Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003076.1 Hibiscus syriacus cultivar Beakdansim tig00006414_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: 167291
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:17255 original size:35 final size:35
Alignment explanation
Indices: 17216--17327 Score: 125
Period size: 35 Copynumber: 3.1 Consensus size: 35
17206 ATTTGTGGTT
* * *
17216 ATATAGTCGTGAAATGATGATAGAAGTTGGTGATG
1 ATATAGGCGTGAAATGGTGATAGAAGATGGTGATG
* *
17251 ATATAGGCGTGCAATGGTGATTGAAGATGGTGATG
1 ATATAGGCGTGAAATGGTGATAGAAGATGGTGATG
* * *
17286 TTATAGGCGTAAAAAATGGTGATGGAAGATGGTGATG
1 ATATAGGCGT--GAAATGGTGATAGAAGATGGTGATG
*
17323 TTATA
1 ATATA
17328 TGTAGTATCT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
35 39 0.59
37 27 0.41
ACGTcount: A:0.33, C:0.04, G:0.33, T:0.30
Consensus pattern (35 bp):
ATATAGGCGTGAAATGGTGATAGAAGATGGTGATG
Found at i:22990 original size:35 final size:35
Alignment explanation
Indices: 22942--23027 Score: 109
Period size: 35 Copynumber: 2.5 Consensus size: 35
22932 TGGTAAGGGA
* * *
22942 TTGGTGGTTATATAGGCGTGAAATGGTGATAGAAG
1 TTGGTGATGATATAGGCGTGAAATGATGATAGAAG
* *
22977 TTGGTGATGATATAGGCGTGCAATGATGATGGAAG
1 TTGGTGATGATATAGGCGTGAAATGATGATAGAAG
* *
23012 ATGGTGATGTTATAGG
1 TTGGTGATGATATAGG
23028 TAGTATCTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.28, C:0.03, G:0.37, T:0.31
Consensus pattern (35 bp):
TTGGTGATGATATAGGCGTGAAATGATGATAGAAG
Found at i:26296 original size:11 final size:11
Alignment explanation
Indices: 26280--26324 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
26270 GTACTACAAC
26280 AAAATAAAAAG
1 AAAATAAAAAG
26291 AAAATAGAAAAG
1 AAAATA-AAAAG
* *
26303 AAAATGAAAAT
1 AAAATAAAAAG
*
26314 AAAAGAAAAAG
1 AAAATAAAAAG
26325 GCTCCTACAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (11 bp):
AAAATAAAAAG
Found at i:39197 original size:23 final size:24
Alignment explanation
Indices: 39171--39223 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
39161 ACTATATGCT
39171 TTATATTTCATAAAATAT-ATA-AC
1 TTATATTT-ATAAAATATAATATAC
* *
39194 TTAT-CTTATAACATATAATATAC
1 TTATATTTATAAAATATAATATAC
39217 TTATATT
1 TTATATT
39224 CATTATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 8 0.33
22 5 0.21
23 10 0.42
24 1 0.04
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.47
Consensus pattern (24 bp):
TTATATTTATAAAATATAATATAC
Found at i:42595 original size:24 final size:24
Alignment explanation
Indices: 42568--42613 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
42558 TCAAACAATT
* * *
42568 TCATGCCTATTGGTCTTTCAAATG
1 TCATACCTATTAGTCTTCCAAATG
*
42592 TCATACCTTTTAGTCTTCCAAA
1 TCATACCTATTAGTCTTCCAAA
42614 AGTTATGATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (24 bp):
TCATACCTATTAGTCTTCCAAATG
Found at i:48413 original size:26 final size:26
Alignment explanation
Indices: 48380--48435 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
48370 AAAGAAATTG
* *
48380 AAGCACTC-CAAAAGAATAAAAAAATA
1 AAGCACTCAAAAAAGAAGAAAAAAA-A
48406 AAGCACTCAGAAAAAGAAGAAAAAAAA
1 AAGCACTCA-AAAAAGAAGAAAAAAAA
48433 AAG
1 AAG
48436 AAAGAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 8 0.31
27 4 0.15
28 14 0.54
ACGTcount: A:0.68, C:0.12, G:0.12, T:0.07
Consensus pattern (26 bp):
AAGCACTCAAAAAAGAAGAAAAAAAA
Found at i:48435 original size:14 final size:16
Alignment explanation
Indices: 48416--48447 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
48406 AAGCACTCAG
48416 AAAAAG-AAGAAA-AA
1 AAAAAGAAAGAAAGAA
48430 AAAAAGAAAGAAAGAA
1 AAAAAGAAAGAAAGAA
48446 AA
1 AA
48448 GTTGAAAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 6 0.38
16 4 0.25
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAGAAAGAA
Found at i:56501 original size:195 final size:195
Alignment explanation
Indices: 56169--56559 Score: 710
Period size: 195 Copynumber: 2.0 Consensus size: 195
56159 CACTGGAGGC
*
56169 TTATTCTTCCTAATGACTTCCATACTCTCTTTTCATATGAATCTGGTGATGTGATCATGCTCACT
1 TTATTCTTCCTAATGACTTCCATACTCTCTTTTCATATGAATCTGGTGATGTGATCATGCCCACT
*
56234 TTGGATCCAGAAGTCATGCTACAAGGTCCTATTACTAGATCAAGGGCCAAACGATTCAGGGAAGT
66 TTGGATCCAGAAGTCATACTACAAGGTCCTATTACTAGATCAAGGGCCAAACGATTCAGGGAAGT
*
56299 ACTCTTAACTAAGTGTATTGAAGCTTTCGATTCATTTAACAACTTGACACCCTCTATTGTTAAGT
131 ACTCTTAACTAAGTGTATTGAAGCTTTCGATTCATTTAACAACTTGACACCCTCTAATGTTAAGT
* *
56364 TTATTCTTCCTAATGACTTCCATACTCTTTTTTCATATGAATCTGGTGATGTGATCATGCCCATT
1 TTATTCTTCCTAATGACTTCCATACTCTCTTTTCATATGAATCTGGTGATGTGATCATGCCCACT
* * *
56429 TTGGATCTAGAAGTCATATTATAAGGTCCTATTACTAGATCAAGGGCCAAACGATTCAGGGAAGT
66 TTGGATCCAGAAGTCATACTACAAGGTCCTATTACTAGATCAAGGGCCAAACGATTCAGGGAAGT
56494 ACTCTTAACTAAGTGTATTGAAGCTTTCGATTCATTTAACAACTTGACACCCTCTAATGTTAAGT
131 ACTCTTAACTAAGTGTATTGAAGCTTTCGATTCATTTAACAACTTGACACCCTCTAATGTTAAGT
56559 T
1 T
56560 ATATAATGTT
Statistics
Matches: 188, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
195 188 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (195 bp):
TTATTCTTCCTAATGACTTCCATACTCTCTTTTCATATGAATCTGGTGATGTGATCATGCCCACT
TTGGATCCAGAAGTCATACTACAAGGTCCTATTACTAGATCAAGGGCCAAACGATTCAGGGAAGT
ACTCTTAACTAAGTGTATTGAAGCTTTCGATTCATTTAACAACTTGACACCCTCTAATGTTAAGT
Found at i:60881 original size:27 final size:26
Alignment explanation
Indices: 60832--60882 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
60822 TTTCTTTCTT
*
60832 TTTTTTTTCTTTTTCTGAGTGCTTGA
1 TTTTTTTTCTTTTTCTGACTGCTTGA
60858 TTTTTTTTCTTCTTT-TGGACTGCTT
1 TTTTTTTTCTT-TTTCT-GACTGCTT
60883 TAATTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.06, C:0.14, G:0.14, T:0.67
Consensus pattern (26 bp):
TTTTTTTTCTTTTTCTGACTGCTTGA
Found at i:60888 original size:28 final size:26
Alignment explanation
Indices: 60832--60893 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
60822 TTTCTTTCTT
* *
60832 TTTTTTTTCTTTTTCTGAGTGCTTGA
1 TTTTTTTTCTTTTTCTGACTGCTTAA
60858 TTTTTTTTCTTCTTT-TGGACTGCTTTAA
1 TTTTTTTTCTT-TTTCT-GACTGC-TTAA
*
60886 TTTCTTTT
1 TTTTTTTT
60894 GCTGATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 12 0.40
27 8 0.27
28 10 0.33
ACGTcount: A:0.08, C:0.13, G:0.11, T:0.68
Consensus pattern (26 bp):
TTTTTTTTCTTTTTCTGACTGCTTAA
Found at i:85629 original size:21 final size:21
Alignment explanation
Indices: 85603--85645 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
85593 TTCATTTATT
85603 TTATTATTCCATGAACTTGCA
1 TTATTATTCCATGAACTTGCA
85624 TTATTATTCCATGAACTTGCA
1 TTATTATTCCATGAACTTGCA
85645 T
1 T
85646 AGGGGACGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (21 bp):
TTATTATTCCATGAACTTGCA
Found at i:89686 original size:2 final size:2
Alignment explanation
Indices: 89679--89703 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
89669 ATCACCAACT
89679 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
89704 TGCTACCATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:94139 original size:28 final size:29
Alignment explanation
Indices: 94089--94152 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
94079 TTTCTTTTCT
* * *
94089 TTTCTTTGCTTTTTTTTTAAGTGCTGGAA
1 TTTCTTTGCTTTCTTTTGAAGTGCTGCAA
* *
94118 TTTCTTT-CTTTCTTTTGCAGTGCTTCAA
1 TTTCTTTGCTTTCTTTTGAAGTGCTGCAA
94146 TTTCTTT
1 TTTCTTT
94153 TTTTATGATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 23 0.77
29 7 0.23
ACGTcount: A:0.11, C:0.16, G:0.12, T:0.61
Consensus pattern (29 bp):
TTTCTTTGCTTTCTTTTGAAGTGCTGCAA
Found at i:106841 original size:19 final size:20
Alignment explanation
Indices: 106817--106867 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
106807 CGGCCAAGAG
* *
106817 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
106836 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
*
106856 AATGTATTTTCA
1 CATGTATTTTCA
106868 AAGGAGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:109799 original size:19 final size:20
Alignment explanation
Indices: 109756--109806 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
109746 GAAATCCTTT
*
109756 TGAAAATACATGATTTTTTATA
1 TGAAAATACATGA--TTTTAAA
109778 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
109797 TGAAGATACA
1 TGAAAATACA
109807 AGCTCTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 14 0.52
22 13 0.48
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:113626 original size:22 final size:21
Alignment explanation
Indices: 113596--113636 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
113586 TATCTCCATT
*
113596 TCATCATCAATACCATCAACA
1 TCATCATCAAGACCATCAACA
*
113617 TCATCCATCAAGACTATCAA
1 TCAT-CATCAAGACCATCAA
113637 TTCCGCAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.41, C:0.32, G:0.02, T:0.24
Consensus pattern (21 bp):
TCATCATCAAGACCATCAACA
Found at i:116070 original size:19 final size:20
Alignment explanation
Indices: 116025--116073 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
116015 AACCCCTTTT
**
116025 AAAATACATGATTTTTGATG
1 AAAATACATGATTTTAAATG
116045 AAAATACATGA-TTTAAATG
1 AAAATACATGATTTTAAATG
*
116064 AAGATACATG
1 AAAATACATG
116074 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (20 bp):
AAAATACATGATTTTAAATG
Found at i:116951 original size:19 final size:18
Alignment explanation
Indices: 116923--116966 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
116913 ATCTAATGTA
*
116923 AACATAACATGAGCTAGAT
1 AACATGACATGAGCTA-AT
*
116942 AACATGACATGGGCTAAT
1 AACATGACATGAGCTAAT
116960 AA-ATGAC
1 AACATGAC
116967 TGATACATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.20
Consensus pattern (18 bp):
AACATGACATGAGCTAAT
Found at i:117873 original size:17 final size:17
Alignment explanation
Indices: 117847--117898 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
117837 ATTAGAGTAC
117847 AAAAAG-AAAGAAAAGA
1 AAAAAGTAAAGAAAAGA
117863 AAAAAGTAAAGAAAAGA
1 AAAAAGTAAAGAAAAGA
*
117880 AGGAAA-T-AAGAAAAGA
1 A-AAAAGTAAAGAAAAGA
117896 AAA
1 AAA
117899 GGAATAGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 1 0.03
16 16 0.50
17 12 0.38
18 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (17 bp):
AAAAAGTAAAGAAAAGA
Found at i:118144 original size:12 final size:14
Alignment explanation
Indices: 118114--118145 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
118104 TAATCTTTTC
118114 TTCTACTTTTCCAT
1 TTCTACTTTTCCAT
118128 TTCTA-TTTTCC-T
1 TTCTACTTTTCCAT
118140 TTCTAC
1 TTCTAC
118146 CCTAACCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 6 0.35
14 5 0.29
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.59
Consensus pattern (14 bp):
TTCTACTTTTCCAT
Found at i:119554 original size:21 final size:20
Alignment explanation
Indices: 119511--119561 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
119501 GGCCAAGAGT
*
119511 ATGTATCTTC-TTTAAAATC
1 ATGTATTTTCATTTAAAATC
119530 ATGTATTTTCATTTAAAAGTC
1 ATGTATTTTCATTTAAAA-TC
119551 ATGTATTTTCA
1 ATGTATTTTCA
119562 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 9 0.31
20 7 0.24
21 13 0.45
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (20 bp):
ATGTATTTTCATTTAAAATC
Found at i:126213 original size:19 final size:20
Alignment explanation
Indices: 126189--126244 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 20
126179 ATAGTATATT
*
126189 ATATATGTAATATATTT-GA
1 ATATATGTAATATATTTACA
* *
126208 ATATATAT-ATATTTTTACA
1 ATATATGTAATATATTTACA
126227 ATATATAGTATATATATT
1 ATATAT-GTA-ATATATT
126245 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 7 0.25
19 14 0.50
20 1 0.04
22 6 0.21
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (20 bp):
ATATATGTAATATATTTACA
Found at i:126243 original size:24 final size:25
Alignment explanation
Indices: 126211--126327 Score: 105
Period size: 24 Copynumber: 4.4 Consensus size: 25
126201 TATTTGAATA
*
126211 TATATATATTTTT-ACAATATATAG
1 TATATATATTTTTAAAAATATATAG
126235 TATATATATTATTTTAAAATATATATAG
1 TATATATA-T-TTTTAAAA-ATATATAG
*
126263 TAGTAGGTATATTATTTTAAAATATATA-
1 TA-TA--TATATT-TTTAAAAATATATAG
*
126291 T-TATATATTATTTAAAAATATGATAT
1 TATATATATT-TTTAAAAATAT-ATAG
126317 TATATATATTT
1 TATATATATTT
126328 AAGAATATAT
Statistics
Matches: 79, Mismatches: 3, Indels: 20
0.77 0.03 0.20
Matches are distributed among these distances:
24 25 0.32
25 4 0.05
26 8 0.10
27 10 0.13
28 11 0.14
29 10 0.13
30 7 0.09
31 4 0.05
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (25 bp):
TATATATATTTTTAAAAATATATAG
Found at i:126258 original size:17 final size:17
Alignment explanation
Indices: 126236--126294 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
126226 AATATATAGT
126236 ATATATATTATTTTAAA
1 ATATATATTATTTTAAA
* **
126253 ATATATA-TA--GTAGT
1 ATATATATTATTTTAAA
**
126267 AGGTATATTATTTTAAA
1 ATATATATTATTTTAAA
126284 ATATATATTAT
1 ATATATATTAT
126295 ATATTATTTA
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
14 7 0.24
15 2 0.07
16 2 0.07
17 18 0.62
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (17 bp):
ATATATATTATTTTAAA
Found at i:126274 original size:31 final size:28
Alignment explanation
Indices: 126208--126326 Score: 117
Period size: 28 Copynumber: 4.3 Consensus size: 28
126198 ATATATTTGA
* *
126208 ATATATATATATTTTTACA-ATATATAGT
1 ATATATAT-TATTTTAAAATATATATAGT
126236 ATATATATTATTTTAAAATATATATAGT
1 ATATATATTATTTTAAAATATATATAGT
126264 AGTAGGTATATTATTTT-AAA-ATATATA-T
1 A-TA--TATATTATTTTAAAATATATATAGT
*
126292 -TATATATTA-TTTAAAA-ATATGATATT
1 ATATATATTATTTTAAAATATAT-ATAGT
126318 ATATATATT
1 ATATATATT
126327 TAAGAATATA
Statistics
Matches: 81, Mismatches: 2, Indels: 17
0.81 0.02 0.17
Matches are distributed among these distances:
23 3 0.04
24 14 0.17
25 3 0.04
26 3 0.04
27 16 0.20
28 19 0.23
29 9 0.11
30 3 0.04
31 11 0.14
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.50
Consensus pattern (28 bp):
ATATATATTATTTTAAAATATATATAGT
Found at i:126328 original size:24 final size:23
Alignment explanation
Indices: 126270--126372 Score: 104
Period size: 24 Copynumber: 4.5 Consensus size: 23
126260 TAGTAGTAGG
*
126270 TATAT-TATTTTAAAATATATAT
1 TATATATATTTAAAAATATATAT
126292 TATATATTATTTAAAAATATGATAT
1 TATATA-TATTTAAAAATAT-ATAT
*
126317 TATATATATTTAAGAATATATAT
1 TATATATATTTAAAAATATATAT
* * **
126340 TCGTATAT-CTT-ATCATATATAT
1 T-ATATATATTTAAAAATATATAT
126362 TATATATATTT
1 TATATATATTT
126373 TTATTTTTTA
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
21 5 0.07
22 17 0.25
23 7 0.10
24 29 0.43
25 10 0.15
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (23 bp):
TATATATATTTAAAAATATATAT
Found at i:126380 original size:7 final size:7
Alignment explanation
Indices: 126370--126400 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
126360 ATTATATATA
126370 TTTTTAT
1 TTTTTAT
126377 TTTTTAT
1 TTTTTAT
126384 TTTTTAT
1 TTTTTAT
126391 TTTTTAT
1 TTTTTAT
126398 TTT
1 TTT
126401 GTTGTACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTAT
Found at i:146930 original size:18 final size:17
Alignment explanation
Indices: 146895--146948 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
146885 AATTATATTT
*
146895 TAGTATTTTATAAAATA
1 TAGTATTTTATAATATA
*
146912 TAGTATTTATATATTATA
1 TAGTATTT-TATAATATA
* *
146930 TAATATTTGTATAGTATA
1 TAGTATTT-TATAATATA
146948 T
1 T
146949 TATATAGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 8 0.26
18 23 0.74
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (17 bp):
TAGTATTTTATAATATA
Found at i:146953 original size:18 final size:18
Alignment explanation
Indices: 146909--146953 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
146899 ATTTTATAAA
* *
146909 ATATAGTATTTATATATT
1 ATATAATATTTATATAGT
*
146927 ATATAATATTTGTATAGT
1 ATATAATATTTATATAGT
*
146945 ATATTATAT
1 ATATAATAT
146954 AGTATGTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (18 bp):
ATATAATATTTATATAGT
Found at i:146966 original size:12 final size:12
Alignment explanation
Indices: 146921--146958 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
146911 ATAGTATTTA
*
146921 TATATTATATAA
1 TATATTATATAG
*
146933 TAT-TTGTATAG
1 TATATTATATAG
146944 TATATTATATAG
1 TATATTATATAG
146956 TAT
1 TAT
146959 GTTCTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (12 bp):
TATATTATATAG
Found at i:146970 original size:23 final size:22
Alignment explanation
Indices: 146919--146970 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
146909 ATATAGTATT
*
146919 TATATATTATATAATATTTGTA
1 TATATATTATATAATATTTCTA
*
146941 TAGTATATTATATAGTATGTTCTA
1 TA-TATATTATATAATAT-TTCTA
146965 TATATA
1 TATATA
146971 AAATATTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 2 0.08
23 18 0.69
24 6 0.23
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (22 bp):
TATATATTATATAATATTTCTA
Found at i:147047 original size:34 final size:35
Alignment explanation
Indices: 147005--147078 Score: 116
Period size: 34 Copynumber: 2.1 Consensus size: 35
146995 TTTTAATATT
147005 ATATATATATATAGT-GTA-TATATTATTTTAGAAA
1 ATATATATATATAGTAGTAGTATATTATTTTA-AAA
147039 ATATATATATATAGTAGTAGGTATATTATTTTAAAA
1 ATATATATATATAGTAGTA-GTATATTATTTTAAAA
147075 ATAT
1 ATAT
147079 TTTTTTATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
34 15 0.41
35 3 0.08
36 7 0.19
37 12 0.32
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.46
Consensus pattern (35 bp):
ATATATATATATAGTAGTAGTATATTATTTTAAAA
Found at i:147051 original size:36 final size:36
Alignment explanation
Indices: 146995--147078 Score: 109
Period size: 36 Copynumber: 2.3 Consensus size: 36
146985 ATAAATAATT
* *
146995 TTTTAATATTATATATATATA-TAGT-GTATATATTA
1 TTTTAAAAATATATATATATAGTAGTAG-ATATATTA
*
147030 TTTTAGAAAATATATATATATAGTAGTAGGTATATTA
1 TTTTA-AAAATATATATATATAGTAGTAGATATATTA
147067 TTTTAAAAATAT
1 TTTTAAAAATAT
147079 TTTTTTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
35 5 0.12
36 21 0.49
37 16 0.37
38 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (36 bp):
TTTTAAAAATATATATATATAGTAGTAGATATATTA
Found at i:147134 original size:10 final size:10
Alignment explanation
Indices: 147117--147156 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
147107 TATACTTAAG
147117 AATATATATT
1 AATATATATT
*
147127 AGTATATATT
1 AATATATATT
147137 AATATATA-T
1 AATATATATT
147146 -ATAT-TATT
1 AATATATATT
147154 AAT
1 AAT
147157 TTTTATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
7 2 0.08
8 5 0.19
9 3 0.12
10 16 0.62
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (10 bp):
AATATATATT
Found at i:153352 original size:108 final size:109
Alignment explanation
Indices: 153163--154013 Score: 512
Period size: 108 Copynumber: 7.6 Consensus size: 109
153153 TGTACCGTCT
* * * *
153163 TTTTAAGTTGATGGGGTCATAGAAATCCGACGA-AA-ATAAGATAGGTTAATTACTTAATTTGTT
1 TTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACATAA-ATAGGTTAATTACTTAATTTGTT
** *
153226 ATCAGTATTATCAACATATTAGGTAACGCCTAAAATGTTACTAAA
65 ATCACCATAATCAACATATTAGGTAACGCCTAAAATGTTACTAAA
* * * * *
153271 TTTTAAGTTAATGGAGCCTTAGAAATCCAACGATAACATAACT-GGTTAATTACTAAATTTGTTA
1 TTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACATAAATAGGTTAATTACTTAATTTGTTA
* * * * * **
153335 TCAACCATAAT-AACATATTATGTAACACTTATGTAACATAATAGGTAGTACCT
66 TC-ACCATAATCAACATATTAGGTAACGC----CT-A-A-AAT-GTTACTA-AA
* * *
153388 TTTTAAAGCTGATGGAACCTTAGAAATCCGATGATAA-TTAAATAGG-TAATTACTTAATTTGTT
1 TTTT-AAGCTGATGGAGCCTTAGAAATCCGACGATAACATAAATAGGTTAATTACTTAATTTGTT
** * * *
153451 ATCAGTATTATCAACATATTAGGTAATGCCTAAAATGTTACCAAAA
65 ATCACCATAATCAACATATTAGGTAACGCCTAAAATGTTA-CTAAA
* * * * * * *
153497 GTTTAAGCTGATGGAGCCTTAAAAATTCGACGATAACAT-AATCGATTAATTAATTGATTTGTTA
1 TTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACATAAATAGGTTAATTACTTAATTTGTTA
** * ** * * * *
153561 TCAACCATAAT-AACATATTAAATAGCGTTTATGTAACGTAATAGATAGTGTAT
66 TC-ACCATAATCAACATATTAGGTAACG----CCTAA---AAT-GTTACT-AAA
* * *
153614 TTTTAAAGCTGATGG-GCCCTTAGAAATCTGACGATAATA-AAATAGGTTAATTACTTAATTTGC
1 TTTT-AAGCTGATGGAG-CCTTAGAAATCCGACGATAACATAAATAGGTTAATTACTTAATTTGT
** * * * * *
153677 TATCAGTATTATCAACATATTAGATAACG-TTGAAAATTTTACCAAA
64 TATCACCATAATCAACATATTAGGTAACGCCT-AAAATGTTACTAAA
* * * * *
153723 GTTTAAGCTGATAGAGCCTTAGAAATCCGATGATAACAT-AATCGGTTAATTACTTGATTTGTTA
1 TTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACATAAATAGGTTAATTACTTAATTTGTTA
* * * * * *
153787 TCAACCATAAT-AACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCACCT
66 TC-ACCATAATCAACATATTAGGTAACGCCTA--AAATGT--TA-CTA--A--A
* * * *
153840 TTTTAAAACTGAT-GAGACCTTAGAAATCTGACGATAACA-AAATATGTTAATTACTTAATTTAT
1 TTTT-AAGCTGATGGAG-CCTTAGAAATCCGACGATAACATAAATAGGTTAATTACTTAATTTGT
* ** * *
153903 TATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTACCAAA
64 TATCACCATAATCAACATATTAGGTAACGCCTAAAATGTTACTAAA
* * * * * * *
153949 ATTTAAGCTAATTGAGCCTTAGAAATCTGAAGATAACAT-AATCA-GTTAATTATTTGATTTGTT
1 TTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACATAAAT-AGGTTAATTACTTAATTTGTT
154012 AT
65 AT
154014 TAACCTAAAA
Statistics
Matches: 562, Mismatches: 128, Indels: 106
0.71 0.16 0.13
Matches are distributed among these distances:
108 212 0.38
109 64 0.11
110 18 0.03
111 5 0.01
112 4 0.01
113 8 0.01
114 5 0.01
115 4 0.01
116 17 0.03
117 65 0.12
118 160 0.28
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (109 bp):
TTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACATAAATAGGTTAATTACTTAATTTGTTA
TCACCATAATCAACATATTAGGTAACGCCTAAAATGTTACTAAA
Found at i:153579 original size:226 final size:226
Alignment explanation
Indices: 153079--154018 Score: 1146
Period size: 226 Copynumber: 4.2 Consensus size: 226
153069 ATATTGAGTT
* * **** * *
153079 TAACATAATCGGTTAATTACTAGAAACATTATCAATCATAATAACATATTAGTTAGCGCTTATAT
1 TAACATAATCGATTAATTACTTGATTTGTTATCAACCATAATAACATATTAG-TAGCGCTTATGT
* * *** * * *
153144 AACATAATA--T-GTACCGTCTTTTTAAGTTGATGGGGTCATAGAAATCCGACGAAAATAAGATA
65 AACATAATAGGTAGTACC-T-TTTTAAAGCTGATGGAACCTTAGAAATCCGACGATAATAAAATA
*
153206 GGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACGCCTAAAATGTTA-CTAA
128 GGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACGCCTAAAATGTTACCAAA
* * *
153270 ATTTTAAGTTAATGGAGCCTTAGAAATCCAACGA
193 AGTTTAAGCTAATGGAGCCTTAGAAATCCGACGA
* ** * *
153304 TAACATAA-CTGGTTAATTACTAAATTTGTTATCAACCATAATAACATATTATGTAACACTTATG
1 TAACATAATC-GATTAATTACTTGATTTGTTATCAACCATAATAACATATTA-GTAGCGCTTATG
* *
153368 TAACATAATAGGTAGTACCTTTTTAAAGCTGATGGAACCTTAGAAATCCGATGATAATTAAATAG
64 TAACATAATAGGTAGTACCTTTTTAAAGCTGATGGAACCTTAGAAATCCGACGATAATAAAATAG
*
153433 G-TAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAATGCCTAAAATGTTACCAAAA
129 GTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACGCCTAAAATGTTACCAAAA
* * *
153497 GTTTAAGCTGATGGAGCCTTAAAAATTCGACGA
194 GTTTAAGCTAATGGAGCCTTAGAAATCCGACGA
* * *
153530 TAACATAATCGATTAATTAATTGATTTGTTATCAACCATAATAACATATTAAATAGCGTTTATGT
1 TAACATAATCGATTAATTACTTGATTTGTTATCAACCATAATAACATATT-AGTAGCGCTTATGT
* * *** ** *
153595 AACGTAATAGATAGTGTATTTTTAAAGCTGATGGGCCCTTAGAAATCTGACGATAATAAAATAGG
65 AACATAATAGGTAGTACCTTTTTAAAGCTGATGGAACCTTAGAAATCCGACGATAATAAAATAGG
* * * *
153660 TTAATTACTTAATTTGCTATCAGTATTATCAACATATTAGATAACG-TTGAAAATTTTACC-AAA
130 TTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACGCCT-AAAATGTTACCAAAA
* * *
153723 GTTTAAGCTGATAGAGCCTTAGAAATCCGATGA
194 GTTTAAGCTAATGGAGCCTTAGAAATCCGACGA
*
153756 TAACATAATCGGTTAATTACTTGATTTGTTATCAACCATAATAACATATTAGGTAGCGCTTATGT
1 TAACATAATCGATTAATTACTTGATTTGTTATCAACCATAATAACATATTA-GTAGCGCTTATGT
* * * * * *
153821 AACGTAATAGGTAGCACCTTTTTAAAACTGAT-GAGACCTTAGAAATCTGACGATAACAAAATAT
65 AACATAATAGGTAGTACCTTTTTAAAGCTGATGGA-ACCTTAGAAATCCGACGATAATAAAATAG
* *
153885 GTTAATTACTTAATTTATTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTACCAAAA
129 GTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACGCCTAAAATGTTACCAAAA
* * *
153950 -TTTAAGCTAATTGAGCCTTAGAAATCTGAAGA
194 GTTTAAGCTAATGGAGCCTTAGAAATCCGACGA
* *
153982 TAACATAATC-AGTTAATTATTTGATTTGTTATTAACC
1 TAACATAATCGA-TTAATTACTTGATTTGTTATCAACC
154019 TAAAATTAAG
Statistics
Matches: 619, Mismatches: 81, Indels: 29
0.85 0.11 0.04
Matches are distributed among these distances:
224 1 0.00
225 119 0.19
226 434 0.70
227 60 0.10
228 5 0.01
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (226 bp):
TAACATAATCGATTAATTACTTGATTTGTTATCAACCATAATAACATATTAGTAGCGCTTATGTA
ACATAATAGGTAGTACCTTTTTAAAGCTGATGGAACCTTAGAAATCCGACGATAATAAAATAGGT
TAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACGCCTAAAATGTTACCAAAAGT
TTAAGCTAATGGAGCCTTAGAAATCCGACGA
Found at i:153650 original size:118 final size:116
Alignment explanation
Indices: 153501--153905 Score: 364
Period size: 118 Copynumber: 3.5 Consensus size: 116
153491 CCAAAAGTTT
* * *
153501 AAGCTGATGGAGCCTTAAAAAT-TCGACGATAACATAATCGATTAATTAATTGATTTGTTATCAA
1 AAGCTGAT-GAGCCTTAGAAATCT-GACGATAACATAATCGGTTAATTACTTGATTTGTTATCAA
* ***
153565 CCATAATAACATATTAAATAGCGTTTATGTAACGTAATAGATAGTGTATTTTTA
64 CCATAATAACATATTAGATAGCG-TTATGTAACGTAATAGATAGCAAATTTTTA
* * * * * * *
153619 AAGCTGATGGGCCCTTAGAAATCTGACGATAATAAAATAGGTTAATTACTTAATTTGCTATC-AG
1 AAGCTGATGAG-CCTTAGAAATCTGACGATAACATAATCGGTTAATTACTTGATTTGTTATCAAC
* * * ** * *
153683 TATTATCAACATATTAGATAACG-T-TG-AA---AAT-TTTACCAAA-GTTT-
65 CATAAT-AACATATTAGATAGCGTTATGTAACGTAATAGATAGCAAATTTTTA
* *
153727 AAGCTGATAGAGCCTTAGAAATCCGATGATAACATAATCGGTTAATTACTTGATTTGTTATCAAC
1 AAGCTGAT-GAGCCTTAGAAATCTGACGATAACATAATCGGTTAATTACTTGATTTGTTATCAAC
* * **
153792 CATAATAACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCACCTTTTTA
65 CATAATAACATATTAGATAGCG-TTATGTAACGTAATAGATAGCAAATTTTTA
* * ** * *
153845 AAACTGATGAGACCTTAGAAATCTGACGATAACAAAATATGTTAATTACTTAATTTATTAT
1 AAGCTGATGAG-CCTTAGAAATCTGACGATAACATAATCGGTTAATTACTTGATTTGTTAT
153906 TAGTATTATC
Statistics
Matches: 223, Mismatches: 48, Indels: 32
0.74 0.16 0.11
Matches are distributed among these distances:
108 65 0.29
109 10 0.04
110 4 0.02
111 5 0.02
112 2 0.01
114 2 0.01
115 5 0.02
116 5 0.02
117 13 0.06
118 111 0.50
119 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (116 bp):
AAGCTGATGAGCCTTAGAAATCTGACGATAACATAATCGGTTAATTACTTGATTTGTTATCAACC
ATAATAACATATTAGATAGCGTTATGTAACGTAATAGATAGCAAATTTTTA
Found at i:154891 original size:229 final size:229
Alignment explanation
Indices: 154490--154940 Score: 681
Period size: 229 Copynumber: 2.0 Consensus size: 229
154480 AGTAAAACGG
* * *
154490 TTTCCTTCAAAGAAATGAGAGTAGTCTCTACTACAAGTATCGATACATTTATATAACCTACAATA
1 TTTCCTTCAAAGAAATGAGAATAGTCTCTACTACAAGTATCGATACATTTATACAACATACAATA
* *
154555 TCATTTTGTACCTATAATATTATATAAAAGTATTAATATTTATTTTCTACCTAAAATATCACTTT
66 TCATTTTCTACCTATAATATTATATAAAAGTATCAATATTTATTTTCTACCTAAAATATCACTTT
* *
154620 CTAACTGTAATCGGTCTCAAATTATTCTTTACTTCAAAAACCCCAAACCCATAAACATAATCCCT
131 ATAACTGTAATCGGTCTCAAATTATTCTTTACTTCAAAAACCCCAAACCCATAAACATAACCCCT
*
154685 ATTTTTGAATATTGTAATACTAAAAAAAATACGA
196 ATTTTTGAATACTGTAATACTAAAAAAAATACGA
* * * *
154719 TTTCCTTCAAAGGAATGAGAATATTCTCTACTACAAGTA-CTGGTACCTTTATACAACATACAAT
1 TTTCCTTCAAAGAAATGAGAATAGTCTCTACTACAAGTATC-GATACATTTATACAACATACAAT
* *
154783 ATCATTTTCTACCTATAATATTATATAAAAGTATCGATATTTATTTTCTACCTATAATATCACTT
65 ATCATTTTCTACCTATAATATTATATAAAAGTATCAATATTTATTTTCTACCTAAAATATCACTT
* * * * *
154848 TATAATTGTAGTCGGTCTCAAA-TATTTCTTTACTTCGAAAACCCCAAACTCATAAACCTAACCC
130 TATAACTGTAATCGGTCTCAAATTA-TTCTTTACTTCAAAAACCCCAAACCCATAAACATAACCC
* *
154912 CTATTTTTTATTACTGTAATACTAAAAAA
194 CTATTTTTGAATACTGTAATACTAAAAAA
154941 TAGGGTTTCG
Statistics
Matches: 199, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
228 3 0.02
229 196 0.98
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.37
Consensus pattern (229 bp):
TTTCCTTCAAAGAAATGAGAATAGTCTCTACTACAAGTATCGATACATTTATACAACATACAATA
TCATTTTCTACCTATAATATTATATAAAAGTATCAATATTTATTTTCTACCTAAAATATCACTTT
ATAACTGTAATCGGTCTCAAATTATTCTTTACTTCAAAAACCCCAAACCCATAAACATAACCCCT
ATTTTTGAATACTGTAATACTAAAAAAAATACGA
Found at i:155373 original size:21 final size:21
Alignment explanation
Indices: 155349--155400 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
155339 ATATTGTCAT
*
155349 GTATCGATACATGTGTCTAAG
1 GTATCGATACATGTGTCTAAA
155370 GTATCGATACATGTGTCTAAA
1 GTATCGATACATGTGTCTAAA
155391 GTATCGATAC
1 GTATCGATAC
155401 TTTGTAGGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (21 bp):
GTATCGATACATGTGTCTAAA
Found at i:155647 original size:20 final size:20
Alignment explanation
Indices: 155622--155724 Score: 79
Period size: 20 Copynumber: 5.1 Consensus size: 20
155612 ATAGCTCTTT
155622 ACCGGTTTTGTCAAATTTCA
1 ACCGGTTTTGTCAAATTTCA
155642 ACCGGTTTTGTC-AATTTCCA
1 ACCGGTTTTGTCAAATTT-CA
*
155662 ATCC-GTTTTGTCCAA-TTCA
1 A-CCGGTTTTGTCAAATTTCA
* * *
155681 TTAACTGTTTTGTCAAA-TTGA
1 --ACCGGTTTTGTCAAATTTCA
* *
155702 ATCCGGATTTCTCAAATTTCA
1 A-CCGGTTTTGTCAAATTTCA
155723 AC
1 AC
155725 ATGTTATATT
Statistics
Matches: 67, Mismatches: 8, Indels: 16
0.74 0.09 0.18
Matches are distributed among these distances:
19 8 0.12
20 37 0.55
21 22 0.33
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (20 bp):
ACCGGTTTTGTCAAATTTCA
Found at i:157344 original size:22 final size:23
Alignment explanation
Indices: 157312--157531 Score: 95
Period size: 22 Copynumber: 10.1 Consensus size: 23
157302 CCCCCAAAAA
157312 ATACTTTATATTTA-ATACTTAT
1 ATACTTTATATTTATATACTTAT
* *
157334 ATATTTTATA-TTATATATTTAT
1 ATACTTTATATTTATATACTTAT
*
157356 ATACTTTATA-TTATATGCTTAT
1 ATACTTTATATTTATATACTTAT
* *
157378 ACACTTTAGTCTTTATA-A--T-T
1 ATACTTTA-TATTTATATACTTAT
157398 ATACTTTATA--TATATAC--AT
1 ATACTTTATATTTATATACTTAT
*
157417 ATA---TATA-TAATATACTTAT
1 ATACTTTATATTTATATACTTAT
*
157436 AT--TTTATATTATTATATATGTATAT
1 ATACTTTATA-T-TTATATA-CT-TAT
* * *
157461 ATACCTTATA-CTAAAT-CTTTAT
1 ATACTTTATATTTATATAC-TTAT
* * *
157483 AAAC-CTATATATATATA-TATAT
1 ATACTTTATATTTATATACT-TAT
*
157505 ATACTTTATAGTTTATATACATAT
1 ATACTTTATA-TTTATATACTTAT
157529 ATA
1 ATA
157532 TATATACATA
Statistics
Matches: 148, Mismatches: 25, Indels: 48
0.67 0.11 0.22
Matches are distributed among these distances:
16 4 0.03
17 10 0.07
18 1 0.01
19 9 0.06
20 12 0.08
21 9 0.06
22 58 0.39
23 12 0.08
24 23 0.16
25 5 0.03
27 5 0.03
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (23 bp):
ATACTTTATATTTATATACTTAT
Found at i:157345 original size:7 final size:7
Alignment explanation
Indices: 157316--157367 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
157306 CAAAAAATAC
157316 TTTATAT
1 TTTATAT
*
157323 TTAATACT
1 TTTATA-T
*
157331 TATATAT
1 TTTATAT
157338 TTTATAT
1 TTTATAT
*
157345 TATATAT
1 TTTATAT
*
157352 TTATATAC
1 TT-TATAT
157360 TTTATAT
1 TTTATAT
157367 T
1 T
157368 ATATGCTTAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
7 24 0.69
8 11 0.31
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTATAT
Found at i:157357 original size:8 final size:8
Alignment explanation
Indices: 157318--157644 Score: 63
Period size: 8 Copynumber: 42.4 Consensus size: 8
157308 AAAAATACTT
157318 TATATTTA
1 TATATTTA
*
157326 -ATACTTA
1 TATATTTA
157333 TATATTT-
1 TATATTTA
157340 TATA-TTA
1 TATATTTA
157347 TATATTTA
1 TATATTTA
*
157355 TATACTT-
1 TATATTTA
157362 TATA-TTA
1 TATATTTA
**
157369 TATGCTTA
1 TATATTTA
*
157377 TACACTTTA
1 TATA-TTTA
* *
157386 -GTCTTTA
1 TATATTTA
157393 TA-A-TTA
1 TATATTTA
*
157399 TA-CTTTA
1 TATATTTA
157406 TATA--TA
1 TATATTTA
* *
157412 TACATATA
1 TATATTTA
*
157420 TATA-TAA
1 TATATTTA
*
157427 TATACTTA
1 TATATTTA
157435 TAT-TTTA
1 TATATTTA
157442 TAT-TATTA
1 TATAT-TTA
157450 TATATGTATA
1 TATAT-T-TA
**
157460 TATACCT-
1 TATATTTA
*
157467 TATA-CTA
1 TATATTTA
* *
157474 AATCTTTA
1 TATATTTA
* **
157482 TAAACCTA
1 TATATTTA
157490 TATA--TA
1 TATATTTA
*
157496 TATATATA
1 TATATTTA
157504 TATACTTTA
1 TATA-TTTA
157513 TAGT-TTATA
1 TA-TATT-TA
* *
157522 TACATATA
1 TATATTTA
*
157530 TATATATA
1 TATATTTA
* *
157538 CATACTTA
1 TATATTTA
157546 TACT-TTATA
1 TA-TATT-TA
* *
157555 TATATATG
1 TATATTTA
*
157563 TACACTTTA
1 TATA-TTTA
*
157572 TATACTTA
1 TATATTTA
157580 TATACTTTA
1 TATA-TTTA
*
157589 TATACTTA
1 TATATTTA
157597 TATACTTTA
1 TATA-TTTA
* *
157606 -GTCTTTA
1 TATATTTA
157613 TA-ATTT-
1 TATATTTA
157619 TAT-TTTA
1 TATATTTA
*
157626 TATATATA
1 TATATTTA
*
157634 TATATATA
1 TATATTTA
157642 TAT
1 TAT
157645 TATAATTGTT
Statistics
Matches: 230, Mismatches: 56, Indels: 66
0.65 0.16 0.19
Matches are distributed among these distances:
6 27 0.12
7 58 0.25
8 102 0.44
9 36 0.16
10 7 0.03
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (8 bp):
TATATTTA
Found at i:157400 original size:44 final size:42
Alignment explanation
Indices: 157312--157419 Score: 105
Period size: 44 Copynumber: 2.5 Consensus size: 42
157302 CCCCCAAAAA
* * *
157312 ATACTTTATATT-TAATACTTATATATTTTATATTATATATTTAT
1 ATACTTTATATTAT-ATACTTATACACTTTATATTATATA-AT-T
* *
157356 ATACTTTATATTATATGCTTATACACTTTAGTCTT-TATAATT
1 ATACTTTATATTATATACTTATACACTTTA-TATTATATAATT
*
157398 ATACTTTATA-TATATACATATA
1 ATACTTTATATTATATACTTATA
157420 TATATAATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
41 10 0.18
42 11 0.20
43 1 0.02
44 29 0.53
45 4 0.07
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (42 bp):
ATACTTTATATTATATACTTATACACTTTATATTATATAATT
Found at i:157471 original size:40 final size:37
Alignment explanation
Indices: 157390--157644 Score: 160
Period size: 36 Copynumber: 7.0 Consensus size: 37
157380 ACTTTAGTCT
* * *
157390 TTATAATTATACTTTATATA-TATACATATATATATA
1 TTATACTTATATTTTATATACTATATATATATATATA
* * *
157426 ATATACTTATATTTTATATTATTATATATGTATATATA
1 TTATACTTATATTTTATA-TACTATATATATATATATA
* *
157464 CCTTATAC-TAAATCTTTATAAACCTATATATATATATATA
1 --TTATACTTATAT-TTTATATA-CTATATATATATATATA
*
157504 -TATACTTTATAGTTTATATAC---ATATATATATATA
1 TTATAC-TTATATTTTATATACTATATATATATATATA
* * * *
157538 -CATACTTATACTTTATATA-TATATGTACACT-T-TA
1 TTATACTTATATTTTATATACTATATATATA-TATATA
* *
157572 -TATACTTATATACTTTATATACT-TATATACTTTAGTCT-
1 TTATACTTATAT--TTTATATACTATATATA-TATA-TATA
* *
157610 TTATAATTTTATTTTATATA-TATATATATATATAT
1 TTATACTTATATTTTATATACTATATATATATATAT
157645 TATAATTGTT
Statistics
Matches: 172, Mismatches: 26, Indels: 43
0.71 0.11 0.18
Matches are distributed among these distances:
33 13 0.08
34 28 0.16
35 8 0.05
36 34 0.20
37 23 0.13
38 22 0.13
39 18 0.10
40 26 0.15
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (37 bp):
TTATACTTATATTTTATATACTATATATATATATATA
Found at i:157575 original size:2 final size:2
Alignment explanation
Indices: 157404--157561 Score: 69
Period size: 2 Copynumber: 79.5 Consensus size: 2
157394 AATTATACTT
* *
157404 TA TA TA TA TA CA TA TA TA TA TA -A TA TA CT- TA TA T- TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* ** * * *
157444 T- TA T- TA TA TA TG TA TA TA TA CC T- TA TA CTA AA TC TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* ** * * *
157484 AA CC TA TA TA TA TA TA TA TA TA TA CTT TA TA GTT TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
* *
157528 TA TA TA TA TA CA TA CT- TA TA CTT TA TA TA TA TA T
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA T
157562 GTACACTTTA
Statistics
Matches: 115, Mismatches: 28, Indels: 26
0.68 0.17 0.15
Matches are distributed among these distances:
1 7 0.06
2 101 0.88
3 7 0.06
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:157600 original size:19 final size:19
Alignment explanation
Indices: 157544--157600 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
157534 TATACATACT
*
157544 TATACTTTATATA-TATATG
1 TATACTTTATATACT-TATA
*
157563 TACACTTTATATAC-T-TA
1 TATACTTTATATACTTATA
157580 TATACTTTATATACTTATA
1 TATACTTTATATACTTATA
157599 TA
1 TA
157601 CTTTAGTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 14 0.44
18 2 0.06
19 16 0.50
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.51
Consensus pattern (19 bp):
TATACTTTATATACTTATA
Found at i:158495 original size:25 final size:26
Alignment explanation
Indices: 158461--158520 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
158451 CATCCCTAGG
158461 GAGAGGGAGAGA-GGGGTAGGGGAAC
1 GAGAGGGAGAGAGGGGGTAGGGGAAC
158486 GAGAGGGAGAGAGGGGGTAGGGGAAC
1 GAGAGGGAGAGAGGGGGTAGGGGAAC
158512 GAGAGGGAG
1 GAGAGGGAG
158521 GGGAAGAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 12 0.35
26 22 0.65
ACGTcount: A:0.32, C:0.03, G:0.62, T:0.03
Consensus pattern (26 bp):
GAGAGGGAGAGAGGGGGTAGGGGAAC
Found at i:160057 original size:20 final size:21
Alignment explanation
Indices: 160032--160070 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
160022 TGATCATGAT
160032 TTGATT-CAAAGAAAATAAAA
1 TTGATTACAAAGAAAATAAAA
*
160052 TTGATTACAAAGAACATAA
1 TTGATTACAAAGAAAATAA
160071 GTAATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.26
Consensus pattern (21 bp):
TTGATTACAAAGAAAATAAAA
Found at i:167259 original size:51 final size:51
Alignment explanation
Indices: 167159--167255 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 51
167149 TAAATCAAAA
* * * * *
167159 GAAGGAAATATTAAATTTTAAAAATGTTATATAAAAAATAAATAAAATAAT
1 GAAGAAAATATTAAATTTCAAAAAAGTAAAATAAAAAATAAATAAAATAAT
*
167210 GAAGAAAATATTAAATTTCAAAAAAGTAAAATAATAAAT-AATAAAA
1 GAAGAAAATATTAAATTTCAAAAAAGTAAAATAAAAAATAAATAAAA
167256 ATAAAAGATA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
50 7 0.17
51 33 0.82
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (51 bp):
GAAGAAAATATTAAATTTCAAAAAAGTAAAATAAAAAATAAATAAAATAAT
Found at i:167274 original size:22 final size:23
Alignment explanation
Indices: 167240--167291 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
167230 AAAAAGTAAA
*
167240 ATAATAAATAATAAAAATAAAAG
1 ATAATAAAAAATAAAAATAAAAG
*
167263 ATAA-AAAAAATAAAAATAAAAC
1 ATAATAAAAAATAAAAATAAAAG
167285 A-AATAAA
1 ATAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 2 0.08
22 20 0.77
23 4 0.15
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (23 bp):
ATAATAAAAAATAAAAATAAAAG
Found at i:167288 original size:15 final size:14
Alignment explanation
Indices: 167237--167291 Score: 65
Period size: 16 Copynumber: 3.6 Consensus size: 14
167227 TCAAAAAAGT
167237 AAAATAATAAATAATA
1 AAAATAA-AAATAA-A
167253 AAAATAAAAGATAAAA
1 AAAATAAAA-AT-AAA
167269 AAAATAAAAATAAA
1 AAAATAAAAATAAA
167283 ACAAATAAA
1 A-AAATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 4 0.11
15 11 0.31
16 19 0.53
17 2 0.06
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (14 bp):
AAAATAAAAATAAA
Done.