Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005665.1 Hibiscus syriacus cultivar Beakdansim tig00013247_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: 61548
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Found at i:11531 original size:110 final size:106
Alignment explanation
Indices: 11320--11553 Score: 283
Period size: 110 Copynumber: 2.2 Consensus size: 106
11310 CCAATTTCAA
* * *
11320 AGCCAAATTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAACG
1 AGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCACAACG
* * * *
11385 AAGGGGCGACTGATTGTCAACAAATAACTTTTCAGTTTCATTCAG
66 AAGGGGCGACTGACTATCAACAAACAACTTTCCAG-TTC--T-AG
* * * * *
11430 AGTCAATTTCAACTTCACAGCGAATGATATTGAACTCGAGACAACACAAGCTCAACTTCATATCG
1 AGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCACAACG
*
11495 AAGGGGCGGA-TGGCTATCAACAAACAA-TTTCCCAGTTCTAG
66 AAGGGGC-GACTGACTATCAACAAACAACTTT-CCAGTTCTAG
11536 AGCCAATTTCAACTTCAC
1 AGCCAATTTCAACTTCAC
11554 GATGGAGAAT
Statistics
Matches: 108, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
106 19 0.18
107 1 0.01
109 6 0.06
110 80 0.74
111 2 0.02
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (106 bp):
AGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCACAACG
AAGGGGCGACTGACTATCAACAAACAACTTTCCAGTTCTAG
Found at i:12915 original size:20 final size:20
Alignment explanation
Indices: 12892--12960 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 20
12882 CCTATATATA
12892 TATTTTAATTATATTTTTTT
1 TATTTTAATTATATTTTTTT
*
12912 TATTTTATTTACTATATTCCTTTT
1 TATTTTAATTA-TAT-TT--TTTT
*
12936 T-TATTTATATTATATTATTTT
1 TAT-TTTA-ATTATATTTTTTT
12957 TATT
1 TATT
12961 ATATATATCT
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
20 10 0.26
21 9 0.23
22 3 0.08
23 2 0.05
24 12 0.31
25 3 0.08
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
TATTTTAATTATATTTTTTT
Found at i:12955 original size:14 final size:14
Alignment explanation
Indices: 12936--12975 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
12926 TATTCCTTTT
12936 TTATTTATATTATA
1 TTATTTATATTATA
*
12950 TTATTTTTATTATA
1 TTATTTATATTATA
12964 TATATCTTATAT
1 T-TAT-TTATAT
12976 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:13129 original size:38 final size:37
Alignment explanation
Indices: 13043--13119 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 37
13033 TATGTATATA
*
13043 TATATATATATTTTTTAATATTATCTTTTATACGTTTT
1 TATATATATATTTTTTAATATTATATTTTATA-GTTTT
*
13081 TATATATATATTTTCTTAATATTCTATTTT-T-GTTTT
1 TATATATATATTTT-TTAATATTATATTTTATAGTTTT
13117 TAT
1 TAT
13120 TTATTTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 8 0.22
38 15 0.42
39 13 0.36
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (37 bp):
TATATATATATTTTTTAATATTATATTTTATAGTTTT
Found at i:13159 original size:18 final size:18
Alignment explanation
Indices: 13114--13174 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
13104 CTATTTTTGT
* *
13114 TTTTATTTATTTA-TATA
1 TTTTATTTTTTTACTTTA
* *
13131 TATTATATTTTTACTTTA
1 TTTTATTTTTTTACTTTA
13149 TTTTATTTTTTT-CTATTA
1 TTTTATTTTTTTACT-TTA
13167 TTTT-TTTT
1 TTTTATTTT
13175 CTTAATATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 16 0.44
18 20 0.56
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATTTTTTTACTTTA
Found at i:13205 original size:37 final size:35
Alignment explanation
Indices: 13164--13247 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 35
13154 TTTTTTTCTA
*
13164 TTATTTTTTTTCTTAATATCATGTATATTT-TTATTTT
1 TTATTTTTTTTCTTAATAT--TATATATTTATTA-TTT
* *
13201 TTATTTGTTTTACTTAGTATTATATATTTATTATTT
1 TTATTT-TTTTTCTTAATATTATATATTTATTATTT
*
13237 TTATTTGTTTT
1 TTATTTTTTTT
13248 AGTAAATACT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
35 3 0.08
36 17 0.43
37 9 0.22
38 11 0.28
ACGTcount: A:0.21, C:0.04, G:0.05, T:0.70
Consensus pattern (35 bp):
TTATTTTTTTTCTTAATATTATATATTTATTATTT
Found at i:13383 original size:18 final size:17
Alignment explanation
Indices: 13362--13400 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
13352 GTTTTTTAAC
13362 ATTTTATTCATTTTGTTT
1 ATTTTATT-ATTTTGTTT
*
13380 ATTTTTATTATTTTTTTT
1 A-TTTTATTATTTTGTTT
13398 ATT
1 ATT
13401 ATTTTTTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 2 0.11
18 10 0.53
19 7 0.37
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.77
Consensus pattern (17 bp):
ATTTTATTATTTTGTTT
Found at i:13398 original size:12 final size:12
Alignment explanation
Indices: 13381--13407 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
13371 ATTTTGTTTA
13381 TTTTTATTATTT
1 TTTTTATTATTT
13393 TTTTTATTATTT
1 TTTTTATTATTT
13405 TTT
1 TTT
13408 ACGTGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTATTATTT
Found at i:13447 original size:26 final size:28
Alignment explanation
Indices: 13387--13448 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 28
13377 TTTATTTTTA
*
13387 TTATTTTTTTTATTATTTTTTACGTGTT
1 TTATTTATTTTATTATTTTTTACGTGTT
* *
13415 TT-GTTATTTTA-TATTTTTT-CTTGTT
1 TTATTTATTTTATTATTTTTTACGTGTT
13440 TTATTTATT
1 TTATTTATT
13449 ATTCTCACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 7 0.24
26 13 0.45
27 7 0.24
28 2 0.07
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (28 bp):
TTATTTATTTTATTATTTTTTACGTGTT
Found at i:20761 original size:18 final size:18
Alignment explanation
Indices: 20730--20766 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20720 AAATTATTTA
20730 ATATAATATAAAATAAAT
1 ATATAATATAAAATAAAT
* *
20748 ATATATTATTAAATAAAT
1 ATATAATATAAAATAAAT
20766 A
1 A
20767 AAATTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATAATATAAAATAAAT
Found at i:20770 original size:23 final size:22
Alignment explanation
Indices: 20740--20785 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
20730 ATATAATATA
*
20740 AAATAAATATATATTATTAAAT
1 AAATAAATATAAATTATTAAAT
* *
20762 AAATAAAATTTAAATTATTTAAT
1 AAAT-AAATATAAATTATTAAAT
20785 A
1 A
20786 GTTACCTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATAAATATAAATTATTAAAT
Found at i:22235 original size:21 final size:21
Alignment explanation
Indices: 22209--22253 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
22199 GATTTCTGGG
* *
22209 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
22230 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
22251 CAA
1 CAA
22254 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:23655 original size:103 final size:103
Alignment explanation
Indices: 23430--23647 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
23420 GTTGAGGGTC
* * *
23430 TATGTGGTCATTCGGGACATATATGCATTCTTTGGAACATGTGTGAAGTCTGGTGAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACAGGTGTGAAGTCTGGTGAGACACATAC
* *
23495 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
23533 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACAGGTGTGAAGTCTGGTGAGACACATAC
*
23598 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
23636 TATGTGGTCCTT
1 TATGTGGTCCTT
23648 ATGGACATTA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACAGGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:23731 original size:23 final size:23
Alignment explanation
Indices: 23663--23723 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
23653 CATTATTATA
*
23663 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
23686 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
23709 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
23724 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:27489 original size:21 final size:21
Alignment explanation
Indices: 27463--27507 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
27453 GATTTCTGGG
* *
27463 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
27484 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
27505 CAA
1 CAA
27508 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:28913 original size:103 final size:103
Alignment explanation
Indices: 28688--28905 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
28678 GTCGAGGGTC
*
28688 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAAGTCTGGTGAGACACATAC
* *
28753 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
28791 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAAGTCTGGTGAGACACATAC
*
28856 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
28894 TATGTGGTCCTT
1 TATGTGGTCCTT
28906 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:28949 original size:23 final size:23
Alignment explanation
Indices: 28922--28981 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
28912 ATTATTATAT
28922 GGCACTATGGTGCAATTCTACGC
1 GGCACTATGGTGCAATTCTACGC
* * *
28945 GGCACTACGGTGCAATTCTATGT
1 GGCACTATGGTGCAATTCTACGC
28968 GGCACT-TCGGTGCA
1 GGCACTAT-GGTGCA
28982 TTTATATGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (23 bp):
GGCACTATGGTGCAATTCTACGC
Found at i:28989 original size:23 final size:23
Alignment explanation
Indices: 28912--28989 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
28902 CCTTATGGAC
* *
28912 ATTATTATATGGCACTATGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
28936 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* *
28959 ATTCTATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
28982 TTTATATG
1 ATTATATG
28990 AGCTGTGGTG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:30358 original size:21 final size:21
Alignment explanation
Indices: 30334--30374 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
30324 CAGAGACAGT
*
30334 TACCAAGGTACTTCATCTACA
1 TACCAAGGTACTTAATCTACA
30355 TACCAAGGTACTTAATCTAC
1 TACCAAGGTACTTAATCTAC
30375 TTCCACTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29
Consensus pattern (21 bp):
TACCAAGGTACTTAATCTACA
Found at i:34010 original size:21 final size:20
Alignment explanation
Indices: 33924--34081 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
33914 AAATGACCAA
**
33924 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
33943 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
33963 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
33983 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
34004 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
34025 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
34045 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
34066 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
34082 ACATATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:34072 original size:20 final size:19
Alignment explanation
Indices: 34047--34100 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 19
34037 GCGATTTTCC
*
34047 AAAATCGCAACGCGAATAT
1 AAAATCGCAACGCGAACAT
34066 GAAAATCGCAACGCGAACAT
1 -AAAATCGCAACGCGAACAT
34086 ATAAATCGCAACGCG
1 A-AAATCGCAACGCG
34101 TATCCGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.44, C:0.24, G:0.19, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCGAACAT
Found at i:34110 original size:20 final size:19
Alignment explanation
Indices: 34087--34318 Score: 221
Period size: 20 Copynumber: 11.6 Consensus size: 19
34077 CGCGAACATA
34087 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
34107 TAAATCGTAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
*
34127 TTAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
* * *
34147 TAAATCGCAACGATAATACA
1 TAAATCGCAACGGT-ATCCG
34167 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACG-GTATCCG
*
34188 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
34208 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
34228 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
34248 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
34268 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
34288 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
34308 TAAATCACAAC
1 TAAATCGCAAC
34319 ACTGAAATTT
Statistics
Matches: 174, Mismatches: 29, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.01
20 156 0.90
21 15 0.09
22 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (19 bp):
TAAATCGCAACGGTATCCG
Found at i:34112 original size:40 final size:39
Alignment explanation
Indices: 34048--34318 Score: 193
Period size: 40 Copynumber: 6.8 Consensus size: 39
34038 CGATTTTCCA
** * *
34048 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACATAT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGAGAAC-TAT
* * * * **
34088 AAATCGCAACGCGTATCCGTAAATCGTAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGAG-AACTAT
* * *
34128 TAATCGCAACGCGTATCCGTAAATCGCAACGATAA-TACAT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGAGAACT--AT
* * **
34168 AAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 -AAATCGCAACGCGAATCCGTAAATCGCAACGAGAA-CTAT
* * * **
34209 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGAGAA-CTAT
* * * **
34249 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGAGAA-CTAT
* * *
34289 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGCGAATCCGTAAATCGCAAC
34319 ACTGAAATTT
Statistics
Matches: 202, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.00
40 164 0.81
41 37 0.18
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (39 bp):
AAATCGCAACGCGAATCCGTAAATCGCAACGAGAACTAT
Found at i:34134 original size:60 final size:60
Alignment explanation
Indices: 34087--34318 Score: 270
Period size: 60 Copynumber: 3.9 Consensus size: 60
34077 CGCGAACATA
* * * * *
34087 TAAATCGCAACGCGT-ATCCGTAAATCGTAACGTGTATCCGTTAATCGCAACGCGTATCCG
1 TAAATCGCAACG-ATAATCCGTAAATCGCAACGTGTATCCGTAAATCGCAACGAGAATCCG
* * * *
34147 TAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGATAATCCGT-AAATCGCAACGTGTATCCGTAAATCGCAACGAGAATCCG
* * * *
34208 TAAATCGCAACGAGAATCTGTAAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCTG
1 TAAATCGCAACGATAATCCGTAAATCGCAACG-TGTATCCGTAAATCGCAACGAGAATCCG
* * * *
34268 TAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCACAAC
1 TAAATCGCAACGATAATCCGTAAATCGCAACGTGTATCCGTAAATCGCAAC
34319 ACTGAAATTT
Statistics
Matches: 146, Mismatches: 22, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
59 1 0.01
60 95 0.65
61 50 0.34
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (60 bp):
TAAATCGCAACGATAATCCGTAAATCGCAACGTGTATCCGTAAATCGCAACGAGAATCCG
Found at i:34179 original size:101 final size:101
Alignment explanation
Indices: 34067--34318 Score: 264
Period size: 101 Copynumber: 2.5 Consensus size: 101
34057 CGCGAATATG
* * * * * *
34067 AAAATCGCAACGCG-AACATATAAATCGCAACGCGT-ATCCGTAAATCGTAACGTGTATCCGTTA
1 AAAATCGCAACGCGTAAC-CATAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCCGTAA
*
34130 ATCGCAACGCGT-ATCCGTAAATCGCAACGATAATACAT
64 ATCGCAACG-ATAATCCGTAAATCGCAACGATAATACAT
* * *
34168 AAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAAT
1 AAAATCGCAACGCGTAACCATAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCCGTAAAT
*
34233 CGCAACGATAATCCGTAAATCGCAACGAGAAT-C-T
66 CGCAACGATAATCCGTAAATCGCAACGATAATACAT
* * * * * *
34267 GTAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTAAATCACAAC
1 -AAAATCGCAACGCGTAA-CCATAAATCGCAACGATAATCCGTAAATCGCAAC
34319 ACTGAAATTT
Statistics
Matches: 129, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
99 3 0.02
100 45 0.35
101 79 0.61
102 2 0.02
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (101 bp):
AAAATCGCAACGCGTAACCATAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCCGTAAAT
CGCAACGATAATCCGTAAATCGCAACGATAATACAT
Found at i:35007 original size:24 final size:24
Alignment explanation
Indices: 34979--35033 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
34969 GTGAGTACTA
* * *
34979 GTCAATATTCGAAATTTGGTCTTG
1 GTCAATATCCGAAATTTGATATTG
* *
35003 GTCAATATCCGGACTTTGATATTG
1 GTCAATATCCGAAATTTGATATTG
35027 GTCAATA
1 GTCAATA
35034 CACGGATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (24 bp):
GTCAATATCCGAAATTTGATATTG
Found at i:35039 original size:24 final size:24
Alignment explanation
Indices: 35000--35046 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
34990 AAATTTGGTC
35000 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
35024 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
35047 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:37576 original size:33 final size:34
Alignment explanation
Indices: 37539--37722 Score: 144
Period size: 33 Copynumber: 5.2 Consensus size: 34
37529 GCAACGAGAG
37539 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACAATGAA
* * *
37572 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCCCAACAATGAA
*
37606 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--C--AATGAA
* * * * *
37644 AATCGCAACGAGAGAATCG-CAAT-GCGA-AATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACAATGAA
*
37677 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--C--AATGAA
37715 AATCGCAA
1 AATCGCAA
37723 CGAGAGAATC
Statistics
Matches: 123, Mismatches: 12, Indels: 27
0.76 0.07 0.17
Matches are distributed among these distances:
31 1 0.01
32 6 0.05
33 47 0.38
34 29 0.24
35 2 0.02
37 1 0.01
38 30 0.24
39 6 0.05
40 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCCCAACAATGAA
Found at i:37593 original size:34 final size:33
Alignment explanation
Indices: 37525--37628 Score: 147
Period size: 33 Copynumber: 3.1 Consensus size: 33
37515 CGGAAATTAC
* *
37525 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCCCAACGAGAAAATCGCAATGCGAAATGAA
37558 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCCCAACGA-GAAAATCGCAATGC-GAAATGAA
* *
37592 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCCCAACGAGAAAATCGCAATGCGAAATGAA
37625 AATC
1 AATC
37629 GCAATGCGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
32 1 0.02
33 33 0.52
34 29 0.45
35 1 0.02
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCCCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:37630 original size:19 final size:19
Alignment explanation
Indices: 37539--37760 Score: 241
Period size: 19 Copynumber: 12.7 Consensus size: 19
37529 GCAACGAGAG
37539 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
37558 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
37572 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
37592 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
37606 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37625 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
37644 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
37658 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37677 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37696 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
37715 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
37729 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
37748 AATCGCATTGCGA
1 AATCGCAATGCGA
37761 TTCTCCCGTT
Statistics
Matches: 172, Mismatches: 10, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
14 42 0.24
15 3 0.02
16 7 0.04
17 6 0.03
18 4 0.02
19 97 0.56
20 13 0.08
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:37652 original size:52 final size:52
Alignment explanation
Indices: 37567--37754 Score: 265
Period size: 52 Copynumber: 3.6 Consensus size: 52
37557 AAATCCCAAC
37567 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
37620 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * * *
37672 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA
* *
37722 ACGAGAGAATCGCAATGCGAAATTAAAATCGCA
1 ATGA-A-AATCGCAATGCGAAATGAAAATCGCA
37755 TTGCGATTCT
Statistics
Matches: 126, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
50 7 0.06
51 7 0.06
52 96 0.76
53 16 0.13
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:37695 original size:71 final size:71
Alignment explanation
Indices: 37606--37760 Score: 292
Period size: 71 Copynumber: 2.2 Consensus size: 71
37596 GCAACGAGAG
37606 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
37671 AATGAA
66 AATGAA
37677 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
*
37742 AATTAA
66 AATGAA
*
37748 AATCGCATTGCGA
1 AATCGCAATGCGA
37761 TTCTCCCGTT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 82 1.00
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
AATGAA
Found at i:37738 original size:33 final size:33
Alignment explanation
Indices: 37625--37754 Score: 197
Period size: 33 Copynumber: 3.8 Consensus size: 33
37615 GCGAAATGAA
37625 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
37658 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
37696 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
37729 AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
37755 TTGCGATTCT
Statistics
Matches: 89, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
33 54 0.61
34 1 0.01
35 2 0.02
36 2 0.02
37 1 0.01
38 29 0.33
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:37760 original size:52 final size:52
Alignment explanation
Indices: 37539--37760 Score: 229
Period size: 52 Copynumber: 4.2 Consensus size: 52
37529 GCAACGAGAG
* * *
37539 AATCGCAATGCGA-AAT-GAAAATCCCAACATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAGAATCG-AAATGCGAA-ACGAAAATCGCAATGC-GAAATGAA
* * * *
37592 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAGAATCGAAATGCGAAACGAAAATCGCAATGCGAAATGAA
* * * *
37644 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAGAATCGAAATGCGAAACGAAAATCGCAATGCGAAATGAA
* *
37696 AATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAGAATCG-AAATGCGAAACGA-A-AATCGCAATGCGAAATGAA
*
37748 AATCGCATTGCGA
1 AATCGCAATGCGA
37761 TTCTCCCGTT
Statistics
Matches: 152, Mismatches: 12, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
50 7 0.05
51 7 0.05
52 101 0.66
53 27 0.18
54 9 0.06
55 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAGAATCGAAATGCGAAACGAAAATCGCAATGCGAAATGAA
Found at i:37809 original size:19 final size:19
Alignment explanation
Indices: 37769--37866 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
37759 GATTCTCCCG
37769 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
37789 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
37808 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
37822 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
37841 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
37860 TTGCGAT
1 TTGCGAT
37867 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:37863 original size:52 final size:53
Alignment explanation
Indices: 37750--37866 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
37740 GAAATTAAAA
37750 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
37803 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
37855 TCGCATTGCGAT
1 TCGCATTGCGAT
37867 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:37992 original size:14 final size:14
Alignment explanation
Indices: 37973--38009 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
37963 CATCAATTAC
37973 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
37987 ACAAATCATCTTTT
1 ACAAATCAACTTTT
38001 ACAAATCAA
1 ACAAATCAA
38010 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:40006 original size:14 final size:14
Alignment explanation
Indices: 39987--40043 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
39977 GCGAAATGAA
*
39987 AATCGCAACGACAG
1 AATCGCAACGAAAG
40001 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
40018 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
40034 AATCGCAACG
1 AATCGCAACG
40044 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:40014 original size:33 final size:33
Alignment explanation
Indices: 39968--40060 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
39958 GCGAAACCAA
*
39968 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
40001 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
40034 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
40061 TGCGATTTGG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:40025 original size:19 final size:19
Alignment explanation
Indices: 39931--40065 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
39921 TAGTTTATTT
* *
39931 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
39951 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
39970 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
39989 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
40003 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
40022 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
40036 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
40055 TCGCAATGCGA
1 TCGCAACGCGA
40066 TTTGGTTTCG
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:40106 original size:33 final size:33
Alignment explanation
Indices: 40061--40151 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
40051 AAAATCGCAA
40061 TGCGA-TTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
40093 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
40126 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
40152 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 5 0.09
33 48 0.87
34 2 0.04
ACGTcount: A:0.08, C:0.19, G:0.29, T:0.45
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:40114 original size:19 final size:19
Alignment explanation
Indices: 40061--40188 Score: 107
Period size: 19 Copynumber: 7.3 Consensus size: 19
40051 AAAATCGCAA
40061 TGCGA-TTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
40079 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
40093 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
40112 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
40126 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
40145 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* * *
40164 TGCAATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
40184 TGCGA
1 TGCGA
40189 AAGTAAACTA
Statistics
Matches: 87, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 7 0.08
19 41 0.47
20 12 0.14
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:40372 original size:93 final size:93
Alignment explanation
Indices: 40236--40704 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
40226 ATGGATTGCA
*
40236 TTAC-TTCAACCAATAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
40300 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
40328 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
40393 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
40421 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
40486 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
40514 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
40579 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
40607 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
40672 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
40700 TTACT
1 TTACT
40705 AAGCAATCTA
Statistics
Matches: 374, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 370 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:42427 original size:14 final size:14
Alignment explanation
Indices: 42408--42461 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
42398 TTGAAATGAA
42408 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
42422 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
42441 AATCGCAACGAGAG
1 AATCGCAACGAGAG
42455 AATCGCA
1 AATCGCA
42462 CGCGAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:42446 original size:19 final size:19
Alignment explanation
Indices: 42422--42485 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
42412 GCAACGAGAG
42422 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
42441 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
42455 AATCGC-ACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
*
42473 AATCGCAATGCGA
1 AATCGCAACGCGA
42486 TTTTGGTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
13 1 0.03
14 8 0.23
15 3 0.09
17 3 0.09
18 7 0.20
19 13 0.37
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:42475 original size:32 final size:33
Alignment explanation
Indices: 42400--42480 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
42390 TCTTTTGGTT
42400 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
42433 GAAATGAAAATCGCAACGAGAGAATCGC-ACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
42465 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
42481 TGCGATTTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 19 0.40
33 28 0.60
ACGTcount: A:0.48, C:0.20, G:0.22, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:42503 original size:19 final size:18
Alignment explanation
Indices: 42481--42539 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
42471 AAAATCGCAA
42481 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
42500 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
42514 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
42533 TGCGATT
1 TGCGATT
42540 CTCTCGTTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 11 0.34
16 1 0.03
17 1 0.03
18 1 0.03
19 18 0.56
ACGTcount: A:0.08, C:0.19, G:0.27, T:0.46
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:42516 original size:14 final size:14
Alignment explanation
Indices: 42497--42553 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
42487 TTTGGTTTCG
*
42497 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
42511 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
42530 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
42544 CGTTGCGATT
1 CGTTGCGATT
42554 TTCATTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:42529 original size:33 final size:33
Alignment explanation
Indices: 42481--42561 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
42471 AAAATCGCAA
** *
42481 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
42514 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
42547 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
42562 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:42594 original size:41 final size:41
Alignment explanation
Indices: 42537--42614 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
42527 TCGCGTTGCG
*
42537 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
42578 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
42615 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:42599 original size:20 final size:21
Alignment explanation
Indices: 42538--42613 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
42528 CGCGTTGCGA
42538 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
42559 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
42579 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
42600 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
42614 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:42735 original size:33 final size:33
Alignment explanation
Indices: 42693--42763 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
42683 AATACTAACT
*
42693 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
42726 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
42759 TGAAA
1 TGAAA
42764 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:42996 original size:22 final size:22
Alignment explanation
Indices: 42944--42998 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
42934 TGGTTGTGAG
**
42944 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
42966 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
42988 GGATTTCTTCG
1 GGATTTCTTCG
42999 CCGTAGAGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:43165 original size:20 final size:20
Alignment explanation
Indices: 43140--43290 Score: 157
Period size: 20 Copynumber: 7.7 Consensus size: 20
43130 GCTTTAATAT
43140 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
43160 CGCGTTGCGATTTATGTATTA
1 CGCGTTGCGATTTACGGA-TA
*
43181 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
43200 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
43220 CACG-TGCGA-TTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
43238 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
43258 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
43278 CGCGTTGCGATTT
1 CGCGTTGCGATTT
43291 TGGAAAATCG
Statistics
Matches: 109, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
18 11 0.10
19 12 0.11
20 83 0.76
21 3 0.03
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:43307 original size:21 final size:21
Alignment explanation
Indices: 43277--43359 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
43267 ATTTTCATAT
*
43277 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
43298 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
43319 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
43340 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
43360 CTGGTTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:43350 original size:42 final size:43
Alignment explanation
Indices: 43257--43355 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
43247 ATTTATGTGT
* *
43257 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
43298 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
43340 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
43356 GAAACTGGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Done.