Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002699.1 Hibiscus syriacus cultivar Beakdansim tig00005574_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: 48826
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1973 original size:16 final size:16
Alignment explanation
Indices: 1952--1982 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1942 GGGTCTATGC
*
1952 GGTCCTTTGGGACATG
1 GGTCCTTCGGGACATG
1968 GGTCCTTCGGGACAT
1 GGTCCTTCGGGACAT
1983 ATGTGTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (16 bp):
GGTCCTTCGGGACATG
Found at i:2309 original size:22 final size:23
Alignment explanation
Indices: 2267--2311 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
2257 TGGGATGTAG
*
2267 ATGAATATGTAAGGTATATATGA
1 ATGAATATGCAAGGTATATATGA
2290 ATGAATAT-CAAGG-ATCATATGA
1 ATGAATATGCAAGGTAT-ATATGA
2312 TGATGTAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 10 0.50
23 8 0.40
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.31
Consensus pattern (23 bp):
ATGAATATGCAAGGTATATATGA
Found at i:2973 original size:23 final size:23
Alignment explanation
Indices: 2901--2976 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
2891 AGAACGTCCT
* *
2901 GAAGGACCACATAGTATTATCCC
1 GAAGGACCACGTAGAATTATCCC
* * *
2924 GAAGGA-CGCGTAGAAATGTCCC
1 GAAGGACCACGTAGAATTATCCC
* *
2946 TAAGGACCACGTAGAATTATTCC
1 GAAGGACCACGTAGAATTATCCC
2969 GAAGGACC
1 GAAGGACC
2977 GCATAGAACC
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 16 0.39
23 25 0.61
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (23 bp):
GAAGGACCACGTAGAATTATCCC
Found at i:8226 original size:38 final size:38
Alignment explanation
Indices: 8184--8307 Score: 121
Period size: 38 Copynumber: 3.3 Consensus size: 38
8174 TTAGAAAACA
* * *
8184 AGTTTTGAAAATATAT-ATATATATATATATATATGTAT
1 AGTTTTGAAAATATATCAAAAATATATATATAT-TATAT
* *
8222 AGTTTTGAAAATATTTCAAAAATATATATGTATTATAT
1 AGTTTTGAAAATATATCAAAAATATATATATATTATAT
* * *
8260 AGTTTGGAAAA-ATTTGAAAACATATATA-ATA-TATAT
1 AGTTTTGAAAATATATCAAAA-ATATATATATATTATAT
8296 AGTTTTTGAAAA
1 AG-TTTTGAAAA
8308 CATTTTTGAA
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
36 7 0.09
37 18 0.24
38 36 0.49
39 13 0.18
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.43
Consensus pattern (38 bp):
AGTTTTGAAAATATATCAAAAATATATATATATTATAT
Found at i:8295 original size:36 final size:38
Alignment explanation
Indices: 8206--8332 Score: 145
Period size: 37 Copynumber: 3.3 Consensus size: 38
8196 ATATATATAT
* * *
8206 ATATATATATATGTATAGTTTTGAAAATATTTCAAAA-
1 ATATATATATATATATAGTTTTGAAAACATTTGAAAAC
* *
8243 ATATATATGTATTATATAGTTTGGAAAA-ATTTGAAAAC
1 ATATATATATA-TATATAGTTTTGAAAACATTTGAAAAC
8281 ATATATA-ATATATATAGTTTTTGAAAACATTTTTGAAAAC
1 ATATATATATATATATAG-TTTTGAAAACA--TTTGAAAAC
8321 ATATAT-TATATA
1 ATATATATATATA
8333 GTTTTTGGAA
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
36 7 0.09
37 28 0.36
38 22 0.29
40 20 0.26
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (38 bp):
ATATATATATATATATAGTTTTGAAAACATTTGAAAAC
Found at i:8315 original size:12 final size:12
Alignment explanation
Indices: 8298--8322 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8288 ATATATATAG
8298 TTTTTGAAAACA
1 TTTTTGAAAACA
8310 TTTTTGAAAACA
1 TTTTTGAAAACA
8322 T
1 T
8323 ATATTATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:8333 original size:36 final size:36
Alignment explanation
Indices: 8252--8404 Score: 172
Period size: 37 Copynumber: 4.2 Consensus size: 36
8242 AATATATATG
*
8252 TATTATATAG-TTTGGAAAA-A--TTTGAAAACATATA
1 TATTATATAGTTTTTGAAAACATTTTTGAAAAC--ATA
8286 TAATATATATAGTTTTTGAAAACATTTTTGAAAACATA
1 T-AT-TATATAGTTTTTGAAAACATTTTTGAAAACATA
*
8324 TATTATATAGTTTTTGGAAAACATTTTTTAAAACATA
1 TATTATATAGTTTTT-GAAAACATTTTTGAAAACATA
* * *
8361 TATTATATGGTTTTTTAAAACATTTTTAAAAAACATA
1 TATTATATAGTTTTTGAAAACATTTTT-GAAAACATA
8398 TA-TATAT
1 TATTATAT
8405 TATATTGTTT
Statistics
Matches: 106, Mismatches: 5, Indels: 14
0.85 0.04 0.11
Matches are distributed among these distances:
34 1 0.01
35 2 0.02
36 35 0.33
37 54 0.51
38 5 0.05
40 9 0.08
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (36 bp):
TATTATATAGTTTTTGAAAACATTTTTGAAAACATA
Found at i:8481 original size:2 final size:2
Alignment explanation
Indices: 8476--8530 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
8466 CATATCGTAA
8476 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
8518 -T TT AT AT TT AT AT
1 AT AT AT AT AT AT AT
8531 TTTATTATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:8545 original size:14 final size:15
Alignment explanation
Indices: 8511--8555 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
8501 TATATATATA
8511 TATATATTTTA-TAT
1 TATATATTTTATTAT
8525 T-TATATTTTATTAT
1 TATATATTTTATTAT
8539 TAT-TA-TTTATTTAT
1 TATATATTTTA-TTAT
8553 TAT
1 TAT
8556 GTTTTTTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 13 0.46
14 14 0.50
15 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATATATTTTATTAT
Found at i:13967 original size:8 final size:8
Alignment explanation
Indices: 13942--13993 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
13932 AGATATAGAG
13942 ATAAAAAA
1 ATAAAAAA
* **
13950 ATCATTAA
1 ATAAAAAA
13958 ATAAAAAA
1 ATAAAAAA
*
13966 ATATAAAA
1 ATAAAAAA
*
13974 ATAAATAA
1 ATAAAAAA
13982 ATAAATAAA
1 ATAAA-AAA
13991 ATA
1 ATA
13994 GAGAGAAGAA
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
8 28 0.85
9 5 0.15
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (8 bp):
ATAAAAAA
Found at i:13982 original size:24 final size:25
Alignment explanation
Indices: 13946--13993 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
13936 ATAGAGATAA
* *
13946 AAAAATCATTAAATAAA-AAAATAT
1 AAAAATAAATAAATAAATAAAATAT
13970 AAAAATAAATAAATAAATAAAATA
1 AAAAATAAATAAATAAATAAAATA
13994 GAGAGAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (25 bp):
AAAAATAAATAAATAAATAAAATAT
Found at i:15325 original size:12 final size:11
Alignment explanation
Indices: 15273--15356 Score: 55
Period size: 12 Copynumber: 6.9 Consensus size: 11
15263 CCCTGCAACA
15273 AAAT-AAAAAT
1 AAATAAAAAAT
15283 AAA-AATAAAAT
1 AAATAA-AAAAT
*
15294 AAGTAATAATAAT
1 AAATAA-AA-AAT
15307 AATAATAAATAAAT
1 -A-AATAAA-AAAT
15321 AAATAACAAAAGGT
1 AAATAA-AAAA--T
15335 AAATAAAAAAT
1 AAATAAAAAAT
15346 AAACTAAAAAA
1 AAA-TAAAAAA
15357 ATAGTTTCCA
Statistics
Matches: 61, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
10 4 0.07
11 11 0.18
12 20 0.33
13 9 0.15
14 12 0.20
15 5 0.08
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:15325 original size:24 final size:25
Alignment explanation
Indices: 15273--15326 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
15263 CCCTGCAACA
*
15273 AAATAAAAATAAAAATAAAATAAGT
1 AAATAAAAATAAAAATAAAATAAAT
* *
15298 -AATAATAATAATAAT-AAATAAAT
1 AAATAAAAATAAAAATAAAATAAAT
15321 AAATAA
1 AAATAA
15327 CAAAAGGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (25 bp):
AAATAAAAATAAAAATAAAATAAAT
Found at i:15465 original size:29 final size:29
Alignment explanation
Indices: 15422--15478 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
15412 ATTATATGTT
*
15422 TTTTTAAAAACGTTTTCAAAATTATATAG
1 TTTTTAAAAACGTTTTCAAAACTATATAG
* *
15451 TTTTTAAAAATGTTTTTAAAACTATATA
1 TTTTTAAAAACGTTTTCAAAACTATATA
15479 TTATAAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (29 bp):
TTTTTAAAAACGTTTTCAAAACTATATAG
Found at i:15552 original size:30 final size:28
Alignment explanation
Indices: 15525--15581 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 28
15515 AGATATATGT
15525 TCTTCAAAATGTTTTTTAAAAACTATATATA
1 TCTTCAAAATG---TTTAAAAACTATATATA
*
15556 TTTTCAAAATGTTTAAAAACTATATA
1 TCTTCAAAATGTTTAAAAACTATATA
15582 ATATATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 15 0.60
31 10 0.40
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (28 bp):
TCTTCAAAATGTTTAAAAACTATATATA
Found at i:15629 original size:38 final size:38
Alignment explanation
Indices: 15548--15741 Score: 184
Period size: 36 Copynumber: 5.2 Consensus size: 38
15538 TTTTAAAAAC
* * *
15548 TATATATATTTTCAAAAT-GTTTAAAAACTATATA--A
1 TATATATTTTTTAAAAATATTTTAAAAACTATATATTA
*
15583 TATATATTTTTTAAAAATATTTTAAAAATTATATATTA
1 TATATATTTTTTAAAAATATTTTAAAAACTATATATTA
* * *
15621 TAT-T-TATTTTCAAAATATTTTAAAAACTATATAATA
1 TATATATTTTTTAAAAATATTTTAAAAACTATATATTA
* * * * *
15657 TATAAATGTTTTCAAACATGTTTTCAAAACTATATATTA
1 TATATAT-TTTTTAAAAATATTTTAAAAACTATATATTA
** *
15696 TATATAGGTTTTAAAAATATTTT-TAAACTATAATATATA
1 TATATATTTTTTAAAAATATTTTAAAAACTAT-ATAT-TA
15735 TATATAT
1 TATATAT
15742 ATATATATAT
Statistics
Matches: 127, Mismatches: 24, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
35 16 0.13
36 45 0.35
37 8 0.06
38 21 0.17
39 37 0.29
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.47
Consensus pattern (38 bp):
TATATATTTTTTAAAAATATTTTAAAAACTATATATTA
Found at i:15735 original size:2 final size:2
Alignment explanation
Indices: 15724--15801 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
15714 ATTTTTAAAC
15724 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15765 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15802 GAGACGAAAA
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15739 original size:39 final size:39
Alignment explanation
Indices: 15548--15741 Score: 192
Period size: 39 Copynumber: 5.2 Consensus size: 39
15538 TTTTAAAAAC
* * *
15548 TATATATATTTTCAAAAT-GTTTAAAAACTATATA-ATA
1 TATATATGTTTTAAAAATATTTTAAAAACTATATATATA
15585 TATAT-T-TTTTAAAAATATTTTAAAAA-T-TATATAT-
1 TATATATGTTTTAAAAATATTTTAAAAACTATATATATA
* * *
15619 TATATTTATTTTCAAAATATTTTAAAAACTATATA-ATA
1 TATATATGTTTTAAAAATATTTTAAAAACTATATATATA
* * * *
15657 TATAAATGTTTTCAAACATGTTTTCAAAACTATATAT-TA
1 TATATATGTTTT-AAAAATATTTTAAAAACTATATATATA
* *
15696 TATATAGGTTTTAAAAATATTTT-TAAACTATAATATATA
1 TATATATGTTTTAAAAATATTTTAAAAACTAT-ATATATA
15735 TATATAT
1 TATATAT
15742 ATATATATAT
Statistics
Matches: 130, Mismatches: 16, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
34 9 0.07
35 13 0.10
36 28 0.22
37 15 0.12
38 26 0.20
39 39 0.30
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.47
Consensus pattern (39 bp):
TATATATGTTTTAAAAATATTTTAAAAACTATATATATA
Found at i:16289 original size:84 final size:83
Alignment explanation
Indices: 16125--16904 Score: 717
Period size: 84 Copynumber: 9.4 Consensus size: 83
16115 TGGTTGATAG
* * * * ** * * *
16125 GCCTTCGATCTGAGTGTAATCGAACTCGGGGGTC-TTT-G-GCAGATAGCCTTTCTCGAGTTAAG
1 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGCAGATAACCCTTCTCGACTTAAG
* *
16187 CTATGCTGTAAATGATGT
66 TTATGCTGCAAATGATGT
* * * * * * *
16205 GCCTTGGAGCTAAACGTAGTCGAACTCGAATGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGA
1 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGT-GCAGATAACCCTTCTCGACTTAA
* *
16270 GTTATGATGTAAATGATGT
65 GTTATGCTGCAAATGATGT
* * * * ** *
16289 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTT-G-GCAGATAACCCTTCTTGACTTAA
1 G-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGCAGATAACCCTTCTCGACTTAA
*
16351 GCTATGCTGCAAATGATGT
65 GTTATGCTGCAAATGATGT
* * ** * *
16370 GCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTATTGGCAGACAACCCTTCTAGACTTAA
1 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGT-GCAGATAACCCTTCTCGACTTAA
* *
16434 GTTGTGCTGCAAATGATAT
65 GTTATGCTGCAAATGATGT
* * *
16453 GCCTTGGAGCTAAGCGTAGTTGAACTCGAAGG-CCTTTGGTTGGCAGATAACCCTTCTCGACTTA
1 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-T-GCAGATAACCCTTCTCGACTTA
*
16517 AGTTATACTGCAAATGATGT
64 AGTTATGCTGCAAATGATGT
* * * ** *
16537 GCCCTCT-AAGCTGAGTGTAATCGAACTCGGGGGTC-TTT-G-GCAGATAGCCCTTCTCGACTTA
1 G-CCT-TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGCAGATAACCCTTCTCGACTTA
*
16598 AGTTATACTGCAAATGATGT
64 AGTTATGCTGCAAATGATGT
* * *
16618 GCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGACTTAA
1 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGT-GCAGATAACCCTTCTCGACTTAA
16683 GTTATGCTGCAAATGATGT
65 GTTATGCTGCAAATGATGT
*** * * ** * *
16702 GCCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTC-TTT-G-GCAGATAGCCATTCTCGACTTAA
1 G-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGCAGATAACCCTTCTCGACTTAA
* *
16764 GCTATGCTGCAAATGATAT
65 GTTATGCTGCAAATGATGT
* * *
16783 GCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTTGTAGATAACCCTTCTCGACTTAA
1 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG-GTGCAGATAACCCTTCTCGACTTAA
*
16848 GTTATGCTGTAAATGATGTT
65 GTTATGCTGCAAATGATG-T
* *** * *
16868 CCCTCAAAGTTGAACGTAGTCGAACTCGAAGGTCTTT
1 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
16905 AGCTGGCAAA
Statistics
Matches: 561, Mismatches: 114, Indels: 45
0.78 0.16 0.06
Matches are distributed among these distances:
79 23 0.04
80 80 0.14
81 125 0.22
82 1 0.00
83 46 0.08
84 179 0.32
85 105 0.19
86 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (83 bp):
GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGCAGATAACCCTTCTCGACTTAAG
TTATGCTGCAAATGATGT
Found at i:16623 original size:165 final size:165
Alignment explanation
Indices: 16160--16904 Score: 786
Period size: 165 Copynumber: 4.5 Consensus size: 165
16150 TCGGGGGTCT
* * * * * *** * * *
16160 TTGGCAGATAGCCTTTCTCGAGTTAAGCTATGCTGTAAATGATGTG-CCTTGGAGCTAAACGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGCGTAA
* * * * * * * *
16224 TCGAACTCGAATGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATGT
66 TCGAACTCGAAGGTC-TTTGG---CAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
* * * * * **
16289 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC---T-
127 G-CCTTGGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTTG
* * * ** *
16325 TTGGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CGT-TGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGCGTAA
* * * * *
16388 TCGAACTCAAAGGTCTTTTATTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
66 TCGAACTCGAAGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
* * *
16453 GCCTTGGAGCTAAGCGTAGTTGAACTCGAAGGCCTTTGG
127 GCCTTGGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTTG
* * *
16492 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCCTCTAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGCGTAA
** * *
16557 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCT
66 TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCT
16622 TGGAGCTGAA-CGTAGTCGAACTCGAAGGTCTTTTG
131 TGGAGCT-AAGCGTAGTCGAACTCGAAGGTCTTTTG
* *
16657 TTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGCGTAA
** * *
16722 TCGAACTCGGGGGTCTTTGGCAGATAGCCATTCTCGACTTAAGCTATGCTGCAAATGATATGCCT
66 TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCT
* *
16787 TGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTG
131 TGGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTTG
* * * * * * *
16822 TTTGTAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTTCCCTCAAAGTTGAACGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGCGTAA
16887 TCGAACTCGAAGGTCTTT
66 TCGAACTCGAAGGTCTTT
16905 AGCTGGCAAA
Statistics
Matches: 502, Mismatches: 67, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
163 24 0.05
164 60 0.12
165 341 0.68
166 5 0.01
167 47 0.09
168 2 0.00
169 23 0.05
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (165 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGCGTAA
TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCT
TGGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTTG
Found at i:23457 original size:25 final size:25
Alignment explanation
Indices: 23421--23468 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
23411 AAAAAAATAA
*
23421 TAAATAATAAATAAA-TAACAAAAGG
1 TAAATAAAAAATAAACTAA-AAAAGG
23446 TAAATAAAAAATAAACTAAAAAA
1 TAAATAAAAAATAAACTAAAAAA
23469 CAGTTTCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (25 bp):
TAAATAAAAAATAAACTAAAAAAGG
Found at i:23560 original size:37 final size:37
Alignment explanation
Indices: 23464--23560 Score: 106
Period size: 36 Copynumber: 2.6 Consensus size: 37
23454 AAATAAACTA
* * *
23464 AAAAACAGTTTCCAAAAATCTATATAATATATATTTTT
1 AAAAAC-GTTTTCAAAATTATATATAATATATATTTTT
** * * *
23502 AAAAATATTTT-AAAATTATATATTATATGTTTTTTT
1 AAAAACGTTTTCAAAATTATATATAATATATATTTTT
23538 AAAAACGTTTTCAAAATTATATA
1 AAAAACGTTTTCAAAATTATATA
23561 GTTTTTAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
36 29 0.60
37 14 0.29
38 5 0.10
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (37 bp):
AAAAACGTTTTCAAAATTATATATAATATATATTTTT
Found at i:23575 original size:28 final size:29
Alignment explanation
Indices: 23533--23588 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
23523 ATTATATGTT
*
23533 TTTTTAAAAACGTTTTCAAAATTATATAG
1 TTTTTAAAAACGTTTTCAAAACTATATAG
* *
23562 TTTTT-AAAATGTTTTTAAAACTATATA
1 TTTTTAAAAACGTTTTCAAAACTATATA
23589 TTATAAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (29 bp):
TTTTTAAAAACGTTTTCAAAACTATATAG
Found at i:23665 original size:36 final size:33
Alignment explanation
Indices: 23624--23770 Score: 103
Period size: 36 Copynumber: 4.3 Consensus size: 33
23614 AACTATATAA
23624 TATATATATATGTTCTTCAAAATATTTTTTAAAAAC
1 TATATATATAT-TT-TTCAAAATA-TTTTTAAAAAC
*
23660 --TATATATA-TTTTC-AAA-ATGTTTAAAAAC
1 TATATATATATTTTTCAAAATATTTTTAAAAAC
*
23688 TATATAATTTATATTTTT-AAAAT-TGTTTTAAAAAT
1 TATAT-A--TATATTTTTCAAAATAT-TTTTAAAAAC
*
23723 TATATATTATATTTATTTTTAAAATA-TTTTAAAAAC
1 TATATA-TATA--T-TTTTCAAAATATTTTTAAAAAC
23759 TATATAATATAT
1 TATAT-ATATAT
23771 AAATGTTTTC
Statistics
Matches: 92, Mismatches: 4, Indels: 32
0.72 0.03 0.25
Matches are distributed among these distances:
28 10 0.11
29 1 0.01
30 6 0.07
31 4 0.04
32 2 0.02
33 9 0.10
34 18 0.20
35 14 0.15
36 22 0.24
37 6 0.07
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (33 bp):
TATATATATATTTTTCAAAATATTTTTAAAAAC
Found at i:23798 original size:39 final size:36
Alignment explanation
Indices: 23555--23852 Score: 215
Period size: 34 Copynumber: 8.2 Consensus size: 36
23545 TTTTCAAAAT
*
23555 TATATAGTTTTTAAAATGTTTTTAAAACTATAT-AT-
1 TATATA-TTTTTAAAATGTTTTAAAAACTATATAATA
* *
23590 TATA-AGTTTTTGAAATGATTTAAAAACTATATAATATA
1 TATATA-TTTTTAAAATGTTTTAAAAACTATAT-A-ATA
* ** *
23628 TATATATGTTCTTCAAAATATTTT-TTAA--A-A-ACTA
1 TATATAT-TT-TT-AAAATGTTTTAAAAACTATATAATA
*
23662 TATATATTTTCAAAATG-TTTAAAAACTATATAAT-
1 TATATATTTTTAAAATGTTTTAAAAACTATATAATA
* *
23696 T-TATATTTTTAAAATTGTTTTAAAAATTATATATTA
1 TATATATTTTTAAAA-TGTTTTAAAAACTATATAATA
* *
23732 TATTTATTTTTAAAATATTTTAAAAACTATATAATA
1 TATATATTTTTAAAATGTTTTAAAAACTATATAATA
* * *
23768 TATAAATGTTTTCAAACATGTTTTCAAAACTATATATTA
1 TATATAT-TTTT-AAA-ATGTTTTAAAAACTATATAATA
* * *
23807 TATATAGGTTTTAAAAATATTTT-TAAACTATAATATATA
1 TATATA--TTTTTAAAATGTTTTAAAAACTAT-ATA-ATA
23846 TATATAT
1 TATATAT
23853 ATATATATAT
Statistics
Matches: 208, Mismatches: 31, Indels: 46
0.73 0.11 0.16
Matches are distributed among these distances:
30 3 0.01
31 7 0.03
32 1 0.00
33 15 0.07
34 38 0.18
35 22 0.11
36 24 0.12
37 27 0.13
38 18 0.09
39 38 0.18
40 7 0.03
41 8 0.04
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (36 bp):
TATATATTTTTAAAATGTTTTAAAAACTATATAATA
Found at i:23846 original size:2 final size:2
Alignment explanation
Indices: 23835--23879 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
23825 ATTTTTAAAC
23835 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23876 TA TA
1 TA TA
23880 AAAGAGACGA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:25654 original size:164 final size:164
Alignment explanation
Indices: 25212--26155 Score: 1212
Period size: 164 Copynumber: 5.7 Consensus size: 164
25202 TATACAAACT
* * *
25212 ATTTGAAGTATAACTTAA-GCTGAGAAGGGTTATCTGCCAACCATAGACCTTCGAGTTCGACTAC
1 ATTTGCAGCATAACTTAAGGCT-AGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTAC
* *
25276 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAAACC
64 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
*
25341 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
129 CCCGAGTTCGATTACACTCAGCTTCGAGGGCATATC
* * ** * * *
25377 ATTTGTAGTATAACTTAAATCAATAAGGGTTATCTGCCAACCAACGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACG
*
25442 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGACAAAGACCC
65 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
25507 CCGAGTTCGATTACACTCAGCTTCGAGGGCATATC
130 CCGAGTTCGATTACACTCAGCTTCGAGGGCATATC
* * * * *
25542 ATTTGCAGCATAACTCAAGGCTGGAAGGGTTATTTTCCACGAAAGACCTTCGAGTTCGACTACGC
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGC
* *
25607 TCAGCTCCAATGTACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCC
66 TCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCC
25672 CGAGTTCGATTACACTCAGCTTCGAGGGCATATC
131 CGAGTTCGATTACACTCAGCTTCGAGGGCATATC
* * *
25706 ATTTGTAGCATAACTAAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACAC
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGC
* * *
25771 TCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGATAAGGGCTATCTGCCAAAGACCCT
66 TCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCC
* * * * * *
25836 CGAGTTCGGTCACATTCAGCTTTGAGGACACATC
131 CGAGTTCGATTACACTCAGCTTCGAGGGCATATC
* * * * * * *
25870 ATTTACAGTATAACTCAAGGCTAGAAGGGTTATTTGTCACCAGAAGACCTTTGAGTTTGACTACG
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCCACCA-AAGACCTTCGAGTTCGACTACG
* * * * * *
25935 CTCAACTCCAAGGCACATCATTTACAGCATAACTCAAGGTTG-GAAGGGTTATCTGTCACCAAAG
65 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAA-GTCGAGAAGGGCTATCTG---CCAAAG
** * * * * * *
25999 ACCTTCAAGTTCGACTACGCTCATC-TCCAAGGCATATC
126 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATC
* * ** *
26037 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAATAAAGACCTTTGAGTTCGACTACGC
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGC
* ** *
26102 TCAGCTCCAAGGCACATCATTTACAGCATAGCCCAAGGT-AAGAAGGGCTATCTG
66 TCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAA-GTCGAGAAGGGCTATCTG
26156 TCAATAAAAT
Statistics
Matches: 684, Mismatches: 88, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
164 303 0.44
165 243 0.36
166 74 0.11
167 41 0.06
168 23 0.03
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (164 bp):
ATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGC
TCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCC
CGAGTTCGATTACACTCAGCTTCGAGGGCATATC
Found at i:25898 original size:81 final size:80
Alignment explanation
Indices: 25212--26131 Score: 600
Period size: 83 Copynumber: 11.2 Consensus size: 80
25202 TATACAAACT
* * * *
25212 ATTTGAAGTATAACTTAAG-CTGAGAAGGGTTATCTGCCAACCATAGACCTTCGAGTTC-GACTA
1 ATTTGCAGCATAACTTAAGTC-GAGAAGGGTTATCTGCC-A--A-AGACCCTCGAGTTCGGTC-A
* * *
25275 CGCTCAGCTCCAAGGCACATC
60 CACTCAGCTTCGAGGCACATC
* * * * *
25296 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAAACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGGTCACACTCA
25361 GCTTCGAGGGCACATC
66 GCTTCGA-GGCACATC
* * * * * * *
25377 ATTTGTAGTATAACTTAAATCAATAAGGGTTATCTGCCAACCAACGACCTTCGAGTTC-GACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-A--AA-GACCCTCGAGTTCGGTC-AC
* * *
25441 GCTCAGCTCCAAGGCACATC
61 ACTCAGCTTCGAGGCACATC
* * * * * *
25461 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGACAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGGTCACACTCA
*
25526 GCTTCGAGGGCATATC
66 GCTTCGA-GGCACATC
* * * * * *
25542 ATTTGCAGCATAACTCAAGGCTG-GAAGGGTTATTTTCCACGAAAGACCTTCGAGTTC-GACTAC
1 ATTTGCAGCATAACTTAAGTC-GAGAAGGGTTA-TCTGC-C-AAAGACCCTCGAGTTCGGTC-AC
* * * * *
25605 GCTCAGCTCCAATGTACATC
61 ACTCAGCTTCGAGGCACATC
* * * * *
25625 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGGTCACACTCA
*
25690 GCTTCGAGGGCATATC
66 GCTTCGA-GGCACATC
* * * * * *
25706 ATTTGTAGCATAACTAAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTC-GACTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG---CCAAAGACCCTCGAGTTCGGTC-ACA
* *
25770 CTCAGCTCCAAGGCACATC
62 CTCAGCTTCGAGGCACATC
* * * * *
25789 ATTTGCAGTATAGCTTAAGTCGATAAGGGCTATCTGCCAAAGACCCTCGAGTTCGGTCACATTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGGTCACACTCA
*
25854 GCTTTGAGGACACATC
66 GCTTCGAGG-CACATC
* * * * * * * * * *
25870 ATTTACAGTATAACTCAAGGCTAGAAGGGTTATTTGTCACCAGAAGACCTTTGAGTT-TGACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG---CCA-AAGACCCTCGAGTTCGGTC-AC
* * * *
25934 GCTCAACTCCAAGGCACATC
61 ACTCAGCTTCGAGGCACATC
* * * * * *
25954 ATTTACAGCATAACTCAAGGTTG-GAAGGGTTATCTGTCACCAAAGACCTTCAAGTTC-GACTAC
1 ATTTGCAGCATAACTTAA-GTCGAGAAGGGTTATCTG---CCAAAGACCCTCGAGTTCGGTC-AC
* * * * *
26017 GCTCATCTCCAAGGCATATC
61 ACTCAGCTTCGAGGCACATC
* * * *
26037 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAATAAAGACCTTTGAGTTC-GACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC---AAAGACCCTCGAGTTCGGTC-ACA
* *
26101 CTCAGCTCCAAGGCACATC
62 CTCAGCTTCGAGGCACATC
*
26120 ATTTACAGCATA
1 ATTTGCAGCATA
26132 GCCCAAGGTA
Statistics
Matches: 659, Mismatches: 142, Indels: 71
0.76 0.16 0.08
Matches are distributed among these distances:
80 100 0.15
81 148 0.22
82 11 0.02
83 183 0.28
84 172 0.26
85 45 0.07
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (80 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGGTCACACTCA
GCTTCGAGGCACATC
Found at i:25919 original size:329 final size:328
Alignment explanation
Indices: 25218--26155 Score: 1249
Period size: 329 Copynumber: 2.8 Consensus size: 328
25208 AACTATTTGA
* * * *
25218 AGTATAACTTAA-GCTGAGAAGGGTTATCTGCCAACCATAGACCTTCGAGTTCGACTACGCTCAG
1 AGTATAACTCAAGGCT-AGAAGGGTTATTTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTCAG
*
25282 CTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAAACCCCCGAG
64 CTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCCGAG
* * *
25347 TTCGATTACACTCAGCTTCGAGGGCACATCATTTGTAGTATAACTTAAA-TCAATAAGGGTTATC
129 TTCGATTACACTCAGCTTCGAGGGCATATCATTTGTAGCATAAC-TAAAGTCAAGAAGGGTTATC
*
25411 TGCCAACCAACGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCT
193 TGCC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCT
* * *
25476 TAAGTCGAGAAGGGCTATCTGACAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
257 TAAGTCGAGAAGGGCTATCTGACAAAGACCCCCGAGTTCGATCACACTCAGCTTCGAGGACACAT
*
25541 CATTTGC
322 CATTTAC
* * *
25548 AGCATAACTCAAGGCTGGAAGGGTTATTT-TCCACGAAAGACCTTCGAGTTCGACTACGCTCAGC
1 AGTATAACTCAAGGCTAGAAGGGTTATTTGT-CACCAAAGACCTTCGAGTTCGACTACGCTCAGC
* * *
25612 TCCAATGTACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGT
65 TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCCGAGT
* *
25677 TCGATTACACTCAGCTTCGAGGGCATATCATTTGTAGCATAACTAAAGGCTAGAAGGGTTATCTG
130 TCGATTACACTCAGCTTCGAGGGCATATCATTTGTAGCATAACTAAAGTCAAGAAGGGTTATCTG
* *
25742 CCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAA
195 CCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAA
* * * * * *
25807 GTCGATAAGGGCTATCTGCCAAAGACCCTCGAGTTCGGTCACATTCAGCTTTGAGGACACATCAT
260 GTCGAGAAGGGCTATCTGACAAAGACCCCCGAGTTCGATCACACTCAGCTTCGAGGACACATCAT
25872 TTAC
325 TTAC
* * *
25876 AGTATAACTCAAGGCTAGAAGGGTTATTTGTCACCAGAAGACCTTTGAGTTTGACTACGCTCAAC
1 AGTATAACTCAAGGCTAGAAGGGTTATTTGTCACCA-AAGACCTTCGAGTTCGACTACGCTCAGC
* * * * **
25941 TCCAAGGCACATCATTTACAGCATAACTCAAGGTTG-GAAGGGTTATCTGTCACCAAAGACCTTC
65 TCCAAGGCACATCATTTGCAGCATAGCTTAA-GTCGAGAAGGGTTATCTG---CCAAAGACCCCC
* * * * * * * * *
26005 AAGTTCGACTACGCTCATC-TCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTA
126 GAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTGTAGCATAACTAAAGTCAAGAAGGGTTA
** * *
26069 TCTGCCAATAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGC
191 TCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGC
** *
26134 CCAAGGT-AAGAAGGGCTATCTG
256 TTAA-GTCGAGAAGGGCTATCTG
26156 TCAATAAAAT
Statistics
Matches: 534, Mismatches: 64, Indels: 19
0.87 0.10 0.03
Matches are distributed among these distances:
328 154 0.29
329 212 0.40
330 25 0.05
331 116 0.22
332 27 0.05
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (328 bp):
AGTATAACTCAAGGCTAGAAGGGTTATTTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
CCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCCGAGTT
CGATTACACTCAGCTTCGAGGGCATATCATTTGTAGCATAACTAAAGTCAAGAAGGGTTATCTGC
CACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG
TCGAGAAGGGCTATCTGACAAAGACCCCCGAGTTCGATCACACTCAGCTTCGAGGACACATCATT
TAC
Found at i:26917 original size:26 final size:26
Alignment explanation
Indices: 26869--26918 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
26859 TTGAAAATGC
* *
26869 TTTTGAAAATATATATAATATATAGT
1 TTTTGAAAACATATATAAAATATAGT
* *
26895 TTTTGAAAACATTTTTAAAATATA
1 TTTTGAAAACATATATAAAATATA
26919 TATAATATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (26 bp):
TTTTGAAAACATATATAAAATATAGT
Found at i:26941 original size:37 final size:37
Alignment explanation
Indices: 26735--27062 Score: 228
Period size: 37 Copynumber: 9.1 Consensus size: 37
26725 TTTTTAAAAA
*
26735 ATATAATTTTTAGAAAACGATTTTTGAAAATATATATATAT
1 ATATAGTTTTT-GAAAAC-ATTTTT-AAAATATATATA-AT
* * ** *
26776 GTATAG-TTTTGAAAATATTTCAAAAATATATATGTATT
1 ATATAGTTTTTGAAAACATTTTTAAAATATATA--TAAT
* *
26814 ATATAG-TTTTGAAAA-A-TTTGAAAACATATATAATAT
1 ATATAGTTTTTGAAAACATTTTTAAAATATATAT-A-AT
*
26850 ATATAGTTTTTGAAAATGC-TTTTGAAAATATATATAAT
1 ATATAGTTTTTGAAAA--CATTTTTAAAATATATATAAT
26888 ATATAGTTTTTGAAAACATTTTTAAAATATATATAAT
1 ATATAGTTTTTGAAAACATTTTTAAAATATATATAAT
26925 ATATAGTTTTTGAAAACA----T---ATAT-TAT-AT
1 ATATAGTTTTTGAAAACATTTTTAAAATATATATAAT
* * *
26953 A-GT--TTTTGGAAAACATTTTTTAAAACATATAT--T
1 ATATAGTTTTTGAAAACA-TTTTTAAAATATATATAAT
* * * * *
26986 ATATGGTTTTTTAAAACATTTTTAAAAAACATATATT
1 ATATAGTTTTTGAAAACATTTTTAAAATATATATAAT
* * * *
27023 ATATGGTTTTTTAAAACATTTTTAAAAAACATAT-AT
1 ATATAGTTTTTGAAAACATTTTTAAAATATATATAAT
27059 ATAT
1 ATAT
27063 TATATTGTTT
Statistics
Matches: 241, Mismatches: 22, Indels: 53
0.76 0.07 0.17
Matches are distributed among these distances:
25 11 0.05
27 1 0.00
28 3 0.01
29 3 0.01
30 5 0.02
33 6 0.02
34 5 0.02
35 15 0.06
36 34 0.14
37 91 0.38
38 37 0.15
39 8 0.03
40 18 0.07
41 4 0.02
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.45
Consensus pattern (37 bp):
ATATAGTTTTTGAAAACATTTTTAAAATATATATAAT
Found at i:26945 original size:24 final size:25
Alignment explanation
Indices: 26918--26968 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
26908 TTTAAAATAT
26918 ATATAATATATAGTTTTT-GAAAAC
1 ATATAATATATAGTTTTTGGAAAAC
*
26942 ATATATTATATAGTTTTTGGAAAAC
1 ATATAATATATAGTTTTTGGAAAAC
26967 AT
1 AT
26969 TTTTTAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (25 bp):
ATATAATATATAGTTTTTGGAAAAC
Found at i:26983 original size:61 final size:62
Alignment explanation
Indices: 26869--27004 Score: 186
Period size: 61 Copynumber: 2.2 Consensus size: 62
26859 TTGAAAATGC
* *
26869 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTTAAAATATATATAATATATAGT
1 TTTTGAAAACATATAT-ATATATAGTTTTTGAAAACATTTTTAAAATACATATAATATATAGT
* * *
26932 TTTTGAAAACATATAT-TATATAGTTTTTGGAAAACATTTTTTAAA-ACATATATTATATGGT
1 TTTTGAAAACATATATATATATAGTTTTT-GAAAACATTTTTAAAATACATATAATATATAGT
*
26993 TTTTTAAAACAT
1 TTTTGAAAACAT
27005 TTTTAAAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
61 36 0.55
62 15 0.23
63 15 0.23
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (62 bp):
TTTTGAAAACATATATATATATAGTTTTTGAAAACATTTTTAAAATACATATAATATATAGT
Found at i:27002 original size:98 final size:100
Alignment explanation
Indices: 26830--27041 Score: 259
Period size: 98 Copynumber: 2.1 Consensus size: 100
26820 TTTTGAAAAA
** *
26830 TTTGAAAACATATATAATATATATAGTTTTTGAAAATGCTTTTGAAAATATATATAATATATAGT
1 TTTGAAAAC--ATATAATATATATAGTTTTTGAAAACACTTTTGAAAACATATAT-ATATATAGT
* *
26895 TTTTGAAAACATTTTTAAAATATATATAATATATAGTT
63 TTTTGAAAACATTTTTAAAAAACATATAATATATAGTT
* * *
26933 TTTGAAAACATAT-AT-TATATAGTTTTTGGAAAACATTTTTTAAAACATATAT-TATATGGTTT
1 TTTGAAAACATATAATATATATAGTTTTT-GAAAACACTTTTGAAAACATATATATATATAGTTT
* * *
26995 TTTAAAACATTTTTAAAAAACATATATTATATGGTT
65 TTGAAAACATTTTTAAAAAACATATAATATATAGTT
*
27031 TTTTAAAACAT
1 TTTGAAAACAT
27042 TTTTAAAAAA
Statistics
Matches: 96, Mismatches: 12, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
98 50 0.52
99 12 0.12
100 21 0.22
101 4 0.04
103 9 0.09
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (100 bp):
TTTGAAAACATATAATATATATAGTTTTTGAAAACACTTTTGAAAACATATATATATATAGTTTT
TGAAAACATTTTTAAAAAACATATAATATATAGTT
Found at i:27085 original size:17 final size:17
Alignment explanation
Indices: 27063--27126 Score: 64
Period size: 15 Copynumber: 4.0 Consensus size: 17
27053 ATATATATAT
27063 TATATTGTTTTTAAAAA
1 TATATTGTTTTTAAAAA
*
27080 TATA-T-TTTTTGAAAA
1 TATATTGTTTTTAAAAA
* *
27095 TATATTATTTTGAAAAA
1 TATATTGTTTTTAAAAA
*
27112 CA-ATTG-TTTTAAAAA
1 TATATTGTTTTTAAAAA
27127 AAAGCATATC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 21 0.54
16 5 0.13
17 13 0.33
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (17 bp):
TATATTGTTTTTAAAAA
Found at i:27146 original size:2 final size:2
Alignment explanation
Indices: 27141--27186 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
27131 CATATCATAA
27141 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27183 AT AT
1 AT AT
27187 TATTTTATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27195 original size:12 final size:12
Alignment explanation
Indices: 27152--27226 Score: 55
Period size: 12 Copynumber: 5.9 Consensus size: 12
27142 TATATATATA
*
27152 TATATATATATATA
1 TATATAT-TAT-TT
*
27166 TATATATATATATA
1 TATATAT-TAT-TT
27180 TATATATTATTT
1 TATATATTATTT
*
27192 TATATTTTATTAT
1 TATATATTATT-T
27205 TAT-TATTATTAT
1 TATATATTATT-T
27217 TAT-TATTATT
1 TATATATTATT
27227 ATTTATTATG
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
12 29 0.51
13 7 0.12
14 21 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATATATTATTT
Found at i:27195 original size:18 final size:18
Alignment explanation
Indices: 27141--27235 Score: 88
Period size: 16 Copynumber: 5.9 Consensus size: 18
27131 CATATCATAA
27141 ATATATATATATA-TA-T
1 ATATATATATATATTATT
27157 ATATATATATATA-TA-T
1 ATATATATATATATTATT
27173 ATATATATATATATTATT
1 ATATATATATATATTATT
*
27191 -T-TATAT-TTTATTATT
1 ATATATATATATATTATT
27206 AT-TAT-TAT-TATTATT
1 ATATATATATATATTATT
*
27221 AT-TAT-TATTTATTAT
1 ATATATATATATATTAT
27236 GTTTTTTTGC
Statistics
Matches: 73, Mismatches: 1, Indels: 10
0.87 0.01 0.12
Matches are distributed among these distances:
15 24 0.33
16 45 0.62
17 3 0.04
18 1 0.01
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATATATATATATTATT
Found at i:27204 original size:3 final size:3
Alignment explanation
Indices: 27184--27235 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
27174 TATATATATA
27184 TAT TAT T-T TA- TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
27230 TAT TAT
1 TAT TAT
27236 GTTTTTTTGC
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.13
3 36 0.80
4 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:28780 original size:2 final size:2
Alignment explanation
Indices: 28773--28802 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28763 TATAATTAAC
28773 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28803 CAATCAGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29466 original size:22 final size:22
Alignment explanation
Indices: 29436--29478 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
29426 CTCTATGGAT
29436 TTATATCTCTCTATACTGTATA
1 TTATATCTCTCTATACTGTATA
* *
29458 TTATCTCTCTCTATATTGTAT
1 TTATATCTCTCTATACTGTAT
29479 GTCATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.53
Consensus pattern (22 bp):
TTATATCTCTCTATACTGTATA
Found at i:31957 original size:2 final size:2
Alignment explanation
Indices: 31950--31977 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31940 CAGTCCCTCA
31950 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31978 GAGTAAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36074 original size:32 final size:31
Alignment explanation
Indices: 36000--36078 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
35990 CTAATTTGAC
* *
36000 TCTTAGGTAGGCTCTACGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
** * **
36031 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACGGCCCTAAGAT-CAT
36063 TCTTAGGTAGGCCCTA
1 TCTTAGGTAGGCCCTA
36079 AACTTTCTTG
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
31 23 0.62
32 14 0.38
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.28
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
Found at i:48566 original size:35 final size:34
Alignment explanation
Indices: 48496--48573 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 34
48486 AAGAAAGTCA
48496 TCAATTACA-TTTAAACCCAAAATCCAAAATGCT
1 TCAATTACATTTTAAACCCAAAATCCAAAATGCT
* * *
48529 TCAATTACATTTTGAACCTCAAATTCCAAAATTCT
1 TCAATTACATTTTAAACC-CAAAATCCAAAATGCT
48564 TCAATTACAT
1 TCAATTACAT
48574 GTCCAACCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 9 0.22
34 7 0.17
35 24 0.60
ACGTcount: A:0.41, C:0.23, G:0.03, T:0.33
Consensus pattern (34 bp):
TCAATTACATTTTAAACCCAAAATCCAAAATGCT
Found at i:48587 original size:35 final size:35
Alignment explanation
Indices: 48511--48589 Score: 104
Period size: 35 Copynumber: 2.3 Consensus size: 35
48501 TACATTTAAA
* * **
48511 CCCAAAATCCAAAATGCTTCAATTACATTTTGAAC
1 CCCAAATTCCAAAATGCTTCAATTACATGTCCAAC
* *
48546 CTCAAATTCCAAAATTCTTCAATTACATGTCCAAC
1 CCCAAATTCCAAAATGCTTCAATTACATGTCCAAC
48581 CCCAAATTC
1 CCCAAATTC
48590 ACAATCCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (35 bp):
CCCAAATTCCAAAATGCTTCAATTACATGTCCAAC
Done.