Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 74 of 132
Found at i:21740830 original size:36 final size:36
Alignment explanation
Indices: 21740790--21740997 Score: 254
Period size: 36 Copynumber: 5.8 Consensus size: 36
21740780 CTATCACAAC
* * * *
21740790 GCATGAATGACATACCTACATATTTACTGTCTCACG
1 GCATGAATAACATACCCACATATTTACTATCTCATG
* * * *
21740826 GCATGGATAACATACCCATATATTTACTGTCACATG
1 GCATGAATAACATACCCACATATTTACTATCTCATG
*
21740862 TCATGAATAACATACCCACATATTTACTATCTCATG
1 GCATGAATAACATACCCACATATTTACTATCTCATG
** * * * * *
21740898 AAATGAATAATATACCCACACATTTATTATCACGTG
1 GCATGAATAACATACCCACATATTTACTATCTCATG
*
21740934 GCATGAATAACATACCTACATATTTACTATCTCATG
1 GCATGAATAACATACCCACATATTTACTATCTCATG
*
21740970 GCATGAATAACATACCTACATATTTACT
1 GCATGAATAACATACCCACATATTTACT
21740998 TTCACAATAG
Statistics
Matches: 146, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 146 1.00
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.32
Consensus pattern (36 bp):
GCATGAATAACATACCCACATATTTACTATCTCATG
Found at i:21740888 original size:72 final size:72
Alignment explanation
Indices: 21740773--21741003 Score: 291
Period size: 72 Copynumber: 3.2 Consensus size: 72
21740763 TTAGCACAAT
* ** * * * *
21740773 ATATTCACTATCACAACGCATGAATGACATACCTACATATTTACTGTCTCACGGCATGGATAACA
1 ATATTTACTATCACATGGCATGAATAACATACCTACATATTTACTATCTCATGGCATGAATAACA
*
21740838 TACCCAT
66 TACCCAC
* * * ** *
21740845 ATATTTACTGTCACATGTCATGAATAACATACCCACATATTTACTATCTCATGAAATGAATAATA
1 ATATTTACTATCACATGGCATGAATAACATACCTACATATTTACTATCTCATGGCATGAATAACA
21740910 TACCCAC
66 TACCCAC
* * *
21740917 ACATTTATTATCACGTGGCATGAATAACATACCTACATATTTACTATCTCATGGCATGAATAACA
1 ATATTTACTATCACATGGCATGAATAACATACCTACATATTTACTATCTCATGGCATGAATAACA
*
21740982 TACCTAC
66 TACCCAC
*
21740989 ATATTTACTTTCACA
1 ATATTTACTATCACA
21741004 ATAGTCATCA
Statistics
Matches: 131, Mismatches: 28, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
72 131 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (72 bp):
ATATTTACTATCACATGGCATGAATAACATACCTACATATTTACTATCTCATGGCATGAATAACA
TACCCAC
Found at i:21752908 original size:52 final size:52
Alignment explanation
Indices: 21752827--21753066 Score: 354
Period size: 52 Copynumber: 4.6 Consensus size: 52
21752817 TTCTCATTTA
** * *
21752827 ATACTCACGATGACACATTTTCATGGGACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCTGTAAAGGATTCAT
*
21752879 ATACTCACGATGACACATAGTCATCGGACCTTATAATCTGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCTGTAAAGGATTCAT
* * * **
21752931 ATACTCACGATGGCACATAGTTATCGAACCTTATAATCAATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCTGTAAAGGATTCAT
* * * *
21752983 ATACTCATGATGACACATAGTTAACGAACCTTATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCTGTAAAGGATTCAT
21753035 ATACTCACGATGACACATAGTCATCGGACCTT
1 ATACTCACGATGACACATAGTCATCGGACCTT
21753067 TTGCATTTAT
Statistics
Matches: 168, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 168 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTTATAATCTGTAAAGGATTCAT
Found at i:21759205 original size:22 final size:21
Alignment explanation
Indices: 21759147--21759206 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 21
21759137 GTAATTTATC
21759147 TTAAATTATTT-T-TATAATT
1 TTAAATTATTTATATATAATT
*
21759166 TTAATAATT-TGTATTATATAAGTT
1 TT-A-AATTATTTA-TATATAA-TT
21759190 TTAAATTATTTATATAT
1 TTAAATTATTTATATAT
21759207 TCATATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 4 0.12
22 10 0.31
23 9 0.28
24 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (21 bp):
TTAAATTATTTATATATAATT
Found at i:21760351 original size:200 final size:200
Alignment explanation
Indices: 21759988--21760351 Score: 514
Period size: 200 Copynumber: 1.8 Consensus size: 200
21759978 CTTAGCCTAG
* * *
21759988 TTACTCTTAAATTTGTCCTATTTTGGTACTGATGTCGCTACATAAGTAATTTTAGGTTGCATCCA
1 TTACCCTTAAATTTGTCATATTTTGGTACTGATGTCGCTACATAAGTAATTTTAGATTGCATCCA
* * * * *
21760053 GGATTGTCGCCACATCTGACAGCTGTCCAGATAAGAACATAAATGTGTGAGTTGTCCAGTCTGGT
66 AGATTGTCGCCACATCTAACAGCTATCCAGATAAGAACAGAAAAGTGTGAGTTGTCCAGTCTGGT
* * *
21760118 ATAACTAACTTGTACGACCAGCGACAGCTTGATTTTGATGAAAGGACACCTGCAAAAGGACAACT
131 ATAACCAACTGGTACGACCAGAGACAGCTTGATTTTGATGAAAGGACACCTGCAAAAGGACAACT
21760183 TGTAC
196 TGTAC
* * *
21760188 TTACCCTTAATTTTGTCATGTTTTGGTACTGATGTCGCT-CAATAAGTAATTTTAGATTGCGTCC
1 TTACCCTTAAATTTGTCATATTTTGGTACTGATGTCGCTAC-ATAAGTAATTTTAGATTGCATCC
* *** * * *
21760252 AAGATTGTTGCTGTATCTAATAGTTATCCGGATAAGAACAGAAAAGTGTGAGTTGTCCAGTCTGG
65 AAGATTGTCGCCACATCTAACAGCTATCCAGATAAGAACAGAAAAGTGTGAGTTGTCCAGTCTGG
*
21760317 TATAACCAACTGGTACGACCCGAGACAGCTTGATT
130 TATAACCAACTGGTACGACCAGAGACAGCTTGATT
21760352 CTACAGAAAA
Statistics
Matches: 141, Mismatches: 22, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
199 1 0.01
200 140 0.99
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Consensus pattern (200 bp):
TTACCCTTAAATTTGTCATATTTTGGTACTGATGTCGCTACATAAGTAATTTTAGATTGCATCCA
AGATTGTCGCCACATCTAACAGCTATCCAGATAAGAACAGAAAAGTGTGAGTTGTCCAGTCTGGT
ATAACCAACTGGTACGACCAGAGACAGCTTGATTTTGATGAAAGGACACCTGCAAAAGGACAACT
TGTAC
Found at i:21772371 original size:13 final size:13
Alignment explanation
Indices: 21772353--21772432 Score: 56
Period size: 13 Copynumber: 6.2 Consensus size: 13
21772343 TTGGTCAAGA
21772353 AAAGTCAACGATC
1 AAAGTCAACGATC
*
21772366 AAAGTCAAAG-TC
1 AAAGTCAACGATC
* * *
21772378 AATGATTAA-GGTC
1 AAAG-TCAACGATC
* *
21772391 AATAGTTAACGGTC
1 AA-AGTCAACGATC
*
21772405 AAAGTCAAAGATC
1 AAAGTCAACGATC
*
21772418 AAGGTCAACGATC
1 AAAGTCAACGATC
21772431 AA
1 AA
21772433 GTTCGACAGG
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
12 6 0.11
13 41 0.76
14 7 0.13
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.20
Consensus pattern (13 bp):
AAAGTCAACGATC
Found at i:21772610 original size:22 final size:23
Alignment explanation
Indices: 21772580--21772626 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
21772570 AACTTCAGTT
21772580 AACGAGTCGAGTCGA-TCAAAGTC
1 AACGAGTCGAGTCGAGTC-AAGTC
21772603 AACG-GTCGAGTCGAGTCAAGTC
1 AACGAGTCGAGTCGAGTCAAGTC
21772625 AA
1 AA
21772627 TTCGGGTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (23 bp):
AACGAGTCGAGTCGAGTCAAGTC
Found at i:21777391 original size:26 final size:26
Alignment explanation
Indices: 21777355--21777406 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
21777345 CAAGACTAAT
21777355 AACCAAAATTTAAAATTCATACTTCC
1 AACCAAAATTTAAAATTCATACTTCC
*
21777381 AACCAAAATTTAAAATTCGTACTTCC
1 AACCAAAATTTAAAATTCATACTTCC
21777407 TTCAAAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.23, G:0.02, T:0.31
Consensus pattern (26 bp):
AACCAAAATTTAAAATTCATACTTCC
Found at i:21777942 original size:47 final size:47
Alignment explanation
Indices: 21777850--21777962 Score: 122
Period size: 47 Copynumber: 2.4 Consensus size: 47
21777840 CATTCACTTG
* * *
21777850 CATCGTAGTGCCTCTGTCAATTACACTGTAGTGACACTATTACTTTT
1 CATCGTAGTGCCTCTGTCAATTACACAGTAGTGACACCATCACTTTT
* * *
21777897 CATCGTAGTG-CTACTGTCACTTGCACAGTAGTGCCACCATCACTTTGT
1 CATCGTAGTGCCT-CTGTCAATTACACAGTAGTGACACCATCACTTT-T
* *
21777945 -ACCATAGTGCCTCTGTCA
1 CATCGTAGTGCCTCTGTCA
21777963 CTTTTCATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
46 2 0.04
47 50 0.91
48 3 0.05
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (47 bp):
CATCGTAGTGCCTCTGTCAATTACACAGTAGTGACACCATCACTTTT
Found at i:21786409 original size:79 final size:79
Alignment explanation
Indices: 21786319--21786588 Score: 357
Period size: 79 Copynumber: 3.4 Consensus size: 79
21786309 TGTTAACAAC
* *
21786319 AAAAATCGAATAAATTATGTTGAACGGCAGGAATAAAATCTTAAAACAAAATTATTTAATTTATT
1 AAAAATCGAATAAATTCTGTTGAACGACAGGAATAAAATCTTAAAACAAAATTATTTAATTTATT
21786384 TCTCTTTGAAAACA
66 TCTCTTTGAAAACA
* * *
21786398 AAAAATCGAATAAATTCTATTGAAC-AGCAAGAATAAAATCCTAAAACAAAATTATTTAATTTAT
1 AAAAATCGAATAAATTCTGTTGAACGA-CAGGAATAAAATCTTAAAACAAAATTATTTAATTTAT
*
21786462 TTCTCTTTGTAAACA
65 TTCTCTTTGAAAACA
* * * * *
21786477 AAAAATCGAATAAATTCTGTTAAACGACATGAATAAAAT-TCTGAAACAGAATT-TTTCAATTAA
1 AAAAATCGAATAAATTCTGTTGAACGACAGGAATAAAATCT-TAAAACAAAATTATTT-AATTTA
*
21786540 TTTCTGTTTGAAAACA
64 TTTCTCTTTGAAAACA
* * *
21786556 GAAAATCAAATAAATTCTGTTGAATGACAGGAA
1 AAAAATCGAATAAATTCTGTTGAACGACAGGAA
21786589 CAAATCTCGA
Statistics
Matches: 167, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
78 3 0.02
79 163 0.98
80 1 0.01
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.32
Consensus pattern (79 bp):
AAAAATCGAATAAATTCTGTTGAACGACAGGAATAAAATCTTAAAACAAAATTATTTAATTTATT
TCTCTTTGAAAACA
Found at i:21786636 original size:78 final size:79
Alignment explanation
Indices: 21786316--21786636 Score: 287
Period size: 79 Copynumber: 4.1 Consensus size: 79
21786306 TATTGTTAAC
* * * * * * *
21786316 AACA-AAAATCGAATAAATTATGTTGAACGGCAGGAATAAAA-TCTTAAAACAAAATTATTTAAT
1 AACAGAAAATCAAATAAATTCTGTTAAACGACAGGAATAAAATTC-TGAAACAGAATTATTCAAT
* *
21786379 TTATTTCTCTTTGAA
65 TAATTTCTATTTGAA
* * * * * * * * *
21786394 AACAAAAAATCGAATAAATTCTATTGAAC-AGCAAGAATAAAATCCTAAAACAAAATTATTTAAT
1 AACAGAAAATCAAATAAATTCTGTTAAACGA-CAGGAATAAAATTCTGAAACAGAATTATTCAAT
* * *
21786458 TTATTTCTCTTTGTA
65 TAATTTCTATTTGAA
* * * *
21786473 AACAAAAAATCGAATAAATTCTGTTAAACGACATGAATAAAATTCTGAAACAGAATTTTTCAATT
1 AACAGAAAATCAAATAAATTCTGTTAAACGACAGGAATAAAATTCTGAAACAGAATTATTCAATT
*
21786538 AATTTCTGTTTGAA
66 AATTTCTATTTGAA
* * *
21786552 AACAGAAAATCAAATAAATTCTGTTGAATGACAGGAA-CAAA-TCTCGAAA-AGAATTATTCAAA
1 AACAGAAAATCAAATAAATTCTGTTAAACGACAGGAATAAAATTCT-GAAACAGAATTATTC-AA
21786614 TTAATTTCTATTT-ACA
64 TTAATTTCTATTTGA-A
21786630 AACAGAA
1 AACAGAA
21786637 TCCAATTTCA
Statistics
Matches: 211, Mismatches: 25, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
77 13 0.06
78 33 0.16
79 163 0.77
80 2 0.01
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (79 bp):
AACAGAAAATCAAATAAATTCTGTTAAACGACAGGAATAAAATTCTGAAACAGAATTATTCAATT
AATTTCTATTTGAA
Found at i:21789063 original size:9 final size:9
Alignment explanation
Indices: 21789050--21789091 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
21789040 AAAAGTATAA
21789050 AAATTACCC
1 AAATTACCC
* *
21789059 GAATTAACC
1 AAATTACCC
21789068 AAATTACCC
1 AAATTACCC
*
21789077 GAATTACCC
1 AAATTACCC
21789086 AAATTA
1 AAATTA
21789092 AGATTTTTAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.45, C:0.26, G:0.05, T:0.24
Consensus pattern (9 bp):
AAATTACCC
Found at i:21789071 original size:18 final size:18
Alignment explanation
Indices: 21789050--21789091 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
21789040 AAAAGTATAA
21789050 AAATTACCCGAATTAACC
1 AAATTACCCGAATTAACC
*
21789068 AAATTACCCGAATTACCC
1 AAATTACCCGAATTAACC
21789086 AAATTA
1 AAATTA
21789092 AGATTTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.26, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATTACCCGAATTAACC
Found at i:21789406 original size:18 final size:18
Alignment explanation
Indices: 21789385--21789420 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
21789375 TTTGATTAAC
*
21789385 CGATCGATTAATCAAATT
1 CGATCGATTAACCAAATT
21789403 CGATCGATTAACCAAATT
1 CGATCGATTAACCAAATT
21789421 TTTTCGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (18 bp):
CGATCGATTAACCAAATT
Found at i:21791119 original size:87 final size:86
Alignment explanation
Indices: 21790968--21791134 Score: 253
Period size: 87 Copynumber: 1.9 Consensus size: 86
21790958 CATTGAGCCG
* * * * * *
21790968 GTGATGTGTTTCAAGGTACAGCTTAGCAGGCTTTGAGTTGGTGATGTGATTCAAGCTACAGCTTA
1 GTGATGTGATTCAAGCTACAGCTTAGCAGGCTATGAATCGGTGATGTGAATCAAGCTACAGCTTA
*
21791033 GTAGGCTATGAGTCGGGAGTCA
66 -CAGGCTATGAGTCGGGAGTCA
*
21791055 GTGATGTGATTCAAGCTACAGCTTAGCAGGCTATGAATCGGTGATGTGAATCAAGCTACGGCTTA
1 GTGATGTGATTCAAGCTACAGCTTAGCAGGCTATGAATCGGTGATGTGAATCAAGCTACAGCTTA
21791120 CAGGCTATGAGTCGG
66 CAGGCTATGAGTCGG
21791135 TGTTATTGTA
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
86 14 0.19
87 58 0.81
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.29
Consensus pattern (86 bp):
GTGATGTGATTCAAGCTACAGCTTAGCAGGCTATGAATCGGTGATGTGAATCAAGCTACAGCTTA
CAGGCTATGAGTCGGGAGTCA
Found at i:21791135 original size:39 final size:40
Alignment explanation
Indices: 21790938--21791136 Score: 213
Period size: 40 Copynumber: 4.8 Consensus size: 40
21790928 GTGATATGTT
* **
21790938 TCAAGCTACAGCTTAGCAGGC-ATTGAGCCGGTGATGTGTT
1 TCAAGCTACAGCTTAGCAGGCTA-TGAGTCGGTGATGTGAA
* * * *
21790978 TCAAGGTACAGCTTAGCAGGCTTTGAGTTGGTGATGTGAT
1 TCAAGCTACAGCTTAGCAGGCTATGAGTCGGTGATGTGAA
* *
21791018 TCAAGCTACAGCTTAGTAGGCTATGAGTCGGGAGTCAGTGATGTGAT
1 TCAAGCTACAGCTTAGCAGGCTATGAGTC----G---GTGATGTGAA
*
21791065 TCAAGCTACAGCTTAGCAGGCTATGAATCGGTGATGTGAA
1 TCAAGCTACAGCTTAGCAGGCTATGAGTCGGTGATGTGAA
*
21791105 TCAAGCTACGGCTTA-CAGGCTATGAGTCGGTG
1 TCAAGCTACAGCTTAGCAGGCTATGAGTCGGTG
21791137 TTATTGTAAA
Statistics
Matches: 137, Mismatches: 14, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
39 16 0.12
40 82 0.60
43 1 0.01
44 1 0.01
47 37 0.27
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.28
Consensus pattern (40 bp):
TCAAGCTACAGCTTAGCAGGCTATGAGTCGGTGATGTGAA
Found at i:21797214 original size:10 final size:10
Alignment explanation
Indices: 21797201--21797232 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
21797191 TCGGGTTTGC
21797201 TCGGAGTTCA
1 TCGGAGTTCA
21797211 TCGGAGTTCA
1 TCGGAGTTCA
21797221 TCGGAGTTCA
1 TCGGAGTTCA
21797231 TC
1 TC
21797233 TTCTTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (10 bp):
TCGGAGTTCA
Found at i:21797419 original size:97 final size:98
Alignment explanation
Indices: 21797243--21797422 Score: 244
Period size: 97 Copynumber: 1.8 Consensus size: 98
21797233 TTCTTTTTTA
*
21797243 TTATTATTTATATTTAGTTTTTTAATTTGACATTTAACTTATTGATTTTTTTTATTTATTTATTT
1 TTATTATTTATATTTAGTTTTTTAATTTGACATTTAACTTATTGATTTTTTTTATTTATTTAGTT
21797308 GTCATTTATTTTCATGCCTAATTCCAATTATTT
66 GTCATTTATTTTCATGCCTAATTCCAATTATTT
* * *
21797341 TTATTGTTTATATTT-GTTTGTTT-ATTTTAGCATTT-ACTT-TTTATTTTTATTTATTTATCTT
1 TTATTATTTATATTTAGTTT-TTTAATTTGA-CATTTAACTTATTGATTTTT-TTTATTTAT-TT
*
21797402 -GTTGTTATTTATTTTCATGCC
62 AGTTGTCATTTATTTTCATGCC
21797423 ATTTTATTGT
Statistics
Matches: 73, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
96 8 0.11
97 41 0.56
98 24 0.33
ACGTcount: A:0.21, C:0.08, G:0.07, T:0.64
Consensus pattern (98 bp):
TTATTATTTATATTTAGTTTTTTAATTTGACATTTAACTTATTGATTTTTTTTATTTATTTAGTT
GTCATTTATTTTCATGCCTAATTCCAATTATTT
Found at i:21797473 original size:37 final size:37
Alignment explanation
Indices: 21797432--21797530 Score: 96
Period size: 37 Copynumber: 2.6 Consensus size: 37
21797422 CATTTTATTG
*
21797432 TTATCTTTTTTTTTTATTTAATTTGCATTTATTGTT-A-
1 TTATCTTTTTTTTTTATTTAATTT--ATTTATTATTAAT
* *
21797469 TTATCTTGTTTGTTTATTT-ATTTATTTATTATTAATTT
1 TTATCTTTTTTTTTTATTTAATTTATTTATTATTAA--T
*
21797507 TTATATTTTTCTTTTTATTTAATT
1 TTATCTTTTT-TTTTTATTTAATT
21797531 ACATGTTAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
34 9 0.18
35 1 0.02
36 4 0.08
37 17 0.34
38 8 0.16
39 8 0.16
40 3 0.06
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (37 bp):
TTATCTTTTTTTTTTATTTAATTTATTTATTATTAAT
Found at i:21801178 original size:15 final size:13
Alignment explanation
Indices: 21801154--21801192 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 13
21801144 TGCAGATGCA
21801154 TACATGCATTCAT
1 TACATGCATTCAT
21801167 TAGCATTGCATTTCAT
1 TA-CA-TGCA-TTCAT
21801183 TACATGCATT
1 TACATGCATT
21801193 AAATTTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 4 0.17
14 6 0.26
15 6 0.26
16 7 0.30
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (13 bp):
TACATGCATTCAT
Found at i:21805186 original size:5 final size:5
Alignment explanation
Indices: 21805176--21805226 Score: 68
Period size: 5 Copynumber: 9.8 Consensus size: 5
21805166 AAATTAGCAA
21805176 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAAG AAAAAG AGAAA- AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG -AAAAG A-AAAG AAAAG
21805223 AAAA
1 AAAA
21805227 AGGAAAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
4 3 0.07
5 26 0.60
6 14 0.33
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:21805205 original size:16 final size:15
Alignment explanation
Indices: 21805175--21805237 Score: 74
Period size: 16 Copynumber: 3.9 Consensus size: 15
21805165 CAAATTAGCA
21805175 AAAAAGAAAAGAAAAG
1 AAAAAGAAAA-AAAAG
21805191 -AAAAGAAAAGAAAAAG
1 AAAAAG-AAA-AAAAAG
21805207 AAAAAGAGAAAAAAAG
1 AAAAAGA-AAAAAAAG
21805223 AAAAAGGAAAAAAAA
1 AAAAA-GAAAAAAAA
21805238 AAGGAGAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.12
16 27 0.64
17 10 0.24
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:21806654 original size:3 final size:3
Alignment explanation
Indices: 21806646--21806688 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
21806636 TTTGTATCAA
*
21806646 AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
21806689 GCTAGTTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:21809457 original size:294 final size:294
Alignment explanation
Indices: 21808908--21809498 Score: 862
Period size: 294 Copynumber: 2.0 Consensus size: 294
21808898 AAGCAACCTT
* * ** *
21808908 TGCTTGTGCTTATGTACAAAGAAAGTTTGTTTAGCACTATTGATTTAGATAAATCTCTTCCTTTT
1 TGCTTATGCTTATGGACAAAGAAAGTTTGTTTAGCACTAACGATTTAGATAAATCTCTTCCTTCT
* * *
21808973 TCTATTGTGTCTTTGTTGTAGGAATTCAAGAATGTGTTTCCAGAAGATATCCCAAGTGGATTGTC
66 TCTATTGTGTCTCTGCTGCAGGAATTCAAGAATGTGTTTCCAGAAGATATCCCAAGTGGATTGTC
* *
21809038 GCCCATTAGAGACATTGAGCATCAAATAGATTTCATTCCCGGAGCCACTACTCTAAATCGACCAG
131 GCCCATTAGAGACATTGAACATCAAATAGATTTCATTCCCGGAGCCACTACTCTAAATCGACCAA
* * * *
21809103 CTTATCGAACCAACCCCGAGGAAACTAAAGAGTTACAAAGGCAAGTTATCGAGCTAATGGAAAAA
196 CTTATCGAACAAACCCCGAGGAAACTAAAGAGCTACAAAGGCAACTTACCGAGCTAATGGAAAAA
* * *
21809168 GGATATGTTCGAGAGAGCCTAAGTCCATGTGTCG
261 GGATATCTTCGAGAGAGCATAAGTCCATGTGCCG
* * *
21809202 TGCTTATGCTTTTGGACAAGGAAAGTTTGTTTAGCACTAACGATTTAGATAACTCTCTTCCTTCT
1 TGCTTATGCTTATGGACAAAGAAAGTTTGTTTAGCACTAACGATTTAGATAAATCTCTTCCTTCT
* * * *
21809267 TCTATTGTGTCTCTGCTGCAGGAATTCGAGGATGTGTTTCCTGAAGATATTCCAAGTGGATTGTC
66 TCTATTGTGTCTCTGCTGCAGGAATTCAAGAATGTGTTTCCAGAAGATATCCCAAGTGGATTGTC
* * * *
21809332 GCCCATTAGAGGA-ATTGAACATCAAATAGATTTTATTCCCGGAGCCACTATTTTGAATCGACCA
131 GCCCATTAGA-GACATTGAACATCAAATAGATTTCATTCCCGGAGCCACTACTCTAAATCGACCA
* * *
21809396 ACTTATC-AGACAAACCCCGATGAAACTAAAGAGCTACAAAGGTAACTTACCGAGTTAATGGAAA
195 ACTTATCGA-ACAAACCCCGAGGAAACTAAAGAGCTACAAAGGCAACTTACCGAGCTAATGGAAA
*
21809460 AAGGGTATCTTCGAGAGAGCATAAGTCCATGTGCCG
259 AAGGATATCTTCGAGAGAGCATAAGTCCATGTGCCG
21809496 TGC
1 TGC
21809499 CTGTGCTATT
Statistics
Matches: 263, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
293 1 0.00
294 260 0.99
295 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (294 bp):
TGCTTATGCTTATGGACAAAGAAAGTTTGTTTAGCACTAACGATTTAGATAAATCTCTTCCTTCT
TCTATTGTGTCTCTGCTGCAGGAATTCAAGAATGTGTTTCCAGAAGATATCCCAAGTGGATTGTC
GCCCATTAGAGACATTGAACATCAAATAGATTTCATTCCCGGAGCCACTACTCTAAATCGACCAA
CTTATCGAACAAACCCCGAGGAAACTAAAGAGCTACAAAGGCAACTTACCGAGCTAATGGAAAAA
GGATATCTTCGAGAGAGCATAAGTCCATGTGCCG
Found at i:21811921 original size:41 final size:41
Alignment explanation
Indices: 21811875--21811957 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
21811865 TATTAGCATG
21811875 TGAAAACTCATTGTTAAAATAGCAAACCAATGGAAGGAGCA
1 TGAAAACTCATTGTTAAAATAGCAAACCAATGGAAGGAGCA
21811916 TGAAAACTCATTGTTAAAATAGCAAACCAATGGAAGGAGCA
1 TGAAAACTCATTGTTAAAATAGCAAACCAATGGAAGGAGCA
21811957 T
1 T
21811958 AGTAATGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.20
Consensus pattern (41 bp):
TGAAAACTCATTGTTAAAATAGCAAACCAATGGAAGGAGCA
Found at i:21811959 original size:22 final size:22
Alignment explanation
Indices: 21811893--21811959 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
21811883 CATTGTTAAA
21811893 ATAGCAAACCAATGGAAGGAGC
1 ATAGCAAACCAATGGAAGGAGC
* * *
21811915 AT-GAAAACTCATTGTTAA--A--
1 ATAGCAAAC-CAATG-GAAGGAGC
21811934 ATAGCAAACCAATGGAAGGAGC
1 ATAGCAAACCAATGGAAGGAGC
21811956 ATAG
1 ATAG
21811960 TAATGAATAC
Statistics
Matches: 32, Mismatches: 6, Indels: 14
0.62 0.12 0.27
Matches are distributed among these distances:
18 2 0.06
19 6 0.19
20 6 0.19
21 6 0.19
22 10 0.31
23 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.16
Consensus pattern (22 bp):
ATAGCAAACCAATGGAAGGAGC
Found at i:21812943 original size:18 final size:18
Alignment explanation
Indices: 21812920--21812964 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
21812910 TTCTTCTCTC
21812920 TTTTCTCTCTT-AAGTTCT
1 TTTTCTCT-TTCAAGTTCT
*
21812938 TTTTCTCTTTCAATTTCT
1 TTTTCTCTTTCAAGTTCT
*
21812956 TTTTTTCTT
1 TTTTCTCTT
21812965 CTCTCTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTCTCTTTCAAGTTCT
Found at i:21812974 original size:21 final size:20
Alignment explanation
Indices: 21812920--21812983 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 20
21812910 TTCTTCTCTC
* *
21812920 TTTTCTCTCTTAAGTTC--T
1 TTTTCTCTCTCAATTTCTTT
*
21812938 TTTTCTCTTTCAATTTCTTT
1 TTTTCTCTCTCAATTTCTTT
*
21812958 TTTTCTTCTCTCTATTTCTTT
1 TTTTC-TCTCTCAATTTCTTT
21812979 TTTTC
1 TTTTC
21812984 GCTCATTTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
18 14 0.37
20 6 0.16
21 18 0.47
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTCTCTCTCAATTTCTTT
Found at i:21824717 original size:48 final size:47
Alignment explanation
Indices: 21824665--21824787 Score: 167
Period size: 48 Copynumber: 2.6 Consensus size: 47
21824655 CAAGGCATTT
21824665 AACAAAGATGCATTTAACGAACAAAACAATGAAT-ATTACAGATTACTA
1 AACAAAGATGCATTTAAC-AACAAAACAATGAATGA-TACAGATTACTA
* * * *
21824713 AACAAAGATGCATTTAACAAACAAAACACTTAATGATGCAGATTATTA
1 AACAAAGATGCATTTAAC-AACAAAACAATGAATGATACAGATTACTA
*
21824761 AACAAAGATGCATTTAACAAAAAAACA
1 AACAAAGATGCATTTAACAACAAAACA
21824788 CTTAATAAAG
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
47 8 0.12
48 59 0.87
49 1 0.01
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.22
Consensus pattern (47 bp):
AACAAAGATGCATTTAACAACAAAACAATGAATGATACAGATTACTA
Found at i:21824739 original size:24 final size:24
Alignment explanation
Indices: 21824665--21824740 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
21824655 CAAGGCATTT
*
21824665 AACAAAGATGCATTTAACGAACAA
1 AACAAAGATGCATTTAACAAACAA
* *
21824689 AAC--A-ATGAATATT-ACAGATTACTA
1 AACAAAGATGCAT-TTAACA-A--ACAA
21824713 AACAAAGATGCATTTAACAAACAA
1 AACAAAGATGCATTTAACAAACAA
21824737 AACA
1 AACA
21824741 CTTAATGATG
Statistics
Matches: 39, Mismatches: 5, Indels: 16
0.65 0.08 0.27
Matches are distributed among these distances:
21 7 0.18
22 4 0.10
24 16 0.41
26 4 0.10
27 8 0.21
ACGTcount: A:0.55, C:0.16, G:0.09, T:0.20
Consensus pattern (24 bp):
AACAAAGATGCATTTAACAAACAA
Found at i:21827342 original size:17 final size:17
Alignment explanation
Indices: 21827320--21827356 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
21827310 GGCAAATCTG
21827320 CTTTTT-TTATTTTCTTT
1 CTTTTTATTATTTT-TTT
21827337 CTTTTTATTATTTTTTT
1 CTTTTTATTATTTTTTT
21827354 CTT
1 CTT
21827357 GAATGCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (17 bp):
CTTTTTATTATTTTTTT
Found at i:21828493 original size:30 final size:30
Alignment explanation
Indices: 21828459--21828560 Score: 150
Period size: 30 Copynumber: 3.4 Consensus size: 30
21828449 GTGTGTATTT
*
21828459 GCAACATGAGTGTTTGCAGCTCCAGTGTTC
1 GCAACATGAGTGTTCGCAGCTCCAGTGTTC
21828489 GCAACATGAGTGTTCGCAGCTCCAGTGTTC
1 GCAACATGAGTGTTCGCAGCTCCAGTGTTC
** * * *
21828519 ATAACTTGCGTGTTCGTAGCTCCAGTGTTC
1 GCAACATGAGTGTTCGCAGCTCCAGTGTTC
21828549 GCAACATGAGTG
1 GCAACATGAGTG
21828561 CTCTCAACAC
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (30 bp):
GCAACATGAGTGTTCGCAGCTCCAGTGTTC
Found at i:21828503 original size:15 final size:15
Alignment explanation
Indices: 21828416--21828506 Score: 58
Period size: 15 Copynumber: 6.1 Consensus size: 15
21828406 CTATGCTCGT
*
21828416 AACACGAGTGTTCGC
1 AACATGAGTGTTCGC
* *
21828431 AACATTAGTGTTCGT
1 AACATGAGTGTTCGC
*** * * *
21828446 ATTGTGTGTATTTGC
1 AACATGAGTGTTCGC
*
21828461 AACATGAGTGTTTGC
1 AACATGAGTGTTCGC
* *
21828476 AGC-TCCAGTGTTCGC
1 AACAT-GAGTGTTCGC
21828491 AACATGAGTGTTCGC
1 AACATGAGTGTTCGC
21828506 A
1 A
21828507 GCTCCAGTGT
Statistics
Matches: 53, Mismatches: 21, Indels: 4
0.68 0.27 0.05
Matches are distributed among these distances:
14 1 0.02
15 51 0.96
16 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (15 bp):
AACATGAGTGTTCGC
Found at i:21828515 original size:15 final size:15
Alignment explanation
Indices: 21828467--21828551 Score: 66
Period size: 15 Copynumber: 5.7 Consensus size: 15
21828457 TTGCAACATG
*
21828467 AGTGTTTGCAGCTCC
1 AGTGTTCGCAGCTCC
* *
21828482 AGTGTTCGCAACAT-G
1 AGTGTTCGCAGC-TCC
21828497 AGTGTTCGCAGCTCC
1 AGTGTTCGCAGCTCC
** * *
21828512 AGTGTTCATAACTTGC
1 AGTGTTCGCAGC-TCC
*
21828528 -GTGTTCGTAGCTCC
1 AGTGTTCGCAGCTCC
21828542 AGTGTTCGCA
1 AGTGTTCGCA
21828552 ACATGAGTGC
Statistics
Matches: 53, Mismatches: 13, Indels: 8
0.72 0.18 0.11
Matches are distributed among these distances:
14 3 0.06
15 47 0.89
16 3 0.06
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.32
Consensus pattern (15 bp):
AGTGTTCGCAGCTCC
Found at i:21828574 original size:30 final size:30
Alignment explanation
Indices: 21828459--21828575 Score: 130
Period size: 30 Copynumber: 3.9 Consensus size: 30
21828449 GTGTGTATTT
21828459 GCAACATGAGTGTT-TGCAGCTCCAGTGTTC
1 GCAACATGAGTGTTCT-CAGCTCCAGTGTTC
*
21828489 GCAACATGAGTGTTCGCAGCTCCAGTGTTC
1 GCAACATGAGTGTTCTCAGCTCCAGTGTTC
** * *
21828519 ATAACTTGCGTGTTCGT-AGCTCCAGTGTTC
1 GCAACATGAGTGTTC-TCAGCTCCAGTGTTC
* * *
21828549 GCAACATGAGTGCTCTCAACACCAGTG
1 GCAACATGAGTGTTCTCAGCTCCAGTG
21828576 CTGGCATCTT
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
29 1 0.01
30 70 0.99
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (30 bp):
GCAACATGAGTGTTCTCAGCTCCAGTGTTC
Found at i:21831020 original size:21 final size:21
Alignment explanation
Indices: 21830996--21831035 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
21830986 AAATCATTCC
21830996 TAAAAC-ATATTAAACATGCAT
1 TAAAACAAT-TTAAACATGCAT
21831017 TAAAACAATTTAAACATGC
1 TAAAACAATTTAAACATGC
21831036 CAATAAGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.28
Consensus pattern (21 bp):
TAAAACAATTTAAACATGCAT
Found at i:21831332 original size:50 final size:50
Alignment explanation
Indices: 21831263--21831392 Score: 156
Period size: 50 Copynumber: 2.6 Consensus size: 50
21831253 TTGATTTAAA
*
21831263 GATGCAAACTTTAACTAACATGGGAGTTACATAATGCATGAT-AGGATTTAT
1 GATGCAAA-TTTAACTAACATGAGAGTTACATAATGCATG-TCAGGATTTAT
* * **
21831314 GATGCATATTTAACTAACATGTA-AGTTACTTAATGCATGTCATTATTTAT
1 GATGCAAATTTAACTAACATG-AGAGTTACATAATGCATGTCAGGATTTAT
*
21831364 GATGCAAACTTAACTAATCATGAGAGTTA
1 GATGCAAATTTAACTAA-CATGAGAGTTA
21831393 ATGGATGTCA
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
49 1 0.01
50 51 0.75
51 16 0.24
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (50 bp):
GATGCAAATTTAACTAACATGAGAGTTACATAATGCATGTCAGGATTTAT
Found at i:21852146 original size:22 final size:22
Alignment explanation
Indices: 21852118--21852164 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
21852108 GTGTGAGGAT
*
21852118 CACCCTTCATCCATGCTTCCAA
1 CACCCTTCATCCATGCTCCCAA
21852140 CACCCTTCATCCATGCTCCCAA
1 CACCCTTCATCCATGCTCCCAA
21852162 CAC
1 CAC
21852165 AAGTGTTCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.49, G:0.04, T:0.23
Consensus pattern (22 bp):
CACCCTTCATCCATGCTCCCAA
Found at i:21854048 original size:18 final size:18
Alignment explanation
Indices: 21854008--21854042 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21853998 CTTGCTCACT
*
21854008 TTCTTTTTCAATTTCAAG
1 TTCTTTATCAATTTCAAG
*
21854026 TTCTTTATCACTTTCAA
1 TTCTTTATCAATTTCAA
21854043 TCTCTTCACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.20, G:0.03, T:0.54
Consensus pattern (18 bp):
TTCTTTATCAATTTCAAG
Found at i:21854072 original size:21 final size:21
Alignment explanation
Indices: 21854034--21854073 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
21854024 AGTTCTTTAT
*
21854034 CACTTTCAATCTCTTCACTCA
1 CACTTTCAATCACTTCACTCA
21854055 CACTTTC-ATCACTCTCACT
1 CACTTTCAATCACT-TCACT
21854074 TTCTTTTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.40, G:0.00, T:0.38
Consensus pattern (21 bp):
CACTTTCAATCACTTCACTCA
Found at i:21854082 original size:21 final size:21
Alignment explanation
Indices: 21854058--21854104 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
21854048 TCACTCACAC
*
21854058 TTTCATCACTCTCACTTTCTT-
1 TTTCATCACGCTCACTTT-TTG
* *
21854079 TTTCCTCACGCTCTCTTTTTG
1 TTTCATCACGCTCACTTTTTG
21854100 TTTCA
1 TTTCA
21854105 GTTTCTTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.11, C:0.32, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTCATCACGCTCACTTTTTG
Found at i:21854130 original size:16 final size:16
Alignment explanation
Indices: 21854092--21854135 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
21854082 CCTCACGCTC
*
21854092 TCTTTTTGTTTCAGTT
1 TCTTTTTCTTTCAGTT
*
21854108 TC-TTTTCTTTCATTT
1 TCTTTTTCTTTCAGTT
*
21854123 TCTTTTTCATTCA
1 TCTTTTTCTTTCA
21854136 CAATTTCTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.09, C:0.18, G:0.05, T:0.68
Consensus pattern (16 bp):
TCTTTTTCTTTCAGTT
Found at i:21854243 original size:14 final size:16
Alignment explanation
Indices: 21854212--21854244 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
21854202 CTCTTTTTTC
21854212 TTCTCTCAAGTTCTTT
1 TTCTCTCAAGTTCTTT
*
21854228 TTCTCTC-ATTTCTTT
1 TTCTCTCAAGTTCTTT
21854243 TT
1 TT
21854245 TTCTTCTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.03, T:0.64
Consensus pattern (16 bp):
TTCTCTCAAGTTCTTT
Found at i:21854253 original size:20 final size:20
Alignment explanation
Indices: 21854225--21854279 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
21854215 TCTCAAGTTC
21854225 TTTTTCTCTCATTTCTTTT-
1 TTTTTCTCTCATTTCTTTTA
21854244 TTTCTTCTCTCTATTTCTTTTA
1 TTT-TTCTCTC-ATTTCTTTTA
*
21854266 TTTTTCGCTCATTT
1 TTTTTCTCTCATTT
21854280 TCTCTCATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 3 0.09
20 11 0.34
21 15 0.47
22 3 0.09
ACGTcount: A:0.07, C:0.22, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTTCTCTCATTTCTTTTA
Found at i:21854270 original size:41 final size:41
Alignment explanation
Indices: 21854225--21854375 Score: 117
Period size: 41 Copynumber: 3.3 Consensus size: 41
21854215 TCTCAAGTTC
*
21854225 TTTTTCTCTCATTTCTTTTTTTCTTCTCTCTATTTCTTTTA
1 TTTTTCGCTCATTTCTTTTTTTCTTCTCTCTATTTCTTTTA
* *
21854266 TTTTTCGCTCATTTTCTCTCATTATCAACTCTTGTCTTTCT-TTTCTTTTA
1 TTTTTCGCTCA-TTTCT-T--TT-T---TTC-T-TCTCTCTATTTCTTTTA
21854316 GCTTCTTTTTCTG-TCATTTCTTTTTTTCTTCTCTCTATTTCTTTTA
1 -----TTTTTC-GCTCATTTCTTTTTTTCTTCTCTCTATTTCTTTTA
21854362 TTTTTCGCTCATTT
1 TTTTTCGCTCATTT
21854376 TCTCTTATTA
Statistics
Matches: 87, Mismatches: 5, Indels: 36
0.68 0.04 0.28
Matches are distributed among these distances:
40 1 0.01
41 22 0.25
42 5 0.06
43 1 0.01
45 8 0.09
46 11 0.13
47 2 0.02
49 2 0.02
50 11 0.13
51 8 0.09
53 1 0.01
54 5 0.06
55 9 0.10
56 1 0.01
ACGTcount: A:0.09, C:0.23, G:0.03, T:0.66
Consensus pattern (41 bp):
TTTTTCGCTCATTTCTTTTTTTCTTCTCTCTATTTCTTTTA
Found at i:21854326 original size:45 final size:45
Alignment explanation
Indices: 21854277--21854429 Score: 146
Period size: 45 Copynumber: 3.3 Consensus size: 45
21854267 TTTTCGCTCA
21854277 TTTTCTCTCATTATCAACTCTTGTCTTTCTTTTCTTTTAGCTTCT
1 TTTTCTCTCATTATCAACTCTTGTCTTTCTTTTCTTTTAGCTTCT
* *** * * * **
21854322 TTTTCTGTCATT-TCTTTTTTTCTTCTCTCTATTTCTTTTATTTTTCGCT
1 TTTTCTCTCATTATCAACTCTT-GTCTTTCT-TTTCTTTTA-GCTT--CT
*
21854371 CATTTTCTCTTATTATCAACTCTTGTCTTTCTTTTCTTTTAGCTTCT
1 --TTTTCTCTCATTATCAACTCTTGTCTTTCTTTTCTTTTAGCTTCT
21854418 TTTTCTCTCATT
1 TTTTCTCTCATT
21854430 CTTTCGTTAA
Statistics
Matches: 80, Mismatches: 20, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
44 5 0.06
45 28 0.35
46 9 0.11
47 4 0.05
49 4 0.05
50 9 0.11
51 16 0.20
52 5 0.06
ACGTcount: A:0.10, C:0.23, G:0.04, T:0.63
Consensus pattern (45 bp):
TTTTCTCTCATTATCAACTCTTGTCTTTCTTTTCTTTTAGCTTCT
Found at i:21854350 original size:96 final size:96
Alignment explanation
Indices: 21854170--21854433 Score: 415
Period size: 96 Copynumber: 2.8 Consensus size: 96
21854160 ACTCTTTGAA
* * * * * **
21854170 TTTTCTCTCATTTTCTCTTATCAACAACTCTTCTCTTTTTTCTTCTCTCAAG-TTCTTTTTCTCT
1 TTTTCGCTCATTTTCTCTTATTATCAACTCTTGTCTTTCTT-TTCT-TTTAGCTTCTTTTTCTCT
21854234 CATTTCTTTTTTTCTTCTCTCTATTTCTTTTAT
64 CATTTCTTTTTTTCTTCTCTCTATTTCTTTTAT
* *
21854267 TTTTCGCTCATTTTCTCTCATTATCAACTCTTGTCTTTCTTTTCTTTTAGCTTCTTTTTCTGTCA
1 TTTTCGCTCATTTTCTCTTATTATCAACTCTTGTCTTTCTTTTCTTTTAGCTTCTTTTTCTCTCA
21854332 TTTCTTTTTTTCTTCTCTCTATTTCTTTTAT
66 TTTCTTTTTTTCTTCTCTCTATTTCTTTTAT
21854363 TTTTCGCTCATTTTCTCTTATTATCAACTCTTGTCTTTCTTTTCTTTTAGCTTCTTTTTCTCTCA
1 TTTTCGCTCATTTTCTCTTATTATCAACTCTTGTCTTTCTTTTCTTTTAGCTTCTTTTTCTCTCA
21854428 -TTCTTT
66 TTTCTTT
21854434 CGTTAAAAGA
Statistics
Matches: 155, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
95 9 0.06
96 111 0.72
97 35 0.23
ACGTcount: A:0.10, C:0.24, G:0.03, T:0.62
Consensus pattern (96 bp):
TTTTCGCTCATTTTCTCTTATTATCAACTCTTGTCTTTCTTTTCTTTTAGCTTCTTTTTCTCTCA
TTTCTTTTTTTCTTCTCTCTATTTCTTTTAT
Found at i:21854377 original size:21 final size:22
Alignment explanation
Indices: 21854331--21854384 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
21854321 TTTTTCTGTC
*
21854331 ATTTCTTTT-TTTCTTCTCTCT
1 ATTTCTTTTATTTCTTCGCTCT
21854352 ATTTCTTTTATTT-TTCGCTC-
1 ATTTCTTTTATTTCTTCGCTCT
*
21854372 ATTTTCTCTTATT
1 A-TTTCTTTTATT
21854385 ATCAACTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 1 0.03
21 25 0.86
22 3 0.10
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.69
Consensus pattern (22 bp):
ATTTCTTTTATTTCTTCGCTCT
Found at i:21855833 original size:22 final size:21
Alignment explanation
Indices: 21855808--21855850 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
21855798 TGGTGGTTTC
21855808 TTTAATGGATTAGTTGGCTAAA
1 TTTAAT-GATTAGTTGGCTAAA
* * *
21855830 TTTAGTGCTTGGTTGGCTAAA
1 TTTAATGATTAGTTGGCTAAA
21855851 AAGAAGTGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.42
Consensus pattern (21 bp):
TTTAATGATTAGTTGGCTAAA
Found at i:21856550 original size:50 final size:50
Alignment explanation
Indices: 21856470--21856625 Score: 154
Period size: 50 Copynumber: 3.1 Consensus size: 50
21856460 TGACATCCAT
* *
21856470 TAACTCTCATGATTAGTTAAGTTTGCATCATAAATAATGACATGCATTAAG
1 TAACTCACATGA-TAGTTAAATTTGCATCATAAATAATGACATGCATTAAG
* * ** *
21856521 TAACTTACATGATAGTTAAATATGCATCATAAATCCT-ATCATGCATTATG
1 TAACTCACATGATAGTTAAATTTGCATCATAAATAATGA-CATGCATTAAG
* * * *
21856571 TAACTCCCATGTTAGTTAAAGTTTGCATCATTAAATCAA-GTCATGCATTTAG
1 TAACTCACATGATAGTTAAA-TTTGCATCA-TAAAT-AATGACATGCATTAAG
21856623 TAA
1 TAA
21856626 TCCATTAGTT
Statistics
Matches: 84, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
49 1 0.01
50 48 0.57
51 18 0.21
52 17 0.20
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (50 bp):
TAACTCACATGATAGTTAAATTTGCATCATAAATAATGACATGCATTAAG
Found at i:21858935 original size:50 final size:50
Alignment explanation
Indices: 21858837--21858973 Score: 170
Period size: 50 Copynumber: 2.7 Consensus size: 50
21858827 TGGATTACTA
*
21858837 AATGCATGACT-TGATTTAATGATGCAAACTTTAACTAACATGGGAGTTACAT
1 AATGCATGA-TATGATTT-ATGATGCAAA-TTTAACTAACATGGAAGTTACAT
* * *
21858889 AATGCATGATATGATTTATGATGCATATTTAACTAACATGTAAGTTACTT
1 AATGCATGATATGATTTATGATGCAAATTTAACTAACATGGAAGTTACAT
* *
21858939 AATGCATG-TCATTATTTATGATGCAAACTTAACTA
1 AATGCATGAT-ATGATTTATGATGCAAATTTAACTA
21858974 GTCATGAGAG
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
49 1 0.01
50 50 0.66
51 10 0.13
52 15 0.20
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (50 bp):
AATGCATGATATGATTTATGATGCAAATTTAACTAACATGGAAGTTACAT
Found at i:21859212 original size:17 final size:17
Alignment explanation
Indices: 21859181--21859213 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21859171 CAAACACTTA
21859181 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
21859198 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
21859214 AGTCCTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:21866972 original size:24 final size:24
Alignment explanation
Indices: 21866945--21866999 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
21866935 GAGAGTTCTC
*
21866945 AAGAGGAAAAAGAAAATGAAAAAA
1 AAGAAGAAAAAGAAAATGAAAAAA
* **
21866969 AAGAAGAAAATGAAAATGAAAAGC
1 AAGAAGAAAAAGAAAATGAAAAAA
21866993 AAGAAGA
1 AAGAAGA
21867000 TACCCATACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.71, C:0.02, G:0.22, T:0.05
Consensus pattern (24 bp):
AAGAAGAAAAAGAAAATGAAAAAA
Found at i:21875259 original size:15 final size:15
Alignment explanation
Indices: 21875222--21875260 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
21875212 CCTTTCATCC
21875222 ATGCTTGCAACACAA
1 ATGCTTGCAACACAA
*
21875237 ATGTTTGCAACATCAA
1 ATGCTTGCAACA-CAA
21875253 A-GCTTGCA
1 ATGCTTGCA
21875261 TTGTGTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (15 bp):
ATGCTTGCAACACAA
Found at i:21877376 original size:30 final size:30
Alignment explanation
Indices: 21877341--21877424 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
21877331 GAACACTAAT
*
21877341 AATGCGAGCA-TGGACCTTGCGAGCTTGGAA
1 AATGCGAGCACTGG-CCTTACGAGCTTGGAA
* **
21877371 GATGCGAGCACTGGTGTTACGAGCTTGGAA
1 AATGCGAGCACTGGCCTTACGAGCTTGGAA
**
21877401 AATGCGAGCACTGGTGTTACGAGC
1 AATGCGAGCACTGGCCTTACGAGC
21877425 ACTCATGTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 45 0.94
31 3 0.06
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.21
Consensus pattern (30 bp):
AATGCGAGCACTGGCCTTACGAGCTTGGAA
Found at i:21877437 original size:30 final size:29
Alignment explanation
Indices: 21877403--21877478 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 29
21877393 GCTTGGAAAA
* *
21877403 TGCGAGCACTGGTGTTACGAGCACTCATGT
1 TGCGAACACTGGTGTT-CGAACACTCATGT
* *
21877433 TGCGAACATTGGAGCTTCGAACACTCATGT
1 TGCGAACACTGGTG-TTCGAACACTCATGT
* *
21877463 TGTGAACACTCGTGTT
1 TGCGAACACTGGTGTT
21877479 GAGAGCATGG
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 2 0.05
30 33 0.89
31 2 0.05
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (29 bp):
TGCGAACACTGGTGTTCGAACACTCATGT
Found at i:21881824 original size:19 final size:19
Alignment explanation
Indices: 21881793--21881832 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
21881783 CTTATCTGAG
*
21881793 TTATTTTCTTTTGAA-AGT
1 TTATTTTCCTTTGAATAGT
21881811 TTATGTTTCCTTTGAATAGT
1 TTAT-TTTCCTTTGAATAGT
21881831 TT
1 TT
21881833 GTTAGTCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 10 0.53
20 5 0.26
ACGTcount: A:0.20, C:0.07, G:0.12, T:0.60
Consensus pattern (19 bp):
TTATTTTCCTTTGAATAGT
Found at i:21894094 original size:16 final size:16
Alignment explanation
Indices: 21894064--21894108 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
21894054 TAAGTCTAAA
21894064 AAAAATCTC-AAAATT
1 AAAAATCTCAAAAATT
* *
21894079 ACAAGTCTCAAAAATT
1 AAAAATCTCAAAAATT
21894095 AAAAATCTCAAAAA
1 AAAAATCTCAAAAA
21894109 CATTTTATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (16 bp):
AAAAATCTCAAAAATT
Found at i:21898146 original size:19 final size:20
Alignment explanation
Indices: 21898124--21898162 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
21898114 CTCACTTTCT
21898124 TTTTTCACT-CTCTCTTTTA
1 TTTTTCACTCCTCTCTTTTA
*
21898143 TTTTTCTCTCGCTCTCTTTT
1 TTTTTCACTC-CTCTCTTTT
21898163 TCCTCAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.05, C:0.28, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTTCACTCCTCTCTTTTA
Found at i:21898220 original size:21 final size:21
Alignment explanation
Indices: 21898194--21898247 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
21898184 AAATTTTCTT
** *
21898194 TTTCAATTTCTTTTCTTTTTC
1 TTTCAATTTCTCGTATTTTTC
*
21898215 TTTCAATCTCTCGTATTTTTC
1 TTTCAATTTCTCGTATTTTTC
*
21898236 TTTCATTTTCTC
1 TTTCAATTTCTC
21898248 TCATTATCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.11, C:0.22, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTCAATTTCTCGTATTTTTC
Found at i:21898289 original size:16 final size:18
Alignment explanation
Indices: 21898265--21898305 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
21898255 CAACTCTTGT
21898265 TTTTC-TTTTCTCTCA-A
1 TTTTCTTTTTCTCTCATA
*
21898281 -TTTCTTTTTGTCTCATA
1 TTTTCTTTTTCTCTCATA
21898298 TTTTCTTT
1 TTTTCTTT
21898306 ACAAGATGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.19
16 9 0.43
17 1 0.05
18 7 0.33
ACGTcount: A:0.10, C:0.20, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTCTTTTTCTCTCATA
Found at i:21899853 original size:36 final size:36
Alignment explanation
Indices: 21899767--21899854 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 36
21899757 TAGCTCAAAA
* * *
21899767 GGCATGTCTATCCATTTGTCTTTAAGGATATGAAAG
1 GGCATGTCTATTCATTTATCTTTAAGGAGATGAAAG
* * * *
21899803 GACATGTCTCTTCATTTATCTTTGAGTAGATGAAAG
1 GGCATGTCTATTCATTTATCTTTAAGGAGATGAAAG
*
21899839 GGCATGTCTTTTCATT
1 GGCATGTCTATTCATT
21899855 AGTCCTTGGA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (36 bp):
GGCATGTCTATTCATTTATCTTTAAGGAGATGAAAG
Found at i:21900255 original size:19 final size:19
Alignment explanation
Indices: 21900228--21900270 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
21900218 AACAGTCAAA
*
21900228 TTAAATAACACACA-CATAT
1 TTAATTAACACA-AGCATAT
*
21900247 TTAATTAACTCAAGCATAT
1 TTAATTAACACAAGCATAT
21900266 TTAAT
1 TTAAT
21900271 AACTAAGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (19 bp):
TTAATTAACACAAGCATAT
Found at i:21900404 original size:51 final size:50
Alignment explanation
Indices: 21900330--21900548 Score: 201
Period size: 50 Copynumber: 4.3 Consensus size: 50
21900320 TAGATTACTA
* **
21900330 AATGCATGA-CTTATTTCAATGATGCAAACTTTAACTAACATGGGAGTTACAT
1 AATGCATGATATTATTT--ATGATGCAAAC-TTAACTAACATGAAAGTTACAT
* * * * * *
21900382 CATGCATGATATAATTTGTGATG-AATATTTAACTAACATGTAAGTTACTT
1 AATGCATGATATTATTTATGATGCAA-ACTTAACTAACATGAAAGTTACAT
* * * * *
21900432 AATGCATG-TCTTTATTTATTATGCAAACTTAACTAACCAAGAGAGTTATAT
1 AATGCATGAT-ATTATTTATGATGCAAACTTAACTAA-CATGAAAGTTACAT
* *
21900483 AATGCATGTTATTATTTATGATGCATACTTAACTAACATGAAAGTTACAT
1 AATGCATGATATTATTTATGATGCAAACTTAACTAACATGAAAGTTACAT
* *
21900533 ATTGCATGATTTTATT
1 AATGCATGATATTATT
21900549 AAATGCAGAA
Statistics
Matches: 133, Mismatches: 28, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
49 1 0.01
50 70 0.53
51 48 0.36
52 9 0.07
53 5 0.04
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.38
Consensus pattern (50 bp):
AATGCATGATATTATTTATGATGCAAACTTAACTAACATGAAAGTTACAT
Found at i:21900478 original size:101 final size:102
Alignment explanation
Indices: 21900324--21900553 Score: 261
Period size: 101 Copynumber: 2.3 Consensus size: 102
21900314 AAATAATAGA
* * * * *
21900324 TTACTAAATGCATGAC-TTATTTCAATGATGCAAACTTTAACTAACATGGGAGTTACATCATGCA
1 TTACTTAATGCATGTCTTTATTT-AATGATGCAAACTTTAACTAACAAGAGAGTTACATAATGCA
* * *
21900388 TGATATAATTTGTGATGAATATTTAACTAACATGTAAG
65 TGATATAATTTATGATGAATACTTAACTAACATGAAAG
* *
21900426 TTACTTAATGCATGTCTTTATTT-ATTATGCAAAC-TTAACTAACCAAGAGAGTTATATAATGCA
1 TTACTTAATGCATGTCTTTATTTAATGATGCAAACTTTAACTAA-CAAGAGAGTTACATAATGCA
* * *
21900489 TGTTATTATTTATGATGCATACTTAACTAACATGAAAG
65 TGATATAATTTATGATGAATACTTAACTAACATGAAAG
* * *
21900527 TTACATATTGCATGAT-TTTATTAAATG
1 TTACTTAATGCATG-TCTTTATTTAATG
21900554 CAGAACACAT
Statistics
Matches: 107, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
100 8 0.07
101 76 0.71
102 17 0.16
103 6 0.06
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (102 bp):
TTACTTAATGCATGTCTTTATTTAATGATGCAAACTTTAACTAACAAGAGAGTTACATAATGCAT
GATATAATTTATGATGAATACTTAACTAACATGAAAG
Found at i:21904728 original size:24 final size:24
Alignment explanation
Indices: 21904699--21904761 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
21904689 AGAAATAATC
21904699 TTTCAATTAAACTCTATTTAATTG
1 TTTCAATTAAACTCTATTTAATTG
*
21904723 TTTCAATTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTATTTAATTG
*
21904747 TTTGAATTAAACTCT
1 TTTCAATTAAACTCT
21904762 TATTACTCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTAATTG
Found at i:21905471 original size:29 final size:29
Alignment explanation
Indices: 21905429--21905489 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
21905419 GTGTCCGTCA
21905429 AAGAGCAGTTCAATCATAAAAAACAACAT
1 AAGAGCAGTTCAATCATAAAAAACAACAT
21905458 AAGAGCAGTTCAATCATAAAAAACAACAT
1 AAGAGCAGTTCAATCATAAAAAACAACAT
21905487 AAG
1 AAG
21905490 GTTTCATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.56, C:0.16, G:0.11, T:0.16
Consensus pattern (29 bp):
AAGAGCAGTTCAATCATAAAAAACAACAT
Found at i:21918182 original size:4 final size:4
Alignment explanation
Indices: 21918173--21918204 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
21918163 TATTGCAGTG
21918173 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
21918205 AGGGTGAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:21918374 original size:6 final size:6
Alignment explanation
Indices: 21918365--21918396 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
21918355 CTTTTTCCTT
*
21918365 TTGGTC TTGGTC TTGGTC TTGGTT TTGGTC TT
1 TTGGTC TTGGTC TTGGTC TTGGTC TTGGTC TT
21918397 AACGAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.12, G:0.31, T:0.56
Consensus pattern (6 bp):
TTGGTC
Found at i:21919387 original size:91 final size:92
Alignment explanation
Indices: 21919288--21919457 Score: 211
Period size: 91 Copynumber: 1.8 Consensus size: 92
21919278 TGAAAAACAA
* *
21919288 TTTATTGGTGCCACCGGTGTGTCAAGCGGCACCGCTTTA-ATTTAAAAAAAA-TAACTTGTCAGA
1 TTTATTGGTACCACCGGTGTGTCAAGCGACACCGCTTTATATTTAAAAAAAATTAAC-TGTCAGA
21919351 AAAAAG-TAGTTGAAACAAAAAAATATTT
65 AAAAAGCT-GTTGAAACAAAAAAATATTT
* * * * * * *
21919379 TTTATTGGTATCATCGGTGTGTTAGGCGACACCGCTTTATTTTTTAAAAAAAATTGACTGTTAGA
1 TTTATTGGTACCACCGGTGTGTCAAGCGACACCGCTTTA-TATTTAAAAAAAATTAACTGTCAGA
21919444 AAAAAGCTGTTGAA
65 AAAAAGCTGTTGAA
21919458 GTAACAAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
91 33 0.50
93 29 0.44
94 4 0.06
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (92 bp):
TTTATTGGTACCACCGGTGTGTCAAGCGACACCGCTTTATATTTAAAAAAAATTAACTGTCAGAA
AAAAGCTGTTGAAACAAAAAAATATTT
Found at i:21922317 original size:13 final size:13
Alignment explanation
Indices: 21922299--21922327 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
21922289 ATGCTTGATG
21922299 TTTAGGTTGGATC
1 TTTAGGTTGGATC
21922312 TTTAGGTTGGATC
1 TTTAGGTTGGATC
21922325 TTT
1 TTT
21922328 TTGTAAAGTG
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:0.14, C:0.07, G:0.28, T:0.52
Consensus pattern (13 bp):
TTTAGGTTGGATC
Found at i:21929700 original size:18 final size:18
Alignment explanation
Indices: 21929669--21929717 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
21929659 AAATTCAAAA
* *
21929669 AATAATTCGAATTAATTCG
1 AATAACTCG-ATTAACTCG
21929688 AATAACTCGATTAACTCG
1 AATAACTCGATTAACTCG
* *
21929706 AAAAACTTGATT
1 AATAACTCGATT
21929718 CGTTTAACTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (18 bp):
AATAACTCGATTAACTCG
Found at i:21930521 original size:13 final size:14
Alignment explanation
Indices: 21930503--21930536 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
21930493 ATGATAATTA
21930503 CTTCTATTT-TATT
1 CTTCTATTTCTATT
21930516 CTTCTATTTCTATT
1 CTTCTATTTCTATT
*
21930530 GTTCTAT
1 CTTCTAT
21930537 ACTCTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.15, C:0.18, G:0.03, T:0.65
Consensus pattern (14 bp):
CTTCTATTTCTATT
Found at i:21933778 original size:18 final size:18
Alignment explanation
Indices: 21933738--21933869 Score: 147
Period size: 18 Copynumber: 7.3 Consensus size: 18
21933728 GAAAGTACTG
* *
21933738 TACTGGCTCATTAGAACA
1 TACTGGCTCGTTAGAGCA
* * *
21933756 AACTGACTCGTTCGAGCA
1 TACTGGCTCGTTAGAGCA
*
21933774 TACTGGCTAGTTAGAGCA
1 TACTGGCTCGTTAGAGCA
*
21933792 TACTGGCTCGTTTGAGCA
1 TACTGGCTCGTTAGAGCA
* * *
21933810 TACTAGCTCATTAGCGCA
1 TACTGGCTCGTTAGAGCA
*
21933828 TACTGGCTCGTTTGAGCA
1 TACTGGCTCGTTAGAGCA
*
21933846 TACTGGCTCGTAAGAGCAA
1 TACTGGCTCGTTAGAGC-A
21933865 TACTG
1 TACTG
21933870 ATTCGTAAGA
Statistics
Matches: 92, Mismatches: 21, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
18 86 0.93
19 6 0.07
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (18 bp):
TACTGGCTCGTTAGAGCA
Found at i:21933788 original size:36 final size:36
Alignment explanation
Indices: 21933738--21933869 Score: 167
Period size: 36 Copynumber: 3.6 Consensus size: 36
21933728 GAAAGTACTG
* * * *
21933738 TACTGGCTCATTAGAACAAACTGACTCGTTCGAGCA
1 TACTGGCTCATTAGAGCATACTGGCTCGTTTGAGCA
21933774 TACTGGCT-AGTTAGAGCATACTGGCTCGTTTGAGCA
1 TACTGGCTCA-TTAGAGCATACTGGCTCGTTTGAGCA
* *
21933810 TACTAGCTCATTAGCGCATACTGGCTCGTTTGAGCA
1 TACTGGCTCATTAGAGCATACTGGCTCGTTTGAGCA
* *
21933846 TACTGGCTCGTAAGAGCAATACTG
1 TACTGGCTCATTAGAGC-ATACTG
21933870 ATTCGTAAGA
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
35 1 0.01
36 75 0.90
37 7 0.08
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (36 bp):
TACTGGCTCATTAGAGCATACTGGCTCGTTTGAGCA
Found at i:21933869 original size:19 final size:18
Alignment explanation
Indices: 21933769--21933956 Score: 144
Period size: 19 Copynumber: 10.2 Consensus size: 18
21933759 TGACTCGTTC
* *
21933769 GAGCATACTGGCTAGTTA
1 GAGCATACTGGCTCGTAA
**
21933787 GAGCATACTGGCTCGTTT
1 GAGCATACTGGCTCGTAA
* * *
21933805 GAGCATACTAGCTCATTA
1 GAGCATACTGGCTCGTAA
* **
21933823 GCGCATACTGGCTCGTTT
1 GAGCATACTGGCTCGTAA
21933841 GAGCATACTGGCTCGTAA
1 GAGCATACTGGCTCGTAA
**
21933859 GAGCAATACTGATTCGTAA
1 GAGC-ATACTGGCTCGTAA
**
21933878 GAGCGATACTATCTCGTAA
1 GAGC-ATACTGGCTCGTAA
* **
21933897 GTGCGATACTATCTCGTAA
1 GAGC-ATACTGGCTCGTAA
*
21933916 GTGCGATACTGGCTCGTAA
1 GAGC-ATACTGGCTCGTAA
*
21933935 -AGGCGATACTGGCTCATAA
1 GA-GC-ATACTGGCTCGTAA
21933954 GAG
1 GAG
21933957 TTAATTACTA
Statistics
Matches: 144, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
18 64 0.44
19 79 0.55
20 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (18 bp):
GAGCATACTGGCTCGTAA
Found at i:21937637 original size:18 final size:18
Alignment explanation
Indices: 21937589--21937679 Score: 76
Period size: 18 Copynumber: 4.9 Consensus size: 18
21937579 TACTGTATTA
21937589 GCTCGTTAGAGCATACTG
1 GCTCGTTAGAGCATACTG
* *
21937607 GCTCATTCA-AGCATAGTG
1 GCTCGTT-AGAGCATACTG
* *
21937625 GCTCGTTTGAGCATATTG
1 GCTCGTTAGAGCATACTG
* * *
21937643 GCTCGTAAGAGTGATATTG
1 GCTCGTTAGAG-CATACTG
*
21937662 GCTCGTAAGAGCAATACT
1 GCTCGTTAGAGC-ATACT
21937680 ATCTCATAAG
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
18 37 0.63
19 22 0.37
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (18 bp):
GCTCGTTAGAGCATACTG
Found at i:21941321 original size:17 final size:17
Alignment explanation
Indices: 21941301--21941339 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
21941291 ACTACAATGT
*
21941301 AAATGCATCGACAAATA
1 AAATGCAGCGACAAATA
* *
21941318 AAATGCAGGGACAATTA
1 AAATGCAGCGACAAATA
21941335 AAATG
1 AAATG
21941340 TGATGACAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.13, G:0.18, T:0.18
Consensus pattern (17 bp):
AAATGCAGCGACAAATA
Found at i:21946939 original size:366 final size:366
Alignment explanation
Indices: 21946263--21946977 Score: 1250
Period size: 366 Copynumber: 2.0 Consensus size: 366
21946253 TTGCGTCAAC
* *
21946263 AATTTTGTAGGTCGAATGGTTGGCATGGGAGTAATAACTGGTGGCTCCTCTTCATTTTGCTCTAC
1 AATTTTGTAGGTCGAATGGTTGGCATGAGAGTAATAACTGGTGGCTCCTCTTCATTTAGCTCTAC
21946328 TGCTTCTTCTTCAGGTACAACTTTTCCTCGTTGCTCTGCTTCATTTGTGTCGACAGGTGCTGTAC
66 TGCTTCTTCTTCAGGTACAACTTTTCCTCGTTGCTCTGCTTCATTTGTGTCGACAGGTGCTGTAC
*
21946393 TGGAATTGCTACATTGTTCAACAGTTTACTTTCCACTCCGAAGAGTAATAGCTTTGCAATGCTCC
131 TGGAATTGCTACATTATTCAACAGTTTACTTTCCACTCCGAAGAGTAATAGCTTTGCAATGCTCC
* *
21946458 TTCTCATTTTGAATTGGATTTTCAATATCACTGGGTAAGACACCTGGTGGTCTCGTGCTCATATT
196 TTCCCATTTTGAATTGGATTTTCAATATCACTGGGTAAGACACCTGGTGGGCTCGTGCTCATATT
* *
21946523 AGAAACTAGTTATCCTACTTATGCTTCCAATGCTCGGATGGAAGAAGAATTTCCTTGCACAATAG
261 AGAAACTAGTTATCCTACTTATGCTTCCAACGCTCGGATGGAAAAAGAATTTCCTTGCACAATAG
21946588 CTTCAGTTCTTGTGATGTGTTAACTGGTGGCATGGAAGAAG
326 CTTCAGTTCTTGTGATGTGTTAACTGGTGGCATGGAAGAAG
*
21946629 AATTTTGTAGGTCGAATGGTTGGCATGAGAGTAATAATTGGTGGCTCCTCTTCATTTAGCTCTAC
1 AATTTTGTAGGTCGAATGGTTGGCATGAGAGTAATAACTGGTGGCTCCTCTTCATTTAGCTCTAC
* *
21946694 TTCTTCTTCTTCAGGTACAACTTTTCCTCGTTGCTCTGCTTCATTTGTGTCGACAGGTGCTGTAT
66 TGCTTCTTCTTCAGGTACAACTTTTCCTCGTTGCTCTGCTTCATTTGTGTCGACAGGTGCTGTAC
* * * *
21946759 TGGAATTGCTGCTTTATTCAATAGTTTGCTTTCCACTCCGAAGAGTAATAGCTTTGCAATGCTCC
131 TGGAATTGCTACATTATTCAACAGTTTACTTTCCACTCCGAAGAGTAATAGCTTTGCAATGCTCC
* * *
21946824 TTCCCCTTTTGAATTGGATTTTCAGTATCACTGGGTAAGGCACCTGGTGGGCTCGTGCTCATATT
196 TTCCCATTTTGAATTGGATTTTCAATATCACTGGGTAAGACACCTGGTGGGCTCGTGCTCATATT
* * *
21946889 AGAAACTAGTTGTCCTATTTGTGCTTCCAACGCTCGGATGGAAAAAGAATTTCCTTGCACAATAG
261 AGAAACTAGTTATCCTACTTATGCTTCCAACGCTCGGATGGAAAAAGAATTTCCTTGCACAATAG
21946954 CTTCAGTTCTTGTGATGTGTTAAC
326 CTTCAGTTCTTGTGATGTGTTAAC
21946978 GCATCAAAGC
Statistics
Matches: 329, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
366 329 1.00
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (366 bp):
AATTTTGTAGGTCGAATGGTTGGCATGAGAGTAATAACTGGTGGCTCCTCTTCATTTAGCTCTAC
TGCTTCTTCTTCAGGTACAACTTTTCCTCGTTGCTCTGCTTCATTTGTGTCGACAGGTGCTGTAC
TGGAATTGCTACATTATTCAACAGTTTACTTTCCACTCCGAAGAGTAATAGCTTTGCAATGCTCC
TTCCCATTTTGAATTGGATTTTCAATATCACTGGGTAAGACACCTGGTGGGCTCGTGCTCATATT
AGAAACTAGTTATCCTACTTATGCTTCCAACGCTCGGATGGAAAAAGAATTTCCTTGCACAATAG
CTTCAGTTCTTGTGATGTGTTAACTGGTGGCATGGAAGAAG
Found at i:21956251 original size:270 final size:270
Alignment explanation
Indices: 21955770--21956307 Score: 1031
Period size: 270 Copynumber: 2.0 Consensus size: 270
21955760 TATTTGTTAA
*
21955770 CGTAGTTCATACACAACTATCCTACGTCTGTGGAGTTTGACCCAGTAAATGATTTTATTCAACAA
1 CGTAGTTCAAACACAACTATCCTACGTCTGTGGAGTTTGACCCAGTAAATGATTTTATTCAACAA
*
21955835 TCATCTAGGTCACCTATTAATTAAAGGCCAATTTACCATTACACCAAGAAGTAATTGCAACCCCA
66 TCATCTAGGTCACCTATTAATTAAAGCCCAATTTACCATTACACCAAGAAGTAATTGCAACCCCA
*
21955900 ATACCGACCCCAATTGTTACAAATCACTAACTCAAATACCTTACAATACAATCAATATAACTCTC
131 ATACCGACCCCAATTGTTACAAATCACTAACTCAAATACCTTACAATACAATCAATAAAACTCTC
21955965 CAAAGAATACTTGGGTCACAAAATAACCACAAGAAAACACAAGAAAGCTGTCGTCAAAGACACTC
196 CAAAGAATACTTGGGTCACAAAATAACCACAAGAAAACACAAGAAAGCTGTCGTCAAAGACACTC
21956030 CAAAACTGCT
261 CAAAACTGCT
*
21956040 CGTAGTTCAAACACAACTGTCCTACGTCTGTGGAGTTTGACCCAGTAAATGATTTTATTCAACAA
1 CGTAGTTCAAACACAACTATCCTACGTCTGTGGAGTTTGACCCAGTAAATGATTTTATTCAACAA
*
21956105 TCATCTAGGTCACCTATTAATTAAAGCCCAATTTACCATTGCACCAAGAAGTAATTGCAACCCCA
66 TCATCTAGGTCACCTATTAATTAAAGCCCAATTTACCATTACACCAAGAAGTAATTGCAACCCCA
21956170 ATACCGACCCCAATTGTTACAAATCACTAACTCAAATACCTTACAATACAATCAATAAAACTCTC
131 ATACCGACCCCAATTGTTACAAATCACTAACTCAAATACCTTACAATACAATCAATAAAACTCTC
21956235 CAAAGAATACTTGGGTCACAAAATAACCACAAGAAAACACAAGAAAGCTGTCGTCAAAGACACTC
196 CAAAGAATACTTGGGTCACAAAATAACCACAAGAAAACACAAGAAAGCTGTCGTCAAAGACACTC
21956300 CAAAACTG
261 CAAAACTG
21956308 TTCTCCAAAG
Statistics
Matches: 263, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
270 263 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.24
Consensus pattern (270 bp):
CGTAGTTCAAACACAACTATCCTACGTCTGTGGAGTTTGACCCAGTAAATGATTTTATTCAACAA
TCATCTAGGTCACCTATTAATTAAAGCCCAATTTACCATTACACCAAGAAGTAATTGCAACCCCA
ATACCGACCCCAATTGTTACAAATCACTAACTCAAATACCTTACAATACAATCAATAAAACTCTC
CAAAGAATACTTGGGTCACAAAATAACCACAAGAAAACACAAGAAAGCTGTCGTCAAAGACACTC
CAAAACTGCT
Found at i:21960158 original size:27 final size:29
Alignment explanation
Indices: 21960109--21960179 Score: 100
Period size: 27 Copynumber: 2.7 Consensus size: 29
21960099 AGTTTAGCTT
21960109 TTACGAGTCTAG-AT-AGAATATCGCT-C
1 TTACGAGTCTAGAATCAGAATATCGCTCC
21960135 TTACGAGTC-AGAATCAGAATATCGCTCC
1 TTACGAGTCTAGAATCAGAATATCGCTCC
21960163 TT-CGAG-CTAGAATCAGA
1 TTACGAGTCTAGAATCAGA
21960180 TTACTCCTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
25 2 0.05
26 12 0.29
27 24 0.59
28 3 0.07
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (29 bp):
TTACGAGTCTAGAATCAGAATATCGCTCC
Found at i:21961378 original size:21 final size:21
Alignment explanation
Indices: 21961341--21961380 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
21961331 TAAAAATTAT
*
21961341 TATTGATTCATATAATTTAAA
1 TATTCATTCATATAATTTAAA
21961362 TATTCATT-ATATGAATTTA
1 TATTCATTCATAT-AATTTA
21961381 CTCGTTGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (21 bp):
TATTCATTCATATAATTTAAA
Found at i:21963870 original size:14 final size:15
Alignment explanation
Indices: 21963847--21963880 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
21963837 TATACATATA
*
21963847 TTTTTTTCTTTTC-C
1 TTTTTCTCTTTTCTC
21963861 TTTTTCTCTTTTCTC
1 TTTTTCTCTTTTCTC
21963876 TTTTT
1 TTTTT
21963881 TATATATGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTCTCTTTTCTC
Found at i:21969051 original size:15 final size:15
Alignment explanation
Indices: 21969016--21969053 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
21969006 GCTCGCAACG
21969016 TGAGTGTTCGCAGCA
1 TGAGTGTTCGCAGCA
*
21969031 TTAGTGTTCGC-GCTA
1 TGAGTGTTCGCAGC-A
21969046 TGAGTGTT
1 TGAGTGTT
21969054 TGCATCTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.37
Consensus pattern (15 bp):
TGAGTGTTCGCAGCA
Found at i:21976349 original size:21 final size:21
Alignment explanation
Indices: 21976325--21976364 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21976315 GTACACGATT
**
21976325 TTGACGTGGCTGCATCTGATC
1 TTGACGTGAATGCATCTGATC
*
21976346 TTGATGTGAATGCATCTGA
1 TTGACGTGAATGCATCTGA
21976365 GTATTCTGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (21 bp):
TTGACGTGAATGCATCTGATC
Found at i:21995025 original size:21 final size:21
Alignment explanation
Indices: 21994991--21995031 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
21994981 ATAAAAAAAG
21994991 AAAAGAAAATGAGT-AGAAAC
1 AAAAGAAAATGAGTAAGAAAC
*
21995011 AAAAGAATCATGAGTAAGAAA
1 AAAAGAA-AATGAGTAAGAAA
21995032 ATAGATAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.63, C:0.05, G:0.20, T:0.12
Consensus pattern (21 bp):
AAAAGAAAATGAGTAAGAAAC
Found at i:21996009 original size:21 final size:21
Alignment explanation
Indices: 21995970--21996010 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21995960 AGACTTTTAC
* *
21995970 CGATACAAGTGACAGTTCTAT
1 CGATACAAATGACACTTCTAT
*
21995991 CGATACAAATGACTCTTCTA
1 CGATACAAATGACACTTCTA
21996011 CTGAAACAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (21 bp):
CGATACAAATGACACTTCTAT
Found at i:21996756 original size:36 final size:36
Alignment explanation
Indices: 21996709--21996851 Score: 259
Period size: 36 Copynumber: 3.9 Consensus size: 36
21996699 TCGTTATTCG
21996709 TTTTACTCCCTGTTGACCCAAAGGTCATGATGTTCA
1 TTTTACTCCCTGTTGACCCAAAGGTCATGATGTTCA
21996745 TTTTACTCCCTGTTGACCCAAAGGTCATGATGTTCA
1 TTTTACTCCCTGTTGACCCAAAGGTCATGATGTTCA
* *
21996781 TTTTACTCCCTGTTGACCCAAAGGTCATTATGCTCA
1 TTTTACTCCCTGTTGACCCAAAGGTCATGATGTTCA
21996817 TTTTACTCCCTGTTGACCCAAAGGTCATGCATGTT
1 TTTTACTCCCTGTTGACCCAAAGGTCATG-ATGTT
21996852 ACTAGTATAC
Statistics
Matches: 102, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 98 0.96
37 4 0.04
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (36 bp):
TTTTACTCCCTGTTGACCCAAAGGTCATGATGTTCA
Found at i:22005133 original size:58 final size:58
Alignment explanation
Indices: 22004973--22005133 Score: 177
Period size: 58 Copynumber: 2.8 Consensus size: 58
22004963 ATATTATATA
* *** *
22004973 TTATGATTTTTATT-AATTCATATTTTAATAATAAT-TATATTAAAAATGTTATTATATTAT
1 TTATTATTTTTATTAAATT-ATA-TTTAATAATAATCT-TATT-AAAATACAATTAAATTAT
* * * *
22005033 ATATTA--TTTATTAAATTGTATTTAATAATAATCATGTTAAAATACAATTAAATTAT
1 TTATTATTTTTATTAAATTATATTTAATAATAATCTTATTAAAATACAATTAAATTAT
22005089 TTATTATTTTTATTAAATTATATTTAATAATAATCTTATTAAAAT
1 TTATTATTTTTATTAAATTATATTTAATAATAATCTTATTAAAAT
22005134 TTAATAGCAA
Statistics
Matches: 84, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
56 19 0.23
57 15 0.18
58 42 0.50
59 4 0.05
60 4 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (58 bp):
TTATTATTTTTATTAAATTATATTTAATAATAATCTTATTAAAATACAATTAAATTAT
Found at i:22005282 original size:44 final size:46
Alignment explanation
Indices: 22005219--22005313 Score: 133
Period size: 44 Copynumber: 2.1 Consensus size: 46
22005209 TATTACAACA
*
22005219 CCATTCCATTCAACCAAAC-AC-AAGAATACT-ATTACAACTCTATT
1 CCATTCCATTCAACCAAACAACTAA-AATACTGATTACAACCCTATT
* *
22005263 CCATTCCATTCAACCAAACAACTAAATTACTGATTACAGCCCTATT
1 CCATTCCATTCAACCAAACAACTAAAATACTGATTACAACCCTATT
22005309 CCATT
1 CCATT
22005314 ACAGCTATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
44 19 0.42
45 7 0.16
46 19 0.42
ACGTcount: A:0.38, C:0.31, G:0.03, T:0.28
Consensus pattern (46 bp):
CCATTCCATTCAACCAAACAACTAAAATACTGATTACAACCCTATT
Found at i:22005316 original size:16 final size:16
Alignment explanation
Indices: 22005295--22005366 Score: 92
Period size: 16 Copynumber: 4.5 Consensus size: 16
22005285 TAAATTACTG
*
22005295 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCC
* *
22005311 ATTACAGCTATATTAC
1 ATTACAGCTCTATTCC
22005327 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
22005343 ATTACAACAT-TATTCC
1 ATTACAGC-TCTATTCC
22005359 ATTACAGC
1 ATTACAGC
22005367 GAACCACACG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
16 47 0.98
17 1 0.02
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:22006356 original size:36 final size:36
Alignment explanation
Indices: 22006302--22006399 Score: 160
Period size: 36 Copynumber: 2.7 Consensus size: 36
22006292 TTATTCGTTT
*
22006302 TACTCCCTGTTGATCCAAAGGTCATGATGCTCATTC
1 TACTCCCTGTTGACCCAAAGGTCATGATGCTCATTC
* * *
22006338 TACTCCCTATTGACCCAAAGGTCATTATGCTCATTT
1 TACTCCCTGTTGACCCAAAGGTCATGATGCTCATTC
22006374 TACTCCCTGTTGACCCAAAGGTCATG
1 TACTCCCTGTTGACCCAAAGGTCATG
22006400 CTTGTTACTA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (36 bp):
TACTCCCTGTTGACCCAAAGGTCATGATGCTCATTC
Found at i:22009538 original size:22 final size:22
Alignment explanation
Indices: 22009485--22009543 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
22009475 TTGTACGAAG
* *
22009485 CACTAGAAGCAGCTACCTTATA
1 CACTAGAAGGATCTACCTTATA
22009507 CACTAGAAGGATCTA-CTTGATA
1 CACTAGAAGGATCTACCTT-ATA
22009529 CACTAGAAGGATCTA
1 CACTAGAAGGATCTA
22009544 TCTAAAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 3 0.09
22 31 0.91
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (22 bp):
CACTAGAAGGATCTACCTTATA
Found at i:22012857 original size:939 final size:942
Alignment explanation
Indices: 22011468--22013335 Score: 2865
Period size: 939 Copynumber: 2.0 Consensus size: 942
22011458 GTCAACGTTG
* * * * *
22011468 GGAGCGGAGCCTCAACGAAGCCATTGTAATAACCTCAACAAAGATATGTTGCTGTGGTAATGCGA
1 GGAGCGGAGCCTCAACGAAGCCATCGCAACAACCTCAACAAAGATACGTTGCTGTGGCAATGCGA
* * * *
22011533 AGCAGAATCGAGCAGCGAGCCTAATGTTCTTTTTGGGTCTCAACGGAGTACTCTTTATTATTAAA
66 AGAAGAATCGAGCAGCGAACCTAATGTTCTTTTTGGGTCTCAACGAAGTACTCTTGATTATTAAA
*
22011598 TTTTGAAAGTTGGAATGTTTAAACAATATTTTGATGCCCTTGAACTAATCATTCGAAGGGTTGTA
131 TTTTGAAAGTTGGAATGTTTAAACAATATTTTGATGCCCTTGAACTAATCATTCGAAGGGTTGGA
* *
22011663 TATTTTAGATCTTTATTTTTGTTTTTATAAAATGTCTGTTAGATCTTCTTCTATAGAATTTCTTA
196 TATTTTAGATCTTTAATTTTATTTTTATAAAATGTCTGTTAGATCTTCTTCTATAGAATTTCTTA
* *
22011728 TTTGAGTTATGTTCTTTGTTTGTAATTCTACGTGCTAGCAATCCTAGACATAAGCTCTTGTTTTA
261 TTTGAGTTATGTTCTTTGTTCGTAATTCTACGTGCTAGCAATCATAGACATAAGCTCTTGTTTTA
* * * *
22011793 CATGTGCATAATCTTAACTAAAAGCATGACAGATTTACTGGAGCATAATTTAGTATTGTGAGCGG
326 CATGTGCATAATCTTAACTAAAAGCAGGACAGATTTACTGGAGCATAATTCAGTATTATGAGCGA
* *
22011858 GGTAATTTGAGAGATACCTGTAGTGACTCTAGACATAGAACCATATTCATAAAGAGTGAGATAAG
391 GGAAATTCGAGAGATACCTGTAGTGACTCTAGACATAGAACCATATTCATAAAGAGTGAGATAAG
*
22011923 TTTTGTTAGGACAATTCATGCTATAGAAATATAATATGGATCAACTGTAAAAGTTGCCATGACAC
456 TTTTGTTAGGACAATTCATGCTATAGAAATATAATATGGATAAACTGTAAAAGTTGCCATGACAC
* * * *
22011988 TAGTAAGCCATTACTTAGTCATTTTGGGGAATTTGTAGAAGTAGAGATTTGCTATAACATTTATA
521 TAGTAAGCCATTACTTAGTCATTCTAGGGAATTTGTAGAAGCAGAG-TTTGCTATAACAATTATA
*
22012053 GATCTGGAATT-T-AG-AT-TTGAG-AAACAATCACAACTTAGTCTTATACTTAGATCTTGCCAA
585 GATCTGGAATTCTAAGAATCTAGAGTAAACAATCACAACTTAGTCTTATACTTAGATCTTGCCAA
*
22012113 TCATTTCTGCTAAGATTGATAAGAACTTAGTAGATTTGAAGCCTTGCTTGTTTGTTTGATCCATT
650 TCATTTCTGCTAAGATTGATAAGAACTTAGTAGATCTGAAGCCTTGCTTGTTTGTTTGATCCATT
* * *
22012178 TACTGTTTTTGCATTTTTTATGACACGCAAGATGCAATCACAAACCTATCTATTATTACATTTTA
715 TACTATTTTTGCATTTGTTATGACACGCAAGATGCAATCACAAACCTATCTACTATTACATTTTA
* *
22012243 TTTGCTTGCACAATTCTTTTGTCAACAATTTAA-GAATTTTTTTTCT-AAAATCCAATCTCTTTG
780 TTTGCTTGCACAATTCTTTTGTCAACAATTTAAGGAA--TTTCTTCTGAAAA-CCAATCTCTCTG
* *
22012306 TGAGG-ACGATACTCTACTTATCACTTTATTACTTGAACGTCTTGTACACTTGCACAGTTGCTAC
842 TG-GGTACGATACTCTACTTATCACTTTATTACTTGAACGTCGTGTACACTTACACAGTTGCTAC
22012370 ATCAATATTCTTTTACATGCAACAATAGCCAACGCTA
906 ATCAATATTCTTTTACATGCAACAATAGCCAACGCTA
* * * *
22012407 GGAGCGGAGCCTCGACGAAGCCATCGCAACCACCTGAGCAAAGATACGTTGCTGTGGCAATGCGA
1 GGAGCGGAGCCTCAACGAAGCCATCGCAACAACCTCAACAAAGATACGTTGCTGTGGCAATGCGA
* * *
22012472 AGAAGAATCGAGCAGCGAACTTGATGTTCTTTTTGGGTCTCAACGAAGTACTCTTGATTGTTAAA
66 AGAAGAATCGAGCAGCGAACCTAATGTTCTTTTTGGGTCTCAACGAAGTACTCTTGATTATTAAA
* *
22012537 TTTTGAAAGTTGGAATGTTTAAACAATATTTT-AGTGCCCTTGAACTAATCATTTGAAGGTTTGG
131 TTTTGAAAGTTGGAATGTTTAAACAATATTTTGA-TGCCCTTGAACTAATCATTCGAAGGGTTGG
* *
22012601 ATATTTTAGATCTTTAATTTTATTTTTATAAAATGTTTGTTAGATCTTCTTCTATTGAATTTCTT
195 ATATTTTAGATCTTTAATTTTATTTTTATAAAATGTCTGTTAGATCTTCTTCTATAGAATTTCTT
* *
22012666 CATTTGAGTTATGTTCTTTGTTCGTAATTCTACGTGCTAGCAATCATAGACGTAGGCTCTTGTTT
260 -ATTTGAGTTATGTTCTTTGTTCGTAATTCTACGTGCTAGCAATCATAGACATAAGCTCTTGTTT
* * * * * * *
22012731 TGCATGTGCATAATCTTAATTGAAAGCAGGATAGATTTGCTGGGGCATAATTCAGTGTTATGAG-
324 TACATGTGCATAATCTTAACTAAAAGCAGGACAGATTTACTGGAGCATAATTCAGTATTATGAGC
* * * *
22012795 TAGGAAATTCGAGAGATACCTGTAGTGACTCTAGACATAGAGCCATGTTCATAAGGAGTGAGATA
389 GAGGAAATTCGAGAGATACCTGTAGTGACTCTAGACATAGAACCATATTCATAAAGAGTGAGATA
* * *
22012860 AGTTTTGTTGGGACAATTCATGCTATAGAAATATAATATGGATAAACTGTAAAATTTTCCATGAC
454 AGTTTTGTTAGGACAATTCATGCTATAGAAATATAATATGGATAAACTGTAAAAGTTGCCATGAC
* *
22012925 ACTGGTAAGCCATTACTTAGTTATTCTAGGGAATTTGTAGAAGCAGAGTTTGCTATAACAATTAT
519 ACTAGTAAGCCATTACTTAGTCATTCTAGGGAATTTGTAGAAGCAGAGTTTGCTATAACAATTAT
* * *
22012990 AGATCTGGAATTCAGACCTAAGAAATCCTAGGGTTAACAATCACAACTTAGTCTTGTACTTAGAT
584 AGATCTGGAATT-----CTAAG-AAT-CTAGAGTAAACAATCACAACTTAGTCTTATACTTAGAT
* *
22013055 CTTGCCAATCATTTTTGCTAAGATTGATAAGTACTTAGTAGATCTGAAGCCTTGCTTGTTTGTTT
642 CTTGCCAATCATTTCTGCTAAGATTGATAAGAACTTAGTAGATCTGAAGCCTTGCTTGTTTGTTT
* * * * *
22013120 GATCCATTTACTATTTTTGCATTTGTTATGACACGCAAGATGCATTCATAAACCTATTTGCTGTT
707 GATCCATTTACTATTTTTGCATTTGTTATGACACGCAAGATGCAATCACAAACCTATCTACTATT
* *
22013185 ACATTTTATTTGCTTGCACAATTCTTTTTTCAACAGTTTAAGGAATTTCTTCTGAAAACCAATCT
772 ACATTTTATTTGCTTGCACAATTCTTTTGTCAACAATTTAAGGAATTTCTTCTGAAAACCAATCT
22013250 CTCTGTGGGTACGATACTCTACTTATCACTTTATTACTTGAACGTCGTGTACACTTACACAGTTG
837 CTCTGTGGGTACGATACTCTACTTATCACTTTATTACTTGAACGTCGTGTACACTTACACAGTTG
22013315 CTACATCAATATTCTTTTACA
902 CTACATCAATATTCTTTTACA
22013336 CGTAATAGTG
Statistics
Matches: 837, Mismatches: 75, Indels: 24
0.89 0.08 0.03
Matches are distributed among these distances:
938 29 0.03
939 396 0.47
940 114 0.14
944 1 0.00
945 2 0.00
947 2 0.00
948 2 0.00
949 97 0.12
950 191 0.23
951 3 0.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.37
Consensus pattern (942 bp):
GGAGCGGAGCCTCAACGAAGCCATCGCAACAACCTCAACAAAGATACGTTGCTGTGGCAATGCGA
AGAAGAATCGAGCAGCGAACCTAATGTTCTTTTTGGGTCTCAACGAAGTACTCTTGATTATTAAA
TTTTGAAAGTTGGAATGTTTAAACAATATTTTGATGCCCTTGAACTAATCATTCGAAGGGTTGGA
TATTTTAGATCTTTAATTTTATTTTTATAAAATGTCTGTTAGATCTTCTTCTATAGAATTTCTTA
TTTGAGTTATGTTCTTTGTTCGTAATTCTACGTGCTAGCAATCATAGACATAAGCTCTTGTTTTA
CATGTGCATAATCTTAACTAAAAGCAGGACAGATTTACTGGAGCATAATTCAGTATTATGAGCGA
GGAAATTCGAGAGATACCTGTAGTGACTCTAGACATAGAACCATATTCATAAAGAGTGAGATAAG
TTTTGTTAGGACAATTCATGCTATAGAAATATAATATGGATAAACTGTAAAAGTTGCCATGACAC
TAGTAAGCCATTACTTAGTCATTCTAGGGAATTTGTAGAAGCAGAGTTTGCTATAACAATTATAG
ATCTGGAATTCTAAGAATCTAGAGTAAACAATCACAACTTAGTCTTATACTTAGATCTTGCCAAT
CATTTCTGCTAAGATTGATAAGAACTTAGTAGATCTGAAGCCTTGCTTGTTTGTTTGATCCATTT
ACTATTTTTGCATTTGTTATGACACGCAAGATGCAATCACAAACCTATCTACTATTACATTTTAT
TTGCTTGCACAATTCTTTTGTCAACAATTTAAGGAATTTCTTCTGAAAACCAATCTCTCTGTGGG
TACGATACTCTACTTATCACTTTATTACTTGAACGTCGTGTACACTTACACAGTTGCTACATCAA
TATTCTTTTACATGCAACAATAGCCAACGCTA
Found at i:22016046 original size:11 final size:11
Alignment explanation
Indices: 22016023--22016092 Score: 60
Period size: 11 Copynumber: 6.6 Consensus size: 11
22016013 ATAAATTTAA
22016023 GAGAGAA-TTT
1 GAGAGAATTTT
22016033 GAGAGAATTTT
1 GAGAGAATTTT
* *
22016044 GAGAGTAGTTT
1 GAGAGAATTTT
22016055 --GAGAATTTT
1 GAGAGAATTTT
22016064 GA-ATG-ATTTAT
1 GAGA-GAATTT-T
22016075 GAGAGAATTTT
1 GAGAGAATTTT
*
22016086 GTGAGAA
1 GAGAGAA
22016093 ATGAGTAAGG
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
9 7 0.15
10 12 0.25
11 24 0.50
12 5 0.10
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.36
Consensus pattern (11 bp):
GAGAGAATTTT
Found at i:22016055 original size:22 final size:21
Alignment explanation
Indices: 22016030--22016086 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 21
22016020 TAAGAGAGAA
22016030 TTTGAGAGAATTTTGAGA-GTAG
1 TTTGAGAGAATTTTGA-ATG-AG
*
22016052 TTT--GAGAATTTTGAATGAT
1 TTTGAGAGAATTTTGAATGAG
22016071 TTATGAGAGAATTTTG
1 TT-TGAGAGAATTTTG
22016087 TGAGAAATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 4 0.13
20 13 0.43
22 13 0.43
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (21 bp):
TTTGAGAGAATTTTGAATGAG
Found at i:22018999 original size:2 final size:2
Alignment explanation
Indices: 22018992--22019016 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22018982 AAGTTATTTA
22018992 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
22019017 TAGAGAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:22022387 original size:22 final size:25
Alignment explanation
Indices: 22022342--22022392 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
22022332 TAATAGAATT
22022342 ATTATTAAAATATGAATTAATAAAA
1 ATTATTAAAATATGAATTAATAAAA
*
22022367 ATTA-TAAAATATAATATTAA-AAAA
1 ATTATTAAAATATGA-ATTAATAAAA
22022391 AT
1 AT
22022393 AATATATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
ATTATTAAAATATGAATTAATAAAA
Found at i:22027734 original size:31 final size:31
Alignment explanation
Indices: 22027696--22027780 Score: 147
Period size: 31 Copynumber: 2.8 Consensus size: 31
22027686 TTTGCCTCAG
22027696 ATTACATTTTAGTTACACTTATGTTTGAAAT
1 ATTACATTTTAGTTACACTTATGTTTGAAAT
22027727 ATTACATTTTAGTTACACTTATGTTTGAAAT
1 ATTACATTTTAGTTACACTTATGTTTGAAAT
*
22027758 GTTACATTTTAG-T-CACTTATGTT
1 ATTACATTTTAGTTACACTTATGTT
22027781 ATCGTTTTGT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 10 0.19
30 1 0.02
31 42 0.79
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (31 bp):
ATTACATTTTAGTTACACTTATGTTTGAAAT
Found at i:22027931 original size:18 final size:18
Alignment explanation
Indices: 22027908--22027950 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
22027898 GAATAGGTTT
22027908 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
22027926 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
22027944 TTAATTA
1 TTAATTA
22027951 CACCTTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:22028523 original size:31 final size:31
Alignment explanation
Indices: 22028488--22028566 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
22028478 TAAAATGAAG
22028488 TTTTAGGTTCCTTAAAAGTTAG-AGAAAAAAA
1 TTTTAGGTTCCTTAAAAGTTAGTA-AAAAAAA
* *
22028519 TTTTAAG-TCTCTTATAAGTTAGTAAAAAAAA
1 TTTTAGGTTC-CTTAAAAGTTAGTAAAAAAAA
* *
22028550 TTTTTGATT-CTTAAAAG
1 TTTTAGGTTCCTTAAAAG
22028567 CTAAAAAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
30 9 0.23
31 28 0.72
32 2 0.05
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (31 bp):
TTTTAGGTTCCTTAAAAGTTAGTAAAAAAAA
Found at i:22028977 original size:13 final size:14
Alignment explanation
Indices: 22028959--22029000 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
22028949 GACCATCCTT
22028959 TGTATTT-CCTTGA
1 TGTATTTGCCTTGA
*
22028972 TGTATTTGGCTTGA
1 TGTATTTGCCTTGA
*
22028986 TGTATTTGGCTTGA
1 TGTATTTGCCTTGA
22029000 T
1 T
22029001 TGATAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 7 0.26
14 20 0.74
ACGTcount: A:0.14, C:0.10, G:0.24, T:0.52
Consensus pattern (14 bp):
TGTATTTGCCTTGA
Found at i:22028986 original size:14 final size:14
Alignment explanation
Indices: 22028967--22029000 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
22028957 TTTGTATTTC
22028967 CTTGATGTATTTGG
1 CTTGATGTATTTGG
22028981 CTTGATGTATTTGG
1 CTTGATGTATTTGG
22028995 CTTGAT
1 CTTGAT
22029001 TGATAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.15, C:0.09, G:0.26, T:0.50
Consensus pattern (14 bp):
CTTGATGTATTTGG
Found at i:22030407 original size:81 final size:81
Alignment explanation
Indices: 22030272--22030435 Score: 319
Period size: 81 Copynumber: 2.0 Consensus size: 81
22030262 TTTATAATAT
22030272 AACAAGAAGTATTTATGGCTTCCACCAAAAAATATCTTGGCAAATTATTTTCACATAACATGGTT
1 AACAAGAAGTATTTATGGCTTCCACCAAAAAATATCTTGGCAAATTATTTTCACATAACATGGTT
22030337 CTAGCCCTTTCCTCTA
66 CTAGCCCTTTCCTCTA
*
22030353 AACAAGAAGTATTTATGGCTTCCACCCAAAAATATCTTGGCAAATTATTTTCACATAACATGGTT
1 AACAAGAAGTATTTATGGCTTCCACCAAAAAATATCTTGGCAAATTATTTTCACATAACATGGTT
22030418 CTAGCCCTTTCCTCTA
66 CTAGCCCTTTCCTCTA
22030434 AA
1 AA
22030436 GTCTTATTTT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.33
Consensus pattern (81 bp):
AACAAGAAGTATTTATGGCTTCCACCAAAAAATATCTTGGCAAATTATTTTCACATAACATGGTT
CTAGCCCTTTCCTCTA
Found at i:22033276 original size:19 final size:18
Alignment explanation
Indices: 22033246--22033285 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
22033236 AACTAAATTA
22033246 ACAAAAAGAAATGCAATG
1 ACAAAAAGAAATGCAATG
*
22033264 ACAAAATAGAAATGCGATG
1 ACAAAA-AGAAATGCAATG
22033283 ACA
1 ACA
22033286 GTAAAATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.57, C:0.12, G:0.17, T:0.12
Consensus pattern (18 bp):
ACAAAAAGAAATGCAATG
Found at i:22058895 original size:18 final size:18
Alignment explanation
Indices: 22058874--22058931 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
22058864 AGGATAAAAG
*
22058874 TATAATAAGTACTAGAAA
1 TATAATAAGTAATAGAAA
*
22058892 TATATATAAAG-AATAAAAA
1 TATA-AT-AAGTAATAGAAA
*
22058911 TATAATAAGTATTAGAAA
1 TATAATAAGTAATAGAAA
22058929 TAT
1 TAT
22058932 GTATATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 3 0.09
18 15 0.45
19 12 0.36
20 3 0.09
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.31
Consensus pattern (18 bp):
TATAATAAGTAATAGAAA
Found at i:22058897 original size:37 final size:37
Alignment explanation
Indices: 22058856--22058936 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
22058846 AATAAACATA
* *
22058856 ATATATAAAGGATAAAAGTATAATAAGTACTAGAAAT
1 ATATATAAAGAATAAAAATATAATAAGTACTAGAAAT
*
22058893 ATATATAAAGAATAAAAATATAATAAGTATTAGAAAT
1 ATATATAAAGAATAAAAATATAATAAGTACTAGAAAT
*
22058930 ATGTATA
1 ATATATA
22058937 TATATATAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.58, C:0.01, G:0.11, T:0.30
Consensus pattern (37 bp):
ATATATAAAGAATAAAAATATAATAAGTACTAGAAAT
Found at i:22058911 original size:19 final size:18
Alignment explanation
Indices: 22058840--22058918 Score: 63
Period size: 19 Copynumber: 4.3 Consensus size: 18
22058830 ATATACAAAG
*
22058840 AATAAA-AATAAACATAAT
1 AATAAAGAATAAAAAT-AT
* *
22058858 ATATAAAGGATAAAAGTAT
1 A-ATAAAGAATAAAAATAT
* *
22058877 AAT-AAGTACTAGAAATAT
1 AATAAAG-AATAAAAATAT
22058895 ATATAAAGAATAAAAATAT
1 A-ATAAAGAATAAAAATAT
22058914 AATAA
1 AATAA
22058919 GTATTAGAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
17 3 0.06
18 15 0.32
19 20 0.43
20 9 0.19
ACGTcount: A:0.65, C:0.03, G:0.08, T:0.25
Consensus pattern (18 bp):
AATAAAGAATAAAAATAT
Found at i:22061129 original size:29 final size:30
Alignment explanation
Indices: 22061057--22061128 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
22061047 TAAATGATTT
22061057 TAAAATTATTAAAATTA-TTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTTAAAATA
* *
22061086 TAAAATAATTAAAATTATTTTTTTGAAATA
1 TAAAATTATTAAAATTATTTTTTTAAAATA
22061116 -ATAAATTATTAAA
1 TA-AAATTATTAAA
22061129 TAATTTTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.45
30 21 0.55
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTTTTTTAAAATA
Found at i:22062165 original size:20 final size:22
Alignment explanation
Indices: 22062140--22062181 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
22062130 AAATAATTTT
22062140 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
22062160 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
22062182 TCATTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:22062169 original size:29 final size:31
Alignment explanation
Indices: 22062106--22062178 Score: 123
Period size: 29 Copynumber: 2.4 Consensus size: 31
22062096 CTTAAAATTA
22062106 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTATTATTTCAAAAAAATAAT
*
22062137 TTTAATAATTTTA-TATTT-TAAAAAATAAT
1 TTTAATAATTTTATTATTTCAAAAAAATAAT
22062166 TTTAATAATTTTA
1 TTTAATAATTTTA
22062179 AAATCATTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 23 0.56
30 5 0.12
31 13 0.32
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTAATAATTTTATTATTTCAAAAAAATAAT
Found at i:22062182 original size:20 final size:20
Alignment explanation
Indices: 22062131--22062187 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
22062121 ATTTCAAAAA
22062131 AATAATTTT--AATAATTTT
1 AATAATTTTAAAATAATTTT
22062149 -AT-ATTTTAAAAAATAATTTT
1 AATAATTTT--AAAATAATTTT
*
22062169 AATAATTTTAAAATCATTT
1 AATAATTTTAAAATAATTT
22062188 GTTGACGTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 5 0.16
17 2 0.06
20 18 0.56
21 2 0.06
22 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAATTTTAAAATAATTTT
Found at i:22077522 original size:21 final size:21
Alignment explanation
Indices: 22077458--22077522 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
22077448 AACATTCACC
*
22077458 GGTTCTGGTTCTGGTGAAACT
1 GGTTCTGGTTCTGGTGAAATT
*
22077479 GGTTCTGGTTCTAGTGAAATT
1 GGTTCTGGTTCTGGTGAAATT
*
22077500 GGTTCTAGTTCTGGT-AAAGTT
1 GGTTCTGGTTCTGGTGAAA-TT
22077521 GG
1 GG
22077523 AGTTTTAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 3 0.08
21 36 0.92
ACGTcount: A:0.17, C:0.11, G:0.32, T:0.40
Consensus pattern (21 bp):
GGTTCTGGTTCTGGTGAAATT
Found at i:22081290 original size:17 final size:18
Alignment explanation
Indices: 22081252--22081292 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
22081242 GCAAATACGT
*
22081252 TGACAAATAAAATACAGA
1 TGACAATTAAAATACAGA
*
22081270 -GACAATTAAAATA-TGA
1 TGACAATTAAAATACAGA
22081286 TGACAAT
1 TGACAAT
22081293 GCAATTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.22
Consensus pattern (18 bp):
TGACAATTAAAATACAGA
Found at i:22083572 original size:18 final size:18
Alignment explanation
Indices: 22083551--22083585 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22083541 AAAATAATTG
22083551 AAATAAAATAAAATAAAA
1 AAATAAAATAAAATAAAA
* *
22083569 AAATTAAATAGAATAAA
1 AAATAAAATAAAATAAA
22083586 TGTAATGACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (18 bp):
AAATAAAATAAAATAAAA
Found at i:22095054 original size:20 final size:21
Alignment explanation
Indices: 22095017--22095055 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
22095007 AAATCGAGCA
*
22095017 TCACTGAGTTAGAAAATGCAG
1 TCACTAAGTTAGAAAATGCAG
22095038 TCACTAAGTTA-AAAATGC
1 TCACTAAGTTAGAAAATGC
22095056 TAAAAATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (21 bp):
TCACTAAGTTAGAAAATGCAG
Found at i:22104372 original size:20 final size:21
Alignment explanation
Indices: 22104335--22104373 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
22104325 AAATCGAGCA
22104335 TCACTAAGTTAGAAAATGCAG
1 TCACTAAGTTAGAAAATGCAG
22104356 TCACTAAGTTA-AAAATGC
1 TCACTAAGTTAGAAAATGC
22104374 TAAAAATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (21 bp):
TCACTAAGTTAGAAAATGCAG
Found at i:22111939 original size:18 final size:18
Alignment explanation
Indices: 22111900--22111941 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
22111890 CCACGAAATA
*
22111900 TTTTTT-TTATTTTTTTC
1 TTTTTTCTTATATTTTTC
22111917 -TTTTTCTTATATTTTTC
1 TTTTTTCTTATATTTTTC
22111934 TTTTTTCT
1 TTTTTTCT
22111942 CTACTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 10 0.45
18 7 0.32
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTCTTATATTTTTC
Found at i:22116948 original size:38 final size:38
Alignment explanation
Indices: 22116906--22116986 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
22116896 TGAGTCTATT
* * *
22116906 CAGAATTGCGCCTAGAATTGTCACTGCATGACGATGTC
1 CAGAATTGCACCCAAAATTGTCACTGCATGACGATGTC
*
22116944 CAGAATTGCACCCAAAATTGTCACTGCATGACGATGTT
1 CAGAATTGCACCCAAAATTGTCACTGCATGACGATGTC
22116982 CAGAA
1 CAGAA
22116987 ATGTCACTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (38 bp):
CAGAATTGCACCCAAAATTGTCACTGCATGACGATGTC
Found at i:22117067 original size:43 final size:43
Alignment explanation
Indices: 22116990--22117105 Score: 153
Period size: 43 Copynumber: 2.7 Consensus size: 43
22116980 TTCAGAAATG
* ** * * *
22116990 TCACTGCATGAACATGCCCAAAATTATCGTCGCATCTAACAGC
1 TCACTGCATGAGCATATCCAGAATTGTCGCCGCATCTAACAGC
*
22117033 TCACTTCATGAGCATATCCAGAATTGTCGCCGCATCTAACAGC
1 TCACTGCATGAGCATATCCAGAATTGTCGCCGCATCTAACAGC
*
22117076 TCGCTGCATGAGCATATCCAGAATTG-CGCC
1 TCACTGCATGAGCATATCCAGAATTGTCGCC
22117106 CAAAATTATC
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
42 4 0.06
43 60 0.94
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (43 bp):
TCACTGCATGAGCATATCCAGAATTGTCGCCGCATCTAACAGC
Done.