Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000180.1 Hibiscus syriacus cultivar Beakdansim tig00000315_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: 84966
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8050 original size:17 final size:18
Alignment explanation
Indices: 8030--8063 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
8020 TTTATAAGGT
8030 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
*
8047 ATATTTTGTTAGTATTT
1 ATATTTTATTAGTATTT
8064 TATTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:17346 original size:32 final size:33
Alignment explanation
Indices: 17274--17347 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
17264 TTATTAAGAA
* * *
17274 AAAATATTATTAATATTTTTAATATATATATAC
1 AAAATTTTATTAATATTTTTAATATACAAATAC
*
17307 AACATTTTATTAATA-TTTTAATATACAAAT-C
1 AAAATTTTATTAATATTTTTAATATACAAATAC
17338 ATAAATTTTA
1 A-AAATTTTA
17348 CTTACTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 2 0.06
32 20 0.57
33 13 0.37
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (33 bp):
AAAATTTTATTAATATTTTTAATATACAAATAC
Found at i:22998 original size:17 final size:17
Alignment explanation
Indices: 22976--23013 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
22966 AAAATAATAG
*
22976 CAATATAAATCACTCAT
1 CAATATAAACCACTCAT
22993 CAATATAAACCACTCAT
1 CAATATAAACCACTCAT
23010 CAAT
1 CAAT
23014 TCTGTCGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (17 bp):
CAATATAAACCACTCAT
Found at i:23278 original size:9 final size:10
Alignment explanation
Indices: 23249--23281 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
23239 TTTTTGAAAA
23249 TTTAATATTAT
1 TTTAATA-TAT
23260 TTTAATATAT
1 TTTAATATAT
23270 TTT-ATATAT
1 TTTAATATAT
23279 TTT
1 TTT
23282 CTATTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 6 0.27
11 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTAATATAT
Found at i:25087 original size:17 final size:17
Alignment explanation
Indices: 25065--25119 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 17
25055 TTTTTTTAGA
25065 TTTTATATTATATATAT
1 TTTTATATTATATATAT
*
25082 TTTTATACTTTTAATATTAT
1 TTTTATA-TTAT-ATA-TAT
*
25102 TTTAATATATATATATAT
1 TTTTATAT-TATATATAT
25120 ATATATAACC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 7 0.23
18 6 0.19
19 7 0.23
20 11 0.35
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTATATTATATATAT
Found at i:28464 original size:194 final size:193
Alignment explanation
Indices: 28217--28843 Score: 954
Period size: 194 Copynumber: 3.2 Consensus size: 193
28207 ATTGAAATTT
* * * * *
28217 GTATCGATACTTTTCTAAGTATATGCACCAAATTATCGATACTTTATGAATTTAAAAGAATCT-C
1 GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAGAAT-TGC
*
28281 AATAATAGCGCCTATAAAGTATTGATACTTTATAAACATGTATCGATACATGACAATATAGCAAG
65 AATAATAGCGCCTATAAAGTATTGATACTTTATAAACATGTATCGATACATGACAATATAACAAG
* *
28346 TAAAAATATGACAAAACCAGTTTCAATATGACAAAACCGGTAAAGAGTTACCAGATATGTTGAAG
130 TAAAAATATGACAAAACCGGTTTCAATATGACAAAACCGGTAAAGAGCTACC-GATATGTTGAAG
*
28411 TTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAGAATTGCA
1 GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAGAATTGCA
* * * * *
28476 ATAATATCGCCTATAAAGT-TTCGATATTTTATAAACATGTATCGATGCATAACAATATAACAGG
66 ATAATAGCGCCTATAAAGTATT-GATACTTTATAAACATGTATCGATACATGACAATATAACAAG
*
28540 TAAAAATATGACAAAACTGGTTTCAATATGACAAAACCGGTAAAGAGCTACCGAATATGTTGAAG
130 TAAAAATATGACAAAACCGGTTTCAATATGACAAAACCGGTAAAGAGCTACCG-ATATGTTGAAG
* *
28605 GTATCGAAACTTTTATAAGTATATGTATCGTATTATCGATACTTTAGGAATTTAAAAGAATTGCA
1 GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAGAATTGCA
* *
28670 ATAATAGCGCTTATAAAGTATCGATACTTTATAAACATGTATCGATACATGACAATATAACAAGC
66 ATAATAGCGCCTATAAAGTATTGATACTTTATAAACATGTATCGATACATGACAATATAACAAG-
* * * *
28735 T-AAAATATGACAAAATCGGTTTCAATATGATAAAACCGGTAAAGCGCTATCGGATATGTTGAAG
130 TAAAAATATGACAAAACCGGTTTCAATATGACAAAACCGGTAAAGAGCTA-CCGATATGTTGAAG
* *
28799 GTATCGATACTTTAATAAGTAAATGTATCATATTATCGATACTTT
1 GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTT
28844 TAAAAGAAAA
Statistics
Matches: 393, Mismatches: 34, Indels: 12
0.90 0.08 0.03
Matches are distributed among these distances:
193 4 0.01
194 385 0.98
195 4 0.01
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.32
Consensus pattern (193 bp):
GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAGAATTGCA
ATAATAGCGCCTATAAAGTATTGATACTTTATAAACATGTATCGATACATGACAATATAACAAGT
AAAAATATGACAAAACCGGTTTCAATATGACAAAACCGGTAAAGAGCTACCGATATGTTGAAG
Found at i:28843 original size:388 final size:388
Alignment explanation
Indices: 28126--28843 Score: 1045
Period size: 388 Copynumber: 1.8 Consensus size: 388
28116 TGCAAAGAAA
** * * *
28126 TATCGATACATAACAATATAAAAGGTTGAAGTTTGACAAAATCGGTTTCAATTTGACAAAACCAG
1 TATCGATACATAACAATATAAAAGGTAAAAATATGACAAAATCGGTTTCAATATGACAAAACCAG
* * *
28191 TAGAAATACCTGAATTATTGAAATTTGTATCGATACTTTTCTAAGTATATGCACCAAATTATCGA
66 TAGAAATACCTGAATTATTGAAA-TGGTATCGAAACTTTTATAAGTATATGCACCAAATTATCGA
* *
28256 TACTTTATGAATTTAAAAGAATCTCAATAATAGCGCCTATAAAGTATTGATACTTTATAAACATG
130 TACTTTAGGAATTTAAAAGAATCTCAATAATAGCGCCTATAAAGTATCGATACTTTATAAACATG
*
28321 TATCGATACATGACAATATAGCAAGTAAAAATATGACAAAACCAGTTTCAATATGACAAAACCGG
195 TATCGATACATGACAATATAACAAGTAAAAATATGACAAAACCAGTTTCAATATGACAAAACCGG
* * * *
28386 TAAAGAGTTACCAGATATGTTGAAGTTATCGATACTTTTATAAGTATATGTATCATATTATCGAT
260 TAAAGAGCTACCAGATATGTTGAAGGTATCGATACTTTAATAAGTAAATGTATCATATTATCGAT
28451 ACTTTAGGAATTTAAAAGAATTGCAATAATATCGCCTATAAAGTTTCGATATTTTATAAACATG
325 ACTTTAGGAATTTAAAAGAATTGCAATAATATCGCCTATAAAGTTTCGATATTTTATAAACATG
* * *
28515 TATCGATGCATAACAATATAACAGGTAAAAATATGACAAAA-CTGGTTTCAATATGACAAAACCG
1 TATCGATACATAACAATATAAAAGGTAAAAATATGACAAAATC-GGTTTCAATATGACAAAACCA
* * * **
28579 GTA-AAGAGCTACC-GAATATGTTG-AA-GGTATCGAAACTTTTATAAGTATATGTATCGTATTA
65 GTAGAA-A--TACCTGAAT-TATTGAAATGGTATCGAAACTTTTATAAGTATATGCACCAAATTA
*
28640 TCGATACTTTAGGAATTTAAAAGAAT-TGCAATAATAGCGCTTATAAAGTATCGATACTTTATAA
126 TCGATACTTTAGGAATTTAAAAGAATCT-CAATAATAGCGCCTATAAAGTATCGATACTTTATAA
* * *
28704 ACATGTATCGATACATGACAATATAACAAGCT-AAAATATGACAAAATCGGTTTCAATATGATAA
190 ACATGTATCGATACATGACAATATAACAAG-TAAAAATATGACAAAACCAGTTTCAATATGACAA
* * *
28768 AACCGGTAAAGCGCTATCGGATATGTTGAAGGTATCGATACTTTAATAAGTAAATGTATCATATT
254 AACCGGTAAAGAGCTACCAGATATGTTGAAGGTATCGATACTTTAATAAGTAAATGTATCATATT
28833 ATCGATACTTT
319 ATCGATACTTT
28844 TAAAAGAAAA
Statistics
Matches: 292, Mismatches: 30, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
387 1 0.00
388 218 0.75
389 59 0.20
390 6 0.02
391 8 0.03
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (388 bp):
TATCGATACATAACAATATAAAAGGTAAAAATATGACAAAATCGGTTTCAATATGACAAAACCAG
TAGAAATACCTGAATTATTGAAATGGTATCGAAACTTTTATAAGTATATGCACCAAATTATCGAT
ACTTTAGGAATTTAAAAGAATCTCAATAATAGCGCCTATAAAGTATCGATACTTTATAAACATGT
ATCGATACATGACAATATAACAAGTAAAAATATGACAAAACCAGTTTCAATATGACAAAACCGGT
AAAGAGCTACCAGATATGTTGAAGGTATCGATACTTTAATAAGTAAATGTATCATATTATCGATA
CTTTAGGAATTTAAAAGAATTGCAATAATATCGCCTATAAAGTTTCGATATTTTATAAACATG
Found at i:30178 original size:36 final size:36
Alignment explanation
Indices: 30121--30221 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 36
30111 TTTCGTCCTA
30121 CTAGGATTCAAACT-CTCAAAAATAGGATAGAATTCTG
1 CTAGGATTC-AACTCCT-AAAAATAGGATAGAATTCTG
*
30158 CTAGGATTCAACTCCTAAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAAATAGGATAGAATTCTG
** * *
30194 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAAAATAGGAT
30222 CCACAAGTAC
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
36 26 0.46
37 31 0.54
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (36 bp):
CTAGGATTCAACTCCTAAAAATAGGATAGAATTCTG
Found at i:30650 original size:11 final size:11
Alignment explanation
Indices: 30630--30713 Score: 55
Period size: 11 Copynumber: 7.3 Consensus size: 11
30620 TATAATTATT
*
30630 TTATTCTAATA
1 TTATTTTAATA
*
30641 TTATTTTAATG
1 TTATTTTAATA
30652 TT-TTTTAA-A
1 TTATTTTAATA
*
30661 GTTATTATATATA
1 -TTATTTTA-ATA
30674 TATATTTATAACTA
1 T-TATTT-TAA-TA
*
30688 TTATATTTATTA
1 TTAT-TTTAATA
*
30700 TTATTTTACTA
1 TTATTTTAATA
30711 TTA
1 TTA
30714 ACGTATATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
10 8 0.14
11 24 0.41
12 8 0.14
13 11 0.19
14 7 0.12
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:30704 original size:15 final size:15
Alignment explanation
Indices: 30662--30704 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
30652 TTTTTTAAAG
30662 TTATTATATATATATAT
1 TTATTAT-TAT-TATAT
* *
30679 TTATAACTATTATAT
1 TTATTATTATTATAT
30694 TTATTATTATT
1 TTATTATTATT
30705 TTACTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 14 0.64
16 3 0.14
17 5 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTATTATTATAT
Found at i:30915 original size:19 final size:18
Alignment explanation
Indices: 30876--30924 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
30866 TTTCATGTAT
*
30876 TTATATTATATTACATTA
1 TTATATTATTTTACATTA
*
30894 TTATTATTATTTTACTTTA
1 TTA-TATTATTTTACATTA
*
30913 TTAAATTATTTT
1 TTATATTATTTT
30925 TTTTCGTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATATTATTTTACATTA
Found at i:34269 original size:8 final size:8
Alignment explanation
Indices: 34196--34263 Score: 55
Period size: 8 Copynumber: 8.0 Consensus size: 8
34186 AATCAAGAAC
34196 AAAAAAGA
1 AAAAAAGA
* *
34204 AAAGAAGC
1 AAAAAAGA
34212 AAAAAAGCAA
1 AAAAAAG--A
*
34222 AAAAAACA
1 AAAAAAGA
34230 AAGAAAAGA
1 AA-AAAAGA
*
34239 GAAACAAGA
1 -AAAAAAGA
*
34248 ACAAAAGA
1 AAAAAAGA
34256 AAAAAAGA
1 AAAAAAGA
34264 GCAAAATCAA
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
8 28 0.61
9 10 0.22
10 8 0.17
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:34933 original size:22 final size:22
Alignment explanation
Indices: 34908--34956 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
34898 CCATCAATCT
* *
34908 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
34930 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
34952 TTTGA
1 TTTGA
34957 CCAAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:35854 original size:35 final size:35
Alignment explanation
Indices: 35808--35910 Score: 143
Period size: 35 Copynumber: 2.9 Consensus size: 35
35798 GTGCTCACCA
35808 TTGTCTCTCTTGAGACAGTTTCCCTTGAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAACAAACT
*
35843 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTG-AAC-AAACT
* * * *
35880 TTTTCTCCCTTGAGACATTTTCTCTTGAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAACA
35911 TAAACATTGA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
35 28 0.46
36 6 0.10
37 27 0.44
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (35 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAACAAACT
Found at i:35907 original size:37 final size:36
Alignment explanation
Indices: 35808--35908 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 36
35798 GTGCTCACCA
35808 TTGTCTCTCTTGAGACAGTTTCCCTTG-AACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
*
35843 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
* * * *
35880 TTTTCTCCCTTGAGACATTTTCTCTTGAA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAA
35909 CATAAACATT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 27 0.46
36 3 0.05
37 29 0.49
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.41
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:36000 original size:37 final size:37
Alignment explanation
Indices: 35941--36011 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
35931 TTGAAATGAG
* *
35941 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
* *
35978 TTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
36012 TAAACATTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
Found at i:36075 original size:102 final size:102
Alignment explanation
Indices: 35826--36214 Score: 626
Period size: 102 Copynumber: 3.9 Consensus size: 102
35816 CTTGAGACAG
* * *
35826 TTTCCCTTGAACA--AACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCC
1 TTTCCCTTGAA-ATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCC
*
35889 TTGAGACATTTTCTCTTG-AACATAAACATT-GAAACA
65 TTGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
* *
35925 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
35990 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
36027 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* *
36092 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
* * * *
36129 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAATTTCCCTCGAAAC-AAATTTTGTCTCCCA
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
36193 TGAGACAGTTTCTCTTGAAACA
66 TGAGACAGTTTCTCTTGAAACA
36215 CAAAATCTTT
Statistics
Matches: 273, Mismatches: 13, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
98 1 0.00
99 11 0.04
100 64 0.23
101 47 0.17
102 150 0.55
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
Found at i:36094 original size:37 final size:37
Alignment explanation
Indices: 36027--36113 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
36017 ATTGGAAACA
** * *
36027 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
36063 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
36100 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
36114 TAAACATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 12 0.27
37 31 0.69
38 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:36197 original size:36 final size:36
Alignment explanation
Indices: 36128--36197 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
36118 CATTGAAAAC
* ** * *
36128 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATA
1 ATTTCCCTCGAAACAAATTTCGTCTCCCATGAGATA
*
36164 ATTTCCCTCGAAACAAATTTTGTCTCCCATGAGA
1 ATTTCCCTCGAAACAAATTTCGTCTCCCATGAGA
36198 CAGTTTCTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (36 bp):
ATTTCCCTCGAAACAAATTTCGTCTCCCATGAGATA
Found at i:37009 original size:109 final size:109
Alignment explanation
Indices: 36821--37285 Score: 551
Period size: 106 Copynumber: 4.4 Consensus size: 109
36811 TAGCTAGAGT
* * *
36821 CAAGTTCAACTTCACAACGAAGGGAC-TCTGGTTG-CCAC-AACAATTTCCCAATTTCGGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAATTTCCCAATTTCAGAACCG
*
36883 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCAAGACAACA
66 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
* *
36927 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTCCAGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAATTTCCCAATTTCAGAACCG
*
36992 ATTTCAACTCCACGACGGAGGATATCGTGCTA-CCGAGAAAACA
66 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
* * * * **
37035 CAAGTCCAACTTCACAACGAAGGGACGGCTGGTTGTCAATGAACAATTT-TCAGTTTCA-TCCGC
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAATTTCCCAATTTCAGAAC-C
* *
37098 GATTTC-ACTCCACGACGGAGGATATCGTGCCACTCGAGACAACA
65 GATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
* * * * * * * *
37142 CAAGTTCAACTTCACAATGAAGGGACAGCT-GTTGTC-ACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAATTTCCCAATTTCAGAACCG
* * * *
37205 ATTTCAACTTCAC-AGCGAAGGATAT--TG-GACTCGAGACAACA
66 ATTTCAACTCCACGA-CGGAGGATATCGTGCTACCCGAGACAACA
* * *
37246 CAAGTTCAAATTCACAATGAAGGGACGGCTGATTGTCAAC
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC
37286 AAGATTTCGT
Statistics
Matches: 312, Mismatches: 36, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
104 41 0.13
105 15 0.05
106 73 0.23
107 72 0.23
108 58 0.19
109 53 0.17
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (109 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAATTTCCCAATTTCAGAACCG
ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
Found at i:37209 original size:106 final size:108
Alignment explanation
Indices: 36821--37283 Score: 545
Period size: 107 Copynumber: 4.4 Consensus size: 108
36811 TAGCTAGAGT
* * *
36821 CAAGTTCAACTTCACAACGAAGGGAC-TCTGGTTGCCAC-AACAATTTCCCAATTTCGGAACCGA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCACAAACAATTTCCCAATTTCAGAACCGA
* *
36884 TTTCAACTCCACGACGGAGGATATCGTGCTACCCAAGACAACA
66 TTTCAACTCCACGACGGAGGATATCGTGCTACTCGAGACAACA
* * *
36927 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTCCAGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTC-ACAAACAATTTCCCAATTTCAGAACCG
*
36992 ATTTCAACTCCACGACGGAGGATATCGTGCTAC-CGAGAAAACA
65 ATTTCAACTCCACGACGGAGGATATCGTGCTACTCGAGACAACA
* * * **
37035 CAAGTCCAACTTCACAACGAAGGGACGGCTGGTTGTCA-ATGAACAATTT-TCAGTTTCA-TCCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCACA--AACAATTTCCCAATTTCAGAAC-
*
37097 CGATTTC-ACTCCACGACGGAGGATATCGTGCCACTCGAGACAACA
63 CGATTTCAACTCCACGACGGAGGATATCGTGCTACTCGAGACAACA
* * * * * * *
37142 CAAGTTCAACTTCACAATGAAGGGACAGCT-GTTGTCACAAACATTTTTCAAATTTCAGAGCCAA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCACAAACAATTTCCCAATTTCAGAACCGA
* * *
37206 TTTCAACTTCAC-AGCGAAGGATAT--TG-GACTCGAGACAACA
66 TTTCAACTCCACGA-CGGAGGATATCGTGCTACTCGAGACAACA
* * *
37246 CAAGTTCAAATTCACAATGAAGGGACGGCTGATTGTCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCA
37284 ACAAGATTTC
Statistics
Matches: 311, Mismatches: 33, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
104 41 0.13
105 15 0.05
106 73 0.23
107 75 0.24
108 53 0.17
109 54 0.17
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (108 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCACAAACAATTTCCCAATTTCAGAACCGA
TTTCAACTCCACGACGGAGGATATCGTGCTACTCGAGACAACA
Found at i:37336 original size:100 final size:102
Alignment explanation
Indices: 36919--37443 Score: 402
Period size: 100 Copynumber: 5.0 Consensus size: 102
36909 GTGCTACCCA
* * * * *
36919 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTC
1 AGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAAC-AA-AAATT-TCAGTT-
* * * * *
36984 CAGAACCGATTTCAACTCCAC-GACGGAGGATATCGTG-CTACCG
62 CAGAGCCAATTTCAACTTCACAG-CGAAGGATATTG-GACT--CG
* * * * * *
37027 AGAAAACACAAGTCCAACTTCACAACGAAGGGACGGCTGGTTGTCAATGAACAATTTTCAGTTTC
1 AGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAA-CAA-AAATTTCAG-TTC
** * * * *
37092 A-TCCGCGATTTC-ACTCCAC-GACGGAGGATATCGTGCCACTCG
63 AGAGC-CAATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCG
* * *
37134 AGACAACACAAGTTCAACTTCACAATGAAGGGACAGCTG-TTGTC-ACAAACATTTTTCAAATTT
1 AGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAACAAA-A-ATTTC--AGTT
37197 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
62 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
* *
37238 AGACAACACAAGTTCAAATTCACAATGAAGGGACGGCTGATTGTCAAC-AAGATTTC-GTTCAGA
1 AGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAACAAAAATTTCAGTTCAGA
* * *
37301 GTCAATTTCAACTTCACAGCGAAAGATATTAGACTCG
66 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
* * ** * * * * *
37338 AGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCATCTAACAATTTCCCGGTTC
1 AGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAAC-AAAAATTT--CAGTT-
* *
37403 CAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTCG
62 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
37444 GAACAATATT
Statistics
Matches: 350, Mismatches: 46, Indels: 44
0.80 0.10 0.10
Matches are distributed among these distances:
100 80 0.23
102 5 0.01
103 5 0.01
104 46 0.13
105 18 0.05
106 73 0.21
107 65 0.19
108 56 0.16
109 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (102 bp):
AGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAACAAAAATTTCAGTTCAGA
GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
Found at i:37442 original size:106 final size:105
Alignment explanation
Indices: 36821--37443 Score: 504
Period size: 106 Copynumber: 5.9 Consensus size: 105
36811 TAGCTAGAGT
* * * * * * *
36821 CAAGTTCAACTTCACAACGAAGGGAC-TCTGGTTG-CCAC-AACAATTTCCCAATTTCGGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACGAACAATTT-CCAGTTCCAGAACCA
* * * *
36883 ATTTCAACTCCAC-GACGGAGGATATCGTGCTACCCAAGACAACA
65 ATTTCAACTTCACAG-CGGAGGATAT--TG-GACTCGAGACAACA
* * * *
36927 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTCCAGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACGAACAA-TTTCCAGTTCCAGAACCA
* * *
36992 ATTTCAACTCCAC-GACGGAGGATATCGTG-CTACCGAGAAAACA
65 ATTTCAACTTCACAG-CGGAGGATATTG-GACT--CGAGACAACA
* * * * * ** *
37035 CAAGTCCAACTTCACAACGAAGGGACGGCTGGTTGTCAATGAACAATTTTCAGTTTCA-TCCGCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACGAACAATTTCCAGTTCCAGAAC-CA
* *
37099 ATTTC-ACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACA
65 ATTTCAACTTCACAG-CGGAGGATAT--TG-GACTCGAGACAACA
* * * * * * * *
37142 CAAGTTCAACTTCACAATGAAGGGACAGCTG-TTGTC-ACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACGAACA-ATTTCCAGTTCCAGAACCA
*
37205 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
65 ATTTCAACTTCACAGCGGAGGATATTGGACTCGAGACAACA
* * * **
37246 CAAGTTCAAATTCACAATGAAGGGACGGCTGATTGTCAAC-AA-GATTT-C-GTT-CAGAGTCAA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACGAACAATTTCCAGTTCCAGAACCAA
* * * *
37306 TTTCAACTTCACAGCGAAAGATATTAGACTCGAGACAGCA
66 TTTCAACTTCACAGCGGAGGATATTGGACTCGAGACAACA
* * * * * * *
37346 CAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCATCTAACAATTTCCCGGTTCCAGAACCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACGAACAATTT-CCAGTTCCAGAACCA
37411 ATTTCAACTTCACAGCGGAGGATATTGGACTCG
65 ATTTCAACTTCACAGCGGAGGATATTGGACTCG
37444 GAACAATATT
Statistics
Matches: 434, Mismatches: 61, Indels: 44
0.81 0.11 0.08
Matches are distributed among these distances:
100 78 0.18
101 4 0.01
102 4 0.01
103 3 0.01
104 43 0.10
105 17 0.04
106 105 0.24
107 76 0.18
108 57 0.13
109 45 0.10
110 2 0.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (105 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACGAACAATTTCCAGTTCCAGAACCAA
TTTCAACTTCACAGCGGAGGATATTGGACTCGAGACAACA
Found at i:37959 original size:35 final size:36
Alignment explanation
Indices: 37903--38001 Score: 112
Period size: 35 Copynumber: 2.8 Consensus size: 36
37893 TTTCGTCCTA
*
37903 CTAGGATTCAAACT-CTCAAAATAGGATAGAA-TCTG
1 CTAGGATTC-AACTCCTAAAAATAGGATAGAATTCTG
*
37938 CTAGGATTCAACTCCTAAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAAATAGGATAGAATTCTG
** * *
37974 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAAAATAGGAT
38002 CCACAAGTAC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
34 4 0.07
35 25 0.45
36 6 0.11
37 20 0.36
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (36 bp):
CTAGGATTCAACTCCTAAAAATAGGATAGAATTCTG
Found at i:38465 original size:23 final size:20
Alignment explanation
Indices: 38439--38479 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
38429 AAGTTATATA
38439 TATATATATTTATAACTATTATT
1 TATAT-TATTT-T-ACTATTATT
38462 TATATTATTTTACTATTA
1 TATATTATTTTACTATTA
38480 ACGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 5 0.28
23 5 0.28
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TATATTATTTTACTATTATT
Found at i:38657 original size:16 final size:16
Alignment explanation
Indices: 38636--38674 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
38626 CATGTATTTA
38636 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
38652 TATTATTTTACTTTAT
1 TATTATATTACATTAT
38668 TAATTAT
1 T-ATTAT
38675 TTTTTTTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:38687 original size:20 final size:20
Alignment explanation
Indices: 38650--38698 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
38640 ATATTACATT
*
38650 ATTATTATTTTACTTTATTA
1 ATTATTATTTTACGTTATTA
* *
38670 ATTATTTTTTTTCGTTATATA
1 ATTATTATTTTACGTTAT-TA
*
38691 TTTATTAT
1 ATTATTAT
38699 ATATATATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTATTATTTTACGTTATTA
Found at i:40006 original size:198 final size:197
Alignment explanation
Indices: 39692--40052 Score: 697
Period size: 198 Copynumber: 1.8 Consensus size: 197
39682 GTCATTAAGA
39692 CGAAGAACTGGAAAGCACTTGCGATGAAATATGATTTAAGCACAATGTGACATATGTTGGCTTGA
1 CGAAGAACTGGAAAGCACTTGCGATGAAATATGATTTAAGCACAATGTGACATATGTTGGCTTGA
39757 AGAGGAAATTAAAAGCATAGTTTACAGGGGTGATACATCCCCGAGCAAGGACAATATAAAGTTGA
66 AGAGGAAATTAAAAGCATAGTTTACAGGGGTGATACATCCCCGAGCAAGGACAATATAAAGTTGA
39822 TTTGCGA-GAAGGCTTGCAAGGTAAATTGAAGTAATATCCATTCCAGTGTTGAAGTCATTAAAGG
131 TTTGCGATGAAGGCTTGCAAGGTAAATTGAAGTAATATCCATTCCAGTGTTGAAGTCATTAAAGG
39886 GT
196 GT
39888 CGAAGAACTGGAAAGCACTTGCGATGAAATATGATTTAAAGCACAATGTGACATATGTTGGGCTT
1 CGAAGAACTGGAAAGCACTTGCGATGAAATATGATTT-AAGCACAATGTGACATATGTT-GGCTT
39953 GAAGAGGAAATTAAAAGCATAGTTTACAGGGGTGATACATCCCCGAGCAAGGACAATATAAAGTT
64 GAAGAGGAAATTAAAAGCATAGTTTACAGGGGTGATACATCCCCGAGCAAGGACAATATAAAGTT
40018 GATTTGCGATGAAGGCTTGCAAGGTAAATTGAAGT
129 GATTTGCGATGAAGGCTTGCAAGGTAAATTGAAGT
40053 TGGCTGAATA
Statistics
Matches: 162, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
196 37 0.23
197 21 0.13
198 79 0.49
199 25 0.15
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (197 bp):
CGAAGAACTGGAAAGCACTTGCGATGAAATATGATTTAAGCACAATGTGACATATGTTGGCTTGA
AGAGGAAATTAAAAGCATAGTTTACAGGGGTGATACATCCCCGAGCAAGGACAATATAAAGTTGA
TTTGCGATGAAGGCTTGCAAGGTAAATTGAAGTAATATCCATTCCAGTGTTGAAGTCATTAAAGG
GT
Found at i:45706 original size:53 final size:53
Alignment explanation
Indices: 45624--45728 Score: 192
Period size: 53 Copynumber: 2.0 Consensus size: 53
45614 ATTGGGGTGG
* *
45624 GGTAATGCGATATTTCAACATGTAGGAGGTGGTCCTAATAATTTACCTCATAA
1 GGTAATGCGATAATTCAACATGTACGAGGTGGTCCTAATAATTTACCTCATAA
45677 GGTAATGCGATAATTCAACATGTACGAGGTGGTCCTAATAATTTACCTCATA
1 GGTAATGCGATAATTCAACATGTACGAGGTGGTCCTAATAATTTACCTCATA
45729 TTTGAAATGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (53 bp):
GGTAATGCGATAATTCAACATGTACGAGGTGGTCCTAATAATTTACCTCATAA
Found at i:51691 original size:23 final size:20
Alignment explanation
Indices: 51645--51695 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
51635 TTAGCATCAT
*
51645 TATTGTTCATACAGTATCGA
1 TATTATTCATACAGTATCGA
51665 TATTATTCATACAGTATCGA
1 TATTATTCATACAGTATCGA
*
51685 TACTATTCATA
1 TATTATTCATA
51696 AAACATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (20 bp):
TATTATTCATACAGTATCGA
Found at i:52224 original size:17 final size:17
Alignment explanation
Indices: 52202--52240 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
52192 AGAAGTCTTG
52202 GAGATTTTGTGAAATTA
1 GAGATTTTGTGAAATTA
*
52219 GAGATTTTGTGAAATTG
1 GAGATTTTGTGAAATTA
52236 GAGAT
1 GAGAT
52241 AGCAACTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.38
Consensus pattern (17 bp):
GAGATTTTGTGAAATTA
Found at i:53734 original size:13 final size:13
Alignment explanation
Indices: 53716--53745 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
53706 GGATAAAGTT
*
53716 AAAACTCAACCAA
1 AAAACTCAAACAA
53729 AAAACTCAAACAA
1 AAAACTCAAACAA
53742 AAAA
1 AAAA
53746 TAGATATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.23, G:0.00, T:0.07
Consensus pattern (13 bp):
AAAACTCAAACAA
Found at i:54032 original size:23 final size:21
Alignment explanation
Indices: 54010--54052 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
54000 ACCAAGAAAG
*
54010 AAGAC-GAAAAATGTGTCACA
1 AAGACAGAAAAATATGTCACA
54030 AAGACAGAAAAATATGTCACA
1 AAGACAGAAAAATATGTCACA
54051 AA
1 AA
54053 ATAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.56, C:0.14, G:0.16, T:0.14
Consensus pattern (21 bp):
AAGACAGAAAAATATGTCACA
Found at i:60271 original size:33 final size:33
Alignment explanation
Indices: 60206--60272 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
60196 TCGTGTTTGA
* **
60206 TTATGTTCATTCGTTATGTTTGTGCAGGTTCGT
1 TTATGTTCATTCATTATGTTTGTGCACATTCGT
* **
60239 TTATGTTCATTTATTATGTTTGTTTACATTCGT
1 TTATGTTCATTCATTATGTTTGTGCACATTCGT
60272 T
1 T
60273 CGTTTATATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.15, C:0.10, G:0.18, T:0.57
Consensus pattern (33 bp):
TTATGTTCATTCATTATGTTTGTGCACATTCGT
Found at i:60287 original size:24 final size:24
Alignment explanation
Indices: 60260--60306 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
60250 TATTATGTTT
* *
60260 GTTTACATTCGTTCGTTTATATTC
1 GTTTACATCCATTCGTTTATATTC
*
60284 GTTTACATCCATTCGTTTCTATT
1 GTTTACATCCATTCGTTTATATT
60307 ATATTCACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.11, T:0.53
Consensus pattern (24 bp):
GTTTACATCCATTCGTTTATATTC
Found at i:62324 original size:30 final size:30
Alignment explanation
Indices: 62263--62327 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
62253 AAACTGGAAA
*
62263 AACCGGCTGAAAATCGATAAAACCGGGTTG
1 AACCGGCTGAAAATCGATAAAACCCGGTTG
* **
62293 AACCGGCTGAAAATCGGTAAAACCCTTTTG
1 AACCGGCTGAAAATCGATAAAACCCGGTTG
62323 AACCG
1 AACCG
62328 CCGATTCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.18
Consensus pattern (30 bp):
AACCGGCTGAAAATCGATAAAACCCGGTTG
Found at i:69410 original size:16 final size:16
Alignment explanation
Indices: 69389--69423 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
69379 AATCCATTAA
69389 TAATTTTAAACCCAAT
1 TAATTTTAAACCCAAT
* *
69405 TAATTTTAAGCTCAAT
1 TAATTTTAAACCCAAT
69421 TAA
1 TAA
69424 AAAAATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (16 bp):
TAATTTTAAACCCAAT
Found at i:74600 original size:21 final size:21
Alignment explanation
Indices: 74574--74683 Score: 150
Period size: 21 Copynumber: 5.2 Consensus size: 21
74564 GTTTCCAGAT
* * *
74574 TCGCAACGCAAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
* *
74595 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
74616 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
74637 TCGTAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
74658 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
74679 TCGCA
1 TCGCA
74684 CAACAAGGAA
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
20 1 0.01
21 78 0.98
22 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:75152 original size:6 final size:6
Alignment explanation
Indices: 75131--75162 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
75121 TCTCGTCTCG
75131 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
75163 ATACCTGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.00, C:0.19, G:0.53, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:75306 original size:42 final size:42
Alignment explanation
Indices: 75247--75470 Score: 385
Period size: 42 Copynumber: 5.3 Consensus size: 42
75237 CGTTGCGATT
*
75247 TTGGACTATCGCTACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
75289 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
75331 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
75373 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
* * *
75415 TTCGACTATTGCAACGAACTTGGAATAAATCGCAACGCGAAT
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
75457 TTGGACTATCGCAA
1 TTGGACTATCGCAA
75471 TGTGAATATG
Statistics
Matches: 170, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 170 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (42 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
Found at i:76447 original size:61 final size:60
Alignment explanation
Indices: 76323--76461 Score: 167
Period size: 60 Copynumber: 2.3 Consensus size: 60
76313 TAAATTTTCT
**
76323 AATTTC-TCCCCTAAACTATGACTATTAGTCTAAATTAGTCCTTAAACTTTTGAACATAAC
1 AATTTCATCCCC-AAACTATGACTATTAGTCTAAATTAGTCCCCAAACTTTTGAACATAAC
* * **
76383 AATTTCATCCCCAAACTATGAC-ATTCATTCTAAATTGGTCCCCAAACTTTTTGAACATTCC
1 AATTTCATCCCCAAACTATGACTATT-AGTCTAAATTAGTCCCCAAAC-TTTTGAACATAAC
*
76444 AATTTCAT-CTCAAACTAT
1 AATTTCATCCCCAAACTAT
76462 ATGTATATAC
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
59 3 0.04
60 42 0.61
61 24 0.35
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (60 bp):
AATTTCATCCCCAAACTATGACTATTAGTCTAAATTAGTCCCCAAACTTTTGAACATAAC
Found at i:76677 original size:60 final size:60
Alignment explanation
Indices: 76613--76765 Score: 175
Period size: 60 Copynumber: 2.6 Consensus size: 60
76603 TAATGTTTGG
*
76613 GGACTAATTTAGAAATAAGGTCATAGTTTAGGGATGAAACTAAAATGTTCAAAAGTTTAA
1 GGACTAATTTAGAAATAAGGTCATAGTTTAGGGATGAAACTAAAATATTCAAAAGTTTAA
* * * ** *
76673 GGACTAATTTAG-AATGAGAGTCATAGTTTAAGGATGAAATTGGAATATTCAATAGTTTAA
1 GGACTAATTTAGAAATAAG-GTCATAGTTTAGGGATGAAACTAAAATATTCAAAAGTTTAA
* * * * *
76733 GGACCAATTTAAAAAGAAGATTATAGTTT-GGGA
1 GGACTAATTTAGAAATAAGGTCATAGTTTAGGGA
76766 ACATATGATG
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
59 8 0.10
60 65 0.84
61 4 0.05
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (60 bp):
GGACTAATTTAGAAATAAGGTCATAGTTTAGGGATGAAACTAAAATATTCAAAAGTTTAA
Found at i:77820 original size:24 final size:25
Alignment explanation
Indices: 77773--77821 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
77763 ATTGATGATC
77773 TAATTTTATAAATCTTTAAATCTTA
1 TAATTTTATAAATCTTTAAATCTTA
*
77798 TAATTTTA-AACTC-TTAAATTCTTA
1 TAATTTTATAAATCTTTAAA-TCTTA
77822 CAATAATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 9 0.41
25 8 0.36
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (25 bp):
TAATTTTATAAATCTTTAAATCTTA
Found at i:80451 original size:118 final size:118
Alignment explanation
Indices: 80243--80484 Score: 484
Period size: 118 Copynumber: 2.1 Consensus size: 118
80233 CTCTCAAATA
80243 AATTAAGATAATTTAAATGATATTATAAAGTTGAGTATTGATATATTTGTGAATCAATAATAATT
1 AATTAAGATAATTTAAATGATATTATAAAGTTGAGTATTGATATATTTGTGAATCAATAATAATT
80308 GAGAATTAAAATATAAGTTTTTAAGAATTACTTAAACCGAAACAAACAGATTG
66 GAGAATTAAAATATAAGTTTTTAAGAATTACTTAAACCGAAACAAACAGATTG
80361 AATTAAGATAATTTAAATGATATTATAAAGTTGAGTATTGATATATTTGTGAATCAATAATAATT
1 AATTAAGATAATTTAAATGATATTATAAAGTTGAGTATTGATATATTTGTGAATCAATAATAATT
80426 GAGAATTAAAATATAAGTTTTTAAGAATTACTTAAACCGAAACAAACAGATTG
66 GAGAATTAAAATATAAGTTTTTAAGAATTACTTAAACCGAAACAAACAGATTG
80479 AATTAA
1 AATTAA
80485 AATCAAATTG
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 124 1.00
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.36
Consensus pattern (118 bp):
AATTAAGATAATTTAAATGATATTATAAAGTTGAGTATTGATATATTTGTGAATCAATAATAATT
GAGAATTAAAATATAAGTTTTTAAGAATTACTTAAACCGAAACAAACAGATTG
Found at i:80561 original size:19 final size:19
Alignment explanation
Indices: 80539--80626 Score: 54
Period size: 20 Copynumber: 4.4 Consensus size: 19
80529 AAAGTTTAAA
80539 AAATTATAAAATATTTATT
1 AAATTATAAAATATTTATT
* *
80558 AAATTTATTAAAAGA-TTATA
1 AAA-TTA-TAAAATATTTATT
*
80578 AAATTATTAATAA-GTTTATCT
1 AAATTA-TAA-AATATTTAT-T
*
80599 AAATACTATAAAATAATTATT
1 AAAT--TATAAAATATTTATT
*
80620 ATATTAT
1 AAATTAT
80627 CGAACTTTTG
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
19 13 0.24
20 16 0.30
21 16 0.30
22 7 0.13
23 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
AAATTATAAAATATTTATT
Found at i:80569 original size:31 final size:31
Alignment explanation
Indices: 80534--80620 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
80524 TGAATAAAGT
80534 TTAAAAAATTATAAAATATTTATTAAATTTA
1 TTAAAAAATTATAAAATATTTATTAAATTTA
* * *
80565 TTAAAAGATTATAAAAT-TATTAATAAGTTTA
1 TTAAAAAATTATAAAATAT-TTATTAAATTTA
* * *
80596 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAATATTTATTA
80621 TATTATCGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.96
32 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (31 bp):
TTAAAAAATTATAAAATATTTATTAAATTTA
Found at i:80576 original size:20 final size:21
Alignment explanation
Indices: 80553--80602 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
80543 TATAAAATAT
80553 TTATTAAATTTATTAA-AAGA
1 TTATTAAATTTATTAATAAGA
* *
80573 TTA-TAAAATTATTAATAAGT
1 TTATTAAATTTATTAATAAGA
80593 TTATCTAAAT
1 TTAT-TAAAT
80603 ACTATAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 9 0.38
22 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (21 bp):
TTATTAAATTTATTAATAAGA
Found at i:83919 original size:41 final size:42
Alignment explanation
Indices: 83864--83972 Score: 116
Period size: 41 Copynumber: 2.6 Consensus size: 42
83854 ACATCATAAC
* *
83864 AATATATAGTATATAATTTAGAAAATATTATACAATTTT-AA
1 AATATATAGTATATAATTTTGAAAATAGTATACAATTTTGAA
* *
83905 AATACTATA-TATATAAGTTTTG-AATTAGTATATAATTTTGAA
1 AATA-TATAGTATATAA-TTTTGAAAATAGTATACAATTTTGAA
* *
83947 AATAATATATTATATAGTTTTGAAAA
1 AAT-ATATAGTATATAATTTTGAAAA
83973 AAAACATTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
41 25 0.45
42 22 0.39
43 9 0.16
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (42 bp):
AATATATAGTATATAATTTTGAAAATAGTATACAATTTTGAA
Found at i:83966 original size:42 final size:41
Alignment explanation
Indices: 83892--83970 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 41
83882 TAGAAAATAT
*
83892 TATACAATTTTAAAATACTATATATATAAGTTTTGAATTAG
1 TATACAATTTTAAAATAATATATATATAAGTTTTGAATTAG
*
83933 TATATAATTTTGAAAATAATATAT-TATATAGTTTTGAA
1 TATACAATTTT-AAAATAATATATATATA-AGTTTTGAA
83971 AAAAAACATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
41 14 0.41
42 20 0.59
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (41 bp):
TATACAATTTTAAAATAATATATATATAAGTTTTGAATTAG
Found at i:84000 original size:34 final size:33
Alignment explanation
Indices: 83957--84082 Score: 113
Period size: 34 Copynumber: 3.9 Consensus size: 33
83947 AATAATATAT
83957 TATATAGTTTTGAAAAAAAACATTTTGAAAATAG
1 TATATAGTTTTG-AAAAAAACATTTTGAAAATAG
* * *
83991 TATATAGTTTTGAGAAATA-A-TTTGAAAATAATA
1 TATATAGTTTTGAAAAAAACATTTTGAAAAT-A-G
*
84024 TATTATAGTTTTG--GAAAACATTTTGAAAATAG
1 TA-TATAGTTTTGAAAAAAACATTTTGAAAATAG
* *
84056 TATGTA-TTTT--AAAAAACAATTTGAAAA
1 TATATAGTTTTGAAAAAAACATTTTGAAAA
84083 ACATTATATT
Statistics
Matches: 77, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
30 18 0.23
31 12 0.16
32 7 0.09
33 9 0.12
34 31 0.40
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (33 bp):
TATATAGTTTTGAAAAAAACATTTTGAAAATAG
Found at i:84052 original size:65 final size:66
Alignment explanation
Indices: 83936--84129 Score: 232
Period size: 65 Copynumber: 2.9 Consensus size: 66
83926 GAATTAGTAT
*
83936 ATAATTTTGAAAATAATATATTATATAGTTTTGAAAAAAAACATTTTGAAAATAGTATATAGTTT
1 ATAA-TTTGAAAATAATATATTATATAGTTTTG---GAAAACATTTTGAAAATAGTATATA-TTT
* *
84001 TGAGAA
61 TAAAAA
*
84007 ATAATTTGAAAATAATATA-T-TATAGTTTTGGAAAACATTTTGAAAATAGTATGTATTTTAAAA
1 ATAATTTGAAAATAATATATTATATAGTTTTGGAAAACATTTTGAAAATAGTATATATTTTAAAA
84070 A
66 A
* * *
84071 ACAATTTGAAAA-ACATTATATTATATAGTTTTGGAAAACATTTAGAAAAATAGTCTATA
1 ATAATTTGAAAATA-A-TATATTATATAGTTTTGGAAAACATTTTG-AAAATAGTATATA
84130 CAATAGTTTG
Statistics
Matches: 110, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
63 1 0.01
64 19 0.17
65 27 0.25
66 1 0.01
67 21 0.19
68 21 0.19
69 1 0.01
70 15 0.14
71 4 0.04
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (66 bp):
ATAATTTGAAAATAATATATTATATAGTTTTGGAAAACATTTTGAAAATAGTATATATTTTAAAA
A
Done.