Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002841.1 Hibiscus syriacus cultivar Beakdansim tig00005847_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: 61405
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:199 original size:20 final size:20
Alignment explanation
Indices: 161--240 Score: 88
Period size: 20 Copynumber: 4.0 Consensus size: 20
151 GTATCCTATT
** *
161 CACTGGTAATCTTTTATTCT
1 CACTGGTAATCTTACATTCC
* *
181 GATTGGTAATCTTACATTCC
1 CACTGGTAATCTTACATTCC
201 CACTGGTAATCTTACATTCC
1 CACTGGTAATCTTACATTCC
* * *
221 TACTAGTACTCTTACATTCC
1 CACTGGTAATCTTACATTCC
241 GTGGACCAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.24, C:0.25, G:0.10, T:0.41
Consensus pattern (20 bp):
CACTGGTAATCTTACATTCC
Found at i:11910 original size:19 final size:20
Alignment explanation
Indices: 11865--11925 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
11855 GTTACAAGCC
11865 TAACTAACAATCTAACTAATTAA
1 TAAC-AACAATCTAACTAA-T-A
**
11888 TAACTGCAATCTAACTAAT-
1 TAACAACAATCTAACTAATA
*
11907 TAACAACAACCTAACTAAT
1 TAACAACAATCTAACTAAT
11926 CAAATAACAG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 16 0.48
21 1 0.03
22 12 0.36
23 4 0.12
ACGTcount: A:0.49, C:0.21, G:0.02, T:0.28
Consensus pattern (20 bp):
TAACAACAATCTAACTAATA
Found at i:13281 original size:27 final size:29
Alignment explanation
Indices: 13228--13281 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 29
13218 AAAATTAGGG
* **
13228 TTTTTTTCATAAATAAAATAATTTTTTAA
1 TTTTTTTCATAAAAAAAATAAAATTTTAA
13257 TTTTTTT-A-AAAAAAAATAAAATTTT
1 TTTTTTTCATAAAAAAAATAAAATTTT
13282 CAAAATTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 14 0.64
28 1 0.05
29 7 0.32
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTTTTTCATAAAAAAAATAAAATTTTAA
Found at i:15396 original size:32 final size:32
Alignment explanation
Indices: 15360--15433 Score: 148
Period size: 32 Copynumber: 2.3 Consensus size: 32
15350 TTGGGGCTTG
15360 AGAGCCTACCTAAGAAAGTTTCTCGGGGCCTC
1 AGAGCCTACCTAAGAAAGTTTCTCGGGGCCTC
15392 AGAGCCTACCTAAGAAAGTTTCTCGGGGCCTC
1 AGAGCCTACCTAAGAAAGTTTCTCGGGGCCTC
15424 AGAGCCTACC
1 AGAGCCTACC
15434 CAAGGGTCAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.26, C:0.30, G:0.24, T:0.20
Consensus pattern (32 bp):
AGAGCCTACCTAAGAAAGTTTCTCGGGGCCTC
Found at i:17640 original size:13 final size:13
Alignment explanation
Indices: 17624--17668 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
17614 AAGTCAACGT
17624 TCAACGGTCAAAG
1 TCAACGGTCAAAG
*
17637 TCAATGGGTCAAAG
1 TCAA-CGGTCAAAG
**
17651 TTGACGGTCAAAG
1 TCAACGGTCAAAG
17664 TCAAC
1 TCAAC
17669 ATGTTGTCTC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (13 bp):
TCAACGGTCAAAG
Found at i:19772 original size:12 final size:12
Alignment explanation
Indices: 19755--19779 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19745 ATATTTTCGA
19755 TAAAATATTATT
1 TAAAATATTATT
19767 TAAAATATTATT
1 TAAAATATTATT
19779 T
1 T
19780 TTTATCGAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:19927 original size:79 final size:78
Alignment explanation
Indices: 19829--19984 Score: 226
Period size: 78 Copynumber: 2.0 Consensus size: 78
19819 AAAAAATAAT
* ** *
19829 ATTTTAGGTAGCGTCCAATATTAACATTTTCAGTAGAAAAAATAATATTTTAGGTAGCGTTTTA-
1 ATTTTAGGTAGCGTCCAATATTAACATTTTCAATAG-AAAAATAATATTTTAAATAACGTTTTAT
19893 CTAAAAATATTAAAC
65 C-AAAAATATTAAAC
*
19908 ATTTTAGGTAGCG-CTCAATATTAATATTTTCAATAGAAAAATAATATTTTAAATAACGTTTTAT
1 ATTTTAGGTAGCGTC-CAATATTAACATTTTCAATAGAAAAATAATATTTTAAATAACGTTTTAT
19972 CAAAAATATTAAA
65 CAAAAATATTAAA
19985 AAAATATTAA
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
78 37 0.53
79 33 0.47
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (78 bp):
ATTTTAGGTAGCGTCCAATATTAACATTTTCAATAGAAAAATAATATTTTAAATAACGTTTTATC
AAAAATATTAAAC
Found at i:24757 original size:180 final size:181
Alignment explanation
Indices: 24323--24795 Score: 630
Period size: 180 Copynumber: 2.6 Consensus size: 181
24313 GATCCAAATT
* * * * * **
24323 AAAAATGTATCGATCCACAACGATATAACAGGTAAAACTATAACAAAACTAATATTGAAATGATA
1 AAAAATGTATCGATCAACAACGATATAACA-GTAAAAATATGATAAAAC-AGTATCAAAATGATA
* * *
24388 AAACCGGTAAAGCGGTACCGGATATATTTAAAGTGTC-AGTACTTTAATATAAGGATCGACACTT
64 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGA-TACTTTAATATAAGGATCGACACTT
* * *
24452 CGTTAATTTAAAAGAGAAATAGTTTTAGCGCCTATAAAGTGTCGATTCTTTAAA
128 CGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
* * * *
24506 AAAAATATATTGATCAACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATG
1 AAAAATGTATCGATCAACAACGATATAACA-GTAAAAATATGATAAAA-CAGTATCAAAATGATA
* * * *
24571 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATTGACACTTT
64 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
24635 GTGAATTTAAAAGATAAGCAGTTTTAGCGCCTATAAAGTGTCGATAC-TT-AA
129 GTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
*
24686 AAAAATGTATCGATCTACAACGATATAACAGATAAAAATATGATAAAAGCAGTATCAAAATGATA
1 AAAAATGTATCGATCAACAACGATATAACAG-TAAAAATATGATAAAA-CAGTATCAAAATGATA
*
24751 AAACCGGTAAAATGATACCGGATATATTAAAAGTGTCGATACTTT
64 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
24796 CGTAAGTAAG
Statistics
Matches: 256, Mismatches: 31, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
179 1 0.00
180 101 0.39
181 2 0.01
182 59 0.23
183 91 0.36
184 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.28
Consensus pattern (181 bp):
AAAAATGTATCGATCAACAACGATATAACAGTAAAAATATGATAAAACAGTATCAAAATGATAAA
ACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGT
GAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
Found at i:26926 original size:15 final size:15
Alignment explanation
Indices: 26906--26938 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
26896 TGGTTGTATT
*
26906 GGGGGATGACGGTGA
1 GGGGGACGACGGTGA
26921 GGGGGACGACGGTGA
1 GGGGGACGACGGTGA
26936 GGG
1 GGG
26939 AAAACAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.09, G:0.64, T:0.09
Consensus pattern (15 bp):
GGGGGACGACGGTGA
Found at i:27046 original size:21 final size:21
Alignment explanation
Indices: 27020--27084 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
27010 AAGACAATCA
*
27020 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
*
27041 AGAGTCAAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
27062 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
27083 AG
1 AG
27085 GCATAAGGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.43, C:0.11, G:0.29, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:27160 original size:33 final size:33
Alignment explanation
Indices: 27118--27183 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
27108 AAATAGATGG
*
27118 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
27151 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
27184 TCTTAAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:27409 original size:33 final size:33
Alignment explanation
Indices: 27371--27443 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
27361 AAAATATGAA
27371 GAAGAAAAGAGGGAGGA-GATAGAAGAAGAGATG
1 GAAGAAAAGAGGGAGGAGGA-AGAAGAAGAGATG
27404 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
1 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
*
27437 AAAGAAA
1 GAAGAAA
27444 TGAAGAAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
33 36 0.95
34 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.41, T:0.04
Consensus pattern (33 bp):
GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
Found at i:27457 original size:33 final size:33
Alignment explanation
Indices: 27391--27458 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
27381 GGGAGGAGAT
* * * *
27391 AGAAGAAGAGATGGAAGAAAAGAGGGAGGAGGA
1 AGAAGAAGAGATGAAAGAAAAGAAGAAGAAGGA
*
27424 AGAAGAAGAGATGAAAGAAATGAAGAAGAAGGA
1 AGAAGAAGAGATGAAAGAAAAGAAGAAGAAGGA
27457 AG
1 AG
27459 TCGATGTCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.40, T:0.04
Consensus pattern (33 bp):
AGAAGAAGAGATGAAAGAAAAGAAGAAGAAGGA
Found at i:29032 original size:19 final size:20
Alignment explanation
Indices: 29008--29056 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
28998 AATGTAGGGT
29008 TAATTTTGTATTA-GATTTA
1 TAATTTTGTATTACGATTTA
29027 TAATTTTGTA-TACGATTTA
1 TAATTTTGTATTACGATTTA
29046 TAATTTTGTAT
1 TAATTTTGTAT
29057 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.07
19 26 0.93
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (20 bp):
TAATTTTGTATTACGATTTA
Found at i:29642 original size:200 final size:200
Alignment explanation
Indices: 29291--29676 Score: 700
Period size: 200 Copynumber: 1.9 Consensus size: 200
29281 AATTTATAAT
29291 ATGGCAAACAAGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAAGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
29356 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCAGTATAAGTATATCGGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCAGTATAAGTATACCGGATTT
* *
29421 ATGAGAGAATATGTATAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTATAATATATGTATCGACACATTTTAATTTTGTGTCGATACTATTGGTCCAG
29486 AATGA
196 AATGA
*
29491 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAAGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
* *
29556 TGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCAGTATAAGTATACCGGATTT
* *
29621 ATGAGAGAATAGGTGTAATATATGTATTGACACATTTTAATTTTGTGTCGATACTA
131 ATGAGAGAATAGGTATAATATATGTATCGACACATTTTAATTTTGTGTCGATACTA
29677 ATTTAAATAT
Statistics
Matches: 178, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
200 178 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAAGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCAGTATAAGTATACCGGATTT
ATGAGAGAATAGGTATAATATATGTATCGACACATTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGA
Found at i:32078 original size:23 final size:23
Alignment explanation
Indices: 32052--32138 Score: 104
Period size: 23 Copynumber: 3.8 Consensus size: 23
32042 CAGATCCTAT
32052 AATTGCACCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* * *
32075 AATTGTACCGGAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACATAG
* *
32098 AATTACACC-AGAGTGCCGCATAG
1 AATTGCACCGA-AGTGCCACATAG
*
32121 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
32139 TATAATAATG
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:32274 original size:103 final size:103
Alignment explanation
Indices: 32154--32366 Score: 399
Period size: 103 Copynumber: 2.1 Consensus size: 103
32144 TAATGTCCAT
32154 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
32219 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
32257 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
32322 GACTTCACACATGTTCCAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
32360 AATGACC
1 AAGGACC
32367 GCGTAGACCC
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:33383 original size:21 final size:21
Alignment explanation
Indices: 33357--33401 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
33347 GATTTCTGGG
* *
33357 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
33378 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
33399 CAA
1 CAA
33402 ACGACAGAAT
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:34115 original size:31 final size:31
Alignment explanation
Indices: 34077--34261 Score: 327
Period size: 31 Copynumber: 6.0 Consensus size: 31
34067 GGGTCGAGGG
34077 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
34108 TTACCTATGTTCTTCGGGACATATAGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
34139 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
34170 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
34201 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
34232 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
34262 GTCCTTCGGG
Statistics
Matches: 149, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
31 148 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:38084 original size:21 final size:21
Alignment explanation
Indices: 38058--38102 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38048 GATTTCTGGG
* *
38058 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
38079 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
38100 CAA
1 CAA
38103 ACGACAGAAT
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:38816 original size:31 final size:31
Alignment explanation
Indices: 38778--38962 Score: 327
Period size: 31 Copynumber: 6.0 Consensus size: 31
38768 GGGTCGAGGG
38778 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
38809 TTACCTATGTTCTTCGGGACATATAGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
38840 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
38871 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
38902 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
38933 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
38963 GTCCTTCGGG
Statistics
Matches: 149, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
31 148 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:40777 original size:22 final size:21
Alignment explanation
Indices: 40752--40811 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
40742 TTCGCTTGAG
*
40752 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
40774 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
40794 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
40812 CCCATAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 17 0.47
21 9 0.25
22 10 0.28
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:43230 original size:184 final size:184
Alignment explanation
Indices: 42826--43541 Score: 1256
Period size: 184 Copynumber: 3.9 Consensus size: 184
42816 ATATCAGCAT
42826 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
* *
42891 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTTTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACC
* * *
42956 CA-ATCGACACTTTTTAATATTGTATCACTACTTTATGTCCAGAATGGATGAAA
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
* *
43009 AAAGTGTTGATACCTTTTCAAAAAGTGTCGATTGAAAAATCATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
* * * * *
43074 ATAGGTAATTTTTTAATATAACTGGTATAAATAAAACAGTTTTATGAGAGAATATGTCTACAACC
66 ATAGGTAATTTTTTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACC
43139 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
*
43193 AAATTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
**
43258 ATAGGTAATTTTTTAATATAATTGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTTTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACC
*
43323 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCTAGAATGGATGAAA
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
*
43377 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCTGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
43442 ATAGGTAATTTTTTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTTTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACC
43507 TATATCGACACTTTTTAATATTGTGTC-CATACTTT
131 TATATCGACACTTTTTAATATTGTGTCGC-TACTTT
43542 TAAGTAACGC
Statistics
Matches: 506, Mismatches: 25, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
183 123 0.24
184 383 0.76
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (184 bp):
AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
ATAGGTAATTTTTTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACC
TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
Found at i:46208 original size:21 final size:22
Alignment explanation
Indices: 46164--46208 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
46154 ATTACATAAC
*
46164 TTTAAAAAAAGTATGGATCCCT
1 TTTAAAAAAAGTATGGATCACT
*
46186 TTTATAAAAAGTATGGA-CACT
1 TTTAAAAAAAGTATGGATCACT
46207 TT
1 TT
46209 CAACATATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (22 bp):
TTTAAAAAAAGTATGGATCACT
Found at i:46700 original size:23 final size:23
Alignment explanation
Indices: 46667--46714 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
46657 AAATAGGTCA
*
46667 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTAATACATT
* *
46690 ATATAAGCGCTACCTAATATATT
1 ATATAAACGCTACCTAATACATT
46713 AT
1 AT
46715 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (23 bp):
ATATAAACGCTACCTAATACATT
Done.