGTGCCC
Statistics
Matches: 68, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
23 1 0.01
24 30 0.44
25 35 0.51
26 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (24 bp):
GCTCATACGAGCTGAAAATGGTAA
Found at i:28487460 original size:13 final size:13
Alignment explanation
Indices: 28487442--28487466 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28487432 TAAGTTATAT
28487442 ATGTGAAAATTTC
1 ATGTGAAAATTTC
28487455 ATGTGAAAATTT
1 ATGTGAAAATTT
28487467 GATAGTTTGA
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:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (13 bp):
ATGTGAAAATTTC
Found at i:28488409 original size:2 final size:2
Alignment explanation
Indices: 28488402--28488465 Score: 112
Period size: 2 Copynumber: 32.0 Consensus size: 2
28488392 TAGTAATTCA
28488402 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28488444 A- AT AGT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT
28488466 GAGTATGAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 57 0.95
3 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28491820 original size:16 final size:17
Alignment explanation
Indices: 28491788--28491822 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28491778 AATTTAGTCG
28491788 AAGTATAAACGATGTAT
1 AAGTATAAACGATGTAT
*
28491805 AAGTATATAC-ATGTAT
1 AAGTATAAACGATGTAT
28491821 AA
1 AA
28491823 ATTATTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (17 bp):
AAGTATAAACGATGTAT
Found at i:28492535 original size:41 final size:41
Alignment explanation
Indices: 28492478--28492759 Score: 392
Period size: 41 Copynumber: 6.9 Consensus size: 41
28492468 AAATAAGATG
28492478 TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
28492519 TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
28492560 TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
28492601 TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
* * * *
28492642 CTTCAGACTTTATGTCTAGCAGGCTT-AGTGCCGGTGAAATG
1 TTTCAGACTTTACGTCTAGCAGGCTTGA-TGCCGGTGAATTA
* * *
28492683 TATCAGACCTTATGTCTAGCAGGCTTTG-TGCCGGTGGAATGTA
1 TTTCAGACTTTACGTCTAGCAGGC-TTGATGCCGGT-GAAT-TA
* * * * *
28492726 --TCGGGCTTTGCGCCTAGCAGGCTTTATGCCGGTG
1 TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTG
28492760 TTTTATACAA
Statistics
Matches: 219, Mismatches: 16, Indels: 13
0.88 0.06 0.05
Matches are distributed among these distances:
40 4 0.02
41 209 0.95
42 5 0.02
43 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (41 bp):
TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
Found at i:28498082 original size:32 final size:32
Alignment explanation
Indices: 28498046--28498107 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
28498036 ACTCTCCTTG
*
28498046 AATGAATCTAGACAAA-TGGTTGTCGAGATTTA
1 AATGAATCTAGACAAACT-GTTGTCCAGATTTA
28498078 AATGAATCTAGACAAACTGTTGTCCAGATT
1 AATGAATCTAGACAAACTGTTGTCCAGATT
28498108 CATTCTAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (32 bp):
AATGAATCTAGACAAACTGTTGTCCAGATTTA
Found at i:28499443 original size:17 final size:16
Alignment explanation
Indices: 28499421--28499477 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
28499411 ATAGATTAAT
28499421 TTATATTTTATATATCA
1 TTATATTTTAT-TATCA
**
28499438 TTATATTAAATTAATCA
1 TTATATTTTATT-ATCA
*
28499455 -AATATTTTATGTATCA
1 TTATATTTTAT-TATCA
28499471 TTATATT
1 TTATATT
28499478 AAATTATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (16 bp):
TTATATTTTATTATCA
Found at i:28499461 original size:33 final size:33
Alignment explanation
Indices: 28499423--28499512 Score: 121
Period size: 33 Copynumber: 2.8 Consensus size: 33
28499413 AGATTAATTT
28499423 ATATTTTATATATCATTATATTAAATTAATCAA
1 ATATTTTATATATCATTATATTAAATTAATCAA
* * *
28499456 ATATTTTATGTATCATTATATTAAATTATTTAA
1 ATATTTTATATATCATTATATTAAATTAATCAA
* *
28499489 ATA--TAATTTATCATTATATTAAAT
1 ATATTTTATATATCATTATATTAAAT
28499513 CATTTAAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
31 19 0.37
33 33 0.63
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (33 bp):
ATATTTTATATATCATTATATTAAATTAATCAA
Found at i:28499504 original size:31 final size:32
Alignment explanation
Indices: 28499433--28499521 Score: 117
Period size: 31 Copynumber: 2.8 Consensus size: 32
28499423 ATATTTTATA
* * *
28499433 TATCATTATATTAAATTAATCAAATATTTTATG
1 TATCATTATATTAAATTATTTAAATA-TTAATG
*
28499466 TATCATTATATTAAATTATTTAAATA-TAATT
1 TATCATTATATTAAATTATTTAAATATTAATG
*
28499497 TATCATTATATTAAATCATTTAAAT
1 TATCATTATATTAAATTATTTAAAT
28499522 TTAGTTCATT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 27 0.53
33 24 0.47
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (32 bp):
TATCATTATATTAAATTATTTAAATATTAATG
Found at i:28504043 original size:14 final size:15
Alignment explanation
Indices: 28504007--28504044 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
28503997 TAAAAATTAA
28504007 AAAAATTAAATGATG
1 AAAAATTAAATGATG
*
28504022 AGAAATTAAATGAT-
1 AAAAATTAAATGATG
28504036 AAAAATTAA
1 AAAAATTAA
28504045 GTATTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (15 bp):
AAAAATTAAATGATG
Found at i:28504274 original size:14 final size:15
Alignment explanation
Indices: 28504231--28504287 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 15
28504221 TGATAAAATG
*
28504231 AAAAATTAAGTGTTA
1 AAAAATTAAGTATTA
*
28504246 AAAAA--AACTAGTTA
1 AAAAATTAAGTA-TTA
28504260 AAAAATT-AGTATTA
1 AAAAATTAAGTATTA
*
28504274 AAAATTTAAGTATT
1 AAAAATTAAGTATT
28504288 GAATTTAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 3 0.09
14 17 0.50
15 14 0.41
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (15 bp):
AAAAATTAAGTATTA
Found at i:28512660 original size:16 final size:17
Alignment explanation
Indices: 28512631--28512662 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28512621 AATATTATTT
28512631 AATTAAATTAATTTTCC
1 AATTAAATTAATTTTCC
28512648 AATTAAA-TAATTTTC
1 AATTAAATTAATTTTC
28512663 TCAACCCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAAATTAATTTTCC
Found at i:28516857 original size:8 final size:8
Alignment explanation
Indices: 28516843--28516895 Score: 52
Period size: 8 Copynumber: 6.2 Consensus size: 8
28516833 AATTAATTTT
28516843 TTAAAAAA
1 TTAAAAAA
*
28516851 TTCAAAACA
1 TT-AAAAAA
28516860 TATAAAAATA
1 T-TAAAAA-A
28516870 TTAAAAAA
1 TTAAAAAA
* *
28516878 TTTAAAAT
1 TTAAAAAA
28516886 TTAAAAAA
1 TTAAAAAA
28516894 TT
1 TT
28516896 TTAATTAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
8 17 0.47
9 16 0.44
10 3 0.08
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (8 bp):
TTAAAAAA
Found at i:28516893 original size:9 final size:9
Alignment explanation
Indices: 28516842--28516896 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
28516832 TAATTAATTT
28516842 TTTAAAAAA
1 TTTAAAAAA
* *
28516851 TTCAAAACA
1 TTTAAAAAA
*
28516860 TAT-AAAAA
1 TTTAAAAAA
28516868 TATTAAAAAA
1 T-TTAAAAAA
28516878 TTT--AAAA
1 TTTAAAAAA
28516885 TTTAAAAAA
1 TTTAAAAAA
28516894 TTT
1 TTT
28516897 TAATTAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
7 7 0.19
8 5 0.14
9 18 0.50
10 6 0.17
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:28516899 original size:17 final size:17
Alignment explanation
Indices: 28516864--28516896 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
28516854 AAAACATATA
28516864 AAAATATTAAAAAATTT
1 AAAATATTAAAAAATTT
28516881 AAAAT-TTAAAAAATTT
1 AAAATATTAAAAAATTT
28516897 TAATTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATATTAAAAAATTT
Found at i:28518487 original size:17 final size:18
Alignment explanation
Indices: 28518465--28518507 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
28518455 TTTTATTGTT
*
28518465 TATTATAAT-AATTTTTA
1 TATTATAATAAATGTTTA
28518482 TATTAT-ATAAATGTTTA
1 TATTATAATAAATGTTTA
*
28518499 TATTTTAAT
1 TATTATAAT
28518508 TTATTCTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 18 0.82
18 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TATTATAATAAATGTTTA
Found at i:28518530 original size:13 final size:13
Alignment explanation
Indices: 28518514--28518544 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28518504 TAATTTATTC
*
28518514 TTAATTTTTAGAT
1 TTAATTTTAAGAT
28518527 TTAATTTTAAGAT
1 TTAATTTTAAGAT
28518540 TTAAT
1 TTAAT
28518545 ATTTCAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (13 bp):
TTAATTTTAAGAT
Found at i:28520222 original size:25 final size:26
Alignment explanation
Indices: 28520194--28520250 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
28520184 TTATTACACA
28520194 TTTAAAAAATATTATATATTAT-TAT
1 TTTAAAAAATATTATATATTATATAT
** *
28520219 TTTAAAATTTATTATGTATTATATAT
1 TTTAAAAAATATTATATATTATATAT
*
28520245 TGTAAA
1 TTTAAA
28520251 GATTCATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 19 0.70
26 8 0.30
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (26 bp):
TTTAAAAAATATTATATATTATATAT
Found at i:28525459 original size:21 final size:21
Alignment explanation
Indices: 28525430--28525474 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28525420 AATAATATAT
* *
28525430 ATATCAGCTTCTATTACAAAA
1 ATATCAGCTCCTATTAAAAAA
*
28525451 ATATTAGCTCCTATTAAAAAA
1 ATATCAGCTCCTATTAAAAAA
28525472 ATA
1 ATA
28525475 GAGCAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (21 bp):
ATATCAGCTCCTATTAAAAAA
Found at i:28526218 original size:26 final size:26
Alignment explanation
Indices: 28526161--28526224 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 26
28526151 AGCTCATTCC
*
28526161 CGTAATTAATTTTCCATATCCTATTT
1 CGTAATTAATTTTCCATACCCTATTT
28526187 CTGTAATTAATTTTCTCAT-CCC-ATTTT
1 C-GTAATTAATTTTC-CATACCCTA-TTT
28526214 CGTAATTAATT
1 CGTAATTAATT
28526225 AAATTTTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
26 12 0.35
27 19 0.56
28 3 0.09
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.50
Consensus pattern (26 bp):
CGTAATTAATTTTCCATACCCTATTT
Found at i:28530489 original size:87 final size:87
Alignment explanation
Indices: 28530367--28530553 Score: 245
Period size: 87 Copynumber: 2.1 Consensus size: 87
28530357 ACTGAATTTT
* * * *
28530367 AAGGAATA-CCTTTGTGGCAAAACTTAGGAAAGGTAAGTCAATGTGGTGAACCTTTGAAAGGAAA
1 AAGGAA-AGCCTTTATGGAAAAACTTAGGAAAGGTAAGCCAATGTAGTGAACCTTTGAAAGGAAA
**
28530431 TGCCTCTATGTTAAAACTCTGGA
65 TGCCTCTATGGCAAAACTCTGGA
*
28530454 CAA-GAAAGCCTTTATGGAAAAACTTA-GAAATGGTAAGCCTATGTAGTGAACCTTTGAAAGGAA
1 -AAGGAAAGCCTTTATGGAAAAACTTAGGAAA-GGTAAGCCAATGTAGTGAACCTTTGAAAGGAA
* *
28530517 ATGCCTTTATGGCAAAACTTTGGA
64 ATGCCTCTATGGCAAAACTCTGGA
28530541 AAGGAAAGCCTTT
1 AAGGAAAGCCTTT
28530554 GTGGCGAGTA
Statistics
Matches: 87, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
86 7 0.08
87 78 0.90
88 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (87 bp):
AAGGAAAGCCTTTATGGAAAAACTTAGGAAAGGTAAGCCAATGTAGTGAACCTTTGAAAGGAAAT
GCCTCTATGGCAAAACTCTGGA
Found at i:28530537 original size:29 final size:28
Alignment explanation
Indices: 28530418--28530558 Score: 95
Period size: 29 Copynumber: 4.9 Consensus size: 28
28530408 TGTGGTGAAC
* **
28530418 CTTTGAAAGGAAATGCCTCTATGTTAAAA
1 CTTTGAAAGGAAA-GCCTTTATGGCAAAA
* *
28530447 CTCTGGACAA-GAAAGCCTTTATGGAAAAA
1 CT-TTGA-AAGGAAAGCCTTTATGGCAAAA
* * * * * ** *
28530476 CTTAGAAATGGTAAGCCTATGTAGTGAAC
1 CTTTGAAA-GGAAAGCCTTTATGGCAAAA
28530505 CTTTGAAAGGAAATGCCTTTATGGCAAAA
1 CTTTGAAAGGAAA-GCCTTTATGGCAAAA
*
28530534 CTTTGGAAAGGAAAGCCTTTGTGGC
1 CTTT-GAAAGGAAAGCCTTTATGGC
28530559 GAGTACTGAA
Statistics
Matches: 85, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
27 2 0.02
28 7 0.08
29 58 0.68
30 16 0.19
31 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (28 bp):
CTTTGAAAGGAAAGCCTTTATGGCAAAA
Found at i:28532307 original size:26 final size:26
Alignment explanation
Indices: 28532271--28532334 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
28532261 AATTCAAATT
28532271 CGGGAATGCTCATACAAGCACATAAA
1 CGGGAATGCTCATACAAGCACATAAA
* *
28532297 CGGGAATGCTCATACGAGTACATAAA
1 CGGGAATGCTCATACAAGCACATAAA
*
28532323 TGGGAA-GCTCAT
1 CGGGAATGCTCAT
28532335 GTGAGCTATG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
25 6 0.17
26 29 0.83
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (26 bp):
CGGGAATGCTCATACAAGCACATAAA
Found at i:28532424 original size:25 final size:25
Alignment explanation
Indices: 28532396--28532480 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
28532386 GAGCAATATT
28532396 GGGAAGCTCCGAAGAGCCATTAATC
1 GGGAAGCTCCGAAGAGCCATTAATC
* * *
28532421 GGGAAGCTCATGAAGAGCCTTTAAAC
1 GGGAAGCTC-CGAAGAGCCATTAATC
* * *
28532447 GGTAAGCTTCGAAAAGCCA-TATATC
1 GGGAAGCTCCGAAGAGCCATTA-ATC
*
28532472 GGGACGCTC
1 GGGAAGCTC
28532481 ATAAGAGTTG
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
24 2 0.04
25 24 0.52
26 20 0.43
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (25 bp):
GGGAAGCTCCGAAGAGCCATTAATC
Found at i:28532444 original size:26 final size:25
Alignment explanation
Indices: 28532396--28532466 Score: 79
Period size: 26 Copynumber: 2.8 Consensus size: 25
28532386 GAGCAATATT
*
28532396 GGGAAGCTCCGAAGAGCCATTAATC
1 GGGAAGCTCCGAAGAGCCATTAAAC
* *
28532421 GGGAAGCTCATGAAGAGCCTTTAAAC
1 GGGAAGCTC-CGAAGAGCCATTAAAC
* * *
28532447 GGTAAGCTTCGAAAAGCCAT
1 GGGAAGCTCCGAAGAGCCAT
28532467 ATATCGGGAC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
25 17 0.46
26 20 0.54
ACGTcount: A:0.34, C:0.21, G:0.27, T:0.18
Consensus pattern (25 bp):
GGGAAGCTCCGAAGAGCCATTAAAC
Found at i:28537122 original size:27 final size:29
Alignment explanation
Indices: 28537034--28537131 Score: 82
Period size: 28 Copynumber: 3.5 Consensus size: 29
28537024 AATGGTTGAA
* *
28537034 ATTATATTTATATTGAAGAATATATTATAA-
1 ATTATATTTATATT-AAAAAT-TATTAAAAT
**
28537064 ATTA-AAAT-TATTAAAAATTATTAAAAT
1 ATTATATTTATATTAAAAATTATTAAAAT
*
28537091 -TT-TATTTATATTAAGAAATTGTTAAAA-
1 ATTATATTTATATTAA-AAATTATTAAAAT
28537118 ATTATATTTATATT
1 ATTATATTTATATT
28537132 GATTAATAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
26 11 0.20
27 11 0.20
28 17 0.31
29 12 0.22
30 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (29 bp):
ATTATATTTATATTAAAAATTATTAAAAT
Found at i:28537146 original size:23 final size:21
Alignment explanation
Indices: 28537108--28537154 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
28537098 ATATTAAGAA
* *
28537108 ATTGTTAAAAATTATATTTAT
1 ATTGTTAAAAAATATATTAAT
28537129 ATTGATTAATAAAATATATTAAT
1 ATTG-TTAA-AAAATATATTAAT
28537152 ATT
1 ATT
28537155 AAACTATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 4 0.18
23 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
ATTGTTAAAAAATATATTAAT
Found at i:28537197 original size:29 final size:26
Alignment explanation
Indices: 28537135--28537197 Score: 63
Period size: 29 Copynumber: 2.3 Consensus size: 26
28537125 TTATATTGAT
*
28537135 TAATAAAATATATTAATATTAAACTA
1 TAATAAAATATATTAATATTAAAATA
* *
28537161 TGATTAAAATAATATTTAATTTTAAAATAA
1 T-AATAAAAT-ATA-TTAATATTAAAAT-A
28537191 TAATAAA
1 TAATAAA
28537198 TTAAAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 1 0.03
27 7 0.24
28 3 0.10
29 16 0.55
30 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (26 bp):
TAATAAAATATATTAATATTAAAATA
Found at i:28537199 original size:18 final size:18
Alignment explanation
Indices: 28537164--28537199 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28537154 TAAACTATGA
* *
28537164 TTAAAATAATATTTAATT
1 TTAAAATAATAATAAATT
28537182 TTAAAATAATAATAAATT
1 TTAAAATAATAATAAATT
28537200 AAAATTAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAAATAATAATAAATT
Found at i:28537203 original size:16 final size:18
Alignment explanation
Indices: 28537163--28537204 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
28537153 TTAAACTATG
*
28537163 ATTAAAATAATATTTAAT
1 ATTAAAATAATATATAAT
*
28537181 TTTAAAATAATA-ATAA-
1 ATTAAAATAATATATAAT
28537197 ATTAAAAT
1 ATTAAAAT
28537205 TAACAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 7 0.33
17 3 0.14
18 11 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTAAAATAATATATAAT
Found at i:28538888 original size:23 final size:23
Alignment explanation
Indices: 28538862--28538905 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
28538852 CGTTTCAATA
*
28538862 GTGTTCTATCATCCGCTTTGGTG
1 GTGTCCTATCATCCGCTTTGGTG
* *
28538885 GTGTCCTATTATTCGCTTTGG
1 GTGTCCTATCATCCGCTTTGG
28538906 CAATGTTCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.09, C:0.20, G:0.25, T:0.45
Consensus pattern (23 bp):
GTGTCCTATCATCCGCTTTGGTG
Found at i:28539750 original size:20 final size:20
Alignment explanation
Indices: 28539714--28539751 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28539704 GTGGAATTTG
*
28539714 TATGAAAATATAGAATTAAA
1 TATGAAAATATAAAATTAAA
28539734 TATGAAGAATA-AAAATTA
1 TATGAA-AATATAAAATTA
28539752 GTCTCGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (20 bp):
TATGAAAATATAAAATTAAA
Found at i:28543420 original size:3 final size:3
Alignment explanation
Indices: 28543412--28543443 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
28543402 AAATTAGTTA
28543412 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28543444 AAGGATAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28543780 original size:31 final size:31
Alignment explanation
Indices: 28543745--28543806 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
28543735 AGGCAAAATA
28543745 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
28543776 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
28543807 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:28543907 original size:3 final size:3
Alignment explanation
Indices: 28543899--28543924 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28543889 GAATTAAGTA
28543899 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
28543925 GATACATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28544567 original size:9 final size:9
Alignment explanation
Indices: 28544549--28544615 Score: 91
Period size: 9 Copynumber: 7.4 Consensus size: 9
28544539 TTTGGTTAAA
28544549 AATTAACCG
1 AATTAACCG
*
28544558 AATTACCCG
1 AATTAACCG
28544567 AATTAACCG
1 AATTAACCG
*
28544576 GATT-ACTCG
1 AATTAAC-CG
28544585 AATTAACCG
1 AATTAACCG
*
28544594 AATTACCCG
1 AATTAACCG
28544603 AATTAACCG
1 AATTAACCG
28544612 AATT
1 AATT
28544616 GAATAACTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
8 2 0.04
9 46 0.92
10 2 0.04
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:28544572 original size:18 final size:18
Alignment explanation
Indices: 28544549--28544615 Score: 116
Period size: 18 Copynumber: 3.7 Consensus size: 18
28544539 TTTGGTTAAA
28544549 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
* *
28544567 AATTAACCGGATTACTCG
1 AATTAACCGAATTACCCG
28544585 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
28544603 AATTAACCGAATT
1 AATTAACCGAATT
28544616 GAATAACTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:28544761 original size:18 final size:18
Alignment explanation
Indices: 28544718--28544761 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
28544708 AATTTTTATG
**
28544718 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
*
28544736 ATTAGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
28544754 CTTGGGTT
1 ATTGGGTT
28544762 TGGATTAGGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:28547235 original size:12 final size:12
Alignment explanation
Indices: 28547220--28547249 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28547210 AATAATTAAA
28547220 TAAATTAGAAAT
1 TAAATTAGAAAT
*
28547232 TAAATTGGAAAT
1 TAAATTAGAAAT
28547244 TAAATT
1 TAAATT
28547250 TATATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (12 bp):
TAAATTAGAAAT
Found at i:28549627 original size:19 final size:20
Alignment explanation
Indices: 28549591--28549633 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
28549581 TTTCTTTGTA
*
28549591 ATAATTTCTTTTAGATA-TT
1 ATAACTTCTTTTAGATATTT
28549610 ATAACTTCTTTTCA-ATATTT
1 ATAACTTCTTTT-AGATATTT
28549630 ATAA
1 ATAA
28549634 ATAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAACTTCTTTTAGATATTT
Found at i:28549959 original size:5 final size:5
Alignment explanation
Indices: 28549949--28549976 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28549939 GGGTAAGAGT
28549949 ATCGG ATCGG ATCGG ATCGG ATCGG ATC
1 ATCGG ATCGG ATCGG ATCGG ATCGG ATC
28549977 CGATGATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.21
Consensus pattern (5 bp):
ATCGG
Found at i:28552185 original size:12 final size:12
Alignment explanation
Indices: 28552168--28552197 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28552158 CGTCCACTTT
28552168 ATCATCATCAAC
1 ATCATCATCAAC
*
28552180 ATCATCATCACC
1 ATCATCATCAAC
28552192 ATCATC
1 ATCATC
28552198 CTCGATTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.27
Consensus pattern (12 bp):
ATCATCATCAAC
Found at i:28564665 original size:17 final size:18
Alignment explanation
Indices: 28564626--28564686 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 18
28564616 CATTATTGAA
28564626 ATTGAAATGGCAAATGAT
1 ATTGAAATGGCAAATGAT
* * *
28564644 GTTGAAGTGG-AAATGCT
1 ATTGAAATGGCAAATGAT
* *
28564661 ATTGAAATAGCAAATGAC
1 ATTGAAATGGCAAATGAT
28564679 A-TGAAATG
1 ATTGAAATG
28564687 AAATATGTAT
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
17 19 0.58
18 14 0.42
ACGTcount: A:0.43, C:0.07, G:0.25, T:0.26
Consensus pattern (18 bp):
ATTGAAATGGCAAATGAT
Found at i:28566252 original size:19 final size:20
Alignment explanation
Indices: 28566228--28566274 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
28566218 AGTGTCTCCC
28566228 AAAACTT-ACACTTGTTGAT
1 AAAACTTGACACTTGTTGAT
***
28566247 AAAACTTGTTTCTTGTTGAT
1 AAAACTTGACACTTGTTGAT
28566267 AAAACTTG
1 AAAACTTG
28566275 TTTCTTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
AAAACTTGACACTTGTTGAT
Found at i:28566263 original size:20 final size:20
Alignment explanation
Indices: 28566238--28566280 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
28566228 AAAACTTACA
28566238 CTTGTTGATAAAACTTGTTT
1 CTTGTTGATAAAACTTGTTT
28566258 CTTGTTGATAAAACTTGTTT
1 CTTGTTGATAAAACTTGTTT
28566278 CTT
1 CTT
28566281 AATTTTGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51
Consensus pattern (20 bp):
CTTGTTGATAAAACTTGTTT
Found at i:28566802 original size:30 final size:31
Alignment explanation
Indices: 28566766--28566824 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
28566756 ACAGTATGGT
*
28566766 GTGGG-CCTAAGCCCAGTACAGTAA-CAGTGA
1 GTGGGCCCT-AGCCCAATACAGTAATCAGTGA
28566796 GTGGGCCCTAGCCCAATACAGTAATCAGT
1 GTGGGCCCTAGCCCAATACAGTAATCAGT
28566825 ACAATGCAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.19
Consensus pattern (31 bp):
GTGGGCCCTAGCCCAATACAGTAATCAGTGA
Found at i:28566985 original size:26 final size:26
Alignment explanation
Indices: 28566956--28567006 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
28566946 GTAATAATGA
*
28566956 CGCAGCGAA-GCTGCCAGTAACAGTAG
1 CGCAGC-AAGGCTGCCAATAACAGTAG
*
28566982 CGCAGCAAGGCTGCCAATAGCAGTA
1 CGCAGCAAGGCTGCCAATAACAGTA
28567007 TATATGGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.31, C:0.27, G:0.29, T:0.12
Consensus pattern (26 bp):
CGCAGCAAGGCTGCCAATAACAGTAG
Found at i:28567212 original size:27 final size:27
Alignment explanation
Indices: 28567182--28567647 Score: 437
Period size: 27 Copynumber: 17.1 Consensus size: 27
28567172 TATAACAGTT
* * * *
28567182 ATTTTACCATTTGGGGGTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
28567209 ATTTTATCCTTCGGGGGTATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
28567236 ATTTTACCCTTCGAAGGTATTTCGTTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
28567263 ATTTTACCCTTCGGGGGTATTTTGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
*
28567290 ATTTTACCTTTC-AGGGGTATTTCGATA
1 ATTTTACCCTTCGA-GGGTATTTCGATA
* * *
28567317 ATTTTACCCTTCAAGGGTATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
*
28567344 ATTTTA-CC--CGAGAGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
28567368 ATTTTACCCTTCGAGGGTATTGGTATTTCGGTT
1 ATTTTACCCTTCGA--G----GGTATTTCGATA
* *
28567401 ATTTTACTCTTCGAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATA
*
28567428 ATTTTACCCTTCGAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
28567455 ATTTTACCCTTCGAGGGTATTTCGGTC
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
28567482 ATTTTATCCTTCGAGGGTATTT-TAGTC
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
* *
28567509 ATTTTACCATTCGAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
28567536 ATTTTACCTTTCG-GGTGTATTTC-AGTT
1 ATTTTACCCTTCGAGG-GTATTTCGA-TA
* *
28567563 ATTTTACCCTTTGAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
28567590 ATTTTACCCTATCGGGGGTATTTC-AGTT
1 ATTTTACCCT-TCGAGGGTATTTCGA-TA
* *
28567618 ATTTTACCCTACG-GGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATA
28567644 ATTT
1 ATTT
28567648 GCCCATAACT
Statistics
Matches: 371, Mismatches: 48, Indels: 41
0.81 0.10 0.09
Matches are distributed among these distances:
24 18 0.05
25 2 0.01
26 19 0.05
27 281 0.76
28 27 0.07
29 1 0.00
31 1 0.00
33 22 0.06
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATA
Found at i:28568467 original size:16 final size:15
Alignment explanation
Indices: 28568424--28568467 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
28568414 CTATTCGGTC
28568424 AAAACAAAATAAGAGA
1 AAAACAAAA-AAGAGA
*
28568440 AAAAAAATAAAAGAGA
1 AAAACAA-AAAAGAGA
28568456 AAAACAAGAAAA
1 AAAACAA-AAAA
28568468 CAAAATAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 22 0.92
17 2 0.08
ACGTcount: A:0.80, C:0.05, G:0.11, T:0.05
Consensus pattern (15 bp):
AAAACAAAAAAGAGA
Found at i:28570362 original size:19 final size:19
Alignment explanation
Indices: 28570338--28570376 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28570328 TCTACACTAT
* *
28570338 AGAAAATATTAAAAAGAAA
1 AGAAAAAATAAAAAAGAAA
*
28570357 AGAAAAAATAAAAAATAAA
1 AGAAAAAATAAAAAAGAAA
28570376 A
1 A
28570377 TATCTATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (19 bp):
AGAAAAAATAAAAAAGAAA
Found at i:28574017 original size:25 final size:24
Alignment explanation
Indices: 28573988--28574037 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
28573978 ATAAGGTATA
28573988 AAATTA-TTATATATAAATTATTAAT
1 AAATTAGTTA-ATATAAATTA-TAAT
*
28574013 AAATTAGTTAATATATATTATAAT
1 AAATTAGTTAATATAAATTATAAT
28574037 A
1 A
28574038 TGTTTTACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 5 0.22
25 15 0.65
26 3 0.13
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
AAATTAGTTAATATAAATTATAAT
Found at i:28574036 original size:12 final size:13
Alignment explanation
Indices: 28573990--28574052 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 13
28573980 AAGGTATAAA
*
28573990 ATTATTATATATAA
1 ATTATTA-ATATAT
28574004 ATTATTAATA-A-
1 ATTATTAATATAT
28574015 ATTAGTTAATATAT
1 ATTA-TTAATATAT
*
28574029 ATTA-TAATATGT
1 ATTATTAATATAT
*
28574041 TTTACTTAATAT
1 ATTA-TTAATAT
28574053 TTAAGTACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
11 4 0.10
12 17 0.40
13 4 0.10
14 17 0.40
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (13 bp):
ATTATTAATATAT
Found at i:28576788 original size:16 final size:16
Alignment explanation
Indices: 28576767--28576797 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28576757 ATCGAGTTAA
28576767 GAAAATTAACTAATTG
1 GAAAATTAACTAATTG
*
28576783 GAAAATTAATTAATT
1 GAAAATTAACTAATT
28576798 AATTAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.35
Consensus pattern (16 bp):
GAAAATTAACTAATTG
Found at i:28576795 original size:20 final size:18
Alignment explanation
Indices: 28576770--28576811 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
28576760 GAGTTAAGAA
28576770 AATTAACTAATTGGAAAATT
1 AATTAACTAATT--AAAATT
*
28576790 AATTAATTAATTAAAATT
1 AATTAACTAATTAAAATT
28576808 AATT
1 AATT
28576812 TATGATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.40
Consensus pattern (18 bp):
AATTAACTAATTAAAATT
Found at i:28584896 original size:2 final size:2
Alignment explanation
Indices: 28584889--28584917 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28584879 ATAATTTACT
28584889 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28584918 TTGCAAGCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28587430 original size:26 final size:26
Alignment explanation
Indices: 28587396--28587445 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
28587386 ACTTTAATAT
28587396 ATATATATACCTATATA-AAAAAACCC
1 ATATATATA-CTATATATAAAAAACCC
* *
28587422 ATATGTATATTATATATAAAAAAC
1 ATATATATACTATATATAAAAAAC
28587446 TATGCGTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (26 bp):
ATATATATACTATATATAAAAAACCC
Found at i:28591829 original size:11 final size:11
Alignment explanation
Indices: 28591812--28591888 Score: 77
Period size: 11 Copynumber: 7.0 Consensus size: 11
28591802 AGATTGAACT
28591812 GAGAGAATTGA
1 GAGAGAATTGA
*
28591823 GTA-AGAATTAA
1 G-AGAGAATTGA
28591834 GAGAGAATTGA
1 GAGAGAATTGA
*
28591845 GAGAGGATTGA
1 GAGAGAATTGA
28591856 GA-ATGAATTGA
1 GAGA-GAATTGA
* *
28591867 GAGAGAGTTGT
1 GAGAGAATTGA
*
28591878 GAGTGAATTGA
1 GAGAGAATTGA
28591889 AAAAGTGGGA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
10 2 0.04
11 49 0.92
12 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (11 bp):
GAGAGAATTGA
Found at i:28591888 original size:33 final size:33
Alignment explanation
Indices: 28591811--28591888 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
28591801 GAGATTGAAC
28591811 TGAGAGAATTGAGTAAGAATTAAGAGAGAATTG
1 TGAGAGAATTGAGTAAGAATTAAGAGAGAATTG
* * * *
28591844 AGAGAGGATTGAG-AATGAATTGAGAGAGAGTTG
1 TGAGAGAATTGAGTAA-GAATTAAGAGAGAATTG
*
28591877 TGAGTGAATTGA
1 TGAGAGAATTGA
28591889 AAAAGTGGGA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
32 2 0.05
33 35 0.95
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.24
Consensus pattern (33 bp):
TGAGAGAATTGAGTAAGAATTAAGAGAGAATTG
Found at i:28598893 original size:15 final size:15
Alignment explanation
Indices: 28598873--28598905 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
28598863 TCGAAATAGT
28598873 TGATAATTGCTTAAA
1 TGATAATTGCTTAAA
28598888 TGATAATTGCTTAAA
1 TGATAATTGCTTAAA
28598903 TGA
1 TGA
28598906 AACTATGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.39
Consensus pattern (15 bp):
TGATAATTGCTTAAA
Found at i:28599432 original size:18 final size:18
Alignment explanation
Indices: 28599406--28599447 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28599396 GATTGGGAAA
* * *
28599406 AGGAAACATATAAGGGTT
1 AGGATACATACAAGGGCT
28599424 AGGATACATACAAGGGCT
1 AGGATACATACAAGGGCT
28599442 AGGATA
1 AGGATA
28599448 TGCACCTGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.29, T:0.19
Consensus pattern (18 bp):
AGGATACATACAAGGGCT
Found at i:28605896 original size:5 final size:5
Alignment explanation
Indices: 28605886--28605911 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28605876 TGAGCATTCG
28605886 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
28605912 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:28606571 original size:17 final size:17
Alignment explanation
Indices: 28606521--28606578 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
28606511 GGGAGAGAAG
*
28606521 TAAAAGTTTAGGGGGAAAA
1 TAAAAGTTT-GAGGG-AAA
*
28606540 TAAAAAGTTT-TGGGAAA
1 T-AAAAGTTTGAGGGAAA
28606557 TAAAAGTTTGAGGGAAA
1 TAAAAGTTTGAGGGAAA
28606574 GTAAA
1 -TAAA
28606579 TAGGGGGAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 8 0.24
17 10 0.29
18 7 0.21
19 1 0.03
20 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (17 bp):
TAAAAGTTTGAGGGAAA
Found at i:28608015 original size:3 final size:3
Alignment explanation
Indices: 28608007--28608042 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
28607997 ATAAATTTCA
*
28608007 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28608043 AATCGTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:28608143 original size:35 final size:35
Alignment explanation
Indices: 28608099--28608169 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
28608089 TACATACACT
* * * * *
28608099 TATACACATACTTTTTTTTGTAATATATATATACA
1 TATAAACATACCTATTTTTATAAAATATATATACA
*
28608134 TATAAACATACCTATTTTTATAAAATATTTATACA
1 TATAAACATACCTATTTTTATAAAATATATATACA
28608169 T
1 T
28608170 GTATATATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.41, C:0.11, G:0.01, T:0.46
Consensus pattern (35 bp):
TATAAACATACCTATTTTTATAAAATATATATACA
Found at i:28608219 original size:44 final size:44
Alignment explanation
Indices: 28608171--28608272 Score: 98
Period size: 44 Copynumber: 2.3 Consensus size: 44
28608161 TTTATACATG
* * *
28608171 TATATATTTATAATACACGCACATATTTCCT-ATTTTTATAAACC
1 TATATATATAT-ATACACACACATATTTCATAATTTTTATAAACC
* ** *
28608215 TATATGTATATATACTTACACATATTTCATAATTTTTATATATATC
1 TATATATATATATACACACACATATTTCATAATTTTTATA-A-ACC
*
28608261 TATGTATATATA
1 TATATATATATA
28608273 CATATTTTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
43 15 0.33
44 18 0.39
45 1 0.02
46 12 0.26
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (44 bp):
TATATATATATATACACACACATATTTCATAATTTTTATAAACC
Found at i:28608273 original size:44 final size:43
Alignment explanation
Indices: 28608190--28608273 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 43
28608180 ATAATACACG
* *
28608190 CACATATTTCCTATTTTTATAAACCTATATGTATATATACTTA
1 CACATATTTCATATTTTTATAAACATATATGTATATATACTTA
* * *
28608233 CACATATTTCATAATTTTTATATATATCTATGTATATATAC
1 CACATATTTCAT-ATTTTTATAAACATATATGTATATATAC
28608274 ATATTTTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 11 0.31
44 24 0.69
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (43 bp):
CACATATTTCATATTTTTATAAACATATATGTATATATACTTA
Found at i:28608411 original size:37 final size:40
Alignment explanation
Indices: 28608326--28608413 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 40
28608316 ATTCTATATA
*
28608326 ATAATTTTAAATATATACTTACATATATTTTTCATATTTCC
1 ATAATTTTATATATATAC-TACATATATTTTTCATATTTCC
* * * *
28608367 ATTATTTTATATATATA-TATATATCTTTTTCAT-TTT-T
1 ATAATTTTATATATATACTACATATATTTTTCATATTTCC
28608404 ATAATTTTAT
1 ATAATTTTAT
28608414 TCATTTTCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
37 9 0.22
38 3 0.07
39 14 0.34
41 15 0.37
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (40 bp):
ATAATTTTATATATATACTACATATATTTTTCATATTTCC
Found at i:28609330 original size:9 final size:9
Alignment explanation
Indices: 28609316--28609352 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28609306 TATAGTTTGA
28609316 TATTCGAAT
1 TATTCGAAT
28609325 TATTCGAAT
1 TATTCGAAT
*
28609334 TATTCGAGT
1 TATTCGAAT
28609343 TATTCGAAT
1 TATTCGAAT
28609352 T
1 T
28609353 CGAAAAGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:28616303 original size:9 final size:9
Alignment explanation
Indices: 28616273--28616320 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
28616263 TTTTTTCCAA
28616273 AAATAAAAAT
1 AAAT-AAAAT
28616283 ACAATAAAAT
1 A-AATAAAAT
*
28616293 AAATAACAT
1 AAATAAAAT
28616302 AAATAAATAT
1 AAATAAA-AT
*
28616312 ATATAAAAT
1 AAATAAAAT
28616321 TAAAAACAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
9 15 0.45
10 15 0.45
11 3 0.09
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (9 bp):
AAATAAAAT
Found at i:28624164 original size:25 final size:25
Alignment explanation
Indices: 28624130--28624258 Score: 97
Period size: 25 Copynumber: 5.2 Consensus size: 25
28624120 TTCAACTCTT
*
28624130 ATGAGCTTCCTGATACTCAGCTCGC
1 ATGAGCTTCCTGATATTCAGCTCGC
* *
28624155 ATGAGCTTCC-CATTGTTCAGCTCGC
1 ATGAGCTTCCTGA-TATTCAGCTCGC
* *
28624180 ATGAGCTTTCC--ATTGTTCAGCTCAC
1 ATGAGC-TTCCTGA-TATTCAGCTCGC
* *
28624205 ATGAGCTTCCTGTTATTCAGCTCGG
1 ATGAGCTTCCTGATATTCAGCTCGC
* * *
28624230 AGGAGCTTACTG-T-TTACAGCTCGT
1 ATGAGCTTCCTGATATT-CAGCTCGC
28624254 ATGAG
1 ATGAG
28624259 TATACATGTA
Statistics
Matches: 87, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
23 2 0.02
24 17 0.20
25 64 0.74
26 4 0.05
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (25 bp):
ATGAGCTTCCTGATATTCAGCTCGC
Found at i:28625220 original size:30 final size:30
Alignment explanation
Indices: 28625171--28625227 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
28625161 TGTGTCTCAA
* *
28625171 CCATGTATGACTCATAGCCAGGTGACACGG
1 CCATGTATGACACACAGCCAGGTGACACGG
*
28625201 CCATGTGTGACACACAGCCAGGTGACA
1 CCATGTATGACACACAGCCAGGTGACA
28625228 TTGTAACAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (30 bp):
CCATGTATGACACACAGCCAGGTGACACGG
Found at i:28625563 original size:25 final size:25
Alignment explanation
Indices: 28625535--28625584 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
28625525 ATATGGTTTT
*
28625535 TATATTAT-TTATAAATGTTATAATA
1 TATATTATATTAT-AATGGTATAATA
28625560 TATATTATATTATAATGGTATAATA
1 TATATTATATTATAATGGTATAATA
28625585 AAACAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (25 bp):
TATATTATATTATAATGGTATAATA
Found at i:28635247 original size:21 final size:21
Alignment explanation
Indices: 28635211--28635252 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28635201 AAAGTTAGTA
* *
28635211 TTAAAGTTTCGTTAATAAATT
1 TTAAAGTTACGATAATAAATT
*
28635232 TTAAAGTTACGATAATTAATT
1 TTAAAGTTACGATAATAAATT
28635253 GAACAAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (21 bp):
TTAAAGTTACGATAATAAATT
Found at i:28640844 original size:21 final size:21
Alignment explanation
Indices: 28640798--28640845 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
28640788 TACAAAAATG
* *
28640798 TAAAAAATTGTAAAATTTATT
1 TAAAAAATTATAAAATGTATT
*
28640819 AAAAAAATTATAAAA-GTACTT
1 TAAAAAATTATAAAATGTA-TT
28640840 TAAAAA
1 TAAAAA
28640846 GGTATTTAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (21 bp):
TAAAAAATTATAAAATGTATT
Found at i:28643177 original size:53 final size:53
Alignment explanation
Indices: 28643109--28643217 Score: 164
Period size: 53 Copynumber: 2.1 Consensus size: 53
28643099 TCATAAATGT
* *
28643109 AAATATGAATATTTTATAGTACAACCTGCTACAGTAGATGTTTGACTGTATCA
1 AAATATGAATATTTTATAGTACAACCTGCTACAATAGATGTTTGACTGTACCA
* * * *
28643162 AAATATGGATCTTTTATAGTACAACTTGTTACAATAGATGTTTGACTGTACCA
1 AAATATGAATATTTTATAGTACAACCTGCTACAATAGATGTTTGACTGTACCA
28643215 AAA
1 AAA
28643218 ATTAATTCAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (53 bp):
AAATATGAATATTTTATAGTACAACCTGCTACAATAGATGTTTGACTGTACCA
Found at i:28643960 original size:33 final size:33
Alignment explanation
Indices: 28643902--28643964 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
28643892 AGACTTTATC
* *
28643902 TTCTGTGTTTACTATCCTAACGGACTATCTTTG
1 TTCTGTGTTTACTACCCCAACGGACTATCTTTG
* *
28643935 TTCTGTGTTTACTGCCCCAATGGACTATCT
1 TTCTGTGTTTACTACCCCAACGGACTATCT
28643965 CTGAGGATGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.17, C:0.24, G:0.16, T:0.43
Consensus pattern (33 bp):
TTCTGTGTTTACTACCCCAACGGACTATCTTTG
Found at i:28650882 original size:20 final size:20
Alignment explanation
Indices: 28650828--28650883 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
28650818 AATCTCGTTT
* **
28650828 TAAAATTATTGATACTTTTA
1 TAAAAATATTGATACTCATA
**
28650848 TAAAAATATCAATACTCATA
1 TAAAAATATTGATACTCATA
28650868 TAAAAATATTGATACT
1 TAAAAATATTGATACT
28650884 TACTGGGTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (20 bp):
TAAAAATATTGATACTCATA
Found at i:28654933 original size:23 final size:24
Alignment explanation
Indices: 28654894--28654941 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
28654884 TTTATTTGAT
28654894 AATATGTTTTGATATAACAAATTAA
1 AATATGTTTTGATATAA-AAATTAA
*
28654919 AATAT-TTTTGA-ATAAAAGTTAA
1 AATATGTTTTGATATAAAAATTAA
28654941 A
1 A
28654942 GTTGAACAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 6 0.27
25 5 0.23
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (24 bp):
AATATGTTTTGATATAAAAATTAA
Found at i:28661008 original size:46 final size:46
Alignment explanation
Indices: 28660941--28661029 Score: 169
Period size: 46 Copynumber: 1.9 Consensus size: 46
28660931 TCAATCAATG
28660941 GCTCAATAATGATTTAGAGATTTAGAAAATGCAAAATATTTCTTAT
1 GCTCAATAATGATTTAGAGATTTAGAAAATGCAAAATATTTCTTAT
*
28660987 GCTCAATAATGATTTAGAGATTTAGGAAATGCAAAATATTTCT
1 GCTCAATAATGATTTAGAGATTTAGAAAATGCAAAATATTTCT
28661030 ATTGTATTCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (46 bp):
GCTCAATAATGATTTAGAGATTTAGAAAATGCAAAATATTTCTTAT
Found at i:28667258 original size:103 final size:104
Alignment explanation
Indices: 28666983--28667342 Score: 564
Period size: 104 Copynumber: 3.5 Consensus size: 104
28666973 TGTATATAAA
** * * * *
28666983 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATGGGTGGTGCTATGTGCG-TGATCCACCATACCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCGTATCT
**
28667047 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
28667087 AGGGGTTGCTAAGTGTTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
28667152 TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
28667191 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGATGCTAAGTGCGATATCCACCGTATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTT
*
28667256 TGAAATGAAAAAGGGGGTTGCTATGGGCTGATT-CCCCG
66 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
28667294 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCG
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCG
28667343 GGATCCACTA
Statistics
Matches: 238, Mismatches: 15, Indels: 7
0.92 0.06 0.03
Matches are distributed among these distances:
103 95 0.40
104 104 0.44
105 38 0.16
106 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTT
TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:28667304 original size:26 final size:26
Alignment explanation
Indices: 28667269--28667320 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
28667259 AATGAAAAAG
*
28667269 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
28667295 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
28667321 TTCAGTGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:28671228 original size:7 final size:7
Alignment explanation
Indices: 28671216--28671244 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
28671206 ATTAATGAAT
28671216 ATTGCTA
1 ATTGCTA
28671223 ATTGCTA
1 ATTGCTA
28671230 ATTGCTA
1 ATTGCTA
28671237 ATTGCTA
1 ATTGCTA
28671244 A
1 A
28671245 ACATGGGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (7 bp):
ATTGCTA
Found at i:28681789 original size:93 final size:93
Alignment explanation
Indices: 28681689--28681875 Score: 365
Period size: 93 Copynumber: 2.0 Consensus size: 93
28681679 ATTAATTCAA
28681689 TAAAATAATAAATGTTTATAACCCAAAAAAATCTAACAAAAATTGTGGGTGTTGTTCATCATGTT
1 TAAAATAATAAATGTTTATAACCCAAAAAAATCTAACAAAAATTGTGGGTGTTGTTCATCATGTT
28681754 TTTCATGTAAGAAAAGAGAAGAATTATG
66 TTTCATGTAAGAAAAGAGAAGAATTATG
*
28681782 TAAAATAATAAATGTTTTTAACCCAAAAAAATCTAACAAAAATTGTGGGTGTTGTTCATCATGTT
1 TAAAATAATAAATGTTTATAACCCAAAAAAATCTAACAAAAATTGTGGGTGTTGTTCATCATGTT
28681847 TTTCATGTAAGAAAAGAGAAGAATTATG
66 TTTCATGTAAGAAAAGAGAAGAATTATG
28681875 T
1 T
28681876 TGTCTTATAT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (93 bp):
TAAAATAATAAATGTTTATAACCCAAAAAAATCTAACAAAAATTGTGGGTGTTGTTCATCATGTT
TTTCATGTAAGAAAAGAGAAGAATTATG
Found at i:28681971 original size:15 final size:14
Alignment explanation
Indices: 28681947--28681981 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
28681937 ATTTAAGTAA
*
28681947 AATTTTGTTTAATT
1 AATTTAGTTTAATT
28681961 ACATTTAGTTTAATT
1 A-ATTTAGTTTAATT
28681976 AATTTA
1 AATTTA
28681982 AAAATCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (14 bp):
AATTTAGTTTAATT
Found at i:28688384 original size:91 final size:91
Alignment explanation
Indices: 28688091--28688420 Score: 360
Period size: 91 Copynumber: 3.6 Consensus size: 91
28688081 TGAAATGTGC
* *
28688091 TACTTAAATGTGATTTAAATGATGTTC-GAAAGTGGTTAGATGACAATTTTAATTGTTGAAAATT
1 TACTTAAAGGTGATTTAAATGAT-TTCTGAAAGTGGTTAAATGACAATTTTAATTGTTGAAAATT
* *
28688155 ATGGTGTCTGATTGTATGCTTTAATGA
65 ATGGTGTCTGATTGTATGCCTTGATGA
* * * * * ** *
28688182 TACTCAAAGGTGATTTAAATTATTTCTAAAAGAT-GTTAATTGGCCGTTTTAATTGTTGGAAATT
1 TACTTAAAGGTGATTTAAATGATTTCTGAAAG-TGGTTAAATGACAATTTTAATTGTTGAAAATT
* **
28688246 ATGGTGTCTGAATGTATGTGTTGATGA
65 ATGGTGTCTGATTGTATGCCTTGATGA
* * * ** *
28688273 TGCTTAAATGTGATTTAAATGATATTC-GAAAGTTGTTAAATGACCGTTTTAATTGCTGAAAATT
1 TACTTAAAGGTGATTTAAATGAT-TTCTGAAAGTGGTTAAATGACAATTTTAATTGTTGAAAATT
*
28688337 ATGGTGTTTGATTGTATGCCTTGATGA
65 ATGGTGTCTGATTGTATGCCTTGATGA
* * ** * *
28688364 TATTTAAAGGTGCTAAAAATGATGTCTGAAAGTGGTAAAATGACAATTTTAATTGTT
1 TACTTAAAGGTGATTTAAATGATTTCTGAAAGTGGTTAAATGACAATTTTAATTGTT
28688421 ATGAATTCAT
Statistics
Matches: 195, Mismatches: 39, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
90 6 0.03
91 185 0.95
92 4 0.02
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (91 bp):
TACTTAAAGGTGATTTAAATGATTTCTGAAAGTGGTTAAATGACAATTTTAATTGTTGAAAATTA
TGGTGTCTGATTGTATGCCTTGATGA
Found at i:28688416 original size:182 final size:182
Alignment explanation
Indices: 28688093--28688420 Score: 442
Period size: 182 Copynumber: 1.8 Consensus size: 182
28688083 AAATGTGCTA
* * *
28688093 CTTAAATGTGATTTAAATGATGTTCGAAAGTGGTTAGATGACAATTTTAATTGTTGAAAATTATG
1 CTTAAATGTGATTTAAATGATATTCGAAAGTGGTTAAATGACAATTTTAATTGCTGAAAATTATG
* ** * * * *
28688158 GTGTCTGATTGTATGCTTTAATGATACTCAAAGGTGATTTAAATTATTTCTAAAAGATGTTAATT
66 GTGTCTGATTGTATGCCTTAATGATACTCAAAGGTGATAAAAATGATGTCTAAAAGATGTAAAAT
* **
28688223 GGCCGTTTTAATTGTTGGAAATTATGGTGTCTGAATGTATGTGTTGATGATG
131 GACAATTTTAATTGTTGGAAATTATGGTGTCTGAATGTATGTGTTGATGATG
* **
28688275 CTTAAATGTGATTTAAATGATATTCGAAAGTTGTTAAATGACCGTTTTAATTGCTGAAAATTATG
1 CTTAAATGTGATTTAAATGATATTCGAAAGTGGTTAAATGACAATTTTAATTGCTGAAAATTATG
* * * * * *
28688340 GTGTTTGATTGTATGCCTTGATGATATTTAAAGGTGCTAAAAATGATGTCTGAAAG-TGGTAAAA
66 GTGTCTGATTGTATGCCTTAATGATACTCAAAGGTGATAAAAATGATGTCTAAAAGAT-GTAAAA
28688404 TGACAATTTTAATTGTT
130 TGACAATTTTAATTGTT
28688421 ATGAATTCAT
Statistics
Matches: 123, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
181 1 0.01
182 122 0.99
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (182 bp):
CTTAAATGTGATTTAAATGATATTCGAAAGTGGTTAAATGACAATTTTAATTGCTGAAAATTATG
GTGTCTGATTGTATGCCTTAATGATACTCAAAGGTGATAAAAATGATGTCTAAAAGATGTAAAAT
GACAATTTTAATTGTTGGAAATTATGGTGTCTGAATGTATGTGTTGATGATG
Found at i:28688782 original size:24 final size:24
Alignment explanation
Indices: 28688732--28688784 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
28688722 TTTCTAGAAG
* *
28688732 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
* *
28688756 ATTTAGCATTTATTAGCATAGTTT
1 ATTTAGCATTTATTAGCATAATAT
28688780 ATTTA
1 ATTTA
28688785 ACTTACTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:28691670 original size:50 final size:50
Alignment explanation
Indices: 28691479--28691719 Score: 195
Period size: 50 Copynumber: 4.7 Consensus size: 50
28691469 GATAATAACA
* * * *
28691479 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATG-TTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGG-GGCTCTCATAT-CGG
* * * * * * *
28691528 TGCCAATGCCATATCTCAGATATGGTCTTACATGAGAGTTTTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGGGCTCTCATATCGG
* *
28691578 TGCCCATGCCATGTCCCAGACATGGTCTTAC--GGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGGG--CTCTCATATCGG
* * *
28691628 TGCCAACGACATGTCCCAGACATGGTCTTACATGGGGGCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGGGCTCTCAT-A--TC---GG
* *
28691684 TGCCAATGCCATGTTCCAAACATGGTCTTACATGGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGG
28691720 ATCTCATCAC
Statistics
Matches: 154, Mismatches: 25, Indels: 19
0.78 0.13 0.10
Matches are distributed among these distances:
48 5 0.03
49 38 0.25
50 71 0.46
52 5 0.03
53 2 0.01
56 33 0.21
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGGGCTCTCATATCGG
Found at i:28691673 original size:100 final size:99
Alignment explanation
Indices: 28691486--28691673 Score: 216
Period size: 100 Copynumber: 1.9 Consensus size: 99
28691476 ACATGCCAAA
* ** * * * * * *
28691486 GCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTACTGCCAATGCCATATCTCAGATAT
1 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTACTGCCAACGACATATCCCAGACAT
* *
28691551 GGTCTTACATGAGAGTTTTCATATCGGTGCCCAT
66 GGTCTTACATGAGAGCTCTCATATCGGTGCCCAT
* *
28691585 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCT-CGGTGCCAACGACATGTCCCAGAC
1 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTAC--TGCCAACGACATATCCCAGAC
* *
28691649 ATGGTCTTACATGGGGGCTCTCATA
64 ATGGTCTTACATGAGAGCTCTCATA
28691674 ATCTCAATGA
Statistics
Matches: 72, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
98 1 0.01
99 34 0.47
100 37 0.51
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (99 bp):
GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTACTGCCAACGACATATCCCAGACAT
GGTCTTACATGAGAGCTCTCATATCGGTGCCCAT
Found at i:28696386 original size:18 final size:17
Alignment explanation
Indices: 28696363--28696401 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
28696353 TTTTATAAAT
*
28696363 TGTGAATTATTTTTGATA
1 TGTGAATTATATTTGA-A
28696381 TGTGAATTATATTTGAA
1 TGTGAATTATATTTGAA
28696398 TGTG
1 TGTG
28696402 GAAGAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Done.