Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001266.1 Hibiscus syriacus cultivar Beakdansim tig00002484_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: 63091
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1388 original size:60 final size:60
Alignment explanation
Indices: 1308--1432 Score: 157
Period size: 60 Copynumber: 2.1 Consensus size: 60
1298 GTCAGGTGAT
* ** *
1308 CATTTTGTAACTTTCAATAGT-TGGAGGATTCAAAAAAGTAACTCCCTATAGTT-AGTGGAC
1 CATTTTATAACTTTCAATAGTCAAGA-GATTCAAAAAAGTAACACCCTATAGTTGAG-GGAC
*
1368 CATTTTATAAC-TTCTAATAGTCAAGAGATTCAACAAAGTAACACCCTATAGTTGAGGGAC
1 CATTTTATAACTTTC-AATAGTCAAGAGATTCAAAAAAGTAACACCCTATAGTTGAGGGAC
1428 CATTT
1 CATTT
1433 ATGTACTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
59 3 0.05
60 50 0.88
61 4 0.07
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (60 bp):
CATTTTATAACTTTCAATAGTCAAGAGATTCAAAAAAGTAACACCCTATAGTTGAGGGAC
Found at i:2343 original size:14 final size:14
Alignment explanation
Indices: 2324--2350 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2314 TGAGTCAATC
2324 CGTTGACTTTGACT
1 CGTTGACTTTGACT
2338 CGTTGACTTTGAC
1 CGTTGACTTTGAC
2351 CAAAAAGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (14 bp):
CGTTGACTTTGACT
Found at i:6422 original size:58 final size:58
Alignment explanation
Indices: 6356--6466 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 58
6346 TCAGGGAGAC
* * *
6356 CATTTTGTAACTTTTAATAGTTGAAG-GACTCAACAGAGCAACACCCTATAGTCGGGAT
1 CATTTTGTAACTTTTAATAG-TCAAGAGACTCAACAAAGCAACACCATATAGTCGGGAT
* *
6414 CATTTTGTAACTTTTAATAGTCAAGAGACTTAACAAAGTAACACCATATAGTC
1 CATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACACCATATAGTC
6467 AAGGGACCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
57 4 0.09
58 43 0.91
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (58 bp):
CATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACACCATATAGTCGGGAT
Found at i:11195 original size:25 final size:25
Alignment explanation
Indices: 11167--11222 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
11157 TTTGAGCTCG
* * *
11167 AGTCGAACTTCAATTTTTTATTTCA
1 AGTCGAACTTCAAGTTTTAAATTCA
* *
11192 AGTCGAATTTTAAGTTTTAAATTCA
1 AGTCGAACTTCAAGTTTTAAATTCA
11217 AGTCGA
1 AGTCGA
11223 GCTTGATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (25 bp):
AGTCGAACTTCAAGTTTTAAATTCA
Found at i:12859 original size:15 final size:15
Alignment explanation
Indices: 12839--12869 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12829 GTATTAGATT
12839 CAATGAATTAATTTG
1 CAATGAATTAATTTG
12854 CAATGAATTAATTTG
1 CAATGAATTAATTTG
12869 C
1 C
12870 GGTTGATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (15 bp):
CAATGAATTAATTTG
Found at i:23830 original size:18 final size:19
Alignment explanation
Indices: 23807--23847 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
23797 AAAATAAATT
*
23807 TAAAATTATACCCAAA-CC
1 TAAAATTATACCAAAACCC
23825 TAAAATTATACCAAAACCC
1 TAAAATTATACCAAAACCC
23844 TAAA
1 TAAA
23848 TCACAATCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (19 bp):
TAAAATTATACCAAAACCC
Found at i:29650 original size:10 final size:10
Alignment explanation
Indices: 29635--29680 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
29625 TTATTTTTTA
29635 AAAAATCAAT
1 AAAAATCAAT
*
29645 AAAAATGAATT
1 AAAAATCAA-T
*
29656 AAAAATGAAT
1 AAAAATCAAT
*
29666 AAAATTCAAT
1 AAAAATCAAT
29676 AAAAA
1 AAAAA
29681 AAAGAATGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 21 0.68
11 10 0.32
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (10 bp):
AAAAATCAAT
Found at i:29680 original size:21 final size:21
Alignment explanation
Indices: 29633--29681 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
29623 ATTTATTTTT
*
29633 TAAAAAATCAATAAAAATGAA
1 TAAAAAATCAATAAAAATCAA
* * *
29654 TTAAAAATGAATAAAATTCAA
1 TAAAAAATCAATAAAAATCAA
29675 TAAAAAA
1 TAAAAAA
29682 AAGAATGTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (21 bp):
TAAAAAATCAATAAAAATCAA
Found at i:30096 original size:249 final size:253
Alignment explanation
Indices: 29804--30304 Score: 793
Period size: 248 Copynumber: 2.0 Consensus size: 253
29794 CATTATTAAC
*
29804 TGTTGTTAAAAAATAATAATTAATGAATAATAATTCATTTGATC-CTTCAATTGTAATTAAAAGT
1 TGTTATTAAAAAATAATAATTAATGAATAATAATTCATTTGATCAC-TCAATTGTAATTAAAA-T
29868 TTATTTTAATATTTTTTATATTTTTAAACAATTAATTTTAAAAGTCAATAAATTTTTCAAAAATA
64 TTATTTTAATATTTTTTATATTTTTAAACAATTAATTTTAAAAGTCAATAAATTTTTCAAAAATA
*
29933 TATAAATATTTATAATTTTTTAAATTA-TAAA-A-CATT-T-ATCATCATC-ATCATTTTGTAAA
129 TATAAA-ATTTATAATTTTTTAAATTACAAAATATCATTATCATCATCATCTATCATTTTGTAAA
*
29992 ATG-AATACTAGTTATAAAACTTTTATAAAATTATTCCTATTTTAAAATACTTACTCTCAAT
193 A-GAAATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTACTCTCAAT
*
30053 TGTTATTAAAAAATAATAATTAATGAATAATAATTTATTTGATCACTCAATTGTAATTAAAATTT
1 TGTTATTAAAAAATAATAATTAATGAATAATAATTCATTTGATCACTCAATTGTAATTAAAATTT
30118 ATTTTAATATTTTTTATATTTTTAAACAATTAATTTTAAAAGTCAATAAATTTTTCAAAAATATA
66 ATTTTAATATTTTTTATATTTTTAAACAATTAATTTTAAAAGTCAATAAATTTTTCAAAAATATA
* *
30183 TGAAATTTATAATTTTTTAAATTACAAAATATTTATTAGCATCATCATCATCATTATCATTTTGT
131 TAAAATTTATAATTTTTTAAATTACAAAATA-TCATT---ATCATCATCATC--TATCATTTTGT
*
30248 AAAAGAAATACTATTTATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTAC
190 AAAAGAAATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTAC
30305 CCCCAATGTT
Statistics
Matches: 231, Mismatches: 7, Indels: 18
0.90 0.03 0.07
Matches are distributed among these distances:
247 20 0.09
248 74 0.32
249 59 0.26
250 1 0.00
251 3 0.01
255 1 0.00
256 9 0.04
258 1 0.00
259 63 0.27
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (253 bp):
TGTTATTAAAAAATAATAATTAATGAATAATAATTCATTTGATCACTCAATTGTAATTAAAATTT
ATTTTAATATTTTTTATATTTTTAAACAATTAATTTTAAAAGTCAATAAATTTTTCAAAAATATA
TAAAATTTATAATTTTTTAAATTACAAAATATCATTATCATCATCATCTATCATTTTGTAAAAGA
AATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTACTCTCAAT
Found at i:37341 original size:59 final size:59
Alignment explanation
Indices: 37231--37343 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 59
37221 ATTTTTAATG
***
37231 TTCTAATTTCATCCTCAAACTATGACTCATGTTCTAAATGAGTCTTTAAACTTTGAACA
1 TTCTAATTTCATCCTCAAACTATGACTCATGTTCTAAATGAGTCCCCAAACTTTGAACA
* * *
37290 TTCTAATTTCATCACT-GAACTATGACTC-TCTTTCTAAATTAGTCCCCAAACTTT
1 TTCTAATTTCATC-CTCAAACTATGACTCAT-GTTCTAAATGAGTCCCCAAACTTT
37344 TTAATATTCC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 1 0.02
59 43 0.93
60 2 0.04
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (59 bp):
TTCTAATTTCATCCTCAAACTATGACTCATGTTCTAAATGAGTCCCCAAACTTTGAACA
Found at i:37612 original size:50 final size:50
Alignment explanation
Indices: 37553--37652 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
37543 ATAAAAGTCT
* *
37553 TAGTTTAGGGATGAAATTGAAATGTTCAAAATTTTG-AGGACTAATTTAGA
1 TAGTTTAGGGATGAAATTGAAATGTTCAAAA-GTTGAAGAACTAATTTAGA
*
37603 TAGTTTAGGGATGAAATTGAAATTTTCAAAAGTTGAAGAACTAATTTAGA
1 TAGTTTAGGGATGAAATTGAAATGTTCAAAAGTTGAAGAACTAATTTAGA
37653 ATCATAGTCC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 3 0.07
50 43 0.93
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (50 bp):
TAGTTTAGGGATGAAATTGAAATGTTCAAAAGTTGAAGAACTAATTTAGA
Found at i:38328 original size:60 final size:59
Alignment explanation
Indices: 38174--38348 Score: 183
Period size: 60 Copynumber: 2.9 Consensus size: 59
38164 GTTTGAAATA
* * **
38174 AAATTGAAATGTTCTAAAAAGTTTGGAGATTAATTTAGAAGGAATGTCATAATTTGGGGATG
1 AAATTGAAATGTT-T-AAAAGTTTGG-GATTAATTTAAAATGAATGTCATAATTTAAGGATG
* * * *
38236 AAATTGAAATGTTCAAAAGTTTGAAGACTAATTTAAAATGACA-GTCATAGTTTAAGGATG
1 AAATTGAAATGTTTAAAAGTTTG-GGATTAATTTAAAATGA-ATGTCATAATTTAAGGATG
* *
38296 AAATTGAAATGTTTAAAAGTTTAGGGATTAATTCAAAAT-AATGATAATAATTT
1 AAATTGAAATGTTTAAAAGTTT-GGGATTAATTTAAAATGAATG-TCATAATTT
38349 GAAGACATGT
Statistics
Matches: 94, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
58 1 0.01
59 2 0.02
60 76 0.81
61 2 0.02
62 13 0.14
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (59 bp):
AAATTGAAATGTTTAAAAGTTTGGGATTAATTTAAAATGAATGTCATAATTTAAGGATG
Found at i:38427 original size:53 final size:53
Alignment explanation
Indices: 38347--38452 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
38337 TGATAATAAT
38347 TTGAAGACATGTGATGCAATTAGCTCTATGTTTTTAGTCTACTAGGTCCAATG
1 TTGAAGACATGTGATGCAATTAGCTCTATGTTTTTAGTCTACTAGGTCCAATG
38400 TTGAAGACATGTGATGCAATTAGCTCTATGTTTTTAGTCTACTAGGTCCAATG
1 TTGAAGACATGTGATGCAATTAGCTCTATGTTTTTAGTCTACTAGGTCCAATG
38453 AGATCCATGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (53 bp):
TTGAAGACATGTGATGCAATTAGCTCTATGTTTTTAGTCTACTAGGTCCAATG
Found at i:45479 original size:48 final size:48
Alignment explanation
Indices: 45423--45531 Score: 150
Period size: 48 Copynumber: 2.3 Consensus size: 48
45413 AAATTAAATA
* *
45423 AACTTAATTATCAAGTAATCTTAAGAC-ACTAAAATTATAATAAAACTT
1 AACTTAATTACCAAGTAATCTTAA-ACTACTAAAATTAAAATAAAACTT
* * *
45471 AACTTAATTACCAAGTAATCTTCAACTAGTAGAATTAAAATAAAACTT
1 AACTTAATTACCAAGTAATCTTAAACTACTAAAATTAAAATAAAACTT
45519 AA-TTAATTACCAA
1 AACTTAATTACCAA
45532 TTATAATTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
47 13 0.24
48 42 0.76
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.32
Consensus pattern (48 bp):
AACTTAATTACCAAGTAATCTTAAACTACTAAAATTAAAATAAAACTT
Found at i:48964 original size:2 final size:2
Alignment explanation
Indices: 48957--49001 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
48947 GTCTTTTATT
* *
48957 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA -A AA 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
48998 TA TA
1 TA TA
49002 CTCACATTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:51533 original size:153 final size:153
Alignment explanation
Indices: 51255--51533 Score: 396
Period size: 153 Copynumber: 1.8 Consensus size: 153
51245 ACAATGTAGA
* * * * *
51255 TCTTTTAACATTAGTGTTTTGCAAGTTAGCTGGGCTCTGAACATTGTTAAAGAACCCTCCATTGC
1 TCTTTTAACATCAGAGTTCTGCAAATTAGCTGGGCTCCGAACATTGTTAAAGAACCCTCCATTGC
* * * * * * *
51320 TACGTTGATCGGCTACATTTGAGATTATCCTCTCCTGATCCTTGATAGTTTGTTCTTCTCCAAAT
66 TACGTTGATCAGCTACATTAGAGATTATCCTCTCCAGAGCCTTCACAGTTAGTTCTTCTCCAAAT
51385 GTTTGTTTCAATAATGTACGTCT
131 GTTTGTTTCAATAATGTACGTCT
* * *
51408 TCTTTTAACATCAGAGTTCTGCAAATTAGCTGGGCTCCGAACATTGTTACAGAAGCCTCCTTTGC
1 TCTTTTAACATCAGAGTTCTGCAAATTAGCTGGGCTCCGAACATTGTTAAAGAACCCTCCATTGC
** *
51473 TTTGTTGATCAGTTACATTAGAGATTATCCTCTCCAGAGCCTTCACAGTTAGTTCTTCTCC
66 TACGTTGATCAGCTACATTAGAGATTATCCTCTCCAGAGCCTTCACAGTTAGTTCTTCTCC
51534 CAGTAAACCT
Statistics
Matches: 108, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
153 108 1.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (153 bp):
TCTTTTAACATCAGAGTTCTGCAAATTAGCTGGGCTCCGAACATTGTTAAAGAACCCTCCATTGC
TACGTTGATCAGCTACATTAGAGATTATCCTCTCCAGAGCCTTCACAGTTAGTTCTTCTCCAAAT
GTTTGTTTCAATAATGTACGTCT
Found at i:51571 original size:153 final size:149
Alignment explanation
Indices: 51257--51690 Score: 362
Period size: 153 Copynumber: 2.9 Consensus size: 149
51247 AATGTAGATC
* * * * *
51257 TTTTAACATTAGTGTTTTGCAAGTTAGCTGGGCTCTGAACATTGTTAAAGAACCCTCCATTGCTA
1 TTTTAACATCAGAGTTCTGCAAATTAGCTGGGCTCCGAACATTGTTAAAGAACCCTCCATTGCTA
* * * * * * *
51322 CGTTGATCGGCTACATTTGAGATTATCCTCTCCTGATCCTTGATAGTTTGTTCTTCTCCAAATGT
66 CGTTGATCAGCTACATTAGAGATTATCCTCTCCAGAGCCTTCACAGTTAGTTCTTCTCCAAATGT
*
51387 TTGTTTCAATAATGTACGTCTT
131 TTCTTTCAATAA-GTAC-TC-T
* * *
51409 CTTTTAACATCAGAGTTCTGCAAATTAGCTGGGCTCCGAACATTGTTACAGAAGCCTCCTTTGCT
1 -TTTTAACATCAGAGTTCTGCAAATTAGCTGGGCTCCGAACATTGTTAAAGAACCCTCCATTGCT
** *
51474 TTGTTGATCAGTTACATTAGAGATTATCCTCTCCAGAGCCTTCACAGTTAGTTCTTCTCCCAGTA
65 ACGTTGATCAGCTACATTAGAGATTATCCTCTCCAGAGCCTTCACAGTTAGTTCTTCT-CC---A
*
51539 AACCT-TTTACTTTCCATAA-TA-T-T
126 AA--TGTTT-CTTTCAATAAGTACTCT
* * * * * *
51562 TTTTGAACATCAGA-TTCCTG-AAAGTTAGCTGAGCTCTGATCATTTTTAAGGAACCCTCCAATG
1 TTTT-AACATCAGAGTT-CTGCAAA-TTAGCTGGGCTCCGAACATTGTTAAAGAACCCTCCATTG
* * * ** * * *
51625 CTACGTTGATCAGTTGCATCT-GGGA-TAGTCCTCTCTTGAGCCTTGATAGTTTGTTCTTCTCCA
63 CTACGTTGATCAGCTACAT-TAGAGATTA-TCCTCTCCAGAGCCTTCACAGTTAGTTCTTCTCCA
51688 AAT
126 AAT
51691 AGTCCCTTCA
Statistics
Matches: 231, Mismatches: 38, Indels: 30
0.77 0.13 0.10
Matches are distributed among these distances:
147 1 0.00
149 3 0.01
152 13 0.06
153 193 0.84
154 3 0.01
155 1 0.00
157 5 0.02
158 3 0.01
159 9 0.04
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (149 bp):
TTTTAACATCAGAGTTCTGCAAATTAGCTGGGCTCCGAACATTGTTAAAGAACCCTCCATTGCTA
CGTTGATCAGCTACATTAGAGATTATCCTCTCCAGAGCCTTCACAGTTAGTTCTTCTCCAAATGT
TTCTTTCAATAAGTACTCT
Found at i:53873 original size:23 final size:24
Alignment explanation
Indices: 53839--53883 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
53829 ACGGTTGATT
53839 TTGATAGTTGACCATTAACTTTGA
1 TTGATAGTTGACCATTAACTTTGA
* *
53863 TTGAT-GTTGACCTTTTACTTT
1 TTGATAGTTGACCATTAACTTT
53884 AACCCTAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.49
Consensus pattern (24 bp):
TTGATAGTTGACCATTAACTTTGA
Found at i:54676 original size:3 final size:3
Alignment explanation
Indices: 54668--54693 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54658 TTGATGAATC
54668 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
54694 GAGAAGTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:55346 original size:28 final size:26
Alignment explanation
Indices: 55324--55374 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
55314 ATTTTATGTT
*
55324 TAGGAGAGAACTTATAAAATTTTAAG
1 TAGGAAAGAACTTATAAAATTTTAAG
*
55350 TATGAAAGAACTTATAAAATTTTAA
1 TAGGAAAGAACTTATAAAATTTTAA
55375 AGGATCGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.33
Consensus pattern (26 bp):
TAGGAAAGAACTTATAAAATTTTAAG
Found at i:58297 original size:132 final size:132
Alignment explanation
Indices: 58110--58957 Score: 954
Period size: 132 Copynumber: 6.5 Consensus size: 132
58100 TGGCGGTCTC
* * * * * * * *
58110 ACAGTTGACTGTTGATCTACGTTGCGAACATTGGCACCAATGGAAAAAGGGTTTATATATGTTTC
1 ACAGTCGACTGCTGGTCTAAGTTGCGAGCATTGGCACCAATGGAGAAAGGGTTTATATTTATTTC
* *
58175 TCTCGGCCTTGGCGGTGTCGGATTCGAGTTGTTCACCGTCGATT-GAATCGAAACAGGAAGTGGT
66 TCTTGGCCTTGGCGGTGTCGGATTCGAGTTGTTCACCGTCGATTGGAA-CGAAACAGGCAGTGGT
58239 CCG
130 CCG
* * * *
58242 GCAGGCGACTGCTGGTCTAAGTTGCGAGCAGTGGCACCAATGGAGAAAGGATTTATATTTATTTC
1 ACAGTCGACTGCTGGTCTAAGTTGCGAGCATTGGCACCAATGGAGAAAGGGTTTATATTTATTTC
* * * *
58307 TCTTAGCCTTGGCGGAGTTGGATT--A---G---A--G-CG-TTGGAACGAAACTGGCAGTGGTC
66 TCTTGGCCTTGGCGGTGTCGGATTCGAGTTGTTCACCGTCGATTGGAACGAAACAGGCAGTGGTC
58360 CG
131 CG
* *
58362 ACAGTCGACTGCTGGTCTAAGTTGCGAGCATTGGCACCAATGGAGAAAGGGTTTCTAGTTATTTC
1 ACAGTCGACTGCTGGTCTAAGTTGCGAGCATTGGCACCAATGGAGAAAGGGTTTATATTTATTTC
** * * *
58427 TCTTGGCCTTGAAGGTGTCGGATTTGAGTTTTTCTCCGTCGATTGGAACGAAACAGGCAGTGGTC
66 TCTTGGCCTTGGCGGTGTCGGATTCGAGTTGTTCACCGTCGATTGGAACGAAACAGGCAGTGGTC
*
58492 TG
131 CG
* * * * * * *
58494 ACAGTCGACTGCTGGTCTACGTTGCAAACTTTGGCACCAAAGGAGAAAGGGTTTATATATGTTTC
1 ACAGTCGACTGCTGGTCTAAGTTGCGAGCATTGGCACCAATGGAGAAAGGGTTTATATTTATTTC
* * * * *
58559 TCTCGGCCTTGGCGGTGTCGGATTCGAGTTGTTCTCCGTCAATTGGAACGAAACAGCCAGTGGTT
66 TCTTGGCCTTGGCGGTGTCGGATTCGAGTTGTTCACCGTCGATTGGAACGAAACAGGCAGTGGTC
58624 CG
131 CG
* * * * * *
58626 ACAGTCGACTGCTGGTCTACGTTGCGAGCGTTGGCTCCAGTGGAAAAAGGGTTTATATTTGTTTC
1 ACAGTCGACTGCTGGTCTAAGTTGCGAGCATTGGCACCAATGGAGAAAGGGTTTATATTTATTTC
** * * * *
58691 TCTTGGCCTTCTCGGTGTCGGATTCGAGTTGTTCCCCGTGGATTGAAACGAAACAGGCAGCGGTC
66 TCTTGGCCTTGGCGGTGTCGGATTCGAGTTGTTCACCGTCGATTGGAACGAAACAGGCAGTGGTC
*
58756 TG
131 CG
* * *** * *
58758 ACCA-TTGACTGCTGATCTAAGTTGCGAGCATTGATTCCAATGGAGAAAGGATTTATATTCATTT
1 A-CAGTCGACTGCTGGTCTAAGTTGCGAGCATTGGCACCAATGGAGAAAGGGTTTATATTTATTT
* *
58822 CTCTTGGCCTCGGCGGTCTCGGATTCGAGTTGTT-ACCCGTCGATTGGAACGAAACAGGCAGTGG
65 CTCTTGGCCTTGGCGGTGTCGGATTCGAGTTGTTCA-CCGTCGATTGGAACGAAACAGGCAGTGG
*
58886 CCCG
129 TCCG
** ** *
58890 ACAGTCGACTGCTGGTCTAACG-TGCGAGCATTGGGTCCAACAGAGAAAGGGTTTACATTTATTT
1 ACAGTCGACTGCTGGTCTAA-GTTGCGAGCATTGGCACCAATGGAGAAAGGGTTTATATTTATTT
58954 CTCT
65 CTCT
58958 CGGCTGCAGC
Statistics
Matches: 599, Mismatches: 100, Indels: 34
0.82 0.14 0.05
Matches are distributed among these distances:
120 97 0.16
121 5 0.01
122 2 0.00
124 1 0.00
127 1 0.00
130 2 0.00
131 4 0.01
132 484 0.81
133 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (132 bp):
ACAGTCGACTGCTGGTCTAAGTTGCGAGCATTGGCACCAATGGAGAAAGGGTTTATATTTATTTC
TCTTGGCCTTGGCGGTGTCGGATTCGAGTTGTTCACCGTCGATTGGAACGAAACAGGCAGTGGTC
CG
Found at i:61012 original size:20 final size:20
Alignment explanation
Indices: 60958--61013 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
60948 TAACGCAAAC
* *
60958 TCCAATTTCGCAACACAGTT
1 TCCAAATTCGCAACTCAGTT
60978 TCCAAATTCGCAACTCAGTT
1 TCCAAATTCGCAACTCAGTT
**
60998 TTGAAATTCGCAACTC
1 TCCAAATTCGCAACTC
61014 GAATTTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.29, G:0.11, T:0.30
Consensus pattern (20 bp):
TCCAAATTCGCAACTCAGTT
Found at i:61324 original size:20 final size:20
Alignment explanation
Indices: 61257--61324 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
61247 AGCAGAATTC
**
61257 GTGTTGCGAATTTCAAAACT
1 GTGTTGCGAATTTGGAAACT
** * *
61277 AAGTTGCGAATCTAGGAAATT
1 GTGTTGCGAAT-TTGGAAACT
61298 CGTGTTGCGAATTTGGAAACT
1 -GTGTTGCGAATTTGGAAACT
61319 GTGTTG
1 GTGTTG
61325 TGAAATTAGA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
20 15 0.42
21 12 0.33
22 9 0.25
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (20 bp):
GTGTTGCGAATTTGGAAACT
Done.