Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold495
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: 586005
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 5
Found at i:304103 original size:16 final size:15
Alignment explanation
Indices: 304091--304123 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
304081 ATAAATATGA
304091 ATAA-ATTTAAATAG
1 ATAACATTTAAATAG
*
304105 ATAACATTTAAATAA
1 ATAACATTTAAATAG
304120 ATAA
1 ATAA
304124 GAAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (15 bp):
ATAACATTTAAATAG
Found at i:313243 original size:2 final size:2
Alignment explanation
Indices: 313236--313304 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
313226 TAACGTTATC
313236 TA TA TA 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 TA TA TA
313278 TA 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 TA T
313305 TAGAATGACA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:314724 original size:2 final size:2
Alignment explanation
Indices: 314708--314741 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
314698 TAATTTTCTA
*
314708 AT AT -T AT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
314742 GACTATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:315409 original size:16 final size:16
Alignment explanation
Indices: 315385--315472 Score: 108
Period size: 16 Copynumber: 5.6 Consensus size: 16
315375 TTAGAGTTTA
315385 AATTATTTTTTATTTG
1 AATTATTTTTTATTTG
315401 -ATTATTTTTTATTTTG
1 AATTATTTTTTA-TTTG
**
315417 -ATTATTTTAAATTTG
1 AATTATTTTTTATTTG
315432 AATTATTTTTTATTTG
1 AATTATTTTTTATTTG
** *
315448 AATTATTTTAAATTTA
1 AATTATTTTTTATTTG
315464 AATTATTTT
1 AATTATTTT
315473 AAATTTAGGT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
15 15 0.24
16 48 0.76
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (16 bp):
AATTATTTTTTATTTG
Found at i:315442 original size:32 final size:32
Alignment explanation
Indices: 315385--315472 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
315375 TTAGAGTTTA
**
315385 AATTATTTTTTATTTG-ATTATTTTTTATTTTG
1 AATTATTTTAAATTTGAATTATTTTTTA-TTTG
315417 -ATTATTTTAAATTTGAATTATTTTTTATTTG
1 AATTATTTTAAATTTGAATTATTTTTTATTTG
*
315448 AATTATTTTAAATTTAAATTATTTT
1 AATTATTTTAAATTTGAATTATTTT
315473 AAATTTAGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
31 17 0.33
32 34 0.67
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (32 bp):
AATTATTTTAAATTTGAATTATTTTTTATTTG
Found at i:315469 original size:48 final size:47
Alignment explanation
Indices: 315385--315478 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 47
315375 TTAGAGTTTA
** **
315385 AATTATTTTTTATTTGATTATTTTTTATTTTGATTATTTTAAATTTG
1 AATTATTTTTTATTTGATTATTTTAAATTTAAATTATTTTAAATTTG
315432 AATTATTTTTTATTTGAATTATTTTAAATTTAAATTATTTTAAATTT
1 AATTATTTTTTATTTG-ATTATTTTAAATTTAAATTATTTTAAATTT
315479 AGGTCTTGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 16 0.38
48 26 0.62
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (47 bp):
AATTATTTTTTATTTGATTATTTTAAATTTAAATTATTTTAAATTTG
Found at i:315473 original size:16 final size:16
Alignment explanation
Indices: 315381--315479 Score: 92
Period size: 16 Copynumber: 6.2 Consensus size: 16
315371 CGATTTAGAG
**
315381 TTTAAATTATTTTTTA
1 TTTAAATTATTTTAAA
* **
315397 TTT-GATTATTTTTTA
1 TTTAAATTATTTTAAA
**
315412 TTTTGATTATTTTAAA
1 TTTAAATTATTTTAAA
* **
315428 TTTGAATTATTTTTTA
1 TTTAAATTATTTTAAA
*
315444 TTTGAATTATTTTAAA
1 TTTAAATTATTTTAAA
315460 TTTAAATTATTTTAAA
1 TTTAAATTATTTTAAA
315476 TTTA
1 TTTA
315480 GGTCTTGACT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
15 14 0.19
16 58 0.81
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:322920 original size:25 final size:25
Alignment explanation
Indices: 322881--322930 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
322871 GGTCATATCC
322881 ATTTTATTTATTTATTATTTATTTT
1 ATTTTATTTATTTATTATTTATTTT
*
322906 ATTTT-TTTATATTATTGTTTATTTT
1 ATTTTATTTAT-TTATTATTTATTTT
322931 TTGAGAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (25 bp):
ATTTTATTTATTTATTATTTATTTT
Found at i:323479 original size:13 final size:13
Alignment explanation
Indices: 323461--323486 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
323451 TTTAAAAGTG
323461 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
323474 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
323487 GTGATTTTTC
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:324263 original size:24 final size:24
Alignment explanation
Indices: 324232--324282 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
324222 TGATTTAAAA
324232 TAAATTAAAATAATTTTTTAAATT
1 TAAATTAAAATAATTTTTTAAATT
*
324256 TAAATTAAAATAATTTTTTGAATT
1 TAAATTAAAATAATTTTTTAAATT
324280 TAA
1 TAA
324283 CTCAAAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
TAAATTAAAATAATTTTTTAAATT
Found at i:324289 original size:24 final size:24
Alignment explanation
Indices: 324232--324290 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
324222 TGATTTAAAA
*
324232 TAAATTAAAATAATTTTTTAAATT
1 TAAATCAAAATAATTTTTTAAATT
* *
324256 TAAATTAAAATAATTTTTTGAATT
1 TAAATCAAAATAATTTTTTAAATT
*
324280 TAACTCAAAAT
1 TAAATCAAAAT
324291 TGATAAGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (24 bp):
TAAATCAAAATAATTTTTTAAATT
Found at i:329391 original size:28 final size:27
Alignment explanation
Indices: 329336--329416 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 27
329326 GCCACCCATT
329336 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
329363 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* * *
329391 TATTTGTCAAATATGGAGGCTTATTT
1 TGTTTGTCAAAAATGGTGG-TTATTT
329417 ATTTGTCAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
26 1 0.02
27 21 0.45
28 22 0.47
29 2 0.04
30 1 0.02
ACGTcount: A:0.22, C:0.07, G:0.23, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:329508 original size:20 final size:20
Alignment explanation
Indices: 329483--329528 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
329473 AAATAAAGGC
*
329483 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
**
329503 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCCTCTCAAGTA
329523 TCCCTC
1 TCCCTC
329529 TTCAATTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.50, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:329825 original size:27 final size:27
Alignment explanation
Indices: 329795--329866 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
329785 AAAATCACTC
*
329795 TTTGTGTTTGTAAAAAAT-GATGGTTAT
1 TTTGTGTTTGTAAAAAATAG-TGATTAT
* * *
329822 TTTGTATTTATAAAAAATAGTGATTCT
1 TTTGTGTTTGTAAAAAATAGTGATTAT
* *
329849 TTTTTGTTTGTCAAAAAT
1 TTTGTGTTTGTAAAAAAT
329867 TATGACTTGT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
27 35 0.97
28 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.15, T:0.50
Consensus pattern (27 bp):
TTTGTGTTTGTAAAAAATAGTGATTAT
Found at i:331950 original size:13 final size:13
Alignment explanation
Indices: 331932--331956 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
331922 CATAAAGTGT
331932 TGTATCGATACAA
1 TGTATCGATACAA
331945 TGTATCGATACA
1 TGTATCGATACA
331957 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:331972 original size:32 final size:33
Alignment explanation
Indices: 331912--331977 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
331902 TTCAACGATT
331912 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
331945 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
331977 T
1 T
331978 ATAAGCTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:332037 original size:13 final size:13
Alignment explanation
Indices: 332019--332043 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
332009 ATTACTCAAA
332019 TGTATCGATACAT
1 TGTATCGATACAT
332032 TGTATCGATACA
1 TGTATCGATACA
332044 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:334293 original size:24 final size:26
Alignment explanation
Indices: 334266--334319 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
334256 ATCAAAATTT
*
334266 ATTCAT-C-GGGGACACTCCAACCCC
1 ATTCATCCAGGGGACACACCAACCCC
*
334290 ATTCTTCCGAGGGGACACACCAACCCC
1 ATTCATCC-AGGGGACACACCAACCCC
334317 ATT
1 ATT
334320 TTCAACCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.20
25 1 0.04
27 19 0.76
ACGTcount: A:0.26, C:0.39, G:0.17, T:0.19
Consensus pattern (26 bp):
ATTCATCCAGGGGACACACCAACCCC
Found at i:337748 original size:15 final size:14
Alignment explanation
Indices: 337710--337748 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
337700 GTTTAAATAA
337710 TTTCTTTTTCATTT
1 TTTCTTTTTCATTT
*
337724 TTTCAATTTTCAATTT
1 TTTC-TTTTTC-ATTT
337740 TTTCTTTTT
1 TTTCTTTTT
337749 TTTTCAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 4 0.19
15 9 0.43
16 8 0.38
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTCTTTTTCATTT
Found at i:338517 original size:3 final size:3
Alignment explanation
Indices: 338505--338534 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
338495 TACTAATCAC
338505 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
338535 AATTTTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:338784 original size:13 final size:13
Alignment explanation
Indices: 338763--338795 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
338753 AACTCTTTTC
338763 TTTTT-TTCGATA
1 TTTTTCTTCGATA
*
338775 TTTTTCTTCGATT
1 TTTTTCTTCGATA
338788 TTTTTCTT
1 TTTTTCTT
338796 TTGAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.09, C:0.12, G:0.06, T:0.73
Consensus pattern (13 bp):
TTTTTCTTCGATA
Found at i:339345 original size:90 final size:90
Alignment explanation
Indices: 339192--339366 Score: 287
Period size: 90 Copynumber: 1.9 Consensus size: 90
339182 ATGCCCATTA
* * * * *
339192 ACCTTAAAACTTTTGCCAGTATCCGAACTTTGGATTTTAACTGTACCATGAGGAAATACATTAGT
1 ACCTTAAAAATATTGCCAGTATCCGAACTATGGATTTCAACTATACCATGAGGAAATACATTAGT
339257 TACAATAAATGGACCAATCCGATTC
66 TACAATAAATGGACCAATCCGATTC
* *
339282 ACCTTAAAAATATTGCCAGTATCCGGACTATGGATTTCAACTATACCATTAGGAAATACATTAGT
1 ACCTTAAAAATATTGCCAGTATCCGAACTATGGATTTCAACTATACCATGAGGAAATACATTAGT
339347 TACAATAAATGGACCAATCC
66 TACAATAAATGGACCAATCC
339367 ATCAAGAATG
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.30
Consensus pattern (90 bp):
ACCTTAAAAATATTGCCAGTATCCGAACTATGGATTTCAACTATACCATGAGGAAATACATTAGT
TACAATAAATGGACCAATCCGATTC
Found at i:340472 original size:19 final size:19
Alignment explanation
Indices: 340448--340484 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
340438 ATCACGATTA
340448 TATCGATACATAAGTTTTG
1 TATCGATACATAAGTTTTG
340467 TATCGATACATAAGTTTT
1 TATCGATACATAAGTTTT
340485 ATACATTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (19 bp):
TATCGATACATAAGTTTTG
Found at i:340548 original size:13 final size:13
Alignment explanation
Indices: 340530--340554 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
340520 ATTACTCAAA
340530 TGTATCGATACAT
1 TGTATCGATACAT
340543 TGTATCGATACA
1 TGTATCGATACA
340555 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:346863 original size:21 final size:21
Alignment explanation
Indices: 346839--346901 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
346829 TCCTAATTTC
346839 AAGTCTACTATATTTGTAAAT
1 AAGTCTACTATATTTGTAAAT
* * *
346860 AAGT-TTC-A-AATTCT--AT
1 AAGTCTACTATATTTGTAAAT
346876 CAAGTCTACTATATTTGTAAAT
1 -AAGTCTACTATATTTGTAAAT
346898 AAGT
1 AAGT
346902 AATTTAGGCA
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
16 2 0.07
17 4 0.13
18 6 0.20
19 2 0.07
20 6 0.20
21 8 0.27
22 2 0.07
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (21 bp):
AAGTCTACTATATTTGTAAAT
Found at i:347096 original size:14 final size:14
Alignment explanation
Indices: 347073--347146 Score: 55
Period size: 14 Copynumber: 5.3 Consensus size: 14
347063 ATTTATTTTA
*
347073 TATATGATATAAAT
1 TATATAATATAAAT
347087 TATATAATATAAA-
1 TATATAATATAAAT
* *
347100 AATATAA-A-AATAA
1 TATATAATATAA-AT
347113 TATATAATATATAAT
1 TATATAATATA-AAT
* *
347128 ATATATTATATAAAC
1 -TATATAATATAAAT
347143 TATA
1 TATA
347147 AAATGGGCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
11 2 0.04
12 2 0.04
13 12 0.25
14 17 0.35
15 4 0.08
16 11 0.23
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (14 bp):
TATATAATATAAAT
Found at i:349595 original size:22 final size:21
Alignment explanation
Indices: 349547--349596 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
349537 CAACTTATGT
349547 TATTTTATTTTATTTATTTTC
1 TATTTTATTTTATTTATTTTC
*
349568 TCATTTTAATTTT-TTATATTTTG
1 T-ATTTT-ATTTTATT-TATTTTC
349591 TATTTT
1 TATTTT
349597 TCTACAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.04
22 12 0.48
23 12 0.48
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (21 bp):
TATTTTATTTTATTTATTTTC
Found at i:351148 original size:13 final size:12
Alignment explanation
Indices: 351129--351171 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
351119 AAATTAAAAT
351129 TTTAAAAATATA
1 TTTAAAAATATA
351141 TTTCAAAAATA-A
1 TTT-AAAAATATA
*
351153 ATTAAAAATATAA
1 TTTAAAAATAT-A
351166 TTTAAA
1 TTTAAA
351172 TAGATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 7 0.27
12 6 0.23
13 13 0.50
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
TTTAAAAATATA
Found at i:353010 original size:20 final size:20
Alignment explanation
Indices: 352979--353027 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
352969 AGAAAGAATT
*
352979 GAAGAAGGATACAAGAGAGG
1 GAAGAGGGATACAAGAGAGG
* **
352999 GATGAGGGATACTTGAGAGG
1 GAAGAGGGATACAAGAGAGG
353019 GAAGAGGGA
1 GAAGAGGGA
353028 GCCTCTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.45, T:0.10
Consensus pattern (20 bp):
GAAGAGGGATACAAGAGAGG
Found at i:355084 original size:21 final size:22
Alignment explanation
Indices: 355058--355103 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
355048 ATCTGTTGAA
* *
355058 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGTGGAGTACT
355079 ACTCCACCTGCTGTGGAGTACT
1 ACTCCACCTGCTGTGGAGTACT
355101 ACT
1 ACT
355104 TGTCTGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGCTGTGGAGTACT
Found at i:357581 original size:20 final size:20
Alignment explanation
Indices: 357556--357594 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
357546 AAGAATTGAA
357556 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAT
**
357576 GAGGGATACTTGAGAGGGA
1 GAGGGATACAAGAGAGGGA
357595 AGAGAGAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.46, T:0.13
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAT
Found at i:357739 original size:27 final size:27
Alignment explanation
Indices: 357675--357745 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
357665 TAACAAGCCT
* * *
357675 CCATATTTGACAAATATAAAGGAAATCA
1 CCATTTTTGACAAATACAAA-GAAACCA
357703 CCATTTTTGACAAATACAAA-ATAACCA
1 CCATTTTTGACAAATACAAAGA-AACCA
357730 CCATTTTTGACAAATA
1 CCATTTTTGACAAATA
357746 AATGGGTGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.28
Consensus pattern (27 bp):
CCATTTTTGACAAATACAAAGAAACCA
Found at i:358771 original size:28 final size:30
Alignment explanation
Indices: 358710--358778 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 30
358700 ATTTTTTTAA
*
358710 AAATAAATTTTTTTATATATTATTATATTC
1 AAATAAATTTTATTATATATTATTATATTC
*
358740 AAATAAATTTGTATTAT-T-TT-TTATATTT
1 AAATAAATTT-TATTATATATTATTATATTC
*
358768 AAATAATTTTT
1 AAATAAATTTT
358779 TTACTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 1 0.03
28 16 0.46
29 2 0.06
30 11 0.31
31 5 0.14
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (30 bp):
AAATAAATTTTATTATATATTATTATATTC
Found at i:358776 original size:18 final size:18
Alignment explanation
Indices: 358755--358789 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
358745 AATTTGTATT
358755 ATTTTTTATA-TTTAAATA
1 ATTTTTT-TACTTTAAATA
358773 ATTTTTTTACTTTAAAT
1 ATTTTTTTACTTTAAAT
358790 GAAAGGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTTTACTTTAAATA
Found at i:362239 original size:25 final size:25
Alignment explanation
Indices: 362211--362259 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
362201 TTCAATTATG
*
362211 ATAA-TAAAAATAATTTATTTTTAAT
1 ATAATTAAAAA-AATTTAATTTTAAT
*
362236 ATAATTAAGAAAATTTAATTTTAA
1 ATAATTAAAAAAATTTAATTTTAA
362260 AAATATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
ATAATTAAAAAAATTTAATTTTAAT
Found at i:362544 original size:18 final size:19
Alignment explanation
Indices: 362511--362546 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
362501 GAATTAAATC
362511 AAATTTGATTTATAAATTT
1 AAATTTGATTTATAAATTT
*
362530 AAATTTTATTT-TAAATT
1 AAATTTGATTTATAAATT
362547 AAAGTCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
AAATTTGATTTATAAATTT
Found at i:364044 original size:149 final size:149
Alignment explanation
Indices: 363774--364053 Score: 497
Period size: 149 Copynumber: 1.9 Consensus size: 149
363764 GACCAACGCG
* * *
363774 CGTTCTCCGATATTCTTAATAGGCAGTCAGAGCCTGCGAATATCCCATCGCATTAAAATCATATT
1 CGTTCTCCGATATTCTTAATAGGCAGTCACAGCCTGCAAATATCCCATCGCATTAAAATCATACT
363839 AACTCTGAAAGTCGTAATTAGATTAAGGAAATATATGGTCTGACAGTAGGTATAACTTGCATAAC
66 AACTCTGAAAGTCGTAATTAGATTAAGGAAATATATGGTCTGACAGTAGGTATAACTTGCATAAC
363904 CCGTCACATTAAAATATCC
131 CCGTCACATTAAAATATCC
* * *
363923 CGTTCTTCGATGTTCTTAATAGGCAGTCACAGCCTGCAAATATCCCGTCGCATTAAAATCATACT
1 CGTTCTCCGATATTCTTAATAGGCAGTCACAGCCTGCAAATATCCCATCGCATTAAAATCATACT
*
363988 AACTCTGAAAGTCGTAATTAGATTAAGGAAATATATGGTCTGATAGTAGGTATAACTTGCATAAC
66 AACTCTGAAAGTCGTAATTAGATTAAGGAAATATATGGTCTGACAGTAGGTATAACTTGCATAAC
364053 C
131 C
364054 ACTCTGTAAG
Statistics
Matches: 124, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 124 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (149 bp):
CGTTCTCCGATATTCTTAATAGGCAGTCACAGCCTGCAAATATCCCATCGCATTAAAATCATACT
AACTCTGAAAGTCGTAATTAGATTAAGGAAATATATGGTCTGACAGTAGGTATAACTTGCATAAC
CCGTCACATTAAAATATCC
Found at i:370365 original size:21 final size:21
Alignment explanation
Indices: 370335--370382 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
370325 AAAATAGTCG
*
370335 ATGCTTACCACCAAGGCAATTT
1 ATGCTCACCACCAAGGC-ATTT
370357 -TGCTCACCACCAAGGCATTT
1 ATGCTCACCACCAAGGCATTT
370377 ATGCTC
1 ATGCTC
370383 GTCGCCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (21 bp):
ATGCTCACCACCAAGGCATTT
Found at i:375966 original size:4 final size:4
Alignment explanation
Indices: 375950--375979 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
375940 TGATATGTAA
375950 AAAT AATAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AA-AT AAAT AAAT AAAT AAAT AAAT A
375980 TATCAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:376041 original size:15 final size:15
Alignment explanation
Indices: 376021--376082 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 15
376011 TTATTAAAAT
376021 TTATATAAATATATA
1 TTATATAAATATATA
376036 TTATATTAAATATGATTA
1 TTATA-TAAATAT-A-TA
* * *
376054 TAACATAAAAATATA
1 TTATATAAATATATA
376069 -TATATAAATA-ATA
1 TTATATAAATATATA
376082 T
1 T
376083 GAATTACTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
13 3 0.08
14 7 0.19
15 7 0.19
16 8 0.22
17 7 0.19
18 5 0.14
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
TTATATAAATATATA
Found at i:376797 original size:9 final size:10
Alignment explanation
Indices: 376771--376812 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
376761 AAAATTTGCA
376771 TATTTATATT
1 TATTTATATT
376781 TATTTATATT
1 TATTTATATT
376791 T-TTTATATT
1 TATTTATATT
376800 ATAATTT-TATT
1 -T-ATTTATATT
376811 TA
1 TA
376813 AAATATTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 9 0.31
10 13 0.45
11 4 0.14
12 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TATTTATATT
Found at i:377268 original size:15 final size:16
Alignment explanation
Indices: 377248--377277 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
377238 ATTATTAATT
377248 TTTTAAA-TTTATCAA
1 TTTTAAACTTTATCAA
377263 TTTTAAACTTTATCA
1 TTTTAAACTTTATCA
377278 TTATTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAACTTTATCAA
Found at i:378158 original size:21 final size:21
Alignment explanation
Indices: 378134--378189 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
378124 TTTTTATCCA
*
378134 AATGTATCAATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
378155 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
378176 AATGTATCGATACA
1 AATGTATCGATACA
378190 AGGTCCCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:378272 original size:19 final size:18
Alignment explanation
Indices: 378221--378310 Score: 75
Period size: 19 Copynumber: 5.1 Consensus size: 18
378211 TTGAATTCCA
378221 ATAA-TTTGTATCGATAC
1 ATAAGTTTGTATCGATAC
* *
378238 ATTCAGTAAATGTATCGATAC
1 A-TAAGT--TTGTATCGATAC
378259 ATAAGTGTTGTATCGATAC
1 ATAAGT-TTGTATCGATAC
378278 --AA---TGTATCGATAC
1 ATAAGTTTGTATCGATAC
378291 ATAAGTTTTGTATCGATAC
1 ATAAG-TTTGTATCGATAC
378310 A
1 A
378311 ATGTATCACT
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
13 11 0.19
15 2 0.03
17 3 0.05
18 2 0.03
19 24 0.41
20 4 0.07
21 12 0.21
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
ATAAGTTTGTATCGATAC
Found at i:378285 original size:13 final size:13
Alignment explanation
Indices: 378267--378291 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
378257 ACATAAGTGT
378267 TGTATCGATACAA
1 TGTATCGATACAA
378280 TGTATCGATACA
1 TGTATCGATACA
378292 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:378287 original size:32 final size:32
Alignment explanation
Indices: 378246--378317 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
378236 ACATTCAGTA
378246 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
378278 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
378310 AATGTATC
1 AATGTATC
378318 ACTAGGAAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:384801 original size:27 final size:28
Alignment explanation
Indices: 384731--384802 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 28
384721 TTTTTTTTCC
* **
384731 TCAAAGTCAA-AGTCAATAATCAACCGA
1 TCAAAGTCAATAGTTAATAATCAACAAA
* *
384758 TCAAAATCAAT-GATTAA-AGTCAACAAA
1 TCAAAGTCAATAG-TTAATAATCAACAAA
384785 TCAAAGTCAATAGTTAAT
1 TCAAAGTCAATAGTTAAT
384803 GGTCAAAGTC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
27 31 0.89
28 4 0.11
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.24
Consensus pattern (28 bp):
TCAAAGTCAATAGTTAATAATCAACAAA
Found at i:385825 original size:2 final size:2
Alignment explanation
Indices: 385818--385843 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
385808 TTATTATCAT
385818 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
385844 CACACATCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:387901 original size:21 final size:21
Alignment explanation
Indices: 387875--387927 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
387865 TAATATCCTA
387875 ACAAAAAAAAACCCT-AAAAC
1 ACAAAAAAAAACCCTCAAAAC
* * *
387895 ACTAAAAAAATACCTTCAAATC
1 AC-AAAAAAAAACCCTCAAAAC
387917 ACAAAAAAAAA
1 ACAAAAAAAAA
387928 TGAAAATTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.07
21 19 0.70
22 6 0.22
ACGTcount: A:0.68, C:0.21, G:0.00, T:0.11
Consensus pattern (21 bp):
ACAAAAAAAAACCCTCAAAAC
Found at i:388418 original size:27 final size:28
Alignment explanation
Indices: 388357--388427 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
388347 AAACAAGCCT
*
388357 CCATATTTGACAAATC-CAAAAGAAACCA
1 CCATTTTTGACAAA-CACAAAAGAAACCA
*
388385 CCATTTTTGACAAACACAAAA-TAACCA
1 CCATTTTTGACAAACACAAAAGAAACCA
*
388412 CCATTTTTTACAAACA
1 CCATTTTTGACAAACA
388428 AATGGGTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.46, C:0.25, G:0.04, T:0.24
Consensus pattern (28 bp):
CCATTTTTGACAAACACAAAAGAAACCA
Found at i:388704 original size:22 final size:22
Alignment explanation
Indices: 388674--388728 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
388664 TTCCATTGAA
* *
388674 AATTATTGATTATTTTTTAT-G
1 AATTTTTGATTATTTTTAATAG
*
388695 CAATTTTTGAGCTATTTTTAATAG
1 -AATTTTTGA-TTATTTTTAATAG
388719 AATTTTTGAT
1 AATTTTTGAT
388729 CAAAAATGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 8 0.30
23 18 0.67
24 1 0.04
ACGTcount: A:0.29, C:0.04, G:0.11, T:0.56
Consensus pattern (22 bp):
AATTTTTGATTATTTTTAATAG
Found at i:391101 original size:17 final size:18
Alignment explanation
Indices: 391076--391128 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
391066 CTATCACTCG
*
391076 TTTAAAAAATTATTATTT
1 TTTAAAAAATTATTATTC
* *
391094 TTTTAAAAATTACTATTC
1 TTTAAAAAATTATTATTC
*
391112 TTT-AAAAACTATTATTC
1 TTTAAAAAATTATTATTC
391129 CATTAAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 12 0.40
18 18 0.60
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAAAAAATTATTATTC
Found at i:391101 original size:18 final size:18
Alignment explanation
Indices: 391080--391127 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
391070 CACTCGTTTA
*
391080 AAAAATTATTATTTTTTT
1 AAAAATTATTATTTCTTT
*
391098 AAAAATTACTA-TTCTTT
1 AAAAATTATTATTTCTTT
*
391115 AAAAACTATTATT
1 AAAAATTATTATT
391128 CCATTAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
AAAAATTATTATTTCTTT
Found at i:391564 original size:14 final size:15
Alignment explanation
Indices: 391537--391569 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
391527 ATATTATTAT
391537 TTAAAAAATAATATA
1 TTAAAAAATAATATA
391552 TTAAAAAAT-ATATA
1 TTAAAAAATAATATA
391566 TTAA
1 TTAA
391570 TACTTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAAAAAATAATATA
Found at i:404556 original size:133 final size:133
Alignment explanation
Indices: 404318--404585 Score: 308
Period size: 133 Copynumber: 2.0 Consensus size: 133
404308 ATTTTGATAG
* * * * * ** *
404318 AAAGAGTTTTATCAAGAACAAAGTAGTCGCTAGTATTGAGCAGTTGTTTATGGATAACTCTTTGA
1 AAAGAATTTTACCAAGAACAAAGTAGTCGCTAGTAATGAACACTTGTTTATAAATAACTCTTCGA
* * * *
404383 GCTGCAAGGTTCTTGGCCATAGGAAGGTGATGCTGAAAATAAC-TTCTAAAAAAGAAATAACCTT
66 GCTGCAAGATTCTTGGCCATAGGAAGATGATGCTGAAAATAACTTTCGAAAAAA-AAATAACATT
404447 GAAC
130 GAAC
* * *
404451 AAAGAATTTTACCAAGTACGAAGTAG-CTGCTAGTAAATGAACACTTGTTTATAAATAATTCTTC
1 AAAGAATTTTACCAAGAACAAAGTAGTC-GCTAGT-AATGAACACTTGTTTATAAATAACTCTTC
* * * * *
404515 GAGTTGCAAGATTCTTGGCCTTA-TAAGATGATGTTGAAAATAACTTTCGAAAAAAAACTAACAT
64 GAGCTGCAAGATTCTTGGCCATAGGAAGATGATGCTGAAAATAACTTTCGAAAAAAAAATAACAT
404579 TGAAC
129 TGAAC
404584 AA
1 AA
404586 TATTATTCAT
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
132 1 0.01
133 60 0.54
134 51 0.46
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (133 bp):
AAAGAATTTTACCAAGAACAAAGTAGTCGCTAGTAATGAACACTTGTTTATAAATAACTCTTCGA
GCTGCAAGATTCTTGGCCATAGGAAGATGATGCTGAAAATAACTTTCGAAAAAAAAATAACATTG
AAC
Found at i:408994 original size:25 final size:25
Alignment explanation
Indices: 408966--409017 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
408956 ATATTACATT
408966 TATTATCAATAAAAATTTAAA-AAAA
1 TATTATCAA-AAAAATTTAAATAAAA
**
408991 TATTATTTAAAAAATTTAAATAAAA
1 TATTATCAAAAAAATTTAAATAAAA
409016 TA
1 TA
409018 ATTTTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
TATTATCAAAAAAATTTAAATAAAA
Found at i:409008 original size:24 final size:25
Alignment explanation
Indices: 408976--409026 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
408966 TATTATCAAT
408976 AAAAATTTAAA-AAAAT-ATTATTTA
1 AAAAATTTAAATAAAATAATT-TTTA
409000 AAAAATTTAAATAAAATAATTTTTA
1 AAAAATTTAAATAAAATAATTTTTA
409025 AA
1 AA
409027 TATTTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 11 0.44
25 11 0.44
26 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
AAAAATTTAAATAAAATAATTTTTA
Found at i:409031 original size:24 final size:23
Alignment explanation
Indices: 408975--409032 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 23
408965 TTATTATCAA
408975 TAAAAATTTAAAAAAATATTATT
1 TAAAAATTTAAAAAAATATTATT
408998 TAAAAAATTTAAATAAAATAATT-TT
1 T-AAAAATTTAAA-AAAAT-ATTATT
*
409023 TAAATATTTA
1 TAAAAATTTA
409033 TTTTGTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 1 0.03
24 19 0.61
25 8 0.26
26 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAAAATTTAAAAAAATATTATT
Found at i:409782 original size:20 final size:21
Alignment explanation
Indices: 409759--409806 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
409749 TTAAAAAAAA
*
409759 ATATTATCATA-TTAAAATTT
1 ATATTATAATATTTAAAATTT
*
409779 ATATT-TAATATTTTAAATTT
1 ATATTATAATATTTAAAATTT
409799 A-ATTATAA
1 ATATTATAA
409807 CATAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATTATAATATTTAAAATTT
Found at i:411112 original size:34 final size:34
Alignment explanation
Indices: 411057--411272 Score: 274
Period size: 34 Copynumber: 6.4 Consensus size: 34
411047 ACGTTAAAAC
* * *
411057 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * * *
411090 TGTTGATTAAATGGGTGATTTAGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
411124 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
411157 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
411191 TGTTGATTAAATGGGTGATTTGATGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
411225 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
411259 TGTTGATTAAATGG
1 TGTTGATTAAATGG
411273 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 39 0.24
34 121 0.76
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:411238 original size:68 final size:67
Alignment explanation
Indices: 411057--411274 Score: 294
Period size: 67 Copynumber: 3.2 Consensus size: 67
411047 ACGTTAAAAC
* * * * *
411057 TGTTGATTAAATGGTGATTT-AGTAGTTTACCATTGTTGATTAAATGGGTGATTTAGTGGTTTGC
1 TGTTGATTAAATGGTGATTTGA-TAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
411121 CAT
65 CAT
* * * * *
411124 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGATAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
411189 AT
66 AT
* * *
411191 TGTTGATTAAATGGGTGATTTGATGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGATAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
411256 CAT
65 CAT
411259 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
411275 GTTTTTACCA
Statistics
Matches: 131, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
67 71 0.54
68 60 0.46
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGATAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:411629 original size:19 final size:19
Alignment explanation
Indices: 411573--411635 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
411563 TGGTTGTCGA
**
411573 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
411592 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
411611 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
411630 GTTACT
1 GGTACT
411636 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:415758 original size:34 final size:34
Alignment explanation
Indices: 415701--415918 Score: 278
Period size: 34 Copynumber: 6.5 Consensus size: 34
415691 AAGTGGGAGA
* * *
415701 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * * *
415734 ATTGTTGATTAAATGGGTGATTTAGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
415768 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
415801 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
415835 ATTGTTGATTAAATGGGTGATTTGATGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
415869 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
415903 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
415919 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 41 0.25
34 121 0.75
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:415884 original size:68 final size:67
Alignment explanation
Indices: 415701--415920 Score: 298
Period size: 67 Copynumber: 3.3 Consensus size: 67
415691 AAGTGGGAGA
* * * * *
415701 ATTGTTGATTAAATGGTGATTT-AGTAGTTTACCATTGTTGATTAAATGGGTGATTTAGTGGTTT
1 ATTGTTGATTAAATGGTGATTTGA-TAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
415765 GCC
65 GCC
* * * * *
415768 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGATAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
415833 CC
66 CC
* * *
415835 ATTGTTGATTAAATGGGTGATTTGATGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGATAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
415900 GCC
65 GCC
415903 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
415921 GTTTTTACCA
Statistics
Matches: 133, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
67 73 0.55
68 60 0.45
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGATAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:416409 original size:13 final size:13
Alignment explanation
Indices: 416387--416487 Score: 53
Period size: 13 Copynumber: 8.5 Consensus size: 13
416377 GTTATTGTAA
*
416387 TATATTTTTATAT
1 TATATATTTATAT
*
416400 TATATATTTATGT
1 TATATATTTATAT
*
416413 T-TA-A-TAAT-T
1 TATATATTTATAT
416422 TATATATTTATA-
1 TATATATTTATAT
416434 TAT-T-TTT-TAT
1 TATATATTTATAT
*
416444 TATATATTTTTAAT
1 TATATATTTAT-AT
*
416458 TTTATA-TTATAAT
1 TATATATTTAT-AT
*
416471 TAAATA-TTATAT
1 TATATATTTATAT
416483 T-TATA
1 TATATA
416488 AATAAAAATT
Statistics
Matches: 70, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
9 4 0.06
10 11 0.16
11 7 0.10
12 14 0.20
13 27 0.39
14 7 0.10
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (13 bp):
TATATATTTATAT
Found at i:416418 original size:30 final size:29
Alignment explanation
Indices: 416362--416465 Score: 99
Period size: 29 Copynumber: 3.6 Consensus size: 29
416352 TAAAAATAAT
* *
416362 TTTTTAT-TTATTATAGTTATTGTAATATA
1 TTTTTATATTA-TATATTTATTTTAATATA
416391 TTTTTATATTATATATTTATGTTTAATA-A
1 TTTTTATATTATATATTTAT-TTTAATATA
* *
416420 TTTATATATTTATATATTT-TTTATTATATA
1 TTTTTATA-TTATATATTTATTT-TAATATA
*
416450 TTTTTA-ATTTTATATT
1 TTTTTATATTATATATT
416466 ATAATTAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
28 10 0.16
29 29 0.45
30 25 0.39
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (29 bp):
TTTTTATATTATATATTTATTTTAATATA
Found at i:416446 original size:22 final size:22
Alignment explanation
Indices: 416368--416468 Score: 80
Period size: 22 Copynumber: 4.4 Consensus size: 22
416358 TAATTTTTTA
416368 TTTATTATAGTTATTGTAATATATTT
1 TTTATTATA--TATT-T-ATATATTT
* *
416394 TTATATTATATATTTATGT-TTA
1 TT-TATTATATATTTATATATTT
* *
416416 ATAATTTATATATTTATATATTT
1 TTTA-TTATATATTTATATATTT
*
416439 TTTATTATATATTTTTA-ATTT
1 TTTATTATATATTTATATATTT
*
416460 TATATTATA
1 TTTATTATA
416469 ATTAAATATT
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
21 13 0.21
22 28 0.45
23 7 0.11
24 1 0.02
25 4 0.06
26 2 0.03
27 7 0.11
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (22 bp):
TTTATTATATATTTATATATTT
Found at i:416448 original size:14 final size:14
Alignment explanation
Indices: 416386--416465 Score: 65
Period size: 14 Copynumber: 5.5 Consensus size: 14
416376 AGTTATTGTA
416386 ATATATTTTTATATT
1 ATATATTTTT-TATT
*
416401 ATATATTTATGT-TT
1 ATATATTT-TTTATT
*
416415 A-ATAATTTATATATTT
1 ATAT-ATTT-TTTA-TT
416431 ATATATTTTTTATT
1 ATATATTTTTTATT
*
416445 ATATATTTTTAATT
1 ATATATTTTTTATT
*
416459 TTATATT
1 ATATATT
416466 ATAATTAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
13 2 0.04
14 31 0.56
15 12 0.22
16 8 0.15
17 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (14 bp):
ATATATTTTTTATT
Found at i:416486 original size:19 final size:18
Alignment explanation
Indices: 416459--416499 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
416449 ATTTTTAATT
* *
416459 TTATATTATAATTAAATA
1 TTATATTATAAATAAAAA
416477 TTATATTTATAAATAAAAA
1 TTATA-TTATAAATAAAAA
416496 TTAT
1 TTAT
416500 TAAATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTATATTATAAATAAAAA
Found at i:416533 original size:24 final size:24
Alignment explanation
Indices: 416506--416552 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
416496 TTATTAAATT
*
416506 ATTAATAAT-TAAATAAATTAATCA
1 ATTAA-AATATAAATAAATAAATCA
*
416530 ATTAAAATATAATTAAATAAATC
1 ATTAAAATATAAATAAATAAATC
416553 TAAAATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (24 bp):
ATTAAAATATAAATAAATAAATCA
Found at i:416920 original size:23 final size:21
Alignment explanation
Indices: 416893--416937 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 21
416883 AAAAATTAAA
416893 ATATATTTTATATATTAATATTT
1 ATATATTTTATA-ATTAA-ATTT
416916 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
416937 A
1 A
416938 AATAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 5 0.23
22 5 0.23
23 12 0.55
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:416927 original size:21 final size:23
Alignment explanation
Indices: 416893--416937 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
416883 AAAAATTAAA
416893 ATATATTTTATAT-ATTAATATTT
1 ATATATTTTATATAATTAA-ATTT
416916 ATATA-TTT-TATAATTAAATTT
1 ATATATTTTATATAATTAAATTT
416937 A
1 A
416938 AATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 8 0.38
22 8 0.38
23 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATATATTTTATATAATTAAATTT
Found at i:417372 original size:21 final size:21
Alignment explanation
Indices: 417346--417391 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
417336 TATTGAAAGT
417346 TGCATTTTTTCATCCAAAAAA
1 TGCATTTTTTCATCCAAAAAA
**
417367 TGCA-TTTTTCATCCAACGAA
1 TGCATTTTTTCATCCAAAAAA
417387 TGCAT
1 TGCAT
417392 CATTTCATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.37
Consensus pattern (21 bp):
TGCATTTTTTCATCCAAAAAA
Found at i:417399 original size:21 final size:20
Alignment explanation
Indices: 417353--417404 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
417343 AGTTGCATTT
*
417353 TTTCATCCAAAAAATGCATT
1 TTTCATCCAAAAAATGCATA
**
417373 TTTCATCCAACGAATGCATCA
1 TTTCATCCAAAAAATGCAT-A
*
417394 TTTCATTCAAA
1 TTTCATCCAAA
417405 GATATCTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.35
Consensus pattern (20 bp):
TTTCATCCAAAAAATGCATA
Found at i:418931 original size:257 final size:257
Alignment explanation
Indices: 418469--418987 Score: 887
Period size: 257 Copynumber: 2.0 Consensus size: 257
418459 CATATAATAA
* *
418469 TCTCATATATGATAACCAAAAAATTCCTAGAAATAGTTATTTTAATAGACTGCACTAGGTATATT
1 TCTCATATATGATAACAAAAAAAATCCTAGAAATAGTTATTTTAATAGACTGCACTAGGTATATT
*
418534 TGTAAATCTTGTTGATTTGCACTTAGCAAATGCAATATTTGATCTTATGCAATAAATTGCATATA
66 TGTAAACCTTGTTGATTTGCACTTAGCAAATGCAATATTTGATCTTATGCAATAAATTGCATATA
*
418599 CTAAATTTTCAATTTTTTGAGAATATTTCAATTAAATATTCTCTCACCTTTTTGGACAGATGTAC
131 CTAAATTTTCAATTATTTGAGAATATTTCAATTAAATATTCTCTCACCTTTTTGGACAGATGTAC
*
418664 ACTCAAATCTATTGGTGTTTTGATAATACTATTATCACATTCAAAAAATTTGTTGAGAATTT
196 ACTAAAATCTATTGGTGTTTTGATAATACTATTATCACATTCAAAAAATTTGTTGAGAATTT
* *
418726 TCTCATATATGATAACAAAAAAAATCTTAGAAATAGTTTTTTATAATAGACTGCAC-AGGTATAT
1 TCTCATATATGATAACAAAAAAAATCCTAGAAATAGTTATTT-TAATAGACTGCACTAGGTATAT
*
418790 TTGTAAACCTTGTTGATTTGCACTTAGCAAATGCAATATTTGATCTTATGTAATAAATTGCATAT
65 TTGTAAACCTTGTTGATTTGCACTTAGCAAATGCAATATTTGATCTTATGCAATAAATTGCATAT
* * *
418855 ACTAAGTTTTCAATTATTTGAGAATATTTCAATTGAATATTCTTTCACCTTTTTGGACAGATGTA
130 ACTAAATTTTCAATTATTTGAGAATATTTCAATTAAATATTCTCTCACCTTTTTGGACAGATGTA
* * * *
418920 CACTAAAATCTATTGGTGTTTTGATGATATTATTATCACATTTAGAAAATTTGTTGAGAATTT
195 CACTAAAATCTATTGGTGTTTTGATAATACTATTATCACATTCAAAAAATTTGTTGAGAATTT
418983 TCTCA
1 TCTCA
418988 ACCAAAAAAG
Statistics
Matches: 246, Mismatches: 15, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
257 233 0.95
258 13 0.05
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (257 bp):
TCTCATATATGATAACAAAAAAAATCCTAGAAATAGTTATTTTAATAGACTGCACTAGGTATATT
TGTAAACCTTGTTGATTTGCACTTAGCAAATGCAATATTTGATCTTATGCAATAAATTGCATATA
CTAAATTTTCAATTATTTGAGAATATTTCAATTAAATATTCTCTCACCTTTTTGGACAGATGTAC
ACTAAAATCTATTGGTGTTTTGATAATACTATTATCACATTCAAAAAATTTGTTGAGAATTT
Found at i:423500 original size:2 final size:2
Alignment explanation
Indices: 423493--423545 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
423483 CCACAAAATT
* * *
423493 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TT TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
423535 TA TA TA TA TA T
1 TA TA TA TA TA T
423546 CCATAAAAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:423779 original size:29 final size:29
Alignment explanation
Indices: 423753--423809 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
423743 ATATTTTATT
* *
423753 AAAATT-AAAATTATTTATATTTATTTAAA
1 AAAATTAAAAAATATATATA-TTATTTAAA
423782 AAAATTAAAAAATATATATATTATTTAA
1 AAAATTAAAAAATATATATATTATTTAA
423810 TTTATTAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
AAAATTAAAAAATATATATATTATTTAAA
Found at i:424023 original size:271 final size:269
Alignment explanation
Indices: 423596--424124 Score: 756
Period size: 271 Copynumber: 2.0 Consensus size: 269
423586 TTGAAGAGAA
* * * * * * * *
423596 AGAATTTTCCGAAAAGATACTTTGCATAAAGGAGAGAGGTATACAACGTACCATAGGAAATTTAG
1 AGAATTTTCCAAAAAGACACTTCGCATAAAGGAGAGAGGAATACAAAGTACAAAAGGAAATTTAA
*
423661 GGGTGTCTATTCACGACAGAAAAAAAATTAAAAATTTATTTTTGAAACATTTATAATATATAAAT
66 GGGTGTCTATTCACGACAG-AAAAAAATTAAAAATTTATATTTGAAACATTTATAATATATAAAT
* * *
423726 TATTAAATTGAATGATGATATTTTATTAAAATTAAAATTATTTATATTTATTTAAAAAAATTAAA
130 TATTAAATTAAATAATAATATTTTATTAAAATTAAAATTATTTATATTTATTTAAAAAAATT-AA
* * *
423791 AAATATATATATTATTTAATTTATTAATGATATATATTTATTATTTGTGTACTC-AATATAAAAT
194 AAA-AT-TATATTATTTAATTTATTAATAATATATATTTATTATCTGTGCA-TCAAATATAAAAT
423855 TTGAAAAAAAAAAG
256 TTGAAAAAAAAAAG
*
423869 AGAATTTTTCAAAAAGACACTTCGCATAAAGGAGAGAGGAATACAAAGTACAAAAGGAAATTTAA
1 AGAATTTTCCAAAAAGACACTTCGCATAAAGGAGAGAGGAATACAAAGTACAAAAGGAAATTTAA
*** * * *
423934 GGGTGTCTATTTGTGACAG-AAAAAATTTAAAATTTATATTTGATATATTTATAATATATAAATT
66 GGGTGTCTATTCACGACAGAAAAAAATTAAAAATTTATATTTGAAACATTTATAATATATAAATT
* * * * *
423998 ATTAAATTAAATAATAATATTTTATTATATTTGAAGTTATTTATATTTATTTAAAAATATTAAAA
131 ATTAAATTAAATAATAATATTTTATTAAAATTAAAATTATTTATATTTATTTAAAAAAATTAAAA
424063 AATTATATTATTTAATTTATTAATAATATATATTTATTATCTGTGCATCAAATATAAAATTT
196 AATTATATTATTTAATTTATTAATAATATATATTTATTATCTGTGCATCAAATATAAAATTT
424125 ATTTTATTTT
Statistics
Matches: 228, Mismatches: 27, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
267 2 0.01
268 53 0.23
269 2 0.01
270 5 0.02
271 94 0.41
273 72 0.32
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (269 bp):
AGAATTTTCCAAAAAGACACTTCGCATAAAGGAGAGAGGAATACAAAGTACAAAAGGAAATTTAA
GGGTGTCTATTCACGACAGAAAAAAATTAAAAATTTATATTTGAAACATTTATAATATATAAATT
ATTAAATTAAATAATAATATTTTATTAAAATTAAAATTATTTATATTTATTTAAAAAAATTAAAA
AATTATATTATTTAATTTATTAATAATATATATTTATTATCTGTGCATCAAATATAAAATTTGAA
AAAAAAAAG
Found at i:424939 original size:37 final size:37
Alignment explanation
Indices: 424898--424971 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
424888 TCTTGACTTT
424898 AAAAGTTTTAAATTTTTTGTTTAAGTTCATTTTTAGC
1 AAAAGTTTTAAATTTTTTGTTTAAGTTCATTTTTAGC
424935 AAAAGTTTTAAATTTTTTGTTTAAGTTCATTTTTAGC
1 AAAAGTTTTAAATTTTTTGTTTAAGTTCATTTTTAGC
424972 TTGACCCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (37 bp):
AAAAGTTTTAAATTTTTTGTTTAAGTTCATTTTTAGC
Found at i:424960 original size:20 final size:20
Alignment explanation
Indices: 424900--424961 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
424890 TTGACTTTAA
424900 AAGTTTTAAATTTTTTGTTT
1 AAGTTTTAAATTTTTTGTTT
* * ***
424920 AAG--TT-CATTTTTAGCAA
1 AAGTTTTAAATTTTTTGTTT
424937 AAGTTTTAAATTTTTTGTTT
1 AAGTTTTAAATTTTTTGTTT
424957 AAGTT
1 AAGTT
424962 CATTTTTAGC
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
17 10 0.34
18 2 0.07
19 2 0.07
20 15 0.52
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.56
Consensus pattern (20 bp):
AAGTTTTAAATTTTTTGTTT
Found at i:431610 original size:29 final size:29
Alignment explanation
Indices: 431575--431638 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
431565 ATCACATAAG
431575 TAAAATAATAATATTTTAATAAATAATTT
1 TAAAATAATAATATTTTAATAAATAATTT
* * *
431604 TAAAATAATATTATTTTAATAATTTATTT
1 TAAAATAATAATATTTTAATAAATAATTT
431633 TAAAAT
1 TAAAAT
431639 TAAAATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TAAAATAATAATATTTTAATAAATAATTT
Found at i:431624 original size:14 final size:14
Alignment explanation
Indices: 431578--431635 Score: 66
Period size: 13 Copynumber: 4.1 Consensus size: 14
431568 ACATAAGTAA
*
431578 AATAATAATATTTT
1 AATAATATTATTTT
*
431592 AATAA-ATAATTTT
1 AATAATATTATTTT
431605 AAAATAATATTATTTT
1 --AATAATATTATTTT
431621 AATAAT-TTATTTT
1 AATAATATTATTTT
431634 AA
1 AA
431636 AATTAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 15 0.39
14 11 0.29
15 5 0.13
16 7 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATAATATTATTTT
Found at i:431649 original size:30 final size:29
Alignment explanation
Indices: 431575--431650 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
431565 ATCACATAAG
431575 TAAAATAATAA-TATTTTAATAAATAATTT
1 TAAAATAA-AATTATTTTAATAAATAATTT
* * *
431604 TAAAATAATATTATTTTAATAATTTATTT
1 TAAAATAAAATTATTTTAATAAATAATTT
431633 TAAAATTAAAATTATTTT
1 TAAAA-TAAAATTATTTT
431651 GATTAATCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
28 1 0.02
29 29 0.71
30 11 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TAAAATAAAATTATTTTAATAAATAATTT
Found at i:431891 original size:12 final size:12
Alignment explanation
Indices: 431874--431933 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 12
431864 TTAAAATGAA
431874 TTAAATTTAAAT
1 TTAAATTTAAAT
*
431886 TTAAA--TAATT
1 TTAAATTTAAAT
**
431896 TTTTATTT--AT
1 TTAAATTTAAAT
431906 TTAAATTTAAAT
1 TTAAATTTAAAT
431918 TTAAA-TTAAAT
1 TTAAATTTAAAT
431929 TTAAA
1 TTAAA
431934 AATTATTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
10 14 0.37
11 11 0.29
12 13 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:431928 original size:5 final size:6
Alignment explanation
Indices: 431874--431933 Score: 58
Period size: 6 Copynumber: 10.8 Consensus size: 6
431864 TTAAAATGAA
* **
431874 TTAAAT TTAAAT TTAAA- -TAATT TTTTAT TT--AT TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
431918 TTAAA- TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAA
431934 AATTATTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
4 7 0.16
5 5 0.11
6 33 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:432487 original size:18 final size:18
Alignment explanation
Indices: 432446--432488 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
432436 CTGATAATAC
432446 ATTAATTATAAGTTTTTA
1 ATTAATTATAAGTTTTTA
* *
432464 CTTAATTAT-ATTTTTTA
1 ATTAATTATAAGTTTTTA
432481 ATATAATT
1 AT-TAATT
432489 CACGTAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
ATTAATTATAAGTTTTTA
Found at i:433653 original size:21 final size:20
Alignment explanation
Indices: 433613--433654 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
433603 AATATTAAAA
*
433613 ATATTTTTATATTGATATTT
1 ATATTTTTATATTGAAATTT
433633 ATATATTTTATAATT-AAATTT
1 ATAT-TTTTAT-ATTGAAATTT
433654 A
1 A
433655 AAAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 12 0.63
22 3 0.16
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATATTTTTATATTGAAATTT
Found at i:435727 original size:43 final size:47
Alignment explanation
Indices: 435680--435788 Score: 118
Period size: 44 Copynumber: 2.4 Consensus size: 47
435670 AGGTAGATTG
* *
435680 ATAATTTATTTAT-TTAAATTATATTTATAT-A-TTTTATTATATT-
1 ATAATTTATTTATATTAAATTATATTCATATAATTTTTAATATATTA
* * * **
435723 ATAATTAATATATAATATTTTATATTCATATAATTTTTAATATATTA
1 ATAATTTATTTATATTAAATTATATTCATATAATTTTTAATATATTA
435770 ATAATTTATATTATATTAA
1 ATAATTTAT-TTATATTAA
435789 TTTTAAAACT
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
43 11 0.22
44 13 0.26
45 1 0.02
46 11 0.22
47 8 0.16
48 6 0.12
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (47 bp):
ATAATTTATTTATATTAAATTATATTCATATAATTTTTAATATATTA
Found at i:435728 original size:29 final size:28
Alignment explanation
Indices: 435684--435745 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
435674 AGATTGATAA
*
435684 TTTATTTATTTAAATT-ATATTTATATAT
1 TTTATTTATTTAAATTAATATATA-ATAT
435712 TTTA-TTATATTATAATTAATATATAATAT
1 TTTATTTAT-TTA-AATTAATATATAATAT
435741 TTTAT
1 TTTAT
435746 ATTCATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
27 4 0.14
28 7 0.24
29 12 0.41
30 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTATTTATTTAAATTAATATATAATAT
Found at i:435733 original size:24 final size:24
Alignment explanation
Indices: 435688--435735 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
435678 TGATAATTTA
*
435688 TTTATTTAAATTATATTTATATAT
1 TTTATTTAAATTATATTAATATAT
*
435712 TTTA-TTATATTATAATTAATATAT
1 TTTATTTAAATTAT-ATTAATATAT
435736 AATATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTATTTAAATTATATTAATATAT
Found at i:435741 original size:24 final size:23
Alignment explanation
Indices: 435697--435741 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
435687 ATTTATTTAA
* **
435697 ATTATATTTATATATTTTATTAT
1 ATTATATTAATATATAATATTAT
435720 ATTATAATTAATATATAATATT
1 ATTAT-ATTAATATATAATATT
435742 TTATATTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTATATTAATATATAATATTAT
Found at i:435778 original size:33 final size:32
Alignment explanation
Indices: 435710--435792 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 32
435700 ATATTTATAT
**
435710 ATTT-TATTATATT-ATAATTAATATATAATA
1 ATTTATATTATATTAATTTTTAATATATAATA
*
435740 TTTTATATTCATA-TAATTTTTAATATATTAATA
1 ATTTATATT-ATATTAATTTTTAATATA-TAATA
435773 ATTTATATTATATTAATTTT
1 ATTTATATTATATTAATTTT
435793 AAAACTTACA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
30 3 0.07
31 5 0.11
32 16 0.36
33 20 0.45
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (32 bp):
ATTTATATTATATTAATTTTTAATATATAATA
Found at i:435786 original size:18 final size:18
Alignment explanation
Indices: 435691--435789 Score: 74
Period size: 18 Copynumber: 5.9 Consensus size: 18
435681 TAATTTATTT
* *
435691 ATTTAAATTATATTTATA
1 ATTTATATTATATTAATA
435709 TATTT-TATTATATT-ATA
1 -ATTTATATTATATTAATA
435726 A-TTA-A-TATA-TAATA
1 ATTTATATTATATTAATA
*
435740 TTTTATATTCATA-TAAT-
1 ATTTATATT-ATATTAATA
*
435757 -TTT-TAATATATTAATA
1 ATTTATATTATATTAATA
435773 ATTTATATTATATTAAT
1 ATTTATATTATATTAAT
435790 TTTAAAACTT
Statistics
Matches: 66, Mismatches: 4, Indels: 21
0.73 0.04 0.23
Matches are distributed among these distances:
13 1 0.02
14 10 0.15
15 13 0.20
16 5 0.08
17 7 0.11
18 26 0.39
19 4 0.06
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATATTATATTAATA
Found at i:435789 original size:15 final size:15
Alignment explanation
Indices: 435681--435791 Score: 56
Period size: 15 Copynumber: 7.4 Consensus size: 15
435671 GGTAGATTGA
435681 TAATTTAT-TTAT-T
1 TAATTTATATTATAT
*
435694 TAAATTATATT-TA-
1 TAATTTATATTATAT
435707 TATATTT-TATTATAT
1 TA-ATTTATATTATAT
* *
435722 TATAATTA-ATATATAA
1 TA-ATTTATAT-TATAT
*
435738 TATTTTATATTCATA-
1 TAATTTATATT-ATAT
* *
435753 TAATTTTTAATATATTAA
1 TAATTTAT-AT-TA-TAT
435771 TAATTTATATTATAT
1 TAATTTATATTATAT
435786 TAATTT
1 TAATTT
435792 TAAAACTTAC
Statistics
Matches: 75, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
13 14 0.19
14 7 0.09
15 26 0.35
16 16 0.21
17 5 0.07
18 7 0.09
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.59
Consensus pattern (15 bp):
TAATTTATATTATAT
Found at i:435793 original size:32 final size:32
Alignment explanation
Indices: 435699--435794 Score: 101
Period size: 32 Copynumber: 3.0 Consensus size: 32
435689 TTATTTAAAT
* *
435699 TATATTTATATATTT-TATTATATT-ATAATTAA
1 TATATTAATA-ATTTATATTATATTAAT-TTTAA
*
435731 TATA-TAATATTTTATATTCATA-TAATTTTTAA
1 TATATTAATAATTTATATT-ATATTAA-TTTTAA
435763 TATATTAATAATTTATATTATATTAATTTTAA
1 TATATTAATAATTTATATTATATTAATTTTAA
435795 AACTTACATT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
30 3 0.06
31 9 0.17
32 25 0.46
33 17 0.31
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (32 bp):
TATATTAATAATTTATATTATATTAATTTTAA
Found at i:436165 original size:18 final size:18
Alignment explanation
Indices: 436118--436218 Score: 55
Period size: 18 Copynumber: 5.4 Consensus size: 18
436108 GATTGGTTTG
*
436118 ATAAAATTAATTTTAATAAA
1 ATAAAATTAATTATAAT--A
*
436138 ATAAAA--AATTATGATA
1 ATAAAATTAATTATAATA
*
436154 ATAAAATTAATTATTATAA
1 ATAAAATTAATTATAAT-A
* *
436173 ATATGAAATTAA-AATTAATG
1 ATA--AAATTAATTA-TAATA
* *
436193 ATAAAAATATATTAAAATA
1 ATAAAATTA-ATTATAATA
436212 ATAAAAT
1 ATAAAAT
436219 AATGGTGAGG
Statistics
Matches: 62, Mismatches: 11, Indels: 17
0.69 0.12 0.19
Matches are distributed among these distances:
16 7 0.11
18 20 0.32
19 14 0.23
20 11 0.18
21 10 0.16
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
ATAAAATTAATTATAATA
Found at i:437070 original size:23 final size:21
Alignment explanation
Indices: 437038--437102 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 21
437028 AATTCATAAG
437038 TAAAAGTTTATTTATATTTAATTA
1 TAAAA-TTTATTTATATTT--TTA
**
437062 TAAAATTTATAAATATTTTTA
1 TAAAATTTATTTATATTTTTA
437083 TAAAATATT-TTTATTATTTT
1 TAAAAT-TTATTTA-TATTTT
437103 AATATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 11 0.31
22 8 0.23
23 11 0.31
24 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TAAAATTTATTTATATTTTTA
Found at i:437084 original size:12 final size:13
Alignment explanation
Indices: 437067--437096 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
437057 AATTATAAAA
437067 TTTAT-AAATATT
1 TTTATAAAATATT
437079 TTTATAAAATATT
1 TTTATAAAATATT
437092 TTTAT
1 TTTAT
437097 TATTTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTATAAAATATT
Found at i:437788 original size:15 final size:16
Alignment explanation
Indices: 437752--437793 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
437742 TTTAATATTT
*
437752 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
437769 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
*
437784 ATAAATTTAT
1 ATAAAATTAT
437794 TTAAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 7 0.30
17 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:437811 original size:23 final size:24
Alignment explanation
Indices: 437770--437825 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 24
437760 TTTAATTAAA
**
437770 TAAAATTATAATTAATAAATTTATT
1 TAAAATTAT-ATTAATAAATAAATT
437795 TAAAATTAT-TTAATAAATAAATT
1 TAAAATTATATTAATAAATAAATT
437818 TAAAATTA
1 TAAAATTA
437826 AAATTTAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 20 0.69
25 9 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TAAAATTATATTAATAAATAAATT
Found at i:437814 original size:27 final size:25
Alignment explanation
Indices: 437770--437819 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
437760 TTTAATTAAA
*
437770 TAAAATTATAATTAATAAATTTATT
1 TAAAATTATAATAAATAAATTTATT
437795 TAAAATTATTTAATAAATAAATTTA
1 TAAAATTA--TAATAAATAAATTTA
437820 AAATTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.36
27 14 0.64
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TAAAATTATAATAAATAAATTTATT
Found at i:437859 original size:17 final size:17
Alignment explanation
Indices: 437839--437872 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
437829 TTTAATCATA
437839 TAAAAAATAAAATAAAT
1 TAAAAAATAAAATAAAT
* *
437856 TAAAACATAACATAAAT
1 TAAAAAATAAAATAAAT
437873 ATAATATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAAAAATAAAATAAAT
Found at i:437888 original size:23 final size:23
Alignment explanation
Indices: 437843--437902 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
437833 ATCATATAAA
437843 AAATAAA-ATAA-ATTAAAACAT
1 AAATAAATATAATATTAAAACAT
437864 AACATAAATATAATATTAAAA-AT
1 AA-ATAAATATAATATTAAAACAT
*
437887 AATTAAAATATAATAT
1 AAAT-AAATATAATAT
437903 GACATAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 2 0.06
22 6 0.18
23 19 0.56
24 7 0.21
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (23 bp):
AAATAAATATAATATTAAAACAT
Found at i:438934 original size:21 final size:23
Alignment explanation
Indices: 438888--438944 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
438878 ACACATAATT
* *
438888 TTTTTCTCTTTTTCTTTCTTTCA
1 TTTTTCTTTTTTTCTTCCTTTCA
438911 TTTTTCTTTTTTTC-TCCTTT-A
1 TTTTTCTTTTTTTCTTCCTTTCA
*
438932 TTTCT-TTTTTTTC
1 TTTTTCTTTTTTTC
438945 AGCCCTACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.26
21 5 0.16
22 5 0.16
23 13 0.42
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTCTTTTTTTCTTCCTTTCA
Found at i:439112 original size:22 final size:22
Alignment explanation
Indices: 439078--439121 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
439068 ATACAAACTC
*
439078 AACATATATAAAAAAATTTAAA
1 AACATATATAAAAAAATATAAA
*
439100 AACAGTATA-AAAATAATATAAA
1 AACA-TATATAAAAAAATATAAA
439122 CACTGTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (22 bp):
AACATATATAAAAAAATATAAA
Found at i:439333 original size:35 final size:32
Alignment explanation
Indices: 439294--439380 Score: 88
Period size: 35 Copynumber: 2.6 Consensus size: 32
439284 ATACACGTAC
*
439294 ATATAAAAATATATATAAATTAAAATAAATTATT-A
1 ATATAAAAA-ATATATAAAATAAAAT--ATT-TTAA
*
439329 ATATATAAAAATATATAAAATATAATATTTTAA
1 ATATA-AAAAATATATAAAATAAAATATTTTAA
439362 ATATAAAAAA-ATAATAAAA
1 ATATAAAAAATAT-ATAAAA
439381 ATATGAATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
31 2 0.04
32 13 0.28
33 9 0.19
35 19 0.40
36 4 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (32 bp):
ATATAAAAAATATATAAAATAAAATATTTTAA
Found at i:439396 original size:33 final size:33
Alignment explanation
Indices: 439294--439396 Score: 102
Period size: 33 Copynumber: 3.1 Consensus size: 33
439284 ATACACGTAC
* * * *
439294 ATATAAAAATATATATAAATTAAAATAAATTATTA
1 ATATAAAAAAATATATAAAATATAAT--ATTATAA
* *
439329 ATATATAAAAATATATAAAATATAATATTTTAA
1 ATATAAAAAAATATATAAAATATAATATTATAA
439362 ATATAAAAAAATA-ATAAAAATATGAAT-TTATAA
1 ATATAAAAAAATATAT-AAAATAT-AATATTATAA
439395 AT
1 AT
439397 TTTTTCTCTC
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
32 2 0.03
33 31 0.53
34 3 0.05
35 22 0.38
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (33 bp):
ATATAAAAAAATATATAAAATATAATATTATAA
Found at i:439414 original size:4 final size:4
Alignment explanation
Indices: 439399--439437 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
439389 TTATAAATTT
* *
439399 TTTC TCTC TTTC TTTC TTTC TTTC TTTT TTTC TTT- TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
439438 AGCTGAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:439663 original size:28 final size:29
Alignment explanation
Indices: 439632--439698 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
439622 AATTTTTAGA
* *
439632 TAAAATAATTTTATTAT-TTTTACTATTT
1 TAAAATAATTTTATGATATTTTAATATTT
* *
439660 TAAATATATTTTTATGATATTTTAATTTTT
1 TAAA-ATAATTTTATGATATTTTAATATTT
*
439690 TATAATAAT
1 TAAAATAAT
439699 ATCAAATACT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 4 0.13
29 15 0.48
30 12 0.39
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (29 bp):
TAAAATAATTTTATGATATTTTAATATTT
Found at i:440810 original size:29 final size:28
Alignment explanation
Indices: 440689--440814 Score: 94
Period size: 29 Copynumber: 4.4 Consensus size: 28
440679 TTCTCAACTT
*
440689 TATTAATTTAC--TTAAATAAATTTATA
1 TATTAATTTACATTTAAATAAATTTTTA
** *
440715 TATTTTTATTGCATTTAAATAAATTTTTAA
1 TATTAAT-TTACATTTAAATAAATTTTT-A
* ** **
440745 TTTTTAAATTTACATTTAAATATGTCATTA
1 -TATT-AATTTACATTTAAATAAATTTTTA
*
440775 TATTTAATTTACATTCAAATAAATTTTTA
1 TA-TTAATTTACATTTAAATAAATTTTTA
440804 CTATTAATTTA
1 -TATTAATTTA
440815 TACATAATAT
Statistics
Matches: 74, Mismatches: 18, Indels: 13
0.70 0.17 0.12
Matches are distributed among these distances:
26 5 0.07
27 3 0.04
29 41 0.55
30 6 0.08
31 18 0.24
32 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.53
Consensus pattern (28 bp):
TATTAATTTACATTTAAATAAATTTTTA
Found at i:440881 original size:14 final size:15
Alignment explanation
Indices: 440856--440900 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
440846 ATTTTTTATT
440856 TAAAATAAAAATTTA
1 TAAAATAAAAATTTA
*
440871 TATAA-AAAAATTTA
1 TAAAATAAAAATTTA
*
440885 AAAAATAAAAATTTA
1 TAAAATAAAAATTTA
440900 T
1 T
440901 TTTAATACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATAAAAATTTA
Found at i:440894 original size:15 final size:15
Alignment explanation
Indices: 440857--440899 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
440847 TTTTTTATTT
*
440857 AAAATAAAAATTTAT
1 AAAATAAAAATTTAA
*
440872 ATAA-AAAAATTTAA
1 AAAATAAAAATTTAA
440886 AAAATAAAAATTTA
1 AAAATAAAAATTTA
440900 TTTTAATACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATAAAAATTTAA
Found at i:441064 original size:14 final size:14
Alignment explanation
Indices: 441047--441074 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
441037 TTTTTGTTTA
441047 AATATAATTTACAT
1 AATATAATTTACAT
441061 AATATAATTTACAT
1 AATATAATTTACAT
441075 TTTCAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATAATTTACAT
Found at i:442832 original size:16 final size:17
Alignment explanation
Indices: 442811--442842 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
442801 TAAAATATTT
442811 ATATAAA-TTTAATATC
1 ATATAAATTTTAATATC
442827 ATATAAATTTTAATAT
1 ATATAAATTTTAATAT
442843 ATTTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATAAATTTTAATATC
Found at i:442881 original size:19 final size:18
Alignment explanation
Indices: 442798--442881 Score: 73
Period size: 19 Copynumber: 4.6 Consensus size: 18
442788 TTACGTAAGT
*
442798 TTTTAAAATATTTATATAA
1 TTTTAATATATTTATAT-A
* *
442817 ATTTAATATCA--TATAAA
1 TTTTAATAT-ATTTATATA
442834 TTTTAATATATTTATATA
1 TTTTAATATATTTATATA
*
442852 TTTAAATTATATTTATATTA
1 TTTTAA-TATATTTATA-TA
*
442872 TTTTTATATA
1 TTTTAATATA
442882 ATATTTTAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
16 1 0.02
17 9 0.17
18 14 0.27
19 21 0.40
20 7 0.13
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAATATATTTATATA
Found at i:442912 original size:61 final size:60
Alignment explanation
Indices: 442834--442965 Score: 144
Period size: 62 Copynumber: 2.2 Consensus size: 60
442824 ATCATATAAA
* * * *
442834 TTTTAATATATTTATATATT-TA-AATTATATTTATATTATT-TTTATATAATATTTTAATTATT
1 TTTTAATATA-CTATATATTACATAATTAT-TTTATATGATTAATTAT-T-ATATTTTAA-TATT
* *
442896 TTTTCATATACTATATATTACATAATTATTTTATATGATTAATTATTATATTTTTATATT
1 TTTTAATATACTATATATTACATAATTATTTTATATGATTAATTATTATATTTTAATATT
442956 TTTTAATATA
1 TTTTAATATA
442966 AAAATTTTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
60 13 0.22
61 16 0.27
62 21 0.35
63 10 0.17
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (60 bp):
TTTTAATATACTATATATTACATAATTATTTTATATGATTAATTATTATATTTTAATATT
Found at i:442915 original size:22 final size:21
Alignment explanation
Indices: 442864--442915 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
442854 TAAATTATAT
442864 TTATATTATTTTTATATAATA
1 TTATATTATTTTTATATAATA
* *
442885 TTTTAATTATTTTTTCATATACTA
1 TTAT-ATTA-TTTTT-ATATAATA
442909 -TATATTA
1 TTATATTA
442916 CATAATTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
23 7 0.28
24 7 0.28
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATATTATTTTTATATAATA
Found at i:442943 original size:20 final size:20
Alignment explanation
Indices: 442907--442955 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
442897 TTTCATATAC
442907 TATATATTACATAATTATTT
1 TATATATTACATAATTATTT
*
442927 TATATGATTA-ATTATTATATT
1 TATAT-ATTACATAATTAT-TT
*
442948 TTTATATT
1 TATATATT
442956 TTTTAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
TATATATTACATAATTATTT
Found at i:443245 original size:17 final size:17
Alignment explanation
Indices: 443219--443251 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
443209 TACATATCTC
443219 ATTTTAATTTTTAATTA
1 ATTTTAATTTTTAATTA
*
443236 ATTTTTATTTTTAATT
1 ATTTTAATTTTTAATT
443252 TATCTTAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTAATTTTTAATTA
Found at i:445308 original size:13 final size:13
Alignment explanation
Indices: 445292--445321 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
445282 TATTAGTATC
445292 TGATATTTATGTT
1 TGATATTTATGTT
445305 TGATATTTATGTT
1 TGATATTTATGTT
445318 TGAT
1 TGAT
445322 TTATAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (13 bp):
TGATATTTATGTT
Done.