Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007933.1 Hibiscus syriacus cultivar Beakdansim tig00110343_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: 282743
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 2 of 2
Found at i:217473 original size:26 final size:27
Alignment explanation
Indices: 217427--217479 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
217417 CAAAAAGAGA
217427 AAAAAGAGAAAAAAAGCAAAGAGAAAAT
1 AAAAAGAGAAAAAAAGCAAAG-GAAAAT
217455 AAAAAGAG-AAAAAA-CAAAGGAAAAT
1 AAAAAGAGAAAAAAAGCAAAGGAAAAT
217480 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 6 0.24
28 8 0.32
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (27 bp):
AAAAAGAGAAAAAAAGCAAAGGAAAAT
Found at i:219194 original size:37 final size:38
Alignment explanation
Indices: 219139--219213 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 38
219129 GAAGATTTTA
* * *
219139 TCTCGCTTGAGATAGTTTCCCTTGAAACA-AAATATTG
1 TCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTG
*
219176 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTG
1 TCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTG
219214 AAAACATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 26 0.79
38 7 0.21
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (38 bp):
TCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTG
Found at i:219367 original size:36 final size:36
Alignment explanation
Indices: 219320--219545 Score: 225
Period size: 36 Copynumber: 6.4 Consensus size: 36
219310 ATTGAAAACA
*
219320 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
219356 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * *
219392 ATTCCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
*** * *
219421 TTTTATTTGAAACAAATTTCATCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** * * *
219457 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* *
219494 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAA
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
219530 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
219546 ATCTTTGAAT
Statistics
Matches: 155, Mismatches: 25, Indels: 20
0.77 0.12 0.10
Matches are distributed among these distances:
28 2 0.01
29 17 0.11
30 2 0.01
31 1 0.01
34 1 0.01
35 1 0.01
36 99 0.64
37 32 0.21
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:219431 original size:101 final size:102
Alignment explanation
Indices: 219139--219507 Score: 485
Period size: 100 Copynumber: 3.6 Consensus size: 102
219129 GAAGATTTTA
* * *
219139 TCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
219204 ATAAACATTGAAAACATTTCCCTTGAAACAAA-TT-G
66 ATAAACATTGAAAACATTTCCCTTGAAACAAATTTCG
*
219239 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
*
219304 ATAAACATTGAAAACATTTCCCTTGAAATAAATTTCG
66 ATAAACATTGAAAACATTTCCCTTGAAACAAATTTCG
* * *
219341 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGATTCCCTTGAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
** * ** *** *
219405 A-AATTATTTGAATATGTTTTATTTGAAACAAATTTCA
66 ATAAACA-TTGAAAACATTTCCCTTGAAACAAATTTCG
* ** * * * *
219442 TCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
219507 A
66 A
219508 AATTTCGTCT
Statistics
Matches: 241, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
100 97 0.40
101 82 0.34
102 62 0.26
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (102 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
ATAAACATTGAAAACATTTCCCTTGAAACAAATTTCG
Found at i:219482 original size:138 final size:138
Alignment explanation
Indices: 219340--219599 Score: 387
Period size: 138 Copynumber: 1.9 Consensus size: 138
219330 AATAAATTTC
*
219340 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGA-TTCCCTTGAAA
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-ATTTCCCTTGAAA
* * * ** *
219404 CAAATTATTTGAATATGTTTTATTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAA
65 CAAAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAA
219469 CTAAGTTTT
130 CTAAGTTTT
*
219478 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTGAAAC
* * * **
219543 AAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCT
219600 CTTAAAACAC
Statistics
Matches: 108, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
137 1 0.01
138 107 0.99
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (138 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTGAAAC
AAAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAAC
TAAGTTTT
Found at i:219608 original size:65 final size:67
Alignment explanation
Indices: 219503--219657 Score: 197
Period size: 65 Copynumber: 2.3 Consensus size: 67
219493 GTTTCTCTTG
* * * **
219503 AAACAAATTTCGTCTCTCTTGAGACAATTTCCCTT-GAA-ACAAAATCTTTGAATTTATTTCCCC
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTAAAACACAAAATCTTCAAATTTATTTCCCC
219566 TA
66 TA
* * *
219568 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTAAAACACAAAATCTTCAAATTTATTTCCCC
219633 TA
66 TA
* *
219635 AAGCAAAATTTTGTTTCCCTTGA
1 AAAC-AAATTTTGTCTCCCTTGA
219658 AACCGTTTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
65 31 0.40
66 2 0.03
67 27 0.35
68 17 0.22
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTAAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:219675 original size:67 final size:68
Alignment explanation
Indices: 219540--219686 Score: 181
Period size: 67 Copynumber: 2.2 Consensus size: 68
219530 TTTCCCTTGA
** * *
219540 AACAAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTAA
1 AACAAAATCTTCAAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAAACAGTTTCTCATAA
219605 AAC
66 AAC
* * * * *
219608 -ACAAAATCTTCAAATTTATTTCCCTTAAAGCAAAATTTTGTTTCCCTTGAAACCGTTT-TCATG
1 AACAAAATCTTCAAATTTATTTCCCCTAAAAC-AAATTTTGTCTCCCTTGAAACAGTTTCTCATA
219671 AAAC
65 AAAC
219675 AACAAATATCTT
1 AACAAA-ATCTT
219687 TGAGATCGTT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
67 34 0.51
68 28 0.42
69 5 0.07
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (68 bp):
AACAAAATCTTCAAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAAACAGTTTCTCATAA
AAC
Found at i:220489 original size:29 final size:29
Alignment explanation
Indices: 220446--220513 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
220436 ATTTATTTTT
* *
220446 GTCCCTCTAAAATTTTATAGGTTTAAGTAC
1 GTCCC-CTAAAATTTTATAAGTTCAAGTAC
* *
220476 GTCCCCTGAAATTTTATAAGTTCAAGTTC
1 GTCCCCTAAAATTTTATAAGTTCAAGTAC
*
220505 GCCCCCTAA
1 GTCCCCTAA
220514 CTTAAAATCC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 27 0.84
30 5 0.16
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (29 bp):
GTCCCCTAAAATTTTATAAGTTCAAGTAC
Found at i:221356 original size:2 final size:2
Alignment explanation
Indices: 221349--221384 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
221339 AATATGTATG
221349 TA TA TA TA TA 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 TA TA TA TA TA
221385 GTACTTATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:223149 original size:24 final size:24
Alignment explanation
Indices: 223119--223419 Score: 292
Period size: 24 Copynumber: 12.8 Consensus size: 24
223109 ACCAGTTCTG
* *
223119 TCTCCACCCCCGGTACCAGTCCAC
1 TCTCCACCTCCGGTACCAGTCCAA
* * *
223143 TCCCCACCTCCGCTACCAGTTCAA
1 TCTCCACCTCCGGTACCAGTCCAA
* * *
223167 TCTCCACCTCCGATAACAGTCCAC
1 TCTCCACCTCCGGTACCAGTCCAA
*
223191 TC-CCTACCTCCGGTACCAGTTCAA
1 TCTCC-ACCTCCGGTACCAGTCCAA
* *
223215 TCTCCACCTCCGTTACCAGTTCAA
1 TCTCCACCTCCGGTACCAGTCCAA
*
223239 TCTCCACCTCCGGTACCAGTCCAT
1 TCTCCACCTCCGGTACCAGTCCAA
223263 TCTCCACCTCC---ACCAGTCCAA
1 TCTCCACCTCCGGTACCAGTCCAA
*
223284 TCTCCACCTCC---ACCAGTCCAC
1 TCTCCACCTCCGGTACCAGTCCAA
*
223305 TCTCCACCTCCGGTACCAGTTCAA
1 TCTCCACCTCCGGTACCAGTCCAA
* *
223329 TCTTCACCTCCGGTACCAGTCCAC
1 TCTCCACCTCCGGTACCAGTCCAA
* * * * **
223353 TCCCCACCTCCTGTTCCACTCCCC
1 TCTCCACCTCCGGTACCAGTCCAA
* * * * *
223377 TCACCTCCTCTGATACCAGTTCAA
1 TCTCCACCTCCGGTACCAGTCCAA
*
223401 TCTCCACCTCCTGTACCAG
1 TCTCCACCTCCGGTACCAG
223420 CCCATTCCCC
Statistics
Matches: 226, Mismatches: 46, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
21 40 0.18
23 2 0.01
24 182 0.81
25 2 0.01
ACGTcount: A:0.19, C:0.48, G:0.09, T:0.24
Consensus pattern (24 bp):
TCTCCACCTCCGGTACCAGTCCAA
Found at i:223325 original size:162 final size:162
Alignment explanation
Indices: 223133--223460 Score: 440
Period size: 162 Copynumber: 2.0 Consensus size: 162
223123 CACCCCCGGT
*
223133 ACCAGTCCACTCCCCACCTCCGCTACCAGTTCAATCTCCACCTCCGATAACAGTCCACTCCCTAC
1 ACCAGTCCACTCCCCACCTCCGCTACCAGTTCAATCTCCACCTCCGATAACAGTCCACTCCCCAC
* * * * *
223198 CTCCGGTACCAGTTCAATCTCCACCTCCGTTACCAGTTCAATCTCCACCTCCGGTACCAGTCCAT
66 CTCCGGTACCACTCCAATCACCACCTCCGATACCAGTTCAATCTCCACCTCCGGTACCAGCCCAT
* * * *
223263 TCTCCACCTCCACCAGTCCAATCTCCACCTCC
131 TCCCCACCACCACCAGTCCAATCACCACCACC
* * * * *
223295 ACCAGTCCACTCTCCACCTCCGGTACCAGTTCAATCTTCACCTCCGGTACCAGTCCACTCCCCAC
1 ACCAGTCCACTCCCCACCTCCGCTACCAGTTCAATCTCCACCTCCGATAACAGTCCACTCCCCAC
* * ** * * *
223360 CTCCTGTTCCACTCCCCTCACCTCCTCTGATACCAGTTCAATCTCCACCTCCTGTACCAGCCCAT
66 CTCCGGTACCACTCCAATCACCACCTCCGATACCAGTTCAATCTCCACCTCCGGTACCAGCCCAT
* *
223425 TCCCCACCACCACCTGTCCATTCACCACCACC
131 TCCCCACCACCACCAGTCCAATCACCACCACC
223457 ACCA
1 ACCA
223461 CCACCACCTG
Statistics
Matches: 142, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
162 142 1.00
ACGTcount: A:0.20, C:0.49, G:0.08, T:0.23
Consensus pattern (162 bp):
ACCAGTCCACTCCCCACCTCCGCTACCAGTTCAATCTCCACCTCCGATAACAGTCCACTCCCCAC
CTCCGGTACCACTCCAATCACCACCTCCGATACCAGTTCAATCTCCACCTCCGGTACCAGCCCAT
TCCCCACCACCACCAGTCCAATCACCACCACC
Found at i:223384 original size:90 final size:89
Alignment explanation
Indices: 223119--223363 Score: 240
Period size: 90 Copynumber: 2.7 Consensus size: 89
223109 ACCAGTTCTG
* * * * * * * * *
223119 TCTCCACCCCCGGTACCAGTCCACTCCCCACCTCCGCTACCAGTTCAATCTCCACCTCCGATAAC
1 TCTCCACCTCCGGTACCAGTTCAATCTCCACCTCCGGTACCAGTCCACTCCCCACCTCC---ACC
* *
223184 AGTCCA-CTCCCTACCTCCGGTACCAGTTCAA
63 ACTCCACCT-CC-ACCTCC---ACCAGTCCAA
* * * *
223215 TCTCCACCTCCGTTACCAGTTCAATCTCCACCTCCGGTACCAGTCCATTCTCCACCTCCACCAGT
1 TCTCCACCTCCGGTACCAGTTCAATCTCCACCTCCGGTACCAGTCCACTCCCCACCTCCACCACT
* *
223280 CCAATCTCCACCTCCACCAGTCCAC
66 CC-ACCTCCACCTCCACCAGTCCAA
*
223305 TCTCCACCTCCGGTACCAGTTCAATCTTCACCTCCGGTACCAGTCCACTCCCCACCTCC
1 TCTCCACCTCCGGTACCAGTTCAATCTCCACCTCCGGTACCAGTCCACTCCCCACCTCC
223364 TGTTCCACTC
Statistics
Matches: 132, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
90 63 0.48
93 13 0.10
94 3 0.02
95 2 0.02
96 51 0.39
ACGTcount: A:0.20, C:0.49, G:0.09, T:0.22
Consensus pattern (89 bp):
TCTCCACCTCCGGTACCAGTTCAATCTCCACCTCCGGTACCAGTCCACTCCCCACCTCCACCACT
CCACCTCCACCTCCACCAGTCCAA
Found at i:231499 original size:25 final size:25
Alignment explanation
Indices: 231469--231518 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
231459 AAAACAAAAG
231469 CTTGAAAGTAAAAATAACAAAGAAA
1 CTTGAAAGTAAAAATAACAAAGAAA
231494 CTTGAAAGTAAAAATAACAAAGAAA
1 CTTGAAAGTAAAAATAACAAAGAAA
231519 GTAAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.64, C:0.08, G:0.12, T:0.16
Consensus pattern (25 bp):
CTTGAAAGTAAAAATAACAAAGAAA
Found at i:235526 original size:19 final size:20
Alignment explanation
Indices: 235499--235542 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
235489 TCGAATAATT
* *
235499 AAATCGAATATATAAT-TTA
1 AAATTGAATATAAAATCTTA
235518 AAATTGAATATAAAATCTTA
1 AAATTGAATATAAAATCTTA
235538 AAATT
1 AAATT
235543 CATTAACACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
AAATTGAATATAAAATCTTA
Found at i:235656 original size:13 final size:13
Alignment explanation
Indices: 235640--235674 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
235630 TAAGATTTTC
235640 TTTTTGAAAATCA
1 TTTTTGAAAATCA
235653 TTTTTG-AAATCA
1 TTTTTGAAAATCA
*
235665 ATTTTGAAAA
1 TTTTTGAAAA
235675 ATTACTCCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:237506 original size:19 final size:20
Alignment explanation
Indices: 237464--237507 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
237454 ATATAGTTTT
*
237464 CAAAAACAACATAACTAAAT
1 CAAAAACAACATAACTAAAA
**
237484 CAAAAACAACA-ATTTAAAA
1 CAAAAACAACATAACTAAAA
237503 CAAAA
1 CAAAA
237508 CTATTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.68, C:0.18, G:0.00, T:0.14
Consensus pattern (20 bp):
CAAAAACAACATAACTAAAA
Found at i:241651 original size:20 final size:21
Alignment explanation
Indices: 241612--241651 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
241602 GAAGCTTTAA
* *
241612 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
241633 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
241652 AAGTAAGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:241816 original size:74 final size:74
Alignment explanation
Indices: 241730--241876 Score: 267
Period size: 74 Copynumber: 2.0 Consensus size: 74
241720 TACTTTCAAG
* * *
241730 TTCAACGTTGGTCTTGGATATGAGGTCTTTTTCATTTTTGAATTTTGAAATATTTTTCTTGTATT
1 TTCAAAGTTGGTCTTGGATATGAGATCTTTTTCATTTTTCAATTTTGAAATATTTTTCTTGTATT
241795 TTGAAAACT
66 TTGAAAACT
241804 TTCAAAGTTGGTCTTGGATATGAGATCTTTTTCATTTTTCAATTTTGAAATATTTTTCTTGTATT
1 TTCAAAGTTGGTCTTGGATATGAGATCTTTTTCATTTTTCAATTTTGAAATATTTTTCTTGTATT
241869 TTGAAAAC
66 TTGAAAAC
241877 AGTTTCTCAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.51
Consensus pattern (74 bp):
TTCAAAGTTGGTCTTGGATATGAGATCTTTTTCATTTTTCAATTTTGAAATATTTTTCTTGTATT
TTGAAAACT
Found at i:246963 original size:7 final size:6
Alignment explanation
Indices: 246943--247012 Score: 54
Period size: 6 Copynumber: 11.7 Consensus size: 6
246933 CGGTTCCTGC
* * * *
246943 AAAATA AAAATA AAAATT AAATTA AACAATA AAAAT- CAAATGA AACA-A
1 AAAATA AAAATA AAAATA AAAATA AA-AATA AAAATA AAAAT-A AAAATA
* *
246991 AAAGTA AAGATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAA
247013 ATATAACGGT
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
5 7 0.15
6 34 0.71
7 7 0.15
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:246975 original size:19 final size:19
Alignment explanation
Indices: 246942--246990 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
246932 TCGGTTCCTG
*
246942 CAAAATAAA-AATAAAAAT
1 CAAATTAAACAATAAAAAT
*
246960 TAAATTAAACAATAAAAAT
1 CAAATTAAACAATAAAAAT
*
246979 CAAATGAAACAA
1 CAAATTAAACAA
246991 AAAGTAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.71, C:0.08, G:0.02, T:0.18
Consensus pattern (19 bp):
CAAATTAAACAATAAAAAT
Found at i:249909 original size:14 final size:14
Alignment explanation
Indices: 249890--249925 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
249880 GTAAAAAGAT
*
249890 AATAAAAGTGATTA
1 AATAAAAGTAATTA
249904 AATAAAAGTAATTA
1 AATAAAAGTAATTA
249918 AAGTAAAA
1 AA-TAAAA
249926 TTAAGAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (14 bp):
AATAAAAGTAATTA
Found at i:251464 original size:18 final size:19
Alignment explanation
Indices: 251441--251479 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
251431 TATCAGTACC
251441 TAGGTA-TCGGTACCC-TAT
1 TAGGTATTC-GTACCCTTAT
251459 TAGGTATTCGTACCCTTAT
1 TAGGTATTCGTACCCTTAT
251478 TA
1 TA
251480 TATTCGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (19 bp):
TAGGTATTCGTACCCTTAT
Found at i:251715 original size:19 final size:20
Alignment explanation
Indices: 251693--251730 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
251683 AATTAAATCA
*
251693 AATATATAAT-TTAAAATTG
1 AATATAAAATCTTAAAATTG
251712 AATATAAAATCTTAAAATT
1 AATATAAAATCTTAAAATT
251731 CATTAATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTG
Found at i:253146 original size:24 final size:24
Alignment explanation
Indices: 253074--253339 Score: 249
Period size: 24 Copynumber: 11.3 Consensus size: 24
253064 ATGGACAGGT
* * * *
253074 GGTGGAGATTGAACTGGTATCAGA
1 GGTGGAGAGTGGACTGGTACCGGA
* * * * * *
253098 GGAGGTGAGGGGAGTGGAACAGGA
1 GGTGGAGAGTGGACTGGTACCGGA
*
253122 GGTGGGGAGTGGACTGGTACCGGA
1 GGTGGAGAGTGGACTGGTACCGGA
* * *
253146 GGTGAAGATTGAACTGGTACCGGA
1 GGTGGAGAGTGGACTGGTACCGGA
253170 GGTGGAGAGTGGACTGGT---GGA
1 GGTGGAGAGTGGACTGGTACCGGA
*
253191 GGTGGAGATTGGACTGGT---GGA
1 GGTGGAGAGTGGACTGGTACCGGA
*
253212 GGTGGAGAATGGACTGGTACCGGA
1 GGTGGAGAGTGGACTGGTACCGGA
* *
253236 GGTGGAGATTGAACTGGTACCGGA
1 GGTGGAGAGTGGACTGGTACCGGA
* *
253260 GGTAGG-GAGTGGACTGTTATCGGA
1 GGT-GGAGAGTGGACTGGTACCGGA
* * *
253284 GGTGGAGATTGAACTGGTAGCGGA
1 GGTGGAGAGTGGACTGGTACCGGA
* *
253308 GGTGGGGAGTGGACTGGTACCGGG
1 GGTGGAGAGTGGACTGGTACCGGA
253332 GGTGGAGA
1 GGTGGAGA
253340 CAGAACTGGT
Statistics
Matches: 196, Mismatches: 41, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
21 40 0.20
23 2 0.01
24 152 0.78
25 2 0.01
ACGTcount: A:0.23, C:0.09, G:0.49, T:0.19
Consensus pattern (24 bp):
GGTGGAGAGTGGACTGGTACCGGA
Found at i:253171 original size:48 final size:48
Alignment explanation
Indices: 253119--253349 Score: 312
Period size: 48 Copynumber: 4.9 Consensus size: 48
253109 GAGTGGAACA
*
253119 GGAGGTGGGGAGTGGACTGGTACCGGAGGTGAAGATTGAACTGGTACC
1 GGAGGTGGGGAGTGGACTGGTACCGGAGGTGGAGATTGAACTGGTACC
* *
253167 GGAGGTGGAGAGTGGACTGGT---GGAGGTGGAGATTGGACTGGT---
1 GGAGGTGGGGAGTGGACTGGTACCGGAGGTGGAGATTGAACTGGTACC
* *
253209 GGAGGTGGAGAATGGACTGGTACCGGAGGTGGAGATTGAACTGGTACC
1 GGAGGTGGGGAGTGGACTGGTACCGGAGGTGGAGATTGAACTGGTACC
* * * *
253257 GGAGGTAGGGAGTGGACTGTTATCGGAGGTGGAGATTGAACTGGTAGC
1 GGAGGTGGGGAGTGGACTGGTACCGGAGGTGGAGATTGAACTGGTACC
* **
253305 GGAGGTGGGGAGTGGACTGGTACCGGGGGTGGAGACAGAACTGGT
1 GGAGGTGGGGAGTGGACTGGTACCGGAGGTGGAGATTGAACTGGT
253350 GGTGGCGGGG
Statistics
Matches: 160, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
42 20 0.12
45 39 0.24
48 101 0.63
ACGTcount: A:0.22, C:0.10, G:0.48, T:0.19
Consensus pattern (48 bp):
GGAGGTGGGGAGTGGACTGGTACCGGAGGTGGAGATTGAACTGGTACC
Found at i:253188 original size:138 final size:139
Alignment explanation
Indices: 253046--253325 Score: 316
Period size: 138 Copynumber: 2.0 Consensus size: 139
253036 GAACAGGTGG
* * * * * *
253046 TGGTGGTGGTGGTGGTGAATGGACAGGT-GGTGGAGATTGAACTGGTATCAGAGGAGGTGAGGGG
1 TGGTGGTGGAGGTGGAGAATGGACAGGTGGGTGGAGAATGAACTGGTACCAGAGGAGGAGAGGGA
* *
253110 AGTGGAACAGGAGGTGGGGAGTGGACTGGTACCGGAGGTGAAGATTGAACTGGTACCGGAGGTGG
66 ACTGGAACAGGAGGTAGGGAGTGGACTGGTACCGGAGGTGAAGATTGAACTGGTACCGGAGGTGG
253175 AGAGTGGAC
131 AGAGTGGAC
* * * * * **
253184 ---TGGTGGAGGTGGAGATTGGACTGGTGGAGGTGGAGAATGGACTGGTACCGGAGGTGGAGATT
1 TGGTGGTGGAGGTGGAGAATGGACAGGT-G-GGTGGAGAATGAACTGGTACCAGAGGAGGAGAGG
* * * * * *
253246 GAACTGGTACCGGAGGTAGGGAGTGGACTGTTATCGGAGGTGGAGATTGAACTGGTAGCGGAGGT
64 GAACTGGAACAGGAGGTAGGGAGTGGACTGGTACCGGAGGTGAAGATTGAACTGGTACCGGAGGT
*
253311 GGGGAGTGGAC
129 GGAGAGTGGAC
253322 TGGT
1 TGGT
253326 ACCGGGGGTG
Statistics
Matches: 114, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
135 21 0.18
138 92 0.81
141 1 0.01
ACGTcount: A:0.22, C:0.08, G:0.49, T:0.21
Consensus pattern (139 bp):
TGGTGGTGGAGGTGGAGAATGGACAGGTGGGTGGAGAATGAACTGGTACCAGAGGAGGAGAGGGA
ACTGGAACAGGAGGTAGGGAGTGGACTGGTACCGGAGGTGAAGATTGAACTGGTACCGGAGGTGG
AGAGTGGAC
Found at i:253233 original size:90 final size:93
Alignment explanation
Indices: 253118--253349 Score: 328
Period size: 90 Copynumber: 2.5 Consensus size: 93
253108 GGAGTGGAAC
*
253118 AGGAGGTGGGGAGTGGACTGGTACCGGAGGTGAAGATTGAACTGGTACCGGAGGT-GGAGAGTGG
1 AGGAGGTGGGGAGTGGACTGGTACCGGAGGTGGAGATTGAACTGGTACCGGAGGTAGG-GAGTGG
* *
253182 ACTG-GT-GGAGGTGGAGATTGGACTGGT
65 ACTGTATCGGAGGTGGAGATTGAACTGGT
* *
253209 -GGAGGTGGAGAATGGACTGGTACCGGAGGTGGAGATTGAACTGGTACCGGAGGTAGGGAGTGGA
1 AGGAGGTGGGGAGTGGACTGGTACCGGAGGTGGAGATTGAACTGGTACCGGAGGTAGGGAGTGGA
253273 CTGTTATCGGAGGTGGAGATTGAACTGGT
66 CTG-TATCGGAGGTGGAGATTGAACTGGT
* **
253302 AGCGGAGGTGGGGAGTGGACTGGTACCGGGGGTGGAGACAGAACTGGT
1 A--GGAGGTGGGGAGTGGACTGGTACCGGAGGTGGAGATTGAACTGGT
253350 GGTGGCGGGG
Statistics
Matches: 124, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
90 61 0.49
91 2 0.02
92 1 0.01
93 20 0.16
96 40 0.32
ACGTcount: A:0.22, C:0.10, G:0.48, T:0.19
Consensus pattern (93 bp):
AGGAGGTGGGGAGTGGACTGGTACCGGAGGTGGAGATTGAACTGGTACCGGAGGTAGGGAGTGGA
CTGTATCGGAGGTGGAGATTGAACTGGT
Found at i:253437 original size:30 final size:30
Alignment explanation
Indices: 253377--253437 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
253367 TGGCACTAGT
* * *
253377 GGTGGAGATTGAATTGGTGGTGAAGTTGGA
1 GGTGGAGATTGAACTGGTGATGAAGATGGA
*
253407 GGTGGAGATTGAACTGGT-ATCGGAGATGGA
1 GGTGGAGATTGAACTGGTGAT-GAAGATGGA
253437 G
1 G
253438 ACGGAACTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.25, C:0.03, G:0.46, T:0.26
Consensus pattern (30 bp):
GGTGGAGATTGAACTGGTGATGAAGATGGA
Found at i:255988 original size:29 final size:29
Alignment explanation
Indices: 255938--256003 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
255928 ATTTTAAGTT
* *
255938 AGGGGACGAACTTGAACTTATAAAATTTC
1 AGGGGACGAACTTAAACCTATAAAATTTC
* *
255967 AGGGGACGTACTTAAACCTATAAAATTTT
1 AGGGGACGAACTTAAACCTATAAAATTTC
255996 AGAGGGAC
1 AG-GGGAC
256004 AAAAATAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 27 0.84
30 5 0.16
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.26
Consensus pattern (29 bp):
AGGGGACGAACTTAAACCTATAAAATTTC
Found at i:257364 original size:22 final size:21
Alignment explanation
Indices: 257338--257381 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
257328 AAGATTATTA
257338 AAATTTTTAAATACCCAATTTT
1 AAATTTTTAAATACCC-ATTTT
* *
257360 AAATTTTTACATACTCATTTT
1 AAATTTTTAAATACCCATTTT
257381 A
1 A
257382 TTAGAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.48
Consensus pattern (21 bp):
AAATTTTTAAATACCCATTTT
Found at i:257840 original size:17 final size:17
Alignment explanation
Indices: 257815--257848 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
257805 TTATTATTAT
*
257815 TTTTTAATATAAAATAA
1 TTTTAAATATAAAATAA
257832 TTTTAAATATAAAATAA
1 TTTTAAATATAAAATAA
257849 AAACATAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTTAAATATAAAATAA
Found at i:267531 original size:25 final size:25
Alignment explanation
Indices: 267495--267550 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
267485 AATGTCAAGT
*
267495 GAAAAG-ATCAAATCAAA-ACAAAGA
1 GAAAAGAAACAAA-CAAATACAAAGA
*
267519 GAAAAGAAACAAAGAAATACAAAGA
1 GAAAAGAAACAAACAAATACAAAGA
*
267544 GCAAAGA
1 GAAAAGA
267551 GAAAAAGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.68, C:0.11, G:0.16, T:0.05
Consensus pattern (25 bp):
GAAAAGAAACAAACAAATACAAAGA
Found at i:267557 original size:25 final size:25
Alignment explanation
Indices: 267512--267559 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
267502 TCAAATCAAA
267512 ACAAAGAGAAAAGAAACAAAGAAAT
1 ACAAAGAGAAAAGAAACAAAGAAAT
*
267537 ACAAAGAGCAAAGAGAA-AAAGAA
1 ACAAAGAGAAAAGA-AACAAAGAA
267560 CAAAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.71, C:0.08, G:0.19, T:0.02
Consensus pattern (25 bp):
ACAAAGAGAAAAGAAACAAAGAAAT
Found at i:267569 original size:14 final size:15
Alignment explanation
Indices: 267511--267572 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
267501 ATCAAATCAA
267511 AACAAAGAG-AAAAG
1 AACAAAGAGAAAAAG
*
267525 AAACAAAGAAATACAAAG
1 -AACAAAGAGA-A-AAAG
*
267543 AGCAAAGAGAAAAAG
1 AACAAAGAGAAAAAG
267558 AACAAA-AGAAAAAG
1 AACAAAGAGAAAAAG
267572 A
1 A
267573 TGACAGAGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
14 9 0.22
15 17 0.43
16 1 0.03
17 9 0.22
18 4 0.10
ACGTcount: A:0.73, C:0.08, G:0.18, T:0.02
Consensus pattern (15 bp):
AACAAAGAGAAAAAG
Found at i:269488 original size:106 final size:106
Alignment explanation
Indices: 269371--269755 Score: 449
Period size: 106 Copynumber: 3.6 Consensus size: 106
269361 TTGAGACATT
*
269371 TTTTTCCTTTGA-CATACAAATTTCGAATTTGATTCAC-TTGAAACAAAAATTAATCTCATTTGA
1 TTTTTCCTTTGAGAATACAAATTTCGAATTTGATTCACATT-AAAC-AAAATTAATCTCATTTGA
269434 GATTGTTATTTCTTTCAAAATAAATTTCGTCTCATTTGAGGCA
64 GATTGTTATTTCTTTCAAAATAAATTTCGTCTCATTTGAGGCA
* * * * *
269477 TTTTTCTTTTGAGAATACAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCTCATTTGAGA
1 TTTTTCCTTTGAGAATACAAATTTCGAATTTGATTCACATTAAACAAAATTAATCTCATTTGAGA
* * ** * * * *** *
269542 TCG--CTTTCTTAAAAAAACAAACTCCGTCTTGCTTGAGACA
66 TTGTTATTTCTT-TCAAAATAAATTTCGTCTCATTTGAGGCA
* *
269582 TTTCTTTCCTTTGA-CATACAAATTTCGAATTTGATTCAC-TTGAAGCAAAAATTAATCTCATTT
1 -TT-TTTCCTTTGAGAATACAAATTTCGAATTTGATTCACATT-AAAC-AAAATTAATCTCATTT
269645 GAGATTGTTATTTCTTTCAAAATAAATTTCGTCTCATTTGAGGCA
62 GAGATTGTTATTTCTTTCAAAATAAATTTCGTCTCATTTGAGGCA
* * * * *
269690 TTTTTCCTTTGAGAATACAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCTCACTTGAGA
1 TTTTTCCTTTGAGAATACAAATTTCGAATTTGATTCACATTAAACAAAATTAATCTCATTTGAGA
269755 T
66 T
269756 CGTTTTCTCA
Statistics
Matches: 226, Mismatches: 42, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
104 6 0.03
105 22 0.10
106 86 0.38
107 82 0.36
108 24 0.11
109 6 0.03
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (106 bp):
TTTTTCCTTTGAGAATACAAATTTCGAATTTGATTCACATTAAACAAAATTAATCTCATTTGAGA
TTGTTATTTCTTTCAAAATAAATTTCGTCTCATTTGAGGCA
Found at i:269592 original size:213 final size:213
Alignment explanation
Indices: 269355--269769 Score: 776
Period size: 213 Copynumber: 1.9 Consensus size: 213
269345 ACAAGTTTCA
*
269355 TCTTGCTTGAGACATTTTTTTCCTTTGACATACAAATTTCGAATTTGATTCACTTGAAACAAAAA
1 TCTTGCTTGAGACATTTCTTTCCTTTGACATACAAATTTCGAATTTGATTCACTTGAAACAAAAA
*
269420 TTAATCTCATTTGAGATTGTTATTTCTTTCAAAATAAATTTCGTCTCATTTGAGGCATTTTTCTT
66 TTAATCTCATTTGAGATTGTTATTTCTTTCAAAATAAATTTCGTCTCATTTGAGGCATTTTTCCT
*
269485 TTGAGAATACAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCTCATTTGAGATCGCTTTC
131 TTGAGAATACAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCTCACTTGAGATCGCTTTC
*
269550 TTAAAAAAACAAACTCCG
196 TCAAAAAAACAAACTCCG
*
269568 TCTTGCTTGAGACATTTCTTTCCTTTGACATACAAATTTCGAATTTGATTCACTTGAAGCAAAAA
1 TCTTGCTTGAGACATTTCTTTCCTTTGACATACAAATTTCGAATTTGATTCACTTGAAACAAAAA
269633 TTAATCTCATTTGAGATTGTTATTTCTTTCAAAATAAATTTCGTCTCATTTGAGGCATTTTTCCT
66 TTAATCTCATTTGAGATTGTTATTTCTTTCAAAATAAATTTCGTCTCATTTGAGGCATTTTTCCT
*
269698 TTGAGAATACAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCTCACTTGAGATCGTTTTC
131 TTGAGAATACAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCTCACTTGAGATCGCTTTC
269763 TCAAAAA
196 TCAAAAA
269770 CAATTTTTGT
Statistics
Matches: 196, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
213 196 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (213 bp):
TCTTGCTTGAGACATTTCTTTCCTTTGACATACAAATTTCGAATTTGATTCACTTGAAACAAAAA
TTAATCTCATTTGAGATTGTTATTTCTTTCAAAATAAATTTCGTCTCATTTGAGGCATTTTTCCT
TTGAGAATACAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCTCACTTGAGATCGCTTTC
TCAAAAAAACAAACTCCG
Found at i:269783 original size:36 final size:36
Alignment explanation
Indices: 269731--269832 Score: 127
Period size: 36 Copynumber: 2.8 Consensus size: 36
269721 GTTTCACATT
**
269731 AAACAAA-GTTGATCTCACTTGAGATCGTTTTCTC-AA
1 AAACAAATGTTG-TCTCACTTGAGA-CAATTTCTCTAA
* * *
269767 AAACAATTTTTGTCTCATTTGAGACAATTTCTCTAA
1 AAACAAATGTTGTCTCACTTGAGACAATTTCTCTAA
269803 AAACAAATGTTGTCTCACTTGAGACAATTT
1 AAACAAATGTTGTCTCACTTGAGACAATTT
269833 TCCAAATTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 7 0.12
36 46 0.82
37 3 0.05
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (36 bp):
AAACAAATGTTGTCTCACTTGAGACAATTTCTCTAA
Found at i:270084 original size:64 final size:66
Alignment explanation
Indices: 269954--270145 Score: 205
Period size: 64 Copynumber: 2.9 Consensus size: 66
269944 ACAGATTTTA
* * * *
269954 TTGAA-AAAAATATTTGAGTATGTTTCTTT-GATAACAAAATTTTGTCTCTTTTGAGAAAATTTC
1 TTGAAGAAAAATCTTTGAGTATGTTTCTTTGGA-AACAAAATTTTGTCTCTTTTAAGACAATTCC
270017 TT
65 TT
* **
270019 TTG-A-AAGAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGACTGTTCCT
1 TTGAAGAAAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGACAATTCCT
270082 T
66 T
* * * * * *
270083 TTGAAGAAAAATCTTTAAGTCTGTTT-TTATGAAAAAAAAAGGTTTGTCACTTTTAAGACAATT
1 TTGAAGAAAAATCTTTGAGTATGTTTCTT-TGGAAACAAAA-TTTTGTCTCTTTTAAGACAATT
270146 TCTCTTAAAA
Statistics
Matches: 106, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
64 54 0.51
65 8 0.08
66 26 0.25
67 18 0.17
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.43
Consensus pattern (66 bp):
TTGAAGAAAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGACAATTCCT
T
Found at i:270185 original size:30 final size:32
Alignment explanation
Indices: 270149--270222 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
270139 GACAATTTCT
270149 CTTAAAACAAA-C-ATCTTTGAGATTGCTTCC
1 CTTAAAACAAACCTATCTTTGAGATTGCTTCC
* * *
270179 CTTAAAACAAAACCTATCTTTGAGTTTGTTTCT
1 CTTAAAAC-AAACCTATCTTTGAGATTGCTTCC
*
270212 CTTGAAACAAA
1 CTTAAAACAAA
270223 AGTCTGTGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 8 0.22
31 3 0.08
32 4 0.11
33 22 0.59
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.35
Consensus pattern (32 bp):
CTTAAAACAAACCTATCTTTGAGATTGCTTCC
Found at i:270238 original size:29 final size:29
Alignment explanation
Indices: 270144--270309 Score: 145
Period size: 29 Copynumber: 5.6 Consensus size: 29
270134 TTTAAGACAA
* * *
270144 TTTCTCTTAAAACAAACATCTTTGAGATTG
1 TTTCTTTTGAAACAAAAATCTTTGAG-TTG
* ** *
270174 CTTCCCTTAAAACAAAACCTATCTTTGAGTTTG
1 TTTCTTTTGAAACAAAA---ATCTTTGAG-TTG
* * *
270207 TTTCTCTTGAAACAAAAGTCTGTGAGTTG
1 TTTCTTTTGAAACAAAAATCTTTGAGTTG
* *
270236 TTTCTTTTGAAATAAAAACCTTTGAGTTG
1 TTTCTTTTGAAACAAAAATCTTTGAGTTG
*
270265 TTTCTTTTG-AACAAAATTCTTTGAGTCTG
1 TTTCTTTTGAAACAAAAATCTTTGAGT-TG
*
270294 TTTCTTTTGAACCAAA
1 TTTCTTTTGAAACAAA
270310 GTTTTGTTTC
Statistics
Matches: 113, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
28 14 0.12
29 47 0.42
30 26 0.23
33 26 0.23
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.42
Consensus pattern (29 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTTG
Found at i:270371 original size:26 final size:27
Alignment explanation
Indices: 270336--270393 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 27
270326 GACAATTTTG
270336 TGAAAAAATCTTTGAG-TCATTTCTTT
1 TGAAAAAATCTTTGAGTTCATTTCTTT
**
270362 TGAAAAAATCTTTGAGTTTGTTTCTTT
1 TGAAAAAATCTTTGAGTTCATTTCTTT
270389 TGAAA
1 TGAAA
270394 CAAAGTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 16 0.55
27 13 0.45
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.47
Consensus pattern (27 bp):
TGAAAAAATCTTTGAGTTCATTTCTTT
Found at i:270399 original size:88 final size:91
Alignment explanation
Indices: 270249--270473 Score: 296
Period size: 88 Copynumber: 2.5 Consensus size: 91
270239 CTTTTGAAAT
* ** * *
270249 AAAAACCTTTGAGTTGTTTCTTTTGAACAAAATTCTTTGAGTCTGTTTCTTTTGAACCAAAGTTT
1 AAAAATCTTTGAGTCATTTCTTTTGAA-AAAA-TCTTTGAGTTTGTTTCTTTTGAAACAAAGTTT
*
270314 TGTTTCTCTTAAGACA-ATTTT-GTGA-
64 TGTCTCTCTTAAGACAGATTTTCGTGAG
270339 AAAAATCTTTGAGTCATTTCTTTTGAAAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAGTTTTG
1 AAAAATCTTTGAGTCATTTCTTTTGAAAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAGTTTTG
* * *
270404 TCTCTCTTGAGACAGTTTTTCTTGAG
66 TCTCTCTTAAGACAGATTTTCGTGAG
* *
270430 AAAAATCTTTGAGTCTATTCCTTTTG-AAAAATCTTTGAGATTGT
1 AAAAATCTTTGAGTC-ATTTCTTTTGAAAAAATCTTTGAGTTTGT
270474 GTCTCTTAAC
Statistics
Matches: 120, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
88 44 0.37
89 8 0.07
90 27 0.22
91 32 0.27
92 9 0.08
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (91 bp):
AAAAATCTTTGAGTCATTTCTTTTGAAAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAGTTTTG
TCTCTCTTAAGACAGATTTTCGTGAG
Found at i:270613 original size:29 final size:29
Alignment explanation
Indices: 270566--270672 Score: 90
Period size: 29 Copynumber: 3.5 Consensus size: 29
270556 CCTTTGAGAT
*
270566 TGTTTCTTTTGAGA-AAAATCCTTGAGTC
1 TGTTTCTTTTGAAACAAAATCCTTGAGTC
*
270594 TGTTTCTTTGGAAACAAAATTTACAATCTTTGAGTC
1 TGTTTCTTTTGAAACAAAA--T-C---C-TTGAGTC
** *
270630 TGTTTCTTTTGAAACATCATCTTTGAGTC
1 TGTTTCTTTTGAAACAAAATCCTTGAGTC
*
270659 GGTTTCTTTTGAAA
1 TGTTTCTTTTGAAA
270673 TCATTATCCC
Statistics
Matches: 64, Mismatches: 7, Indels: 15
0.74 0.08 0.17
Matches are distributed among these distances:
28 12 0.19
29 24 0.38
31 1 0.02
32 1 0.02
33 1 0.02
34 1 0.02
35 1 0.02
36 23 0.36
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (29 bp):
TGTTTCTTTTGAAACAAAATCCTTGAGTC
Found at i:270791 original size:43 final size:42
Alignment explanation
Indices: 270731--270931 Score: 104
Period size: 43 Copynumber: 4.5 Consensus size: 42
270721 TCATCTCCTG
*
270731 ACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCCCTAGATA
1 ACCAGA-CTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATA
* * ** * *
270774 ACCAGACGTCCTCATCACATAGAAATCGTGTTATCGCCCTTCCTAAATA
1 ACCAGAC-TCCTCATCACGTAGGAGCCGTG---TC-ACC--CCTAGATA
* * * * *
270823 TGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCC-CG---
1 --ACCAG-ACTCCTCATCACGTAGGAGCCGTGTCA-CCCCTAGATA
* *
270865 ACCAGATCTCCTCATCGCGTAGGAGCCGTGTCATCCCTAGATA
1 ACCAGA-CTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATA
* *
270908 ACCAGCCGTCCTCATCGCGTAGGA
1 ACCAGAC-TCCTCATCACGTAGGA
270932 ACCGAGTTAT
Statistics
Matches: 117, Mismatches: 24, Indels: 34
0.67 0.14 0.19
Matches are distributed among these distances:
39 4 0.03
40 27 0.23
42 2 0.02
43 44 0.38
46 4 0.03
47 2 0.02
48 4 0.03
49 7 0.06
51 21 0.18
52 2 0.02
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (42 bp):
ACCAGACTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATA
Found at i:270895 original size:40 final size:40
Alignment explanation
Indices: 270826--270901 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
270816 CTAAATATGG
* * *
270826 CCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGA
1 CCAGAACTCCTCATCACGTAGGAGCCGTGTCATCCCCCGA
* *
270866 CCAGATCTCCTCATCGCGTAGGAGCCGTGTCATCCC
1 CCAGAACTCCTCATCACGTAGGAGCCGTGTCATCCC
270902 TAGATAACCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.24
Consensus pattern (40 bp):
CCAGAACTCCTCATCACGTAGGAGCCGTGTCATCCCCCGA
Found at i:270941 original size:134 final size:133
Alignment explanation
Indices: 270688--271041 Score: 521
Period size: 134 Copynumber: 2.6 Consensus size: 133
270678 ATCCCTAGAG
* * *
270688 ATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCTCCTGACCAGATCTCTTCATCACGTAG
1 ATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCCTCATCACGTAG
* * *
270753 GAGCCGTGTCACCCCTAGATAACCAGACGTCCTCATCACATAGAAATCGTGTTATCGCCCTTCCT
66 GAGCCGTGTCA-CCCTAGATAACCAGACGTCCTCATCACATAGAAACCGAGTTATCACCCTTCCT
270818 AAAT
130 AAAT
*
270822 ATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCCTCATCGCGTAG
1 ATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCCTCATCACGTAG
* * * *
270887 GAGCCGTGTCATCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACCCTTCCT
66 GAGCCGTGTCA-CCCTAGATAACCAGACGTCCTCATCACATAGAAACCGAGTTATCACCCTTCCT
270952 AAAT
130 AAAT
* * *
270956 ATGGCCAAGAACTCTTCATCACGTATGAG-CAGTGTCATCCCTCGACCAGATTTCCTCATCACAT
1 ATGGCC-AGAACTCTTCATCACGTATGAGTC-GTGTCATCCCCCGACCAGATCTCCTCATCACGT
*
271020 AGGAACCGTGTCACCCTTAGAT
64 AGGAGCCGTGTCACCC-TAGAT
271042 GACCCGAACT
Statistics
Matches: 200, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
134 132 0.66
135 68 0.34
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (133 bp):
ATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCGACCAGATCTCCTCATCACGTAG
GAGCCGTGTCACCCTAGATAACCAGACGTCCTCATCACATAGAAACCGAGTTATCACCCTTCCTA
AAT
Found at i:271074 original size:43 final size:40
Alignment explanation
Indices: 270963--271078 Score: 108
Period size: 43 Copynumber: 2.8 Consensus size: 40
270953 AATATGGCCA
270963 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
** * * * * * *
271003 AGATTTCCTCATCACATAGGAACCGTGTCA-CCCTTAGATGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCC-T---CGACC
*
271046 CGAACTCTTCATCACGTATGAGCAGTGTCATCC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCC
271079 TCAACAACCA
Statistics
Matches: 55, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
39 3 0.05
40 24 0.44
43 26 0.47
44 2 0.04
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (40 bp):
AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
Found at i:271236 original size:3 final size:3
Alignment explanation
Indices: 271228--271273 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
271218 CGGTTCTTTT
*
271228 TTA TTA TTA TTA TTA TTAA TTA ATA TTA TTA TTAA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TT-A TTA TTA TTA TTA
271274 CATATTTGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:271254 original size:16 final size:16
Alignment explanation
Indices: 271230--271273 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
271220 GTTCTTTTTT
271230 ATTATTATTATTATTA
1 ATTATTATTATTATTA
*
271246 ATTAATATTATTATTA
1 ATTATTATTATTATTA
271262 ATT-TTATTATTA
1 ATTATTATTATTA
271274 CATATTTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATTATTATTATTA
Found at i:271268 original size:25 final size:25
Alignment explanation
Indices: 271229--271279 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
271219 GGTTCTTTTT
271229 TATTATTATTATTATTAATTA-ATAT
1 TATTATTATTATTATT-ATTACATAT
271254 TATTATTAATT-TTATTATTACATAT
1 TATTATT-ATTATTATTATTACATAT
271279 T
1 T
271280 TGCAGGCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 4 0.17
25 17 0.71
26 3 0.12
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (25 bp):
TATTATTATTATTATTATTACATAT
Found at i:276169 original size:42 final size:42
Alignment explanation
Indices: 276118--276312 Score: 178
Period size: 42 Copynumber: 4.6 Consensus size: 42
276108 TGTATCTCAA
* *
276118 TGGCATTTGTTATAAAAACGCCGCAATAAAGGCGAACCTAAG
1 TGGCGTTTGTTATAAAAACGCCGCAATAGAGGCGAACCTAAG
* * * * * * *
276160 TGGTGTTTGTCACT-AAAATGCCGCTATAGAGTCGTACCTTAG
1 TGGCGTTTGTTA-TAAAAACGCCGCAATAGAGGCGAACCTAAG
* * * *
276202 TGGCATTTATTATAAAAACACTGCAATAGAGGCGAACCCTAA-
1 TGGCGTTTGTTATAAAAACGCCGCAATAGAGGCGAA-CCTAAG
* * ** * *
276244 TGGTGTTTGTTATTAAAACGCCGCAATAGATCCGTACCTTAG
1 TGGCGTTTGTTATAAAAACGCCGCAATAGAGGCGAACCTAAG
*
276286 TGGCGTTTGTTATTAAAACGCCGCAAT
1 TGGCGTTTGTTATAAAAACGCCGCAAT
276313 TTATTTCTTC
Statistics
Matches: 118, Mismatches: 31, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
41 5 0.04
42 108 0.92
43 5 0.04
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (42 bp):
TGGCGTTTGTTATAAAAACGCCGCAATAGAGGCGAACCTAAG
Found at i:276187 original size:84 final size:83
Alignment explanation
Indices: 276074--276312 Score: 302
Period size: 84 Copynumber: 2.9 Consensus size: 83
276064 ATGTCAAATT
* * * *
276074 TAATGGTGTTT-TCACTAAAACGTCGCTATAGATCTGTATCTCAATGGCATTTGTTATAAAAACG
1 TAATGGTGTTTGTCACTAAAACGCCGCTATAGATC-GTACCTTAGTGGCATTTGTTATAAAAACG
276138 CCGCAATAAAGGCGAA-CC
65 CCGCAATAAAGGCGAACCC
* *
276156 TAAGTGGTGTTTGTCACTAAAATGCCGCTATAGAGTCGTACCTTAGTGGCATTTATTATAAAAAC
1 TAA-TGGTGTTTGTCACTAAAACGCCGCTATAGA-TCGTACCTTAGTGGCATTTGTTATAAAAAC
* * *
276221 ACTGCAATAGAGGCGAACCC
64 GCCGCAATAAAGGCGAACCC
* * * * *
276241 TAATGGTGTTTGTTATTAAAACGCCGCAATAGATCCGTACCTTAGTGGCGTTTGTTATTAAAACG
1 TAATGGTGTTTGTCACTAAAACGCCGCTATAGAT-CGTACCTTAGTGGCATTTGTTATAAAAACG
276306 CCGCAAT
65 CCGCAAT
276313 TTATTTCTTC
Statistics
Matches: 134, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
82 3 0.02
83 9 0.07
84 115 0.86
85 7 0.05
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (83 bp):
TAATGGTGTTTGTCACTAAAACGCCGCTATAGATCGTACCTTAGTGGCATTTGTTATAAAAACGC
CGCAATAAAGGCGAACCC
Found at i:278796 original size:42 final size:42
Alignment explanation
Indices: 278750--278837 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
278740 CAACTGTGGC
278750 GTTTTACCTT-AAAATGTCACTAAATTA-TCTACCTTTTGCGGA
1 GTTTTA-CTTAAAAATGTCACTAAATTACT-TACCTTTTGCGGA
*
278792 GTTTTACTTAAAAATGTCACTAAATTACTTACCTTTTGCGGC
1 GTTTTACTTAAAAATGTCACTAAATTACTTACCTTTTGCGGA
278834 GTTT
1 GTTT
278838 GTTCCCAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
41 3 0.07
42 39 0.91
43 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (42 bp):
GTTTTACTTAAAAATGTCACTAAATTACTTACCTTTTGCGGA
Found at i:278883 original size:43 final size:42
Alignment explanation
Indices: 278809--278916 Score: 117
Period size: 43 Copynumber: 2.5 Consensus size: 42
278799 TTAAAAATGT
* * * * *
278809 CACTAAATTACTTACCTTTTGCGGCGTTTGTTCCCAAAACGA
1 CACTAAATGACTAACCTTTTGTGGCGGTTGTTCCAAAAACGA
* * *
278851 CACTAAATGACATAACCTTTTGTGTCGGTTGTTCCAAAAATGC
1 CACTAAATGAC-TAACCTTTTGTGGCGGTTGTTCCAAAAACGA
*
278894 CGCTAAATGACCTAACCTTTTGT
1 CACTAAATGA-CTAACCTTTTGT
278917 AGCATTTTTG
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
42 10 0.18
43 44 0.80
44 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (42 bp):
CACTAAATGACTAACCTTTTGTGGCGGTTGTTCCAAAAACGA
Found at i:279968 original size:12 final size:12
Alignment explanation
Indices: 279951--279975 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
279941 TAGTTGAACA
279951 ATCTTCATATGC
1 ATCTTCATATGC
279963 ATCTTCATATGC
1 ATCTTCATATGC
279975 A
1 A
279976 CGTCTGTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (12 bp):
ATCTTCATATGC
Done.