Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002928.1 Hibiscus syriacus cultivar Beakdansim tig00006050_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: 56701
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6160 original size:32 final size:35
Alignment explanation
Indices: 6082--6161 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 35
6072 CACAAGATGT
*
6082 GATTTCAACTTCACAACGAAAGATATCCAATTCAAA
1 GATTTCAACTTCACAACGAAAGA-AGCCAATTCAAA
*
6118 G--TTCAACTTCACAACGAATG-AGCC-A-TCAAA
1 GATTTCAACTTCACAACGAAAGAAGCCAATTCAAA
6148 GATTTCAACTTCAC
1 GATTTCAACTTCAC
6162 GAAGAATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 6 0.15
31 1 0.03
32 14 0.35
34 18 0.45
36 1 0.03
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (35 bp):
GATTTCAACTTCACAACGAAAGAAGCCAATTCAAA
Found at i:6946 original size:27 final size:27
Alignment explanation
Indices: 6897--6957 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
6887 ATTATTTGAC
* *
6897 TATATAT-TTATTTATAATGTATATTA
1 TATATATATTATTTATAATATATAATA
* * *
6923 TATATATATTGTTTATATTATATAATG
1 TATATATATTATTTATAATATATAATA
6950 TATATATA
1 TATATATA
6958 GCACGTTGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (27 bp):
TATATATATTATTTATAATATATAATA
Found at i:13407 original size:4 final size:4
Alignment explanation
Indices: 13400--13426 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
13390 ATATATTATA
13400 ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATA
13427 ATATATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:14207 original size:17 final size:17
Alignment explanation
Indices: 14187--14219 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
14177 ATATTTATTT
*
14187 ATATAAAATATAATATA
1 ATATAAAAAATAATATA
14204 ATATAAAAAATAATAT
1 ATATAAAAAATAATAT
14220 TATGATAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:14257 original size:16 final size:17
Alignment explanation
Indices: 14238--14274 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
14228 TAAAATATTA
14238 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
14254 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
14271 TTTT
1 TTTT
14275 CATCCCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Found at i:15822 original size:23 final size:23
Alignment explanation
Indices: 15796--15852 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
15786 TATTAGGTTT
15796 AAATCGATAATATCATTAATTTG
1 AAATCGATAATATCATTAATTTG
15819 AAATCGATAATATCATTAATTTG
1 AAATCGATAATATCATTAATTTG
15842 AAATCGATAAT
1 AAATCGATAAT
15853 GCTTATGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (23 bp):
AAATCGATAATATCATTAATTTG
Found at i:16052 original size:21 final size:20
Alignment explanation
Indices: 16027--16065 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16017 AACTGATGCC
*
16027 GTAATTATACCTAGTTTTGAT
1 GTAA-TATACCTAATTTTGAT
*
16048 GTAATATTCCTAATTTTG
1 GTAATATACCTAATTTTG
16066 TATTTCTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (20 bp):
GTAATATACCTAATTTTGAT
Found at i:18542 original size:20 final size:19
Alignment explanation
Indices: 18497--18544 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
18487 TGACCAACAA
* *
18497 AATT-GCAACGCGATCTCG
1 AATTCGCAACGCGAACTCC
18515 AATTCGCAACGCGAACTCC
1 AATTCGCAACGCGAACTCC
18534 AATTTCGCAAC
1 AA-TTCGCAAC
18545 TTAGTTTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 4 0.15
19 14 0.54
20 8 0.31
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (19 bp):
AATTCGCAACGCGAACTCC
Found at i:18577 original size:20 final size:20
Alignment explanation
Indices: 18554--18644 Score: 148
Period size: 20 Copynumber: 4.5 Consensus size: 20
18544 CTTAGTTTCC
*
18554 AAAATCGCAACGTGAATAGT
1 AAAATCGCAACGCGAATAGT
18574 AAAATCGCAACGCGAATAGT
1 AAAATCGCAACGCGAATAGT
18594 AAAATCGCAACGCGAATAGT
1 AAAATCGCAACGCGAATAGT
18614 AAAATCGCAACGCGAATTTAG-
1 AAAATCGCAACGCGAA--TAGT
18635 AAAATCGCAA
1 AAAATCGCAA
18645 AATCGCGTTG
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
20 55 0.81
21 10 0.15
22 3 0.04
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGAATAGT
Found at i:19108 original size:40 final size:40
Alignment explanation
Indices: 19061--19206 Score: 224
Period size: 40 Copynumber: 3.6 Consensus size: 40
19051 TTCACGTTGC
19061 GAATTTGACTATCGCGTTGCGAATTTAACTTTTGTATTGT
1 GAATTTGACTATCGCGTTGCGAATTTAACTTTTGTATTGT
19101 GAATTTGACTATCGCGTTGCGAATTTAACTTTTGTATTGT
1 GAATTTGACTATCGCGTTGCGAATTTAACTTTTGTATTGT
* * * *
19141 GAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGC
1 GAATTTGACTATCGCGTTGCGAATTTAACTTTTGTATTGT
19181 G-ATTT-ACATATTCGCGTTGCGAATTT
1 GAATTTGAC-TA-TCGCGTTGCGAATTT
19207 GTTGATCATT
Statistics
Matches: 100, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
38 2 0.02
39 6 0.06
40 92 0.92
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.43
Consensus pattern (40 bp):
GAATTTGACTATCGCGTTGCGAATTTAACTTTTGTATTGT
Found at i:19164 original size:20 final size:20
Alignment explanation
Indices: 18994--19207 Score: 150
Period size: 20 Copynumber: 10.7 Consensus size: 20
18984 CATATAGATT
* *
18994 CGTTGCG-ATTTTACTATTCA
1 CGTTGCGAATTTGACTA-TCG
* * *
19014 CGTTGTG-ATTTTACTATTCA
1 CGTTGCGAATTTGACTA-TCG
* * *
19034 CGTTGCGATTTTTACTATTCA
1 CGTTGCGAATTTGACTA-TCG
19055 CGTTGCGAATTTGACTATCG
1 CGTTGCGAATTTGACTATCG
* * *
19075 CGTTGCGAATTTAACTTTTG
1 CGTTGCGAATTTGACTATCG
** *
19095 TATTGTGAATTTGACTATCG
1 CGTTGCGAATTTGACTATCG
* * *
19115 CGTTGCGAATTTAACTTTTG
1 CGTTGCGAATTTGACTATCG
** *
19135 TATTGTGAATTTGACTATCG
1 CGTTGCGAATTTGACTATCG
19155 CGTTGCGAATTTGACTTAT-G
1 CGTTGCGAATTTGAC-TATCG
*
19175 TGTTGCG-ATTT-ACATATTCG
1 CGTTGCGAATTTGAC-TA-TCG
19195 CGTTGCGAATTTG
1 CGTTGCGAATTTG
19208 TTGATCATTT
Statistics
Matches: 155, Mismatches: 33, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
18 4 0.03
19 5 0.03
20 112 0.72
21 34 0.22
ACGTcount: A:0.21, C:0.15, G:0.20, T:0.44
Consensus pattern (20 bp):
CGTTGCGAATTTGACTATCG
Found at i:21030 original size:3 final size:3
Alignment explanation
Indices: 21022--21046 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
21012 TATTTCCTTC
21022 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
21047 TTTTGTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:21235 original size:3 final size:3
Alignment explanation
Indices: 21227--21271 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
21217 CATTGTTTGG
21227 TAT TAT TAT TAT TAT TAT 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
21272 GTGATAATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:24137 original size:23 final size:23
Alignment explanation
Indices: 24049--24137 Score: 87
Period size: 23 Copynumber: 4.0 Consensus size: 23
24039 CAACTCGTAA
*
24049 TTTGCACCGAAGTGCCACATAA-
1 TTTGCACCGAAGTACCACATAAG
* *
24071 -TTGTC-CCGAAGGACCACATATG
1 TTTG-CACCGAAGTACCACATAAG
*
24093 TTTGCACCGAAGTACCAAATAAG
1 TTTGCACCGAAGTACCACATAAG
*
24116 TTTGCACC-ACAGTGCCACATAA
1 TTTGCACCGA-AGTACCACATAA
24138 TTGTCCCGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
21 16 0.30
22 3 0.06
23 35 0.65
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (23 bp):
TTTGCACCGAAGTACCACATAAG
Found at i:27101 original size:42 final size:43
Alignment explanation
Indices: 27055--27206 Score: 150
Period size: 42 Copynumber: 3.6 Consensus size: 43
27045 AGTAGAAGTC
* *
27055 GGGCTATAAGCA-GGTGAAGTAGGGCTTTACGATGGAGATGTG
1 GGGCTATAAGCAGGGTGAAGTTGGGCTGTACGATGGAGATGTG
* * * *
27097 GGGCTAT-AGGAGGGTGAGGTTGGGCTGTACGAAGGAGATGTT
1 GGGCTATAAGCAGGGTGAAGTTGGGCTGTACGATGGAGATGTG
* * * * * **
27139 GGGCTCTATG-ATGGTGATGTTGGGCTGTATGATGGAGAACTG
1 GGGCTATAAGCAGGGTGAAGTTGGGCTGTACGATGGAGATGTG
*
27181 GGGCTATACGCA-GGTGAAGTTGGGCT
1 GGGCTATAAGCAGGGTGAAGTTGGGCT
27207 ATATGCAGGT
Statistics
Matches: 89, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
41 3 0.03
42 84 0.94
43 2 0.02
ACGTcount: A:0.22, C:0.10, G:0.43, T:0.26
Consensus pattern (43 bp):
GGGCTATAAGCAGGGTGAAGTTGGGCTGTACGATGGAGATGTG
Found at i:27214 original size:21 final size:21
Alignment explanation
Indices: 27049--27227 Score: 103
Period size: 21 Copynumber: 8.5 Consensus size: 21
27039 TTACCCAGTA
* *
27049 GAAGTCGGGCTATAAGCA-GGT
1 GAAGTTGGGCTATACG-ATGGT
* * *
27070 GAAGTAGGGCTTTACGATGGA
1 GAAGTTGGGCTATACGATGGT
* * * *
27091 GATGTGGGGCTATAGGAGGGT
1 GAAGTTGGGCTATACGATGGT
* * * *
27112 GAGGTTGGGCTGTACGAAGGA
1 GAAGTTGGGCTATACGATGGT
* * *
27133 GATGTTGGGCTCTATGATGGT
1 GAAGTTGGGCTATACGATGGT
* * * *
27154 GATGTTGGGCTGTATGATGGA
1 GAAGTTGGGCTATACGATGGT
* *
27175 GAACTGGGGCTATACGCA-GGT
1 GAAGTTGGGCTATACG-ATGGT
*
27196 GAAGTTGGGCTATATGCA-GGT
1 GAAGTTGGGCTATACG-ATGGT
27217 GAAGTTGGGCT
1 GAAGTTGGGCT
27228 GTAGCTCGGG
Statistics
Matches: 124, Mismatches: 32, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
20 1 0.01
21 122 0.98
22 1 0.01
ACGTcount: A:0.22, C:0.10, G:0.42, T:0.26
Consensus pattern (21 bp):
GAAGTTGGGCTATACGATGGT
Found at i:27363 original size:21 final size:21
Alignment explanation
Indices: 27339--27428 Score: 72
Period size: 21 Copynumber: 4.3 Consensus size: 21
27329 GACTGTAAGT
* *
27339 AGGTGACGTGGGACTATATCC
1 AGGTGACGTAGGACTATAACC
* *
27360 AGGTGATGTAGGACTGTAACC
1 AGGTGACGTAGGACTATAACC
* * * *
27381 AGGAGATGTATGACTGTAACC
1 AGGTGACGTAGGACTATAACC
* * * *
27402 AGGAGAGGTAGGACTGTAGCC
1 AGGTGACGTAGGACTATAACC
27423 AGGTGA
1 AGGTGA
27429 TGATGGACTG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.29, C:0.14, G:0.36, T:0.21
Consensus pattern (21 bp):
AGGTGACGTAGGACTATAACC
Found at i:27404 original size:42 final size:42
Alignment explanation
Indices: 27349--27449 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
27339 AGGTGACGTG
* * * *
27349 GGACTATATCCAGGTGATGTAGGACTGTAACCAGGAGATGTAT
1 GGACTGTAACCAGGAGAGGTAGGACTGTAACCAGGAGATG-AT
* *
27392 -GACTGTAACCAGGAGAGGTAGGACTGTAGCCAGGTGATGAT
1 GGACTGTAACCAGGAGAGGTAGGACTGTAACCAGGAGATGAT
* *
27433 GGACTGTATCCTGGAGA
1 GGACTGTAACCAGGAGA
27450 TGACATAGGC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.04
42 47 0.96
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.23
Consensus pattern (42 bp):
GGACTGTAACCAGGAGAGGTAGGACTGTAACCAGGAGATGAT
Found at i:27436 original size:21 final size:22
Alignment explanation
Indices: 27349--27452 Score: 99
Period size: 21 Copynumber: 4.9 Consensus size: 22
27339 AGGTGACGTG
* * *
27349 GGACTATATCCAGGTGATG-TA
1 GGACTGTAACCAGGAGATGATA
27370 GGACTGTAACCAGGAGATG-TA
1 GGACTGTAACCAGGAGATGATA
* *
27391 TGACTGTAACCAGGAGA-GGTA
1 GGACTGTAACCAGGAGATGATA
* *
27412 GGACTGTAGCCAGGTGATGAT-
1 GGACTGTAACCAGGAGATGATA
* *
27433 GGACTGTATCCTGGAGATGA
1 GGACTGTAACCAGGAGATGA
27453 CATAGGCGAG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
20 1 0.01
21 67 0.96
22 2 0.03
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (22 bp):
GGACTGTAACCAGGAGATGATA
Found at i:32154 original size:88 final size:95
Alignment explanation
Indices: 32030--32244 Score: 239
Period size: 88 Copynumber: 2.3 Consensus size: 95
32020 TCTTTAAAGC
* * * * * *
32030 AATTGGTTAAAAGCTCCAGCTTTATGGATAAGATTCAGCTAGCCTTATAAAGGTGA-T-T-ATA-
1 AATTGGCTAAACGCCCCGGCTTTATGGATAAGATTCAACTAGCCTGATAAAGGTGATTCTAATAT
*
32091 ATA-AAGT-T-TT-AGTTGTCCCTCTAGAGC
66 ATACAA-TATATTAAGTTGTCCCTCTAGAGA
* * *
32118 AATTGGCTAAACGCCTCGGCTTTATGGATAATATTCAACTAGCCTGATACAGGTGATTCTAATAT
1 AATTGGCTAAACGCCCCGGCTTTATGGATAAGATTCAACTAGCCTGATAAAGGTGATTCTAATA-
32183 CTATACAATAATATTAAGTTGTCCCTCTAGAGA
65 -TATACAAT-ATATTAAGTTGTCCCTCTAGAGA
*
32216 AATTGGTTAAACGCCCCGGCTTTATGGAT
1 AATTGGCTAAACGCCCCGGCTTTATGGAT
32245 TCAGCTAGCC
Statistics
Matches: 104, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
88 47 0.45
89 1 0.01
90 1 0.01
91 3 0.03
94 4 0.04
95 2 0.02
96 1 0.01
97 2 0.02
98 43 0.41
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (95 bp):
AATTGGCTAAACGCCCCGGCTTTATGGATAAGATTCAACTAGCCTGATAAAGGTGATTCTAATAT
ATACAATATATTAAGTTGTCCCTCTAGAGA
Found at i:33476 original size:84 final size:84
Alignment explanation
Indices: 33335--34289 Score: 987
Period size: 84 Copynumber: 11.4 Consensus size: 84
33325 TAAAGAAACT
* * * * * * *
33335 ATTTGTAGCATAACTCAAGG-TCAAAAGGGTTATCTACCAATAAAAGACCATCGAGTTCAATTAC
1 ATTTGCAGCATAACTCAAGGCT-AGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTAC
* * * *
33399 ACTCAGCTCAAAGGCATAAC
65 GCTCAGCTCCAAGGCACATC
* * * * *
33419 ATTTGCAGTATAGCTCAAGGCGAGAAAGGCTATCTTCCAACAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACG
*
33484 CTCAGCTCCAAGTCACATC
66 CTCAGCTCCAAGGCACATC
* *
33503 ATTTGCAGCATTACTCAAGGACTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAC
1 ATTTGCAGCATAACTCAAGG-CTAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTAC
*
33568 GCTCAGCTCTAAGGCACATC
65 GCTCAGCTCCAAGGCACATC
* * * * *
33588 ATTTGCAGCATAGCTCAAAGCTAGAAGGGTTATCTACCACCAAAAGACCTTCGAGTTCGACTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACG
*
33653 CTCAG-T--AAGGCACATT
66 CTCAGCTCCAAGGCACATC
* * * *
33669 ATTTGCAGCATAACTCAAGGCTAGAAGGGTT-TTTTGCCAACCAAATACCTTCGAGTTCGGCTAC
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTT-CCAACAAAAGACCTTCGAGTTCGACTAC
*
33733 GCTCAGCTCCAAGGAACATC
65 GCTCAGCTCCAAGGCACATC
* * * * * * * * * *
33753 ATTTACAGTATAACTTAAGGCTAGAAGGGCTATCTACCACCAAACGACCTTCAAGTTCAACTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACG
*
33818 CTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
* * * * *
33837 ATTTGCATCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGAACTTCGAGCTCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACG
* *
33902 CTCAGCTCCAAGGTACATT
66 CTCAGCTCCAAGGCACATC
* * * ** * * * *
33921 ATTTGCAGCATAGCTCAAGGCAATAAGGGTTAT-TTGTTACCAAACGACATTCGAATTCGACTAC
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTT-CCAACAAAAGACCTTCGAGTTCGACTAC
* *
33985 GCCCAGCTCCAAGGCATATC
65 GCTCAGCTCCAAGGCACATC
* * *
34005 ATTTGCAGCATAAATCAAGGCTAGAAGGGTTATCTGT-CAACCAAAGACCTTCGAGTTCGACAAC
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCT-TCCAACAAAAGACCTTCGAGTTCGACTAC
*
34069 GTTCAGCTCCAAGGCACATC
65 GCTCAGCTCCAAGGCACATC
* * * * * * *
34089 ATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTGCCACCAAAAGACCTACGAGTTCGATTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACG
34154 CTCAGCT--AAGGGCACATC
66 CTCAGCTCCAA-GGCACATC
* * * * * * *
34172 ATTTACATCATAACTAAAGGCTAGAAAGGTTAT-TTGTCAAC-AAAGACCTTTGAGTTCGATTAC
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTT-CCAACAAAAGACCTTCGAGTTCGACTAC
* * *
34235 ACTCGGCTCAAAGGCACATC
65 GCTCAGCTCCAAGGCACATC
* * * * * *
34255 ATTTACAGCTTAGCTCAAGGCAAGAAAGGCTATCT
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCT
34290 GTCAATAAAA
Statistics
Matches: 717, Mismatches: 138, Indels: 32
0.81 0.16 0.04
Matches are distributed among these distances:
80 2 0.00
81 67 0.09
82 31 0.04
83 75 0.10
84 463 0.65
85 78 0.11
86 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (84 bp):
ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATC
Found at i:33906 original size:168 final size:168
Alignment explanation
Indices: 33335--34289 Score: 1132
Period size: 168 Copynumber: 5.7 Consensus size: 168
33325 TAAAGAAACT
* * * ** * * *
33335 ATTTGTAGCATAACTCAAGG-TCAAAAGGGTTATCTACCAATAAAAGACCATCGAGTTCAATTAC
1 ATTTGCAGCATAACTCAAGGCT-AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * * * * * * *
33399 ACTCAGCTCAAAGGCATAACATTTGCAGTATAGCTCAAGGCGAGAAAGGCTATCTTCCAACAAAA
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTACCACCAAAA
* *
33464 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGTCACATC
130 GACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATC
* *
33503 ATTTGCAGCATTACTCAAGGACTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAC
1 ATTTGCAGCATAACTCAAGG-CTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * *
33568 GCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTCAAAGCTAGAAGGGTTATCTACCACCAAAA
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTACCACCAAAA
*
33633 GACCTTCGAGTTCGACTACACTCAG-T--AAGGCACATT
130 GACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATC
* * * *
33669 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTTTTTGCCAACCAAATACCTTCGAGTTCGGCTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * * * * *
33734 CTCAGCTCCAAGGAACATCATTTACAGTATAACTTAAGGCTAGAAGGGCTATCTACCACCAAACG
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTACCACCAAAAG
* * *
33799 ACCTTCAAGTTCAACTACACTCAGCTCCAAGGCATATC
131 ACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATC
* * *
33837 ATTTGCATCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGAACTTCGAGCTCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * * * * * *** *
33902 CTCAGCTCCAAGGTACATTATTTGCAGCATAGCTCAAGGCAATAAGGGTTATTTGTTACCAAACG
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTACCACCAAAAG
* * * * *
33967 ACATTCGAATTCGACTACGCCCAGCTCCAAGGCATATC
131 ACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATC
* * *
34005 ATTTGCAGCATAAATCAAGGCTAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACAACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
34070 TTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTGCCACCAAAAG
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTACCACCAAAAG
* *
34135 ACCTACGAGTTCGATTACACTCAGCT--AAGGGCACATC
131 ACCTTCGAGTTCGACTACACTCAGCTCCAA-GGCACATC
* * * * * * * * *
34172 ATTTACATCATAACTAAAGGCTAGAAAGGTTATTTGTCAA-CAAAGACCTTTGAGTTCGATTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * * * * *
34236 CTCGGCTCAAAGGCACATCATTTACAGCTTAGCTCAAGGCAAGAAAGGCTATCT
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCT
34290 GTCAATAAAA
Statistics
Matches: 674, Mismatches: 107, Indels: 14
0.85 0.13 0.02
Matches are distributed among these distances:
165 118 0.18
166 97 0.14
167 41 0.06
168 303 0.45
169 114 0.17
170 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (168 bp):
ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTACCACCAAAAG
ACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATC
Found at i:37224 original size:6 final size:7
Alignment explanation
Indices: 37207--37244 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
37197 CGAATCGAAT
37207 ATTTTAA
1 ATTTTAA
37214 ATTTT-A
1 ATTTTAA
37220 ATTTTAA
1 ATTTTAA
37227 ATTTT-A
1 ATTTTAA
37233 ATTTTAA
1 ATTTTAA
37240 ATTTT
1 ATTTT
37245 CGCAACTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 12 0.41
7 17 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (7 bp):
ATTTTAA
Found at i:37225 original size:13 final size:13
Alignment explanation
Indices: 37207--37244 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
37197 CGAATCGAAT
37207 ATTTTAAATTTTA
1 ATTTTAAATTTTA
37220 ATTTTAAATTTTA
1 ATTTTAAATTTTA
37233 ATTTTAAATTTT
1 ATTTTAAATTTT
37245 CGCAACTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTTTAAATTTTA
Found at i:41477 original size:36 final size:36
Alignment explanation
Indices: 41427--41534 Score: 180
Period size: 36 Copynumber: 3.0 Consensus size: 36
41417 CAAAACAAAG
*
41427 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
* *
41463 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
*
41499 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
41535 ATCTTTGAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
Found at i:41667 original size:138 final size:138
Alignment explanation
Indices: 41419--41753 Score: 428
Period size: 138 Copynumber: 2.4 Consensus size: 138
41409 AATTTACTCA
* * ** * * * *
41419 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT-GAAATAAATTTTGTCTCCCTTGAGACAG
1 AAACAAA-TTTTATCTCCCTTGAGACAAATTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
*
41483 TTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAATAAAATCTTTGAATATG
65 TTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATG
*
41548 TTTT-CCTT
130 TTTTACATT
* *
41556 GAAAC-AATTTTCATCTCCTTTGAGACAAATTCTTTTGGAACTAAGTTTTGTCTCTCTAT-AGGC
1 -AAACAAATTTT-ATCTCCCTTGAGACAAATTCTTTTGGAACTAAGTTTTGTCTCTCT-TGAGAC
* *
41619 AGTTTCTCTTGAAA-AAATATTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
63 AGTTTCCCTTGAAACAAAT-TTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
41683 ATGTTTTACATT
127 ATGTTTTACATT
* * **
41695 AAACAAATTTTGTCTCCCTTGAGATAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGA
1 AAACAAATTTTATCTCCCTTGAGACAAATTCTTTTGGAACTAAGTTTTGTCTCTCTTGA
41754 AACAAATTTT
Statistics
Matches: 171, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
136 4 0.02
137 25 0.15
138 132 0.77
139 10 0.06
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.41
Consensus pattern (138 bp):
AAACAAATTTTATCTCCCTTGAGACAAATTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGT
TTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
TTTACATT
Found at i:41763 original size:21 final size:21
Alignment explanation
Indices: 41739--41811 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
41729 TGGAACTAAG
41739 TTTTGTCTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAAACAAA
*
41760 TTTTGTCTCTCTTGAGAC-AA
1 TTTTGTCTCTCTTGAAACAAA
41780 --TT-TC-C-CTTGAAACAAA
1 TTTTGTCTCTCTTGAAACAAA
41796 GTTTTGTCTCTCTTGA
1 -TTTTGTCTCTCTTGA
41812 TACAGTTTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
15 7 0.16
16 3 0.07
17 2 0.05
18 2 0.05
19 2 0.05
20 4 0.09
21 18 0.42
22 5 0.12
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (21 bp):
TTTTGTCTCTCTTGAAACAAA
Found at i:41789 original size:36 final size:37
Alignment explanation
Indices: 41749--41830 Score: 130
Period size: 37 Copynumber: 2.2 Consensus size: 37
41739 TTTTGTCTCT
41749 CTTGAAACAAA-TTTTGTCTCTCTTGAGACAATTTCC
1 CTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCC
* * *
41785 CTTGAAACAAAGTTTTGTCTCTCTTGATACAGTTTCT
1 CTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCC
41822 CTTGAAACA
1 CTTGAAACA
41831 CACAAAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 11 0.26
37 31 0.74
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (37 bp):
CTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCC
Found at i:41798 original size:58 final size:58
Alignment explanation
Indices: 41695--41811 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 58
41685 GTTTTACATT
* * ** * *
41695 AAACAAATTTTGTCTCCCTTGAGATAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTG
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTG
*
41753 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTG
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTG
41811 A
1 A
41812 TACAGTTTCT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (58 bp):
AAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTG
Found at i:42019 original size:84 final size:84
Alignment explanation
Indices: 41872--42028 Score: 217
Period size: 84 Copynumber: 1.9 Consensus size: 84
41862 GAAACACCAA
* **
41872 ACCTTCAAGTTCGGATACACTCAGCTCAAAGGAACATCATTTGTAGCATAGCTCAAGGAAAGAAG
1 ACCTTCAAGTTCGGATACACTAAGCTCAAAGGAACATCATTTACAGCATAGCTCAAGGAAAGAAG
*
41937 GGTTATCTTCCGACCAAAT
66 GGCTATCTTCCGACCAAAT
* * * * *
41956 ACCTTCCAGTTC-GATTACACTAAGCTCAAGGGCACATCATTTACAGCATAGCTCGAGGCAAGAA
1 ACCTTCAAGTTCGGA-TACACTAAGCTCAAAGGAACATCATTTACAGCATAGCTCAAGGAAAGAA
42020 GGGCTATCT
65 GGGCTATCT
42029 GTCAATAAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
83 2 0.03
84 61 0.97
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (84 bp):
ACCTTCAAGTTCGGATACACTAAGCTCAAAGGAACATCATTTACAGCATAGCTCAAGGAAAGAAG
GGCTATCTTCCGACCAAAT
Found at i:42614 original size:13 final size:14
Alignment explanation
Indices: 42596--42625 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
42586 ACATAGTATG
42596 TATATTA-TGTTGT
1 TATATTACTGTTGT
42609 TATATTACTGTTGT
1 TATATTACTGTTGT
42623 TAT
1 TAT
42626 TAAACTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.23, C:0.03, G:0.13, T:0.60
Consensus pattern (14 bp):
TATATTACTGTTGT
Found at i:43838 original size:14 final size:13
Alignment explanation
Indices: 43819--43872 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 13
43809 TCTTTGAATA
43819 TTTTTTATTTCTTT
1 TTTTTTATTT-TTT
43833 TTTTTTATTTTTT
1 TTTTTTATTTTTT
* * *
43846 TCTTTGACTTATTT
1 TTTTTTA-TTTTTT
*
43860 TGTTTTATTTTTT
1 TTTTTTATTTTTT
43873 ATTTATTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
13 13 0.39
14 20 0.61
ACGTcount: A:0.09, C:0.06, G:0.04, T:0.81
Consensus pattern (13 bp):
TTTTTTATTTTTT
Found at i:43849 original size:37 final size:38
Alignment explanation
Indices: 43808--43883 Score: 102
Period size: 37 Copynumber: 2.0 Consensus size: 38
43798 CTTTTTTATG
* *
43808 TTCTTTGA-ATATTTTTTATTTCTTTTTT-TTTATTTTT
1 TTCTTTGACATATTTTGT-TTTATTTTTTATTTATTTTT
*
43845 TTCTTTGACTTATTTTGTTTTATTTTTTATTTATTTTT
1 TTCTTTGACATATTTTGTTTTATTTTTTATTTATTTTT
43883 T
1 T
43884 CAATTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 17 0.50
38 17 0.50
ACGTcount: A:0.13, C:0.05, G:0.04, T:0.78
Consensus pattern (38 bp):
TTCTTTGACATATTTTGTTTTATTTTTTATTTATTTTT
Found at i:44719 original size:16 final size:17
Alignment explanation
Indices: 44695--44734 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
44685 TATATATATC
44695 TATTATTTTATATTTTA
1 TATTATTTTATATTTTA
*
44712 TATT-TTTTATCTTTTA
1 TATTATTTTATATTTTA
44728 TTATTAT
1 -TATTAT
44735 ATTTCCCGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 11 0.55
17 8 0.40
18 1 0.05
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTATTTTATATTTTA
Found at i:44938 original size:3 final size:3
Alignment explanation
Indices: 44930--45109 Score: 94
Period size: 3 Copynumber: 60.0 Consensus size: 3
44920 TATTGTTTTC
*
44930 ATT ATT ATT AGT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ACTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
* * * *
44975 ATT TTT ATT -TT ATT -TT -TT ATT CTT CATCT -TT ATT -TT TTT CTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -AT-T ATT ATT ATT ATT ATT
* * *
45017 -TAT ATT -TGT TTT ATTT ATT ATCT ATT -TGT ATT -TT CTT CTT ATT
1 AT-T ATT AT-T ATT A-TT ATT AT-T ATT AT-T ATT ATT ATT ATT ATT
* *
45060 TTT ATT TTT ATTT ATT -TAT ATAT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT A-TT ATT AT-T AT-T ATT ATT ATT ATT ATT ATT ATT ATT
45107 ATT
1 ATT
45110 CTTTTTTTCA
Statistics
Matches: 144, Mismatches: 13, Indels: 40
0.73 0.07 0.20
Matches are distributed among these distances:
2 17 0.12
3 105 0.73
4 21 0.15
5 1 0.01
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:45123 original size:6 final size:5
Alignment explanation
Indices: 44941--45161 Score: 65
Period size: 6 Copynumber: 39.4 Consensus size: 5
44931 TTATTATTAG
*
44941 TATTAT TATTAT TATTAT TATTAT TATTT TA-CT TATTTT TATTT TATTTTT
1 TATT-T TATT-T TATT-T TATT-T TATTT TATTT TA-TTT TATTT TA--TTT
* *
44992 TATTCT TCATCTT TATTTT TTTCTT TATATT TGTTT TA-TT TATTAT CTATTT
1 TATT-T T-AT-TT TA-TTT TAT-TT TAT-TT TATTT TATTT TATT-T -TATTT
*
45044 GTATTT TCTTCT TATTTT TATTT T-TATT TATTT ATATATAT TATTAT TATTAT
1 -TATTT TATT-T TA-TTT TATTT TAT-TT TATTT -TAT-T-T TATT-T TATT-T
* * * *
45097 TATTAT TATTAT TCTTT T-TTT CATTT TATTTT TATTT TTTATT TATTG
1 TATT-T TATT-T TATTT TATTT TATTT TA-TTT TATTT TAT-TT TATTT
*
45145 TA-TT CATTT TATCTT TA
1 TATTT TATTT TAT-TT TA
45162 CCCTTTTATT
Statistics
Matches: 172, Mismatches: 19, Indels: 48
0.72 0.08 0.20
Matches are distributed among these distances:
4 13 0.08
5 45 0.26
6 92 0.53
7 20 0.12
8 2 0.01
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.71
Consensus pattern (5 bp):
TATTT
Found at i:47850 original size:37 final size:37
Alignment explanation
Indices: 47800--47876 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
47790 GACCAGCTAT
*
47800 TTGATGAGAATGGTTGTTTGTGTGTATGAGTCTTATC
1 TTGATGAGAATGGTTGTTTGTGTGTATGAGTCTTACC
47837 TTGATGAGAATGGTTGTTTGTGTGTATGAGTCTTACC
1 TTGATGAGAATGGTTGTTTGTGTGTATGAGTCTTACC
47874 TTG
1 TTG
47877 TGTAATGGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.18, C:0.06, G:0.30, T:0.45
Consensus pattern (37 bp):
TTGATGAGAATGGTTGTTTGTGTGTATGAGTCTTACC
Found at i:47963 original size:57 final size:57
Alignment explanation
Indices: 47899--48010 Score: 215
Period size: 57 Copynumber: 2.0 Consensus size: 57
47889 CTACATCTTT
47899 GATATCGATATGGTGTACTATTTTTCCACCATTAGATGTAGGGATGCTTTTTGAAAA
1 GATATCGATATGGTGTACTATTTTTCCACCATTAGATGTAGGGATGCTTTTTGAAAA
*
47956 GATATCGATATGGTGTATTATTTTTCCACCATTAGATGTAGGGATGCTTTTTGAA
1 GATATCGATATGGTGTACTATTTTTCCACCATTAGATGTAGGGATGCTTTTTGAA
48011 TGATGCTCAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (57 bp):
GATATCGATATGGTGTACTATTTTTCCACCATTAGATGTAGGGATGCTTTTTGAAAA
Found at i:48764 original size:50 final size:49
Alignment explanation
Indices: 48657--48854 Score: 215
Period size: 50 Copynumber: 4.0 Consensus size: 49
48647 CATATACCAG
*
48657 TGTA-AGTGTGTGTTAAGTGCTACA-TTTTTTATTTTATT-ACTTACACCAT
1 TGTATAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTT--A-CAT
* *
48706 TGTA-AGTATGTGTTAAGTGTTACACTTTTTTATTTTATTCACTTATAT
1 TGTATAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACAT
** * * *
48754 TGATATAGTATGTGTTAAGTTATACACTTTTTTGTTTAATTCACTTACACC
1 TG-TATAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACA-T
* *
48805 GGTATAAGTATGTGTTAAGTGCTACACTTGTTTATTTTTATTCACTTACA
1 TGTAT-AGTATGTGTTAAGTGCTACACTTTTTTA-TTTTATTCACTTACA
48855 CCGGTGTAAG
Statistics
Matches: 127, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
48 4 0.03
49 25 0.20
50 55 0.43
51 29 0.23
52 14 0.11
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.49
Consensus pattern (49 bp):
TGTATAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACAT
Found at i:48887 original size:101 final size:99
Alignment explanation
Indices: 48656--48888 Score: 270
Period size: 101 Copynumber: 2.3 Consensus size: 99
48646 ACATATACCA
* * * * *
48656 GTGTAAGTGTGTGTTAAGTGCTACATTTTTTATTTTATTACTTACACCATTGTAAGTATGTGTTA
1 GTGTAAGTATGTGTTAAGT-TTACATTTTTTATTTAATTACTTACACCAGTATAAGTATGTGTTA
* * * **
48721 AGTGTTACACTTTTTTATTTTATTCACTTATATTG
65 AGTGCTACACTTGTTTATTTTATTCACTTACACCG
* * * *
48756 ATAT-AGTATGTGTTAAGTTATACACTTTTTTGTTTAATTCACTTACACCGGTATAAGTATGTGT
1 GTGTAAGTATGTGTTAAGTT-TACA-TTTTTTATTTAATT-ACTTACACCAGTATAAGTATGTGT
48820 TAAGTGCTACACTTGTTTATTTTTATTCACTTACACCG
63 TAAGTGCTACACTTGTTTA-TTTTATTCACTTACACCG
*
48858 GTGTAAGTATGTGTTAAATATTACATTTTTT
1 GTGTAAGTATGTGTTAAGT-TTACATTTTTT
48889 TAAAGTGAGT
Statistics
Matches: 110, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
99 17 0.15
100 14 0.13
101 38 0.35
102 23 0.21
103 17 0.15
104 1 0.01
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (99 bp):
GTGTAAGTATGTGTTAAGTTTACATTTTTTATTTAATTACTTACACCAGTATAAGTATGTGTTAA
GTGCTACACTTGTTTATTTTATTCACTTACACCG
Found at i:49150 original size:29 final size:28
Alignment explanation
Indices: 49108--49170 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
49098 TTTTTAAAGT
*
49108 AATTTTTATAAATTTGACACCTTAAAAAA
1 AATTTTTATAAA-TTGACACCTCAAAAAA
* *
49137 AATTCTTTA-AAATTGATACCTCAAAATA
1 AATT-TTTATAAATTGACACCTCAAAAAA
49165 AATTTT
1 AATTTT
49171 CTAACTTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 2 0.07
28 17 0.57
29 7 0.23
30 4 0.13
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (28 bp):
AATTTTTATAAATTGACACCTCAAAAAA
Found at i:49902 original size:60 final size:60
Alignment explanation
Indices: 49809--49935 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
49799 ATTGATATTA
** * * *
49809 ATAGTTTGGGGATAAAATTGGAATGTTCAAAAGTTTAATGACTAATTT-AGAATGAGATTC
1 ATAGTTTGGGGATAAAATTAAAATGTTCAAAAGTTCAAAGACTAATTTGA-AATGAGAGTC
* * *
49869 ATAGTTTTGGGATAAAATTAAAATGTTTAAAAGTTCAAAGACTAATTTGAAATGAGGGTC
1 ATAGTTTGGGGATAAAATTAAAATGTTCAAAAGTTCAAAGACTAATTTGAAATGAGAGTC
49929 ATAGTTT
1 ATAGTTT
49936 ATGGATATAT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 57 0.98
61 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.35
Consensus pattern (60 bp):
ATAGTTTGGGGATAAAATTAAAATGTTCAAAAGTTCAAAGACTAATTTGAAATGAGAGTC
Found at i:53962 original size:3 final size:3
Alignment explanation
Indices: 53956--54057 Score: 109
Period size: 3 Copynumber: 33.3 Consensus size: 3
53946 CCATTTTGAT
* *
53956 TTA TTA TTA TTA TTA TTA CTAA TTA TTA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
54002 TAAA ATA TTA TTA TTA TTA -TA TTA -AA TATA TTA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
54047 TTA TTAA TTA T
1 TTA TT-A TTA T
54058 ATATATACAC
Statistics
Matches: 83, Mismatches: 10, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
2 3 0.04
3 72 0.87
4 8 0.10
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Done.