Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008426.1 Hibiscus syriacus cultivar Beakdansim tig00111210_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: 4445546
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 18
Found at i:419223 original size:26 final size:26
Alignment explanation
Indices: 419184--419233 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
419174 ATTTGTGTTG
* * * *
419184 CGAAATTAATATTCGTGTTTCGAATT
1 CGAAAATAAAATTCGCGTTGCGAATT
419210 CGAAAATAAAATTCGCGTTGCGAA
1 CGAAAATAAAATTCGCGTTGCGAA
419234 AATAAACGCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (26 bp):
CGAAAATAAAATTCGCGTTGCGAATT
Found at i:419224 original size:19 final size:20
Alignment explanation
Indices: 419202--419239 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
419192 ATATTCGTGT
419202 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
419221 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
419240 CGCGTTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:420237 original size:14 final size:15
Alignment explanation
Indices: 420217--420254 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
420207 TAATATAATT
420217 TTTTATTTATGAATA
1 TTTTATTTATGAATA
*
420232 -TTTATTT-TGATTA
1 TTTTATTTATGAATA
420245 TTTTATTTAT
1 TTTTATTTAT
420255 AATTTTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
13 5 0.25
14 14 0.70
15 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (15 bp):
TTTTATTTATGAATA
Found at i:420268 original size:20 final size:21
Alignment explanation
Indices: 420235--420274 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
420225 ATGAATATTT
420235 ATTTTGATTATTTTATTTATA
1 ATTTTGATTATTTTATTTATA
420256 ATTTTGA-TATTTTATTTAT
1 ATTTTGATTATTTTATTTAT
420275 TTTTGTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
ATTTTGATTATTTTATTTATA
Found at i:421950 original size:54 final size:53
Alignment explanation
Indices: 421892--422043 Score: 196
Period size: 54 Copynumber: 2.8 Consensus size: 53
421882 TTCCATATTT
* *
421892 AGTTAATTGAACTTGTAAAAATATATATAGTTAATGAAAAATTATGTAATGTTG
1 AGTTAATT-AACTTGCAAAAATATATTTAGTTAATGAAAAATTATGTAATGTTG
* * *
421946 AGTTAAGCTAACTTGCAAAAATATATTTAGTTGATGAAAAAGTATGTAATGTTG
1 AGTTAA-TTAACTTGCAAAAATATATTTAGTTAATGAAAAATTATGTAATGTTG
* *
422000 AGTTAATCAAACTTGCAAAAATATGTTTAGTTAATCGGAAAAAT
1 AGTTAAT-TAACTTGCAAAAATATATTTAGTTAAT--GAAAAAT
422044 AAATTACAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
54 77 0.92
55 1 0.01
56 6 0.07
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (53 bp):
AGTTAATTAACTTGCAAAAATATATTTAGTTAATGAAAAATTATGTAATGTTG
Found at i:425442 original size:13 final size:13
Alignment explanation
Indices: 425424--425449 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
425414 GAAGAGGGAG
425424 GAAATGAAGAAGA
1 GAAATGAAGAAGA
425437 GAAATGAAGAAGA
1 GAAATGAAGAAGA
425450 TGGAGAGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.08
Consensus pattern (13 bp):
GAAATGAAGAAGA
Found at i:430460 original size:21 final size:21
Alignment explanation
Indices: 430434--430493 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
430424 ATAGTGCAGG
*
430434 GGCAGTATCGATACTCCCTTT
1 GGCAGTATTGATACTCCCTTT
430455 GGCAGTATTGATACTCCCTTT
1 GGCAGTATTGATACTCCCTTT
430476 GGCAGTATTGATACTCCC
1 GGCAGTATTGATACTCCC
430494 AGTCAAAATC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (21 bp):
GGCAGTATTGATACTCCCTTT
Found at i:431573 original size:19 final size:20
Alignment explanation
Indices: 431530--431573 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
431520 GAGATACATT
*
431530 TTCATCACCATCATCCATCAAC
1 TTCAACACCATCATCCAT--AC
431552 TTCAACACCATCATCCAT-C
1 TTCAACACCATCATCCATAC
431571 TTC
1 TTC
431574 CATTGAACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
22 17 0.81
ACGTcount: A:0.30, C:0.41, G:0.00, T:0.30
Consensus pattern (20 bp):
TTCAACACCATCATCCATAC
Found at i:448477 original size:21 final size:19
Alignment explanation
Indices: 448453--448499 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
448443 AGGAAGAATG
448453 AATAAAATAGAAAATGAGAGA
1 AATAAAAT-G-AAATGAGAGA
448474 AATAAAATGAAATGAGAGA
1 AATAAAATGAAATGAGAGA
*
448493 TATAAAA
1 AATAAAA
448500 GCTATCATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.64
20 1 0.04
21 8 0.32
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (19 bp):
AATAAAATGAAATGAGAGA
Found at i:453742 original size:23 final size:23
Alignment explanation
Indices: 453677--453742 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
453667 AAACAATCAA
* * *
453677 AAAATGTGTCA-AAAGACACAAG
1 AAAACGTGTCATAAAGACATATG
*
453699 AAAACGTGTCATAAAGGCATATG
1 AAAACGTGTCATAAAGACATATG
* * *
453722 AAAATGTGTTATATAGACATA
1 AAAACGTGTCATAAAGACATA
453743 CTAAAAATAA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 10 0.29
23 25 0.71
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.23
Consensus pattern (23 bp):
AAAACGTGTCATAAAGACATATG
Found at i:453919 original size:14 final size:15
Alignment explanation
Indices: 453900--453934 Score: 54
Period size: 14 Copynumber: 2.3 Consensus size: 15
453890 TGATTCAATC
453900 TTAATATATTT-TTA
1 TTAATATATTTATTA
453914 TTAATATATTTATTA
1 TTAATATATTTATTA
453929 TCTAAT
1 T-TAAT
453935 CTAATATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
15 4 0.21
16 4 0.21
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
TTAATATATTTATTA
Found at i:454920 original size:12 final size:12
Alignment explanation
Indices: 454903--454927 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
454893 CATTCGCTCC
454903 CAAGCGTAAATG
1 CAAGCGTAAATG
454915 CAAGCGTAAATG
1 CAAGCGTAAATG
454927 C
1 C
454928 GGGAGATCAG
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:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CAAGCGTAAATG
Found at i:456523 original size:12 final size:14
Alignment explanation
Indices: 456501--456553 Score: 79
Period size: 14 Copynumber: 3.6 Consensus size: 14
456491 TCCGTTCAAA
456501 CTTTCTCTCTCGTT
1 CTTTCTCTCTCGTT
456515 CTTTCTCTCTCGTT
1 CTTTCTCTCTCGTT
*
456529 CTTTCTCTCCCCCGTT
1 CTTTCTCT--CTCGTT
456545 CTTTCTCTC
1 CTTTCTCTC
456554 CCCCACATCG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
14 23 0.64
16 13 0.36
ACGTcount: A:0.00, C:0.42, G:0.06, T:0.53
Consensus pattern (14 bp):
CTTTCTCTCTCGTT
Found at i:456525 original size:16 final size:16
Alignment explanation
Indices: 456504--456553 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
456494 GTTCAAACTT
456504 TCTCTCTCGTTC-TT-
1 TCTCTCTCGTTCTTTC
456518 TCTCTCTCGTTCTTTC
1 TCTCTCTCGTTCTTTC
* *
456534 TCTCCCCCGTTCTTTC
1 TCTCTCTCGTTCTTTC
456550 TCTC
1 TCTC
456554 CCCCACATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 12 0.38
15 2 0.06
16 18 0.56
ACGTcount: A:0.00, C:0.42, G:0.06, T:0.52
Consensus pattern (16 bp):
TCTCTCTCGTTCTTTC
Found at i:456554 original size:16 final size:16
Alignment explanation
Indices: 456511--456557 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
456501 CTTTCTCTCT
*
456511 CGTTCTTTCTCT--CT
1 CGTTCTTTCTCTCCCC
456525 CGTTCTTTCTCTCCCC
1 CGTTCTTTCTCTCCCC
456541 CGTTCTTTCTCTCCCC
1 CGTTCTTTCTCTCCCC
456557 C
1 C
456558 ACATCGAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 12 0.40
16 18 0.60
ACGTcount: A:0.00, C:0.47, G:0.06, T:0.47
Consensus pattern (16 bp):
CGTTCTTTCTCTCCCC
Found at i:457046 original size:12 final size:12
Alignment explanation
Indices: 457029--457058 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
457019 TAAAATAATG
457029 ATAAAACAAAAA
1 ATAAAACAAAAA
*
457041 ATAAAACAAATA
1 ATAAAACAAAAA
457053 ATAAAA
1 ATAAAA
457059 ATGGTGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (12 bp):
ATAAAACAAAAA
Found at i:457527 original size:117 final size:117
Alignment explanation
Indices: 457186--457922 Score: 957
Period size: 117 Copynumber: 6.4 Consensus size: 117
457176 TCTGATCAGC
* * * ** * * *
457186 TGAGTTTTTCTCATTATGAACTCTTCATTGGGGATGTTAATCCACTTCATTCTATGATGGAAT-C
1 TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCATTCTGTGATGGAATCC
* *
457250 -ACCAAGGTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTCCTTCGTCGGA
66 AACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGA
* *** *
457301 TGAGTTCTTCTCATTATGAACTCTCCAATGGAAATGTTGAT-CGGTTTATTCTGTGATGGAAT-C
1 TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCATTCTGTGATGGAATCC
* * * *
457364 AAGCTAAGGTTGAACAAGTTTTTCTCATTATGAACTTTTTCTCCCTCGTTGGA
66 AA-CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGA
* **
457417 TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCTTTCTGTGATGGAATTG
1 TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCATTCTGTGATGGAATCC
** ** *
457482 AACCAATATTGAGTAAGTTATTCTCATTATGAACTTCTTCTCCCTCGTCGGA
66 AACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGA
* * * * *
457534 TGAGTTCTTATCATTATGAACTCTCAACTGTAAATGTTAATCCACCTCCTTCTGTGATGGAATCC
1 TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCATTCTGTGATGGAATCC
* * *
457599 AACCAAGGTTGAACAAGTTGTTCTCATTATGAACTTATTCTCCCTCGTCGAA
66 AACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGA
* * * *
457651 TGAGTTATTCTCATTATGAACTTTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGGAATCA
1 TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCATTCTGTGATGGAATCC
* * * *
457716 AACCAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTTTCCCTCATTGGA
66 AACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGA
* * *
457768 TAAG---TTCTCATTATGAACTCTCTACTGGAAATGTTGATCCACCTCATTCTGTGATGGAATCG
1 TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCATTCTGTGATGGAATCC
* * *
457830 AACCAAGGTTGAACAGGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGA
66 AACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGA
* *
457882 TAAGTTCTTCTCATTATGAACTCTCAACTGGAAATGTTGAT
1 TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAT
457923 TGTCTTATCT
Statistics
Matches: 547, Mismatches: 68, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
114 125 0.23
115 36 0.07
116 84 0.15
117 300 0.55
118 2 0.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.37
Consensus pattern (117 bp):
TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCATTCTGTGATGGAATCC
AACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGA
Found at i:457835 original size:348 final size:346
Alignment explanation
Indices: 457196--457919 Score: 1013
Period size: 348 Copynumber: 2.1 Consensus size: 346
457186 TGAGTTTTTC
* ** *
457196 TCATTATGAACTCTTC-ATTGGGGATGTTAATCCACTTCATTCTATGATGGAATCACCAAGGTTG
1 TCATTATGAACTC-TCAACTGGAAATGTTAATCCACCTCATTCTATGATGGAATCACCAAGGTTG
* * * *
457260 AAAAAGTTCTTCTCATTATGAACTTCTTCTCCTTCGTCGGATGAGTTCTTCTCATTATGAACTCT
65 AAAAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTCGAATGAGTTATTCTCATTATGAACTCT
*** * * * *
457325 CCAATGGAAATGTTGATCGGTTTATTCTGTGATGGAATCAAGCTAAGGTTGAACAAGTTTTTCTC
130 CCAATGGAAATGTTGATCACCTCATTCTGTGATGGAATCAAACCAAGGTTGAACAAGTTCTTCTC
* *
457390 ATTATGAACTTTTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTT
195 ATTATGAACTTTTTCTCCCTCATTGGATAAG-T-TTCTCATTATGAACTCTCCACTGGAAATGTT
* * * **
457455 GATCCACCTCTTTCTGTGATGGAATTGAACCAATATTGAGTAAGTTATTCTCATTATGAACTTCT
258 GATCCACCTCATTCTGTGATGGAATCGAACCAAGATTGAACAAGTTATTCTCATTATGAACTTCT
* *
457520 TCTCCCTCGTCGGATGAGTTCTTA
323 TCTCCCTCATCGGATAAGTTCTTA
* * *
457544 TCATTATGAACTCTCAACTGTAAATGTTAATCCACCTCCTTCTGTGATGGAATCCAACCAAGGTT
1 TCATTATGAACTCTCAACTGGAAATGTTAATCCACCTCATTCTATGATGGAAT-C-ACCAAGGTT
* * *
457609 GAACAAGTTGTTCTCATTATGAACTTATTCTCCCTCGTCGAATGAGTTATTCTCATTATGAACTT
64 GAAAAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTCGAATGAGTTATTCTCATTATGAACTC
* *
457674 TCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGGAATCAAACCAAGGTTGAACAAGTTCTTC
129 TCCAATGGAAATGTTGAT-CACCTCATTCTGTGATGGAATCAAACCAAGGTTGAACAAGTTCTTC
* *
457739 TCATTATGAA-TTTCTTTTCCCTCATTGGATAAG-TTCTCATTATGAACTCTCTACTGGAAATGT
193 TCATTATGAACTTT-TTCTCCCTCATTGGATAAGTTTCTCATTATGAACTCTCCACTGGAAATGT
* * *
457802 TGATCCACCTCATTCTGTGATGGAATCGAACCAAGGTTGAACAGGTTCTTCTCATTATGAACTTC
257 TGATCCACCTCATTCTGTGATGGAATCGAACCAAGATTGAACAAGTTATTCTCATTATGAACTTC
* *
457867 TTCTCCCTCATTGGATAAGTTCTTC
322 TTCTCCCTCATCGGATAAGTTCTTA
457892 TCATTATGAACTCTCAACTGGAAATGTT
1 TCATTATGAACTCTCAACTGGAAATGTT
457920 GATTGTCTTA
Statistics
Matches: 331, Mismatches: 40, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
347 2 0.01
348 177 0.53
349 1 0.00
350 87 0.26
351 64 0.19
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (346 bp):
TCATTATGAACTCTCAACTGGAAATGTTAATCCACCTCATTCTATGATGGAATCACCAAGGTTGA
AAAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTCGAATGAGTTATTCTCATTATGAACTCTC
CAATGGAAATGTTGATCACCTCATTCTGTGATGGAATCAAACCAAGGTTGAACAAGTTCTTCTCA
TTATGAACTTTTTCTCCCTCATTGGATAAGTTTCTCATTATGAACTCTCCACTGGAAATGTTGAT
CCACCTCATTCTGTGATGGAATCGAACCAAGATTGAACAAGTTATTCTCATTATGAACTTCTTCT
CCCTCATCGGATAAGTTCTTA
Found at i:457874 original size:231 final size:229
Alignment explanation
Indices: 457186--457922 Score: 949
Period size: 231 Copynumber: 3.2 Consensus size: 229
457176 TCTGATCAGC
* * * ** * * *
457186 TGAGTTTTTCTCATTATGAACTCTTCATTGGGGATGTTAATCCACTTCATTCTATGATGGAATC-
1 TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCATTCTGTGATGGAATCA
*
457250 ACCAAGGTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTCCTTCGTCGGATGAGTTCTTCTCAT
66 ACCAAGGTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAG---TTCTCAT
*** * *
457315 TATGAACTCTCCAA-TGGAAATGTTGAT-CGGTTTATTCTGTGATGGAATCAAGCTAAGGTTGAA
128 TATGAACTCT-CAACTGGAAATGTTGATCCACCTCATTCTGTGATGGAATCAA-CCAAGGTTGAA
* *
457378 CAAGTTTTTCTCATTATGAACTTTTTCTCCCTCGTTGGA
191 CAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGA
* *
457417 TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCTTTCTGTGATGGAATTG
1 TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCATTCTGTGATGGAA-TC
** ** *
457482 AACCAATATTGAGTAAGTTATTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTATCA
65 AACCAAGGTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTC---TCA
* * *
457547 TTATGAACTCTCAACTGTAAATGTTAATCCACCTCCTTCTGTGATGGAATCCAACCAAGGTTGAA
127 TTATGAACTCTCAACTGGAAATGTTGATCCACCTCATTCTGTGATGGAAT-CAACCAAGGTTGAA
* * *
457612 CAAGTTGTTCTCATTATGAACTTATTCTCCCTCGTCGAA
191 CAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGA
* * *
457651 TGAGTTATTCTCATTATGAACTTTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGGAATCA
1 TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCATTCTGTGATGGAATC-
* * * * * *
457716 AACCAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTTTCCCTCATTGGATAAGTTCTCATTA
65 AACCAAGGTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTCATTA
* *
457781 TGAACTCTCTACTGGAAATGTTGATCCACCTCATTCTGTGATGGAATCGAACCAAGGTTGAACAG
130 TGAACTCTCAACTGGAAATGTTGATCCACCTCATTCTGTGATGGAATC-AACCAAGGTTGAACAA
* *
457846 GTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGA
194 GTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGA
* *
457882 TAAGTTCTTCTCATTATGAACTCTCAACTGGAAATGTTGAT
1 TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAT
457923 TGTCTTATCT
Statistics
Matches: 440, Mismatches: 56, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
230 4 0.01
231 185 0.42
232 4 0.01
233 75 0.17
234 169 0.38
235 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.37
Consensus pattern (229 bp):
TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCATTCTGTGATGGAATCA
ACCAAGGTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTCATTAT
GAACTCTCAACTGGAAATGTTGATCCACCTCATTCTGTGATGGAATCAACCAAGGTTGAACAAGT
TCTTCTCATTATGAACTTATTCTCCCTCGTTGGA
Found at i:458272 original size:36 final size:36
Alignment explanation
Indices: 458225--458567 Score: 188
Period size: 36 Copynumber: 9.3 Consensus size: 36
458215 GGGAAACCTG
* *
458225 TCTCAAGTGAGACAAAATTGGTTTTAAGAAAAACCA
1 TCTCAAGTGAGACAAAATTTGTTTTAAGAAAAACTA
* *** * * *
458261 TCTCAAGTGAGATACTTTTTGTTTCAAGGAAAACTG
1 TCTCAAGTGAGACAAAATTTGTTTTAAGAAAAACTA
* * *
458297 TCTCAAGCGAGAC-AAAGTTGTTTTTAAGAAAAACCA
1 TCTCAAGTGAGACAAAATTTG-TTTTAAGAAAAACTA
* * ** * *
458333 TCTCGAGTGAGATAAAATTTCTTGTTTTAAGGGAAATTG
1 TCTCAAGTGAGACAAAA--T-TTGTTTTAAGAAAAACTA
* * * ** *
458372 TCTCTAGTGAGGA-GAAACTAATTTTAAGAAAAACCA
1 TCTCAAGTGA-GACAAAATTTGTTTTAAGAAAAACTA
* * * ** *
458408 TCTCAAGTAAGATAAAATTTCTTGTTTCAAGGGAAACTG
1 TCTCAAGTGAGACAAAA--T-TTGTTTTAAGAAAAACTA
* * * * * *
458447 TCTCTAGTGGGACGAAACTTGTTTTGAGAAAAACAA
1 TCTCAAGTGAGACAAAATTTGTTTTAAGAAAAACTA
* * * *
458483 TCTCAAGTGAGATAAATTTTGTTTCAAGGGAAAACTA
1 TCTCAAGTGAGACAAAATTTGTTTTAA-GAAAAACTA
* * *
458520 TATCTAGTGAGACAAAAGTTGTTTTAAGAAAAA-TA
1 TCTCAAGTGAGACAAAATTTGTTTTAAGAAAAACTA
458555 CTCTCAAGTGAGA
1 -TCTCAAGTGAGA
458568 TAACTTTCTG
Statistics
Matches: 215, Mismatches: 80, Indels: 24
0.67 0.25 0.08
Matches are distributed among these distances:
35 7 0.03
36 127 0.59
37 31 0.14
39 45 0.21
40 5 0.02
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (36 bp):
TCTCAAGTGAGACAAAATTTGTTTTAAGAAAAACTA
Found at i:458309 original size:72 final size:73
Alignment explanation
Indices: 458168--458576 Score: 407
Period size: 75 Copynumber: 5.5 Consensus size: 73
458158 ATAAGAAACA
* * * * * * *
458168 TGTTTTAAGAGAAGCTC-TCTCGAGTGAGATAAAATTTCTTATTTTAAGGGAAACCTGTCTCAAG
1 TGTTTTAAGAAAAAC-CATCTCAAGTGAGAT-AAATTTCTTGTTTCAA-GGAAAACTGTCTCTAG
458232 TGAGACAAAAT
63 TGAGACAAAAT
* * *
458243 TGGTTTTAAGAAAAACCATCTCAAGTGAGAT-ACTTT-TTGTTTCAAGGAAAACTGTCTCAAGCG
1 T-GTTTTAAGAAAAACCATCTCAAGTGAGATAAATTTCTTGTTTCAAGGAAAACTGTCTCTAGTG
*
458306 AGACAAAGT
65 AGACAAAAT
* * * *
458315 TGTTTTTAAGAAAAACCATCTCGAGTGAGATAAAATTTCTTGTTTTAAGGGAAATTGTCTCTAGT
1 TG-TTTTAAGAAAAACCATCTCAAGTGAGAT-AAATTTCTTGTTTCAAGGAAAACTGTCTCTAGT
* *
458380 GAGGAGAAACT
64 GA-GACAAAAT
** * *
458391 AATTTTAAGAAAAACCATCTCAAGTAAGATAAAATTTCTTGTTTCAAGGGAAACTGTCTCTAGTG
1 TGTTTTAAGAAAAACCATCTCAAGTGAGAT-AAATTTCTTGTTTCAAGGAAAACTGTCTCTAGTG
* *
458456 GGACGAAACT
65 AGAC-AAAAT
* * * *
458466 TGTTTTGAGAAAAACAATCTCAAGTGAGATAAA-TT-TTGTTTCAAGGGAAAACTATATCTAGTG
1 TGTTTTAAGAAAAACCATCTCAAGTGAGATAAATTTCTTGTTTCAA-GGAAAACTGTCTCTAGTG
458529 AGACAAAAGT
65 AGACAAAA-T
* *
458539 TGTTTTAAGAAAAA-TACTCTCAAGTGAGATAACTTTCT
1 TGTTTTAAGAAAAACCA-TCTCAAGTGAGATAAATTTCT
458577 GATCTTTGCT
Statistics
Matches: 282, Mismatches: 39, Indels: 26
0.81 0.11 0.07
Matches are distributed among these distances:
71 1 0.00
72 65 0.23
73 56 0.20
74 15 0.05
75 115 0.41
76 30 0.11
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (73 bp):
TGTTTTAAGAAAAACCATCTCAAGTGAGATAAATTTCTTGTTTCAAGGAAAACTGTCTCTAGTGA
GACAAAAT
Found at i:460110 original size:5 final size:5
Alignment explanation
Indices: 460097--460214 Score: 52
Period size: 5 Copynumber: 23.2 Consensus size: 5
460087 ATTGGATATG
* * *
460097 TTTTC TTTTT TTTTC -TTTC GTCTCTC TTTTC TTTT- TTTCC TTTT- TTTTC
1 TTTTC TTTTC TTTTC TTTTC -T-TTTC TTTTC TTTTC TTTTC TTTTC TTTTC
* * *
460146 TATTTTT TTTTC TGTT- TTTTC -TTTC TTTTTC TCTGTT- TTTTC TTCTC
1 --TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC T-T-TTC TTTTC TTTTC
460193 TTTTCC TTTTTC TTTT- TTTTC T
1 TTTT-C -TTTTC TTTTC TTTTC T
460215 CTATTTTTAT
Statistics
Matches: 85, Mismatches: 12, Indels: 32
0.66 0.09 0.25
Matches are distributed among these distances:
4 24 0.28
5 39 0.46
6 9 0.11
7 13 0.15
ACGTcount: A:0.01, C:0.19, G:0.03, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:460152 original size:12 final size:11
Alignment explanation
Indices: 460128--460222 Score: 61
Period size: 12 Copynumber: 8.4 Consensus size: 11
460118 CTCTCTTTTC
*
460128 TTTTTTTC-CT
1 TTTTTTTCTTT
460138 TTTTTTTCTATT
1 TTTTTTTCT-TT
460150 TTTTTTTC--T
1 TTTTTTTCTTT
*
460159 GTTTTTTCTTT
1 TTTTTTTCTTT
*
460170 CTTTTTCTCTGTT
1 -TTTTTTTCT-TT
460183 TTTTCTTCTCTTT
1 TTTT-TT-TCTTT
*
460196 TCCTTTTTCTTT
1 T-TTTTTTCTTT
* *
460208 TTTTTCTCTAT
1 TTTTTTTCTTT
460219 TTTT
1 TTTT
460223 ATGTTTTTTC
Statistics
Matches: 67, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
9 8 0.12
10 8 0.12
11 12 0.18
12 26 0.39
13 8 0.12
14 5 0.07
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:460154 original size:21 final size:20
Alignment explanation
Indices: 460128--460212 Score: 86
Period size: 21 Copynumber: 4.3 Consensus size: 20
460118 CTCTCTTTTC
*
460128 TTTTTTTCCTTTTTTTTCTAT
1 TTTTTTTCCTGTTTTTTCT-T
*
460149 TTTTTTTTCTGTTTTTTCTT
1 TTTTTTTCCTGTTTTTTCTT
*
460169 TCTTTTTCTCTGTTTTTTCTT
1 TTTTTTTC-CTGTTTTTTCTT
* *
460190 CTCTTTTCC---TTTTTCTT
1 TTTTTTTCCTGTTTTTTCTT
460207 TTTTTT
1 TTTTTT
460213 CTCTATTTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
17 12 0.22
20 8 0.15
21 34 0.63
ACGTcount: A:0.01, C:0.16, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTTTTTCCTGTTTTTTCTT
Found at i:460164 original size:31 final size:31
Alignment explanation
Indices: 460123--460203 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
460113 TTCGTCTCTC
460123 TTTTCTTTTTTTCCTTTTTTTTCTAT-TTTT
1 TTTTCTTTTTTTCCTTTTTTTTCTATGTTTT
*
460153 TTTTCTGTTTTTT-CTTTCTTTTTCTCTGTTTT
1 TTTTCT-TTTTTTCCTTT-TTTTTCTATGTTTT
*
460185 TTCTTC-TCTTTTCCTTTTT
1 TT-TTCTTTTTTTCCTTTTT
460204 CTTTTTTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
30 10 0.23
31 21 0.48
32 10 0.23
33 3 0.07
ACGTcount: A:0.01, C:0.17, G:0.02, T:0.79
Consensus pattern (31 bp):
TTTTCTTTTTTTCCTTTTTTTTCTATGTTTT
Found at i:460228 original size:45 final size:45
Alignment explanation
Indices: 460137--460232 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 45
460127 CTTTTTTTCC
* *
460137 TTTTTT-TTCTATTTTTTTTTCTGTTTTTTCTTTCTTTTTCTCTG
1 TTTTTTCTTCTATTTTTTTTTCTGTTTTTTCTCTCTTTTTCTATG
*
460181 TTTTTTCTTCTCTTTTCCTTTTTCT-TTTTTT-TCTCTATTTT-TATG
1 TTTTTTCTTCTATTTT--TTTTTCTGTTTTTTCTCTCT-TTTTCTATG
460226 TTTTTTC
1 TTTTTTC
460233 GCTATATCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
44 6 0.13
45 22 0.49
46 10 0.22
47 7 0.16
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (45 bp):
TTTTTTCTTCTATTTTTTTTTCTGTTTTTTCTCTCTTTTTCTATG
Found at i:460231 original size:21 final size:21
Alignment explanation
Indices: 460125--460232 Score: 80
Period size: 21 Copynumber: 5.0 Consensus size: 21
460115 CGTCTCTCTT
*
460125 TTCT-TTTTTTCCTTTTTTTTC
1 TTCTCTTTTTT-CTGTTTTTTC
*
460146 TAT-TTTTTTTTCTGTTTTTTC
1 T-TCTCTTTTTTCTGTTTTTTC
460167 TT-TCTTTTTCTCTGTTTTTTC
1 TTCTCTTTTT-TCTGTTTTTTC
* *
460188 TTCTCTTTTCCTT-TTTCTTTTTT
1 TTCTCTTTT--TTCTGT-TTTTTC
*
460211 TTCTCTATTTTTATGTTTTTTC
1 TTCTCT-TTTTTCTGTTTTTTC
460233 GCTATATCTT
Statistics
Matches: 72, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
20 7 0.10
21 25 0.35
22 22 0.31
23 14 0.19
24 4 0.06
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.78
Consensus pattern (21 bp):
TTCTCTTTTTTCTGTTTTTTC
Found at i:462071 original size:149 final size:149
Alignment explanation
Indices: 461798--462089 Score: 431
Period size: 149 Copynumber: 2.0 Consensus size: 149
461788 TTAAAACTTT
* * * *
461798 TACTTCATCTTCTACTTCCAGAAATCTTTCGAGCTGGTTTGTGATCTTCAACTGTTGGCTTCAAC
1 TACTTCATCTCCTACTTCCAGAAATCTTTCGACCTGGTTCGTAATCTTCAACTGTTGGCTTCAAC
* * * * * *
461863 GTTGAATCGTCTCGAGTCTAACTTGTTACCTCAGCAGGCAGATGTCTGGCTCGTCTCCTTGGTAG
66 GTTGAATCGTCTCGAGTCCAACTTGTTACCTCAGCAAGCAAATGTATGGCTCATCTCCTTGGTAA
461928 GTAGACTCCCTCTAGCTAC
131 GTAGACTCCCTCTAGCTAC
* * *
461947 TACTTTATCTCCTACTTCCAGAAATCTTTCGACCTGGTTCGTAATCTTTAATTGTTGGCTTCAAC
1 TACTTCATCTCCTACTTCCAGAAATCTTTCGACCTGGTTCGTAATCTTCAACTGTTGGCTTCAAC
* * * *
462012 GTTGAATCGTCTTGAGTCCAACTTGTTACCTCATCAAGTAAATGTATGGCTCATTTCCTTGGTAA
66 GTTGAATCGTCTCGAGTCCAACTTGTTACCTCAGCAAGCAAATGTATGGCTCATCTCCTTGGTAA
462077 GTAGACTCCCTCT
131 GTAGACTCCCTCT
462090 TGAGGTTACT
Statistics
Matches: 126, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
149 126 1.00
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.37
Consensus pattern (149 bp):
TACTTCATCTCCTACTTCCAGAAATCTTTCGACCTGGTTCGTAATCTTCAACTGTTGGCTTCAAC
GTTGAATCGTCTCGAGTCCAACTTGTTACCTCAGCAAGCAAATGTATGGCTCATCTCCTTGGTAA
GTAGACTCCCTCTAGCTAC
Found at i:466685 original size:35 final size:34
Alignment explanation
Indices: 466639--466824 Score: 264
Period size: 35 Copynumber: 5.3 Consensus size: 34
466629 AAAGTTTGCA
*
466639 TCGATTCAAGTCGAACGGAAGAAAGCATCACACTT
1 TCGATTCAAGTCGAACGGAAG-AAGCATCGCACTT
* *
466674 TCGATTCAAGTCGAACGGAAGGAAGCGTTGCACTT
1 TCGATTCAAGTCGAACGGAA-GAAGCATCGCACTT
*
466709 TCGATTCAAGTAGAACGGAATGAAGCATCGCACTT
1 TCGATTCAAGTCGAACGGAA-GAAGCATCGCACTT
* *
466744 TCGATTTAAGTCGAATGGAATGAAGCATCGCACTT
1 TCGATTCAAGTCGAACGGAA-GAAGCATCGCACTT
*
466779 TCGATTCATGTCGAACGGAAGGAAGCATCGCACTT
1 TCGATTCAAGTCGAACGGAA-GAAGCATCGCACTT
466814 TCGATTCAAGT
1 TCGATTCAAGT
466825 GTTCATCTTT
Statistics
Matches: 135, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
35 134 0.99
36 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (34 bp):
TCGATTCAAGTCGAACGGAAGAAGCATCGCACTT
Found at i:468420 original size:51 final size:50
Alignment explanation
Indices: 468329--468433 Score: 129
Period size: 51 Copynumber: 2.1 Consensus size: 50
468319 AGCAGTAAAG
** * ** *
468329 CGCGCCCCCTGCACTGCGTTATACGATGATTTGGCGCCACGTGGGGTATAA
1 CGCGCCCCCTGCACCACGCTATACGATGAGCTGGCACCACGT-GGGTATAA
* *
468380 CGCGCCCCCTGCACCACGCTATACGGTGAGCTGGCACCACGTGGGTATAG
1 CGCGCCCCCTGCACCACGCTATACGATGAGCTGGCACCACGTGGGTATAA
468430 CGCG
1 CGCG
468434 TCCGTATAGC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
50 11 0.24
51 35 0.76
ACGTcount: A:0.17, C:0.33, G:0.30, T:0.19
Consensus pattern (50 bp):
CGCGCCCCCTGCACCACGCTATACGATGAGCTGGCACCACGTGGGTATAA
Found at i:468557 original size:49 final size:51
Alignment explanation
Indices: 468479--468601 Score: 189
Period size: 49 Copynumber: 2.5 Consensus size: 51
468469 CACGTAGGGG
**
468479 TATAGCGCGGATCAGGTACCGCGCTATACCTTTACTCCT-A-ATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCGCTATACCTTTACTCCTGACATAATTTTA
*
468528 TATAGTGCGGGGCAGGTACCGCGAC-ATACCTTTACTCCTGACATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCG-CTATACCTTTACTCCTGACATAATTTTA
468579 TATAGCGCGGGGCAGGTACCGCG
1 TATAGCGCGGGGCAGGTACCGCG
468602 TTTTGTATAA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
49 34 0.51
50 2 0.03
51 31 0.46
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (51 bp):
TATAGCGCGGGGCAGGTACCGCGCTATACCTTTACTCCTGACATAATTTTA
Found at i:473922 original size:109 final size:110
Alignment explanation
Indices: 473737--473948 Score: 363
Period size: 109 Copynumber: 1.9 Consensus size: 110
473727 AATTAATTCT
* * *
473737 TAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTAAATTAAAA
1 TAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTAAATTAAAA
*
473802 CATTAAAATGTTACCGTATCAGCAAAGTGTCGAGATATTTAATTA
66 CATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATATTTAATTA
*
473847 TAATATAATAATCATGCATTAAATAAAT-AACTAAATATTATTAATAATTTAAATTAAATTAAAA
1 TAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTAAATTAAAA
*
473911 CGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 CATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
473949 ATGATTTCCA
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
109 70 0.73
110 26 0.27
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.35
Consensus pattern (110 bp):
TAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTAAATTAAAA
CATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATATTTAATTA
Found at i:474087 original size:10 final size:10
Alignment explanation
Indices: 474072--474103 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
474062 ACCTTAAAAA
474072 GAGAGAATTT
1 GAGAGAATTT
474082 GAGAGAATTT
1 GAGAGAATTT
474092 GAGAGAATTT
1 GAGAGAATTT
474102 GA
1 GA
474104 TGTGATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:476937 original size:6 final size:6
Alignment explanation
Indices: 476916--476949 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
476906 GGCTCGGCTC
476916 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
476950 ACGTGTCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.36
6 18 0.64
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:480063 original size:137 final size:133
Alignment explanation
Indices: 479828--480157 Score: 361
Period size: 137 Copynumber: 2.5 Consensus size: 133
479818 TATGATATCA
* *
479828 ATACTTTAAATGTTG--AAAA--GATACAAAAAGATCAAAATTTAAAATATCGATATATGTGATG
1 ATACTTTAAATATTGAAAAAATTGATA-AAAAAGATCAAAATTTAAAATATCGATA-CT-T-ATG
* ** * *
479889 AGATTTAGTTTTATATATGAAAATTGCTGAAGGTGATTGATAGTTAAAATATTGATACTTATGCG
62 AGATTTACTTTTATATATGAAAATTAATGAAGATGATTGATAGTT-AAATA-TCATACTTATGCG
479954 ATAAT-TATCG
125 ATAATGT-T-G
* * * *
479964 ATACTTTTAAATATTGATAAAGTTGATAAAAAAAATCAAAATTTAAAATATCGATACTTATGTGA
1 ATAC-TTTAAATATTGAAAAAATTGATAAAAAAGATCAAAATTTAAAATATCGATACTTATGAGA
*
480029 -TTACTTTGTATAT-TGAAAAATTAATGAAGATGATTGATAGTTAAATATCATACTTATGCGGTA
65 TTTACTTT-TATATATG-AAAATTAATGAAGATGATTGATAGTTAAATATCATACTTATGCGATA
480092 ATGTTG
128 ATGTTG
** * *
480098 ATACTTTAAATATTGAAAAAATTGAT-AAAAAGATTGAAATTTAAAATATCAATTCTTATG
1 ATACTTTAAATATTGAAAAAATTGATAAAAAAGATCAAAATTTAAAATATCGATACTTATG
480158 CGATGATGAT
Statistics
Matches: 168, Mismatches: 18, Indels: 20
0.82 0.09 0.10
Matches are distributed among these distances:
132 29 0.17
133 20 0.12
134 5 0.03
135 17 0.10
136 18 0.11
137 43 0.26
138 1 0.01
139 4 0.02
140 27 0.16
141 4 0.02
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.37
Consensus pattern (133 bp):
ATACTTTAAATATTGAAAAAATTGATAAAAAAGATCAAAATTTAAAATATCGATACTTATGAGAT
TTACTTTTATATATGAAAATTAATGAAGATGATTGATAGTTAAATATCATACTTATGCGATAATG
TTG
Found at i:480142 original size:69 final size:74
Alignment explanation
Indices: 480038--480198 Score: 190
Period size: 73 Copynumber: 2.3 Consensus size: 74
480028 ATTACTTTGT
* * * * *
480038 ATATTG-AAAAATTAATGAAGATGATTGATAGTT-AAATATC-ATACTTATGCGGTAATG-TTGA
1 ATATTGAAAAAATTAATGAAAAAGATTGAAAGTTAAAATATCAATACTTATGCGATAATGATCGA
480099 TAC-TTTAA
66 TACTTTTAA
* * * *
480107 ATATTGAAAAAATTGAT-AAAAAGATTGAAATTTAAAATATCAATTCTTATGCGATGATGATCGA
1 ATATTGAAAAAATTAATGAAAAAGATTGAAAGTTAAAATATCAATACTTATGCGATAATGATCGA
*
480171 TACTTTTAT
66 TACTTTTAA
480180 ATATTGAAAAAATTAATGA
1 ATATTGAAAAAATTAATGA
480199 GAATGTTTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
69 18 0.24
70 16 0.21
71 14 0.19
72 6 0.08
73 20 0.27
74 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.37
Consensus pattern (74 bp):
ATATTGAAAAAATTAATGAAAAAGATTGAAAGTTAAAATATCAATACTTATGCGATAATGATCGA
TACTTTTAA
Found at i:480680 original size:71 final size:69
Alignment explanation
Indices: 480481--480699 Score: 176
Period size: 71 Copynumber: 3.1 Consensus size: 69
480471 CATAATATAT
* * * *
480481 GTATCAATATTTTAACTATCGAACATCTTCATCAACTTTTTCAATATAAAAAGTA-CTGATCATC
1 GTATCAATATTTTAACT-TTGATC-T-TTCTTCAACTTTTTCAATAT-TAAAGTATC-GATCATC
*
480545 GTCGCATAA
61 GTCACATAA
** * ** * * *
480554 GTATTGATATTTTAAATTTGATCTTT-TTACAATCAATTT-AGTATTTAAAATTATCGATCATTG
1 GTATCAATATTTTAACTTTGATCTTTCTT-CAA-CTTTTTCAATA-TT-AAAGTATCGATCATCG
480617 TCACATAA
62 TCACATAA
*
480625 GTATCAATATTTTAACTTTAGATCTTATCTTCAACTTTTTCAATATTAAAGTATCGATCATCAT-
1 GTATCAATATTTTAACTTT-GATCTT-TCTTCAACTTTTTCAATATTAAAGTATCGATCATCGTC
480689 ACATTAA
64 ACA-TAA
480696 GTAT
1 GTAT
480700 TGATATTTAA
Statistics
Matches: 114, Mismatches: 22, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
69 1 0.01
70 11 0.10
71 62 0.54
72 17 0.15
73 21 0.18
74 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42
Consensus pattern (69 bp):
GTATCAATATTTTAACTTTGATCTTTCTTCAACTTTTTCAATATTAAAGTATCGATCATCGTCAC
ATAA
Found at i:480706 original size:71 final size:68
Alignment explanation
Indices: 480512--480713 Score: 187
Period size: 71 Copynumber: 2.9 Consensus size: 68
480502 AACATCTTCA
* *
480512 TCAACTTTTTCAATATAAAAAGTA-CTGATCATCGTCGCATAAGTATTGATATTTTAAATTTGAT
1 TCAACTTTTTCAATAT-TAAAGTATC-GATCATCGTCACATAAGTATTGATATTTTAAATTTGAT
480576 CTTTT
64 CTTTT
** * * * ** *
480581 TACAATCAATTT-AGTATTTAAAATTATCGATCATTGTCACATAAGTATCAATATTTTAACTTTA
1 T-CAA-CTTTTTCAATA-TT-AAAGTATCGATCATCGTCACATAAGTATTGATATTTTAAATTT-
480645 GATCTTATCT
61 GATCTT-T-T
*
480655 TCAACTTTTTCAATATTAAAGTATCGATCATCAT-ACATTAAGTATTGATA-TTTAAATTT
1 TCAACTTTTTCAATATTAAAGTATCGATCATCGTCACA-TAAGTATTGATATTTTAAATTT
480714 TGAAATGCTT
Statistics
Matches: 104, Mismatches: 19, Indels: 19
0.73 0.13 0.13
Matches are distributed among these distances:
69 1 0.01
70 17 0.16
71 64 0.62
72 13 0.12
73 7 0.07
74 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (68 bp):
TCAACTTTTTCAATATTAAAGTATCGATCATCGTCACATAAGTATTGATATTTTAAATTTGATCT
TTT
Found at i:483801 original size:16 final size:17
Alignment explanation
Indices: 483775--483813 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
483765 ATAAATATGC
483775 AAAAT-TTAATTTT-TA
1 AAAATATTAATTTTATA
*
483790 GAAATATTAATTTTATA
1 AAAATATTAATTTTATA
483807 AAAATAT
1 AAAATAT
483814 ATAAACAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 4 0.20
16 8 0.40
17 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
AAAATATTAATTTTATA
Found at i:484440 original size:11 final size:12
Alignment explanation
Indices: 484424--484463 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
484414 TAAAAGTTGA
484424 AAATAA-AAATT
1 AAATAATAAATT
484435 AAATAATAAATT
1 AAATAATAAATT
*
484447 -AATAGTAAA-T
1 AAATAATAAATT
484457 AAATAAT
1 AAATAAT
484464 TTACCCTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 1 0.04
11 19 0.76
12 5 0.20
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (12 bp):
AAATAATAAATT
Found at i:485133 original size:29 final size:29
Alignment explanation
Indices: 485101--485158 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
485091 AGTTTTTTTG
485101 AAAAATATTTTACATAAAATAAATTATCT
1 AAAAATATTTTACATAAAATAAATTATCT
** *
485130 AAAAATATTTTATGTAAAATGAATTATCT
1 AAAAATATTTTACATAAAATAAATTATCT
485159 CGAAGTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (29 bp):
AAAAATATTTTACATAAAATAAATTATCT
Found at i:485504 original size:24 final size:24
Alignment explanation
Indices: 485436--485504 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
485426 ACCATTAAAT
*
485436 TTAATATT-TATTATAATATTTTA
1 TTAATATTATATTATAATATTATA
* *
485459 TTAACATAATATTA-AATTATTATA
1 TTAATATTATATTATAA-TATTATA
485483 TTAATATTATATGTATAA-ATTA
1 TTAATATTATAT-TATAATATTA
485505 ATTTTATTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 8 0.22
24 25 0.68
25 2 0.05
26 2 0.05
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (24 bp):
TTAATATTATATTATAATATTATA
Found at i:493618 original size:2 final size:2
Alignment explanation
Indices: 493613--493644 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
493603 CGCGTGCATC
493613 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
493645 TAAAACAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:493729 original size:11 final size:11
Alignment explanation
Indices: 493713--493742 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
493703 TAATTTTAAG
493713 ATTTTTATTTT
1 ATTTTTATTTT
493724 ATTTTTATTTT
1 ATTTTTATTTT
493735 -TTTTTATT
1 ATTTTTATT
493743 ATTTGGATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:494256 original size:22 final size:22
Alignment explanation
Indices: 494199--494257 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
494189 ACGCGATTCT
494199 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
494221 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
494242 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
494258 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:494318 original size:20 final size:20
Alignment explanation
Indices: 494242--494372 Score: 131
Period size: 20 Copynumber: 6.5 Consensus size: 20
494232 GCGATTTTCC
*
494242 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
494262 GTA-AATCGCAATGCGAATAT
1 G-ACTATCGCAATGCGATTAT
*
494282 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
*
494302 GACTATCGCAATGCGATTCT
1 GACTATCGCAATGCGATTAT
** *
494322 GACTATCGCAACACGATTCT
1 GACTATCGCAATGCGATTAT
* *
494342 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTAT
*
494362 GACTGTCGCAA
1 GACTATCGCAA
494373 CACTGAATTT
Statistics
Matches: 101, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
19 1 0.01
20 99 0.98
21 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:494330 original size:40 final size:40
Alignment explanation
Indices: 494184--494372 Score: 141
Period size: 40 Copynumber: 4.7 Consensus size: 40
494174 GTTTCCAGAT
* * **
494184 TCGCAACGCGATTCTGACTATCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTCTGACTATCGCAATGCGATTATGAC-AA
** * *
494224 TTCGCGTTGCGATTTTCCGACTATCGCAATGCGAATATGTA-AA
1 -TCGCAATGCGA--TTCTGACTATCGCAATGCGATTATG-ACAA
* * * *
494267 TCGCAATGCGAATATGTA-AATCGCAATGCGATTATGACTA
1 TCGCAATGCGATTCTG-ACTATCGCAATGCGATTATGACAA
** * *
494307 TCGCAATGCGATTCTGACTATCGCAACACGATTCTGACTA
1 TCGCAATGCGATTCTGACTATCGCAATGCGATTATGACAA
* *
494347 TCGCAACGCGATTCTGACTGTCGCAA
1 TCGCAATGCGATTCTGACTATCGCAA
494373 CACTGAATTT
Statistics
Matches: 117, Mismatches: 24, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
39 2 0.02
40 75 0.64
41 9 0.08
42 9 0.08
43 21 0.18
44 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (40 bp):
TCGCAATGCGATTCTGACTATCGCAATGCGATTATGACAA
Found at i:495231 original size:24 final size:24
Alignment explanation
Indices: 495176--495238 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
495166 TACTAGTCGG
*
495176 TATTCGAAATTTGATCTTGGTCAA
1 TATTCGGAATTTGATCTTGGTCAA
** *
495200 TACCCGGACTTTGATCTTGGTCAA
1 TATTCGGAATTTGATCTTGGTCAA
*
495224 TATTCGGATTTTGAT
1 TATTCGGAATTTGAT
495239 GATGTTTCAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (24 bp):
TATTCGGAATTTGATCTTGGTCAA
Found at i:497508 original size:18 final size:18
Alignment explanation
Indices: 497485--497520 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
497475 AAGAAAAAGG
*
497485 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
497503 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
497521 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:497931 original size:54 final size:53
Alignment explanation
Indices: 497818--497955 Score: 204
Period size: 54 Copynumber: 2.6 Consensus size: 53
497808 CATCATTGAA
* *
497818 TATCGCAACGCGAATTTGATTATCGCAACTCAAAATCGCAACGCAAATTCGAC
1 TATCGCAACGCGAATTTGACTATCGCAACGCAAAATCGCAACGCAAATTCGAC
* * * * *
497871 TATCGCAACACGAATATGACTATCGCAACGCAAAAATCGCAACGCGAATTTGTC
1 TATCGCAACGCGAATTTGACTATCGCAACGC-AAAATCGCAACGCAAATTCGAC
497925 TATCGCAACGCGAATTTGACTATCGCAACGC
1 TATCGCAACGCGAATTTGACTATCGCAACGC
497956 GAATTTGATT
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
53 27 0.36
54 48 0.64
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.22
Consensus pattern (53 bp):
TATCGCAACGCGAATTTGACTATCGCAACGCAAAATCGCAACGCAAATTCGAC
Found at i:497987 original size:94 final size:94
Alignment explanation
Indices: 497852--498034 Score: 244
Period size: 94 Copynumber: 1.9 Consensus size: 94
497842 GCAACTCAAA
*
497852 ATCGCAACGCAAATTCGACTATCGCAACACGAATATGACTATCGCAACGCA-AAAATCGCAACGC
1 ATCGCAACGCAAATTCGACTATCGCAACACGAATATGACTATCGCAACG-AGAAAATCGCAAAGC
* * *
497916 GAATTTGTCTATCGCAACGCGAATTTGACT
65 GAATTAGACTATCGCAACACGAATTTGACT
* * * * *
497946 ATCGCAACGCGAATTTGATTATCGCAACGA-GTATTTGACTATCGCAACGAGAAAATCGCAAAGC
1 ATCGCAACGCAAATTCGACTATCGCAAC-ACGAATATGACTATCGCAACGAGAAAATCGCAAAGC
*
498010 GTATTAGACTATCGCAACACGAATT
65 GAATTAGACTATCGCAACACGAATT
498035 AACTTTCGCG
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
93 1 0.01
94 75 0.97
95 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (94 bp):
ATCGCAACGCAAATTCGACTATCGCAACACGAATATGACTATCGCAACGAGAAAATCGCAAAGCG
AATTAGACTATCGCAACACGAATTTGACT
Found at i:497996 original size:20 final size:20
Alignment explanation
Indices: 497813--497994 Score: 165
Period size: 20 Copynumber: 9.8 Consensus size: 20
497803 TTACACATCA
*
497813 TTGAATATCGCAACGCGAAT
1 TTGACTATCGCAACGCGAAT
* *
497833 TTGATTATCGCAACTC-AA-
1 TTGACTATCGCAACGCGAAT
*
497851 ---A--ATCGCAACGCAAAT
1 TTGACTATCGCAACGCGAAT
* *
497866 TCGACTATCGCAACACGAAT
1 TTGACTATCGCAACGCGAAT
*
497886 ATGACTATCGCAACGC-AA-
1 TTGACTATCGCAACGCGAAT
*
497904 ---A-AATCGCAACGCGAAT
1 TTGACTATCGCAACGCGAAT
*
497920 TTGTCTATCGCAACGCGAAT
1 TTGACTATCGCAACGCGAAT
497940 TTGACTATCGCAACGCGAAT
1 TTGACTATCGCAACGCGAAT
* * *
497960 TTGATTATCGCAACGAGTAT
1 TTGACTATCGCAACGCGAAT
497980 TTGACTATCGCAACG
1 TTGACTATCGCAACG
497995 AGAAAATCGC
Statistics
Matches: 133, Mismatches: 16, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
13 9 0.07
14 12 0.09
15 4 0.03
18 1 0.01
19 4 0.03
20 103 0.77
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
TTGACTATCGCAACGCGAAT
Found at i:498035 original size:20 final size:20
Alignment explanation
Indices: 497852--498035 Score: 85
Period size: 20 Copynumber: 9.8 Consensus size: 20
497842 GCAACTCAAA
* * *
497852 ATCGCAACGCAAATTCGACT
1 ATCGCAACACGAATTAGACT
497872 ATCGCAACACGAA-TATGACT
1 ATCGCAACACGAATTA-GACT
*
497892 ATCGCAACGC-AA--A-A--
1 ATCGCAACACGAATTAGACT
* * *
497906 ATCGCAACGCGAATTTGTCT
1 ATCGCAACACGAATTAGACT
* *
497926 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAATTAGACT
* * *
497946 ATCGCAACGCGAATTTGATT
1 ATCGCAACACGAATTAGACT
* *
497966 ATCGCAACGA-GTATTTGACT
1 ATCGCAAC-ACGAATTAGACT
497986 ATCGC-A-ACGAGA--A-A--
1 ATCGCAACACGA-ATTAGACT
*
498000 ATCGCAA-AGCGTATTAGACT
1 ATCGCAACA-CGAATTAGACT
498020 ATCGCAACACGAATTA
1 ATCGCAACACGAATTA
498036 ACTTTCGCGT
Statistics
Matches: 131, Mismatches: 15, Indels: 36
0.72 0.08 0.20
Matches are distributed among these distances:
14 15 0.11
15 5 0.04
16 4 0.03
17 2 0.02
18 3 0.02
19 5 0.04
20 96 0.73
21 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACACGAATTAGACT
Found at i:498062 original size:20 final size:21
Alignment explanation
Indices: 498037--498090 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
498027 CACGAATTAA
498037 CTTTCGCGTTGCGATTTTG-G
1 CTTTCGCGTTGCGATTTTGAG
*
498057 CTTTCGCATTGCGATTTTGAG
1 CTTTCGCGTTGCGATTTTGAG
*
498078 -TTTAGCGTTGCGA
1 CTTTCGCGTTGCGA
498091 AAGTGTACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.11, C:0.19, G:0.28, T:0.43
Consensus pattern (21 bp):
CTTTCGCGTTGCGATTTTGAG
Found at i:498246 original size:14 final size:14
Alignment explanation
Indices: 498209--498247 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
498199 TCAATATTAA
*
498209 ACAAATCAACTTTT
1 ACAAATCAATTTTT
498223 ACAAATCAATTTTT
1 ACAAATCAATTTTT
*
498237 ATAAATCAATT
1 ACAAATCAATT
498248 AAACAAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (14 bp):
ACAAATCAATTTTT
Found at i:500330 original size:20 final size:20
Alignment explanation
Indices: 500305--500352 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
500295 GCGATTCTTT
500305 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
500325 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
500345 CGTTGCGA
1 CGTTGCGA
500353 AAGTAAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:502272 original size:20 final size:20
Alignment explanation
Indices: 502217--502284 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
502207 TCTGAAACTT
*
502217 AAAATCGCAACACAAAAATG
1 AAAATCGCAACACGAAAATG
502237 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * *
502257 ACTATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
502276 AAAATCGCA
1 AAAATCGCA
502285 TTGCGATTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 7 0.17
20 34 0.83
ACGTcount: A:0.51, C:0.24, G:0.13, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:502697 original size:22 final size:22
Alignment explanation
Indices: 502670--502712 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
502660 GAGATAGACG
502670 GATTTCACCGGAGATGGGGACT
1 GATTTCACCGGAGATGGGGACT
**
502692 GATTTCGTCGGAGATGGGGAC
1 GATTTCACCGGAGATGGGGAC
502713 GGATGTCGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.40, T:0.23
Consensus pattern (22 bp):
GATTTCACCGGAGATGGGGACT
Found at i:502919 original size:20 final size:20
Alignment explanation
Indices: 502886--503020 Score: 110
Period size: 20 Copynumber: 6.7 Consensus size: 20
502876 GCGCTTTGAA
* *
502886 AATCGCATTACGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
502906 CATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
502926 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
* * *
502946 AATCGCATTGCGAT-TTACAT
1 AATCGCGTTGCGATAGT-CAG
* * * *
502966 ATTCACATTGCGATAGTCGGAA
1 AATCGCGTTGCGATAGTC--AG
***
502988 AATCGTAATGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
503008 AATCGCGTTGCGA
1 AATCGCGTTGCGA
503021 ATCTGGAAAC
Statistics
Matches: 92, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
19 1 0.01
20 75 0.82
21 1 0.01
22 15 0.16
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:510132 original size:105 final size:105
Alignment explanation
Indices: 509945--510158 Score: 329
Period size: 105 Copynumber: 2.0 Consensus size: 105
509935 GGTGGAGTGA
* * *
509945 TTATCATATACTGTAGTGTTATCGGTGGGTACACTAGTATATTTTTCAGGTATAATTGCACTTTG
1 TTATCATATACTGTAGTGTTACCGGTGGGTACACTAGTATATTTTTCAGATATAATTGCACCTTG
* *
510010 TGTGTATATTATGATTCCGATGTGATAGCACTGTGTGTGC
66 TATGCATATTATGATTCCGATGTGATAGCACTGTGTGTGC
* * * * *
510050 TTATGATATACTGTGGTGTTACCGGTGGGTACACTAGTATATTTTTCAGATGTGATTTCACCTTG
1 TTATCATATACTGTAGTGTTACCGGTGGGTACACTAGTATATTTTTCAGATATAATTGCACCTTG
*
510115 TATGCATATTATTATTCCGATGTGATAGCACTGTGTGTGC
66 TATGCATATTATGATTCCGATGTGATAGCACTGTGTGTGC
510155 TTAT
1 TTAT
510159 ATTGTTCATA
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
105 98 1.00
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.42
Consensus pattern (105 bp):
TTATCATATACTGTAGTGTTACCGGTGGGTACACTAGTATATTTTTCAGATATAATTGCACCTTG
TATGCATATTATGATTCCGATGTGATAGCACTGTGTGTGC
Found at i:511810 original size:24 final size:24
Alignment explanation
Indices: 511782--511827 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
511772 TATGAATAAA
511782 TTGTATCAATAAAAGATTGCCTAT
1 TTGTATCAATAAAAGATTGCCTAT
511806 TTGTATCAATAAAAGATTGCCT
1 TTGTATCAATAAAAGATTGCCT
511828 TAAATAGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (24 bp):
TTGTATCAATAAAAGATTGCCTAT
Found at i:523357 original size:17 final size:17
Alignment explanation
Indices: 523337--523372 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
523327 ATTAAAGGGT
*
523337 TAGTTAGATTAATGAAC
1 TAGTTAGATGAATGAAC
*
523354 TAGTTATATGAATGAAC
1 TAGTTAGATGAATGAAC
523371 TA
1 TA
523373 ACTTTATAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.36
Consensus pattern (17 bp):
TAGTTAGATGAATGAAC
Found at i:527475 original size:46 final size:46
Alignment explanation
Indices: 527424--527515 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
527414 GGAAATTACA
*
527424 TTATTATCCTCGGATAGAGTAGGGTCAGAGTTTTTTCACCTTCCAG
1 TTATTATCCTCGGATAGAGTAGGATCAGAGTTTTTTCACCTTCCAG
527470 TTATTATCCTCGGATAGAGTAGGATCAGAGTTTTTTCACCTTCCAG
1 TTATTATCCTCGGATAGAGTAGGATCAGAGTTTTTTCACCTTCCAG
527516 CCAAACTCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (46 bp):
TTATTATCCTCGGATAGAGTAGGATCAGAGTTTTTTCACCTTCCAG
Found at i:533069 original size:24 final size:24
Alignment explanation
Indices: 533007--533088 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
532997 AATTATGTTA
*
533007 TGATACCTGACCTGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
* *
533031 TGGTA-TTGACATGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
* *
533054 TGATACATGACCTGGATTCTGATA
1 TGATACTTGACCTGGATTCTGATC
533078 TGATACTTGAC
1 TGATACTTGAC
533089 TTGAATTATG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 20 0.41
24 29 0.59
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (24 bp):
TGATACTTGACCTGGATTCTGATC
Found at i:535231 original size:5 final size:5
Alignment explanation
Indices: 535194--535218 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
535184 ACCGGTCATA
535194 ACCCG ACCCG ACCCG ACCCG ACCCG
1 ACCCG ACCCG ACCCG ACCCG ACCCG
535219 TTTACCCGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:535260 original size:13 final size:13
Alignment explanation
Indices: 535208--535263 Score: 76
Period size: 13 Copynumber: 4.3 Consensus size: 13
535198 GACCCGACCC
535208 GACCCGACCCGTT
1 GACCCGACCCGTT
*
535221 TACCCGACCCGTT
1 GACCCGACCCGTT
* **
535234 TACCCGACTAGTT
1 GACCCGACCCGTT
535247 GACCCGACCCGTT
1 GACCCGACCCGTT
535260 GACC
1 GACC
535264 TATTGACCGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.18, C:0.43, G:0.20, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:537605 original size:24 final size:24
Alignment explanation
Indices: 537578--537668 Score: 130
Period size: 24 Copynumber: 3.8 Consensus size: 24
537568 TCAAATTTGA
* *
537578 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
*
537602 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* *
537625 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
537649 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
537669 TTGAATTATG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 20 0.34
24 38 0.66
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:537638 original size:47 final size:48
Alignment explanation
Indices: 537578--537668 Score: 148
Period size: 47 Copynumber: 1.9 Consensus size: 48
537568 TCAAATTTGA
* *
537578 ATTCTGTTATGATACCTGACCTGGATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
*
537625 ATTCTGATCTGATACATGACCTGGATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGAC
537669 TTGAATTATG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 35 0.88
48 5 0.12
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
Found at i:543202 original size:3 final size:3
Alignment explanation
Indices: 543196--543230 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
543186 ACGACGAGAG
* *
543196 AGA AGA AGA AGA AGA AGA AGA AGA ACA AGA GGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
543231 CAATCTTAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.63, C:0.03, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:543745 original size:22 final size:22
Alignment explanation
Indices: 543704--543745 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
543694 ATTTACCATC
543704 AAAATACTTCCATTATAATTTT
1 AAAATACTTCCATTATAATTTT
*
543726 AAAATGACTTCTATTA-AATT
1 AAAAT-ACTTCCATTATAATT
543746 GGATTATGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAATACTTCCATTATAATTTT
Found at i:544881 original size:15 final size:12
Alignment explanation
Indices: 544851--544875 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
544841 TTTGGTAGAA
544851 AAATAATATTTT
1 AAATAATATTTT
544863 AAATAATATTTT
1 AAATAATATTTT
544875 A
1 A
544876 TCAAATTCGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:544936 original size:21 final size:21
Alignment explanation
Indices: 544896--544936 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
544886 TAAAACGCCC
**
544896 AATAATAATATTTTTGATAAA
1 AATAATAATATTTTAAATAAA
544917 AATAATAATATTTTAAATAA
1 AATAATAATATTTTAAATAA
544937 TTTTTTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AATAATAATATTTTAAATAAA
Found at i:546355 original size:78 final size:78
Alignment explanation
Indices: 546257--546422 Score: 278
Period size: 78 Copynumber: 2.1 Consensus size: 78
546247 AAATTTTTGT
* * *
546257 AACGCGACTTACCGATATAGGTAAACACAACTATTCGCAACTCAGTTTTCAAATTCGCAACTCGA
1 AACGCGAATTACCAATATAGGTAAACACAACTATTCGCAACTCAGTTTTCAAATTCGCAACACGA
546322 ATTCGGATTTCGC
66 ATTCGGATTTCGC
*
546335 AACGCGAATTACCAATATAGGTAAATACAACTATTCGCAACTCAGTTTTCAAATTCGCAACACGA
1 AACGCGAATTACCAATATAGGTAAACACAACTATTCGCAACTCAGTTTTCAAATTCGCAACACGA
*
546400 ATTCGGATTTCGT
66 ATTCGGATTTCGC
*
546413 AACTCGAATT
1 AACGCGAATT
546423 CTTCAATTTC
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 82 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (78 bp):
AACGCGAATTACCAATATAGGTAAACACAACTATTCGCAACTCAGTTTTCAAATTCGCAACACGA
ATTCGGATTTCGC
Found at i:547076 original size:20 final size:20
Alignment explanation
Indices: 547011--547066 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
547001 CTACATCGGT
*
547011 AATTCGCGTTGCGAAAATGA
1 AATTCGCTTTGCGAAAATGA
547031 AATTCGCTTTGCGAAAATGA
1 AATTCGCTTTGCGAAAATGA
547051 AATTCGCTTTGCGAAA
1 AATTCGCTTTGCGAAA
547067 TCCGAATTCG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (20 bp):
AATTCGCTTTGCGAAAATGA
Found at i:547188 original size:20 final size:20
Alignment explanation
Indices: 547159--547208 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
547149 TCATGTTCGA
547159 GTTGCGAATTCTAATTCTGT
1 GTTGCGAATTCTAATTCTGT
*
547179 GTTGCAAATTCTAATTCTGT
1 GTTGCGAATTCTAATTCTGT
547199 GTTGCGAATT
1 GTTGCGAATT
547209 TGTTGGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.44
Consensus pattern (20 bp):
GTTGCGAATTCTAATTCTGT
Found at i:555801 original size:2 final size:2
Alignment explanation
Indices: 555790--555846 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
555780 TTAAACGAAA
555790 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
555831 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
555847 TACAAATATT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:558385 original size:24 final size:24
Alignment explanation
Indices: 558358--558490 Score: 142
Period size: 24 Copynumber: 5.5 Consensus size: 24
558348 TATATCAAAA
* * *
558358 ATCAAAACATAATTCATGTCAAGT
1 ATCAAATCAGAATCCATGTCAAGT
* * *
558382 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAATCAGAATCCATGTCAAGT
* *
558406 ATCATATCAGAATCCAAGTCAAGT
1 ATCAAATCAGAATCCATGTCAAGT
*
558430 ATCAGATCAGAATCCATGTC-AGAT
1 ATCAAATCAGAATCCATGTCAAG-T
* *
558454 ATCAAATCATAATCCATGACAAGT
1 ATCAAATCAGAATCCATGTCAAGT
*
558478 ATCATATCAGAAT
1 ATCAAATCAGAAT
558491 TCAAATCGAA
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
23 2 0.02
24 89 0.96
25 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (24 bp):
ATCAAATCAGAATCCATGTCAAGT
Found at i:558506 original size:72 final size:72
Alignment explanation
Indices: 558372--558508 Score: 179
Period size: 72 Copynumber: 1.9 Consensus size: 72
558362 AAACATAATT
* * * *
558372 CATGTCAAGTATCATATCAAAATCCAGGTCAAGTATCATATCAGAATCCAAGTCAAGTATCAGAT
1 CATGTCAAGTATCAAATCAAAATCCAGGACAAGTATCATATCAGAATCCAAATCAAGAATCAGAT
558437 CAGAATC
66 CAGAATC
* * *
558444 CATGTC-AGATATCAAATCATAATCCATGACAAGTATCATATCAGAATTCAAATCGAA-AATCAG
1 CATGTCAAG-TATCAAATCAAAATCCAGGACAAGTATCATATCAGAATCCAAATC-AAGAATCAG
558507 AT
64 AT
558509 AAAATATTCA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
71 2 0.04
72 52 0.93
73 2 0.04
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (72 bp):
CATGTCAAGTATCAAATCAAAATCCAGGACAAGTATCATATCAGAATCCAAATCAAGAATCAGAT
CAGAATC
Found at i:563255 original size:24 final size:24
Alignment explanation
Indices: 563242--563360 Score: 184
Period size: 24 Copynumber: 5.0 Consensus size: 24
563232 AAACATAATT
* *
563242 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCAGATCAGAATC
* *
563266 CAGGTCAAGTATTAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
*
563290 CAAGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
*
563314 CATGTCAGGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
563338 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCAGATCAGAAT
563361 TCAAATCGAA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 86 1.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (24 bp):
CATGTCAAGTATCAGATCAGAATC
Found at i:565865 original size:17 final size:17
Alignment explanation
Indices: 565843--565885 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
565833 TGGTCAACAG
*
565843 TGGTCAACACCGGTCAA
1 TGGTCAACACAGGTCAA
*
565860 TGGTCAACGCAGGTCAA
1 TGGTCAACACAGGTCAA
565877 TGGTCAACA
1 TGGTCAACA
565886 GTCGACCGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (17 bp):
TGGTCAACACAGGTCAA
Found at i:581111 original size:2 final size:2
Alignment explanation
Indices: 581104--581135 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
581094 TAGCGTTAAC
581104 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
581136 TGAGGAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:584487 original size:15 final size:15
Alignment explanation
Indices: 584467--584511 Score: 90
Period size: 15 Copynumber: 3.0 Consensus size: 15
584457 TAGTGTTATT
584467 TAGATCAGATGTACC
1 TAGATCAGATGTACC
584482 TAGATCAGATGTACC
1 TAGATCAGATGTACC
584497 TAGATCAGATGTACC
1 TAGATCAGATGTACC
584512 ACTTTGCGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (15 bp):
TAGATCAGATGTACC
Found at i:595918 original size:21 final size:21
Alignment explanation
Indices: 595892--595932 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
595882 CATCCGCCTG
*
595892 AGATTCGACCCGACCAAAACA
1 AGATTCCACCCGACCAAAACA
*
595913 AGATTCCACCCGACCCAAAC
1 AGATTCCACCCGACCAAAAC
595933 CCGACCCGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.39, G:0.12, T:0.10
Consensus pattern (21 bp):
AGATTCCACCCGACCAAAACA
Found at i:604065 original size:2 final size:2
Alignment explanation
Indices: 604002--604052 Score: 54
Period size: 2 Copynumber: 26.5 Consensus size: 2
603992 ATTTTGTTTT
* *
604002 TA TA TA TA TA TA TA T- TCC TA T- TT TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
604042 TA TA TA TA TA T
1 TA TA TA TA TA T
604053 GTGTGTGTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 3 0.07
2 39 0.91
3 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:604262 original size:36 final size:36
Alignment explanation
Indices: 604124--604297 Score: 168
Period size: 36 Copynumber: 4.6 Consensus size: 36
604114 CGGAAAAACG
* *
604124 ATTTTAAAAAATAAGTATATATTATATAGTTTTTGAAAAC
1 ATTTT-AAAAAT-A-TATATAATATATAGTTTTT-AAAAT
* * * * *
604164 GTTTTTAAAATATATATAGTATATGGTTTTGAAAAAT
1 ATTTTAAAAATATATATAATATATAGTTTT-TAAAAT
* *
604201 ATTTTGAAAACATTTATATATTATATAGTTTTTAAAAT
1 ATTTT-AAAA-ATATATATAATATATAGTTTTTAAAAT
* *
604239 ATTTTAAAAGTATATATAATATATAGTTTTTAAAAC
1 ATTTTAAAAATATATATAATATATAGTTTTTAAAAT
* *
604275 ATTTTAAAAACATATATTATATA
1 ATTTTAAAAATATATATAATATA
604298 AAACATTTTT
Statistics
Matches: 112, Mismatches: 19, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
36 43 0.38
37 28 0.25
38 14 0.12
39 23 0.21
40 4 0.04
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (36 bp):
ATTTTAAAAATATATATAATATATAGTTTTTAAAAT
Found at i:604308 original size:29 final size:29
Alignment explanation
Indices: 604269--604345 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
604259 ATATAGTTTT
604269 TAAAACA--TTTTAAAAACATATAT-TATA
1 TAAAACATTTTTTAAAAACATATATATA-A
* **
604296 TAAAACATTTTTTGAAAATTTATATATAA
1 TAAAACATTTTTTAAAAACATATATATAA
*
604325 TATATA-ATTTTTTAAAAACAT
1 TA-AAACATTTTTTAAAAACAT
604346 TTTTGAAAAC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
27 7 0.18
29 28 0.72
30 4 0.10
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (29 bp):
TAAAACATTTTTTAAAAACATATATATAA
Found at i:604360 original size:69 final size:67
Alignment explanation
Indices: 604240--604403 Score: 194
Period size: 68 Copynumber: 2.4 Consensus size: 67
604230 TTTTAAAATA
* *
604240 TTTTAAAAGTATATATAATATAT-AGTTTTTAAAACATTTTAAAAACATATATTA-TAT-AAAAC
1 TTTTAAAA-TATATATAATATATAATTTTTTAAAACATTTTAAAAACATATATAATTATGAAAAC
604302 ATT
65 ATT
* *
604305 TTTTGAAAATTTATATATAATATATAATTTTTTAAAAACATTTTTGAAAAC-TATATAATTTTGA
1 TTTT-AAAA--TATATATAATATATAATTTTTT-AAAACA-TTTTAAAAACATATATAATTATGA
604369 AAACATT
61 AAACATT
604376 TTTTAAAA-AGTATATAATATATAATTTT
1 TTTTAAAATA-TATATAATATATAATTTT
604404 AAAATAGTTT
Statistics
Matches: 86, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
65 4 0.05
66 4 0.05
67 15 0.17
68 24 0.28
69 12 0.14
70 15 0.17
71 12 0.14
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (67 bp):
TTTTAAAATATATATAATATATAATTTTTTAAAACATTTTAAAAACATATATAATTATGAAAACA
TT
Found at i:604390 original size:30 final size:29
Alignment explanation
Indices: 604325--604393 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
604315 TTATATATAA
*
604325 TATATAATTTTTTAAAAACATTTTTGAAAAC
1 TATATAA--TTTTAAAAACATTTTTAAAAAC
* *
604356 TATATAATTTTGAAAACATTTTTTAAAAAG
1 TATATAATTTTAAAAACA-TTTTTAAAAAC
604386 TATATAAT
1 TATATAAT
604394 ATATAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 10 0.29
30 17 0.50
31 7 0.21
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (29 bp):
TATATAATTTTAAAAACATTTTTAAAAAC
Found at i:604433 original size:23 final size:25
Alignment explanation
Indices: 604410--604457 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
604400 TTTTAAAATA
*
604410 GTTTT-GAAATTATATATTATATAG
1 GTTTTGGAAAATATATATTATATAG
* *
604434 GTTTTGGAAAATATTTTTTATATA
1 GTTTTGGAAAATATATATTATATA
604458 TAATATATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (25 bp):
GTTTTGGAAAATATATATTATATAG
Found at i:609146 original size:60 final size:58
Alignment explanation
Indices: 609082--609205 Score: 126
Period size: 58 Copynumber: 2.1 Consensus size: 58
609072 TAAAGTACAT
* * * *
609082 AAATGAACCCTTGATTATATGGTATT-ATTTTGTCGAGT-CTAATAACTATTAAAAGTTATA
1 AAATGAACCC-TCACTATAGGGTATTGATTTGGT-GAGTACTAA-AA-TATTAAAAGTTATA
** * *
609142 AAATGCTCCCTCACTATAGGGTGTTGATTTGGTGAGTACTCAAATATTAAAAGTTATA
1 AAATGAACCCTCACTATAGGGTATTGATTTGGTGAGTACTAAAATATTAAAAGTTATA
609200 AAATGA
1 AAATGA
609206 TCACCGACTA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
58 19 0.36
59 17 0.32
60 17 0.32
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (58 bp):
AAATGAACCCTCACTATAGGGTATTGATTTGGTGAGTACTAAAATATTAAAAGTTATA
Found at i:612241 original size:23 final size:23
Alignment explanation
Indices: 612214--612282 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
612204 CACCACAAAT
*
612214 CGTATAAATGCACCAAAGTGCCA
1 CGTATAAATGCACCGAAGTGCCA
* * *
612237 CGTATAATTGCACCGTAGTGCCG
1 CGTATAAATGCACCGAAGTGCCA
* *
612260 CATAGAAATGCACCGAAGTGCCA
1 CGTATAAATGCACCGAAGTGCCA
612283 TATAAGGTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (23 bp):
CGTATAAATGCACCGAAGTGCCA
Found at i:612770 original size:2 final size:2
Alignment explanation
Indices: 612763--612802 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
612753 ATTCATCTTC
612763 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
612803 CATTTTTTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:614000 original size:19 final size:19
Alignment explanation
Indices: 613976--614024 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
613966 TAAGGGGATA
613976 CATCGATGCACTCCTTATG
1 CATCGATGCACTCCTTATG
613995 CATCGATGCACTCCTTATG
1 CATCGATGCACTCCTTATG
614014 CATCGATGCAC
1 CATCGATGCAC
614025 CAATTGCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (19 bp):
CATCGATGCACTCCTTATG
Found at i:617407 original size:23 final size:23
Alignment explanation
Indices: 617373--617441 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
617363 CACCACAGCT
*
617373 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
617396 CGTA-AAATTGCACCGTAGTGCCG
1 CGTAGAAA-TGCACCGAAGTGCCA
617419 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
617442 TATAAGGTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.08
23 34 0.85
24 3 0.08
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:617841 original size:2 final size:2
Alignment explanation
Indices: 617834--617875 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
617824 CTTATCCTAG
617834 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
617876 TCACATGTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:617940 original size:2 final size:2
Alignment explanation
Indices: 617933--617957 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
617923 TTCATCTTCC
617933 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
617958 CATTTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:619086 original size:24 final size:20
Alignment explanation
Indices: 619029--619066 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
619019 TTTCCCTTGA
619029 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
619049 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
619067 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:619164 original size:45 final size:45
Alignment explanation
Indices: 619093--619196 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 45
619083 TGCACTACCC
* * * * *
619093 ATGCATCGATACACAAATTACCTTCGATATTTTCAT-TTTAAGGGG
1 ATGCATCGATGCACAAATTACATTCGAT-GTTTCATCTTTAAAGAG
* * *
619138 ATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGAG
1 ATGCATCGATGCACAAATTACATTCGATGTTTCATCTTTAAAGAG
619183 -TGCATCGATGCACA
1 ATGCATCGATGCACA
619197 TTGAATATGC
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
44 18 0.37
45 31 0.63
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (45 bp):
ATGCATCGATGCACAAATTACATTCGATGTTTCATCTTTAAAGAG
Found at i:620889 original size:32 final size:31
Alignment explanation
Indices: 620853--620944 Score: 103
Period size: 32 Copynumber: 2.9 Consensus size: 31
620843 TAAGGTGACA
* *
620853 CTTGGGCAGGCTTTGAGGCCCCAAGGTATTTC
1 CTTGGGAAGGCTTT-AGGCCCCAAGGTATTCC
* * * *
620885 CTTGGGTAGGATCTAAAGCCCCAAGGTATTCC
1 CTTGGGAAGGCT-TTAGGCCCCAAGGTATTCC
620917 CTTGGGAAGGCTCTTAGGCCCCAAGGTA
1 CTTGGGAAGGCT-TTAGGCCCCAAGGTA
620945 CACTCTTGGG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 49 0.98
33 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (31 bp):
CTTGGGAAGGCTTTAGGCCCCAAGGTATTCC
Found at i:626690 original size:32 final size:31
Alignment explanation
Indices: 626654--626784 Score: 127
Period size: 32 Copynumber: 4.1 Consensus size: 31
626644 TAAGGTGACA
*
626654 CTTGGTTAGGCTCTAAGGCCCCAAGGTATTTC
1 CTTGG-TAGGCTCTAAGGCCCCAAGGTATTCC
*
626686 CTTGGGTAGGCTCTAAGGCCCCAATGTATTCC
1 CTT-GGTAGGCTCTAAGGCCCCAAGGTATTCC
* * ** *
626718 CTTAGGTAGGCTATTAGGCCCCAAGGTACACT
1 CTT-GGTAGGCTCTAAGGCCCCAAGGTATTCC
* * * *
626750 CTTGAGTACGTTCTCAGGCCCCAAGGTAATCC
1 CTTG-GTAGGCTCTAAGGCCCCAAGGTATTCC
626782 CTT
1 CTT
626785 AGGTTGTCAT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
31 1 0.01
32 78 0.96
33 2 0.02
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (31 bp):
CTTGGTAGGCTCTAAGGCCCCAAGGTATTCC
Found at i:627378 original size:31 final size:30
Alignment explanation
Indices: 627338--627404 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
627328 TATTATTGGA
*
627338 TATTGTTGAA-TTATATTTTTAATTTATAAAT
1 TATTTTTGAACTTATA-TTTT-ATTTATAAAT
*
627369 TATTTTTGAACTTGTATTTTATTTATAAAT
1 TATTTTTGAACTTATATTTTATTTATAAAT
627399 TATTTT
1 TATTTT
627405 ACATTTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 16 0.48
31 13 0.39
32 4 0.12
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.61
Consensus pattern (30 bp):
TATTTTTGAACTTATATTTTATTTATAAAT
Found at i:629582 original size:13 final size:13
Alignment explanation
Indices: 629564--629594 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
629554 CTCAAAATCG
629564 AAAATTTATTTAT
1 AAAATTTATTTAT
*
629577 AAAATTTATTTTT
1 AAAATTTATTTAT
629590 AAAAT
1 AAAAT
629595 GTGTACCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAATTTATTTAT
Found at i:630423 original size:3 final size:3
Alignment explanation
Indices: 630415--630439 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
630405 TAACGAAAAT
630415 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
630440 AACCCTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:631083 original size:43 final size:46
Alignment explanation
Indices: 630961--631085 Score: 159
Period size: 47 Copynumber: 2.8 Consensus size: 46
630951 TATAAAATCC
*
630961 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAGATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAGATA
* * *
631006 CTTACTATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAGATA
* *
631053 CTTGCCA-TT-ATT-CATAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
631086 GCATACTTAC
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
43 20 0.28
44 3 0.04
45 9 0.13
46 2 0.03
47 37 0.52
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAGATA
Found at i:640449 original size:14 final size:15
Alignment explanation
Indices: 640432--640461 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
640422 AGGAAGAATG
640432 ATTTTATAG-AGAAA
1 ATTTTATAGCAGAAA
640446 ATTTTATAGCAGAAA
1 ATTTTATAGCAGAAA
640461 A
1 A
640462 AGTAAAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.50, C:0.03, G:0.13, T:0.33
Consensus pattern (15 bp):
ATTTTATAGCAGAAA
Found at i:640603 original size:14 final size:14
Alignment explanation
Indices: 640579--640631 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
640569 CGTTTTGTTA
*
640579 TAAATCCTAAATCG
1 TAAACCCTAAATCG
* *
640593 TAAACCTTAAATTG
1 TAAACCCTAAATCG
*
640607 TAAACCCTAAATTG
1 TAAACCCTAAATCG
*
640621 TGAACCCTAAA
1 TAAACCCTAAA
640632 CACTAACCCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (14 bp):
TAAACCCTAAATCG
Found at i:640812 original size:7 final size:7
Alignment explanation
Indices: 640797--640869 Score: 83
Period size: 7 Copynumber: 10.4 Consensus size: 7
640787 TATGTTTATA
*
640797 TAAATCC
1 TAAACCC
640804 TAAACCC
1 TAAACCC
640811 TAAACCC
1 TAAACCC
640818 TAAACCC
1 TAAACCC
640825 TAAACCC
1 TAAACCC
**
640832 TAAACTT
1 TAAACCC
*
640839 TAAACCA
1 TAAACCC
*
640846 TAAACAC
1 TAAACCC
**
640853 TAAACTA
1 TAAACCC
640860 TAAACCC
1 TAAACCC
640867 TAA
1 TAA
640870 TATAAATAGA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 55 1.00
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:640826 original size:21 final size:21
Alignment explanation
Indices: 640795--640869 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 21
640785 TATATGTTTA
*
640795 TATAAATCCTAAACCCTAAAC
1 TATAAACCCTAAACCCTAAAC
**
640816 CCTAAACCCTAAACCCTAAAC
1 TATAAACCCTAAACCCTAAAC
* * *
640837 TTTAAACCATAAACACTAAAC
1 TATAAACCCTAAACCCTAAAC
640858 TATAAACCCTAA
1 TATAAACCCTAA
640870 TATAAATAGA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (21 bp):
TATAAACCCTAAACCCTAAAC
Found at i:641705 original size:24 final size:23
Alignment explanation
Indices: 641678--641726 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
641668 CATATAAACC
641678 ATGTATAGTATATATAAACTATAT
1 ATGTATAGTATATATAAA-TATAT
*
641702 ATGTATAGTATATATATATATAT
1 ATGTATAGTATATATAAATATAT
641725 AT
1 AT
641727 AAACTATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (23 bp):
ATGTATAGTATATATAAATATAT
Found at i:641708 original size:467 final size:468
Alignment explanation
Indices: 640819--641735 Score: 1397
Period size: 467 Copynumber: 2.0 Consensus size: 468
640809 CCTAAACCCT
* *
640819 AAACCCTAAACCCTAAACTTTAAACCATAAACACTAAACTATAAACCCTAATATAAATAGACTAA
1 AAACCCTAAACCATAAACTTTAAACCATAAACACTAAACCATAAACCCTAATATAAATAGACTAA
*
640884 CACTAATGCATATCTATTTGTAATAAAAGAGTGGGCTTATGTATTGGGCCTATGTAAATTAATGT
66 CACTAATGCATATCTATTTGTAATAAAAGAGTGGGCTTATGTATTGGGCCTATGTAAACTAATGT
* * * *
640949 AAATGGACTAACACTATTGTAAATTGACTTATTTTTTTGTTTTATTATTTCTTATTCATAACAAC
131 AAATGGACTAACACTATTGCAAATGGACTTATTTTTTAGTTTTATTATTACTTATTCATAACAAC
*
641014 AAAATAAATAGGCTATTAATGTGAATTAATCTAACATGCAACTAAAATACTAATTATGCAAATGA
196 AAAATAAATAGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGA
*
641079 AATTAATATGACATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTT
261 AATTAATATGACATGCACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTT
* * *
641144 AACACCTAATTAATCATGTTTTATATTATTTACATTTAAATAATTTTATTAATTTTATTAAATAA
326 AACACCTAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAATTGTATCAAATAA
*** * *
641209 TTTTATATAATATGTATGTATAAACCATGTATAGTATATATA-A-ACTATATAAATTATATTACT
391 TACCATATAATATGTATATATAAACCATGTATAGTATATATATATA-TATATAAACTATATTACT
641272 TATATAGTTTATAA
455 TATATAGTTTATAA
* * *
641286 AAACCCTAAATCATAAA-TTATAAA-CACTAAACACTAAACCATAAACCCTAATATGAATGGACT
1 AAACCCTAAACCATAAACTT-TAAACCA-TAAACACTAAACCATAAACCCTAATATAAATAGACT
* *
641349 AGCACTAATGCATA-CATATTTGTAATAAAAGAGTGGGTTTATGTATTGGGCCTATGTAAACTAA
64 AACACTAATGCATATC-TATTTGTAATAAAAGAGTGGGCTTATGTATTGGGCCTATGTAAACTAA
*
641413 TGTAAATGGACTATCACTATTGCAAATGGACTTATTTTTTAGTTTTATTATTACTTATTCATAAC
128 TGTAAATGGACTAACACTATTGCAAATGGACTTATTTTTTAGTTTTATTATTACTTATTCATAAC
*
641478 AACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAA
193 AACAAAATAAATAGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAA
* *
641543 TGAAATT-A-ATGACATGCACTACTATTTATGAACCATATAGTATGCAATGTGACATTCTAATTA
258 TGAAATTAATATGACATGCACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTA
*
641606 TTTAACACCTAATTAATCATGTTTTATATAATTTATATTTAAATAATTTTATATAATATGTA-CA
323 TTTAACACCTAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTAT-TAAT-TGTATCA
* * *
641670 TATAA-ACCATGT-ATA-GTATATATAAACTATATATGTATAGTATATATATATATATATAAACT
386 AATAATACCATATAATATGTATATATAAAC----CATGTATAGTATATATATATATATATAAACT
641732 ATAT
447 ATAT
641736 ACAATAAATT
Statistics
Matches: 409, Mismatches: 30, Indels: 21
0.89 0.07 0.05
Matches are distributed among these distances:
463 11 0.03
464 3 0.01
465 105 0.26
466 15 0.04
467 260 0.64
468 14 0.03
469 1 0.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (468 bp):
AAACCCTAAACCATAAACTTTAAACCATAAACACTAAACCATAAACCCTAATATAAATAGACTAA
CACTAATGCATATCTATTTGTAATAAAAGAGTGGGCTTATGTATTGGGCCTATGTAAACTAATGT
AAATGGACTAACACTATTGCAAATGGACTTATTTTTTAGTTTTATTATTACTTATTCATAACAAC
AAAATAAATAGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGA
AATTAATATGACATGCACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTT
AACACCTAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAATTGTATCAAATAA
TACCATATAATATGTATATATAAACCATGTATAGTATATATATATATATATAAACTATATTACTT
ATATAGTTTATAA
Found at i:641821 original size:7 final size:7
Alignment explanation
Indices: 641811--641876 Score: 55
Period size: 7 Copynumber: 9.7 Consensus size: 7
641801 TAGTTTATAG
641811 AAACCCT
1 AAACCCT
641818 AAACCCT
1 AAACCCT
* *
641825 AAATCAT
1 AAACCCT
*
641832 -AATCCT
1 AAACCCT
**
641838 AAACTTT
1 AAACCCT
641845 AAA-CCT
1 AAACCCT
641851 AAACCCT
1 AAACCCT
*
641858 AAACACT
1 AAACCCT
*
641865 AAACCAT
1 AAACCCT
641872 AAACC
1 AAACC
641877 ATAATGTAAA
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
6 9 0.20
7 37 0.80
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (7 bp):
AAACCCT
Found at i:641851 original size:13 final size:13
Alignment explanation
Indices: 641811--641876 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
641801 TAGTTTATAG
641811 AAACCCTAAACCCT
1 AAACCCTAAA-CCT
* * *
641825 AAATCATAATCCT
1 AAACCCTAAACCT
**
641838 AAACTTTAAACCT
1 AAACCCTAAACCT
641851 AAACCCTAAACACT
1 AAACCCTAAAC-CT
*
641865 AAACCATAAACC
1 AAACCCTAAACC
641877 ATAATGTAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
13 22 0.54
14 19 0.46
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (13 bp):
AAACCCTAAACCT
Found at i:641858 original size:20 final size:21
Alignment explanation
Indices: 641811--641876 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 21
641801 TAGTTTATAG
* *
641811 AAACCCTAAACCCTAAATCAT
1 AAACCCTAAACACTAAACCAT
* **
641832 -AATCCTAAACTTTAAACC-T
1 AAACCCTAAACACTAAACCAT
641851 AAACCCTAAACACTAAACCAT
1 AAACCCTAAACACTAAACCAT
641872 AAACC
1 AAACC
641877 ATAATGTAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
19 1 0.03
20 29 0.81
21 6 0.17
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (21 bp):
AAACCCTAAACACTAAACCAT
Found at i:642065 original size:14 final size:14
Alignment explanation
Indices: 642046--642092 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
642036 ATTTTTTCTT
642046 TATATAAATTAAAC
1 TATATAAATTAAAC
642060 TATAT-AATT----
1 TATATAAATTAAAC
642069 TATATAAATTAAAC
1 TATATAAATTAAAC
*
642083 TATATTAATT
1 TATATAAATT
642093 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:642071 original size:23 final size:24
Alignment explanation
Indices: 642044--642093 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
642034 TTATTTTTTC
642044 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
642067 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
642091 TTT
1 TTT
642094 TCCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:642158 original size:22 final size:24
Alignment explanation
Indices: 642115--642166 Score: 81
Period size: 22 Copynumber: 2.2 Consensus size: 24
642105 ATTAGTCATG
642115 TTTTATCTAATTTACATTAAATAA
1 TTTTATCTAATTTACATTAAATAA
*
642139 TTTTAT-TAATTT-TATTAAATAA
1 TTTTATCTAATTTACATTAAATAA
642161 TTTTAT
1 TTTTAT
642167 ATTATAGGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 15 0.56
23 6 0.22
24 6 0.22
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTATCTAATTTACATTAAATAA
Found at i:642386 original size:16 final size:16
Alignment explanation
Indices: 642365--642411 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
642355 TCATTTACAG
*
642365 GTCAGGTTAAAAACAT
1 GTCAGGTTGAAAACAT
642381 GTCAGGTTGAAAACAT
1 GTCAGGTTGAAAACAT
642397 GTCAGGTTGAAAACA
1 GTCAGGTTGAAAACA
642412 GGTCGGGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (16 bp):
GTCAGGTTGAAAACAT
Found at i:643718 original size:5 final size:5
Alignment explanation
Indices: 643708--643732 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
643698 ATTTCGTCAC
643708 AATTA AATTA AATTA AATTA AATTA
1 AATTA AATTA AATTA AATTA AATTA
643733 TAATATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:643921 original size:33 final size:33
Alignment explanation
Indices: 643846--643921 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
643836 TACTAGGACT
**
643846 AAATAAT-TTTGTCACAATTTATTATTGTGAAA
1 AAATAATATTTGTCACAATTTATTATAATGAAA
* * *
643878 AAATATTATTTGTCACAATTTTTTATAATGAGA
1 AAATAATATTTGTCACAATTTATTATAATGAAA
*
643911 AATTAATATTT
1 AAATAATATTT
643922 ATTATAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (33 bp):
AAATAATATTTGTCACAATTTATTATAATGAAA
Found at i:644221 original size:195 final size:196
Alignment explanation
Indices: 643842--644247 Score: 548
Period size: 195 Copynumber: 2.1 Consensus size: 196
643832 TTTTTACTAG
* * *
643842 GACTAAATAATTTTGTCACAATTTATTATTGTGAAAAAATATTATTTGTCACAATTTTTTATAAT
1 GACTAAATAAATTTGTCACAATTGATTATTGTGAAAAAATATTATTTGTCACAACTTTTTATAAT
* *
643907 GAGAAATTAATATTTATTATAAATTGTTATTTTGATTAAATAAATTTGTCAAAAGTTGTTATTTT
66 GAGAAATTAATATTTATTATAAATTGTTATTATAATT--ATAAATTTGTCAAAAGTTGTTATTTT
* * *
643972 GAGAAAATGTTGTGACGAAATAAATTTTACATAAATTTTTATTTTAATTAAATTTAATATGTTAT
129 GAGAAAATATTGTGACGAAATAAATTTGACATAAATTTTTATTTTAACTAAATTTAATATGTTAT
644037 TGT
194 TGT
* * * * *
644040 GACTAAATAAATTTGTTATAATTGATTATTGTG-AAAAATATTATTTTTCATAACTTTTTATATT
1 GACTAAATAAATTTGTCACAATTGATTATTGTGAAAAAATATTATTTGTCACAACTTTTTATAAT
* * *
644104 GAGAAATTAATATTTATTATAATTTGTTATTATAACTT-TAAATTTGTCATAATTTGTTATTTTG
66 GAGAAATTAATATTTATTATAAATTGTTATTATAA-TTATAAATTTGTCAAAAGTTGTTATTTTG
* * * *
644168 ATAAAATATT-TAGACTAAATAAATTTGACATAATTTTTTATTTTAACTAAATTTAATTTGTTAT
130 AGAAAATATTGT-GACGAAATAAATTTGACATAAATTTTTATTTTAACTAAATTTAATATGTTAT
*
644232 TTT
194 TGT
* *
644235 GTCTATATAAATT
1 GACTAAATAAATT
644248 ATCATAATTT
Statistics
Matches: 183, Mismatches: 23, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
194 1 0.01
195 92 0.50
197 59 0.32
198 31 0.17
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (196 bp):
GACTAAATAAATTTGTCACAATTGATTATTGTGAAAAAATATTATTTGTCACAACTTTTTATAAT
GAGAAATTAATATTTATTATAAATTGTTATTATAATTATAAATTTGTCAAAAGTTGTTATTTTGA
GAAAATATTGTGACGAAATAAATTTGACATAAATTTTTATTTTAACTAAATTTAATATGTTATTG
T
Done.