Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003016.1 Hibiscus syriacus cultivar Beakdansim tig00006260_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: 72143
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5283 original size:5 final size:5
Alignment explanation
Indices: 5273--5310 Score: 67
Period size: 5 Copynumber: 7.4 Consensus size: 5
5263 AAAGATGTAC
5273 AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG AAAGGG AA
1 AAGGG AAGGG AAGGG AAGGG AAGGG AAGGG -AAGGG AA
5311 ACCTTGCGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (5 bp):
AAGGG
Found at i:5904 original size:21 final size:21
Alignment explanation
Indices: 5878--5923 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
5868 TTGATGACAT
5878 GTTTTCTGTTCTTAATTTTTG
1 GTTTTCTGTTCTTAATTTTTG
5899 GTTTTCTGTTCTTAATTTTTG
1 GTTTTCTGTTCTTAATTTTTG
5920 GTTT
1 GTTT
5924 GTGAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.09, C:0.09, G:0.15, T:0.67
Consensus pattern (21 bp):
GTTTTCTGTTCTTAATTTTTG
Found at i:7489 original size:44 final size:44
Alignment explanation
Indices: 7434--7519 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
7424 TATGATAGTG
* * *
7434 CCCCGATGGACATGAGTAACATAATAGTGTAATGATAACATAGC
1 CCCCGAGGGACATGAGTAACATAATAGGGCAATGATAACATAGC
*
7478 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATA
1 CCCCGAGGGACATGAGTAACATAATAGGGCAATGATAACATA
7520 TTCTCTGACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (44 bp):
CCCCGAGGGACATGAGTAACATAATAGGGCAATGATAACATAGC
Found at i:7643 original size:43 final size:43
Alignment explanation
Indices: 7595--7679 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
7585 TGAATAGTGC
* *
7595 CCCCGAGGGACATGAGTGACATAATAGGGTAATGATAACATAA
1 CCCCGAGGGACATGAGTGACATAATAGGGCAACGATAACATAA
7638 CCCCGAGGGACATGAGTGACATAATAGGGCAACGATAACATA
1 CCCCGAGGGACATGAGTGACATAATAGGGCAACGATAACATA
7680 TCTGACAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (43 bp):
CCCCGAGGGACATGAGTGACATAATAGGGCAACGATAACATAA
Found at i:10830 original size:13 final size:13
Alignment explanation
Indices: 10812--10837 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10802 ACCTAAATAA
10812 TTATTTAAAAATT
1 TTATTTAAAAATT
10825 TTATTTAAAAATT
1 TTATTTAAAAATT
10838 ATTTTATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTATTTAAAAATT
Found at i:10852 original size:22 final size:24
Alignment explanation
Indices: 10824--10886 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
10814 ATTTAAAAAT
*
10824 TTTATTTAAAAATTATT-TTA-TA
1 TTTATTTAAAAATTATTAATATTA
*
10846 TTTATTTAATATAATAATTAATATTA
1 TTTATTTAA-A-AATTATTAATATTA
*
10872 TTTATATAAAAATTA
1 TTTATTTAAAAATTA
10887 ATTATTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 9 0.27
23 1 0.03
24 10 0.30
25 3 0.09
26 10 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTATTTAAAAATTATTAATATTA
Found at i:10880 original size:21 final size:23
Alignment explanation
Indices: 10847--10893 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
10837 TATTTTATAT
*
10847 TTATTTAATATAATAATTAA-TA
1 TTATTTAATATAAAAATTAATTA
10869 TTATTT-ATATAAAAATTAATTA
1 TTATTTAATATAAAAATTAATTA
10891 TTA
1 TTA
10894 ATTTTCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTATTTAATATAAAAATTAATTA
Found at i:12320 original size:24 final size:23
Alignment explanation
Indices: 12288--12336 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
12278 AAAATTTCAG
*
12288 GAGCTCGATTGAAGCTCGAGACTC
1 GAGCTCGATTGAAACTCGA-ACTC
12312 GAGCTCGATTGAAACTCGAACTC
1 GAGCTCGATTGAAACTCGAACTC
12335 GA
1 GA
12337 TTCAAGCTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (23 bp):
GAGCTCGATTGAAACTCGAACTC
Found at i:12346 original size:17 final size:17
Alignment explanation
Indices: 12308--12351 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
12298 GAAGCTCGAG
* *
12308 ACTCGAGCTCGATTGAA
1 ACTCGAACTCGATTCAA
12325 ACTCGAACTCGATTCAA
1 ACTCGAACTCGATTCAA
*
12342 GCTCGAACTC
1 ACTCGAACTC
12352 AAACTTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.23
Consensus pattern (17 bp):
ACTCGAACTCGATTCAA
Found at i:13183 original size:54 final size:54
Alignment explanation
Indices: 13123--13259 Score: 220
Period size: 54 Copynumber: 2.5 Consensus size: 54
13113 TACCTCCTGG
*
13123 GGGGTATCGGTATCCTCTGAGCAATCTGTTATTTATCGGAGCCAAATCTTACAT
1 GGGGTATCGGTACCCTCTGAGCAATCTGTTATTTATCGGAGCCAAATCTTACAT
* * *
13177 GGGGTATCGGTACCCTCCGAGCAATCTGTTATTTCTCTGAGCCAAATCTTACAT
1 GGGGTATCGGTACCCTCTGAGCAATCTGTTATTTATCGGAGCCAAATCTTACAT
*
13231 GGTGGTATCGGTACCCTCTGGGCAATCTG
1 GG-GGTATCGGTACCCTCTGAGCAATCTG
13260 GTTTTTCAGT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
54 52 0.68
55 24 0.32
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.31
Consensus pattern (54 bp):
GGGGTATCGGTACCCTCTGAGCAATCTGTTATTTATCGGAGCCAAATCTTACAT
Found at i:13697 original size:37 final size:36
Alignment explanation
Indices: 13649--13722 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
13639 GAAGTTTACA
*
13649 AAATATGACAACACATCTAAATTTATAAAAAGATGAC
1 AAATATGACAACACATCCAAATTTAT-AAAAGATGAC
* *
13686 AAATATGACAACATATCCAAATTTATACAAGATGAC
1 AAATATGACAACACATCCAAATTTATAAAAGATGAC
13722 A
1 A
13723 CTATTTTCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 10 0.29
37 24 0.71
ACGTcount: A:0.53, C:0.15, G:0.08, T:0.24
Consensus pattern (36 bp):
AAATATGACAACACATCCAAATTTATAAAAGATGAC
Found at i:16160 original size:7 final size:7
Alignment explanation
Indices: 16148--16244 Score: 68
Period size: 7 Copynumber: 13.7 Consensus size: 7
16138 AATCAGATTA
16148 AGGGTTT
1 AGGGTTT
16155 AGGGTTT
1 AGGGTTT
**
16162 AGGACTT
1 AGGGTTT
16169 AGGGGTTT
1 A-GGGTTT
**
16177 ATAGTTT
1 AGGGTTT
*
16184 AGGATTT
1 AGGGTTT
16191 AGGGTTT
1 AGGGTTT
*
16198 AAGGTTT
1 AGGGTTT
*
16205 AAGGTTT
1 AGGGTTT
***
16212 AAATTTT
1 AGGGTTT
*
16219 AGAGTTT
1 AGGGTTT
* *
16226 AGGATTA
1 AGGGTTT
16233 AGGGTTT
1 AGGGTTT
16240 AGGGT
1 AGGGT
16245 GTAATCTAAA
Statistics
Matches: 69, Mismatches: 20, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
7 64 0.93
8 5 0.07
ACGTcount: A:0.25, C:0.01, G:0.33, T:0.41
Consensus pattern (7 bp):
AGGGTTT
Found at i:16175 original size:22 final size:21
Alignment explanation
Indices: 16148--16205 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
16138 AATCAGATTA
*
16148 AGGGTTTAGGGTTTAGGACTT
1 AGGGTTTAAGGTTTAGGACTT
*
16169 AGGGGTTTATA-GTTTAGGATTT
1 A-GGGTTTA-AGGTTTAGGACTT
16191 AGGGTTTAAGGTTTA
1 AGGGTTTAAGGTTTA
16206 AGGTTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 13 0.41
22 18 0.56
ACGTcount: A:0.22, C:0.02, G:0.34, T:0.41
Consensus pattern (21 bp):
AGGGTTTAAGGTTTAGGACTT
Found at i:16197 original size:21 final size:21
Alignment explanation
Indices: 16143--16241 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
16133 CATATAATCA
* *
16143 GATTAAGGGTTTAGGGTTTAG
1 GATTTAGGGTTTAGAGTTTAG
* *
16164 GACTTAGGGGTTTATAGTTTAG
1 GATTTA-GGGTTTAGAGTTTAG
16186 GATTTAGGGTTTA-AGGTTTAAG
1 GATTTAGGGTTTAGA-GTTT-AG
***
16208 G-TTTAAATTTTAGAGTTTAG
1 GATTTAGGGTTTAGAGTTTAG
*
16228 GATTAAGGGTTTAG
1 GATTTAGGGTTTAG
16242 GGTGTAATCT
Statistics
Matches: 61, Mismatches: 12, Indels: 10
0.73 0.14 0.12
Matches are distributed among these distances:
20 4 0.07
21 35 0.57
22 22 0.36
ACGTcount: A:0.26, C:0.01, G:0.31, T:0.41
Consensus pattern (21 bp):
GATTTAGGGTTTAGAGTTTAG
Found at i:16787 original size:21 final size:21
Alignment explanation
Indices: 16763--16802 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16753 CCCTTAGTCT
*
16763 TAAATCATAAACCCTAAACCC
1 TAAACCATAAACCCTAAACCC
* *
16784 TAAACCTTGAACCCTAAAC
1 TAAACCATAAACCCTAAAC
16803 TCTATCACAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.33, G:0.03, T:0.20
Consensus pattern (21 bp):
TAAACCATAAACCCTAAACCC
Found at i:17794 original size:14 final size:14
Alignment explanation
Indices: 17775--17804 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17765 TATAATCATC
*
17775 AATAATGTATTTTT
1 AATAATGTAATTTT
17789 AATAATGTAATTTT
1 AATAATGTAATTTT
17803 AA
1 AA
17805 AAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:25637 original size:3 final size:3
Alignment explanation
Indices: 25620--25662 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
25610 TTACAAAAAG
25620 ATT ATTT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
25663 CTTTTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:27675 original size:65 final size:65
Alignment explanation
Indices: 27542--27701 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 65
27532 TGCACTAAAA
* * * *
27542 GTGCATTGATGCATCAAGTGCATTCGAT-ATTTCAAAATAGCCAGAGTGCATCGATGCATAGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATAGCTG
* * *
27606 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCAT-GGT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATAGCT
*
27669 AT
65 -G
* *
27671 GTGCATCGATGCATGAAATGGATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
27702 CAATTTAATT
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 28 0.34
65 52 0.63
66 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATAGCTG
Found at i:27740 original size:65 final size:63
Alignment explanation
Indices: 27542--27742 Score: 178
Period size: 65 Copynumber: 3.1 Consensus size: 63
27532 TGCACTAAAA
* * * * * *
27542 GTGCATTGATGCATCAAGTGCATTCGATATTTCA-AAATAGC-CAGAGTGCATCGATGCATAGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTT
27605 G
63 G
27606 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
27671 -
63 G
* * ** *
27671 GTGCATCGATGCATGAAATGGATTCGATG-TTCAATTTAAT-TCATGGTGTATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
27734 TG
62 TG
27736 GTGCATC
1 GTGCATC
27743 ACTCTGAAAA
Statistics
Matches: 116, Mismatches: 11, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 47 0.41
65 57 0.49
66 5 0.04
67 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:28196 original size:20 final size:20
Alignment explanation
Indices: 28152--28311 Score: 97
Period size: 20 Copynumber: 7.8 Consensus size: 20
28142 AATGACCAAT
* *
28152 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
28171 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
28191 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
* **
28211 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
28232 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
28255 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
28275 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
28295 AGAGTCGCAACGCGATT
1 AAAATCGCAACGCGATT
28312 GACGTTGAAA
Statistics
Matches: 108, Mismatches: 28, Indels: 9
0.74 0.19 0.06
Matches are distributed among these distances:
19 17 0.16
20 64 0.59
21 13 0.12
23 14 0.13
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:29117 original size:6 final size:6
Alignment explanation
Indices: 29101--29138 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
29091 TCTCGTCTCG
29101 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
29139 AATACGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:29250 original size:20 final size:20
Alignment explanation
Indices: 29225--29522 Score: 170
Period size: 20 Copynumber: 14.6 Consensus size: 20
29215 ATCTTTTTAA
29225 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
29245 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
29265 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
29285 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* *
29305 CATTGCGATTTTCTTCTAAATCA
1 CGTTGCGA--TT-TTCTAAATCG
* * *
29328 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
29348 CATTGCGATTATATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
29368 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
29388 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
29411 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
29432 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
29450 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
29472 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
29492 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
29511 CGTTGCGATTTT
1 CGTTGCGATTTT
29523 ATTGGTCATT
Statistics
Matches: 219, Mismatches: 48, Indels: 23
0.76 0.17 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 153 0.70
21 14 0.06
22 6 0.03
23 27 0.12
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:29271 original size:40 final size:40
Alignment explanation
Indices: 29227--29418 Score: 240
Period size: 40 Copynumber: 4.7 Consensus size: 40
29217 CTTTTTAACG
29227 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * *
29267 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* *
29307 TTGCGATTTTCTTCTAAATCACGTTGCGACTCTCTCAATCGCA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * *
29350 TTGCGATTATATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
29390 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGA
29419 ACTTGGAAGC
Statistics
Matches: 127, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
40 74 0.58
41 2 0.02
42 4 0.03
43 47 0.37
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (40 bp):
TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
Found at i:29332 original size:83 final size:83
Alignment explanation
Indices: 29235--29418 Score: 323
Period size: 83 Copynumber: 2.2 Consensus size: 83
29225 CGTTGCGATT
* * *
29235 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATAAATCGCATTGCGATTCTATC
*
29300 AGTCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
*
29318 TTCTAAATCACGTTGCGACTCTCTCAATCGCATTGCGATTATATAAATCGCATTGCGATTCTATC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATAAATCGCATTGCGATTCTATC
29383 AATCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
29401 TTCTAAATCGCGTTGCGA
1 TTCTAAATCGCGTTGCGA
29419 ACTTGGAAGC
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 95 1.00
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.36
Consensus pattern (83 bp):
TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATAAATCGCATTGCGATTCTATC
AATCGCATTGCGATTTTC
Found at i:29512 original size:19 final size:20
Alignment explanation
Indices: 29472--29522 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
29462 TTCTTTTTAA
*
29472 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
29492 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
29511 CGTTGCGATTTT
1 CGTTGCGATTTT
29523 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:31252 original size:23 final size:22
Alignment explanation
Indices: 31222--31303 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 22
31212 GCATGGCCTT
31222 GTGCATCGATGCACATACAAGG
1 GTGCATCGATGCACATACAAGG
* *
31244 CGTGCATCGGTGCATCA-AC-ATG
1 -GTGCATCGATGCA-CATACAAGG
* * *
31266 ATGAATCGATGCACATTAAAAGG
1 GTGCATCGATGCACA-TACAAGG
31289 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
31304 TGTTAAGTGT
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
20 2 0.04
21 10 0.22
22 3 0.07
23 16 0.36
24 14 0.31
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.21
Consensus pattern (22 bp):
GTGCATCGATGCACATACAAGG
Found at i:35177 original size:22 final size:21
Alignment explanation
Indices: 35135--35174 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35125 GAGTTTATTT
*
35135 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
35156 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
35175 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:37314 original size:65 final size:64
Alignment explanation
Indices: 37116--37316 Score: 232
Period size: 65 Copynumber: 3.1 Consensus size: 64
37106 TGCACTAAAA
* * ** *
37116 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCGTGGTTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTTG
*
37180 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGATGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGT
37243 AT-
63 -TG
* *
37245 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGG-TT
37309 G
64 G
37310 GTGCATC
1 GTGCATC
37317 ACTTTGAAAA
Statistics
Matches: 118, Mismatches: 9, Indels: 19
0.81 0.06 0.13
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 52 0.44
65 57 0.48
66 1 0.01
67 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTTG
Found at i:37927 original size:59 final size:59
Alignment explanation
Indices: 37822--37938 Score: 177
Period size: 59 Copynumber: 2.0 Consensus size: 59
37812 TTTGTAATTA
*
37822 CTATTTTAGTCCTTTAAGTTTCTATTTTTTCTATTTATCCCTTTAAGTTTCTATTTTTC
1 CTATTTTAGTCCCTTAAGTTTCTATTTTTTCTATTTATCCCTTTAAGTTTCTATTTTTC
37881 CTATTTTAGTCCCTTAAGTTTCTATTTTTGT-T-TTCTAGTCCC-TTAAGTTTCTATTTTT
1 CTATTTTAGTCCCTTAAGTTTCTATTTTT-TCTATT-TA-TCCCTTTAAGTTTCTATTTTT
37939 TTAATTTGGA
Statistics
Matches: 54, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
58 2 0.04
59 47 0.87
60 5 0.09
ACGTcount: A:0.16, C:0.17, G:0.07, T:0.60
Consensus pattern (59 bp):
CTATTTTAGTCCCTTAAGTTTCTATTTTTTCTATTTATCCCTTTAAGTTTCTATTTTTC
Found at i:37986 original size:88 final size:88
Alignment explanation
Indices: 37828--37996 Score: 223
Period size: 88 Copynumber: 1.9 Consensus size: 88
37818 ATTACTATTT
* ** * * * *
37828 TAGTCCTTTAAGTTTCTATTTTTTCTATTTATCCCTTTAAGTTTCTATTTTTCCTATTTTAGTCC
1 TAGTCCCTTAAGTTTCTATTTTTTCTATTTAGACCTTTAAATTCCTATTTGTACTATTTTAGTCC
37893 CTTAAGTTTCTATTTTTGTTTTC
66 CTTAAGTTTCTATTTTTGTTTTC
* * *
37916 TAGTCCCTTAAGTTTCTATTTTTT-TAATTTGGACCTTTAAATTCCTGTTTGTACTATTTTGGTC
1 TAGTCCCTTAAGTTTCTATTTTTTCT-ATTTAGACCTTTAAATTCCTATTTGTACTATTTTAGTC
*
37980 CTTTAAGTTTCTATTTT
65 CCTTAAGTTTCTATTTT
37997 CCTATTCTGG
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
87 1 0.01
88 68 0.99
ACGTcount: A:0.17, C:0.16, G:0.09, T:0.58
Consensus pattern (88 bp):
TAGTCCCTTAAGTTTCTATTTTTTCTATTTAGACCTTTAAATTCCTATTTGTACTATTTTAGTCC
CTTAAGTTTCTATTTTTGTTTTC
Found at i:38002 original size:29 final size:29
Alignment explanation
Indices: 37822--38011 Score: 179
Period size: 29 Copynumber: 6.5 Consensus size: 29
37812 TTTGTAATTA
37822 CTATTTTAGTCCTTTAAGTTTCTATTTTTT
1 CTATTTTAGTCCTTTAAGTTTCTA-TTTTT
37852 CTA-TTTA-TCCCTTTAAGTTTCTATTTTT
1 CTATTTTAGT-CCTTTAAGTTTCTATTTTT
*
37880 CCTATTTTAGTCCCTTAAGTTTCTATTTTT
1 -CTATTTTAGTCCTTTAAGTTTCTATTTTT
* *
37910 GT-TTTCTAGTCCCTTAAGTTTCTATTTTT
1 CTATTT-TAGTCCTTTAAGTTTCTATTTTT
* * * * * * * *
37939 TTAATTTGGACCTTTAAATTCCTGTTTGTA
1 CTATTTTAGTCCTTTAAGTTTCTATTT-TT
* *
37969 CTATTTTGGTCCTTTAAGTTTCTATTTTC
1 CTATTTTAGTCCTTTAAGTTTCTATTTTT
* *
37998 CTATTCTGGTCCTT
1 CTATTTTAGTCCTT
38012 GTAATTATAA
Statistics
Matches: 134, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
28 9 0.07
29 75 0.56
30 49 0.37
31 1 0.01
ACGTcount: A:0.16, C:0.17, G:0.09, T:0.57
Consensus pattern (29 bp):
CTATTTTAGTCCTTTAAGTTTCTATTTTT
Found at i:38436 original size:20 final size:20
Alignment explanation
Indices: 38411--38472 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
38401 AAAATGCTAA
38411 AGTGTACCGATACACTCTGC
1 AGTGTACCGATACACTCTGC
38431 AGTGTATCC-ATACA-T-TG-
1 AGTGTA-CCGATACACTCTGC
*
38448 -GTGTACCGATACACACTGC
1 AGTGTACCGATACACTCTGC
38467 AGTGTA
1 AGTGTA
38473 TCCATACCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
15 2 0.06
16 10 0.29
18 4 0.11
19 1 0.03
20 16 0.46
21 2 0.06
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (20 bp):
AGTGTACCGATACACTCTGC
Found at i:38459 original size:36 final size:36
Alignment explanation
Indices: 38412--38580 Score: 142
Period size: 36 Copynumber: 4.9 Consensus size: 36
38402 AAATGCTAAA
*
38412 GTGTACCGATACACTCTGCAGTGTATCCATACATTG
1 GTGTACCGATACACACTGCAGTGTATCCATACATTG
*
38448 GTGTACCGATACACACTGCAGTGTATCCATACCCTT-
1 GTGTACCGATACACACTGCAGTGTATCCATA-CATTG
* * * * * * *
38484 ATG-ACTGCTCAAACAC--C---GAAT--GTA-ATTA
1 GTGTACCGAT-ACACACTGCAGTGTATCCATACATTG
* *
38512 GTGTACCGATACACCCTGCAGTGTATCCATACACTG
1 GTGTACCGATACACACTGCAGTGTATCCATACATTG
*
38548 GTGTACCGATACACTCTGCAGTGTATCCATACA
1 GTGTACCGATACACACTGCAGTGTATCCATACA
38581 CCCTGGCTGC
Statistics
Matches: 102, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
27 2 0.02
28 6 0.06
29 6 0.06
30 1 0.01
31 3 0.03
33 3 0.03
34 1 0.01
35 6 0.06
36 71 0.70
37 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (36 bp):
GTGTACCGATACACACTGCAGTGTATCCATACATTG
Found at i:38536 original size:20 final size:20
Alignment explanation
Indices: 38511--38585 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
38501 GAATGTAATT
38511 AGTGTA-CCGATACACCCTGC
1 AGTGTATCC-ATACACCCTGC
38531 AGTGTATCCATACA--CTG-
1 AGTGTATCCATACACCCTGC
*
38548 -GTGTA-CCGATACACTCTGC
1 AGTGTATCC-ATACACCCTGC
38567 AGTGTATCCATACACCCTG
1 AGTGTATCCATACACCCTG
38586 GCTGCAACGA
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
15 2 0.04
16 10 0.21
18 6 0.13
20 25 0.53
21 4 0.09
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (20 bp):
AGTGTATCCATACACCCTGC
Found at i:38559 original size:16 final size:17
Alignment explanation
Indices: 38511--38562 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 17
38501 GAATGTAATT
38511 AGTGTACCGATACACCCTG
1 AGTGTACCGATACA--CTG
38530 CAGTGTATCC-ATACACTG
1 -AGTGTA-CCGATACACTG
38548 -GTGTACCGATACACT
1 AGTGTACCGATACACT
38563 CTGCAGTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.07
16 12 0.40
18 3 0.10
20 11 0.37
21 2 0.07
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (17 bp):
AGTGTACCGATACACTG
Found at i:38651 original size:21 final size:21
Alignment explanation
Indices: 38625--38665 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
38615 TTTGAATTTA
*
38625 ATGAAGGTGTACCGATACCCT
1 ATGAAGGGGTACCGATACCCT
*
38646 ATGAAGGGGTATCGATACCC
1 ATGAAGGGGTACCGATACCC
38666 CATGTTATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (21 bp):
ATGAAGGGGTACCGATACCCT
Found at i:39018 original size:34 final size:34
Alignment explanation
Indices: 38953--39019 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
38943 TGTAAAAGGA
* *
38953 AAGGTTCTAGTTGAGCCCTTGAAAAGCTAGGGAT
1 AAGGTTCTAGTTGAGCCCGTGAAAAACTAGGGAT
* *
38987 AAGGTTCTAGTTTAGCCCGTGAAAAATTAGGGA
1 AAGGTTCTAGTTGAGCCCGTGAAAAACTAGGGA
39020 GTTGTAAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.27
Consensus pattern (34 bp):
AAGGTTCTAGTTGAGCCCGTGAAAAACTAGGGAT
Found at i:47343 original size:43 final size:43
Alignment explanation
Indices: 47261--47411 Score: 171
Period size: 42 Copynumber: 3.5 Consensus size: 43
47251 AGCTTTACCA
* * * ** *
47261 CGGCATTTTTGGATACAAACGCCGC-GAAAGGAAAGATCTATAG
1 CGGCGTTTTTGGA-ACAAACGCCACAAAAAGTCAATATCTATAG
* * *
47304 CTGCGTTTTTGGAACGAACGCCTCAAAAAGTCAATATCTATAG
1 CGGCGTTTTTGGAACAAACGCCACAAAAAGTCAATATCTATAG
*
47347 CGGCG-TTTTGGAACAAACGCCACAAAAGGTCAATATCTATAG
1 CGGCGTTTTTGGAACAAACGCCACAAAAAGTCAATATCTATAG
*
47389 CGGCGTTTGTGGATACAAACGCC
1 CGGCGTTTTTGGA-ACAAACGCC
47412 GCTAATTACC
Statistics
Matches: 92, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
42 48 0.52
43 35 0.38
44 9 0.10
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (43 bp):
CGGCGTTTTTGGAACAAACGCCACAAAAAGTCAATATCTATAG
Found at i:49892 original size:41 final size:41
Alignment explanation
Indices: 49835--50299 Score: 461
Period size: 41 Copynumber: 11.3 Consensus size: 41
49825 TTGTGTTTAC
*
49835 AAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
49876 AAACACCACTGAAGTACGAGTCTTTAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * *
49917 AAACGCCACTGAAGTATGAGTCTATAGCGGCGTTTATATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * * *
49958 AAACGCCACTGAATTACGAGTCTTTAGCAGCATTTGTAAACA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA-A
* * *
50000 CAAACACCACTAAAGTACGAGTCGTTAGCGGCGTTTGTACAA
1 -AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * ** * *
50042 AAACGCCACTAATGAACTCGTTTTTAGCGGCGTTTGTACAAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTA-TAA
* * *
50084 AAACGCCACTAAAGTACGAGT-TGTTAACGACGTTTGTACAA
1 AAACGCCACTAAAGTACGAGTCT-TTAGCGGCGTTTGTATAA
* * * * * * *
50125 AAACACCAATAATGAACTCA-TTTTTAGCGGCGTTTGTACAAAA
1 AAACGCCACTAAAGTAC-GAGTCTTTAGCGGCGTTTGT--ATAA
50168 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * * * *
50209 AACCCCCACTAAATTAC-AATCTTTAGCGACGTTTATATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * *
50249 AAACGCCACTAAAATATGAGTATTTAGCGGCGTTT-TAAAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
50289 AAACGCCACTA
1 AAACGCCACTA
50300 TAGCACATGT
Statistics
Matches: 347, Mismatches: 67, Indels: 21
0.80 0.15 0.05
Matches are distributed among these distances:
40 48 0.14
41 197 0.57
42 37 0.11
43 65 0.19
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
Found at i:50197 original size:167 final size:165
Alignment explanation
Indices: 49835--50261 Score: 452
Period size: 167 Copynumber: 2.6 Consensus size: 165
49825 TTGTGTTTAC
* *
49835 AAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAAAAACACCACTGAAGTACGAGTCTT
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACACCACT-AAGAACGAGTCTT
* * * * * * *
49900 TAGCGACGTTTGTATAAAAACGCCACTGAAGTATGAGTCTATAGCGGCGTTTATATAAAAACGCC
65 TAGCGACGTTTGTAAAAAAACGCCACTAAAGTACGAGTCTATAACGACGTTTATACAAAAACACC
* * * *
49965 ACTGAATTACGAGTCTTTAGCAGCATTTGTAAACAC
130 AATGAATAACCAGTCTTTAGCAGCATTTGTAAACAA
* * * * ** *
50001 AAACACCACTAAAGTACGAGTCGTTAGCGGCGTTTGTACAAAAACGCCACTAATGAACTCGTTTT
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACACCACTAA-GAACGAGTCTT
* * *
50066 TAGCGGCGTTTGTACAAAAAACGCCACTAAAGTACGAGT-TGTTAACGACGTTTGTACAAAAACA
65 TAGCGACGTTTGTA-AAAAAACGCCACTAAAGTACGAGTCT-ATAACGACGTTTATACAAAAACA
* * *
50130 CCAAT-AATGAACTCA-TTTTTAGCGGCGTTTGTACAA-AA
128 CCAATGAAT-AAC-CAGTCTTTAGCAGCATTTGTA-AACAA
* * *
50168 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAACCCCCACTAA-ATTAC-AATCT
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACACCACTAAGA--ACGAGTCT
* *
50231 TTAGCGACGTTTATATAAAAACGCCACTAAA
64 TTAGCGACGTTTGTAAAAAAACGCCACTAAA
50262 ATATGAGTAT
Statistics
Matches: 216, Mismatches: 37, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
165 18 0.08
166 85 0.39
167 110 0.51
168 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (165 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACACCACTAAGAACGAGTCTTT
AGCGACGTTTGTAAAAAAACGCCACTAAAGTACGAGTCTATAACGACGTTTATACAAAAACACCA
ATGAATAACCAGTCTTTAGCAGCATTTGTAAACAA
Found at i:50234 original size:83 final size:82
Alignment explanation
Indices: 49835--50299 Score: 445
Period size: 84 Copynumber: 5.6 Consensus size: 82
49825 TTGTGTTTAC
* * *
49835 AAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAAAAACACCACTGAAGTACGAGTCTT
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACACCACT-AATTACGAATCTT
* *
49900 TAGCGACGTTTGT-ATAA
65 TAGCGGCGTTTGTAAAAA
* * * * * *
49917 AAACGCCACTGAAGTATGAGTCTATAGCGGCGTTTATATAAAAACGCCACTGAATTACGAGTCTT
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACACCACT-AATTACGAATCTT
* * *
49982 TAGCAGCATTTGTAAACAC
65 TAGCGGCGTTTGTAAA-AA
* * * * * *** *
50001 AAACACCACTAAAGTACGAGTCGTTAGCGGCGTTTGTACAAAAACGCCACTAATGAACTCGTTTT
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACACCACTAAT-TACGAATCTT
*
50066 TAGCGGCGTTTGTACAAA
65 TAGCGGCGTTTGTAAAAA
* * * * * ** *
50084 AAACGCCACTAAAGTACGAGT-TGTTAACGACGTTTGTACAAAAACACCAATAATGAACTCATTT
1 AAACGCCACTAAAGTACGAGTCT-TTAGCGGCGTTTGTATAAAAACACCACTAAT-TACGAATCT
50148 TTAGCGGCGTTTGTACAAAA
64 TTAGCGGCGTTTGTA-AAAA
* *
50168 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAACCCCCACTAAATTAC-AATCTT
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACACCACT-AATTACGAATCTT
* * *
50232 TAGCGACGTTTAT-ATAA
65 TAGCGGCGTTTGTAAAAA
* * * * *
50249 AAACGCCACTAAAATATGAGTATTTAGCGGCGTTT-TAAAAAAACGCCACTA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACACCACTA
50300 TAGCACATGT
Statistics
Matches: 323, Mismatches: 53, Indels: 17
0.82 0.13 0.04
Matches are distributed among these distances:
79 1 0.00
80 12 0.04
81 35 0.11
82 68 0.21
83 91 0.28
84 112 0.35
85 4 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (82 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACACCACTAATTACGAATCTTT
AGCGGCGTTTGTAAAAA
Found at i:60184 original size:22 final size:23
Alignment explanation
Indices: 60156--60210 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
60146 GGGCGCTATA
60156 CCTATAAATA-CCCCCAAACCTC
1 CCTATAAATACCCCCCAAACCTC
*
60178 CCTATAAATACCCCCCTAACCTC
1 CCTATAAATACCCCCCAAACCTC
60201 CCTATAAATA
1 CCTATAAATA
60211 TCTCATCATC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 10 0.32
23 21 0.68
ACGTcount: A:0.36, C:0.42, G:0.00, T:0.22
Consensus pattern (23 bp):
CCTATAAATACCCCCCAAACCTC
Found at i:60344 original size:17 final size:18
Alignment explanation
Indices: 60308--60348 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
60298 ATATTATGTA
*
60308 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
60326 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
60343 TTTACT
1 TTTACT
60349 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:64470 original size:22 final size:23
Alignment explanation
Indices: 64442--64490 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
64432 TTCAACCTAA
64442 ATTTTTTTAT-TTTTTATTAAAT
1 ATTTTTTTATATTTTTATTAAAT
*
64464 A-TTTTTTATATTTTTATTTAAT
1 ATTTTTTTATATTTTTATTAAAT
64486 -TTTTT
1 ATTTTT
64491 AAATAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (23 bp):
ATTTTTTTATATTTTTATTAAAT
Found at i:65290 original size:9 final size:9
Alignment explanation
Indices: 65276--65309 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
65266 TTATTTTTTA
65276 AAAATAAAT
1 AAAATAAAT
65285 AAAATATAAT
1 AAAATA-AAT
65295 AAAAATAAAT
1 -AAAATAAAT
65305 AAAAT
1 AAAAT
65310 TCAATAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 11 0.48
10 6 0.26
11 6 0.26
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATAAAT
Found at i:65297 original size:20 final size:20
Alignment explanation
Indices: 65274--65322 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
65264 ATTTATTTTT
65274 TAAAAATAAATAAAATAT-AA
1 TAAAAATAAATAAAAT-TCAA
65294 TAAAAATAAATAAAATTCAA
1 TAAAAATAAATAAAATTCAA
*
65314 TAAACATAA
1 TAAAAATAA
65323 TGTAAAGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (20 bp):
TAAAAATAAATAAAATTCAA
Found at i:66559 original size:21 final size:19
Alignment explanation
Indices: 66518--66562 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
66508 ATATTTTTAG
*
66518 TTATTATTTTTATTGAATT
1 TTATTATTTTTATTCAATT
*
66537 TTATTCATTTTTAATTCATTT
1 TTATT-ATTTTT-ATTCAATT
66558 TTATT
1 TTATT
66563 GTATTTGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 6 0.27
21 11 0.50
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (19 bp):
TTATTATTTTTATTCAATT
Found at i:66568 original size:11 final size:10
Alignment explanation
Indices: 66518--66562 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
66508 ATATTTTTAG
66518 TTATT-ATTT
1 TTATTCATTT
* *
66527 TTATTGAATT
1 TTATTCATTT
66537 TTATTCATTT
1 TTATTCATTT
66547 TTAATTCATTT
1 TT-ATTCATTT
66558 TTATT
1 TTATT
66563 GTATTTGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 5 0.16
10 16 0.52
11 10 0.32
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (10 bp):
TTATTCATTT
Found at i:67023 original size:22 final size:21
Alignment explanation
Indices: 66997--67041 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
66987 CTATAATATC
66997 ATCAATTAAAAATAATTTTTAA
1 ATCAA-TAAAAATAATTTTTAA
** *
67019 ATCAATACTAATATTTTTTAA
1 ATCAATAAAAATAATTTTTAA
67040 AT
1 AT
67042 TTCAAAATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (21 bp):
ATCAATAAAAATAATTTTTAA
Done.