Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006513.1 Hibiscus syriacus cultivar Beakdansim tig00015867_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: 291456
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
File 2 of 2
Found at i:212260 original size:2 final size:2
Alignment explanation
Indices: 212253--212279 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
212243 TGCACCTTTC
212253 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 A
212280 CACACATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:212618 original size:30 final size:30
Alignment explanation
Indices: 212559--212862 Score: 529
Period size: 30 Copynumber: 10.1 Consensus size: 30
212549 GAAGGACCTA
* * *
212559 TCCAGAGGTCACAAAGA-CCCCAGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
* * *
212588 TCCAGAGGTCATAAAGATCTTTGATAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
212618 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
212648 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
212678 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
212708 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
212738 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
212768 TCCAGAGGTCATAAAGATCCTCAGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
212798 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
212828 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
212859 TCCA
1 TCCA
212863 TATGTCTCGA
Statistics
Matches: 262, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
29 16 0.06
30 237 0.90
31 9 0.03
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:214080 original size:21 final size:21
Alignment explanation
Indices: 214050--214094 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
214040 ATTCTGTCGT
* *
214050 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
214071 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
214092 TTG
1 TTG
214095 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:217141 original size:2 final size:2
Alignment explanation
Indices: 217134--217172 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
217124 TGCACCTTTC
217134 AT 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 AT A
217173 CTTCTATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:218644 original size:24 final size:24
Alignment explanation
Indices: 218617--218663 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
218607 TCCCACGTTT
*
218617 TTATATTCCTTAAAAAGAGAGAAA
1 TTATATTCCTTAAAAAAAGAGAAA
218641 TTATATTCCTTAAAAAAAGAGAA
1 TTATATTCCTTAAAAAAAGAGAA
218664 TAAAAATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.30
Consensus pattern (24 bp):
TTATATTCCTTAAAAAAAGAGAAA
Found at i:221765 original size:59 final size:58
Alignment explanation
Indices: 221481--221763 Score: 294
Period size: 58 Copynumber: 4.9 Consensus size: 58
221471 TCTAATACGA
* * *
221481 AAATTCATACACTTAGTATGAATTTC-T--CAGTTT-GCAC-CCATAGTGCCACTACA--G
1 AAATTCATACACTTAGTATG-ATTTCTTAACATTTTAGCACACGA-AGTGCC-CTATATGG
* ** * *
221535 AAATTCATACACTTAGTATGATTTCTTAACGTTTTAGCACACGAAACGCTCTATAAGG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCACACGAAGTGCCCTATATGG
* ** * *
221593 AAATTCATACACTTAGTATAATTTCTTAACATTTTAGCGTATGAAACT-CCCTATATGG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCACACG-AAGTGCCCTATATGG
* * *
221651 AAATTTATACACTTAGTATGATTTCTTATCATTTTAGCACACGAAGTGCCCTATCTGG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCACACGAAGTGCCCTATATGG
* * *
221709 AAATTCATACACTAAGTATGATTTCCTTATCATTTTAGCACAGGAAGTGCCCTAT
1 AAATTCATACACTTAGTATGATTT-CTTAACATTTTAGCACACGAAGTGCCCTAT
221764 CTTTAGCACA
Statistics
Matches: 192, Mismatches: 27, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
53 5 0.03
54 21 0.11
56 8 0.04
57 10 0.05
58 117 0.61
59 31 0.16
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (58 bp):
AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCACACGAAGTGCCCTATATGG
Found at i:221768 original size:23 final size:23
Alignment explanation
Indices: 221742--221788 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
221732 TCCTTATCAT
*
221742 TTTAGCACAGGAAGTGCCCTATC
1 TTTAGCACACGAAGTGCCCTATC
*
221765 TTTAGCACACGAAGTGCCTTATC
1 TTTAGCACACGAAGTGCCCTATC
221788 T
1 T
221789 GGAAATTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (23 bp):
TTTAGCACACGAAGTGCCCTATC
Found at i:221820 original size:82 final size:82
Alignment explanation
Indices: 221683--221847 Score: 276
Period size: 82 Copynumber: 2.0 Consensus size: 82
221673 TTCTTATCAT
221683 TTTAGCACACGAAGTGCCCTATCTGGAAATTCATACACTAAGTATGATTTCCTTATCATTTTAGC
1 TTTAGCACACGAAGTGCCCTATCTGGAAATTCATACACTAAGTATGATTTCCTTATCATTTTAGC
*
221748 ACAGGAAGTGCCCTATC
66 ACACGAAGTGCCCTATC
* * * *
221765 TTTAGCACACGAAGTGCCTTATCTGGAAATTCATACATTTAGTATGATTTCCTTATCATTTTAGT
1 TTTAGCACACGAAGTGCCCTATCTGGAAATTCATACACTAAGTATGATTTCCTTATCATTTTAGC
*
221830 ACACGAAGTGCCTTATC
66 ACACGAAGTGCCCTATC
221847 T
1 T
221848 GGAAACTCAT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.35
Consensus pattern (82 bp):
TTTAGCACACGAAGTGCCCTATCTGGAAATTCATACACTAAGTATGATTTCCTTATCATTTTAGC
ACACGAAGTGCCCTATC
Found at i:221901 original size:141 final size:140
Alignment explanation
Indices: 221648--221904 Score: 415
Period size: 141 Copynumber: 1.8 Consensus size: 140
221638 ACTCCCTATA
* *
221648 TGGAAATTTATACACTTAGTATGATTTCTTATCATTTTAGCACACGAAGTGCCCTATCTGGAAAT
1 TGGAAATTCATACACTTAGTATGATTTCTTATCATTTTAGCACACGAAGTGCCCTATCTGGAAAC
* * *
221713 TCATACACTAAGTATGATTTCCTTATCATTTTAGCACAGGAAGTGCCCTATCTTTAGCACACGAA
66 TCATACACTAAGTATGATTTCCTTATCATTATAGCACACGAAATGCCCTATCTTTAGCACACGAA
221778 GTGCCTTATC
131 GTGCCTTATC
* * *
221788 TGGAAATTCATACATTTAGTATGATTTCCTTATCATTTTAGTACACGAAGTGCCTTATCTGGAAA
1 TGGAAATTCATACACTTAGTATGATTT-CTTATCATTTTAGCACACGAAGTGCCCTATCTGGAAA
* *
221853 CTCATACACTTAGTATGATTTCCTTATCATTATAGCACACTAAATGCCCTAT
65 CTCATACACTAAGTATGATTTCCTTATCATTATAGCACACGAAATGCCCTAT
221905 ATGGAAATTC
Statistics
Matches: 106, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
140 25 0.24
141 81 0.76
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (140 bp):
TGGAAATTCATACACTTAGTATGATTTCTTATCATTTTAGCACACGAAGTGCCCTATCTGGAAAC
TCATACACTAAGTATGATTTCCTTATCATTATAGCACACGAAATGCCCTATCTTTAGCACACGAA
GTGCCTTATC
Found at i:221913 original size:200 final size:198
Alignment explanation
Indices: 221591--221965 Score: 536
Period size: 200 Copynumber: 1.9 Consensus size: 198
221581 CGCTCTATAA
** * *
221591 GGAAATTCATACACTTAGTATAATTTCTTAACATTTTAGCGTATGAAACTCCCTATATGGAAATT
1 GGAAATTCATACACTTAGTATAATTTCTTAACATTTTAGCACACGAAACTCCCTATATGGAAACT
* * * *
221656 TATACACTTAGTATGATTTCTTATCATTTTAGCACACGAAGTGCCCTATCTGGAAATTCATACAC
66 CATACACTTAGTATGATTTCTTATCATTATAGCACACGAAATGCCCTATATGGAAATTCATACAC
* *
221721 TAAGTATGATTTCCTTATCATTTTAGCACAGGAAGTGCCCTATCTTTAGCACACGAAGTGCCTTA
131 TAAGTATGATTTCCTTATCATTTTAGCAAACGAAGTGCCCTATCTTTAGCACACGAAGTGCCTTA
221786 TCT
196 TCT
* * * * * * *
221789 GGAAATTCATACATTTAGTATGATTTCCTTATCATTTTAGTACACG-AAGTGCCTTATCTGGAAA
1 GGAAATTCATACACTTAGTATAATTT-CTTAACATTTTAGCACACGAAACT-CCCTATATGGAAA
*
221853 CTCATACACTTAGTATGATTTCCTTATCATTATAGCACACTAAATGCCCTATATGGAAATTCATA
64 CTCATACACTTAGTATGATTT-CTTATCATTATAGCACACGAAATGCCCTATATGGAAATTCATA
* *
221918 CACTTAGTATGATTTCCTTATCATTTTAGCAAACGTAGTGCCCTATCT
128 CACTAAGTATGATTTCCTTATCATTTTAGCAAACGAAGTGCCCTATCT
221966 GGAAATTCAT
Statistics
Matches: 154, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
198 27 0.18
199 44 0.29
200 83 0.54
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (198 bp):
GGAAATTCATACACTTAGTATAATTTCTTAACATTTTAGCACACGAAACTCCCTATATGGAAACT
CATACACTTAGTATGATTTCTTATCATTATAGCACACGAAATGCCCTATATGGAAATTCATACAC
TAAGTATGATTTCCTTATCATTTTAGCAAACGAAGTGCCCTATCTTTAGCACACGAAGTGCCTTA
TCT
Found at i:222273 original size:59 final size:59
Alignment explanation
Indices: 221765--222254 Score: 793
Period size: 59 Copynumber: 8.3 Consensus size: 59
221755 GTGCCCTATC
* * *
221765 TTTAGCACACGAAGTGCCTTATCTGGAAATTCATACATTTAGTATGATTTCCTTATCAT
1 TTTAGCACACTAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
* * * *
221824 TTTAGTACACGAAGTGCCTTATCTGGAAACTCATACACTTAGTATGATTTCCTTATCAT
1 TTTAGCACACTAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
* * *
221883 TATAGCACACTAAATGCCCTATATGGAAATTCATACACTTAGTATGATTTCCTTATCAT
1 TTTAGCACACTAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
*
221942 TTTAGCAAACGT-AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
1 TTTAGCACAC-TAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
*
222001 TTTAGCACACGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
1 TTTAGCACACTAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
* *
222060 TTTAGCACACTATGTGCCTTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
1 TTTAGCACACTAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
*
222119 TTTAGCACACTAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCTTTATCAT
1 TTTAGCACACTAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
* * *
222178 TTTAGCACACTAAGTGCCCTATCTAGAAATTCATACACTTAGTATAATTTCCTTATTAT
1 TTTAGCACACTAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
*
222237 TTTAGCACACTTAGTGCC
1 TTTAGCACACTAAGTGCC
222255 ATTTGGTAAT
Statistics
Matches: 402, Mismatches: 27, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
59 401 1.00
60 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (59 bp):
TTTAGCACACTAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
Found at i:227743 original size:29 final size:29
Alignment explanation
Indices: 227701--227866 Score: 171
Period size: 28 Copynumber: 5.8 Consensus size: 29
227691 ACCCGACCCA
*
227701 GTGATATTTTGGGAATTATTTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAT
227730 GTGACATTTTGGGAATTA-TTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAT
*
227758 ATGACATTTTGGGAATT-TTTT-AAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAT
* * *
227785 AGTGACATTCTGGTAATTATTTT-TAAAAT
1 -GTGACATTTTGGGAATTATTTTGAAAAAT
* **
227814 GATGACATTTTGGAAATTA-TTTGTAAAACG
1 G-TGACATTTTGGGAATTATTTTG-AAAAAT
* *
227844 GTGATATTTTTGGTAATTATTTT
1 GTGACA-TTTTGGGAATTATTTT
227867 TAATAAAGGT
Statistics
Matches: 116, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
27 6 0.05
28 47 0.41
29 45 0.39
30 15 0.13
31 3 0.03
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.45
Consensus pattern (29 bp):
GTGACATTTTGGGAATTATTTTGAAAAAT
Found at i:227762 original size:28 final size:28
Alignment explanation
Indices: 227706--227841 Score: 166
Period size: 29 Copynumber: 4.8 Consensus size: 28
227696 ACCCAGTGAT
*
227706 ATTTTGGGAATTATTTTGAAAAATGTGAC
1 ATTTTGGGAATTA-TTTGAAAAATATGAC
227735 ATTTTGGGAATTATTTGAAAAATATGAC
1 ATTTTGGGAATTATTTGAAAAATATGAC
*
227763 ATTTTGGGAATT-TTTTAAAAATAGTGAC
1 ATTTTGGGAATTATTTGAAAAATA-TGAC
* * **
227791 ATTCTGGTAATTATTTTTAAAATGATGAC
1 ATTTTGGGAATTATTTGAAAAAT-ATGAC
* *
227820 ATTTTGGAAATTATTTGTAAAA
1 ATTTTGGGAATTATTTGAAAAA
227842 CGGTGATATT
Statistics
Matches: 96, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
27 10 0.10
28 40 0.42
29 45 0.47
30 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.43
Consensus pattern (28 bp):
ATTTTGGGAATTATTTGAAAAATATGAC
Found at i:227891 original size:30 final size:30
Alignment explanation
Indices: 227798--227891 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 30
227788 GACATTCTGG
* * * * *
227798 TAATTATTTTTAAAATGATGACATTTTGGA
1 TAATTATTTGTAAAAAGGTGATATTTTTGA
* *
227828 -AATTATTTGTAAAACGGTGATATTTTTGG
1 TAATTATTTGTAAAAAGGTGATATTTTTGA
* *
227857 TAATTATTTTTAATAAAGGTTATATTTTT-A
1 TAATTATTTGTAA-AAAGGTGATATTTTTGA
227887 TAATT
1 TAATT
227892 TTCGAATGTG
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 23 0.44
30 16 0.31
31 13 0.25
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (30 bp):
TAATTATTTGTAAAAAGGTGATATTTTTGA
Found at i:235223 original size:19 final size:19
Alignment explanation
Indices: 235199--235235 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
235189 GGGTGATGTT
235199 TTGACCGGTCTGAACCGAG
1 TTGACCGGTCTGAACCGAG
*
235218 TTGACCGGTCTGACCCGA
1 TTGACCGGTCTGAACCGA
235236 TCTGACCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.30, G:0.30, T:0.22
Consensus pattern (19 bp):
TTGACCGGTCTGAACCGAG
Found at i:235241 original size:19 final size:18
Alignment explanation
Indices: 235200--235270 Score: 58
Period size: 19 Copynumber: 3.9 Consensus size: 18
235190 GGTGATGTTT
*
235200 TGACCGGTCTGAACCGAGT-
1 TGACCGGT-TGACCCGA-TC
235219 TGACCGGTCTGACCCGATC
1 TGACCGGT-TGACCCGATC
*
235238 TGACCTGTTGA-CCGA-C
1 TGACCGGTTGACCCGATC
*
235254 TCGACCTGTTGACCCGA
1 T-GACCGGTTGACCCGA
235271 CCCGACCCAG
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.04
17 14 0.30
18 8 0.17
19 23 0.49
ACGTcount: A:0.18, C:0.32, G:0.27, T:0.23
Consensus pattern (18 bp):
TGACCGGTTGACCCGATC
Found at i:235276 original size:18 final size:18
Alignment explanation
Indices: 235228--235277 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
235218 TTGACCGGTC
* *
235228 TGACCCGATCTGACCTGT
1 TGACCCGACCCGACCTGT
*
235246 TGA-CCGACTCGACCTGT
1 TGACCCGACCCGACCTGT
235263 TGACCCGACCCGACC
1 TGACCCGACCCGACC
235278 CAGTGACATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.18, C:0.40, G:0.22, T:0.20
Consensus pattern (18 bp):
TGACCCGACCCGACCTGT
Found at i:235323 original size:28 final size:28
Alignment explanation
Indices: 235279--235445 Score: 167
Period size: 29 Copynumber: 5.8 Consensus size: 28
235269 GACCCGACCC
235279 AGTGACATTTTGGGAATTATTTTGAAAA
1 AGTGACATTTTGGGAATTATTTTGAAAA
*
235307 AGTAACATTTTGGGAATTATTTTGAAAA
1 AGTGACATTTTGGGAATTATTTTGAAAA
* *
235335 AGGTGATATTTTGGGAATT-TTTATAAAAA
1 A-GTGACATTTTGGGAATTATTT-TGAAAA
* * * *
235364 CAATGACATTCTGGTAATTATTTTTAAAA
1 -AGTGACATTTTGGGAATTATTTTGAAAA
*
235393 CGATGACATTTTGGGAATTA-TTTGTAAAA
1 AG-TGACATTTTGGGAATTATTTTG-AAAA
* * *
235422 TGATGATATTTTGGTAATTATTTT
1 AG-TGACATTTTGGGAATTATTTT
235446 TAATAAAAGT
Statistics
Matches: 115, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
28 34 0.30
29 74 0.64
30 7 0.06
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.43
Consensus pattern (28 bp):
AGTGACATTTTGGGAATTATTTTGAAAA
Found at i:235385 original size:58 final size:56
Alignment explanation
Indices: 235280--235457 Score: 187
Period size: 58 Copynumber: 3.1 Consensus size: 56
235270 ACCCGACCCA
* * * *
235280 GTGACATTTTGGGAATTATTTTGAAAAAGTAACATTTTGGGAATTATTTTGAAAAAG
1 GTGACATTTTGGGAATTATTTT-AAAAAATGACATTTTGGTAATTATTTTTAAAAAG
* * *
235337 GTGATATTTTGGGAATT-TTTATAAAAACAATGACATTCTGGTAATTATTTTTAAAACG
1 GTGACATTTTGGGAATTATTT-T-AAAA-AATGACATTTTGGTAATTATTTTTAAAAAG
* * * *
235395 ATGACATTTTGGGAATTATTTGTAAAATGATGATATTTTGGTAATTATTTTTAATAAAA
1 GTGACATTTTGGGAATTATTT-TAAAA-AATGACATTTTGGTAATTATTTTTAA-AAAG
235454 GTGA
1 GTGA
235458 TTTTTGTAAT
Statistics
Matches: 99, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
56 3 0.03
57 21 0.21
58 66 0.67
59 9 0.09
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.42
Consensus pattern (56 bp):
GTGACATTTTGGGAATTATTTTAAAAAATGACATTTTGGTAATTATTTTTAAAAAG
Found at i:235462 original size:29 final size:28
Alignment explanation
Indices: 235286--235463 Score: 112
Period size: 29 Copynumber: 6.2 Consensus size: 28
235276 CCCAGTGACA
* * *
235286 TTTTGGGAATTA-TTTTGAAAAAGTAACA
1 TTTTGGGAATTATTTTTAAAAAAGTGA-T
* *
235314 TTTTGGGAATTATTTTGAAAAAGGTGAT
1 TTTTGGGAATTATTTTTAAAAAAGTGAT
* * *
235342 ATTTTGGGAATT-TTTATAAAAACAATGACA
1 -TTTTGGGAATTATTTTTAAAAA-AGTGA-T
* * * *
235372 TTCTGGTAATTATTTTT-AAAACGATGACA
1 TTTTGGGAATTATTTTTAAAAAAG-TGA-T
* *
235401 TTTTGGGAATTATTTGT-AAAATGATGAT
1 TTTTGGGAATTATTTTTAAAAAAG-TGAT
*
235429 ATTTTGGTAATTATTTTTAATAAAAGTGAT
1 -TTTTGGGAATTATTTTTAA-AAAAGTGAT
235459 TTTTG
1 TTTTG
235464 TAATTTTTGA
Statistics
Matches: 118, Mismatches: 23, Indels: 17
0.75 0.15 0.11
Matches are distributed among these distances:
28 20 0.17
29 85 0.72
30 9 0.08
31 4 0.03
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.44
Consensus pattern (28 bp):
TTTTGGGAATTATTTTTAAAAAAGTGAT
Found at i:237619 original size:23 final size:23
Alignment explanation
Indices: 237586--237643 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
237576 CAGCCGAAAC
* *
237586 TGCCACATAGAATTTGCATCGAA
1 TGCCACATAGAATATGCACCGAA
*
237609 TGCCACGTAGAATATGCACCGAA
1 TGCCACATAGAATATGCACCGAA
*
237632 GTTCCACATAGA
1 -TGCCACATAGA
237644 TTTGTCCCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (23 bp):
TGCCACATAGAATATGCACCGAA
Found at i:237693 original size:24 final size:24
Alignment explanation
Indices: 237635--237714 Score: 74
Period size: 23 Copynumber: 3.4 Consensus size: 24
237625 CACCGAAGTT
237635 CCACATAG-ATTTGTCCCAAATGA
1 CCACATAGAATTTGTCCCAAATGA
* * *
237658 CCGCGTAAAATTTGTCCCAAATGA
1 CCACATAGAATTTGTCCCAAATGA
* * * *
237682 TCATATAGAA-TTGTCCCGAAGGA
1 CCACATAGAATTTGTCCCAAATGA
*
237705 CCACGTAGAA
1 CCACATAGAA
237715 CCCTCGACTC
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
23 23 0.53
24 20 0.47
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (24 bp):
CCACATAGAATTTGTCCCAAATGA
Found at i:237881 original size:57 final size:57
Alignment explanation
Indices: 237814--237973 Score: 171
Period size: 57 Copynumber: 2.8 Consensus size: 57
237804 TCAAACTGTC
* * * *
237814 ATTTGTTCACATAAAACATATATTCATAGTACTTCACATAGCATTACTCAATTTATA
1 ATTTATTCACATAAAACATATATTCATAGTATTTCACATAGCATTACTAAACTTATA
* * *
237871 ATTTATTCACATAAAACA-ATTACTT-ATTGCATTTCACATAGCATTACTAAACTTATC
1 ATTTATTCACATAAAACATA-TA-TTCATAGTATTTCACATAGCATTACTAAACTTATA
* * * * * *
237928 ATTTATTCACATAGATCATATACTCATCGTGTTTCATATAGCATTA
1 ATTTATTCACATAAAACATATATTCATAGTATTTCACATAGCATTA
237974 TTATTATCAT
Statistics
Matches: 85, Mismatches: 14, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
56 2 0.02
57 80 0.94
58 3 0.04
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (57 bp):
ATTTATTCACATAAAACATATATTCATAGTATTTCACATAGCATTACTAAACTTATA
Found at i:239395 original size:14 final size:14
Alignment explanation
Indices: 239376--239405 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
239366 GATACCAGTG
239376 AGGAATTGATCGTT
1 AGGAATTGATCGTT
239390 AGGAATTGATCGTT
1 AGGAATTGATCGTT
239404 AG
1 AG
239406 CCGATGTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (14 bp):
AGGAATTGATCGTT
Found at i:247898 original size:6 final size:6
Alignment explanation
Indices: 247887--247916 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
247877 GAGCTAGCCT
247887 TGGCTC TGGCTC TGGCTC TGGCTC TGGCTC
1 TGGCTC TGGCTC TGGCTC TGGCTC TGGCTC
247917 CAGCAACGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (6 bp):
TGGCTC
Found at i:252822 original size:3 final size:3
Alignment explanation
Indices: 252808--252868 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
252798 ATATTTAAAA
* * * **
252808 AAT AAT ATAT AAT AAT TAT TAT AAT AAT ACT AAT AAT AAT AAT TTT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
252854 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
252869 TTTAAATGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (3 bp):
AAT
Found at i:252869 original size:18 final size:18
Alignment explanation
Indices: 252838--252873 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
252828 ATAATAATAC
252838 TAATAATAATAATTTTAA
1 TAATAATAATAATTTTAA
252856 TAATAATAATAATTTTAA
1 TAATAATAATAATTTTAA
252874 ATGAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATAATAATAATTTTAA
Found at i:257372 original size:20 final size:20
Alignment explanation
Indices: 257343--257385 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
257333 GAATGCACTG
257343 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
257363 ATGCATCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
257383 ATG
1 ATG
257386 AATTGAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.35, G:0.16, T:0.19
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:257438 original size:64 final size:65
Alignment explanation
Indices: 257343--257551 Score: 216
Period size: 65 Copynumber: 3.2 Consensus size: 65
257333 GAATGCACTG
* * *
257343 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CAATCCATGAATTGAACATCGAATGCATTT
1 ATGCATCGATGCA-CAAGCCATGCATCGATGCACTCAATCTATGAATTGAACATCGAATGCATTT
257407 T
65 T
* * *
257408 ATGCATCGATGCACATA-CCATGCATTGATGCACTCAGGGTTTTATGAA---AACATCGAATGCA
1 ATGCATCGATGCACA-AGCCATGCATCGATGCACTCA---ATCTATGAATTGAACATCGAATGCA
*
257469 TTTG
62 TTTT
* ** *
257473 ATGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTAT--TTTGAAACATCGAATGCATTT
1 ATGCATCGATGCACAAGCCATGCATCGATGCACTCAATCTATGAATTG-AACATCGAATGCATTT
257536 T
65 T
257537 ATGCATCGATGCACA
1 ATGCATCGATGCACA
257552 CTTAGTGCAC
Statistics
Matches: 121, Mismatches: 13, Indels: 21
0.78 0.08 0.14
Matches are distributed among these distances:
62 3 0.02
64 49 0.40
65 63 0.52
68 6 0.05
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (65 bp):
ATGCATCGATGCACAAGCCATGCATCGATGCACTCAATCTATGAATTGAACATCGAATGCATTTT
Found at i:257464 original size:65 final size:64
Alignment explanation
Indices: 257391--257551 Score: 245
Period size: 65 Copynumber: 2.5 Consensus size: 64
257381 CCATGAATTG
* * *
257391 AACATCGAATGCATTTTATGCATCGATGCACATA-CCATGCATTGATGCACTCAGGGT-TTTATG
1 AACATCGAATGCATTTTATGCATCGATGCACA-AGACATGCATCGATGCACTCAGGCTATTT-TG
257454 AA
64 -A
*
257456 AACATCGAATGCATTTGATGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTTTGA
1 AACATCGAATGCATTTTATGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTTTGA
257520 AACATCGAATGCATTTTATGCATCGATGCACA
1 AACATCGAATGCATTTTATGCATCGATGCACA
257552 CTTAGTGCAC
Statistics
Matches: 89, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
64 33 0.37
65 53 0.60
66 3 0.03
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTTTGA
Found at i:262580 original size:20 final size:20
Alignment explanation
Indices: 262552--262599 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
262542 TCTATAAAAT
* * *
262552 TAAATCCTTCGGGTGATTTA
1 TAAAACCTTCGGGTCATCTA
*
262572 TAAAACCTTCGGGTCATCTG
1 TAAAACCTTCGGGTCATCTA
262592 TAAAACCT
1 TAAAACCT
262600 CAGGGTAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (20 bp):
TAAAACCTTCGGGTCATCTA
Found at i:262684 original size:119 final size:119
Alignment explanation
Indices: 262329--262705 Score: 601
Period size: 119 Copynumber: 3.2 Consensus size: 119
262319 TTTTCCACAT
** * *
262329 ATTTATAAAACCTTCATGTCCTCTGTAAAACCTCAGGGTATGATGTTTTCGCATGCAAATGAGAA
1 ATTTATAAAACCTTCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAATGAGAA
**
262394 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCAAGTG
66 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
* *
262448 ATTTATAAGACCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAATGAGAA
1 ATTTATAAAACCTTCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAATGAGAA
* *
262513 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTATAAAATTAAATCCTTCGGGTG
66 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
* *
262567 ATTTATAAAACCTTCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTTGCATGAAAATGAGAA
1 ATTTATAAAACCTTCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAATGAGAA
* *
262632 AGCAATTTTCAAAGTTTCTTATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
66 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
* *
262686 ATTAATTAAATCCTTCGGGT
1 ATTTA-TAAAACCTTCGGGT
262706 GATTAATTAA
Statistics
Matches: 237, Mismatches: 20, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
119 224 0.95
120 13 0.05
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (119 bp):
ATTTATAAAACCTTCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAATGAGAA
AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
Found at i:262694 original size:21 final size:21
Alignment explanation
Indices: 262668--262726 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
262658 TGTTCTAGAA
*
262668 AATTAAATCCTCCGGGTGATT
1 AATTAAATCCTTCGGGTGATT
262689 AATTAAATCCTTCGGGTGATT
1 AATTAAATCCTTCGGGTGATT
262710 AATTAAATCCTTCGGGT
1 AATTAAATCCTTCGGGT
262727 CATCCATAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (21 bp):
AATTAAATCCTTCGGGTGATT
Found at i:262955 original size:19 final size:18
Alignment explanation
Indices: 262927--262962 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
262917 ACTATTAATA
262927 ATAATATATTATTATTAT
1 ATAATATATTATTATTAT
262945 ATAATTATATTATTATTA
1 ATAA-TATATTATTATTA
262963 CAAATAGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATAATATATTATTATTAT
Found at i:263072 original size:17 final size:17
Alignment explanation
Indices: 263050--263086 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
263040 TACAAGTACA
* *
263050 ACCCGGTCTAGGCCCAG
1 ACCCGGTCCAAGCCCAG
263067 ACCCGGTCCAAGCCCAG
1 ACCCGGTCCAAGCCCAG
263084 ACC
1 ACC
263087 ACCCAAACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.46, G:0.24, T:0.08
Consensus pattern (17 bp):
ACCCGGTCCAAGCCCAG
Found at i:264871 original size:3 final size:3
Alignment explanation
Indices: 264860--264917 Score: 70
Period size: 3 Copynumber: 20.7 Consensus size: 3
264850 CTATTAATAA
* *
264860 TAT TA- TAT TAT TAT TAT TAT TA- TAC TAT TAT TAT TAT TA- TAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
264905 TA- TAT TAT TAT TA
1 TAT TAT TAT TAT TA
264918 AAAATAATAC
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
2 8 0.17
3 40 0.83
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:264877 original size:14 final size:14
Alignment explanation
Indices: 264860--264917 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
264850 CTATTAATAA
264860 TATTATATTATTAT
1 TATTATATTATTAT
*
264874 TATTAT-TATACTAT
1 TATTATAT-TATTAT
264888 TATTATTATTA-TAT
1 TATTA-TATTATTAT
*
264902 AATTATATTATTAT
1 TATTATATTATTAT
264916 TA
1 TA
264918 AAAATAATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
13 6 0.16
14 27 0.73
15 3 0.08
16 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTATATTATTAT
Found at i:264880 original size:17 final size:17
Alignment explanation
Indices: 264860--264915 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 17
264850 CTATTAATAA
264860 TATTATATTATTATTAT
1 TATTATATTATTATTAT
*
264877 TATTATACTATTATTAT
1 TATTATATTATTATTAT
*
264894 TATTATATAATTA-TAT
1 TATTATATTATTATTAT
264910 TATTAT
1 TATTAT
264916 TAAAAATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
16 9 0.25
17 27 0.75
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTATATTATTATTAT
Found at i:266187 original size:29 final size:30
Alignment explanation
Indices: 266127--266196 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
266117 TTTTGTAATA
266127 TTTATAA-TTAACACTATTAATTTTGATAT
1 TTTATAATTTAACACTATTAATTTTGATAT
266156 TTTATAATTTAACCACTA-TAATTTT-A-ACT
1 TTTATAATTTAA-CACTATTAATTTTGATA-T
*
266185 TTTATATTTTAA
1 TTTATAATTTAA
266197 ATAATTATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 1 0.03
29 20 0.54
30 11 0.30
31 5 0.14
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (30 bp):
TTTATAATTTAACACTATTAATTTTGATAT
Found at i:283089 original size:42 final size:42
Alignment explanation
Indices: 283042--283150 Score: 182
Period size: 42 Copynumber: 2.6 Consensus size: 42
283032 TCGAATTTCT
*
283042 GTGTTTGTTTCACGTAATTCATTTTTCGAAAAATGTTTTCCC
1 GTGTTTGTTTCACGTAATTCATTTTTCGAAAAATGTTTTCCA
* *
283084 GTGTTTGTTTCACGTAATTCGTTTTTCGAAAAATGTTTTTCA
1 GTGTTTGTTTCACGTAATTCATTTTTCGAAAAATGTTTTCCA
*
283126 GTGTTTGTTTCACGTAATTGATTTT
1 GTGTTTGTTTCACGTAATTCATTTT
283151 CCTGAACGTA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (42 bp):
GTGTTTGTTTCACGTAATTCATTTTTCGAAAAATGTTTTCCA
Found at i:283388 original size:21 final size:20
Alignment explanation
Indices: 283341--283387 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
283331 TATTATTTAT
*
283341 TAATTTATTAATATTTATAA
1 TAATATATTAATATTTATAA
*
283361 TAATATATT-ATATTTTTAA
1 TAATATATTAATATTTATAA
*
283380 TATTATAT
1 TAATATAT
283388 AAAATAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TAATATATTAATATTTATAA
Found at i:283402 original size:31 final size:30
Alignment explanation
Indices: 283338--283418 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 30
283328 AAATATTATT
283338 TATTA-ATTTATTAATATT-TAT-AATAATA
1 TATTATATTT-TTAATATTATATAAATAATA
283366 TATTATATTTTTAATATTATATAAAATAATCA
1 TATTATATTTTTAATATTATAT-AAATAAT-A
* *
283398 -ATTATA-TTATAATAATATATA
1 TATTATATTTTTAATATTATATA
283419 TATTTTTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
28 13 0.28
29 8 0.17
30 12 0.26
31 12 0.26
32 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (30 bp):
TATTATATTTTTAATATTATATAAATAATA
Found at i:283428 original size:23 final size:23
Alignment explanation
Indices: 283355--283441 Score: 86
Period size: 23 Copynumber: 3.7 Consensus size: 23
283345 TTATTAATAT
283355 TTATAATAATATATTATATTTTTA
1 TTATAATAATATA-TATATTTTTA
* * * *
283379 ATATTATATAAAATA-ATCAATTATA
1 TTA-TA-ATAATATATAT-ATTTTTA
283404 TTATAATAATATATATATTTTTA
1 TTATAATAATATATATATTTTTA
*
283427 TTTTAATAATATATA
1 TTATAATAATATATA
283442 ATAAAAAATT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
23 26 0.52
24 8 0.16
25 9 0.18
26 7 0.14
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATAATAATATATATATTTTTA
Found at i:283464 original size:28 final size:28
Alignment explanation
Indices: 283418--283496 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 28
283408 AATAATATAT
*
283418 ATATTTTTAT-TTTAATAATATATAATAAAA
1 ATATTTATATATTTAAT-A-AT-TAATAAAA
*
283448 A-ATTTTATATATTTAATAATTAATAATA
1 ATA-TTTATATATTTAATAATTAATAAAA
*
283476 TTATTTATATATTTAAATAAT
1 ATATTTATATATTT-AATAAT
283497 ATTTTAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
28 18 0.43
29 10 0.24
30 8 0.19
31 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATATTTATATATTTAATAATTAATAAAA
Found at i:283476 original size:19 final size:20
Alignment explanation
Indices: 283454--283506 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
283444 AAAAAATTTT
283454 ATATATTTAATAATT-AATA
1 ATATATTTAATAATTAAATA
*
283473 ATATTATTTATATATTTAAATA
1 ATA-TATTTA-ATAATTAAATA
283495 ATAT-TTTAATAA
1 ATATATTTAATAA
283507 AGATATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 6 0.21
20 10 0.34
21 6 0.21
22 7 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATTTAATAATTAAATA
Found at i:283496 original size:22 final size:20
Alignment explanation
Indices: 283457--283499 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
283447 AAATTTTATA
283457 TATTTAATAATTAATAATAT
1 TATTTAATAATTAATAATAT
*
283477 TATTTATATATTTAAATAATAT
1 TATTTA-ATAATT-AATAATAT
283499 T
1 T
283500 TTAATAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTTAATAATTAATAATAT
Found at i:283527 original size:23 final size:23
Alignment explanation
Indices: 283501--283545 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
283491 AATAATATTT
283501 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
283524 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
283546 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:283634 original size:28 final size:27
Alignment explanation
Indices: 283603--283661 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
283593 TTTATTTCAC
* *
283603 TAAAA-TATACAAATTAATATTTTATTAA
1 TAAAATTATA-AAAATAATA-TTTAATAA
*
283631 TAAAATTATAAAAATACTATTTAATAA
1 TAAAATTATAAAAATAATATTTAATAA
283658 TAAA
1 TAAA
283662 TAAATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 11 0.41
28 12 0.44
29 4 0.15
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (27 bp):
TAAAATTATAAAAATAATATTTAATAA
Found at i:283865 original size:14 final size:14
Alignment explanation
Indices: 283832--283864 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
283822 AAATGTAATT
283832 CATTTTACGGAAAA
1 CATTTTACGGAAAA
*
283846 CATTTTCCGGAAAA
1 CATTTTACGGAAAA
283860 C-TTTT
1 CATTTT
283865 TTCAGAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (14 bp):
CATTTTACGGAAAA
Found at i:283910 original size:15 final size:15
Alignment explanation
Indices: 283874--283968 Score: 104
Period size: 15 Copynumber: 6.4 Consensus size: 15
283864 TTTCAGAAAT
**
283874 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
283889 G-AATTCAAGTTCCA
1 GTAATTCAAATTCCA
**
283903 GTAATTCATTTTTCCA
1 GTAATTCA-AATTCCA
*
283919 GTAA-TCAAATTTCA
1 GTAATTCAAATTCCA
*
283933 GTAATTCAAATTTCA
1 GTAATTCAAATTCCA
283948 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
283963 GTAATT
1 GTAATT
283969 TATTTTTCCG
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
14 20 0.29
15 40 0.58
16 9 0.13
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:283918 original size:30 final size:31
Alignment explanation
Indices: 283874--283977 Score: 135
Period size: 30 Copynumber: 3.5 Consensus size: 31
283864 TTTCAGAAAT
*
283874 GTAATTCA-TTTTCCAG-AATTCAAGTTCCA
1 GTAATTCATTTTTCCAGTAATTCAAATTCCA
*
283903 GTAATTCATTTTTCCAGTAA-TCAAATTTCA
1 GTAATTCATTTTTCCAGTAATTCAAATTCCA
**
283933 GTAATTCAAATTT-CAGTAATTCAAATTCCA
1 GTAATTCATTTTTCCAGTAATTCAAATTCCA
*
283963 GTAATTTATTTTTCC
1 GTAATTCATTTTTCC
283978 GAAAATCAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
29 14 0.22
30 46 0.73
31 3 0.05
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (31 bp):
GTAATTCATTTTTCCAGTAATTCAAATTCCA
Found at i:283985 original size:60 final size:59
Alignment explanation
Indices: 283874--283986 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 59
283864 TTTCAGAAAT
* * *
283874 GTAATTCATTTTCCAGAATTCAAGTTCCAGTAATTCATTTTTCCAGTAATCAAATTTCA
1 GTAATTCAATTTCCAGAATTCAAATTCCAGTAATTCATTTTTCCAGAAATCAAATTTCA
*
283933 GTAATTCAAATTT-CAGTAATTCAAATTCCAGTAATTTATTTTTCC-GAAAATCAA
1 GTAATTC-AATTTCCAG-AATTCAAATTCCAGTAATTCATTTTTCCAG-AAATCAA
283987 TTACAGCCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
59 11 0.23
60 36 0.77
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (59 bp):
GTAATTCAATTTCCAGAATTCAAATTCCAGTAATTCATTTTTCCAGAAATCAAATTTCA
Found at i:285383 original size:16 final size:17
Alignment explanation
Indices: 285364--285397 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
285354 AAAATAAGAA
285364 AGAAAG-AAAAGAAAAG
1 AGAAAGCAAAAGAAAAG
*
285380 AGAAAGCAAACGAAAAG
1 AGAAAGCAAAAGAAAAG
285397 A
1 A
285398 CAATCTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.71, C:0.06, G:0.24, T:0.00
Consensus pattern (17 bp):
AGAAAGCAAAAGAAAAG
Found at i:287044 original size:24 final size:23
Alignment explanation
Indices: 286982--287045 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
286972 AACATATAAA
* *
286982 TGAACGATAAACAAAAATGTTCG
1 TGAACGATAAACGAACATGTTCG
* *
287005 TGAACGCTAAATGAACATGTTCG
1 TGAACGATAAACGAACATGTTCG
*
287028 TGAACATATAAACGAACA
1 TGAAC-GATAAACGAACA
287046 CATTTGCCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 24 0.73
24 9 0.27
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (23 bp):
TGAACGATAAACGAACATGTTCG
Done.