Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold472
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: 529027
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:360010 original size:20 final size:20
Alignment explanation
Indices: 359967--360012 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
359957 AAATCTTTTG
359967 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
359988 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
360008 CAAAA
1 CAAAA
360013 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:362409 original size:13 final size:13
Alignment explanation
Indices: 362391--362416 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
362381 TACACCAAGT
362391 ATGTATCGATACA
1 ATGTATCGATACA
362404 ATGTATCGATACA
1 ATGTATCGATACA
362417 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:362414 original size:32 final size:33
Alignment explanation
Indices: 362373--362436 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
362363 TAGCCAAACT
* **
362373 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
362405 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
362437 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:363537 original size:140 final size:143
Alignment explanation
Indices: 363349--363643 Score: 395
Period size: 140 Copynumber: 2.1 Consensus size: 143
363339 GTTAACATTT
* * *
363349 ATTTATTATTTTATTTTTGTATTCTCAGAAATTTCATTTCGTACCTTAATA-AGGACCCAA-AAA
1 ATTT-TTATTTAATTTTTGTATTCTCAGAAAATTCATTTCGTACCTTAATAGAGAACCCAACAAA
* * * *
363412 TATGCAAAAAGATTTGAAGATTTCTATACCCTTGCG-AAAACTATAGAAATATTAAAAAT-CTAA
65 TATG--AAAAGATTTGAAGATTTCTACACCCCTACGAAAAACCATAGAAATATTAAAAATACTAA
363475 AAAAATTAAGATAATA
128 AAAAATTAAGATAATA
* * *
363491 ATTTTTATTTAATTTTT-TAATTTTCA-AAAATTCATTTCGTACCTTAATAGAGAACCGAACAGA
1 ATTTTTATTTAATTTTTGT-ATTCTCAGAAAATTCATTTCGTACCTTAATAGAGAACCCAACAAA
* * *
363554 TATGAAAAGTTTTGAAGATTTCTACACCCCTACGAAAAACCATAGGAATATTAAAAATATTAAAA
65 TATGAAAAGATTTGAAGATTTCTACACCCCTACGAAAAACCATAGAAATATTAAAAATACTAAAA
363619 AAATTAAGATAATA
130 AAATTAAGATAATA
363633 ATTTTTATTTA
1 ATTTTTATTTA
363644 GTGATAAAAT
Statistics
Matches: 135, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
140 49 0.36
141 46 0.34
142 40 0.30
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.37
Consensus pattern (143 bp):
ATTTTTATTTAATTTTTGTATTCTCAGAAAATTCATTTCGTACCTTAATAGAGAACCCAACAAAT
ATGAAAAGATTTGAAGATTTCTACACCCCTACGAAAAACCATAGAAATATTAAAAATACTAAAAA
AATTAAGATAATA
Found at i:364359 original size:11 final size:11
Alignment explanation
Indices: 364343--364392 Score: 68
Period size: 10 Copynumber: 4.7 Consensus size: 11
364333 GTTTTTTATA
364343 TTTTCTCTCTT
1 TTTTCTCTCTT
*
364354 TTTTCTTTC-T
1 TTTTCTCTCTT
*
364364 TTTTCTTTCTT
1 TTTTCTCTCTT
364375 TTTTCTCT-TT
1 TTTTCTCTCTT
364385 TTTTCTCT
1 TTTTCTCT
364393 ACTTGCTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
10 20 0.56
11 16 0.44
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTCTCTCTT
Found at i:364369 original size:21 final size:21
Alignment explanation
Indices: 364343--364392 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
364333 GTTTTTTATA
364343 TTTTCTCTCTTTTTTCT-TTCT
1 TTTTCTCTCTTTTTTCTCTT-T
*
364364 TTTTCTTTCTTTTTTCTCTTT
1 TTTTCTCTCTTTTTTCTCTTT
364385 TTTTCTCT
1 TTTTCTCT
364393 ACTTGCTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTCTCTCTTTTTTCTCTTT
Found at i:365088 original size:166 final size:163
Alignment explanation
Indices: 364876--365302 Score: 422
Period size: 166 Copynumber: 2.6 Consensus size: 163
364866 AATATAAACA
* * *
364876 AAAAAATTCAAAATTCGTGAAATAATTTA-AATTTTTCAAAACTGATTTAATGTGAATTTAATGA
1 AAAAAA-TGAAAATTCGTGAAATAA-CTAGAAATTTTCAAAACTGATTTAATGTGAATTTAATGA
* * *
364940 GAATATTAGATGAATTTTAAAAATTTTAAACAAAGAAAAATTTTCTT-GAAAATATTTA-GGGAT
64 CAATATTA-ATGAATTTTAAAAATTTTAAAC-AAGAAAAA-TTTCTTCGAAAACATTTATGGAAT
*
365003 AGAAAACTCAATTTTTCGAAAATAG-GAAAATTTCAAAAG
126 AGAAAACTCAATTTTTCGAAAACAGAG-AAATTT-AAAAG
* * * *
365042 AAAAAATGAAAAACTT-TTGAAAATGAA-T-GAAATTTTCAAAACTGATTTAAAAG-GAGTCTAA
1 AAAAAATG-AAAA-TTCGTG-AAAT-AACTAGAAATTTTCAAAACTGATTT-AATGTGAATTTAA
* * *
365103 TGACAATGTTATATGAATTTTAAAAACTTTGAATCAAGAAAAATTTCTTCGAAAACATTTATGGA
61 TGACAATATTA-ATGAATTTTAAAAA-TTTTAAACAAGAAAAATTTCTTCGAAAACATTTATGGA
* * * *
365168 ATAGAAAATTCAGTTTTTTGAAAACAGAGACATTTAAAAG
124 ATAGAAAACTCAATTTTTCGAAAACAGAGAAATTTAAAAG
* * * *
365208 AAAAAATGAAAATTCGGTGAAATAACTAGAATTTTTCAAAACTAATTTAATAGTG-ATTAAATAA
1 AAAAAATGAAAATTC-GTGAAATAACTAGAAATTTTCAAAACTGATTTAAT-GTGAATTTAATGA
* *
365272 TAACATTTAATGAATTTTAAAAATTTTAAAC
64 CAATA-TTAATGAATTTTAAAAATTTTAAAC
365303 CAATTAAAAT
Statistics
Matches: 213, Mismatches: 31, Indels: 35
0.76 0.11 0.13
Matches are distributed among these distances:
164 4 0.02
165 24 0.11
166 133 0.62
167 49 0.23
168 3 0.01
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.33
Consensus pattern (163 bp):
AAAAAATGAAAATTCGTGAAATAACTAGAAATTTTCAAAACTGATTTAATGTGAATTTAATGACA
ATATTAATGAATTTTAAAAATTTTAAACAAGAAAAATTTCTTCGAAAACATTTATGGAATAGAAA
ACTCAATTTTTCGAAAACAGAGAAATTTAAAAG
Found at i:366289 original size:38 final size:38
Alignment explanation
Indices: 366159--366327 Score: 141
Period size: 38 Copynumber: 4.5 Consensus size: 38
366149 ACATCACCGA
* * **
366159 TTAAGAATAGT-AGTTTTTGTTTCGAACCGTGCCATTAG
1 TTAAGAATAGTGA-TTTTTGTTTCAAACTGTGCCAACAG
* *
366197 TTTAA-AATAGT-AGTTTTTGTTTCAAACTATGCC-ACCG
1 -TTAAGAATAGTGA-TTTTTGTTTCAAACTGTGCCAACAG
* * * *
366234 ATAAGAATAATGGTTTTTG-TTCTAAACTGTGCCAACGG
1 TTAAGAATAGTGATTTTTGTTTC-AAACTGTGCCAACAG
* * *
366272 TTAAGAATAGTGATTTTTGTTTCGAACTGTTCCACCAG
1 TTAAGAATAGTGATTTTTGTTTCAAACTGTGCCAACAG
*
366310 TTGAGAATAGTGATTTTT
1 TTAAGAATAGTGATTTTT
366328 ATTCTGATCT
Statistics
Matches: 106, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
36 6 0.06
37 21 0.20
38 72 0.68
39 7 0.07
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (38 bp):
TTAAGAATAGTGATTTTTGTTTCAAACTGTGCCAACAG
Found at i:370061 original size:15 final size:15
Alignment explanation
Indices: 370038--370071 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
370028 ACTTAATTTA
*
370038 AGTTGAGTCATTTTG
1 AGTTAAGTCATTTTG
370053 AGTTAAGTCATTTTG
1 AGTTAAGTCATTTTG
370068 AGTT
1 AGTT
370072 TAGGTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (15 bp):
AGTTAAGTCATTTTG
Found at i:370281 original size:35 final size:35
Alignment explanation
Indices: 370241--370362 Score: 93
Period size: 35 Copynumber: 3.3 Consensus size: 35
370231 TATAATAATG
370241 TTTATGTAATTTTGATAAAAATTCTTAGGTAATAT
1 TTTATGTAATTTTGATAAAAATTCTTAGGTAATAT
* * * * ** *
370276 TTTATGTAACTAGTAATGTTTATATATAATGT-GATAATAT
1 TTTATGTAA-T--T-TTG-ATAAAAATTCT-TAGGTAATAT
** *
370316 TTTATGTAATTTTGAGGAAAATTCTTAAGTAATAT
1 TTTATGTAATTTTGATAAAAATTCTTAGGTAATAT
370351 TTTATGTAATTT
1 TTTATGTAATTT
370363 ATAATATTTT
Statistics
Matches: 63, Mismatches: 17, Indels: 14
0.67 0.18 0.15
Matches are distributed among these distances:
34 1 0.02
35 31 0.49
36 3 0.05
37 1 0.02
38 1 0.02
39 3 0.05
40 22 0.35
41 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.49
Consensus pattern (35 bp):
TTTATGTAATTTTGATAAAAATTCTTAGGTAATAT
Found at i:370381 original size:75 final size:77
Alignment explanation
Indices: 370232--370381 Score: 207
Period size: 75 Copynumber: 2.0 Consensus size: 77
370222 TATATGTGAT
* * *
370232 ATAATAATGTTTATGTAATTTTGATAAAAATTCTTAGGTAATATTTTATGTAACTAGTAATGTTT
1 ATAATAATGTTTATGTAATTTTGAGAAAAATTCTTAAGTAATATTTTATGTAACTAGTAATATTT
370297 ATATATAATGTG
66 ATATATAATGTG
* *
370309 ATAAT-AT-TTTATGTAATTTTGAGGAAAATTCTTAAGTAATATTTTATGTAATTTA-TAATATT
1 ATAATAATGTTTATGTAATTTTGAGAAAAATTCTTAAGTAATATTTTATGTAA-CTAGTAATATT
* *
370371 TTTATGTAATG
65 TATATATAATG
370382 CGGTAAGGTA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
75 56 0.86
76 4 0.06
77 5 0.08
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (77 bp):
ATAATAATGTTTATGTAATTTTGAGAAAAATTCTTAAGTAATATTTTATGTAACTAGTAATATTT
ATATATAATGTG
Found at i:370405 original size:75 final size:75
Alignment explanation
Indices: 370235--370405 Score: 170
Period size: 75 Copynumber: 2.3 Consensus size: 75
370225 ATGTGATATA
* * ** * *
370235 ATAATGTT-TATGTAATTTTGATAAAAATTCTTAGGTAATATTTTATGTAACTAGTAATGTTTAT
1 ATAATATTATATGTAACTTTGAGGAAAATTCTTAAGTAATATTTTATGTAACTAGTAATATTTAT
*
370299 ATATAATGTG
66 ATATAATGCG
* * * *
370309 ATAATATTTTATGTAATTTTGAGGAAAATTCTTAAGTAATATTTTATGTAATTTA-TAATATTTT
1 ATAATATTATATGTAACTTTGAGGAAAATTCTTAAGTAATATTTTATGTAA-CTAGTAATATTTA
*
370373 TATGTAATGCG
65 TATATAATGCG
*
370384 GTAAGGTATTATA-G-AACTTTGA
1 ATAA--TATTATATGTAACTTTGA
370406 TGAACCACAT
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
74 7 0.09
75 65 0.80
76 3 0.04
77 6 0.07
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (75 bp):
ATAATATTATATGTAACTTTGAGGAAAATTCTTAAGTAATATTTTATGTAACTAGTAATATTTAT
ATATAATGCG
Found at i:371466 original size:2 final size:2
Alignment explanation
Indices: 371459--371483 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
371449 TTAAGTAATG
371459 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
371484 GTAACTGCAA
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:371651 original size:25 final size:23
Alignment explanation
Indices: 371603--371652 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
371593 ATATCTAGGT
**
371603 AATTGAAATAATATTGTATTAAA
1 AATTGAAATAATATTGTAAAAAA
371626 AATTGAAAATAATATGTGTAAAAAA
1 AATTG-AAATAATAT-TGTAAAAAA
371651 AA
1 AA
371653 GATTAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.22
24 9 0.39
25 9 0.39
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (23 bp):
AATTGAAATAATATTGTAAAAAA
Found at i:372394 original size:22 final size:22
Alignment explanation
Indices: 372369--372415 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
372359 ATATTAAAAT
*
372369 TATTTTTA-CATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
372391 TATTTTTATAATTAAATTTATA
1 TATTTTTATAATTAAATTTATA
372413 TAT
1 TAT
372416 ATAAATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:372414 original size:14 final size:14
Alignment explanation
Indices: 372392--372491 Score: 53
Period size: 14 Copynumber: 6.7 Consensus size: 14
372382 ATATTTATAT
*
372392 ATTTTTATAATTAA
1 ATTTATATAATTAA
372406 ATTTATAT-ATATAA
1 ATTTATATAAT-TAA
372420 ATATTATTATTAATTAA
1 AT-TTA-TA-TAATTAA
*
372437 ATATTAAATAATATTAA
1 AT-TTATAT-A-ATTAA
*
372454 A-TTA-ATATTTATA
1 ATTTATATAATTA-A
*
372467 TATTTTTATAATTAA
1 -ATTTATATAATTAA
*
372482 ATTTAAATAA
1 ATTTATATAA
372492 AAATATTATT
Statistics
Matches: 68, Mismatches: 7, Indels: 22
0.70 0.07 0.23
Matches are distributed among these distances:
12 3 0.04
13 4 0.06
14 23 0.34
15 10 0.15
16 10 0.15
17 16 0.24
18 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTTATATAATTAA
Found at i:372424 original size:38 final size:38
Alignment explanation
Indices: 372381--372498 Score: 120
Period size: 38 Copynumber: 3.2 Consensus size: 38
372371 TTTTTACATT
372381 AATATTTATATATTTTTATAATTAAATTTATATATATA
1 AATATTTATATATTTTTATAATTAAATTTATATATATA
* * * * *
372419 AATA-TTAT-TATTAATTAAATATTAAA-TAATATTAAATT
1 AATATTTATATATT-TTTATA-ATTAAATTTATA-TATATA
*
372457 AATATTTATATATTTTTATAATTAAATTTA-A-ATAAA
1 AATATTTATATATTTTTATAATTAAATTTATATATATA
372493 AATATT
1 AATATT
372499 ATTTTTTTAA
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
36 12 0.19
37 12 0.19
38 25 0.40
39 10 0.16
40 4 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (38 bp):
AATATTTATATATTTTTATAATTAAATTTATATATATA
Found at i:372449 original size:10 final size:11
Alignment explanation
Indices: 372422--372462 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
372412 ATATATAAAT
*
372422 ATTATTATT-A
1 ATTAATATTAA
372432 ATTAAATATTAA
1 ATT-AATATTAA
372444 A-TAATATTAA
1 ATTAATATTAA
372454 ATTAATATT
1 ATTAATATT
372463 TATATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 12 0.44
11 13 0.48
12 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTAATATTAA
Found at i:372464 original size:76 final size:76
Alignment explanation
Indices: 372378--372519 Score: 225
Period size: 76 Copynumber: 1.9 Consensus size: 76
372368 TTATTTTTAC
*
372378 ATTAATATTTATATATTTTTATAATTAAATTTATATATATAAATATTA-TTATTAATTAAA-TAT
1 ATTAATATTTATATATTTTTATAATTAAATTTA-A-ATAAAAATATTATTTATTAATTAAATTAT
372441 TAAATAATATTAA
64 TAAATAATATTAA
*
372454 ATTAATATTTATATATTTTTATAATTAAATTTAAATAAAAATATTATTTTTTTAATTAAATTATT
1 ATTAATATTTATATATTTTTATAATTAAATTTAAATAAAAATATTA-TTTATTAATTAAATTATT
372519 A
65 A
372520 TCGAATCAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
74 11 0.18
75 1 0.02
76 44 0.72
77 5 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (76 bp):
ATTAATATTTATATATTTTTATAATTAAATTTAAATAAAAATATTATTTATTAATTAAATTATTA
AATAATATTAA
Found at i:373106 original size:3 final size:3
Alignment explanation
Indices: 373098--373134 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
373088 TTTTATGACC
373098 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
373135 ATAAAAATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:376804 original size:1 final size:1
Alignment explanation
Indices: 376798--376822 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
376788 CGCGTCTCTT
376798 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
376823 ACAATTCCGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:381005 original size:2 final size:2
Alignment explanation
Indices: 380998--381024 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
380988 ATTGCGATTC
380998 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
381025 GTTTGACTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:381547 original size:16 final size:16
Alignment explanation
Indices: 381521--381557 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
381511 TCCGAACATA
*
381521 AAAATATTCTTAATCT
1 AAAATAATCTTAATCT
*
381537 GAAATAATCTTAATCT
1 AAAATAATCTTAATCT
381553 AAAAT
1 AAAAT
381558 TACTCAAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.38
Consensus pattern (16 bp):
AAAATAATCTTAATCT
Found at i:383140 original size:2 final size:2
Alignment explanation
Indices: 383133--383159 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
383123 ATTTTCTAAT
383133 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
383160 GCCAAAACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:385717 original size:25 final size:25
Alignment explanation
Indices: 385668--385716 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
385658 ATTGAAGCTT
*
385668 TTCAAGAGTTTCTCATTAAAAAAAA
1 TTCAAGAATTTCTCATTAAAAAAAA
*
385693 TTCAAGAATTTCT-TTTAAAAAAAA
1 TTCAAGAATTTCTCATTAAAAAAAA
385717 AATTAACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (25 bp):
TTCAAGAATTTCTCATTAAAAAAAA
Found at i:386111 original size:2 final size:2
Alignment explanation
Indices: 386104--386135 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
386094 TCTAGTTTAT
386104 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
386136 ATAAACGCTT
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):
TA
Found at i:386557 original size:4 final size:4
Alignment explanation
Indices: 386531--386573 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
386521 TCAAGACTAT
* * * *
386531 TATA TACA TACA TACA TACA TATA TATA TATA TATA TATA TAT
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TAT
386574 TTTTTTCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (4 bp):
TATA
Found at i:386573 original size:12 final size:12
Alignment explanation
Indices: 386531--386572 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
386521 TCAAGACTAT
*
386531 TATATACATACA
1 TATATACATATA
*
386543 TACATACATATA
1 TATATACATATA
*
386555 TATATATATATA
1 TATATACATATA
386567 TATATA
1 TATATA
386573 TTTTTTTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (12 bp):
TATATACATATA
Found at i:388145 original size:2 final size:2
Alignment explanation
Indices: 388133--388171 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
388123 ATTTAATTTA
*
388133 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
388172 ATTTTCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:389171 original size:2 final size:2
Alignment explanation
Indices: 389166--389197 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
389156 GATATATGTG
389166 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
389198 GGAGTTGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:391105 original size:13 final size:13
Alignment explanation
Indices: 391087--391119 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
391077 ATAAAAAGAT
391087 ATATATCTTT-AAA
1 ATATAT-TTTAAAA
391100 ATATATTTTAAAA
1 ATATATTTTAAAA
391113 ATATATT
1 ATATATT
391120 AAATGGGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 3 0.16
13 16 0.84
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATTTTAAAA
Found at i:391681 original size:24 final size:23
Alignment explanation
Indices: 391627--391681 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
391617 AAATTAAAAT
391627 TTTAAATATTAATATAATATATA
1 TTTAAATATTAATATAATATATA
*
391650 -TTAAATATT-TTATAATATTTATA
1 TTTAAATATTAATATAATA--TATA
391673 TTTAAATAT
1 TTTAAATAT
391682 ATCATACTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 7 0.25
22 9 0.32
23 4 0.14
24 8 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTAAATATTAATATAATATATA
Found at i:391696 original size:24 final size:24
Alignment explanation
Indices: 391644--391698 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
391634 ATTAATATAA
* * *
391644 TATATATTAAATATTTTATAATATT
1 TATAT-TTAAATATATCATAATATC
*
391669 TATATTTAAATATATCATACTATC
1 TATATTTAAATATATCATAATATC
391693 TATATT
1 TATATT
391699 ATTATATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (24 bp):
TATATTTAAATATATCATAATATC
Found at i:392029 original size:31 final size:29
Alignment explanation
Indices: 391991--392051 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 29
391981 TTAAATTATT
391991 TTTTAAATAAAAA-ACTTTAATATTTAAAAAA
1 TTTTAAATAAAAATA--TTAA-ATTTAAAAAA
392022 TTTTAAATAAAAATATTAAATTTAAAAAA
1 TTTTAAATAAAAATATTAAATTTAAAAAA
392051 T
1 T
392052 AAATTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 11 0.38
30 4 0.14
31 13 0.45
32 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (29 bp):
TTTTAAATAAAAATATTAAATTTAAAAAA
Found at i:392047 original size:19 final size:19
Alignment explanation
Indices: 392023--392061 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
392013 TTTAAAAAAT
*
392023 TTTAAATAA-AAATATTAAA
1 TTTAAAAAATAAAT-TTAAA
392042 TTTAAAAAATAAATTTAAA
1 TTTAAAAAATAAATTTAAA
392061 T
1 T
392062 AAATTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TTTAAAAAATAAATTTAAA
Found at i:392929 original size:17 final size:18
Alignment explanation
Indices: 392907--392944 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
392897 ACTTCAATGG
392907 CAGTAGCA-GTGCAGCTT
1 CAGTAGCAGGTGCAGCTT
392924 CAGTAGCAGGTGCAGCTT
1 CAGTAGCAGGTGCAGCTT
392942 CAG
1 CAG
392945 ATCATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.21
Consensus pattern (18 bp):
CAGTAGCAGGTGCAGCTT
Found at i:394210 original size:13 final size:13
Alignment explanation
Indices: 394192--394216 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
394182 ATTTTGCTTA
394192 GTATCGATACATT
1 GTATCGATACATT
394205 GTATCGATACAT
1 GTATCGATACAT
394217 AAAACTGACA
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):
GTATCGATACATT
Found at i:394261 original size:10 final size:10
Alignment explanation
Indices: 394246--394298 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
394236 TCTCATTTTT
394246 TCACTGTTCA
1 TCACTGTTCA
394256 TCACTGTTCA
1 TCACTGTTCA
* * *
394266 TGTATTGATACA
1 T-CACTG-TTCA
394278 TCACTGTTCA
1 TCACTGTTCA
394288 TCACTGTTCA
1 TCACTGTTCA
394298 T
1 T
394299 GTATCGACAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 25 0.71
11 6 0.17
12 4 0.11
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:399403 original size:13 final size:13
Alignment explanation
Indices: 399372--399412 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
399362 AGGGTTATAA
399372 AAAATTATAAATATT
1 AAAATT-TAAAT-TT
399387 AAAATTTAAATTT
1 AAAATTTAAATTT
*
399400 AAAATTAAAATTT
1 AAAATTTAAATTT
399413 TTTAAATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 14 0.56
14 5 0.20
15 6 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAAATTTAAATTT
Found at i:402423 original size:19 final size:17
Alignment explanation
Indices: 402394--402463 Score: 60
Period size: 18 Copynumber: 4.2 Consensus size: 17
402384 AAATTATACT
402394 AAATAATTA-ATATTATAA
1 AAAT-ATTATATATTA-AA
402412 AAATATTATA-ATTAAA
1 AAATATTATATATTAAA
402428 TAAA-A-TAT-TATTAAA
1 -AAATATTATATATTAAA
*
402443 AAATATAATAATATTAAA
1 AAATATTAT-ATATTAAA
402461 AAA
1 AAA
402464 ATAGCAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
14 3 0.07
15 10 0.23
16 5 0.11
17 11 0.25
18 15 0.34
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATTATATATTAAA
Found at i:402446 original size:18 final size:18
Alignment explanation
Indices: 402411--402463 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
402401 TAATATTATA
*
402411 AAAATATTA-TAATTAAAT
1 AAAATATTATTAA-AAAAT
402429 AAAATATTATTAAAAAAT
1 AAAATATTATTAAAAAAT
* *
402447 ATAATAATATTAAAAAA
1 AAAATATTATTAAAAAA
402464 ATAGCAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 28 0.90
19 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATATTATTAAAAAAT
Found at i:402455 original size:21 final size:18
Alignment explanation
Indices: 402427--402466 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
402417 TTATAATTAA
402427 ATAAAATATTATTAAAAAAT
1 ATAAAATATTA--AAAAAAT
402447 ATAATAATATTAAAAAAAT
1 ATAA-AATATTAAAAAAAT
402466 A
1 A
402467 GCAAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 4 0.21
21 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAAAATATTAAAAAAAT
Found at i:402461 original size:29 final size:29
Alignment explanation
Indices: 402393--402454 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 29
402383 AAAATTATAC
402393 TAAATAATTAATATTATAAAAATATTATAAT
1 TAAATAA--AATATTATAAAAATATTATAAT
*
402424 TAAATAAAATATTATTAAAAAATATAATAAT
1 TAAATAAAATATTA-T-AAAAATATTATAAT
402455 ATTAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.25
30 1 0.04
31 20 0.71
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
TAAATAAAATATTATAAAAATATTATAAT
Found at i:405079 original size:17 final size:17
Alignment explanation
Indices: 405056--405090 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
405046 GAGAGAGAAA
405056 AAAAAAAGGAAAAAAAAG
1 AAAAAAA-GAAAAAAAAG
*
405074 AAAAAAATAAAAAAAAG
1 AAAAAAAGAAAAAAAAG
405091 TTTTTAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAAG
Found at i:405638 original size:49 final size:49
Alignment explanation
Indices: 405570--405677 Score: 171
Period size: 49 Copynumber: 2.2 Consensus size: 49
405560 AATATATTAA
* *
405570 ATTTACTTTCTTACAATTTATATTTAGGCAATTTACTTTATTTGCATTT
1 ATTTACTTTCTTACAATTTACATTTAGGCAATATACTTTATTTGCATTT
*
405619 ATTTACTTTCTTACAATTTACATTTATGCAATATACTTTATTTGCATTT
1 ATTTACTTTCTTACAATTTACATTTAGGCAATATACTTTATTTGCATTT
*
405668 TTTTCACTTT
1 ATTT-ACTTT
405678 ATTTCATGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
49 49 0.91
50 5 0.09
ACGTcount: A:0.26, C:0.14, G:0.05, T:0.56
Consensus pattern (49 bp):
ATTTACTTTCTTACAATTTACATTTAGGCAATATACTTTATTTGCATTT
Found at i:410489 original size:28 final size:28
Alignment explanation
Indices: 410453--410526 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
410443 TTAAAATTAA
*
410453 ATTTTAATAATTTATATTATATTT-ACAT
1 ATTTTAAT-ATTTATATTATATTTAAAAT
*
410481 ATTTTAATATATTATAATTTTATTTAAAAT
1 ATTTTAATAT-TTAT-ATTATATTTAAAAT
410511 ATTTT-ATATTTATATT
1 ATTTTAATATTTATATT
410527 CATTAAACCA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
27 5 0.12
28 16 0.39
29 12 0.29
30 8 0.20
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTTTAATATTTATATTATATTTAAAAT
Found at i:412144 original size:3 final size:3
Alignment explanation
Indices: 412136--412167 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
412126 TTTAATGAGG
412136 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
412168 TGGTTTGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:413010 original size:22 final size:22
Alignment explanation
Indices: 412985--413039 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
412975 TGTATATAAA
*
412985 TATAGTGATATGTTTATAGTGT
1 TATAATGATATGTTTATAGTGT
* * * *
413007 TATAATGATAAGTATAAAGTAT
1 TATAATGATATGTTTATAGTGT
413029 TATAATGATAT
1 TATAATGATAT
413040 TTACATAGTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (22 bp):
TATAATGATATGTTTATAGTGT
Found at i:415726 original size:323 final size:326
Alignment explanation
Indices: 415316--416187 Score: 946
Period size: 322 Copynumber: 2.7 Consensus size: 326
415306 TCATTATGCG
* * * * *
415316 ATTTTCTACTACGTAAATTCTTTT-GGAAGGATTTTTCTTGGTTTTTAA-TTTTAAAATTCTTCA
1 ATTTTCTACTCCATAAATTGTTTTAAG-AGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCA
415379 AATATTACCATTTATTTTATATTAATTTAATTTTAAAAAATTCATTCATTTTCATGAGTTTTTGA
65 AATATTA-CATTTA-TTTATATTAATTTAATTTTAAAAAATTCATTCATTTTCATGAGTTTTTGA
* * *
415444 TTTTTTCCTTGAAATTCTCTTTTTTTCAAAATA-GGTGTTTTCTACTCCGTAATTTTTTAAGAGG
128 TTTTTTCCTTGAAATTCTCTTTTTTT-GAAATACGATGTTTTCTACTCCGTAATTTTTTAAGGGG
* * ** * *
415508 ATTTTTTTTGGTTTTTAATTTTTAAAA-TTATTCAAATATTACCATTTATTTTGTGTTAATTTAT
192 ATTTTTCTTGGTTTTTAATTTTTAAAACTCA-TCAAATATTACCATTTATTTCATATTAATTCA-
* * *
415572 GTTTC-AAAAATTCATTCATATTCATGAGGTTTTGATTTTTTT-CTT-AAA-TT-TTTTTC-GAA
255 GTTTCAAAAAATTCATTCATATTCATGAGATTTTAATTTTTTTCCTTGAAACTTCCTTTTCTGAA
**
415631 ATACGGT
320 ATACAAT
* *
415638 GTTTTCTACTCCAT-AATTTTTTTCAAGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCA
1 ATTTTCTACTCCATAAATTGTTTT-AAGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCA
* * * * * *
415702 AATATTATCATTTATTTCATATTAA-ATCATTTTTAAAAATTCATTTATTTTCATTCA-TTTTTT
65 AATATTA-CATTTATTT-ATATTAATTTAATTTTAAAAAATTCATTCATTTTCA-TGAGTTTTTG
*
415765 ATTTTTTCCTTGAAATT-TCCTTTTTTTGAAATACGACGTTTTCTACTCCGTAATTTGTTTCAAG
127 ATTTTTTCCTTGAAATTCT-CTTTTTTTGAAATACGATGTTTTCTACTCCGTAATTT-TTT-AAG
* *
415829 GGGATTTTTCTTGGTTTTTATTTTTTAAAACTCATCAAATATTATCATTTATTTCATATTAATTC
189 GGGATTTTTCTTGGTTTTTAATTTTTAAAACTCATCAAATATTACCATTTATTTCATATTAATTC
* ***
415894 AGTTTCAAAAAATTCATTCATTTTCATTCTATTTTAATTTTTTTCCTTGAAACTTCCCCTTTTCT
254 AGTTTCAAAAAATTCATTCATATTCATGAGATTTTAATTTTTTTCCTTGAAACTT--CCTTTTCT
415959 GAAATACAAT
317 GAAATACAAT
* * * * * *
415969 ATTTTCTATTGCGTAAATTGTTTTGAG-GGAATTTTTCTGGGTTTTCAATTTTTAAAATTCATC-
1 ATTTTCTACTCCATAAATTGTTTTAAGAGG-ATTTTTCTTGGTTTTTAATTTTTAAAATTCATCA
* * *
416032 AA-A--A-A--TATTTAT-TTAATTTAGTTTTCAAAAATTCATTCATTTTTATGAGTTTTTGATT
65 AATATTACATTTATTTATATTAATTTAATTTTAAAAAATTCATTCATTTTCATGAGTTTTTGA--
* * * *
416090 TTTTTTCCTTGAAACTTCTTTTTTTTTGAAATACGATGTTTTTTACTCCATAAATTTTTT-GGGG
128 TTTTTTCCTTGAAA-TTCTCTTTTTTTGAAATACGATGTTTTCTACTCCGT-AATTTTTTAAGGG
* **
416154 GATTTGTCTTGGTTTAAAATTTTTAAAACTCATC
191 GATTTTTCTTGGTTTTTAATTTTTAAAACTCATC
416188 TAATGTTGTT
Statistics
Matches: 464, Mismatches: 59, Indels: 53
0.81 0.10 0.09
Matches are distributed among these distances:
321 20 0.04
322 139 0.30
323 83 0.18
324 102 0.22
325 39 0.08
326 9 0.02
327 3 0.01
329 1 0.00
330 9 0.02
331 51 0.11
332 8 0.02
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (326 bp):
ATTTTCTACTCCATAAATTGTTTTAAGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAA
ATATTACATTTATTTATATTAATTTAATTTTAAAAAATTCATTCATTTTCATGAGTTTTTGATTT
TTTCCTTGAAATTCTCTTTTTTTGAAATACGATGTTTTCTACTCCGTAATTTTTTAAGGGGATTT
TTCTTGGTTTTTAATTTTTAAAACTCATCAAATATTACCATTTATTTCATATTAATTCAGTTTCA
AAAAATTCATTCATATTCATGAGATTTTAATTTTTTTCCTTGAAACTTCCTTTTCTGAAATACAA
T
Found at i:416582 original size:13 final size:13
Alignment explanation
Indices: 416564--416601 Score: 55
Period size: 11 Copynumber: 3.2 Consensus size: 13
416554 GTCAGCTAGC
416564 AAAGAGAGAAGAA
1 AAAGAGAGAAGAA
416577 AAAGAGA-AAG-A
1 AAAGAGAGAAGAA
416588 AAAGAGAGAA-AA
1 AAAGAGAGAAGAA
416600 AA
1 AA
416602 GAAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 8 0.35
12 8 0.35
13 7 0.30
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AAAGAGAGAAGAA
Found at i:416604 original size:20 final size:22
Alignment explanation
Indices: 416568--416610 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
416558 GCTAGCAAAG
416568 AGAGAAGAAAAAGAGAAAGAAA
1 AGAGAAGAAAAAGAGAAAGAAA
416590 AGAG-AGAAAAA-AGAAAGAAA
1 AGAGAAGAAAAAGAGAAAGAAA
416610 A
1 A
416611 ATAGTGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.48
21 7 0.33
22 4 0.19
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (22 bp):
AGAGAAGAAAAAGAGAAAGAAA
Found at i:416608 original size:24 final size:24
Alignment explanation
Indices: 416564--416609 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
416554 GTCAGCTAGC
*
416564 AAAGAGAGAAGAAAAAGAGAAAGA
1 AAAGAGAGAAGAAAAAAAGAAAGA
416588 AAAGAGAGAA-AAAAGAAAGAAA
1 AAAGAGAGAAGAAAA-AAAGAAA
416610 AATAGTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (24 bp):
AAAGAGAGAAGAAAAAAAGAAAGA
Found at i:419100 original size:30 final size:31
Alignment explanation
Indices: 419038--419115 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 31
419028 GATACATTGA
**
419038 AGAATGTATTAATACATTTGGGTCAAAAACCC
1 AGAATGTATCGATACATTTGGGTC-AAAACCC
419070 AGAATGTATCGATACATTTGGGTC-AAACCC
1 AGAATGTATCGATACATTTGGGTCAAAACCC
*
419100 AAAATGTATCGATACA
1 AGAATGTATCGATACA
419116 ATGAAAATGT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 21 0.49
32 22 0.51
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (31 bp):
AGAATGTATCGATACATTTGGGTCAAAACCC
Found at i:419764 original size:20 final size:21
Alignment explanation
Indices: 419734--419772 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
419724 TTCTATGTTA
*
419734 ATACAATAAGTTAATGTATTG
1 ATACAATAAGTGAATGTATTG
419755 ATAC-ATAAGTGAATGTAT
1 ATACAATAAGTGAATGTAT
419773 CATACATGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (21 bp):
ATACAATAAGTGAATGTATTG
Found at i:419884 original size:20 final size:20
Alignment explanation
Indices: 419836--419895 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
419826 TTCTGAAAAA
*
419836 ATTGTATCGATACATGCTTGC
1 ATTGTATCGATACAT-TTTGC
* *
419857 AATGTATCGATACATTTTTC
1 ATTGTATCGATACATTTTGC
*
419877 ATTGTATCAATACATTTTG
1 ATTGTATCGATACATTTTG
419896 AGTTTTTAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (20 bp):
ATTGTATCGATACATTTTGC
Found at i:426043 original size:13 final size:13
Alignment explanation
Indices: 426027--426052 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
426017 AGGGTAGTTT
426027 TGTATCGATACAA
1 TGTATCGATACAA
426040 TGTATCGATACAA
1 TGTATCGATACAA
426053 AACTTATGTA
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:426703 original size:9 final size:9
Alignment explanation
Indices: 426689--426723 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
426679 ACACTGGACT
426689 TAAAGATGA
1 TAAAGATGA
426698 TAAAGATGA
1 TAAAGATGA
426707 -AAAGAGTGA
1 TAAAGA-TGA
426716 TAAAGATG
1 TAAAGATG
426724 CCAATATGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 5 0.21
9 14 0.58
10 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.26, T:0.20
Consensus pattern (9 bp):
TAAAGATGA
Found at i:426919 original size:52 final size:53
Alignment explanation
Indices: 426783--426925 Score: 166
Period size: 52 Copynumber: 2.8 Consensus size: 53
426773 ATGATAAAGG
* *
426783 TGCTAATATGCTGATTCAAGGCCAGCGATATT-GAGCTTAAAGATGCGAAGAA
1 TGCTAATATGCTGATTCAAGGCCAGCGACATTAGAGCTTAAAGATGAGAAGAA
* * * * *
426835 TGTTAATATACTGATTTAGGGCCAGCGACATTAGA-CTTGAAGATGAGAAGAA
1 TGCTAATATGCTGATTCAAGGCCAGCGACATTAGAGCTTAAAGATGAGAAGAA
* * * *
426887 TGCTAATGTGCTAATTCAAAGCCAGTGACATTAG-GCTTA
1 TGCTAATATGCTGATTCAAGGCCAGCGACATTAGAGCTTA
426926 GGAATGTTAA
Statistics
Matches: 73, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
52 71 0.97
53 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (53 bp):
TGCTAATATGCTGATTCAAGGCCAGCGACATTAGAGCTTAAAGATGAGAAGAA
Found at i:427019 original size:101 final size:95
Alignment explanation
Indices: 426891--427123 Score: 238
Period size: 101 Copynumber: 2.4 Consensus size: 95
426881 GAAGAATGCT
* * * * *
426891 AATGTGCTAATTCAAAGCCAGTGACATTAGGCTT-AGGAATGTTAAAGATGACAATATGCTGACT
1 AATGTGCTGATTCAAGGCCAGTGACATTAGGCTTAAAG-ATGGTAAAGACGACAATATGCTGACT
*
426955 CAAGGTC-GACGATATCAGACTTCAAGCTGAAGGTGCC
65 CAAGGCCAG-CGATATCAGACTT--A----AAGGTGCC
* * * * *
426992 AATGTACTGATTCAAGGCCAGTGACATT-GGACTTAAAGATGGTAAAGGCGCCAATGTGCTGATT
1 AATGTGCTGATTCAAGGCCAGTGACATTAGG-CTTAAAGATGGTAAAGACGACAATATGCTGACT
*
427056 CAAGGCCAGCGATATTAGACTTAAAGGTGCC
65 CAAGGCCAGCGATATCAGACTTAAAGGTGCC
* *
427087 AATGTGCTGATTCAAGGTCAGCGACATTAGGCTTAAA
1 AATGTGCTGATTCAAGGCCAGTGACATTAGGCTTAAA
427124 AGAGATGCCA
Statistics
Matches: 113, Mismatches: 15, Indels: 14
0.80 0.11 0.10
Matches are distributed among these distances:
95 39 0.35
96 2 0.02
99 1 0.01
100 2 0.02
101 66 0.58
102 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (95 bp):
AATGTGCTGATTCAAGGCCAGTGACATTAGGCTTAAAGATGGTAAAGACGACAATATGCTGACTC
AAGGCCAGCGATATCAGACTTAAAGGTGCC
Found at i:427095 original size:43 final size:43
Alignment explanation
Indices: 427034--427123 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
427024 TTAAAGATGG
*
427034 TAAAGGCGCCAATGTGCTGATTCAAGGCCAGCGATATTAGACT
1 TAAAGGCGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACT
* * *
427077 TAAAGGTGCCAATGTGCTGATTCAAGGTCAGCGACATTAGGCT
1 TAAAGGCGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACT
427120 TAAA
1 TAAA
427124 AGAGATGCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (43 bp):
TAAAGGCGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACT
Found at i:427165 original size:32 final size:31
Alignment explanation
Indices: 427129--427441 Score: 374
Period size: 32 Copynumber: 9.8 Consensus size: 31
427119 TTAAAAGAGA
*
427129 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGC-TTTGAAAAGGT
* *
427161 TGCCACCAACTTGTGTGGGCTTTAAAAAGGGC
1 TGCCACCAACTTGTGTGGGCTTTGAAAA-GGT
*
427193 TACCACCAACTTGTGTGGGCTTTGAAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTG-AAAAGGT
* * *
427225 TGCCTCCAACTTGTGTTGGCTTTGAAGAAAGT
1 TGCCACCAACTTGTGTGGGCTTTGAA-AAGGT
* *
427257 TGCCACCAGCTTGTGTGGGCTTTGGAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTT-GAAAAGGT
* *
427289 TACCACCAACTTATGTGGGCTTTGAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAA-AAGGT
*
427321 TGCCACCAGCTTGTGTGGGCTTTGAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAA-AAGGT
*
427353 TGCCACCAGCTTGTGTGGGCTTTGAAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTG-AAAAGGT
* * * *
427385 TTCCACCAGCTTGTGTGGGCTTTGGAGAAGTT
1 TGCCACCAACTTGTGTGGGCTTT-GAAAAGGT
* *
427417 TACCACCAATTTGTGTGGGCTTTGA
1 TGCCACCAACTTGTGTGGGCTTTGA
427442 GGAAGGTTTC
Statistics
Matches: 246, Mismatches: 28, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
31 12 0.05
32 225 0.91
33 9 0.04
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (31 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAAGGT
Found at i:427298 original size:96 final size:96
Alignment explanation
Indices: 427129--427449 Score: 448
Period size: 96 Copynumber: 3.3 Consensus size: 96
427119 TTAAAAGAGA
* *
427129 TGCCACCAACTTGTGTGGGCTTTTGAA-AGGGTTGCCACCAACTTGTGTGGGCTTT-AAAAAGGG
1 TGCCACCAACTTGTGTGGGC-TTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGAAAAA-GG
* *
427192 CTACCACCAACTTGTGTGGGCTTTGAAAAAGGT
64 TTACCACCAACTTGTGTGGGCTTTGAAGAAGGT
* * * * *
427225 TGCCTCCAACTTGTGTTGGCTTTGAAGAAAGTTGCCACCAGCTTGTGTGGGCTTTGGAGAAGGTT
1 TGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGAAAAAGGTT
*
427290 ACCACCAACTTATGTGGGCTTTGAAGAAGGT
66 ACCACCAACTTGTGTGGGCTTTGAAGAAGGT
*
427321 TGCCACCAGCTTGTGTGGGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGAAAAAGGTT
1 TGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGAAAAAGGTT
* * * *
427386 TCCACCAGCTTGTGTGGGCTTTGGAGAAGTT
66 ACCACCAACTTGTGTGGGCTTTGAAGAAGGT
* * *
427417 TACCACCAATTTGTGTGGGCTTTGAGGAAGGTT
1 TGCCACCAACTTGTGTGGGCTTTGAAGAAGGTT
427450 TCTCTATTGG
Statistics
Matches: 198, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
95 6 0.03
96 189 0.95
97 3 0.02
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (96 bp):
TGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGAAAAAGGTT
ACCACCAACTTGTGTGGGCTTTGAAGAAGGT
Found at i:427451 original size:64 final size:64
Alignment explanation
Indices: 427129--427449 Score: 421
Period size: 64 Copynumber: 5.0 Consensus size: 64
427119 TTAAAAGAGA
* * *
427129 TGCCACCAACTTGTGTGGGCTTTTGA-AAGGGTTGCCACCAACTTGTGTGGGCTTT-AAAAAGGG
1 TGCCACCAGCTTGTGTGGGCTTTGGAGAA-GGTTGCCACCAACTTGTGTGGGCTTTGAAGAA-GG
*
427192 C
64 T
* * * * * * *
427193 TACCACCAACTTGTGTGGGCTTTGAAAAAGGTTGCCTCCAACTTGTGTTGGCTTTGAAGAAAGT
1 TGCCACCAGCTTGTGTGGGCTTTGGAGAAGGTTGCCACCAACTTGTGTGGGCTTTGAAGAAGGT
* *
427257 TGCCACCAGCTTGTGTGGGCTTTGGAGAAGGTTACCACCAACTTATGTGGGCTTTGAAGAAGGT
1 TGCCACCAGCTTGTGTGGGCTTTGGAGAAGGTTGCCACCAACTTGTGTGGGCTTTGAAGAAGGT
* * *
427321 TGCCACCAGCTTGTGTGGGCTTTGAAGAAGGTTGCCACCAGCTTGTGTGGGCTTTGAAAAAGGT
1 TGCCACCAGCTTGTGTGGGCTTTGGAGAAGGTTGCCACCAACTTGTGTGGGCTTTGAAGAAGGT
* * * * *
427385 TTCCACCAGCTTGTGTGGGCTTTGGAGAAGTTTACCACCAATTTGTGTGGGCTTTGAGGAAGGT
1 TGCCACCAGCTTGTGTGGGCTTTGGAGAAGGTTGCCACCAACTTGTGTGGGCTTTGAAGAAGGT
427449 T
1 T
427450 TCTCTATTGG
Statistics
Matches: 225, Mismatches: 30, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
64 219 0.97
65 6 0.03
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (64 bp):
TGCCACCAGCTTGTGTGGGCTTTGGAGAAGGTTGCCACCAACTTGTGTGGGCTTTGAAGAAGGT
Found at i:429026 original size:5 final size:5
Alignment explanation
Indices: 429018--429058 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
429008 TGTTTGCTGT
429018 TTTTG TTTT- TTTTG -TTTG TTTT- TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
429059 TTTCTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 12 0.36
5 21 0.64
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (5 bp):
TTTTG
Found at i:429026 original size:22 final size:22
Alignment explanation
Indices: 429001--429057 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 22
428991 CTTTCTTCCT
429001 TTTTTTTTGTTTGCTGTTTTTG
1 TTTTTTTTGTTTGCTGTTTTTG
* *
429023 TTTTTTTTGTTTGTTTTTTTTG
1 TTTTTTTTGTTTGCTGTTTTTG
429045 TTTTGTTTTGTTT
1 TTTT-TTTTGTTT
429058 TTTTCTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 24 0.75
23 8 0.25
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82
Consensus pattern (22 bp):
TTTTTTTTGTTTGCTGTTTTTG
Found at i:429029 original size:9 final size:9
Alignment explanation
Indices: 429015--429070 Score: 62
Period size: 9 Copynumber: 6.1 Consensus size: 9
429005 TTTTGTTTGC
429015 TGTTTTTGTT
1 TGTTTTT-TT
429025 T-TTTTTGTT
1 TGTTTTT-TT
429034 TGTTTTTTT
1 TGTTTTTTT
429043 TGTTTTGTTT
1 TGTTTT-TTT
429053 TG-TTTTTT
1 TGTTTTTTT
*
429061 TCTTTTTTT
1 TGTTTTTTT
429070 T
1 T
429071 ACAAAGGACT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
8 4 0.10
9 27 0.64
10 11 0.26
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (9 bp):
TGTTTTTTT
Found at i:429035 original size:13 final size:13
Alignment explanation
Indices: 429019--429070 Score: 70
Period size: 13 Copynumber: 3.9 Consensus size: 13
429009 GTTTGCTGTT
429019 TTTGTTTTTTTTG
1 TTTGTTTTTTTTG
429032 TTTGTTTTTTTTG
1 TTTGTTTTTTTTG
429045 TTTTGTTTTGTTTT-
1 -TTTGTTTT-TTTTG
*
429059 TTTCTTTTTTTT
1 TTTGTTTTTTTT
429071 ACAAAGGACT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
12 4 0.11
13 20 0.56
14 8 0.22
15 4 0.11
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.87
Consensus pattern (13 bp):
TTTGTTTTTTTTG
Found at i:429037 original size:19 final size:19
Alignment explanation
Indices: 429000--429068 Score: 86
Period size: 19 Copynumber: 3.5 Consensus size: 19
428990 CCTTTCTTCC
429000 TTTTTTTTTGTTTGCTGTTTT
1 TTTTTTTTTGTTT--TGTTTT
429021 TGTTTTTTTTG-TTTGTTTT
1 T-TTTTTTTTGTTTTGTTTT
*
429040 TTTTGTTTTGTTTTGTTTT
1 TTTTTTTTTGTTTTGTTTT
429059 TTTCTTTTTT
1 TTT-TTTTTT
429069 TTACAAAGGA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
18 8 0.19
19 18 0.42
20 5 0.12
21 3 0.07
22 9 0.21
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.84
Consensus pattern (19 bp):
TTTTTTTTTGTTTTGTTTT
Found at i:429059 original size:18 final size:17
Alignment explanation
Indices: 429000--429070 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 17
428990 CCTTTCTTCC
429000 TTTTTTTTTG-TTTGCTGT
1 TTTTTTTTTGTTTTG-T-T
*
429018 TTTTGTTTT-TTTTGTT
1 TTTTTTTTTGTTTTGTT
429034 TGTTTTTTTTGTTTTGTT
1 T-TTTTTTTTGTTTTGTT
*
429052 TTGTTTTTTTCTTTT-TT
1 TT-TTTTTTTGTTTTGTT
429069 TT
1 TT
429071 ACAAAGGACT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
16 2 0.04
17 13 0.28
18 31 0.67
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.85
Consensus pattern (17 bp):
TTTTTTTTTGTTTTGTT
Found at i:429066 original size:27 final size:27
Alignment explanation
Indices: 429018--429070 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
429008 TGTTTGCTGT
*
429018 TTTTGTTTTTTTTGTTTGTTTTTTTTG
1 TTTTGTTTTTTTTGTTTCTTTTTTTTG
429045 TTTTGTTTTGTTTT-TTTCTTTTTTTT
1 TTTTGTTTT-TTTTGTTTCTTTTTTTT
429071 ACAAAGGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (27 bp):
TTTTGTTTTTTTTGTTTCTTTTTTTTG
Found at i:449163 original size:33 final size:33
Alignment explanation
Indices: 449104--449166 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
449094 TATCGTTGTT
* *
449104 TGTATCGATACATGGGATATTGTATCGATATAA
1 TGTATCGATACATGGAAAATTGTATCGATATAA
449137 TGTATCGATACATGGTAAAATT-TATCGATA
1 TGTATCGATACATGG-AAAATTGTATCGATA
449167 CATTGTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 23 0.85
34 4 0.15
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.37
Consensus pattern (33 bp):
TGTATCGATACATGGAAAATTGTATCGATATAA
Found at i:449190 original size:20 final size:20
Alignment explanation
Indices: 449139--449193 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
449129 CGATATAATG
*
449139 TATCGATACATGGTAAAATT
1 TATCGATACATTGTAAAATT
449159 TATCGATACATTGTAAAATT
1 TATCGATACATTGTAAAATT
449179 TATCGATACATTGTA
1 TATCGATACATTGTA
449194 CCCAATGGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (20 bp):
TATCGATACATTGTAAAATT
Found at i:450358 original size:13 final size:13
Alignment explanation
Indices: 450340--450364 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
450330 CATAAAGTGT
450340 TGTATCGATACAA
1 TGTATCGATACAA
450353 TGTATCGATACA
1 TGTATCGATACA
450365 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:450380 original size:32 final size:33
Alignment explanation
Indices: 450320--450388 Score: 122
Period size: 32 Copynumber: 2.1 Consensus size: 33
450310 TTCAACGATT
450320 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
450353 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
450385 TGTA
1 TGTA
450389 AGCTACTGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 22 0.63
33 13 0.37
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:450488 original size:52 final size:52
Alignment explanation
Indices: 450446--450626 Score: 308
Period size: 52 Copynumber: 3.5 Consensus size: 52
450436 CACTGATCTT
*
450446 TGTATCGATACATGCAGGCAATTTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
450498 TGTATTGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACAATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
450550 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATATACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
450602 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
450627 TCATATTTCG
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 121 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:464333 original size:1 final size:1
Alignment explanation
Indices: 464327--464421 Score: 73
Period size: 1 Copynumber: 95.0 Consensus size: 1
464317 CGTCCTCCAC
* * * * * * * *
464327 AAAAAAAAACAAAACAAAACAAAAAAAAAACAAAAAACAAAAAACAAAAAAACAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* ** * *
464392 ACAAAGCAAAAAAAAAAACAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
464422 CAACAACAAC
Statistics
Matches: 69, Mismatches: 25, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.86, C:0.13, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:464345 original size:15 final size:14
Alignment explanation
Indices: 464325--464421 Score: 106
Period size: 15 Copynumber: 6.5 Consensus size: 14
464315 GGCGTCCTCC
464325 ACAAAAAAAAACAAA
1 ACAAAAAAAAA-AAA
464340 ACAAAACAAAAAAAAA
1 AC-AAA-AAAAAAAAA
*
464356 ACAAAAAACAAAAA
1 ACAAAAAAAAAAAA
464370 ACAAAAAAACAAAAA
1 ACAAAAAAA-AAAAA
464385 ACAAAAAACAAAGCAAA
1 ACAAAAAA-AAA--AAA
*
464402 A-AAAAAAACAAAA
1 ACAAAAAAAAAAAA
464415 ACAAAAA
1 ACAAAAA
464422 CAACAACAAC
Statistics
Matches: 72, Mismatches: 3, Indels: 15
0.80 0.03 0.17
Matches are distributed among these distances:
13 4 0.06
14 21 0.29
15 22 0.31
16 15 0.21
17 10 0.14
ACGTcount: A:0.86, C:0.13, G:0.01, T:0.00
Consensus pattern (14 bp):
ACAAAAAAAAAAAA
Found at i:464351 original size:6 final size:6
Alignment explanation
Indices: 464327--464445 Score: 104
Period size: 6 Copynumber: 19.7 Consensus size: 6
464317 CGTCCTCCAC
464327 AAAA-A AAAAC- AAAAC- AAAACA AAAA-A AAAACAA AAAACAA AAAACAAA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAAC-A AAAAC-A AAAAC--A
* *
464375 AAAACAA AAAACA AAAA-A CAAAGCA AAAAAA AAAACA AAAACA AAAACA
1 AAAAC-A AAAACA AAAACA -AAAACA AAAACA AAAACA AAAACA AAAACA
* * *
464424 ACAACA ACAACA ACAACA AAAA
1 AAAACA AAAACA AAAACA AAAA
464446 GGGTCCAGAT
Statistics
Matches: 101, Mismatches: 6, Indels: 13
0.84 0.05 0.11
Matches are distributed among these distances:
5 20 0.20
6 53 0.52
7 21 0.21
8 7 0.07
ACGTcount: A:0.83, C:0.16, G:0.01, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:464426 original size:3 final size:3
Alignment explanation
Indices: 464408--464442 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
464398 CAAAAAAAAA
* *
464408 AAC AAA AAC AAA AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
464443 AAAGGGTCCA
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:0.74, C:0.26, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:464426 original size:15 final size:15
Alignment explanation
Indices: 464328--464445 Score: 88
Period size: 15 Copynumber: 7.9 Consensus size: 15
464318 GTCCTCCACA
*
464328 AAAAAAAAC-AAAAC
1 AAAAACAACAAAAAC
*
464342 -AAAACAA-AAAAAA
1 AAAAACAACAAAAAC
*
464355 AACAAAAAACAAAAAAC
1 AA-AAACAAC-AAAAAC
464372 AAAAA-AACAAAAAAC
1 AAAAACAAC-AAAAAC
464387 AAAAAACAA-AGCAAAA-
1 -AAAAACAACA--AAAAC
464403 AAAAA-AACAAAAAC
1 AAAAACAACAAAAAC
*
464417 AAAAACAACAACAAC
1 AAAAACAACAAAAAC
*
464432 AACAACAACAAAAA
1 AAAAACAACAAAAA
464446 GGGTCCAGAT
Statistics
Matches: 85, Mismatches: 7, Indels: 23
0.74 0.06 0.20
Matches are distributed among these distances:
13 14 0.16
14 8 0.09
15 42 0.49
16 8 0.09
17 13 0.15
ACGTcount: A:0.83, C:0.16, G:0.01, T:0.00
Consensus pattern (15 bp):
AAAAACAACAAAAAC
Found at i:465946 original size:59 final size:57
Alignment explanation
Indices: 465880--466773 Score: 976
Period size: 59 Copynumber: 15.2 Consensus size: 57
465870 CACTCTTTTT
* * *
465880 CAAAGCCCACAAATCAGTGGCACCCTTCTCCCAAAGCCCACAAGTCAGTGGCAACCTTC
1 CAAAGCCCACAAGTCAGTGGCA-CCTT-TTCCAAAGCCCACAAGTCAGTGGCACCCTTC
* ** * *
465939 AAAAGCCCACAAAACAGTGACGCCTTTCTCTCAAAGCCCACAAGTCAGTGGCACCCTTC
1 CAAAGCCCACAAGTCAGTGGCACCTTT-TC-CAAAGCCCACAAGTCAGTGGCACCCTTC
* * **
465998 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAGTTAGTGGCATCTTTTC
1 ---CAAAGCCCACAAGTCAGTGGCA-CCTTTTCCAAAGCCCACAAGTCAGTGGCA-CCCTTC
*
466060 CAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCACCC--TTC
* *
466119 CAAAGCCCACAAGTCAGTGGCAACC--TTCAAAAGCCCACAAATCAGTGGCACCCTTCTC
1 CAAAGCCCACAAGTCAGTGGC-ACCTTTTCCAAAGCCCACAAGTCAGTGGCACCC-T-TC
* *
466177 TCAAAACCCACAAGTCAGTGGCAACC--TT-CAAAG-CCACAAGTCAGTGGCACCTTTTTC
1 -CAAAGCCCACAAGTCAGTGGC-ACCTTTTCCAAAGCCCACAAGTCAGTGGCACC--CTTC
* * **
466234 CAAAGCCCACAAGTTAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCA-CCCTTC
* *
466292 CAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAATGGCACCCTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCACCC--TTC
* * **
466351 AAAAGCCCACAAGTCAGTGGTACCCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTC
1 CAAAGCCCACAAGTCAGTGGCA-CCTTTTCCAAAGCCCACAAGTCAGTGGCA-CCCTTC
*
466410 CAAAGCCCACAAGTCAGTGGCACCCTTTTCTAAAGCCCACAAGTCAGTGGCACCCTCTTC
1 CAAAGCCCACAAGTCAGTGGCA-CCTTTTCCAAAGCCCACAAGTCAGTGGCA-CC-CTTC
* **
466470 CAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCA-CCCTTC
* * * *
466528 CAAAGCCCACAAGTCAGTGGTATCTTTTCAAAAGCCCACAAGTCAGTGGCACCTTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCACC--CTTC
* * * * * *
466587 CAAAGCCCACAAGTTAGTGGTATCTTTTCAAAAGCTCACAAGTCAATGGCACCCTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCACCC--TTC
* * *
466646 CAAAGCCCGCAAGTCAGTGGCATCTTTTCCAAAGCCCACAGGTCAGTGGCACCCTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCACCC--TTC
* * * * *
466705 CAAAGCCCACAAGTCAATGG--CCTCTTCAAAAGCCCACAAGTTAGTGGCAACCTTC
1 CAAAGCCCACAAGTCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTC
* *
466760 AAAAGCACACAAGT
1 CAAAGCCCACAAGT
466774 TGGTGCAACC
Statistics
Matches: 731, Mismatches: 76, Indels: 60
0.84 0.09 0.07
Matches are distributed among these distances:
55 17 0.02
56 19 0.03
57 53 0.07
58 174 0.24
59 364 0.50
60 55 0.08
61 22 0.03
62 22 0.03
63 5 0.01
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.22
Consensus pattern (57 bp):
CAAAGCCCACAAGTCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTC
Found at i:466067 original size:29 final size:29
Alignment explanation
Indices: 465874--466758 Score: 1097
Period size: 29 Copynumber: 30.1 Consensus size: 29
465864 AGATATCACT
* *
465874 CTTTTTCAAAGCCCACAAATCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCA-C
*
465904 CTTCTCCCAAAGCCCACAAGTCAGTGGCAAC
1 CTT-TTCCAAAGCCCACAAGTCAGTGGC-AC
* ** * *
465935 C--TTCAAAAGCCCACAAAACAGTGACGC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAC
465962 CTTTCTCTCAAAGCCCACAAGTCAGTGGCACC
1 CTTT-TC-CAAAGCCCACAAGTCAGTGGCA-C
*
465994 CTTCTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTT-TTCCAAAGCCCACAAGTCAGTGGCA-C
* * *
466025 CTTTTTCAAAGCCCACAAGTTAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAC
*
466054 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAC
466083 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCA-C
466113 CTTTTCCAAAGCCCACAAGTCAGTGGCAAC
1 CTTTTCCAAAGCCCACAAGTCAGTGGC-AC
* *
466143 C--TTCAAAAGCCCACAAATCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCA-C
* *
466171 CTTCTCTCAAAACCCACAAGTCAGTGGCAAC
1 CTTTTC-CAAAGCCCACAAGTCAGTGGC-AC
466202 C--TT-CAAAG-CCACAAGTCAGTGGCAC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAC
* *
466227 CTTTTTCCAAAGCCCACAAGTTAGTGGCAT
1 C-TTTTCCAAAGCCCACAAGTCAGTGGCAC
*
466257 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAC
*
466286 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAC
*
466315 CTTTTCCAAAGCCCACAAGTCAATGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCA-C
* *
466345 CTTTTCAAAAGCCCACAAGTCAGTGGTACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCA-C
*
466375 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAC
466404 CTTTTCCAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCA-C
*
466434 CTTTTCTAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCA-C
* *
466464 CTCTTCCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAC
*
466493 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAC
* *
466522 CTTTTCCAAAGCCCACAAGTCAGTGGTAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAC
*
466551 CTTTTCAAAAGCCCACAAGTCAGTGGCAC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAC
* * *
466580 CTTTTTCCAAAGCCCACAAGTTAGTGGTAT
1 C-TTTTCCAAAGCCCACAAGTCAGTGGCAC
* * *
466610 CTTTTCAAAAGCTCACAAGTCAATGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCA-C
* *
466640 CTTTTCCAAAGCCCGCAAGTCAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAC
*
466669 CTTTTCCAAAGCCCACAGGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCA-C
*
466699 CTTTTCCAAAGCCCACAAGTCAATGG--C
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAC
* * *
466726 CTCTTCAAAAGCCCACAAGTTAGTGGCAAC
1 CTTTTCCAAAGCCCACAAGTCAGTGGC-AC
466756 CTT
1 CTT
466759 CAAAAGCACA
Statistics
Matches: 753, Mismatches: 74, Indels: 56
0.85 0.08 0.06
Matches are distributed among these distances:
25 3 0.00
26 15 0.02
27 30 0.04
28 45 0.06
29 304 0.40
30 260 0.35
31 88 0.12
32 7 0.01
33 1 0.00
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.22
Consensus pattern (29 bp):
CTTTTCCAAAGCCCACAAGTCAGTGGCAC
Found at i:466877 original size:49 final size:48
Alignment explanation
Indices: 466816--467183 Score: 442
Period size: 49 Copynumber: 7.8 Consensus size: 48
466806 GGTGGCAACT
*
466816 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCA
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CTTCA
* *
466865 TCTTTAAGTCCAATGTAGCTGGCCTTAAATCAGCACATTGG----T-A
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCA
* * *
466908 CCTTTAAGTCCAATATAGCTGGCCTTGAGTCAGCATATTGGCACCTTCA
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CTTCA
*
466957 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C-
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCA
* *
467001 -CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCT
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CTTCA
*
467049 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C-
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCA
* *
467093 -CTTTAAGTCCAATATAGCTGGCCTTGAATCAGTATATTGGCACATTTTCCA
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC---TT-CA
* *
467144 TCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
467184 ACATCCTTTT
Statistics
Matches: 275, Mismatches: 23, Indels: 39
0.82 0.07 0.12
Matches are distributed among these distances:
43 116 0.42
44 1 0.00
45 2 0.01
47 1 0.00
48 1 0.00
49 118 0.43
50 1 0.00
52 35 0.13
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (48 bp):
TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCA
Found at i:466927 original size:43 final size:43
Alignment explanation
Indices: 466866--467124 Score: 311
Period size: 43 Copynumber: 5.7 Consensus size: 43
466856 GCACCTTCAT
* *
466866 CTTTAAGTCCAATGTAGCTGGCCTTAAATCAGCACATTGGTAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGTAC
* * *
466909 CTTTAAGTCCAATATAGCTGGCCTTGAGTCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG-----T-AC
* *
466958 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGTAC
* *
467001 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG----TAC
* *
467048 TTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGTAC
467093 CTTTAAGTCCAATATAGCTGGCCTTGAATCAG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAG
467125 TATATTGGCA
Statistics
Matches: 185, Mismatches: 19, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
43 106 0.57
45 1 0.01
47 1 0.01
48 1 0.01
49 76 0.41
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGTAC
Found at i:466974 original size:92 final size:92
Alignment explanation
Indices: 466817--467192 Score: 644
Period size: 92 Copynumber: 4.0 Consensus size: 92
466807 GTGGCAACTT
466817 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
* *
466882 GCTGGCCTTAAATCAGCACATTGGTAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
*
466909 CTTTAAGTCCAATATAGCTGGCCTTGAGTCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
466974 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
*
467001 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
467066 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
467093 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGTATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC--CTT-CATCTTTAAGTCCAAT
*
467158 GTAGCTGGCCTTGAATCAGCACATTGACATC
63 GTAGCTGGCCTTGAATCAGCACATTGGCA-C
467189 CTTT
1 CTTT
467193 TTCTCATCTT
Statistics
Matches: 270, Mismatches: 10, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
92 221 0.82
94 2 0.01
95 42 0.16
96 5 0.02
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (92 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:467863 original size:19 final size:19
Alignment explanation
Indices: 467831--467926 Score: 123
Period size: 19 Copynumber: 5.3 Consensus size: 19
467821 AATTTATATT
467831 GATACATAAAGTGTTGTATC
1 GATACAT-AAGTGTTGTATC
467851 GATACATAAGTGTTGTATC
1 GATACATAAGTGTTGTATC
467870 GATACATAAGTGTTGTATC
1 GATACATAAGTGTTGTATC
*
467889 GATAC--AA----TATATC
1 GATACATAAGTGTTGTATC
*
467902 GATACATAAGTTTTGTATC
1 GATACATAAGTGTTGTATC
467921 GATACA
1 GATACA
467927 ATGTAAGCTA
Statistics
Matches: 68, Mismatches: 2, Indels: 13
0.82 0.02 0.16
Matches are distributed among these distances:
13 10 0.15
15 2 0.03
17 2 0.03
19 47 0.69
20 7 0.10
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (19 bp):
GATACATAAGTGTTGTATC
Found at i:467907 original size:32 final size:32
Alignment explanation
Indices: 467825--467928 Score: 118
Period size: 32 Copynumber: 3.0 Consensus size: 32
467815 TTCAATAATT
*
467825 TATATTGATACATAAAGTGTTGTATCGATACATAA
1 TATATCGATACAT-AAGTGTTGTATCGATAC--AA
*
467860 GTGTTGTATCGATACATAAGTGTTGTATCGATACAA
1 ----TATATCGATACATAAGTGTTGTATCGATACAA
*
467896 TATATCGATACATAAGTTTTGTATCGATACAA
1 TATATCGATACATAAGTGTTGTATCGATACAA
467928 T
1 T
467929 GTAAGCTACT
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
32 31 0.51
36 2 0.03
38 17 0.28
39 11 0.18
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (32 bp):
TATATCGATACATAAGTGTTGTATCGATACAA
Found at i:468030 original size:52 final size:52
Alignment explanation
Indices: 467947--468149 Score: 352
Period size: 52 Copynumber: 3.9 Consensus size: 52
467937 CTGCCAAAAA
* * *
467947 ATGTATCGATACATTACTCAAATGTATCGATACATGCAGGCAAGTTTGCCCAG
1 ATGTATCGATACACTA-TAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
468000 ATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
*
468052 ATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAA
1 ATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
*
468104 ATGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTT
1 ATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTT
468150 TCATATTTCG
Statistics
Matches: 145, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 130 0.90
53 15 0.10
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (52 bp):
ATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
Found at i:476708 original size:13 final size:13
Alignment explanation
Indices: 476690--476738 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
476680 ATGTTCTAAG
*
476690 TATCGATAAATTA
1 TATCGATAAACTA
*
476703 TATCGATACACTA
1 TATCGATAAACTA
* *
476716 TATCGATACACTG
1 TATCGATAAACTA
476729 TATCGATAAA
1 TATCGATAAA
476739 AGGGGTACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (13 bp):
TATCGATAAACTA
Found at i:479430 original size:13 final size:13
Alignment explanation
Indices: 479412--479436 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
479402 CATGGGACAT
479412 TGTATCGATACAA
1 TGTATCGATACAA
479425 TGTATCGATACA
1 TGTATCGATACA
479437 TGATAAAATG
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:479441 original size:20 final size:20
Alignment explanation
Indices: 479418--479457 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
479408 ACATTGTATC
*
479418 GATACAATGTATCGATACAT
1 GATAAAATGTATCGATACAT
*
479438 GATAAAATGTATCGGTACAT
1 GATAAAATGTATCGATACAT
479458 TGTGCCCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (20 bp):
GATAAAATGTATCGATACAT
Found at i:480375 original size:27 final size:27
Alignment explanation
Indices: 480342--480403 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
480332 TTATGTGGGG
480342 ACCCTTTTAAGCCCACAACTCCGTGGC
1 ACCCTTTTAAGCCCACAACTCCGTGGC
* *
480369 ACCCTTTTAAGTCCACGACTCCGTGGC
1 ACCCTTTTAAGCCCACAACTCCGTGGC
480396 ACCCTTTT
1 ACCCTTTT
480404 TTCCTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.19, C:0.39, G:0.15, T:0.27
Consensus pattern (27 bp):
ACCCTTTTAAGCCCACAACTCCGTGGC
Found at i:480454 original size:33 final size:34
Alignment explanation
Indices: 480371--480454 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 34
480361 TCCGTGGCAC
* * *
480371 CCTTTTAAGTCCACGACTCCGTGGCACCCTTTTTT
1 CCTTTTAAGTCCACAACTACGTGGCA-CCTCTTTT
*
480406 CCTTTAAAG-CTCACAACTACGTGGCA-CTCTTTT
1 CCTTTTAAGTC-CACAACTACGTGGCACCTCTTTT
480439 CCTTTTAAGTCCACAA
1 CCTTTTAAGTCCACAA
480455 ATCGGTGGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
33 19 0.45
34 2 0.05
35 21 0.50
ACGTcount: A:0.21, C:0.32, G:0.12, T:0.35
Consensus pattern (34 bp):
CCTTTTAAGTCCACAACTACGTGGCACCTCTTTT
Found at i:480463 original size:33 final size:33
Alignment explanation
Indices: 480371--480464 Score: 93
Period size: 33 Copynumber: 2.8 Consensus size: 33
480361 TCCGTGGCAC
* *
480371 CCTTTTAAGTCCACGACTCCGTGGCACCCTTTTTT
1 CCTTTTAAGTCCACAACT-CGTGGCA-CCTCTTTT
*
480406 CCTTTAAAG-CTCACAACTACGTGGCA-CTCTTTT
1 CCTTTTAAGTC-CACAACT-CGTGGCACCTCTTTT
*
480439 CCTTTTAAGTCCACAAATCGGTGGCA
1 CCTTTTAAGTCCACAACTC-GTGGCA
480465 ACCTTCTTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
32 1 0.02
33 26 0.52
34 2 0.04
35 21 0.42
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.33
Consensus pattern (33 bp):
CCTTTTAAGTCCACAACTCGTGGCACCTCTTTT
Found at i:480516 original size:32 final size:33
Alignment explanation
Indices: 480450--480547 Score: 155
Period size: 32 Copynumber: 3.0 Consensus size: 33
480440 CTTTTAAGTC
*
480450 CACAAATCGGTGGCAA-CCTTCTTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTC-TCTAAAGCCCA
480483 CACAAGTCGGTGGCAACCCTTCTC-AAAGCCCA
1 CACAAGTCGGTGGCAACCCTTCTCTAAAGCCCA
*
480515 CACAAGTCGGTGGCAACCATTCTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTCTCTAAAGCCCA
480548 ATATAGCTGG
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
32 31 0.51
33 25 0.41
34 5 0.08
ACGTcount: A:0.30, C:0.35, G:0.17, T:0.18
Consensus pattern (33 bp):
CACAAGTCGGTGGCAACCCTTCTCTAAAGCCCA
Found at i:480604 original size:49 final size:49
Alignment explanation
Indices: 480545--481063 Score: 661
Period size: 49 Copynumber: 10.8 Consensus size: 49
480535 TCTCTAAAGC
*
480545 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGT
* *
480594 CCAATGTAGCTGGCCTTGAATCAGCACATTGG---C---ACCTTTAAGC
1 CCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGT
* * * * *
480637 CCAATATCGCCGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGT
* *
480686 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGT
* * * *
480735 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGT
* *
480784 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGT
* * * *
480833 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGT
*
480882 CCAATGTAGCTGG-CTTGAATCAGCATATTGGCACC-TCACCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGT
*
480929 CCAATGTAGCTGGCCTTGAATCAGCACATTGG---C---ACCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGT
* *
480972 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ACCTTTAAGT
* * *
481024 TCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTT
1 CCAATGTAGCTGGCCTTGAATCAGCATATTGGCA-CCTTT
481064 TTCTCATCTT
Statistics
Matches: 414, Mismatches: 39, Indels: 31
0.86 0.08 0.06
Matches are distributed among these distances:
43 77 0.19
45 1 0.00
46 3 0.01
47 24 0.06
48 37 0.09
49 228 0.55
52 42 0.10
53 2 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
CCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGT
Found at i:480768 original size:98 final size:98
Alignment explanation
Indices: 480545--481120 Score: 739
Period size: 98 Copynumber: 5.9 Consensus size: 98
480535 TCTCTAAAGC
* * * * *
480545 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGTCCAATGTAGCTGGCCT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCT
* *
480610 TGAATCAGCACATTGGCA-C-----CTTTAAGC
66 TGAATCAGCATATTGGCACCTTTATCTTTAAGT
* * * *
480637 CCAATATCGCCGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCT
480702 TGAATCAGCATATTGGCACCTTTATCTTTAAGT
66 TGAATCAGCATATTGGCACCTTTATCTTTAAGT
* * *
480735 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCT
480800 TGAATCAGCATATTGGCACCTTTATCTTTAAGT
66 TGAATCAGCATATTGGCACCTTTATCTTTAAGT
* *
480833 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGG-CT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCT
* *
480897 TGAATCAGCATATTGGCACC-TCACCTTTAAGT
66 TGAATCAGCATATTGGCACCTTTATCTTTAAGT
480929 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAGCTGGCCT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCT
480988 TGAATCAGCATATTGGCACCTTTTCCATCTTTAAGT
66 TGAATCAGCATATTGGCACC-TTT--ATCTTTAAGT
* * * * *
481024 TCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CC----T-TCATCTTTAAGTCCAATATAGC
* * *
481089 TGGCCGTGAATCAACATATTGGCATCTTTATC
60 TGGCCTTGAATCAGCATATTGGCACCTTTATC
481121 ACTTTTCTCA
Statistics
Matches: 430, Mismatches: 31, Indels: 34
0.87 0.06 0.07
Matches are distributed among these distances:
90 20 0.05
91 22 0.05
92 78 0.18
93 2 0.00
95 41 0.10
96 43 0.10
97 22 0.05
98 157 0.37
104 3 0.01
105 1 0.00
106 3 0.01
107 38 0.09
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (98 bp):
CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCT
TGAATCAGCATATTGGCACCTTTATCTTTAAGT
Found at i:480847 original size:147 final size:144
Alignment explanation
Indices: 480545--481054 Score: 761
Period size: 147 Copynumber: 3.6 Consensus size: 144
480535 TCTCTAAAGC
*
480545 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGTCCAATGTAGCTGGCCT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCT
* * *
480610 TGAATCAGCACATTGGCACCT----TTAAGCCCAATATCGCCGGCCTTGAATCAGCATATTGGCA
66 TGAATCAGCACATTGGCACCTCACCTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
480671 CCTTCATCTTTAAGT
131 CCTT-ATCTTTAAGT
480686 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCT
*
480751 TGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
66 TGAATCAGCACATTGGCACC-TCACC-TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
480816 CACCTTTATCTTTAAGT
129 CACC-TTATCTTTAAGT
* * * *
480833 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGG-CT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCT
* * *
480897 TGAATCAGCATATTGGCACCTCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGC
66 TGAATCAGCACATTGGCACCTCACC-TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC
480962 A-C----CTTTAAGT
130 ACCTTATCTTTAAGT
*
480972 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGG
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTTTAAGTCCAATGTAGCTGG
481037 CCTTGAATCAGCACATTG
63 CCTTGAATCAGCACATTG
481055 ACATCCTTTT
Statistics
Matches: 338, Mismatches: 20, Indels: 20
0.89 0.05 0.05
Matches are distributed among these distances:
139 41 0.12
140 2 0.01
141 83 0.25
142 23 0.07
143 16 0.05
144 1 0.00
145 43 0.13
146 20 0.06
147 107 0.32
148 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (144 bp):
CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCT
TGAATCAGCACATTGGCACCTCACCTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
CCTTATCTTTAAGT
Found at i:481042 original size:52 final size:53
Alignment explanation
Indices: 480964--481117 Score: 193
Period size: 52 Copynumber: 2.9 Consensus size: 53
480954 ACATTGGCAC
480964 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * * *
481016 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAT
* * * * * *
481071 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
481118 ATCACTTTTC
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
52 38 0.45
53 5 0.06
54 6 0.07
55 36 0.42
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.36
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:481043 original size:95 final size:91
Alignment explanation
Indices: 480874--481063 Score: 292
Period size: 95 Copynumber: 2.0 Consensus size: 91
480864 GCACCTTCAT
*
480874 CTTTAAGTCCAATGTAGCTGGCTTGAATCAGCATATTGGCACCTCACCTTTAAGTCCAATGTAGC
1 CTTTAAGTCCAATATAGCTGGCTTGAATCAGCATATTGGCACCTCACCTTTAAGTCCAATGTAGC
*
480939 TGGCCTTGAATCAGCACATTGGCA-C
66 TGGCCTTGAATCAGCACATTGACATC
* *
480964 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGG-CTTGAATCAGCATATTGGCACC---T-CACCTTTAAGTCCAAT
481029 GTAGCTGGCCTTGAATCAGCACATTGACATC
61 GTAGCTGGCCTTGAATCAGCACATTGACATC
481060 CTTT
1 CTTT
481064 TTCTCATCTT
Statistics
Matches: 90, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
90 20 0.22
91 22 0.24
94 1 0.01
95 42 0.47
96 5 0.06
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (91 bp):
CTTTAAGTCCAATATAGCTGGCTTGAATCAGCATATTGGCACCTCACCTTTAAGTCCAATGTAGC
TGGCCTTGAATCAGCACATTGACATC
Found at i:481175 original size:67 final size:68
Alignment explanation
Indices: 481067--481193 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 68
481057 ATCCTTTTTC
* * *
481067 TCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
481131 TCT
66 TCT
* * * * *
481134 TCATCTTTAAGTCCTATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTT
481194 AAAACCCAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
67 47 0.92
68 4 0.08
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (68 bp):
TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
TCT
Found at i:482006 original size:13 final size:13
Alignment explanation
Indices: 481988--482012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
481978 CATAAAATGT
481988 TGTATCGATACAA
1 TGTATCGATACAA
482001 TGTATCGATACA
1 TGTATCGATACA
482013 TATTTTTTTT
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:482096 original size:13 final size:13
Alignment explanation
Indices: 482078--482102 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
482068 ATTACTCAAA
482078 TGTATCGATACAT
1 TGTATCGATACAT
482091 TGTATCGATACA
1 TGTATCGATACA
482103 CCGATCTTTG
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:482167 original size:52 final size:52
Alignment explanation
Indices: 482111--482231 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
482101 CACCGATCTT
*
482111 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
482163 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
482215 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
482232 ATAAATTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:488967 original size:24 final size:24
Alignment explanation
Indices: 488940--488985 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
488930 CTTGCATGTA
*
488940 AAATTTAAGGTTTCTTAAAACCTT
1 AAATTTAAGGTTTCCTAAAACCTT
488964 AAATTTAAGGTTTCCTAAAACC
1 AAATTTAAGGTTTCCTAAAACC
488986 CTAATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (24 bp):
AAATTTAAGGTTTCCTAAAACCTT
Found at i:489765 original size:32 final size:32
Alignment explanation
Indices: 489718--489807 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
489708 AATTTCTTGC
* *
489718 AATTCTGTATCTATTATTGAATAAATTATTGT
1 AATTTTGTATTTATTATTGAATAAATTATTGT
*
489750 AATTTTGTATTTATTATTGAATAAATTCTTGT
1 AATTTTGTATTTATTATTGAATAAATTATTGT
489782 AATTTTGTATTTATTTATTGAATAAA
1 AATTTTGTATTTA-TTATTGAATAAA
489808 AATTCTAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 42 0.78
33 12 0.22
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.53
Consensus pattern (32 bp):
AATTTTGTATTTATTATTGAATAAATTATTGT
Found at i:491595 original size:11 final size:10
Alignment explanation
Indices: 491574--491607 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
491564 AATTCGTTTA
491574 TAAAATTATT
1 TAAAATTATT
491584 TAAAACTTATT
1 TAAAA-TTATT
491595 TAAAGATTATT
1 TAAA-ATTATT
491606 TA
1 TA
491608 TCATTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.23
11 16 0.73
12 1 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (10 bp):
TAAAATTATT
Found at i:492823 original size:14 final size:14
Alignment explanation
Indices: 492790--492821 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
492780 TTATATTATA
492790 TAAAAA-TAAATAT
1 TAAAAATTAAATAT
492803 TAAAAATTAAA-AT
1 TAAAAATTAAATAT
492816 TAAAAA
1 TAAAAA
492822 ATATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
TAAAAATTAAATAT
Found at i:493230 original size:23 final size:24
Alignment explanation
Indices: 493191--493261 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 24
493181 TATTTTGATT
*
493191 TTATTATTATAAA-AAAATATTAAA
1 TTATAATTA-AAATAAAATATTAAA
* *
493215 -TATGATTAAAATAAAAAATTAAA
1 TTATAATTAAAATAAAATATTAAA
*
493238 TTTATAATTAAAATTAAATTATTA
1 -TTATAATTAAAA-TAAAATATTA
493262 TGATAAACTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 3 0.08
23 17 0.45
25 10 0.26
26 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (24 bp):
TTATAATTAAAATAAAATATTAAA
Found at i:493247 original size:25 final size:25
Alignment explanation
Indices: 493190--493251 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 25
493180 TTATTTTGAT
* *
493190 TTTATTATTATAAA-AAAATATTAAA
1 TTTATAATTA-AAATAAAAAATTAAA
*
493215 --TATGATTAAAATAAAAAATTAAA
1 TTTATAATTAAAATAAAAAATTAAA
493238 TTTATAATTAAAAT
1 TTTATAATTAAAAT
493252 TAAATTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 3 0.10
23 17 0.55
25 11 0.35
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
TTTATAATTAAAATAAAAAATTAAA
Found at i:494000 original size:11 final size:11
Alignment explanation
Indices: 493984--494026 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
493974 ATGTATATAA
*
493984 AATATAATTAT
1 AATATAAATAT
*
493995 AATATAAAAAT
1 AATATAAATAT
494006 AATATAAATAT
1 AATATAAATAT
494017 AATATAAATA
1 AATATAAATA
494027 ATTATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AATATAAATAT
Found at i:494015 original size:17 final size:18
Alignment explanation
Indices: 493978--494023 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 18
493968 AATTGAATGT
493978 ATATAAAATATAATTATA
1 ATATAAAATATAATTATA
493996 ATATAAAA-ATAA-TATA
1 ATATAAAATATAATTATA
*
494012 A-ATATAATATAA
1 ATATAAAATATAA
494024 ATAATTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 5 0.19
16 9 0.35
17 4 0.15
18 8 0.31
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATATAAAATATAATTATA
Found at i:495235 original size:106 final size:107
Alignment explanation
Indices: 495047--495265 Score: 343
Period size: 106 Copynumber: 2.1 Consensus size: 107
495037 CAAATCTACT
*
495047 TTTAATCAATTTTTATTAGGTTATTTATGCTTGATCAACATCTCTAGAGCGGCCACAAGTGATAA
1 TTTAATCAACTTTTATTAGGTTATTTATGCTTGATCAACATCTCTAGAGCGGCCACAAGTGATAA
* *
495112 AAAATTAGATCTCATTAATTAGTTCAATT-AAAATTAATAAA
66 AAAATTAAATCTCATTAATCAGTTCAATTAAAAATTAATAAA
* * * *
495153 TTTAATCAACTTTTATTAGGTTATTTATGTTTGATCAGCATCTCTAGAGCTGTCACAAGTGATAA
1 TTTAATCAACTTTTATTAGGTTATTTATGCTTGATCAACATCTCTAGAGCGGCCACAAGTGATAA
*
495218 AAAATTAAAT-TCGATTAATCAGTTCAGTTAAAAATTAATAAA
66 AAAATTAAATCTC-ATTAATCAGTTCAATTAAAAATTAATAAA
495260 TTTAAT
1 TTTAAT
495266 AATATAATGA
Statistics
Matches: 103, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
105 2 0.02
106 83 0.81
107 18 0.17
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.39
Consensus pattern (107 bp):
TTTAATCAACTTTTATTAGGTTATTTATGCTTGATCAACATCTCTAGAGCGGCCACAAGTGATAA
AAAATTAAATCTCATTAATCAGTTCAATTAAAAATTAATAAA
Found at i:495600 original size:7 final size:7
Alignment explanation
Indices: 495553--495591 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
495543 ACACATTATT
495553 ATTTTT-
1 ATTTTTA
*
495559 ATTCTT-
1 ATTTTTA
495565 ATTTTTA
1 ATTTTTA
495572 ATTTTTA
1 ATTTTTA
495579 ATTTTTA
1 ATTTTTA
495586 ATTTTT
1 ATTTTT
495592 TTAAATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 10 0.33
7 20 0.67
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTTTTA
Found at i:497474 original size:22 final size:22
Alignment explanation
Indices: 497440--497485 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
497430 GGAATATTAT
497440 AAAAAACAAAAAAAAAGAAAAG
1 AAAAAACAAAAAAAAAGAAAAG
**
497462 AAAAAA-AAGAAAAGGAGAAAAG
1 AAAAAACAA-AAAAAAAGAAAAG
497484 AA
1 AA
497486 TTGAGAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAACAAAAAAAAAGAAAAG
Found at i:497482 original size:14 final size:14
Alignment explanation
Indices: 497448--497475 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
497438 ATAAAAAACA
497448 AAAAAAAAGAAAAG
1 AAAAAAAAGAAAAG
497462 AAAAAAAAGAAAAG
1 AAAAAAAAGAAAAG
497476 GAGAAAAGAA
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:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAAG
Found at i:497557 original size:44 final size:40
Alignment explanation
Indices: 497509--497615 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 40
497499 TGATAGAGAT
497509 GATAAGAAAATAAAAATAAAAAAGAAAGAAAATTATTTAAAGAA
1 GATAA-AAAATAAAAA-AAAAAAG-AA-AAAATTATTTAAAGAA
* *
497553 GATAAAAAATGAAAACAAAAAGAAAAAATTATTTAAAGAA
1 GATAAAAAATAAAAAAAAAAAGAAAAAATTATTTAAAGAA
* **
497593 TCATAAAGCA-AAAAAAAAAAAGA
1 -GATAAAAAATAAAAAAAAAAAGA
497616 TGGGTCATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
40 27 0.49
41 8 0.15
42 6 0.11
43 9 0.16
44 5 0.09
ACGTcount: A:0.71, C:0.03, G:0.10, T:0.16
Consensus pattern (40 bp):
GATAAAAAATAAAAAAAAAAAGAAAAAATTATTTAAAGAA
Found at i:497588 original size:40 final size:44
Alignment explanation
Indices: 497509--497592 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 44
497499 TGATAGAGAT
497509 GATAAGAAAATAAAAATAAAAAAGAAAGAAAATTATTTAAAGAA
1 GATAAGAAAATAAAAATAAAAAAGAAAGAAAATTATTTAAAGAA
* *
497553 GATAA-AAAATGAAAA-CAAAAAG-AA-AAAATTATTTAAAGAA
1 GATAAGAAAATAAAAATAAAAAAGAAAGAAAATTATTTAAAGAA
497593 TCATAAAGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 16 0.42
41 2 0.05
42 6 0.16
43 9 0.24
44 5 0.13
ACGTcount: A:0.70, C:0.01, G:0.11, T:0.18
Consensus pattern (44 bp):
GATAAGAAAATAAAAATAAAAAAGAAAGAAAATTATTTAAAGAA
Found at i:504300 original size:32 final size:32
Alignment explanation
Indices: 504227--504334 Score: 134
Period size: 32 Copynumber: 3.5 Consensus size: 32
504217 TTTTTTGGTA
* *
504227 TTTTTTCTAAAGTCCACATCTCTGTGGCA-CCC
1 TTTTTT-TAAAGTCCATATCTCTATGGCACCCC
*
504259 ---TTTTAAAGTCCATATCTCTATAGCACCCC
1 TTTTTTTAAAGTCCATATCTCTATGGCACCCC
* *
504288 TTTTTTTAAAGTCCATAACTCCATGGCACCCC
1 TTTTTTTAAAGTCCATATCTCTATGGCACCCC
504320 TTTTTTTAAAGTCCA
1 TTTTTTTAAAGTCCA
504335 CAACTCCATG
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
28 19 0.29
29 6 0.09
32 41 0.62
ACGTcount: A:0.24, C:0.29, G:0.09, T:0.38
Consensus pattern (32 bp):
TTTTTTTAAAGTCCATATCTCTATGGCACCCC
Found at i:504356 original size:30 final size:30
Alignment explanation
Indices: 504227--504746 Score: 233
Period size: 31 Copynumber: 17.2 Consensus size: 30
504217 TTTTTTGGTA
* **
504227 TTTTTTCTAAAGTCCACATCTCTGTGGCACC
1 TTTTTT-TAAAGTCCACAACTCCATGGCACC
* * * * *
504258 --CTTTTAAAGTCCATATCTCTATAGCACCCC
1 TTTTTTTAAAGTCCACAACTCCATGGCA--CC
*
504288 TTTTTTTAAAGTCCATAACTCCATGGCACCCC
1 TTTTTTTAAAGTCCACAACTCCATGGCA--CC
* *
504320 TTTTTTTAAAGTCCACAACTCCATGGTACTT
1 TTTTTTTAAAGTCCACAACTCCATGGCAC-C
* ** * *
504351 TTTTTTTTAAGTTTACAACTTCATGGTACC
1 TTTTTTTAAAGTCCACAACTCCATGGCACC
* *
504381 TTCTTTTTTAAGTCAACAACTCCATGGCACC
1 TT-TTTTTAAAGTCCACAACTCCATGGCACC
** * * *
504412 TTTTTAAAAAATCCACAACTCCGTGCCACCC
1 TTTTTTTAAAGTCCACAACTCCATGGCA-CC
* * *
504443 TCTTTTTT-AAGTTCACAACTTCGTGGCACC
1 T-TTTTTTAAAGTCCACAACTCCATGGCACC
* * *
504473 TCTTTTTAAA-TCCACAACTCTATAGCA-C
1 TTTTTTTAAAGTCCACAACTCCATGGCACC
* *
504501 TATCTTTTT-AAGTCCACAATTCCGTGGCACCC
1 T-T-TTTTTAAAGTCCACAACTCCATGGCA-CC
* * *** *
504533 TTTTTTAAAAGTTCACAACTTTGTGGTACC
1 TTTTTTTAAAGTCCACAACTCCATGGCACC
*
504563 -TTTTTTAAAGTCCACAACTCCAAGGCACC
1 TTTTTTTAAAGTCCACAACTCCATGGCACC
* * * ** *
504592 --CTTTTAAAATCAACAACTTTATAGCACC
1 TTTTTTTAAAGTCCACAACTCCATGGCACC
* *
504620 --CTTTTACAA-TCCACAACTCCATGGAATCC
1 TTTTTTTA-AAGTCCACAACTCCATGGCA-CC
* * * * *
504649 -CTTTTCAAAGCCCACAAGT-TAGTGGCATCC
1 TTTTTTTAAAGTCCACAACTCCA-TGGCA-CC
* * *
504679 TTTTTTTTAAAGCCCACAAGT-TAGTGGCATCC
1 -TTTTTTTAAAGTCCACAACTCCA-TGGCA-CC
* * * *
504711 TTTTTCTAAAGCCCACAAGTCAATGGCACC
1 TTTTTTTAAAGTCCACAACTCCATGGCACC
*
504741 CTTTTT
1 TTTTTT
504747 AAATCCTACA
Statistics
Matches: 385, Mismatches: 81, Indels: 47
0.75 0.16 0.09
Matches are distributed among these distances:
28 60 0.16
29 51 0.13
30 77 0.20
31 110 0.29
32 87 0.23
ACGTcount: A:0.27, C:0.28, G:0.10, T:0.35
Consensus pattern (30 bp):
TTTTTTTAAAGTCCACAACTCCATGGCACC
Done.