Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000604.1 Hibiscus syriacus cultivar Beakdansim tig00001173_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: 104974
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:6551 original size:36 final size:36
Alignment explanation
Indices: 6480--6552 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
6470 GTTGGAAAAT
* * *
6480 ATTTATATGTTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
6516 ATTTATATATTTT-TATTATAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCT-TTA-AAAATTGAAAATCATAAA
6552 A
1 A
6553 ATGTTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 1 0.03
36 21 0.66
37 10 0.31
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
Found at i:9160 original size:6 final size:6
Alignment explanation
Indices: 9149--9176 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
9139 AGAAACGCCC
9149 ATGAAG ATGAAG ATGAAG ATGAAG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGA
9177 TAAGAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.32, T:0.18
Consensus pattern (6 bp):
ATGAAG
Found at i:12948 original size:2 final size:2
Alignment explanation
Indices: 12941--12966 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12931 TCTAACTTAT
12941 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
12967 ATCACTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15590 original size:19 final size:20
Alignment explanation
Indices: 15550--15591 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
15540 ACTCCATCCG
15550 ATTCAATATTATAGTATAATT
1 ATTCAATATTATAG-ATAATT
15571 ATTCAATATTATAG-TAATT
1 ATTCAATATTATAGATAATT
15590 AT
1 AT
15592 AATAATATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
21 14 0.67
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (20 bp):
ATTCAATATTATAGATAATT
Found at i:19482 original size:2 final size:2
Alignment explanation
Indices: 19475--19518 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
19465 GAGATTATTC
19475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19517 AT
1 AT
19519 TATTATTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20327 original size:226 final size:220
Alignment explanation
Indices: 19914--20363 Score: 667
Period size: 226 Copynumber: 2.0 Consensus size: 220
19904 TATTCAGGTT
*
19914 GGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTAAGTGTGATATTCGGGTCGGGTCGAG
1 GGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTAAGTGTGATATTCGGGTC--G-AGAG
* * *
19979 TTCGGGTTTAGGGTGAAAAAGACCCGACCCGAATATATATATAATTTTACCTTATATATTAGGAA
63 TTAGGGTTTAGGGTGAAAAAGACCCGACCCGAATAAAAATATAATTTTACCTTATATATTAGGAA
20044 TAATTACAATAATACCCCTCTATATATAATTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAA
128 TAATTACAATAATACCCCTCTATATATAATTTTTTCAATTAAGT-ACTGTTTTTATTGAATAAAA
*
20109 ATAATTTTTTTATTATTT-TGGTCGGGTC
192 ATAATTTTTTTATTATTTCGGGTCGGGTC
20137 GGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTC-A
1 GGGTCGGGTGAAACTTTA-TTT--T--GGTCGGGTCGG-TTTTTTAAGTGTGATATTCGGGTCGA
*
20201 G-GTTAGGGTTTAGGGTGAAAAATACCCGACCCGACCCA-AAAAATATAATTTTACCTTATATAT
60 GAGTTAGGGTTTAGGGTGAAAAAGACCCGACCCGA---ATAAAAATATAATTTTACCTTATATA-
*
20264 TTAGGAATAATTACAATAATACCCCTCTATATATATTTTTTTTCAATTAAGT-CTGTTTTTATTG
121 TTAGGAATAATTACAATAATACCCCTCTATATATA-ATTTTTTCAATTAAGTACTGTTTTTATTG
20328 AATAAAAATAATTTTTTTATTATTTCGGGTCGGGTC
185 AATAAAAATAATTTTTTTATTATTTCGGGTCGGGTC
20364 AGGTTTCTAA
Statistics
Matches: 208, Mismatches: 7, Indels: 20
0.89 0.03 0.09
Matches are distributed among these distances:
223 18 0.09
224 34 0.16
225 1 0.00
226 60 0.29
227 45 0.22
228 26 0.12
229 24 0.12
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (220 bp):
GGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTAAGTGTGATATTCGGGTCGAGAGTTA
GGGTTTAGGGTGAAAAAGACCCGACCCGAATAAAAATATAATTTTACCTTATATATTAGGAATAA
TTACAATAATACCCCTCTATATATAATTTTTTCAATTAAGTACTGTTTTTATTGAATAAAAATAA
TTTTTTTATTATTTCGGGTCGGGTC
Found at i:35098 original size:13 final size:13
Alignment explanation
Indices: 35080--35117 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
35070 TTATAACGGT
35080 AAAAATTAATAAA
1 AAAAATTAATAAA
35093 AAAAATTAAT--A
1 AAAAATTAATAAA
35104 AAAAATTAATAAA
1 AAAAATTAATAAA
35117 A
1 A
35118 TAATAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.48
13 12 0.52
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATTAATAAA
Found at i:35106 original size:11 final size:11
Alignment explanation
Indices: 35080--35117 Score: 58
Period size: 11 Copynumber: 3.3 Consensus size: 11
35070 TTATAACGGT
35080 AAAAATTAATAAA
1 AAAAATTAAT--A
35093 AAAAATTAATA
1 AAAAATTAATA
35104 AAAAATTAATA
1 AAAAATTAATA
35115 AAA
1 AAA
35118 TAATAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 15 0.60
13 10 0.40
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAATTAATA
Found at i:36168 original size:20 final size:20
Alignment explanation
Indices: 36143--36186 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
36133 TTAGTTCACG
36143 GAATGTAAAATTACCAGTAA
1 GAATGTAAAATTACCAGTAA
* * *
36163 GAATGTAAGATTATCAGTGA
1 GAATGTAAAATTACCAGTAA
36183 GAAT
1 GAAT
36187 AGGATTGCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.27
Consensus pattern (20 bp):
GAATGTAAAATTACCAGTAA
Found at i:37714 original size:34 final size:31
Alignment explanation
Indices: 37634--37722 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 31
37624 TTAGTATTTT
* *
37634 TTTAAATAATTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTTTTATTAATATA
* *
37666 TTTATGTAAATATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTTATT--AAT-ATA
*
37700 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTTTTTTA
37723 GAATTATTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 8 0.17
32 13 0.28
33 3 0.06
34 23 0.49
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTTTATTAATATA
Found at i:37885 original size:17 final size:17
Alignment explanation
Indices: 37863--37916 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
37853 AATGTTAATA
37863 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
37880 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
37897 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
37914 TTT
1 TTT
37917 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:39530 original size:21 final size:21
Alignment explanation
Indices: 39501--39591 Score: 114
Period size: 21 Copynumber: 4.3 Consensus size: 21
39491 GCCATCTCCG
39501 CAGGGTTACATTCCGAGCCCT
1 CAGGGTTACATTCCGAGCCCT
* *
39522 CAAGGTTACATTCCAAGCCCGT
1 CAGGGTTACATTCCGAGCCC-T
*
39544 -AGGGTTACATTCCGAGCCCA
1 CAGGGTTACATTCCGAGCCCT
*
39564 CAGGGTTACATTCCTAGCCCGT
1 CAGGGTTACATTCCGAGCCC-T
39586 -AGGGTT
1 CAGGGTT
39592 TTATACCATA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
21 59 0.98
22 1 0.02
ACGTcount: A:0.22, C:0.30, G:0.24, T:0.24
Consensus pattern (21 bp):
CAGGGTTACATTCCGAGCCCT
Found at i:39549 original size:42 final size:42
Alignment explanation
Indices: 39502--39591 Score: 153
Period size: 42 Copynumber: 2.1 Consensus size: 42
39492 CCATCTCCGC
*
39502 AGGGTTACATTCCGAGCCCTCAAGGTTACATTCCAAGCCCGT
1 AGGGTTACATTCCGAGCCCACAAGGTTACATTCCAAGCCCGT
* *
39544 AGGGTTACATTCCGAGCCCACAGGGTTACATTCCTAGCCCGT
1 AGGGTTACATTCCGAGCCCACAAGGTTACATTCCAAGCCCGT
39586 AGGGTT
1 AGGGTT
39592 TTATACCATA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.24
Consensus pattern (42 bp):
AGGGTTACATTCCGAGCCCACAAGGTTACATTCCAAGCCCGT
Found at i:40217 original size:34 final size:34
Alignment explanation
Indices: 40112--40218 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
40102 ATAAATGTTT
*
40112 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* *
40146 TAAAAATAAAAATAATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* * * *
40180 TTAAAATATAAATTATAGTATTCAAAATTTAACA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
40214 TTAAA
1 TTAAA
40219 TTTCAACTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (34 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAAA
Found at i:41014 original size:127 final size:128
Alignment explanation
Indices: 40614--41218 Score: 1061
Period size: 128 Copynumber: 4.7 Consensus size: 128
40604 ACAATCCATC
*
40614 TAGTGTCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
40679 GGAAGGCGCG-CCCCGGGAACGCGTCTTCAAGTCCACTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
40741 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGAAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
40806 GGAAGGCGCACCCCCGAGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTATTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
40869 TAGTGTCCCCGAGAGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
40934 AGAAGGCGC-CCCTCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
40996 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
41061 GGAAGGCGCCCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
** *
41124 TAGTGTCCATGAGGGACATGAGTGGCATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
41189 GGAAGGCGCGCCCCCGGGAACGTGCCTTCA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCA
41219 TGTGAATAGT
Statistics
Matches: 455, Mismatches: 21, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
127 194 0.43
128 261 0.57
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (128 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:41065 original size:255 final size:255
Alignment explanation
Indices: 40614--41218 Score: 1068
Period size: 255 Copynumber: 2.4 Consensus size: 255
40604 ACAATCCATC
*
40614 TAGTGTCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
40679 GGAAGGCGCGCCCCGGGAACGCGTCTTCAAGTCCACTGAGAAATAATAGGTACTGATATGAATAG
66 GGAAGGCGCGCCCCGGGAACGCGCCTTCAAGTCCACTGAGAAATAATAGGTACTGATATGAATAG
40744 TGTCCCCGAGGGACATGAGTGACATAATAGGGAAATGATAACATATTCTCTGACAAAATAATGGA
131 TGTCCCCGAGGGACATGAGTGACATAATAGGGAAATGATAACATATTCTCTGACAAAATAATGGA
*
40809 AGGCGCACCCCCGAGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTATTGATATGAA
196 AGGCGCACCCCCGAGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
40869 TAGTGTCCCCGAGAGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
40934 AGAAGGCGC-CCCTCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
66 GGAAGGCGCGCCC-CGGGAACGCGCCTTCAAGTCCACTGAGAAATAATAGGTACTGATATGAATA
*
40998 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
130 GTGTCCCCGAGGGACATGAGTGACATAATAGGGAAATGATAACATATTCTCTGACAAAATAATGG
* *
41063 AAGGCGCCCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
195 AAGGCGCACCCCCGAGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
** *
41124 TAGTGTCCATGAGGGACATGAGTGGCATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
41189 GGAAGGCGCGCCCCCGGGAACGTGCCTTCA
66 GGAAGGCGCG-CCCCGGGAACGCGCCTTCA
41219 TGTGAATAGT
Statistics
Matches: 332, Mismatches: 15, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
254 3 0.01
255 311 0.94
256 15 0.05
257 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (255 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCGGGAACGCGCCTTCAAGTCCACTGAGAAATAATAGGTACTGATATGAATAG
TGTCCCCGAGGGACATGAGTGACATAATAGGGAAATGATAACATATTCTCTGACAAAATAATGGA
AGGCGCACCCCCGAGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:41312 original size:8 final size:8
Alignment explanation
Indices: 41299--41339 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
41289 TCACAAGCGT
41299 TCAAATTC
1 TCAAATTC
41307 TCAAATTC
1 TCAAATTC
* *
41315 CCAAACTC
1 TCAAATTC
41323 T-AAATTC
1 TCAAATTC
41330 TCAAATTC
1 TCAAATTC
41338 TC
1 TC
41340 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:49766 original size:2 final size:2
Alignment explanation
Indices: 49759--49822 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
49749 ATAATACCAA
49759 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49801 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
49823 CGAGTGAGAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51486 original size:124 final size:122
Alignment explanation
Indices: 51244--51469 Score: 280
Period size: 124 Copynumber: 1.8 Consensus size: 122
51234 AAAATTAAAA
* * **
51244 AAAACATATAATAATATTAATTCCATATATATAATAGCTAAATATGGGAGAGGGAAAAATATATA
1 AAAACATATAATAATATTAATACCATATATATAATAACTAAATAT-GGAGAGAAAAAAATATATA
* * *
51309 ATAATAATAGAAAAAATTAAATAATAATTAGCGTATAAAGTAAAATAAATAAAGTTAAT
65 ATAATAATAGAAAAAACTAAATAATAAATA-CATATAAAGTAAAATAAATAAAGTTAAT
51368 AAAACATATAATAATATTAATACCATATATATATATAACTAAATAT-GAGA-AAAAAAATCTATA
1 AAAACATATAATAATATTAATACCATATATATA-ATAACTAAATATGGAGAGAAAAAAA--TATA
* *
51431 TAATAGTAAT-GGAAAAACTAAATAATGAAGATA-ATATAA
63 TAATAATAATAGAAAAAACTAAATAAT-AA-ATACATATAA
51470 TAAGAAAAAG
Statistics
Matches: 88, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
122 5 0.06
123 23 0.26
124 47 0.53
125 13 0.15
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.29
Consensus pattern (122 bp):
AAAACATATAATAATATTAATACCATATATATAATAACTAAATATGGAGAGAAAAAAATATATAA
TAATAATAGAAAAAACTAAATAATAAATACATATAAAGTAAAATAAATAAAGTTAAT
Found at i:53552 original size:105 final size:105
Alignment explanation
Indices: 53277--53747 Score: 890
Period size: 105 Copynumber: 4.5 Consensus size: 105
53267 GTATTGTTCA
53277 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
*
53342 CAGTGGTCCCTTCGTCGTGAAGTTGAAC-TGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
53381 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
*
53446 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
53486 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
*
53551 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
53591 TAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
53656 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
53696 TAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAAT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAAT
53748 ACAACCAGCC
Statistics
Matches: 362, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
104 93 0.26
105 269 0.74
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:63992 original size:20 final size:20
Alignment explanation
Indices: 63954--63997 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
63944 ATGGTTAGTA
*
63954 AAATAAAAATAAATGGAAAT
1 AAATAAAAATAAATAGAAAT
63974 AAATAAAAATAACA-AGAAAT
1 AAATAAAAATAA-ATAGAAAT
63994 AAAT
1 AAAT
63998 GGCAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (20 bp):
AAATAAAAATAAATAGAAAT
Found at i:65026 original size:25 final size:26
Alignment explanation
Indices: 64997--65049 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
64987 TAATAATAAT
64997 AAAGATATA-AAAAAATAAAAAAAAA
1 AAAGATATATAAAAAATAAAAAAAAA
* * *
65022 AAAGATATATAAATAGTAATAAAAAA
1 AAAGATATATAAAAAATAAAAAAAAA
65048 AA
1 AA
65050 CTAAATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (26 bp):
AAAGATATATAAAAAATAAAAAAAAA
Found at i:65061 original size:28 final size:29
Alignment explanation
Indices: 65010--65064 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
65000 GATATAAAAA
*
65010 AATAAAAAAAAAAAAGATATATAAATAGT
1 AATAAAAAAAAAAAAGATAAATAAATAGT
**
65039 AATAAAAAAAACTAA-ATAAATAAATA
1 AATAAAAAAAAAAAAGATAAATAAATA
65065 ACTATAATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (29 bp):
AATAAAAAAAAAAAAGATAAATAAATAGT
Found at i:65307 original size:19 final size:19
Alignment explanation
Indices: 65285--65321 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
65275 GGGAGAGAGG
65285 GAAAAA-TATAATAATAATA
1 GAAAAATTA-AATAATAATA
65304 GAAAAATTAAATAATAAT
1 GAAAAATTAAATAATAAT
65322 TATAGCGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
GAAAAATTAAATAATAATA
Found at i:67129 original size:2 final size:2
Alignment explanation
Indices: 67122--67146 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
67112 CGAGGGATTT
67122 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
67147 TAATTAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:68076 original size:2 final size:2
Alignment explanation
Indices: 68069--68094 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
68059 CCCTAGTTTA
68069 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
68095 TATTTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74364 original size:25 final size:26
Alignment explanation
Indices: 74336--74391 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
74326 ATAAAGAGAT
74336 TTAATTAAAAT-AA-TATTTGAATCTA
1 TTAATTAAAATAAATTATTT-AATCTA
*
74361 TTAATTAAATTAAATTATTTAATCTA
1 TTAATTAAAATAAATTATTTAATCTA
74387 -TAATT
1 TTAATT
74392 TAGAGTGTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 15 0.54
26 8 0.29
27 5 0.18
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (26 bp):
TTAATTAAAATAAATTATTTAATCTA
Found at i:74671 original size:2 final size:2
Alignment explanation
Indices: 74664--74700 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
74654 TTATTATTGA
74664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
74701 GTTTATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:75350 original size:18 final size:17
Alignment explanation
Indices: 75327--75360 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
75317 ATTTAAATTA
*
75327 TAATTATTATTGTATTTT
1 TAATTA-TATTATATTTT
75345 TAATTATATTATATTT
1 TAATTATATTATATTT
75361 ATTATAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TAATTATATTATATTTT
Found at i:75368 original size:20 final size:19
Alignment explanation
Indices: 75323--75373 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
75313 AGAGATTTAA
*
75323 ATTATAATTATTATTGTATT
1 ATTATAATTA-TATTATATT
75343 -TT-TAATTATATTATATTT
1 ATTATAATTATATTATA-TT
*
75361 ATTATAATAATAT
1 ATTATAATTATAT
75374 AATAAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 6 0.23
18 8 0.31
19 4 0.15
20 8 0.31
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTATAATTATATTATATT
Found at i:78012 original size:12 final size:12
Alignment explanation
Indices: 77977--78012 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
77967 CTGTTTCAAC
77977 TATATATTTATT
1 TATATATTTATT
*
77989 TATTTATTTATT
1 TATATATTTATT
*
78001 TATATATGTATT
1 TATATATTTATT
78013 GCATTTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (12 bp):
TATATATTTATT
Found at i:79893 original size:29 final size:28
Alignment explanation
Indices: 79831--79915 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 28
79821 CAGTACCGGG
*
79831 GGTAGGTCGCCATGCA-CCCGGCGACCT
1 GGTAGGTCGCCATGCAGCCCAGCGACCT
***
79858 ACCAGGTCGCCATGCACGCCCAGCGACCT
1 GGTAGGTCGCCATGCA-GCCCAGCGACCT
*
79887 GGTAGGTCGCCATGCATGCCCTGCGACCT
1 GGTAGGTCGCCATGCA-GCCCAGCGACCT
79916 ACCAGCCAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
27 13 0.28
29 34 0.72
ACGTcount: A:0.16, C:0.39, G:0.29, T:0.15
Consensus pattern (28 bp):
GGTAGGTCGCCATGCAGCCCAGCGACCT
Found at i:80166 original size:29 final size:29
Alignment explanation
Indices: 80118--80205 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
80108 TCCCCATGAA
**
80118 TCCTTGGTCGCCCCGAGTGCATGGCGACC
1 TCCTTGGTCGCCGGGAGTGCATGGCGACC
*
80147 TCCTTGGTCGCCGGGCGTGCATGGCGACC
1 TCCTTGGTCGCCGGGAGTGCATGGCGACC
**** *
80176 TAGGAGGTCGCTGGGAGTGCATGGCGACC
1 TCCTTGGTCGCCGGGAGTGCATGGCGACC
80205 T
1 T
80206 ATGGTTGGGT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.11, C:0.31, G:0.38, T:0.20
Consensus pattern (29 bp):
TCCTTGGTCGCCGGGAGTGCATGGCGACC
Found at i:85829 original size:63 final size:63
Alignment explanation
Indices: 85761--85888 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 63
85751 ATTTGAAAAC
85761 CAAAACTCATATGTTTTTATAGTCTTTAATACTCAACCTAAAACTTTTAAGATTAAAAACTAT
1 CAAAACTCATATGTTTTTATAGTCTTTAATACTCAACCTAAAACTTTTAAGATTAAAAACTAT
* *
85824 CAAAACTCATGTGTTTTTATAGTCTTTAATACTCAACCTAAAACTTTTAAGATTAAAAATTAT
1 CAAAACTCATATGTTTTTATAGTCTTTAATACTCAACCTAAAACTTTTAAGATTAAAAACTAT
85887 CA
1 CA
85889 TTTTAACCTC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (63 bp):
CAAAACTCATATGTTTTTATAGTCTTTAATACTCAACCTAAAACTTTTAAGATTAAAAACTAT
Found at i:102222 original size:2 final size:2
Alignment explanation
Indices: 102215--102239 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
102205 TAGTAATGAA
102215 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
102240 GAAACTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.