Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002786.1 Hibiscus syriacus cultivar Beakdansim tig00005741_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: 242387
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:148602 original size:21 final size:20
Alignment explanation
Indices: 148578--148625 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
148568 ATTTTAGAAA
*
148578 TTTAGATTCTAAAATTTATAT
1 TTTAGATT-TAAAATTTAAAT
*
148599 TTTAGGATTTAAGATTTAAAT
1 TTTA-GATTTAAAATTTAAAT
148620 TTTAGA
1 TTTAGA
148626 AATTTAGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 18 0.75
22 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTAGATTTAAAATTTAAAT
Found at i:148608 original size:14 final size:14
Alignment explanation
Indices: 148534--148609 Score: 62
Period size: 14 Copynumber: 5.3 Consensus size: 14
148524 TTTCTTAAGG
*
148534 TTTAAATTTTAGATA
1 TTTATATTTTAGA-A
* * *
148549 TTTAGATTCTAAAA
1 TTTATATTTTAGAA
148563 TTTATATTTTAGAAA
1 TTTATATTTTAG-AA
* * *
148578 TTTAGATTCTAAAA
1 TTTATATTTTAGAA
*
148592 TTTATATTTTAGGA
1 TTTATATTTTAGAA
148606 TTTA
1 TTTA
148610 AGATTTAAAT
Statistics
Matches: 47, Mismatches: 13, Indels: 3
0.75 0.21 0.05
Matches are distributed among these distances:
14 26 0.55
15 21 0.45
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (14 bp):
TTTATATTTTAGAA
Found at i:148613 original size:29 final size:28
Alignment explanation
Indices: 148534--148623 Score: 110
Period size: 29 Copynumber: 3.1 Consensus size: 28
148524 TTTCTTAAGG
* *
148534 TTTAAATTTTAGATATTTAGATTCTAAAA
1 TTTATATTTTAG-GATTTAGATTCTAAAA
*
148563 TTTATATTTTAGAAATTTAGATTCTAAAA
1 TTTATATTTTAG-GATTTAGATTCTAAAA
*
148592 TTTATATTTTAGGATTTAAGATT-TAAAT
1 TTTATATTTTAGGATTT-AGATTCTAAAA
148620 TTTA
1 TTTA
148624 GAAATTTAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
28 12 0.21
29 44 0.79
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (28 bp):
TTTATATTTTAGGATTTAGATTCTAAAA
Found at i:148634 original size:21 final size:21
Alignment explanation
Indices: 148578--148636 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
148568 ATTTTAGAAA
* *
148578 TTTAG-ATTCTAAAATTTATAT
1 TTTAGAATT-TAAGATTTAAAT
*
148599 TTTAGGATTTAAGATTTAAAT
1 TTTAGAATTTAAGATTTAAAT
148620 TTTAGAAATTT-AGATTT
1 TTTAG-AATTTAAGATTT
148637 TAAGGTCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 26 0.79
22 7 0.21
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (21 bp):
TTTAGAATTTAAGATTTAAAT
Found at i:149041 original size:46 final size:43
Alignment explanation
Indices: 148971--149070 Score: 139
Period size: 46 Copynumber: 2.3 Consensus size: 43
148961 TCATTCAAAA
148971 AATTATTAATTTGTTAATAAATAATAAAAAAGATGATAAATTATT
1 AATTATTAATTTGTTAATAAATAATAAAAAAGAT--TAAATTATT
*
149016 AATCTATTAATTT-TCTAATAAATAATAAAAAATATTAAATTATT
1 AAT-TATTAATTTGT-TAATAAATAATAAAAAAGATTAAATTATT
*
149060 AATTAATAATT
1 AATTATTAATT
149071 ATTATTTTAC
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
43 7 0.14
44 12 0.24
45 4 0.08
46 28 0.55
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (43 bp):
AATTATTAATTTGTTAATAAATAATAAAAAAGATTAAATTATT
Found at i:155850 original size:2 final size:2
Alignment explanation
Indices: 155845--155872 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
155835 CAAAAAACTA
155845 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
155873 TATGTACGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:155993 original size:21 final size:20
Alignment explanation
Indices: 155967--156021 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
155957 AAATAAAATT
155967 ATAATATATATACTTTTAAAA
1 ATAATATATATA-TTTTAAAA
* * *
155988 ATAATACATATATTTTCAAT
1 ATAATATATATATTTTAAAA
156008 ATATATATATATAT
1 ATA-ATATATATAT
156022 AATGTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.31
21 20 0.69
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAATATATATATTTTAAAA
Found at i:156011 original size:2 final size:2
Alignment explanation
Indices: 156006--156084 Score: 71
Period size: 2 Copynumber: 42.0 Consensus size: 2
155996 TATATTTTCA
* * * *
156006 AT AT AT AT AT AT AT AT A- AT GT TT AT -T TT A- AA AT ACT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
156045 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
156085 GTATCTTTCA
Statistics
Matches: 65, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
1 6 0.09
2 57 0.88
3 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
AT
Found at i:156122 original size:22 final size:21
Alignment explanation
Indices: 156094--156135 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
156084 TGTATCTTTC
*
156094 AAAATATAACGTATATATTTTA
1 AAAATAT-ACATATATATTTTA
156116 AAAATATACATATATATTTT
1 AAAATATACATATATATTTT
156136 TCAAAACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (21 bp):
AAAATATACATATATATTTTA
Found at i:156141 original size:23 final size:23
Alignment explanation
Indices: 156081--156155 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
156071 TATATATATT
* *
156081 ATATGTATCTTTC-AAAATATAAC
1 ATATATATTTTTCAAAAATAT-AC
*
156104 GTATATA-TTTT-AAAAATATAC
1 ATATATATTTTTCAAAAATATAC
*
156125 ATATATATTTTTCAAAACAAATA-
1 ATATATATTTTTCAAAA-ATATAC
156148 ATATATAT
1 ATATATAT
156156 ATATCCTCGA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
21 8 0.19
22 14 0.33
23 17 0.40
24 4 0.09
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (23 bp):
ATATATATTTTTCAAAAATATAC
Found at i:156888 original size:28 final size:28
Alignment explanation
Indices: 156856--156939 Score: 159
Period size: 28 Copynumber: 3.0 Consensus size: 28
156846 ACTCCCCTTT
156856 GCGAGTTAAGTCATGCCGAAAAATTATC
1 GCGAGTTAAGTCATGCCGAAAAATTATC
156884 GCGAGTTAAGTCATGCCGAAAAATTATC
1 GCGAGTTAAGTCATGCCGAAAAATTATC
*
156912 GCGAGTTAAGTTATGCCGAAAAATTATC
1 GCGAGTTAAGTCATGCCGAAAAATTATC
156940 TCGAATAAGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (28 bp):
GCGAGTTAAGTCATGCCGAAAAATTATC
Found at i:157179 original size:70 final size:71
Alignment explanation
Indices: 156952--157302 Score: 367
Period size: 71 Copynumber: 4.9 Consensus size: 71
156942 GAATAAGACT
* * * * * *
156952 AAATGTTTCAAGAGAAAATATCTCAAATGAGATAAAATTTTGTTTC-CATAGAAAT-TGTCTTGG
1 AAAT-TTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTCAGAT-G-AATCTGTCTCGA
157015 GTGAGAC--
63 GTGAGACAA
* * **
157022 AAATTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGCTTCGGCCGAATCTGTCTCGAGTG
1 AAATTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTCAGATGAATCTGTCTCGAGTG
157087 AGACAA
66 AGACAA
* *
157093 AACA-TTTCAGGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTCAG-TGAATCTGTCTAGAGT
1 AA-ATTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTCAGATGAATCTGTCTCGAGT
157156 GAGACAA
65 GAGACAA
* * * *
157163 AAATTTTCAAGCGAAAATATTTTAAGTGAGATGAAATTTTGTTTCGAGAT-AAACTGTCTCGAGT
1 AAATTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTC-AGATGAATCTGTCTCGAGT
157227 GAGACAA
65 GAGACAA
* ** * * *
157234 AAATTTTCAAGGAAAAAAAATATCTCAAGTGAGATGCGATTTTTTTTCAAGAT-AAACTATCTCG
1 AAATTTTCAAGG---GAAAATATCTCAAGTGAGATGAAATTTTGTTTC-AGATGAATCTGTCTCG
157298 AGTGA
62 AGTGA
157303 AAATATTTCT
Statistics
Matches: 241, Mismatches: 29, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
68 3 0.01
69 52 0.22
70 64 0.27
71 74 0.31
72 2 0.01
74 46 0.19
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (71 bp):
AAATTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTCAGATGAATCTGTCTCGAGTG
AGACAA
Found at i:157220 original size:141 final size:142
Alignment explanation
Indices: 156952--157269 Score: 384
Period size: 141 Copynumber: 2.2 Consensus size: 142
156942 GAATAAGACT
* * * *
156952 AAATGTTTCAA-G-AGAAAATATCTCAAATGAGATAAAATTTTGTTTCCATAGAAATTGTCTTGG
1 AAAT-TTTCAAGGAAGAAAATATCTCAAGTGAGATGAAATTTTGTTTCCATAGAAATTGTCTAGA
* * *
157015 GTGAGACAAATTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGCTTCGGCCGAATCTGTC
65 GTGAGACAAATTTTCAAGCGAAAATATCTCAAGTGAGATGAAATTTTGCTTCGGCAGAAACTGTC
157080 TCGAGTGAGACAA
130 TCGAGTGAGACAA
*
157093 AACA-TTTC-AGG-GGAAAATATCTCAAGTGAGATGAAATTTTGTTT-CAGT-G-AATCTGTCTA
1 AA-ATTTTCAAGGAAGAAAATATCTCAAGTGAGATGAAATTTTGTTTCCA-TAGAAAT-TGTCTA
* * * *
157152 GAGTGAGACAAAAATTTTCAAGCGAAAATATTTTAAGTGAGATGAAATTTTGTTTCGAG-ATAAA
63 GAGTGAGAC--AAATTTTCAAGCGAAAATATCTCAAGTGAGATGAAATTTTGCTTCG-GCAGAAA
157216 CTGTCTCGAGTGAGACAA
125 CTGTCTCGAGTGAGACAA
*
157234 AAATTTTCAAGGAAAAAAAATATCTCAAGTGAGATG
1 AAATTTTCAAGG-AAGAAAATATCTCAAGTGAGATG
157270 CGATTTTTTT
Statistics
Matches: 152, Mismatches: 14, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
138 3 0.02
139 17 0.11
140 37 0.24
141 70 0.46
142 5 0.03
144 20 0.13
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.30
Consensus pattern (142 bp):
AAATTTTCAAGGAAGAAAATATCTCAAGTGAGATGAAATTTTGTTTCCATAGAAATTGTCTAGAG
TGAGACAAATTTTCAAGCGAAAATATCTCAAGTGAGATGAAATTTTGCTTCGGCAGAAACTGTCT
CGAGTGAGACAA
Found at i:157317 original size:52 final size:53
Alignment explanation
Indices: 157250--157355 Score: 142
Period size: 52 Copynumber: 2.0 Consensus size: 53
157240 TCAAGGAAAA
** *
157250 AAAATATCTCAAGTGAGATGCGATTTTT-TTTCAAGATAAACTATCTCGAGTG
1 AAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAGAAACTATCTCGAGTG
* * * *
157302 AAAATATTTCTAGTGAGATGAAATTTTTGTTTCAAGAGAAACTGTCTGGAGTG
1 AAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAGAAACTATCTCGAGTG
157355 A
1 A
157356 GACGAATTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 24 0.52
53 22 0.48
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (53 bp):
AAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAGAAACTATCTCGAGTG
Found at i:157402 original size:126 final size:125
Alignment explanation
Indices: 157175--157421 Score: 293
Period size: 126 Copynumber: 2.0 Consensus size: 125
157165 ATTTTCAAGC
* *
157175 GAAAATATTTTAAGTGAGATGAAATTTTGTTTCGAGATAAACTGTCTCGAGTGAGACAAAAATTT
1 GAAAATATTTTAAGTGAGATGAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACAAAAATTT
* *** *
157240 TCAAGGAAAAAAAATATCTCAAGTGAGATGCGATTTTT-TTTCAAGATAAACTATCTCGAGT
66 TCAAGG--AAAAAATATCTCAAGTAAGATAAAATTTTTGTTTCAAGAGAAACTATCTCGAGT
* ***
157301 GAAAATATTTCT-AGTGAGATGAAATTTTTGTTTCAAGAGAAACTGTCTGGAGTGAGACGAATTT
1 GAAAATATTT-TAAGTGAGATGAAA-TTTTGTTTCAAGAGAAACTGTCTCGAGTGAGAC-AAAAA
* * *
157365 TGTTTTAAGG-AAAACTATCTCAAGTAAGATAAAATTTTTGTTTCAAGGGAAACTATC
63 T-TTTCAAGGAAAAAATATCTCAAGTAAGATAAAATTTTTGTTTCAAGAGAAACTATC
157422 CCAATCGAGA
Statistics
Matches: 102, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
126 46 0.45
127 46 0.45
128 3 0.03
129 7 0.07
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.34
Consensus pattern (125 bp):
GAAAATATTTTAAGTGAGATGAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACAAAAATTT
TCAAGGAAAAAATATCTCAAGTAAGATAAAATTTTTGTTTCAAGAGAAACTATCTCGAGT
Found at i:157411 original size:74 final size:72
Alignment explanation
Indices: 157317--157624 Score: 235
Period size: 74 Copynumber: 4.3 Consensus size: 72
157307 ATTTCTAGTG
* * * * *
157317 AGATGAAATTTTTGTTTCAAGAGAAACTGTCTGGAGTGAGACGAATTTTGTTTTAAGGAAAACTA
1 AGATAAAATTTTTGTTTCAAG-GAAACTGTCTCGAGTGAGAAGAAATTTGTTTTGAGGAAAACTA
157382 TCTCAAGT
65 TCTCAAGT
* * * * *
157390 AAGATAAAATTTTTGTTTCAAGGGAAACTATC-CCAATCGAGATGTAAATTT-TTTTGAGGAAAT
1 -AGATAAAATTTTTGTTTCAA-GGAAACTGTCTCGAGT-GAGAAG-AAATTTGTTTTGAGGAAAA
157453 CTATCTCAAGT
62 CTATCTCAAGT
* * *
157464 -G----AATTTTTGTTTCAAGGAAATTGTCTTGAGTGAGAAGAAAATTGTTTTCGAGGAAAACTA
1 AGATAAAATTTTTGTTTCAAGGAAACTGTCTCGAGTGAGAAGAAATTTGTTTT-GAGGAAAACTA
157524 TCTCAAGT
65 TCTCAAGT
* * * * ** *
157532 GAGATAAAA--ATTATTTC-A-GAGAATTGTCTCAAGTGAGATTAAATTTGTTCTTGAGGAAAGC
1 -AGATAAAATTTTTGTTTCAAGGA-AACTGTCTCGAGTGAGAAGAAATTTGTT-TTGAGGAAAAC
* *
157593 TATATCGAGT
63 TATCTCAAGT
*
157603 GAGAT-AAATTTTTGTTTTAAGG
1 -AGATAAAATTTTTGTTTCAAGG
157625 GAAATTTGTC
Statistics
Matches: 186, Mismatches: 30, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
66 5 0.03
67 17 0.09
68 34 0.18
70 6 0.03
71 45 0.24
72 14 0.08
73 3 0.02
74 56 0.30
75 6 0.03
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.35
Consensus pattern (72 bp):
AGATAAAATTTTTGTTTCAAGGAAACTGTCTCGAGTGAGAAGAAATTTGTTTTGAGGAAAACTAT
CTCAAGT
Found at i:164060 original size:23 final size:23
Alignment explanation
Indices: 164003--164060 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
163993 CACTAGACTA
* * *
164003 TCTAACCTGCCAATCCAAAGCCC
1 TCTAAACTGCCTATCCAAAGACC
*
164026 TCTAAACTGCCTATTCAAAGACC
1 TCTAAACTGCCTATCCAAAGACC
164049 TCTAAACTGCCT
1 TCTAAACTGCCT
164061 TTGCATGGCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.31, C:0.36, G:0.09, T:0.24
Consensus pattern (23 bp):
TCTAAACTGCCTATCCAAAGACC
Found at i:175553 original size:13 final size:14
Alignment explanation
Indices: 175526--175554 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
175516 TTGTGACAAA
175526 ATTTATTTGTAATT
1 ATTTATTTGTAATT
175540 ATTTATTT-TAATT
1 ATTTATTTGTAATT
175553 AT
1 AT
175555 AGTGACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (14 bp):
ATTTATTTGTAATT
Found at i:176565 original size:40 final size:40
Alignment explanation
Indices: 176509--176613 Score: 158
Period size: 40 Copynumber: 2.6 Consensus size: 40
176499 GGAAGGAACC
* *
176509 GTGGATTTCCCGGAATGCCTCGTGGGAGGCAGATTG-ACAA
1 GTGGATTTCCCAGAATGCCTCGTGGGAGGAAGA-TGCACAA
176549 GTGGATTTCCCAGAATGCCTCGTGGGAGGAAGATGCACAA
1 GTGGATTTCCCAGAATGCCTCGTGGGAGGAAGATGCACAA
* *
176589 GTGGATTTCCCAAAATGCGTCGTGG
1 GTGGATTTCCCAGAATGCCTCGTGG
176614 ATTTCCCCGA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
39 2 0.03
40 58 0.97
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.23
Consensus pattern (40 bp):
GTGGATTTCCCAGAATGCCTCGTGGGAGGAAGATGCACAA
Found at i:184743 original size:41 final size:41
Alignment explanation
Indices: 184686--184764 Score: 133
Period size: 41 Copynumber: 1.9 Consensus size: 41
184676 ATTCTAAGTA
*
184686 AACTTTTGGAGTTTCATC-TTCCATTGAATTAATAACTAGTG
1 AACTTTTGGAGTTTCATCTTTCC-TTGAATTAACAACTAGTG
184727 AACTTTTGGAGTTTCATCTTTCCTTGAATTAACAACTA
1 AACTTTTGGAGTTTCATCTTTCCTTGAATTAACAACTA
184765 ATTTACCGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
41 32 0.89
42 4 0.11
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (41 bp):
AACTTTTGGAGTTTCATCTTTCCTTGAATTAACAACTAGTG
Found at i:185968 original size:15 final size:15
Alignment explanation
Indices: 185950--185991 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
185940 TCAGTGTTGC
185950 TGTTATTGGAGTCGT
1 TGTTATTGGAGTCGT
**
185965 TGTTAAAGGAGTCGT
1 TGTTATTGGAGTCGT
185980 TGTTATTGGAGT
1 TGTTATTGGAGT
185992 ATAGGAGGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.19, C:0.05, G:0.33, T:0.43
Consensus pattern (15 bp):
TGTTATTGGAGTCGT
Found at i:186521 original size:24 final size:24
Alignment explanation
Indices: 186477--186528 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
186467 TATTTGGACA
* *
186477 TATTTTATATTATGTTAAAATTTT
1 TATTCTATATTATGTTAAAATATT
*
186501 TATTCTATATTAT-TATGAAATATT
1 TATTCTATATTATGT-TAAAATATT
186525 TATT
1 TATT
186529 TTAATCATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (24 bp):
TATTCTATATTATGTTAAAATATT
Found at i:189747 original size:54 final size:54
Alignment explanation
Indices: 189713--190081 Score: 576
Period size: 54 Copynumber: 6.8 Consensus size: 54
189703 CCATAGGATC
* * * *
189713 ATTCATAAATATATTATGAATTCCGTGGATTGCACACTTAGTGCCGAAATGGTT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAATGGTT
*
189767 ATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGCCGAAATGGTT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAATGGTT
* *
189821 ATTCATCAACATATGATGAATTCCGTGAATTGTACACTTAGTGCCGAAACGGTT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAATGGTT
* * **
189875 ATTCATCAATATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACAGTT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAATGGTT
* * *
189929 ATTCATCAACATAAGATGAATTCCGTGAATTGCACACTTAGTGCCAAAATTGTT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAATGGTT
* * * *
189983 ATTTATCAACATATGATGAATTTCGTGAATTGCACACTTAGTGTCGAAACGGTT
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAATGGTT
190037 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCC
1 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCC
190082 TATTTGTTAA
Statistics
Matches: 287, Mismatches: 28, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 287 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (54 bp):
ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAATGGTT
Found at i:193566 original size:16 final size:17
Alignment explanation
Indices: 193536--193571 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
193526 ACAAATATAA
*
193536 TAAAAATAAGTAAATGT
1 TAAAAATAAGAAAATGT
193553 TAAAAATAA-AAAATGT
1 TAAAAATAAGAAAATGT
193569 TAA
1 TAA
193572 TGCATCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (17 bp):
TAAAAATAAGAAAATGT
Found at i:194961 original size:18 final size:18
Alignment explanation
Indices: 194931--195091 Score: 66
Period size: 18 Copynumber: 8.9 Consensus size: 18
194921 AAAATTAATA
194931 ATATATA-TATATATATT
1 ATATATACTATATATATT
* *
194948 ATATGTACTATATATTTT
1 ATATATACTATATATATT
* *
194966 GTATATACTATACGGTATATA
1 ATATATACTATA---TATATT
* * *
194987 ATATATA-TGT-TTTCA-A
1 ATATATACTATATAT-ATT
* * *
195003 AAATATACCATATAATACAT
1 ATATATACTATAT-ATA-TT
*
195023 ATATTTA-TATATATATAT
1 ATATATACTATATATAT-T
195041 ATATATA-TATATATATT
1 ATATATACTATATATATT
* * * *
195058 A-AAATAATACATATACT
1 ATATATACTATATATATT
195075 ACTATATACTATATATA
1 A-TATATACTATATATA
195092 ATATCTACAC
Statistics
Matches: 105, Mismatches: 25, Indels: 26
0.67 0.16 0.17
Matches are distributed among these distances:
16 13 0.12
17 19 0.18
18 40 0.38
19 16 0.15
20 7 0.07
21 10 0.10
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (18 bp):
ATATATACTATATATATT
Found at i:195033 original size:2 final size:2
Alignment explanation
Indices: 195012--195095 Score: 70
Period size: 2 Copynumber: 43.0 Consensus size: 2
195002 AAAATATACC
* *
195012 AT AT A- AT AC AT AT AT TT 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
* *
195053 AT AT -T A- AA AT A- AT AC AT AT ACT ACT AT AT ACT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT A-T A-T AT AT A-T AT AT AT AT
195092 AT AT
1 AT AT
195096 CTACACTTCT
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
1 5 0.07
2 56 0.82
3 7 0.10
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:195169 original size:18 final size:18
Alignment explanation
Indices: 195128--195182 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
195118 TAATATGTAT
**
195128 TATGTATGTAATATTATAAA
1 TATGTATGT-ATA-TATATG
* *
195148 TATGTGTGTGTATATATG
1 TATGTATGTATATATATG
195166 TATGTATGTATATATAT
1 TATGTATGTATATATAT
195183 ACACACGTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 19 0.66
19 2 0.07
20 8 0.28
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (18 bp):
TATGTATGTATATATATG
Found at i:195485 original size:2 final size:2
Alignment explanation
Indices: 195478--195512 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
195468 TGTCTGCATA
195478 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 A
195513 CGTTAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:197556 original size:21 final size:22
Alignment explanation
Indices: 197534--197620 Score: 110
Period size: 21 Copynumber: 4.1 Consensus size: 22
197524 AAATGGATTG
197534 AAGGG-TTAAGTCCTTTTGATGA
1 AAGGGCTTAA-TCCTTTTGATGA
*
197556 AAGGACTT-ATCCTTTTGATGA
1 AAGGGCTTAATCCTTTTGATGA
*
197577 AAGGGCTTAA-CCTCTTGATGA
1 AAGGGCTTAATCCTTTTGATGA
*
197598 AAGGGCTTAAT-CTTTTCATGA
1 AAGGGCTTAATCCTTTTGATGA
197619 AA
1 AA
197621 AGATTTAATC
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
21 49 0.86
22 6 0.11
23 2 0.04
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (22 bp):
AAGGGCTTAATCCTTTTGATGA
Found at i:197738 original size:35 final size:35
Alignment explanation
Indices: 197690--197761 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
197680 TAAATTAAAA
197690 AATAAGTCCATTCACCAAGTGACATGACTTATTAT
1 AATAAGTCCATTCACCAAGTGACATGACTTATTAT
* *
197725 AATAAGTCTATTCACCAAGTGACTTGACTTATTAT
1 AATAAGTCCATTCACCAAGTGACATGACTTATTAT
197760 AA
1 AA
197762 ATAGCATCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (35 bp):
AATAAGTCCATTCACCAAGTGACATGACTTATTAT
Found at i:201211 original size:21 final size:21
Alignment explanation
Indices: 201185--201251 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
201175 TAAGTCCTTT
201185 TGAAAGGATTTATCCTTTTGA
1 TGAAAGGATTTATCCTTTTGA
** *
201206 TGAAAGGGCTTAACCTTTTCG-
1 TGAAAGGATTTATCCTTTT-GA
* *
201227 TGAAATGATTTAAT-CTTTTCA
1 TGAAAGGATTT-ATCCTTTTGA
201248 TGAA
1 TGAA
201252 GAGAATTGTT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
21 33 0.94
22 2 0.06
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (21 bp):
TGAAAGGATTTATCCTTTTGA
Found at i:206726 original size:83 final size:83
Alignment explanation
Indices: 206587--206743 Score: 260
Period size: 83 Copynumber: 1.9 Consensus size: 83
206577 ACACCGATGG
* **
206587 TTAAATCATGAACCGGTTGGAATCTTTTGTCAGTAAACTGCAAGACCAAACATGATTTTCCCACG
1 TTAAATCATGAACCGATTGGAATCACTTGTCAGTAAACTGCAAGACCAAACATGATTTTCCCACG
206652 CCTGTAAAAGAAACCCGA
66 CCTGTAAAAGAAACCCGA
* **
206670 TTAAATCATGAACCGATTGGAATCACTTGTCGGTAAACTGCAAGAGTAAACATGATTTTCCCACG
1 TTAAATCATGAACCGATTGGAATCACTTGTCAGTAAACTGCAAGACCAAACATGATTTTCCCACG
206735 CCTGTAAAA
66 CCTGTAAAA
206744 AAAAACCCCA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 68 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (83 bp):
TTAAATCATGAACCGATTGGAATCACTTGTCAGTAAACTGCAAGACCAAACATGATTTTCCCACG
CCTGTAAAAGAAACCCGA
Found at i:209326 original size:26 final size:26
Alignment explanation
Indices: 209297--209349 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
209287 AACTTTAGTT
* *
209297 GAATAGTTTGATTGTTTTGTAATTCA
1 GAATAGTTTGATTATATTGTAATTCA
209323 GAATAGTTTGATTATATTGTAATTCA
1 GAATAGTTTGATTATATTGTAATTCA
209349 G
1 G
209350 TCTTTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.47
Consensus pattern (26 bp):
GAATAGTTTGATTATATTGTAATTCA
Found at i:220843 original size:55 final size:55
Alignment explanation
Indices: 220759--221235 Score: 627
Period size: 55 Copynumber: 8.5 Consensus size: 55
220749 AATATGTTGC
* * *
220759 AATTTCCGAATTGGCACTATGTGTGCAACCTCACGAAATTAATAATGAGTTTATG
1 AATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
220814 AATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
1 AATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* *
220869 AATTTTATGAATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCAAAATTAGTTTATG
1 -A----AT---TTT-CGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
*
220933 AA-TTTCTGTATTGGCATTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
1 AATTTTC-GTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * *
220988 AATTTAT-GTATTGGCATTATGTGTGCAACCTCATGAAATTCATAATGAGTTTATA
1 AATTT-TCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* *
221043 AATTTCCGTATTGACACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
1 AATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * * *
221098 AATTTTCGTATTGTCACTATGTGTGTAACTTCACGAAATTCATAATAAGTTTATG
1 AATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * * * *
221153 AATTTCCGTATTGGTACTATGTGTGCAACCCCA-TATAATTCATAATGAGTTTGTG
1 AATTTTCGTATTGGCACTATGTGTGCAACCTCACGA-AATTCATAATGAGTTTATG
**
221208 AATTACCGTATTGGCACTATGTGTGCAA
1 AATTTTCGTATTGGCACTATGTGTGCAA
221236 AACCATGGAA
Statistics
Matches: 377, Mismatches: 31, Indels: 28
0.86 0.07 0.06
Matches are distributed among these distances:
54 2 0.01
55 317 0.84
56 3 0.01
57 1 0.00
59 1 0.00
60 2 0.01
63 4 0.01
64 47 0.12
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.37
Consensus pattern (55 bp):
AATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
Found at i:226754 original size:20 final size:20
Alignment explanation
Indices: 226729--226778 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
226719 ATTTAAAGAA
*
226729 GTATCGATACCGAG-GTGTAG
1 GTATCGATACCAAGAG-GTAG
226749 GTATCGATACCAAGAGGTAG
1 GTATCGATACCAAGAGGTAG
226769 GTATCGATAC
1 GTATCGATAC
226779 TATAATCAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (20 bp):
GTATCGATACCAAGAGGTAG
Found at i:227711 original size:55 final size:55
Alignment explanation
Indices: 227182--227704 Score: 731
Period size: 55 Copynumber: 9.5 Consensus size: 55
227172 TATATGTTGT
* *
227182 AATTTCCATATTGGCATTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
*
227237 AATTTCTGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* **
227292 AATTTACGTATTGATACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * *
227347 AATTTCTGTATTGGCACTATATGTGTAACCTCACGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* *
227402 AATTTCTGTATTGGCATTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * * *
227457 AATTTCGGTATTGGCACTATGTATACAACCTCACGAAATTTATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * ** *
227512 AATTTCCGTATTGGCATTATGTGTGAAACCTCATAAAACTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * **
227567 AATTTTCGTATTGCCACTATGTGTGCAACCTCGTGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * * * * * *
227622 AATTTCTGTATTGGCACTCTGTGTGTAACCCCATGTAATTCATAATGAGTTTGTG
1 AATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * * *
227677 AATTACCATATCGACACTATGTGTGCAA
1 AATTTCCGTATTGGCACTATGTGTGCAA
227705 AACCATGGAA
Statistics
Matches: 415, Mismatches: 53, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 415 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (55 bp):
AATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
Found at i:229604 original size:20 final size:20
Alignment explanation
Indices: 229579--229623 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
229569 AAATGGTTCG
229579 ATTTC-ACACTCTTAACATCA
1 ATTTCAACACTC-TAACATCA
*
229599 ATTTCAACACTCTAACATTA
1 ATTTCAACACTCTAACATCA
229619 ATTTC
1 ATTTC
229624 CAGCATAGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTTCAACACTCTAACATCA
Found at i:234229 original size:40 final size:41
Alignment explanation
Indices: 234181--234275 Score: 138
Period size: 42 Copynumber: 2.3 Consensus size: 41
234171 ATAATATGAG
* *
234181 AATGTTATATGAG-ATATGAGAAACGGTATATGAAAGTGAT
1 AATGTTATATGAGAATATAAGAAAAGGTATATGAAAGTGAT
*
234221 AATGTTATATGAGATATATAAGAAAAGGTATGTGAAAGTGAT
1 AATGTTATATGAGA-ATATAAGAAAAGGTATATGAAAGTGAT
*
234263 AATGTGATATGAG
1 AATGTTATATGAG
234276 TCTCTATGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 13 0.27
42 36 0.73
ACGTcount: A:0.43, C:0.01, G:0.25, T:0.31
Consensus pattern (41 bp):
AATGTTATATGAGAATATAAGAAAAGGTATATGAAAGTGAT
Found at i:238400 original size:20 final size:20
Alignment explanation
Indices: 238351--238394 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
238341 CCAAATGGCC
*
238351 CAATTTC-ATACTCTAACAT
1 CAATTTCAACACTCTAACAT
238370 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
238390 TAATT
1 CAATT
238395 CTAACATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Done.