Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006616.1 Hibiscus syriacus cultivar Beakdansim tig00016238_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 102633
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7034 original size:14 final size:14
Alignment explanation
Indices: 7015--7044 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
7005 TGTAAGTTAT
7015 CAAGGCAGTTAGGA
1 CAAGGCAGTTAGGA
7029 CAAGGCAGTTAGGA
1 CAAGGCAGTTAGGA
7043 CA
1 CA
7045 GCTGTAGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.33, T:0.13
Consensus pattern (14 bp):
CAAGGCAGTTAGGA
Found at i:7251 original size:29 final size:29
Alignment explanation
Indices: 7174--7266 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
7164 AACAATATTA
*
7174 ATAATATTACTAATAATAAT-TT-TAATT
1 ATAATATTAATAATAATAATATTATAATT
* *
7201 TTAATTGTTATAATAATAATAATAGTTA-AATT
1 ATAA-T-AT-TAATAATAATAATA-TTATAATT
* *
7233 ATAATATTAATAATTATAATATTATATTT
1 ATAATATTAATAATAATAATATTATAATT
7262 ATAAT
1 ATAAT
7267 CGGATAAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
27 3 0.06
28 4 0.08
29 22 0.42
30 13 0.25
31 1 0.02
32 9 0.17
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (29 bp):
ATAATATTAATAATAATAATATTATAATT
Found at i:7495 original size:53 final size:53
Alignment explanation
Indices: 7414--7638 Score: 317
Period size: 53 Copynumber: 4.2 Consensus size: 53
7404 CCTCTTCTTT
*
7414 GAACAATCTTC-GACTAGCAGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
1 GAACAATCTTCTGCCTA-CAGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* * * *
7467 GAACAGTCTTCTGCCTACAGGTTTGCTCCCTCTTGCTTCAGGGAGTAGAGCTA
1 GAACAATCTTCTGCCTACAGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* * * * * *
7520 GAATAATCTTCTACCTACGGGTTCGTTCCCTCTTGCTTTAGGGAGTAGAACTT
1 GAACAATCTTCTGCCTACAGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* *
7573 GAACAATCTTCTGTCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
1 GAACAATCTTCTGCCTACAGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
7626 GAACAATCTTCTG
1 GAACAATCTTCTG
7639 GCGGGATTCT
Statistics
Matches: 151, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
53 147 0.97
54 4 0.03
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (53 bp):
GAACAATCTTCTGCCTACAGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
Found at i:8188 original size:42 final size:42
Alignment explanation
Indices: 8140--8265 Score: 191
Period size: 42 Copynumber: 3.0 Consensus size: 42
8130 TTACAAATTA
*
8140 CCCGAAGGATTTAATCATCAAGCTCGAAAGACTTACTGATGG
1 CCCGAAGGACTTAATCATCAAGCTCGAAAGACTTACTGATGG
* *
8182 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGACTTAATCATCAAGCTCGAAAGACTTACTGATGG
* *
8224 CTCGAAGGACTTAATCATTATA-CTCGAAAGACTTACTGATGG
1 CCCGAAGGACTTAATCATCA-AGCTCGAAAGACTTACTGATGG
8266 TTTTACTTCA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (42 bp):
CCCGAAGGACTTAATCATCAAGCTCGAAAGACTTACTGATGG
Found at i:8190 original size:122 final size:120
Alignment explanation
Indices: 8004--8222 Score: 305
Period size: 122 Copynumber: 1.8 Consensus size: 120
7994 AATCTTCCGA
** *
8004 GAAGGCTTAAAATAGCCCGAAGGACTTATCATCTTGCTAAAAAGACTTACAAATGACCTGAAGGA
1 GAAGGCTTAAAATAGCCCGAAGGACTTATCATCAAGCTAAAAAGACTTACAAATGACCCGAAGGA
*
8069 TTTCATCATCATGCTCGAAAAACTTACTGATGTATTTGCTTCACTACTCTTCGGT
66 CTTCATCATCATGCTCGAAAAACTTACTGATGTATTTGCTTCACTACTCTTCGGT
* ** ** *
8124 GAAGGCTTACAAATTA-CCCGAAGGATTTAATCATCAAGCTCGAAAGACTTACTGATGGCCCGAA
1 GAAGGCTTA-AAA-TAGCCCGAAGGACTT-ATCATCAAGCTAAAAAGACTTACAAATGACCCGAA
*
8188 GGACTTCATCATCATGCTCGAAAGACTTACTGATG
63 GGACTTCATCATCATGCTCGAAAAACTTACTGATG
8223 GCTCGAAGGA
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
120 9 0.11
121 14 0.16
122 62 0.73
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (120 bp):
GAAGGCTTAAAATAGCCCGAAGGACTTATCATCAAGCTAAAAAGACTTACAAATGACCCGAAGGA
CTTCATCATCATGCTCGAAAAACTTACTGATGTATTTGCTTCACTACTCTTCGGT
Found at i:8192 original size:20 final size:20
Alignment explanation
Indices: 8161--8265 Score: 88
Period size: 20 Copynumber: 5.0 Consensus size: 20
8151 TAATCATCAA
8161 GCTCGAAAGACTTACTGATG
1 GCTCGAAAGACTTACTGATG
* * *
8181 GCCCGAAGGACTTCATCATCAT-
1 GCTCGAAAGACTT-A-C-TGATG
8203 GCTCGAAAGACTTACTGATG
1 GCTCGAAAGACTTACTGATG
* *
8223 GCTCGAAGGACTTAATCATTAT-
1 GCTCGAAAGACTT-A-C-TGATG
*
8245 ACTCGAAAGACTTACTGATG
1 GCTCGAAAGACTTACTGATG
8265 G
1 G
8266 TTTTACTTCA
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
19 6 0.09
20 25 0.38
21 4 0.06
22 24 0.37
23 6 0.09
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (20 bp):
GCTCGAAAGACTTACTGATG
Found at i:8335 original size:160 final size:160
Alignment explanation
Indices: 8018--8396 Score: 467
Period size: 160 Copynumber: 2.3 Consensus size: 160
8008 GCTTAAAATA
* ** ** * * * *
8018 GCCCGAAGGACTTATCATCTTGCTAAAAAGACTTACAAATGACCTGAAGGATTTCATCATCATGC
1 GCCCGAAGGACTTATCATCATGCTCGAAAGACTTACTGATGGCC-GAAGGACTTAATCATCATAC
* *
8083 TCGAAAAACTTACTGATGTATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGG
65 TCGAAAAACTTACTGATGTATTTACTTCACTACTCTTCCGTGAAGG--TACAAATTACCCGAAGG
8148 ATTTAATCATCAAGCTCGAAAGACTTACTGATG
128 ATTTAATCATCAAGCTCGAAAGACTTACTGATG
*
8181 GCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCTCGAAGGACTTAATCATTATA
1 GCCCGAAGGACTT-ATCATCATGCTCGAAAGACTTACTGATGGC-CGAAGGACTTAATCATCATA
* *
8246 CTCGAAAGACTTACTGATGGT-TTTACTTCACTACTCTTCCGTGAA-G-ACAAATTACCCTAAGG
64 CTCGAAAAACTTACTGAT-GTATTTACTTCACTACTCTTCCGTGAAGGTACAAATTACCCGAAGG
*
8308 ATTTAATCATCATGCTCGAAAGACTTACTGATG
128 ATTTAATCATCAAGCTCGAAAGACTTACTGATG
* * * * * * *
8341 GCCCTAAAGATTTAAGCATCATGCTCGAAAGGCTTATTGGTGGCCCGAAGGACTTA
1 GCCCGAAGGACTT-ATCATCATGCTCGAAAGACTTACTGATGG-CCGAAGGACTTA
8397 CTAAGTGCAA
Statistics
Matches: 189, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
160 93 0.49
161 1 0.01
163 14 0.07
164 78 0.41
165 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.28
Consensus pattern (160 bp):
GCCCGAAGGACTTATCATCATGCTCGAAAGACTTACTGATGGCCGAAGGACTTAATCATCATACT
CGAAAAACTTACTGATGTATTTACTTCACTACTCTTCCGTGAAGGTACAAATTACCCGAAGGATT
TAATCATCAAGCTCGAAAGACTTACTGATG
Found at i:8347 original size:42 final size:42
Alignment explanation
Indices: 8300--8392 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
8290 AGACAAATTA
*
8300 CCCTAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCTAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
* * * *
8342 CCCTAAAGATTTAAGCATCATGCTCGAAAGGCTTATTGGTGG
1 CCCTAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
*
8384 CCCGAAGGA
1 CCCTAAGGA
8393 CTTACTAAGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (42 bp):
CCCTAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
Found at i:16986 original size:302 final size:302
Alignment explanation
Indices: 16436--17030 Score: 1037
Period size: 302 Copynumber: 2.0 Consensus size: 302
16426 CCTAAAACCG
* *
16436 TACCTAGTCTATTAATTAATGTCTTTGCAATGAACTTTACAAATTCGAACTTAATTTGATCTTTG
1 TACCTAGTCGATTAATTAATATCTTTGCAATGAACTTTACAAATTCGAACTTAATTTGATCTTTG
* * *
16501 ATCCCATAAAACAAAGATGTGAATTTAATAATGTTCAAAAGCACTCAAATAAATTAAATTAAGAT
66 ATCCCATAAAACAAAGATGTGAATTTAATAATGTTAAAAAGAACTAAAATAAATTAAATTAAGAT
16566 TACCAAGCCGTTTTAGAAAGATAAAGAATGTTCGGTTATTTACAAATATCGAGACCAGATCTTAA
131 TACCAAGCCGTTTTAGAAAGATAAAGAATGTTCGGTTATTTACAAATATCGAGACCAGATCTTAA
*
16631 AAGCTATAACAACATTTTCTCGTTAAATTTAAATAGTCGAACATTTATTTTTCTTCCATTCCCAA
196 AAGCTATAACAACATTTTCTCGATAAATTTAAATAGTCGAACATTTATTTTTCTTCCATTCCCAA
16696 ATTTTAAAGTGATGGATCAATTTTTAGGCATCAATAAAATGA
261 ATTTTAAAGTGATGGATCAATTTTTAGGCATCAATAAAATGA
*
16738 TACCTAGTCGATTAATTAATATCTTTGCAATGAACTTTACAAATTCGAACTTAATTTGATTTTTG
1 TACCTAGTCGATTAATTAATATCTTTGCAATGAACTTTACAAATTCGAACTTAATTTGATCTTTG
16803 ATCCCATAAAACAAAGATGTGAATTTAATAATGTTAAAAAGAACTAAAATAAATTAAATTAAGAT
66 ATCCCATAAAACAAAGATGTGAATTTAATAATGTTAAAAAGAACTAAAATAAATTAAATTAAGAT
* * * *
16868 TATCAAGTCGTTTTAGAAAGATAAAGAATGTTTGGTTATTTACATATATCGAGACCAGATCTTAA
131 TACCAAGCCGTTTTAGAAAGATAAAGAATGTTCGGTTATTTACAAATATCGAGACCAGATCTTAA
* * * * *
16933 AAGCTATAACAACCTTTTCTCGATAAATTTATATAGTTGAACATTTCTTTTTCTTTCATTCCCAA
196 AAGCTATAACAACATTTTCTCGATAAATTTAAATAGTCGAACATTTATTTTTCTTCCATTCCCAA
*
16998 ATTTTAAAGTGATTGATCAATTTTTAGGCATCA
261 ATTTTAAAGTGATGGATCAATTTTTAGGCATCA
17031 TTAATGGGAT
Statistics
Matches: 276, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
302 276 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.36
Consensus pattern (302 bp):
TACCTAGTCGATTAATTAATATCTTTGCAATGAACTTTACAAATTCGAACTTAATTTGATCTTTG
ATCCCATAAAACAAAGATGTGAATTTAATAATGTTAAAAAGAACTAAAATAAATTAAATTAAGAT
TACCAAGCCGTTTTAGAAAGATAAAGAATGTTCGGTTATTTACAAATATCGAGACCAGATCTTAA
AAGCTATAACAACATTTTCTCGATAAATTTAAATAGTCGAACATTTATTTTTCTTCCATTCCCAA
ATTTTAAAGTGATGGATCAATTTTTAGGCATCAATAAAATGA
Found at i:31660 original size:92 final size:92
Alignment explanation
Indices: 31503--31672 Score: 295
Period size: 92 Copynumber: 1.8 Consensus size: 92
31493 TATCAAGTGA
* * *
31503 GAACAATATTAAAAATATGAAATTTCATTTAGAAACCTTATAACTTAGGGTATCATAAGACTTGC
1 GAACAATATTAAAAATATGAAATTTCACTTAGAAACCCTATAACTTAGGGAATCATAAGACTTGC
31568 CTTGTGTGATGTTCGAGAAACAAGAAG
66 CTTGTGTGATGTTCGAGAAACAAGAAG
* *
31595 GAACATTATTAAAAATGTGAAATTTCACTTAGAAACCCTATAACTTAGGGAATCATAAGACTTGC
1 GAACAATATTAAAAATATGAAATTTCACTTAGAAACCCTATAACTTAGGGAATCATAAGACTTGC
31660 CTTGTGTGATGTT
66 CTTGTGTGATGTT
31673 TGGGAAATAG
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 73 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (92 bp):
GAACAATATTAAAAATATGAAATTTCACTTAGAAACCCTATAACTTAGGGAATCATAAGACTTGC
CTTGTGTGATGTTCGAGAAACAAGAAG
Found at i:33008 original size:18 final size:18
Alignment explanation
Indices: 32968--33002 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
32958 TAACTCACGC
*
32968 ATACACACACAAATAAAT
1 ATACACACAAAAATAAAT
32986 ATACACACAAAAATAAA
1 ATACACACAAAAATAAA
33003 GTTACATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.20, G:0.00, T:0.14
Consensus pattern (18 bp):
ATACACACAAAAATAAAT
Found at i:34758 original size:20 final size:20
Alignment explanation
Indices: 34729--34773 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
34719 GTTTGTATCT
*
34729 TCTCTGTTTTTTTTTCTGTC
1 TCTCTCTTTTTTTTTCTGTC
34749 TCTCTCTTTTTTTTTCTGTC
1 TCTCTCTTTTTTTTTCTGTC
34769 TCTCT
1 TCTCT
34774 GTCCCGTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.00, C:0.24, G:0.07, T:0.69
Consensus pattern (20 bp):
TCTCTCTTTTTTTTTCTGTC
Found at i:35207 original size:3 final size:3
Alignment explanation
Indices: 35199--35260 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
35189 AATATATATT
* *
35199 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35247 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
35261 TTATTATTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:35265 original size:3 final size:3
Alignment explanation
Indices: 35259--35287 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
35249 ATAATAATAA
35259 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
35288 ATAATATGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:35830 original size:113 final size:113
Alignment explanation
Indices: 35610--36289 Score: 997
Period size: 113 Copynumber: 6.0 Consensus size: 113
35600 ATAGAATTAT
* * * * *
35610 GCAAAAAGTTGAACAAGTTCTTCTTATTAAGAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA--A-TTCTT
* * * * * *
35675 CTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAA
63 CTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAG
35726 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
35791 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAG
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAG
* *
35839 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
*
35904 ATTATGAACTTTCTCTGGAAAAGCTTATCCATCAAATGATGGATTCAG
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAG
* *
35952 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
36017 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAG
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAG
* * * *
36065 GTAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
* * * *
36130 ATTATGAAC-TTCTCTGGCAAAA-ATAATCCATCAAGTGATGAATTCAG
66 ATTATGAACTTTCTCTGG-AAAAGCTGATCCATCAAATGATGGATTCAG
* *
36177 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATGATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA--A-TTCTT
* * * *
36242 CTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAAATGATAGATT
63 CTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATT
36290 TGAATCTTTG
Statistics
Matches: 527, Mismatches: 30, Indels: 14
0.92 0.05 0.02
Matches are distributed among these distances:
112 82 0.16
113 345 0.65
114 1 0.00
115 21 0.04
116 78 0.15
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAG
Found at i:37187 original size:84 final size:84
Alignment explanation
Indices: 37017--37413 Score: 733
Period size: 84 Copynumber: 4.7 Consensus size: 84
37007 GTAATTTTTA
* * * *
37017 CCAAACCAGATTAGATAACTCAAAGAACACTTTCAAAAGATGCTATTG-GCAAATTCATCTTCCA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
37081 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
37100 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
37165 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
37184 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
37249 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
*
37268 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCTA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
37333 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
*
37352 CCAAATCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGAGCAAATTCATCTT
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTT
37414 TCAGTTAATG
Statistics
Matches: 307, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
83 44 0.14
84 263 0.86
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (84 bp):
CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
AATTCAATGATTGGTTCTG
Found at i:38203 original size:19 final size:20
Alignment explanation
Indices: 38179--38220 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
38169 AATAGAAAAG
*
38179 AATAAATTGAATTTCCAA-A
1 AATAAATTGAATCTCCAATA
38198 AATAAATTGAATCTCCAATA
1 AATAAATTGAATCTCCAATA
38218 AAT
1 AAT
38221 TGAACTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (20 bp):
AATAAATTGAATCTCCAATA
Found at i:38583 original size:16 final size:15
Alignment explanation
Indices: 38555--38593 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
38545 TGACCCCCCC
38555 TTTTTCTTTTTTTCT
1 TTTTTCTTTTTTTCT
*
38570 TTTTTTTTTCTTTTCT
1 TTTTTCTTT-TTTTCT
*
38586 TTTCTCTT
1 TTTTTCTT
38594 CAAGCATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTCTTTTTTTCT
Found at i:50908 original size:21 final size:22
Alignment explanation
Indices: 50876--50921 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
50866 GTTTGTATCT
50876 TCTCTGTTTTTTTTTCTGTCTC
1 TCTCTGTTTTTTTTTCTGTCTC
50898 TCTCT-TTTTTTTTTCTGTCTC
1 TCTCTGTTTTTTTTTCTGTCTC
50919 TCT
1 TCT
50922 GTCCCGTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.00, C:0.24, G:0.07, T:0.70
Consensus pattern (22 bp):
TCTCTGTTTTTTTTTCTGTCTC
Found at i:51356 original size:3 final size:3
Alignment explanation
Indices: 51348--51436 Score: 151
Period size: 3 Copynumber: 29.7 Consensus size: 3
51338 AATATATATT
* *
51348 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
51396 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
51437 TGGATAAAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:52777 original size:3 final size:3
Alignment explanation
Indices: 52764--52809 Score: 67
Period size: 3 Copynumber: 15.0 Consensus size: 3
52754 CTGGGTTTTA
52764 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT CATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT
52810 GTTAAAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.05
3 33 0.82
4 5 0.12
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:54673 original size:25 final size:24
Alignment explanation
Indices: 54645--54691 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
54635 TTGACTAAAT
54645 TTTTATAATAATAGTTAATTTATTA
1 TTTTATAATAATAG-TAATTTATTA
**
54670 TTTTATTTTAATAGTAATTTAT
1 TTTTATAATAATAGTAATTTAT
54692 GTTTCTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTTATAATAATAGTAATTTATTA
Found at i:59278 original size:3 final size:3
Alignment explanation
Indices: 59272--59312 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
59262 TATTATTATT
* *
59272 TAA TAA TAA TAA TAA TAG TAA TAA -AA GAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59313 AAGGATGGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:59793 original size:42 final size:42
Alignment explanation
Indices: 59719--59819 Score: 125
Period size: 42 Copynumber: 2.4 Consensus size: 42
59709 AGGTCTTATG
* * * * *
59719 AATGGCCCGAAGGACTT-ATCATCTTGCTCGAAAGGCATA-T
1 AATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACATACT
*
59759 AGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 A-ATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACATACT
59802 AATGACCCGAAGGATTTA
1 AATGACCCGAAGGATTTA
59820 CAAAGCAAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 1 0.02
41 14 0.27
42 35 0.67
43 2 0.04
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.24
Consensus pattern (42 bp):
AATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACATACT
Found at i:59820 original size:20 final size:21
Alignment explanation
Indices: 59761--59821 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
59751 AGGCATATAG
*
59761 ATGACCCGAAGGATTTAAGCATC
1 ATGACCCGAAGGATTT-A-CATA
* * *
59784 ATG-CTCGAAAGACTTAC-TA
1 ATGACCCGAAGGATTTACATA
59803 ATGACCCGAAGGATTTACA
1 ATGACCCGAAGGATTTACA
59822 AAGCAAGAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
19 4 0.14
20 12 0.41
21 1 0.03
22 9 0.31
23 3 0.10
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (21 bp):
ATGACCCGAAGGATTTACATA
Found at i:60076 original size:42 final size:42
Alignment explanation
Indices: 59981--60087 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 42
59971 TCCCGAAGGT
* * * * * *
59981 CTTATGGATGGCCCGAAGG-TCTAATCATCTTGCTCGAAAGG
1 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
60022 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
*
60064 CTTACT-GGTGACCCGAAGGATTTA
1 CTTA-TAGATGACCCGAAGGATTTA
60088 TTTTAATCTC
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
41 17 0.30
42 39 0.68
43 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (42 bp):
CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
Found at i:60541 original size:227 final size:225
Alignment explanation
Indices: 59959--60543 Score: 839
Period size: 228 Copynumber: 2.6 Consensus size: 225
59949 AAAATCTCAT
* * * *
59959 TTGAAAACATCATC-CCGAAGGTCTTATGGATGGCCCGAAGGTCTAATCATCTTGCTCGAAAGGC
1 TTGAAAACATCAGCACTGAAGGTCTTATGGATGG-CCGAAGGTCTTATCATCTTACTCGAAAGGC
* *
60023 TTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGGTGACCCGAAGGATTTA
65 TTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTA
* * * * *
60088 TTTTAATCTCGAGTGAGACAAATTTCTATTTCAAGTGAAACTTTCTCTAGCAAGACATTGTTGAT
130 CTTTAATCTCGAGTGAAACAAATTACTATTTCAAGTGAAACTTTCTCAAGCAAGACATTGATGAT
* *
60153 TCGAAATGTCATGAATCAAACAACATAAATG
195 TCGAAATGTCATGAATCAAACAACAGAAATA
* * *
60184 TTGAAAACATTCAGCACTGAAAGGTCTTATGGATGGACCGAAGGTCCTATCATCTTTCTCAAAAG
1 TTGAAAACA-TCAGCACTG-AAGGTCTTATGGATGG-CCGAAGGTCTTATCATCTTACTCGAAAG
* * * * * *
60249 GCTTACAAATGATCCGAATGATTTAAGCATCATGCTCTAAAGACTTATTGATGACTCGAAGGATT
63 GCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATT
** * *
60314 TACTTTAATCTCGAGTGAAACAAATTACTATTTTGAGTTAAACTTTCTCAAGCAATACATTGATG
128 TACTTTAATCTCGAGTGAAACAAATTACTATTTCAAGTGAAACTTTCTCAAGCAAGACATTGATG
* **
60379 ATTCGAAATGTCGTGAATCAAACAATGGAAATA
193 ATTCGAAATGTCATGAATCAAACAACAGAAATA
60412 TTGAAAACATCAAGCACTGAAGGTCTTATGGATGGCTCGAAGGTCTTATCATCTTACTCGAAAGG
1 TTGAAAACATC-AGCACTGAAGGTCTTATGGATGGC-CGAAGGTCTTATCATCTTACTCGAAAGG
*
60477 CTTACAGATAACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTT
64 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTT
60542 AC
129 AC
60544 AAAGCAATAA
Statistics
Matches: 316, Mismatches: 39, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
225 9 0.03
226 5 0.02
227 105 0.33
228 197 0.62
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (225 bp):
TTGAAAACATCAGCACTGAAGGTCTTATGGATGGCCGAAGGTCTTATCATCTTACTCGAAAGGCT
TACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTAC
TTTAATCTCGAGTGAAACAAATTACTATTTCAAGTGAAACTTTCTCAAGCAAGACATTGATGATT
CGAAATGTCATGAATCAAACAACAGAAATA
Found at i:62288 original size:40 final size:39
Alignment explanation
Indices: 62201--62329 Score: 105
Period size: 40 Copynumber: 3.2 Consensus size: 39
62191 GATACGAACG
* * **
62201 TTCAAAATGTGTTCAACATTACTTCTTGCTGATGTGTTCT
1 TTCAAAATG-ATTCAACATTACTTCTTGATGATGTGAGCT
* *
62241 TTCAAAATGATTCAACACTTTCTTTTTGATGATGTGAGCT
1 TTCAAAATGATTCAACA-TTACTTCTTGATGATGTGAGCT
* *** ** * *
62281 TTTAAAATGCCCCAACATTTACTTCTTTTTTATATGAGCT
1 TTCAAAATGATTCAACA-TTACTTCTTGATGATGTGAGCT
62321 TTCAAAATG
1 TTCAAAATG
62330 CCCCACATGG
Statistics
Matches: 70, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
39 7 0.10
40 63 0.90
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.43
Consensus pattern (39 bp):
TTCAAAATGATTCAACATTACTTCTTGATGATGTGAGCT
Found at i:63639 original size:19 final size:20
Alignment explanation
Indices: 63611--63672 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 20
63601 CTTGATTCAA
63611 TTTC-TTTTCTTCTTCTTTT
1 TTTCATTTTCTTCTTCTTTT
*
63630 TTT-ATTTTCTTTTTCATCTTT
1 TTTCATTTTCTTCTTC-T-TTT
* *
63651 TTTCTTTTTCATCTCTCTTTT
1 TTTCATTTTCTTCT-TCTTTT
63672 T
1 T
63673 CTTTTTTCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 13 0.38
20 1 0.03
21 10 0.29
22 8 0.24
23 2 0.06
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTCATTTTCTTCTTCTTTT
Found at i:63653 original size:16 final size:18
Alignment explanation
Indices: 63634--63678 Score: 67
Period size: 16 Copynumber: 2.6 Consensus size: 18
63624 TCTTTTTTTA
63634 TTTTCTTTTTCA-TCT-T
1 TTTTCTTTTTCACTCTCT
63650 TTTTCTTTTTCATCTCTCT
1 TTTTCTTTTTCA-CTCTCT
63669 TTTTCTTTTT
1 TTTTCTTTTT
63679 TCCTTTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.46
18 3 0.12
19 11 0.42
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTCTTTTTCACTCTCT
Found at i:70938 original size:3 final size:3
Alignment explanation
Indices: 70932--71002 Score: 83
Period size: 3 Copynumber: 24.0 Consensus size: 3
70922 TATTATTATT
* * * *
70932 TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA GAA GAA GAA GAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
70978 -AA -AA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
71003 ATGATGGACA
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 4 0.06
3 57 0.89
4 3 0.05
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (3 bp):
TAA
Found at i:77252 original size:3 final size:3
Alignment explanation
Indices: 77244--77295 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
77234 TCTACAAAAA
* *
77244 TAT TAT TAT TAA TAT CAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
77292 TAT T
1 TAT T
77296 TTGTTTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:83062 original size:15 final size:15
Alignment explanation
Indices: 83044--83147 Score: 89
Period size: 15 Copynumber: 7.3 Consensus size: 15
83034 ATATCAAATA
*
83044 AAAAAAGAAGCAAAG
1 AAAAAAGAAACAAAG
*
83059 AAAAAAGAAGCAAAG
1 AAAAAAGAAACAAAG
83074 AAAAAA-AAACAAAG
1 AAAAAAGAAACAAAG
83088 AGAAAAA-AGAA-AAA-
1 A-AAAAAGA-AACAAAG
*
83102 AAGAAA-AAA-AAAG
1 AAAAAAGAAACAAAG
*
83115 AAAAAAGAAA-AATG
1 AAAAAAGAAACAAAG
*
83129 -AAAAATAAACAAAG
1 AAAAAAGAAACAAAG
83143 AAAAA
1 AAAAA
83148 GGGACAAGAG
Statistics
Matches: 77, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
12 5 0.06
13 18 0.23
14 18 0.23
15 34 0.44
16 2 0.03
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.02
Consensus pattern (15 bp):
AAAAAAGAAACAAAG
Found at i:83098 original size:38 final size:35
Alignment explanation
Indices: 83043--83147 Score: 110
Period size: 34 Copynumber: 3.0 Consensus size: 35
83033 AATATCAAAT
*
83043 AAAAAAAGAAGCAAAGAAAAAAGAAGCAAAGAAAAAA
1 AAAAAAAGAA-AAAAGAAAAAA-AAGCAAAGAAAAAA
83080 AAACAAAGAGAAAAAAG-AAAAAAAG-AAA-AAAAAA
1 AAA-AAA-AGAAAAAAGAAAAAAAAGCAAAGAAAAAA
* *
83114 GAAAAAAGAAAAATGAAAAATAAA-CAAAGAAAAA
1 AAAAAAAGAAAAAAGAAAAA-AAAGCAAAGAAAAA
83148 GGGACAAGAG
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
32 8 0.14
33 7 0.12
34 14 0.24
35 8 0.14
36 3 0.05
37 8 0.14
38 7 0.12
39 4 0.07
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.02
Consensus pattern (35 bp):
AAAAAAAGAAAAAAGAAAAAAAAGCAAAGAAAAAA
Found at i:83126 original size:31 final size:32
Alignment explanation
Indices: 83071--83133 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
83061 AAAAGAAGCA
* *
83071 AAGAAAAAAAAA-CAAAGAGAAAAAAGAAAAA
1 AAGAAAAAAAAAGAAAAAAGAAAAAAGAAAAA
*
83102 AAGAAAAAAAAAGAAAAAAGAAAAATGAAAAA
1 AAGAAAAAAAAAGAAAAAAGAAAAAAGAAAAA
83134 TAAACAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.84, C:0.02, G:0.13, T:0.02
Consensus pattern (32 bp):
AAGAAAAAAAAAGAAAAAAGAAAAAAGAAAAA
Found at i:83133 original size:8 final size:7
Alignment explanation
Indices: 83044--83147 Score: 81
Period size: 7 Copynumber: 14.7 Consensus size: 7
83034 ATATCAAATA
83044 AAAAAAG
1 AAAAAAG
*
83051 AAGCAAAG
1 AA-AAAAG
83059 AAAAAAG
1 AAAAAAG
*
83066 AAGCAAAG
1 AA-AAAAG
*
83074 AAAAAAA
1 AAAAAAG
83081 AACAAAGAG
1 AA-AAA-AG
83090 AAAAAAG
1 AAAAAAG
83097 -AAAAA-
1 AAAAAAG
*
83102 AAGAAA-
1 AAAAAAG
83108 AAAAAAG
1 AAAAAAG
83115 AAAAAAG
1 AAAAAAG
*
83122 AAAAATG
1 AAAAAAG
83129 AAAAATA-
1 AAAAA-AG
*
83136 AACAAAG
1 AAAAAAG
83143 AAAAA
1 AAAAA
83148 GGGACAAGAG
Statistics
Matches: 77, Mismatches: 12, Indels: 16
0.73 0.11 0.15
Matches are distributed among these distances:
6 15 0.19
7 41 0.53
8 18 0.23
9 3 0.04
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:83142 original size:21 final size:20
Alignment explanation
Indices: 83045--83147 Score: 68
Period size: 23 Copynumber: 4.9 Consensus size: 20
83035 TATCAAATAA
* *
83045 AAAAAGAAGCAAAGAAAAAAG
1 AAAAAGAA-AAAAGAAAAATG
* *
83066 AAGCAAAGAAAAAAAAACAAAGAG
1 AA--AAAGAAAAAAGAA-AAA-TG
83090 AAAAAAGAAAAAA-AGAAAA--
1 -AAAAAGAAAAAAGA-AAAATG
83109 AAAAAGAAAAAAGAAAAATG
1 AAAAAGAAAAAAGAAAAATG
*
83129 AAAAATAAACAAAGAAAAA
1 AAAAAGAAA-AAAGAAAAA
83148 GGGACAAGAG
Statistics
Matches: 69, Mismatches: 3, Indels: 20
0.75 0.03 0.22
Matches are distributed among these distances:
18 16 0.23
19 1 0.01
20 8 0.12
21 11 0.16
22 9 0.13
23 20 0.29
24 2 0.03
25 2 0.03
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAAAAGAAAAATG
Found at i:83143 original size:46 final size:46
Alignment explanation
Indices: 83039--83147 Score: 114
Period size: 46 Copynumber: 2.3 Consensus size: 46
83029 TGAAAATATC
** *
83039 AAATAAAAAAAGAAGCAAAGAAAAAAGAAGCAAAGAAAAAAAAACAA
1 AAAT-AAAAAAGAAAAAAAGAAAAAAAAAGCAAAGAAAAAAAAACAA
* * **
83086 AGAGAAAAAAGAAAAAAAGAAAAAAAAAG-AAA-AAAGAAAAATGAA
1 AAATAAAAAAGAAAAAAAGAAAAAAAAAGCAAAGAAA-AAAAAACAA
83131 AAATAAACAAAGAAAAA
1 AAATAAA-AAAGAAAAA
83148 GGGACAAGAG
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
44 3 0.06
45 15 0.29
46 31 0.61
47 2 0.04
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.03
Consensus pattern (46 bp):
AAATAAAAAAGAAAAAAAGAAAAAAAAAGCAAAGAAAAAAAAACAA
Found at i:84489 original size:59 final size:59
Alignment explanation
Indices: 84410--84528 Score: 193
Period size: 59 Copynumber: 2.0 Consensus size: 59
84400 ATATGGATAT
* *
84410 GTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGGTTCTAA
1 GTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGGCTCTAA
* * *
84469 GTGTTCTATCGAACCCTCCTAGTTGGAATGAAAAGGAAAACTCGATAATATGGCTCTAA
1 GTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGGCTCTAA
84528 G
1 G
84529 CAACCCTCCT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (59 bp):
GTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGGCTCTAA
Found at i:87621 original size:59 final size:59
Alignment explanation
Indices: 87543--87663 Score: 179
Period size: 59 Copynumber: 2.1 Consensus size: 59
87533 AATAGATGAA
* **
87543 TAAGGGTCCTATCGAACCCTCCTAGTTGCAATGAAAAGGAAAACTCGATAATATGGCTC
1 TAAGGGTCCTATCAAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATGGCTC
* ** *
87602 TAAGTGTCCTATCAAACCCTGTTAGTCACAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGGGTCCTATCAAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATGGCTC
87661 TAA
1 TAA
87664 CCAACCCTCC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (59 bp):
TAAGGGTCCTATCAAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATGGCTC
Found at i:89844 original size:20 final size:20
Alignment explanation
Indices: 89819--89880 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
89809 TTTTGAAACA
89819 AATTTTGTCTCGCTAGAGAC
1 AATTTTGTCTCGCTAGAGAC
* *
89839 AATTTT-TCT-G--AAAAAC
1 AATTTTGTCTCGCTAGAGAC
*
89855 AAATTTTGTCTCGCTTGAGAC
1 -AATTTTGTCTCGCTAGAGAC
89876 AATTT
1 AATTT
89881 CTCTCAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
16 4 0.12
17 6 0.19
18 4 0.12
19 4 0.12
20 11 0.34
21 3 0.09
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (20 bp):
AATTTTGTCTCGCTAGAGAC
Found at i:89902 original size:36 final size:37
Alignment explanation
Indices: 89814--89917 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
89804 GAAATTTTTG
* *
89814 AAACAAATTTTGTCTCGCTAGAGACAATTTTTCTGAA
1 AAACAAATTTTGTCTCGCTTGAGACAATTTCTCTGAA
*
89851 AAACAAATTTTGTCTCGCTTGAGACAATTTCTCT-CA
1 AAACAAATTTTGTCTCGCTTGAGACAATTTCTCTGAA
* * *
89887 AAATAAATTTCGTCTCGCTTGAGACAGTTTC
1 AAACAAATTTTGTCTCGCTTGAGACAATTTC
89918 CCCTCAGATG
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
36 29 0.48
37 32 0.52
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (37 bp):
AAACAAATTTTGTCTCGCTTGAGACAATTTCTCTGAA
Found at i:90128 original size:21 final size:21
Alignment explanation
Indices: 90096--90135 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
90086 ACACAAATTT
*
90096 CAAAGATTATTTTACTTGAAA
1 CAAAGATTATTTCACTTGAAA
90117 CAAA-ATTAATTTCACTTGA
1 CAAAGATT-ATTTCACTTGA
90136 GATTGTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (21 bp):
CAAAGATTATTTCACTTGAAA
Found at i:90473 original size:66 final size:66
Alignment explanation
Indices: 90227--90496 Score: 301
Period size: 70 Copynumber: 4.0 Consensus size: 66
90217 AACAAAATTG
* *
90227 ATAAAACATTGAGATTGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACACTTTCTCTTGAA
1 ATAAAACTTTGAGATTGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAATTTCTCTTGAA
90292 AC
65 AC
* * * *
90294 ATAAAAAAACTTTGAGATTGTTACTCTTGAAACAAAGTTTTGCCTCTCTTGGGACAATTT-TACT
1 AT---AAAACTTTGAGATTGTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAATTTCT-CT
90358 TGAAATC
61 TGAAA-C
* * * *
90365 -TAAAATTGTTTAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTCTTTAGACAATTTCTCTTGAA
1 ATAAAACT-TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAA
90429 AC
65 AC
* ** * ** *
90431 ATACAACTTTGAGATCCTTTCCCTTGAAACAAATTATGTCTCTCTTGAGACGGTTTCCCTTGAAA
1 ATAAAACTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAA
90496 C
66 C
90497 TATTATCCCT
Statistics
Matches: 169, Mismatches: 25, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
66 50 0.30
67 39 0.23
68 22 0.13
69 4 0.02
70 53 0.31
71 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (66 bp):
ATAAAACTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAA
C
Found at i:90853 original size:134 final size:133
Alignment explanation
Indices: 90504--90863 Score: 386
Period size: 134 Copynumber: 2.7 Consensus size: 133
90494 AACTATTATC
* * *
90504 CCTAAATATGTCCAACCATCCTCATCACGTAGGAACTGTGTCATTCC-CCGACCATACCTCCTCA
1 CCTAAAAATGGCCTACCATCCTCATCACGTAGGAACTGTGTCA-TCCACCGACC-TACCTCCTCA
* * * * ** * *
90568 TCACGTAGGAGCTGCGTCA-ACCTCAGAAAACCAGTTGTCCTTATAACGTAGGAACCGTGTTATC
64 TCACGTAGGAGCAGTGTCACCCCT-AGACAACCAGTCATCCTCATAACGTAGGAAACGTGTTATC
90632 ACCATT
128 ACCATT
* * * * * *
90638 CCTAAAAATGGCATGCCATCCTCATCACGTAGGAATTATGTCATCCACTGACCAAACCTCCTCAT
1 CCTAAAAATGGCCTACCATCCTCATCACGTAGGAACTGTGTCATCCACCGACC-TACCTCCTCAT
* ** *
90703 CACGTAGGTA-CCGTGTCACCCCTAGACAACCAGTCATCCTCATCGCGTAGGAAATGTGTTATCA
65 CACGTAGG-AGCAGTGTCACCCCTAGACAACCAGTCATCCTCATAACGTAGGAAACGTGTTATCA
90767 CTC-TT
129 C-CATT
* * * *
90772 CCTAAAGATGGCCTACCGTCCTCATCGCGTAGGAACTGTGTCATCCACCGACCTGATCTCCTCAT
1 CCTAAAAATGGCCTACCATCCTCATCACGTAGGAACTGTGTCATCCACCGACCT-ACCTCCTCAT
* *
90837 CACGTAAGAGCAGTGTCACCCTTAGAC
65 CACGTAGGAGCAGTGTCACCCCTAGAC
90864 GACTATAACT
Statistics
Matches: 187, Mismatches: 33, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
133 4 0.02
134 178 0.95
135 5 0.03
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.25
Consensus pattern (133 bp):
CCTAAAAATGGCCTACCATCCTCATCACGTAGGAACTGTGTCATCCACCGACCTACCTCCTCATC
ACGTAGGAGCAGTGTCACCCCTAGACAACCAGTCATCCTCATAACGTAGGAAACGTGTTATCACC
ATT
Found at i:91056 original size:3 final size:3
Alignment explanation
Indices: 91048--91126 Score: 115
Period size: 3 Copynumber: 26.3 Consensus size: 3
91038 TCTGCAAAAA
* *
91048 TAT TAT TAT TAA TAT CAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
91095 TAT TAT TAT TAT TAT TAC TAT TAT TAAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT T
91127 TTGTTTACAT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.03
3 63 0.93
4 3 0.04
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:96538 original size:17 final size:17
Alignment explanation
Indices: 96518--96552 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
96508 TCTGGGTGTT
96518 TCATTTTCTTATACACA
1 TCATTTTCTTATACACA
96535 TCATTTTCTTATACACA
1 TCATTTTCTTATACACA
96552 T
1 T
96553 TAAATTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.49
Consensus pattern (17 bp):
TCATTTTCTTATACACA
Found at i:99494 original size:27 final size:26
Alignment explanation
Indices: 99454--99505 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
99444 AGAAGGTGCA
99454 CTGACTAGAACTTCTAGAAAACTGCCG
1 CTGACTAGAACTTCTAG-AAACTGCCG
* *
99481 CTGACTGGACCTTCTAGAAACTGCC
1 CTGACTAGAACTTCTAGAAACTGCC
99506 ACGTCAGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (26 bp):
CTGACTAGAACTTCTAGAAACTGCCG
Done.