Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold181
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: 2212501
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 130279 characters in sequence are not A, C, G, or T
File 2 of 6
Found at i:394481 original size:50 final size:49
Alignment explanation
Indices: 394276--394482 Score: 218
Period size: 50 Copynumber: 4.1 Consensus size: 49
394266 CCTTACATGC
* *
394276 GACCTATCATTCCGATACACATAGTAACCTGCACATAGTACTACACATGT
1 GACCTATCA-TCCGATACACATAGTAGCCTGCACATAGTACTACACACGT
* **
394326 GACCATTTTCATCCGATACACGGAG-AGCCTGCACATAGTACTACACACGT
1 GACC--TATCATCCGATACACATAGTAGCCTGCACATAGTACTACACACGT
** * * * * * *
394376 GATCAAAGTTATCTGGTACGCATAGTAGCCTGCACATAGTACTACACATGC
1 GA-CCTA-TCATCCGATACACATAGTAGCCTGCACATAGTACTACACACGT
* *
394427 GACCTATCATTCCGGTACACGTAGTAGCCTGCACATAGTACTACACACGT
1 GACCTATCA-TCCGATACACATAGTAGCCTGCACATAGTACTACACACGT
394477 GACCTA
1 GACCTA
394483 GCAACTTCAC
Statistics
Matches: 127, Mismatches: 24, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
49 2 0.02
50 83 0.65
51 38 0.30
52 4 0.03
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (49 bp):
GACCTATCATCCGATACACATAGTAGCCTGCACATAGTACTACACACGT
Found at i:398411 original size:17 final size:18
Alignment explanation
Indices: 398389--398430 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
398379 TATATTTGTG
398389 TATATATAATGTATG-AA
1 TATATATAATGTATGTAA
*
398406 TATATAT-ATGTGTGTAA
1 TATATATAATGTATGTAA
398423 TATATATA
1 TATATATA
398431 TAAATTCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (18 bp):
TATATATAATGTATGTAA
Found at i:398431 original size:17 final size:17
Alignment explanation
Indices: 398379--398431 Score: 67
Period size: 15 Copynumber: 3.3 Consensus size: 17
398369 GTTTGGATGT
*
398379 TATATTTGTGT-ATATA
1 TATATGTGTGTAATATA
*
398395 TA-ATGTATG-AATATA
1 TATATGTGTGTAATATA
398410 TATATGTGTGTAATATA
1 TATATGTGTGTAATATA
398427 TATAT
1 TATAT
398432 AAATTCTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 12 0.39
16 8 0.26
17 11 0.35
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (17 bp):
TATATGTGTGTAATATA
Found at i:398710 original size:76 final size:76
Alignment explanation
Indices: 398630--398829 Score: 183
Period size: 78 Copynumber: 2.6 Consensus size: 76
398620 GAAATTAGGG
* * *
398630 ATGTATATATTAGATTTGAATATGTATGAGTATACATGTATAAGTTCATGTTTTG-ATTATAAGT
1 ATGTATATATTAGATTCGAATATGTATGAGTATACATGTATAAGTTCATGTATTGAAAT-TAAGT
*
398694 ATGCAA-TTATTT
65 ATG-AATTTATAT
* * * * * * *
398706 ATGTATATGA-TAGACTCGAATATATATATAAATATACATGTATAAATTCTTGTATTGAAATTAG
1 ATGTATAT-ATTAGATTCG-A-ATATGTATGAGTATACATGTATAAGTTCATGTATTGAAATTAA
398770 GTATGAATTTATAT
63 GTATGAATTTATAT
* * * *
398784 ATGTATATGTGAGGTTCGAATGTGTATG-GTTATACATGTATAAGTT
1 ATGTATATATTAGATTCGAATATGTATGAG-TATACATGTATAAGTT
398830 TTATATTGAA
Statistics
Matches: 97, Mismatches: 20, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
76 35 0.36
77 5 0.05
78 55 0.57
79 2 0.02
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.43
Consensus pattern (76 bp):
ATGTATATATTAGATTCGAATATGTATGAGTATACATGTATAAGTTCATGTATTGAAATTAAGTA
TGAATTTATAT
Found at i:399344 original size:281 final size:280
Alignment explanation
Indices: 398842--399403 Score: 1043
Period size: 281 Copynumber: 2.0 Consensus size: 280
398832 ATATTGAATC
398842 AAAGGAATGAAATTATTAGCTTAGATTATTTTAATATCTTCAAATGTAGGATATGTTTTCTTTGG
1 AAAGGAATGAAATTATTAGCTTAGATTATTTTAATATCTTCAAATGTAGGATATGTTTTCTTTGG
*
398907 ATTAAATTTGATGCCATGAAATGTATAAATATTTAAGTAATTCGTAGGTTAAATGTACATTAATT
66 ATTAAATTTGATGCCATGAAATGTATAAATATTTAAGTAATTCGCAGGTTAAATGTACATTAATT
*
398972 AAGGTATGTTATAAGAAAATAGTATAATACTAGTAGTAGGATCTAAAGTATAAAGTTATATATAT
131 AAGGTACGTTATAAGAAAATAGTATAATACTAGTAGTAGGATCTAAAGTATAAAGTTATATATAT
*
399037 ATAAGTATTCGGTTGGATCATTGAGTTATCGAGATGGGTTTTGTGATTGAACTTTATATACCAAG
196 ATAAGTATTCGGTTGGATCATTGAGTTATCGAGATGGATTTTGTGATTGAACTTTATATACCAAG
399102 GTGGTTCAAAGATATAAGTT
261 GTGGTTCAAAGATATAAGTT
* *
399122 AAAGGAATGAAATTATTAGCTTAGATTATTTTAATATGTTCGAATGTAGGATATGTTTTCTTTGG
1 AAAGGAATGAAATTATTAGCTTAGATTATTTTAATATCTTCAAATGTAGGATATGTTTTCTTTGG
*
399187 ATTAAATTTTGATGCCATGAAATGTATATATATTTAAGTAATTCGCAGGTTAAATGTACATTAAT
66 ATTAAA-TTTGATGCCATGAAATGTATAAATATTTAAGTAATTCGCAGGTTAAATGTACATTAAT
399252 TAAGGTACGTTATAAGAAAATAGTATAATACTAGTAGTAGGATCTAAAGTATAAAGTTATATATA
130 TAAGGTACGTTATAAGAAAATAGTATAATACTAGTAGTAGGATCTAAAGTATAAAGTTATATATA
* *
399317 TATAAGTATTTGGTTGGATCATTGAGTTATTGAGATGGATTTTGTGATTGAACTTTATATACCAA
195 TATAAGTATTCGGTTGGATCATTGAGTTATCGAGATGGATTTTGTGATTGAACTTTATATACCAA
399382 GGTGGTTCAAAGATATAAGTT
260 GGTGGTTCAAAGATATAAGTT
399403 A
1 A
399404 TAAATTTTTG
Statistics
Matches: 273, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
280 69 0.25
281 204 0.75
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.39
Consensus pattern (280 bp):
AAAGGAATGAAATTATTAGCTTAGATTATTTTAATATCTTCAAATGTAGGATATGTTTTCTTTGG
ATTAAATTTGATGCCATGAAATGTATAAATATTTAAGTAATTCGCAGGTTAAATGTACATTAATT
AAGGTACGTTATAAGAAAATAGTATAATACTAGTAGTAGGATCTAAAGTATAAAGTTATATATAT
ATAAGTATTCGGTTGGATCATTGAGTTATCGAGATGGATTTTGTGATTGAACTTTATATACCAAG
GTGGTTCAAAGATATAAGTT
Found at i:399558 original size:41 final size:41
Alignment explanation
Indices: 399501--399689 Score: 256
Period size: 41 Copynumber: 4.6 Consensus size: 41
399491 CAGGCTTTGG
* * *
399501 GCCTAGCAAGCTAAGTGATGGTGAACTGAATCAGATTATAA
1 GCCTAGCAGGCTAAGTGACGGTGAACTGAATCAGGTTATAA
*
399542 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGACGGTGAACTGAATCAGGTTATAA
* *
399583 GCCTAGCAGGCTAAGTGACGGTGATCTAAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGACGGTGAACTGAATCAGGTTATAA
* * *
399624 GCCTAGCAGGCTAATTGCCGGT-AATCTGAATCAGGTTATCA
1 GCCTAGCAGGCTAAGTGACGGTGAA-CTGAATCAGGTTATAA
*
399665 GCTTAGCAGGCTAAGT-ACCGGTGAA
1 GCCTAGCAGGCTAAGTGA-CGGTGAA
399690 TCTGTTTAAA
Statistics
Matches: 130, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
40 1 0.01
41 127 0.98
42 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (41 bp):
GCCTAGCAGGCTAAGTGACGGTGAACTGAATCAGGTTATAA
Found at i:399859 original size:2 final size:2
Alignment explanation
Indices: 399852--399900 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
399842 GAAATTGTTG
* * *
399852 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
399894 TA TA TA T
1 TA TA TA T
399901 GCATACTTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:401904 original size:27 final size:27
Alignment explanation
Indices: 401874--401927 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
401864 TTAATACATT
401874 TTTATACTAATCTCATAAATATTCATA
1 TTTATACTAATCTCATAAATATTCATA
*
401901 TTTATACTAATCTTATAAATATTCATA
1 TTTATACTAATCTCATAAATATTCATA
401928 CTTAATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (27 bp):
TTTATACTAATCTCATAAATATTCATA
Found at i:404200 original size:24 final size:23
Alignment explanation
Indices: 404171--404225 Score: 94
Period size: 24 Copynumber: 2.4 Consensus size: 23
404161 GTTAGGTAAA
404171 ATCTTAAAATAAAGATATAGTTAT
1 ATCTTAAAATAAAGATATAGTT-T
404195 ATCTTAAAATAAAGATATAGTTT
1 ATCTTAAAATAAAGATATAGTTT
404218 AT-TTAAAA
1 ATCTTAAAA
404226 CTATCTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 6 0.19
23 3 0.10
24 22 0.71
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (23 bp):
ATCTTAAAATAAAGATATAGTTT
Found at i:406450 original size:41 final size:41
Alignment explanation
Indices: 406373--406696 Score: 409
Period size: 41 Copynumber: 7.9 Consensus size: 41
406363 TGAGTTTTTG
* *
406373 GGGCCTTTAGCGGCGTTTTTTCAA-AAACGCCGCTAATGCTC
1 GGGCCTTTAGCGGCG-TTTTTGAAGAAGCGCCGCTAATGCTC
* * * * **
406414 TGGTCTTTAGCGGCGTTTTTGAAGAAGCACCACTAATTATC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* *
406455 GGGCCTTTAGCAGCGTTTTTGGAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* * * * *
406496 TGGCCTTTAGCAGCGTTTTTGGATAAGCGCCACTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* * * *
406537 GGGACTTTAGCTGC-TTTTTGTAGAAGCCCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
*
406577 GGGCCTTTAGCGGCGTTTTTTGAAGAAGCGCCGCTAATGGTC
1 GGGCCTTTAGCGGCG-TTTTTGAAGAAGCGCCGCTAATGCTC
* *
406619 GGGCCTTTAGCGGCGTTTTTGGAGAAGTGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
*
406660 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAAT
406697 AATAATAAAA
Statistics
Matches: 243, Mismatches: 37, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
40 41 0.17
41 164 0.67
42 38 0.16
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
Found at i:411364 original size:31 final size:31
Alignment explanation
Indices: 411328--411395 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
411318 CACTCTGTTG
411328 AGTTGCCATTCTCTATCCCTTCTAATTTATC
1 AGTTGCCATTCTCTATCCCTTCTAATTTATC
**
411359 AGTTGCCATTCTCTATGTCTTCTAATTTATC
1 AGTTGCCATTCTCTATCCCTTCTAATTTATC
411390 AGTTGC
1 AGTTGC
411396 AAGAAATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.19, C:0.25, G:0.10, T:0.46
Consensus pattern (31 bp):
AGTTGCCATTCTCTATCCCTTCTAATTTATC
Found at i:414050 original size:43 final size:43
Alignment explanation
Indices: 413983--414081 Score: 144
Period size: 43 Copynumber: 2.3 Consensus size: 43
413973 TTGTGTTATT
* * *
413983 TTTAGCGACGTTTTTGCGAGAAGCGCCGCTAAAGGTAGTGGTC
1 TTTAGCGGCGTTTGTGCGAAAAGCGCCGCTAAAGGTAGTGGTC
* **
414026 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGCGAAAAGCGCCGCTAAAGGTAGTGGTC
414069 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
414082 TTAGAAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGCGAAAAGCGCCGCTAAAGGTAGTGGTC
Found at i:415365 original size:13 final size:13
Alignment explanation
Indices: 415347--415372 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
415337 CCACAGCCCA
415347 CATGCCCATGTGG
1 CATGCCCATGTGG
415360 CATGCCCATGTGG
1 CATGCCCATGTGG
415373 GTTCACACCC
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:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
CATGCCCATGTGG
Found at i:417120 original size:28 final size:28
Alignment explanation
Indices: 417088--417144 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
417078 CAAAAACACC
417088 TGATCAGCTATAGAGTACTCAATATCCT
1 TGATCAGCTATAGAGTACTCAATATCCT
* *
417116 TGATCAGCTGTAGAGTATTCAATATCCT
1 TGATCAGCTATAGAGTACTCAATATCCT
417144 T
1 T
417145 TCTTTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (28 bp):
TGATCAGCTATAGAGTACTCAATATCCT
Found at i:420920 original size:20 final size:19
Alignment explanation
Indices: 420891--420929 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
420881 AACCAACCTT
420891 GGGTATTGGGTTGGGTTTA
1 GGGTATTGGGTTGGGTTTA
*
420910 GGGTCATTGGGTTGTGTTTA
1 GGGT-ATTGGGTTGGGTTTA
420930 TAAAGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.10, C:0.03, G:0.44, T:0.44
Consensus pattern (19 bp):
GGGTATTGGGTTGGGTTTA
Found at i:424124 original size:12 final size:12
Alignment explanation
Indices: 424102--424137 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
424092 CCAGAGTAGG
424102 TTTGTAAAAAAAA
1 TTTG-AAAAAAAA
424115 TTTGAAAAAAAA
1 TTTGAAAAAAAA
424127 -TTGAAAAAAAA
1 TTTGAAAAAAAA
424138 AAGAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.48
12 8 0.35
13 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (12 bp):
TTTGAAAAAAAA
Found at i:428509 original size:12 final size:11
Alignment explanation
Indices: 428492--428521 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
428482 GTAGGTTCGT
*
428492 AAAAAAATTTG
1 AAAAAAAATTG
428503 AAAAAAAATTG
1 AAAAAAAATTG
428514 AAAAAAAA
1 AAAAAAAA
428522 GGAACAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:435914 original size:20 final size:20
Alignment explanation
Indices: 435851--436017 Score: 112
Period size: 20 Copynumber: 8.3 Consensus size: 20
435841 GCATCATTGA
435851 TGCAAAACAGGGGCACAGATG
1 TGCAAAA-AGGGGCACAGATG
** *
435872 TGCAGTCAA-GGGCACCA-AAG
1 TGCA-AAAAGGGGCA-CAGATG
*
435892 TGCAAAAAGGGACACAGATG
1 TGCAAAAAGGGGCACAGATG
* * *
435912 TGCAAGAAGGGGCACCGATA
1 TGCAAAAAGGGGCACAGATG
*
435932 TGCAAACAAGGGTGCA-A-ATA
1 TGCAAA-AAGGG-GCACAGATG
*
435952 TGCAAACAGGGGCACAGATG
1 TGCAAAAAGGGGCACAGATG
* * *
435972 TGCAAATAA-AGGTACCGATG
1 TGCAAA-AAGGGGCACAGATG
*
435992 TGCAAATAGGGGCATC-GATG
1 TGCAAAAAGGGGCA-CAGATG
436012 TGCAAA
1 TGCAAA
436018 CATAAATAAT
Statistics
Matches: 113, Mismatches: 22, Indels: 23
0.72 0.14 0.15
Matches are distributed among these distances:
18 3 0.03
19 10 0.09
20 82 0.73
21 14 0.12
22 4 0.04
ACGTcount: A:0.38, C:0.18, G:0.31, T:0.13
Consensus pattern (20 bp):
TGCAAAAAGGGGCACAGATG
Found at i:437374 original size:28 final size:28
Alignment explanation
Indices: 437342--437466 Score: 196
Period size: 28 Copynumber: 4.5 Consensus size: 28
437332 GACTTTCGAT
437342 ACTAAGTGTGCGAGTTTAATTGTAAAGC
1 ACTAAGTGTGCGAGTTTAATTGTAAAGC
*
437370 ACTAAGTGTGCTAGTTTAATTGTAAAGC
1 ACTAAGTGTGCGAGTTTAATTGTAAAGC
*
437398 ACTAAGTGTGCGAGTTTAATGGTAAAGC
1 ACTAAGTGTGCGAGTTTAATTGTAAAGC
* * **
437426 ACTAAGTGTGCGAGTTTGATTATTGAGC
1 ACTAAGTGTGCGAGTTTAATTGTAAAGC
437454 ACTAAGTGTGCGA
1 ACTAAGTGTGCGA
437467 ACTTATTAAA
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 89 1.00
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.32
Consensus pattern (28 bp):
ACTAAGTGTGCGAGTTTAATTGTAAAGC
Found at i:438221 original size:23 final size:23
Alignment explanation
Indices: 438192--438388 Score: 171
Period size: 23 Copynumber: 8.5 Consensus size: 23
438182 TGATGCTTAA
*
438192 ATGCTGCCCAATTTCTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * *
438215 ATACTGCTCAATTTGTTGCATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * * *
438238 ATGCTGTCTAATTTTTATGCT-TAA
1 ATGCTGCCCAATTTGT-TG-TATAT
* * * *
438262 ATGCTTCTCAATTTGGTATATAT
1 ATGCTGCCCAATTTGTTGTATAT
438285 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * * * *
438308 AAGCTGTCCAATTTTGGTGTAAAA
1 ATGCTGCCCAA-TTTGTTGTATAT
* *
438332 ATACTGCTCAATTTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
*
438355 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
*
438378 ATGCTGTCCAA
1 ATGCTGCCCAA
438389 ATTTTGGTGT
Statistics
Matches: 131, Mismatches: 39, Indels: 8
0.74 0.22 0.04
Matches are distributed among these distances:
22 1 0.01
23 100 0.76
24 30 0.23
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (23 bp):
ATGCTGCCCAATTTGTTGTATAT
Found at i:438297 original size:70 final size:70
Alignment explanation
Indices: 438178--438394 Score: 274
Period size: 70 Copynumber: 3.1 Consensus size: 70
438168 TGTTCATGTT
* * * * *
438178 ATTTTGATGCTTAAATGCTGCCCAATTTCTTGTATATATACTGCTCAATTTGTTGCATATATGCT
1 ATTTTGATGCTTAAATGCTGCTCAATTTGTTGTATATATGCTGCCCAATTTGTTGTATATATGCT
*
438243 GTCTA
66 GTCCA
* * * * *
438248 ATTTTTATGCTTAAATGCTTCTCAATTTGGTATATATATGCTGCCCAATTTGTTGTATATAAGCT
1 ATTTTGATGCTTAAATGCTGCTCAATTTGTTGTATATATGCTGCCCAATTTGTTGTATATATGCT
438313 GTCCA
66 GTCCA
* * * *
438318 ATTTTGGTG-TAAAAATACTGCTCAATTTGTTGTATATATGCTGCCCAAATTGTTGTATATATGC
1 ATTTTGATGCT-TAAATGCTGCTCAATTTGTTGTATATATGCTGCCCAATTTGTTGTATATATGC
438382 TGTCCAA
65 TGTCC-A
438389 ATTTTG
1 ATTTTG
438395 GTGTGAAAAT
Statistics
Matches: 125, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
69 1 0.01
70 117 0.94
71 7 0.06
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (70 bp):
ATTTTGATGCTTAAATGCTGCTCAATTTGTTGTATATATGCTGCCCAATTTGTTGTATATATGCT
GTCCA
Found at i:438389 original size:23 final size:23
Alignment explanation
Indices: 438192--438446 Score: 160
Period size: 23 Copynumber: 10.9 Consensus size: 23
438182 TGATGCTTAA
* *
438192 ATGCTGCCCAATTTCTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* *
438215 ATACTG-CTCAATTTGTTGCATAT
1 ATGCTGTC-CAATTTGTTGTATAT
* * *
438238 ATGCTGTCTAATTTTTATGCT-TAA
1 ATGCTGTCCAATTTGT-TG-TATAT
* *
438262 ATGCT-TCTCAATTTGGTATATAT
1 ATGCTGTC-CAATTTGTTGTATAT
*
438285 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * * *
438308 AAGCTGTCCAATTTTGGTGTAAAA
1 ATGCTGTCCAA-TTTGTTGTATAT
*
438332 ATACTG-CTCAATTTGTTGTATAT
1 ATGCTGTC-CAATTTGTTGTATAT
* *
438355 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* *
438378 ATGCTGTCCAAATTTTGGTGTGA-AA
1 ATGCTGTCC-AA-TTTGTTGT-ATAT
* * * * *
438403 ATGCTGTCTAGTTTGGTATATAA
1 ATGCTGTCCAATTTGTTGTATAT
* *
438426 ATGCTGTCCAAATTGATGTAT
1 ATGCTGTCCAATTTGTTGTAT
438447 GAGGGCTGTC
Statistics
Matches: 178, Mismatches: 40, Indels: 28
0.72 0.16 0.11
Matches are distributed among these distances:
22 3 0.02
23 123 0.69
24 36 0.20
25 15 0.08
26 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (23 bp):
ATGCTGTCCAATTTGTTGTATAT
Found at i:438392 original size:47 final size:46
Alignment explanation
Indices: 438192--438388 Score: 171
Period size: 47 Copynumber: 4.2 Consensus size: 46
438182 TGATGCTTAA
* * * * *
438192 ATGCTGCCCAATTTCTTGTATATATACTGCTCAATTTGTTGCATAT
1 ATGCTGCCCAATTTGTTGTATATATGCTGCCCAATTTGGTGTATAT
* * * * * * *
438238 ATGCTGTCTAATTTTTATGCT-TAAATGCTTCTCAATTTGGTATATAT
1 ATGCTGCCCAATTTGT-TG-TATATATGCTGCCCAATTTGGTGTATAT
* * * *
438285 ATGCTGCCCAATTTGTTGTATATAAGCTGTCCAATTTTGGTGTAAAA
1 ATGCTGCCCAATTTGTTGTATATATGCTGCCCAA-TTTGGTGTATAT
* * * *
438332 ATACTGCTCAATTTGTTGTATATATGCTGCCCAAATTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATATATGCTGCCCAATTTGGTGTATAT
*
438378 ATGCTGTCCAA
1 ATGCTGCCCAA
438389 ATTTTGGTGT
Statistics
Matches: 116, Mismatches: 31, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
45 1 0.01
46 40 0.34
47 74 0.64
48 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (46 bp):
ATGCTGCCCAATTTGTTGTATATATGCTGCCCAATTTGGTGTATAT
Found at i:438437 original size:71 final size:71
Alignment explanation
Indices: 438210--438446 Score: 257
Period size: 70 Copynumber: 3.4 Consensus size: 71
438200 CAATTTCTTG
* * * * * * ** *
438210 TATATATACTGCTCAATTTGTTGCATATATGCTGTCTAATTTTTATGCT-TAAATGCT-TCTCAA
1 TATATATGCTGCCCAAATTGTTGTATATAAGCTGTCCAATTTTGGTG-TAAAAATGCTGTCTCAA
438273 TTTGGTA
65 TTTGGTA
* *
438280 TATATATGCTGCCCAATTTGTTGTATATAAGCTGTCCAATTTTGGTGTAAAAATACTG-CTCAAT
1 TATATATGCTGCCCAAATTGTTGTATATAAGCTGTCCAATTTTGGTGTAAAAATGCTGTCTCAAT
* *
438344 TTGTTG
66 TTGGTA
* * *
438350 TATATATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTGAAAATGCTGTCT-AG
1 TATATATGCTGCCCAAATTGTTGTATATAAGCTGTCC-AATTTTGGTGTAAAAATGCTGTCTCAA
438414 TTTGGTA
65 TTTGGTA
* * *
438421 TATAAATGCTGTCCAAATTGATGTAT
1 TATATATGCTGCCCAAATTGTTGTAT
438447 GAGGGCTGTC
Statistics
Matches: 142, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
69 1 0.01
70 91 0.64
71 48 0.34
72 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.43
Consensus pattern (71 bp):
TATATATGCTGCCCAAATTGTTGTATATAAGCTGTCCAATTTTGGTGTAAAAATGCTGTCTCAAT
TTGGTA
Found at i:443222 original size:22 final size:22
Alignment explanation
Indices: 443178--443220 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
443168 TTTCGAAATT
*
443178 TAAAATATTTTGATAATTTAAA
1 TAAAACATTTTGATAATTTAAA
443200 TAAAACATTTTGA-AATTTAAA
1 TAAAACATTTTGATAATTTAAA
443221 ATCATCTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (22 bp):
TAAAACATTTTGATAATTTAAA
Found at i:445886 original size:22 final size:22
Alignment explanation
Indices: 445842--445884 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
445832 TTTCGAAATT
*
445842 TAAAATATTTTGATAATTTAAA
1 TAAAACATTTTGATAATTTAAA
445864 TAAAACATTTTGA-AATTTAAA
1 TAAAACATTTTGATAATTTAAA
445885 ATCATCTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (22 bp):
TAAAACATTTTGATAATTTAAA
Found at i:447236 original size:31 final size:31
Alignment explanation
Indices: 447181--447246 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
447171 AACAACAGAG
447181 TGACTTAAATAAAAACTTTTGAATAGTCCAA
1 TGACTTAAATAAAAACTTTTGAATAGTCCAA
* * *
447212 TGACTTGAATGAAAA-TTTTCGAATAGTTCAA
1 TGACTTAAATAAAAACTTTT-GAATAGTCCAA
447243 TGAC
1 TGAC
447247 CAACTTATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTGAATAGTCCAA
Found at i:459261 original size:9 final size:9
Alignment explanation
Indices: 459244--459273 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
459234 ATTAATTCCC
459244 TTTTCTTTA
1 TTTTCTTTA
*
459253 TTTTGTTTA
1 TTTTCTTTA
459262 TTTTCTTTA
1 TTTTCTTTA
459271 TTT
1 TTT
459274 GATTGTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (9 bp):
TTTTCTTTA
Found at i:459273 original size:75 final size:75
Alignment explanation
Indices: 459153--459355 Score: 255
Period size: 75 Copynumber: 2.7 Consensus size: 75
459143 TATCGTATTT
* * *
459153 TTTTGCCATCAATTTCCTTGTCTTTGTTTT-TTTATTTTATTTATTTGATTTTTTAATTGTCATC
1 TTTTGCCATCAATTCCCTTTTCTTTATTTTGTTTATTTTATTTATTTGATTTTTTAATTGTCATC
** *
459217 ATTGTCTCTA
66 ATTACCTATA
* * * *
459227 TTTTGCCATTAATTCCCTTTTCTTTATTTTGTTTATTTTCTTTATTTGATTGTTTAGTTGTCATC
1 TTTTGCCATCAATTCCCTTTTCTTTATTTTGTTTATTTTATTTATTTGATTTTTTAATTGTCATC
*
459292 ATTACCTATG
66 ATTACCTATA
* * * *
459302 TTTTGCCATCAAATCCTTTTTCTTTCTTTTGTTTATTTTTATTTATTTTATTTT
1 TTTTGCCATCAATTCCCTTTTCTTTATTTTGTTTA-TTTTATTTATTTGATTTT
459356 GTTTTAGTTT
Statistics
Matches: 109, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
74 26 0.24
75 68 0.62
76 15 0.14
ACGTcount: A:0.16, C:0.14, G:0.07, T:0.63
Consensus pattern (75 bp):
TTTTGCCATCAATTCCCTTTTCTTTATTTTGTTTATTTTATTTATTTGATTTTTTAATTGTCATC
ATTACCTATA
Found at i:463328 original size:17 final size:17
Alignment explanation
Indices: 463308--463348 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
463298 TTTGGGCGTA
*
463308 TGGGCCACACGGGCATG
1 TGGGCCACACGGGAATG
*
463325 TGGGCCCATACGGGAATG
1 TGGG-CCACACGGGAATG
463343 TGGGCC
1 TGGGCC
463349 CAAAATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.17, C:0.27, G:0.41, T:0.15
Consensus pattern (17 bp):
TGGGCCACACGGGAATG
Found at i:463343 original size:18 final size:18
Alignment explanation
Indices: 463316--463350 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
463306 TATGGGCCAC
*
463316 ACGGGCATGTGGGCCCAT
1 ACGGGAATGTGGGCCCAT
463334 ACGGGAATGTGGGCCCA
1 ACGGGAATGTGGGCCCA
463351 AAATTTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.26, G:0.40, T:0.14
Consensus pattern (18 bp):
ACGGGAATGTGGGCCCAT
Found at i:470263 original size:6 final size:6
Alignment explanation
Indices: 470252--470286 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
470242 GGTTTTCTTC
470252 AAAATG AAAATG AAAATG AAAATAG AGAAATG AAA
1 AAAATG AAAATG AAAATG AAAAT-G A-AAATG AAA
470287 TCATTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.70
7 4 0.15
8 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:470334 original size:13 final size:14
Alignment explanation
Indices: 470316--470349 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
470306 ATTTTCTCCC
*
470316 AAATGAAAAA-GAA
1 AAATGAAAAATAAA
470329 AAATGAAAAATAAA
1 AAATGAAAAATAAA
470343 AAATGAA
1 AAATGAA
470350 TTTATGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (14 bp):
AAATGAAAAATAAA
Found at i:470336 original size:7 final size:7
Alignment explanation
Indices: 470316--470349 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
470306 ATTTTCTCCC
470316 AAATGAA
1 AAATGAA
470323 AAA-GAA
1 AAATGAA
470329 AAATGAA
1 AAATGAA
*
470336 AAATAAA
1 AAATGAA
470343 AAATGAA
1 AAATGAA
470350 TTTATGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAATGAA
Found at i:476419 original size:75 final size:75
Alignment explanation
Indices: 476317--476497 Score: 245
Period size: 75 Copynumber: 2.4 Consensus size: 75
476307 CTTTCAGTGG
* * *
476317 TATCGCAATATCCTCTTTAGGTATCGCGATATCTACCCTCCAAGGAAAACCTCCAAATTTAAATA
1 TATCGCAATATCCTCTTTGGGTATCGCGATATCCACCCTCCAAGGAAAACCCCCAAATTTAAATA
* **
476382 CTGCCTTAGA
66 ATGCCCGAGA
* ** * *
476392 TATTGCGGTATCCTCTTTGGGTATCGCGATATCCACCCTCCAAGGAAGACCCCCAAGTTTAAATA
1 TATCGCAATATCCTCTTTGGGTATCGCGATATCCACCCTCCAAGGAAAACCCCCAAATTTAAATA
476457 ATGCCCGAGA
66 ATGCCCGAGA
*
476467 TATCGCAATATCCTCTTCTGGGTATCACGAT
1 TATCGCAATATCCTCTT-TGGGTATCGCGAT
476498 CACTTTTATT
Statistics
Matches: 90, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
75 78 0.87
76 12 0.13
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (75 bp):
TATCGCAATATCCTCTTTGGGTATCGCGATATCCACCCTCCAAGGAAAACCCCCAAATTTAAATA
ATGCCCGAGA
Found at i:481892 original size:25 final size:25
Alignment explanation
Indices: 481864--481911 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
481854 CAAGCGAGTC
481864 ATATCAGGAAGCTCACAAAGAGCCT
1 ATATCAGGAAGCTCACAAAGAGCCT
** * *
481889 ATATTGGGACGCTCATAAAGAGC
1 ATATCAGGAAGCTCACAAAGAGC
481912 TACGGTATGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.19
Consensus pattern (25 bp):
ATATCAGGAAGCTCACAAAGAGCCT
Found at i:482003 original size:64 final size:64
Alignment explanation
Indices: 481895--482014 Score: 159
Period size: 64 Copynumber: 1.9 Consensus size: 64
481885 GCCTATATTG
* * * * * * *
481895 GGACGCTCATAAAGAGCTACGGTATGTCTGCAATATATGTAGGATCAATATCGATCATATAACA
1 GGACGCTCACAAAGAGCTACGGTATATCCGCAAAACATGCAGGATCAATACCGATCATATAACA
* *
481959 GGACGCTTACAAAGAGCTGCGGTATATCCGCAAAACATGCAGGATCAATACCGATC
1 GGACGCTCACAAAGAGCTACGGTATATCCGCAAAACATGCAGGATCAATACCGATC
482015 GGGATGCTCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 47 1.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.23
Consensus pattern (64 bp):
GGACGCTCACAAAGAGCTACGGTATATCCGCAAAACATGCAGGATCAATACCGATCATATAACA
Found at i:486696 original size:16 final size:16
Alignment explanation
Indices: 486677--486723 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
486667 TTTGAAGGTA
*
486677 ATTATTTATTAAATAT
1 ATTATTAATTAAATAT
* *
486693 ATTATAAATCAAATAT
1 ATTATTAATTAAATAT
486709 ATTTATTAATTAAAT
1 A-TTATTAATTAAAT
486724 GAAACGAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTATTAATTAAATAT
Found at i:491277 original size:45 final size:44
Alignment explanation
Indices: 491227--491319 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
491217 GGTTCGCTGT
*
491227 AATGGAATAGAGGC-GTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGA-ACTGTAATAGT-ATTC-ATGTGTTTGGTTGAATGG
*
491272 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
491316 AATG
1 AATG
491320 ATATTGTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 1 0.02
44 24 0.55
45 19 0.43
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
Found at i:501429 original size:44 final size:43
Alignment explanation
Indices: 501377--501493 Score: 139
Period size: 44 Copynumber: 2.7 Consensus size: 43
501367 TATGAGTTAT
* *
501377 CGTGTAAGACCACGTCTGGAACATTGGCATGGAT-TTGAGATTTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGATGTT-AGA-TTA
* *
501421 CGTGTAAGACC-CTGTCTGGGACAGTGGCATCGATGTTTGATTA
1 CGTGTAAGACCAC-GTCTGGGACATTGGCATCGATGTTAGATTA
* *
501464 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACATTGGCAT
501494 TATACGAGCT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
43 29 0.46
44 32 0.51
45 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCGATGTTAGATTA
Found at i:502801 original size:6 final size:6
Alignment explanation
Indices: 502790--502814 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
502780 AGATGTCTAT
502790 TATACA TATACA TATACA TATACA T
1 TATACA TATACA TATACA TATACA T
502815 CCATAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (6 bp):
TATACA
Found at i:513728 original size:28 final size:29
Alignment explanation
Indices: 513687--513743 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
513677 ATTCCTGGGA
*
513687 TATTTTCTCAGAACTCATCTCGTCAAAAT
1 TATTTTCTCAGAACCCATCTCGTCAAAAT
513716 TATTTT-TCAGAACCCATCTCGTCAAAAT
1 TATTTTCTCAGAACCCATCTCGTCAAAAT
513744 AAATTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (29 bp):
TATTTTCTCAGAACCCATCTCGTCAAAAT
Found at i:513759 original size:29 final size:28
Alignment explanation
Indices: 513688--513751 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
513678 TTCCTGGGAT
* *
513688 ATTTTCTCAGAACTCATCTCGTCAAAATT
1 ATTTT-TCAGAACCCATCTCGTCAAAATA
513717 ATTTTTCAGAACCCATCTCGTCAAAATAA
1 ATTTTTCAGAACCCATCTCGTCAAAAT-A
513746 ATTTTT
1 ATTTTT
513752 TTGAACCCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 21 0.66
29 11 0.34
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (28 bp):
ATTTTTCAGAACCCATCTCGTCAAAATA
Found at i:513887 original size:19 final size:18
Alignment explanation
Indices: 513859--513896 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
513849 CTAAAACACT
513859 AATTAAT-AAACACTTAAA
1 AATTAATAAAACAC-TAAA
513877 AATTAAATAAAACACTAAA
1 AATT-AATAAAACACTAAA
513896 A
1 A
513897 CGCTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 8 0.44
20 6 0.33
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.24
Consensus pattern (18 bp):
AATTAATAAAACACTAAA
Found at i:513924 original size:22 final size:21
Alignment explanation
Indices: 513887--513962 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 21
513877 AATTAAATAA
*
513887 AACACTAAAACGCTAATTTAAT
1 AACACT-AAACCCTAATTTAAT
513909 GAACACTAAACCCTAA-TTAA-
1 -AACACTAAACCCTAATTTAAT
513929 AAC-CTTAAACCCTAATTTAAT
1 AACAC-TAAACCCTAATTTAAT
*
513950 ATACCCTAAACCC
1 A-ACACTAAACCC
513963 CTAAAAAACG
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
18 1 0.02
19 13 0.28
20 4 0.09
21 5 0.11
22 17 0.36
23 7 0.15
ACGTcount: A:0.46, C:0.26, G:0.03, T:0.25
Consensus pattern (21 bp):
AACACTAAACCCTAATTTAAT
Found at i:513959 original size:41 final size:42
Alignment explanation
Indices: 513842--513962 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 42
513832 TTATTTTTCC
* * * *** *
513842 TAAAACTCTAAAACACTAA-TTAATAAACACTTAAAAATTAAA
1 TAAAACACTAAAACCCTAATTTAATGAACAC-TAAACCCTAAT
*
513884 TAAAACACTAAAACGCTAATTTAATGAACACTAAACCCTAAT
1 TAAAACACTAAAACCCTAATTTAATGAACACTAAACCCTAAT
* *
513926 TAAAAC-CTTAAACCCTAATTTAAT-ATACCCTAAACCC
1 TAAAACACTAAAACCCTAATTTAATGA-ACACTAAACCC
513963 CTAAAAAACG
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.01
41 26 0.39
42 30 0.45
43 10 0.15
ACGTcount: A:0.51, C:0.21, G:0.02, T:0.26
Consensus pattern (42 bp):
TAAAACACTAAAACCCTAATTTAATGAACACTAAACCCTAAT
Found at i:514393 original size:19 final size:19
Alignment explanation
Indices: 514369--514414 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
514359 GAAACTCCTC
514369 TAATATATTAT-TATATAAA
1 TAATATATTATGTATAT-AA
514388 TAATATATTATGTATATAA
1 TAATATATTATGTATATAA
514407 TAATATAT
1 TAATATAT
514415 AAATACATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TAATATATTATGTATATAA
Found at i:514396 original size:16 final size:16
Alignment explanation
Indices: 514377--514419 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
514367 TCTAATATAT
514377 TATTATATAAATAATA
1 TATTATATAAATAATA
* *
514393 TATTATGTATATAATA
1 TATTATATAAATAATA
514409 -A-TATATAAATA
1 TATTATATAAATA
514420 CATTTAAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 8 0.35
15 1 0.04
16 14 0.61
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TATTATATAAATAATA
Found at i:516146 original size:20 final size:20
Alignment explanation
Indices: 516117--516159 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
516107 AAAAAAAGAG
516117 AAATAGTAAATTATCAGAA-A
1 AAATAGTAAATTA-CAGAATA
*
516137 AAATATTAAATTACAGAATA
1 AAATAGTAAATTACAGAATA
516157 AAA
1 AAA
516160 GAATTTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.26
Consensus pattern (20 bp):
AAATAGTAAATTACAGAATA
Found at i:526581 original size:31 final size:31
Alignment explanation
Indices: 526545--526603 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
526535 AAAATATATT
* * *
526545 TTTTATACTTTTTTAATTTTTTGAAAATACC
1 TTTTATAATTTTTTAAGTTTTTCAAAATACC
*
526576 TTTTATAATTTTTTGAGTTTTTCAAAAT
1 TTTTATAATTTTTTAAGTTTTTCAAAAT
526604 TTAAAAACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (31 bp):
TTTTATAATTTTTTAAGTTTTTCAAAATACC
Found at i:529088 original size:23 final size:24
Alignment explanation
Indices: 529048--529092 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
529038 GAAATACTTG
529048 AGGATTCAATAAGTAATTAAACTA
1 AGGATTCAATAAGTAATTAAACTA
529072 AGGATCTCAA-AA-TAATTAAAC
1 AGGAT-TCAATAAGTAATTAAAC
529093 CATTGTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.45
24 7 0.35
25 4 0.20
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (24 bp):
AGGATTCAATAAGTAATTAAACTA
Found at i:531006 original size:27 final size:28
Alignment explanation
Indices: 530968--531031 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
530958 CAAAATGGGA
* *
530968 AAATAAAATTAA-AAATC-AAAACTACAC
1 AAATAACATTAACAAA-CGAAAACCACAC
*
530995 AAATAACATTAACAAACGAAAACCACTC
1 AAATAACATTAACAAACGAAAACCACAC
531023 AAATAACAT
1 AAATAACAT
531032 GCATATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 12 0.38
28 20 0.62
ACGTcount: A:0.62, C:0.19, G:0.02, T:0.17
Consensus pattern (28 bp):
AAATAACATTAACAAACGAAAACCACAC
Found at i:532835 original size:50 final size:49
Alignment explanation
Indices: 532772--532916 Score: 139
Period size: 50 Copynumber: 2.9 Consensus size: 49
532762 TCTTGAGAAA
* *
532772 ATTGTCTCTATAGTTGCGACATTCCATTGATGAAGTTACGACATCAAGCT
1 ATTGTCTCCATAGTTGCGACATTCC-TTGATGAAGTCACGACATCAAGCT
* * * * * * *
532822 GTTGTCTCCATAGTCGTGACATTCCCT-ACTAAAGTCGCAACATCAAGCT
1 ATTGTCTCCATAGTTGCGACATTCCTTGA-TGAAGTCACGACATCAAGCT
* * * *
532871 ACTGTCTCCATAGTTGCAATATTCCCTTGTTGAAGTCACGACATCA
1 ATTGTCTCCATAGTTGCGACATT-CCTTGATGAAGTCACGACATCA
532917 TGATATTACT
Statistics
Matches: 72, Mismatches: 20, Indels: 6
0.73 0.20 0.06
Matches are distributed among these distances:
48 1 0.01
49 34 0.47
50 37 0.51
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (49 bp):
ATTGTCTCCATAGTTGCGACATTCCTTGATGAAGTCACGACATCAAGCT
Found at i:544102 original size:23 final size:23
Alignment explanation
Indices: 544069--544120 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
544059 ATAAGTGTCA
* *
544069 CACTGATATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCAAAGCTAC
544092 CACTGAAATGTAGCCAAAGCTAC
1 CACTGAAATGTAGCCAAAGCTAC
544115 CACTGA
1 CACTGA
544121 TCAATAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (23 bp):
CACTGAAATGTAGCCAAAGCTAC
Found at i:545589 original size:16 final size:16
Alignment explanation
Indices: 545568--545599 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
545558 TGATTGAAAG
*
545568 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
545584 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
545600 GCAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:550413 original size:46 final size:46
Alignment explanation
Indices: 550323--550443 Score: 192
Period size: 46 Copynumber: 2.7 Consensus size: 46
550313 AATACAAACC
* *
550323 AAGATAATTTTATT-A-ATATGCTAATGGAATAATAAATGAATTTT
1 AAGATAATTTTATTAATATATACTAATGGAACAATAAATGAATTTT
*
550367 AAGATAATTTTATTAATATATACTAATGGAACAATAAATGAGTTTT
1 AAGATAATTTTATTAATATATACTAATGGAACAATAAATGAATTTT
*
550413 AAGATAATTTTGTTAATATATACTAATGGAA
1 AAGATAATTTTATTAATATATACTAATGGAA
550444 TTTTTAGAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 14 0.20
45 1 0.01
46 56 0.79
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (46 bp):
AAGATAATTTTATTAATATATACTAATGGAACAATAAATGAATTTT
Found at i:557251 original size:54 final size:53
Alignment explanation
Indices: 557193--557359 Score: 164
Period size: 54 Copynumber: 3.2 Consensus size: 53
557183 AAAGAAAAAA
*
557193 ATATATATAGAAATAATAACATATGGATAGAAAGTATAATATATATATACGTAC
1 ATATATATAGAAATAATAAAATATGGATAGAAAGTATAAT-TATATATACGTAC
** * * * * *
557247 ATATATAT-GAGTTAATAAATATATAGATCATAAAG-ATAATGAT-T-T-CATAT
1 ATATATATAGAAATAATAAA-ATATGGAT-AGAAAGTATAATTATATATACGTAC
* * *
557297 ATATATCTAGAAATTATAAAATATGTATAGAAAGTATAATGTATATATACGTAC
1 ATATATATAGAAATAATAAAATATGGATAGAAAGTATAAT-TATATATACGTAC
557351 ATATATATA
1 ATATATATA
557360 TAAGGTAATA
Statistics
Matches: 86, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
49 5 0.06
50 21 0.24
51 11 0.13
52 2 0.02
53 11 0.13
54 31 0.36
55 5 0.06
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (53 bp):
ATATATATAGAAATAATAAAATATGGATAGAAAGTATAATTATATATACGTAC
Found at i:557308 original size:104 final size:105
Alignment explanation
Indices: 557193--557392 Score: 303
Period size: 104 Copynumber: 1.9 Consensus size: 105
557183 AAAGAAAAAA
* *
557193 ATATATATAGAAATAATAACATATGGATAGAAAGTATAATATATATATACGTAC-ATATATATGA
1 ATATATATAGAAATAATAAAATATGGATAGAAAGTATAATATATATATACGTACAATATATATAA
* * *
557257 GTTAATAAATATATAGATCATAAAGATAATGATTTCATAT
66 GGTAATAAATATATAAATCATAAAAATAATGATTTCATAT
* * * *
557297 ATATATCTAGAAATTATAAAATATGTATAGAAAGTATAATGTATATATACGTACATATATATATA
1 ATATATATAGAAATAATAAAATATGGATAGAAAGTATAATATATATATACGTACA-ATATATATA
557362 AGGTAATAAATATATAAATCATAAAAATAAT
65 AGGTAATAAATATATAAATCATAAAAATAAT
557393 AATTACATGT
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
104 49 0.58
106 36 0.42
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.34
Consensus pattern (105 bp):
ATATATATAGAAATAATAAAATATGGATAGAAAGTATAATATATATATACGTACAATATATATAA
GGTAATAAATATATAAATCATAAAAATAATGATTTCATAT
Found at i:557345 original size:20 final size:20
Alignment explanation
Indices: 557297--557345 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
557287 GATTTCATAT
* *
557297 ATATATCTAGAAATTATAAA
1 ATATATATAGAAAGTATAAA
* *
557317 ATATGTATAGAAAGTATAAT
1 ATATATATAGAAAGTATAAA
*
557337 GTATATATA
1 ATATATATA
557346 CGTACATATA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (20 bp):
ATATATATAGAAAGTATAAA
Found at i:558990 original size:43 final size:40
Alignment explanation
Indices: 558890--559000 Score: 123
Period size: 43 Copynumber: 2.7 Consensus size: 40
558880 ATTTACTTTG
*
558890 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGA
1 TCTGCT-CACTGCAACTTCAGGGAGATAAGACTAGATGCAA
* * * * *
558931 TCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGGTTGTAA
1 TCTGCTCACTGCAACTTCAGGGAGATAAGA-C--TAGATGCAA
*
558974 TCTGCTCACTGCAACTTTAGGGAGATA
1 TCTGCTCACTGCAACTTCAGGGAGATA
559001 GGATTGGTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
40 22 0.38
41 7 0.12
43 29 0.50
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (40 bp):
TCTGCTCACTGCAACTTCAGGGAGATAAGACTAGATGCAA
Found at i:559089 original size:44 final size:44
Alignment explanation
Indices: 559041--559223 Score: 129
Period size: 44 Copynumber: 4.2 Consensus size: 44
559031 TCTTGGAAAA
*
559041 ATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAG
1 ATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGGAG
* * ** * * * * * * *
559085 ATAAGATCTACAATCTTCAACCTACTCCGCTGCTACTCAAGGAG
1 ATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGGAG
* ** ** * * *
559129 ACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAAAG
1 ATAAGATTTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-GAG
*
559173 ATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAG
1 ATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGGAG
559217 ATAAGAT
1 ATAAGAT
559224 CTACAATCTT
Statistics
Matches: 95, Mismatches: 38, Indels: 12
0.66 0.26 0.08
Matches are distributed among these distances:
42 6 0.06
43 3 0.03
44 78 0.82
45 4 0.04
46 4 0.04
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (44 bp):
ATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGGAG
Found at i:559163 original size:132 final size:131
Alignment explanation
Indices: 559011--559272 Score: 488
Period size: 132 Copynumber: 2.0 Consensus size: 131
559001 GGATTGGTTT
559011 CTTAAATCTGCTTCCCACTATCTTGGAAAAATAAGATTTGCCGTCTTCGATCTGCTCCACTACTG
1 CTTAAATCTGCTTCCCACTATCTTGGAAAAATAAGATTTGCCGTCTTCGATCTGCTCCACTACTG
559076 CTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTACTCAAGGAGACAAGGCTTGGT
66 CTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTACTCAAGGAGACAAGGC-TGGT
559141 GG
130 GG
*
559143 CTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTG
1 CTTAAATCTGCTTCCCACTATCTTGGAAAAATAAGATTTGCCGTCTTCGATCTGCTCCACTACTG
* *
559208 CTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTGGTG
66 CTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTACTCAAGGAGACAAGGCTGGTG
559273 TCTTCGATCT
Statistics
Matches: 127, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
131 5 0.04
132 122 0.96
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (131 bp):
CTTAAATCTGCTTCCCACTATCTTGGAAAAATAAGATTTGCCGTCTTCGATCTGCTCCACTACTG
CTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTACTCAAGGAGACAAGGCTGGTG
G
Found at i:559234 original size:44 final size:44
Alignment explanation
Indices: 559054--559261 Score: 111
Period size: 44 Copynumber: 4.7 Consensus size: 44
559044 AGATTTGCCG
*
559054 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
* * * * * * * * * ***
559098 TCTTCAACCTACTCCGCTGCTACTCAAGGAGACAAG-GCT-TGG
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
* * * * **
559140 TGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAAAGATAAGATTTGCCG
1 T--CTTCAATCTGC-T-CCACTACTGCTTAGG-GAGATAAGATCTACAA
*
559186 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
* * * * *
559230 TCTTCAACCTACTCCGCTGCTGCTCAGGGAGA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGA
559262 CAAGGCTGGT
Statistics
Matches: 115, Mismatches: 39, Indels: 20
0.66 0.22 0.11
Matches are distributed among these distances:
42 7 0.06
43 5 0.04
44 92 0.80
45 5 0.04
46 6 0.05
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (44 bp):
TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
Found at i:559359 original size:44 final size:44
Alignment explanation
Indices: 559299--559720 Score: 427
Period size: 44 Copynumber: 9.5 Consensus size: 44
559289 CTCTCGGTGC
* * *
559299 AGGAAGGCAAGATCTGCTATCTTCGATCTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAT
** * * *
559343 ATAAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAATAT
* * *
559388 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATAT
* * * *
559432 AGGAAGACAGGATCTGCCATCTTCGATCTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAT
* * * * *
559476 ACGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAATAT
* * *
559521 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATAT
* * * * * * *
559565 AGGAAGATAGGATCTGGTACCTTTGATCTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAT
* * * *
559609 ATGAAGACAATATCTGCTTTCTTCGATCTACTTCAGCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCA-CACCAATAT
* * *
559654 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATAT
*
559698 AGGAAGACAAGATTTGCTATCTT
1 AGGAAGACAAGATCTGCTATCTT
559721 TACGGATCTG
Statistics
Matches: 302, Mismatches: 67, Indels: 17
0.78 0.17 0.04
Matches are distributed among these distances:
43 3 0.01
44 204 0.68
45 95 0.31
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (44 bp):
AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAT
Found at i:559401 original size:89 final size:89
Alignment explanation
Indices: 559299--559720 Score: 422
Period size: 89 Copynumber: 4.8 Consensus size: 89
559289 CTCTCGGTGC
* * ** *
559299 AGGAAGGCAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATAAAGACAAGATCTGCTTTC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTATC
*
559364 TTCGATCTACTTCGCCACCAGTAT
66 TTCGATCTACTTCGCCACCAATAT
* * * * * *
559388 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGCCAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATACAGGAAGACAAGATCTGCTAT
* * *
559452 CTTCGATCTACTTC-ACGCCAATAC
65 CTTCGATCTACTTCGCCACCAATAT
* * * * * **
559476 ACGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGC-AT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAATACAGGAAGACAAGATCTGCTAT
* *
559540 CTTCGATCCACTTCGCTACCAATAT
65 CTTCGATCTACTTCGCCACCAATAT
* * * * * * * * *
559565 AGGAAGATAGGATCTGGTACCTTTGATCTACTTCACGCCAATACATGAAGACAATATCTGCTTTC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTATC
*
559630 TTCGATCTACTTCAG-CACCAGTAT
66 TTCGATCTACTTC-GCCACCAATAT
* * * * *
559654 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATATAGGAAGACAAGATTTGCTAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATACAGGAAGACAAGATCTGCTAT
559718 CTT
65 CTT
559721 TACGGATCTG
Statistics
Matches: 266, Mismatches: 60, Indels: 14
0.78 0.18 0.04
Matches are distributed among these distances:
88 85 0.32
89 179 0.67
90 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (89 bp):
AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTATC
TTCGATCTACTTCGCCACCAATAT
Found at i:559446 original size:133 final size:133
Alignment explanation
Indices: 559299--559720 Score: 711
Period size: 133 Copynumber: 3.2 Consensus size: 133
559289 CTCTCGGTGC
* *
559299 AGGAAGGCAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATAAAGACAAGATCTGCTTTC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC
559364 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAA
66 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAA
559429 TAT
131 TAT
* * * *
559432 AGGAAGACAGGATCTGCCATCTTCGATCTACTTCACGCCAATACACGAAGATAAGATCTGCTTTC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC
559497 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAA
66 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAA
559562 TAT
131 TAT
* * * * * *
559565 AGGAAGATAGGATCTGGTACCTTTGATCTACTTCACGCCAATACATGAAGACAATATCTGCTTTC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC
559630 TTCGATCTACTTCAG-CACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCA
66 TTCGATCTACTTC-GCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCA
559694 ATAT
130 ATAT
*
559698 AGGAAGACAAGATTTGCTATCTT
1 AGGAAGACAAGATCTGCTATCTT
559721 TACGGATCTG
Statistics
Matches: 269, Mismatches: 19, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
133 268 1.00
134 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (133 bp):
AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC
TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAA
TAT
Found at i:567179 original size:20 final size:20
Alignment explanation
Indices: 567156--567193 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
567146 AAATATATAT
*
567156 ATAGAAATTATAAAATATGG
1 ATAGAAAGTATAAAATATGG
*
567176 ATAGAAAGTATAATATAT
1 ATAGAAAGTATAAAATAT
567194 ATATACGTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (20 bp):
ATAGAAAGTATAAAATATGG
Found at i:567208 original size:50 final size:50
Alignment explanation
Indices: 567154--567312 Score: 189
Period size: 50 Copynumber: 3.1 Consensus size: 50
567144 AAAAATATAT
567154 ATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATACGTAC
1 ATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATACGTAC
* * * *
567204 ATATATATAAGTTAATAAATATATAGATCATAAAG-ATAATGATTATATATA--TAT
1 ATATAGA-AA-TT-ATAAA-ATATGGAT-AGAAAGTATAAT-A-TATATATACGTAC
*
567258 ATATAGAAATTATAAAATATGTATAGAAAGTATAATATATATATACGTAC
1 ATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATACGTAC
567308 ATATA
1 ATATA
567313 TATAAGGTAA
Statistics
Matches: 90, Mismatches: 9, Indels: 20
0.76 0.08 0.17
Matches are distributed among these distances:
48 8 0.09
49 6 0.07
50 24 0.27
51 7 0.08
52 4 0.04
53 7 0.08
54 20 0.22
55 6 0.07
56 8 0.09
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.35
Consensus pattern (50 bp):
ATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATACGTAC
Found at i:567208 original size:54 final size:54
Alignment explanation
Indices: 567150--567316 Score: 206
Period size: 54 Copynumber: 3.2 Consensus size: 54
567140 AAAGAAAAAT
567150 ATATATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATACGTAC
1 ATATATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATACGTAC
* * *
567204 ATATATAT--AAGTTAATAAATATATAGATCATAAAG-ATAATGAT-TATATA--T--
1 ATATATATAGAAATT-ATAAA-ATATGGAT-AGAAAGTATAAT-ATATATATACGTAC
*
567254 ATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATATATACGTAC
1 ATATATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATACGTAC
567308 ATATATATA
1 ATATATATA
567317 AGGTAATAAA
Statistics
Matches: 94, Mismatches: 7, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
49 7 0.07
50 25 0.27
51 5 0.05
52 10 0.11
53 5 0.05
54 35 0.37
55 7 0.07
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (54 bp):
ATATATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATACGTAC
Found at i:567269 original size:104 final size:104
Alignment explanation
Indices: 567148--567360 Score: 390
Period size: 104 Copynumber: 2.0 Consensus size: 104
567138 ATAAAGAAAA
567148 ATATATATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATACGTACATATATATA
1 ATATATATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATACGTACATATATATA
* *
567213 AGTTAATAAATATATAGATCATAAAGATAATGATTATAT
66 AGGTAATAAATATATAGATCATAAAGATAATGATTACAT
*
567252 ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATATATACGTACATATATATA
1 ATATATATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATACGTACATATATATA
*
567317 AGGTAATAAATATATAGATTATAAAGATAATGATTACAT
66 AGGTAATAAATATATAGATCATAAAGATAATGATTACAT
567356 ATATA
1 ATATA
567361 AATTATAAAA
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 105 1.00
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (104 bp):
ATATATATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATACGTACATATATATA
AGGTAATAAATATATAGATCATAAAGATAATGATTACAT
Found at i:567282 original size:20 final size:20
Alignment explanation
Indices: 567254--567302 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
567244 GATTATATAT
*
567254 ATATATATAGAAATTATAAA
1 ATATATATAGAAAGTATAAA
* *
567274 ATATGTATAGAAAGTATAAT
1 ATATATATAGAAAGTATAAA
567294 ATATATATA
1 ATATATATA
567303 CGTACATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (20 bp):
ATATATATAGAAAGTATAAA
Found at i:567333 original size:50 final size:50
Alignment explanation
Indices: 567176--567334 Score: 157
Period size: 52 Copynumber: 3.1 Consensus size: 50
567166 TAAAATATGG
*
567176 ATAGAAAGTATAATATATATATACGTACATATATATAAGTTAATAAATAT
1 ATAGAAAGTATAATATATATATACGTACATATATATAAGATAATAAATAT
* * *
567226 ATAGATCATAAAG-ATAATGAT-TATATA--TATATATATAGAA-ATTATAAAATATGT
1 ATAG-----AAAGTATAAT-ATATATATACGTACATATATATAAGATAAT-AAATA--T
*
567280 ATAGAAAGTATAATATATATATACGTACATATATATAAGGTAATAAATAT
1 ATAGAAAGTATAATATATATATACGTACATATATATAAGATAATAAATAT
567330 ATAGA
1 ATAGA
567335 TTATAAAGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 28
0.71 0.07 0.23
Matches are distributed among these distances:
49 6 0.07
50 21 0.24
51 3 0.03
52 32 0.37
53 3 0.03
54 16 0.18
55 6 0.07
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.35
Consensus pattern (50 bp):
ATAGAAAGTATAATATATATATACGTACATATATATAAGATAATAAATAT
Found at i:568976 original size:42 final size:43
Alignment explanation
Indices: 568881--569017 Score: 197
Period size: 43 Copynumber: 3.2 Consensus size: 43
568871 AGAAATAAAT
* * *
568881 GCCGCTATAGATCATGACCTTTAGCGACGCTTTTCCCACAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCATTTCCCACAAAC
*
568924 GCCGCTATAGATCAGGACCTTTAGCGGCGCATTT-GCACAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCATTTCCCACAAAC
* *
568966 GCCGCTATAGATCAAGG-CCTTTAGCAGCGCCTTTCCCACAAAC
1 GCCGCTATAGATC-AGGACCTTTAGCGGCGCATTTCCCACAAAC
569009 GCCGCTATA
1 GCCGCTATA
569018 ACTCAAGACC
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
42 35 0.41
43 50 0.59
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.23
Consensus pattern (43 bp):
GCCGCTATAGATCAGGACCTTTAGCGGCGCATTTCCCACAAAC
Found at i:569103 original size:42 final size:43
Alignment explanation
Indices: 569031--569129 Score: 121
Period size: 42 Copynumber: 2.3 Consensus size: 43
569021 CAAGACCTGG
* * * *
569031 AAAAATCGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTC-C
1 AAAAA-CGCCACTATAGAACAAGACCTTTAGCGACGC-TTCTCGC
*
569075 ACAAACGCCACTATAGAACAAG-CCTTTAGCGACGCTTCTCGC
1 AAAAACGCCACTATAGAACAAGACCTTTAGCGACGCTTCTCGC
569117 AAAAACGCCACTA
1 AAAAACGCCACTA
569130 AAAACATAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
41 4 0.08
42 25 0.52
43 15 0.31
44 4 0.08
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.21
Consensus pattern (43 bp):
AAAAACGCCACTATAGAACAAGACCTTTAGCGACGCTTCTCGC
Found at i:569149 original size:114 final size:114
Alignment explanation
Indices: 568923--569132 Score: 273
Period size: 114 Copynumber: 1.8 Consensus size: 114
568913 TTCCCACAAA
* * * *
568923 CGCCGCTATAGATCAGGACCTTTAGCGGCGCATTTGCACAAACGCCGCTATAGATCAAGGCCTTT
1 CGCCGCTATAGATCAAGACCTTTAGCGGCGCATTTCCACAAACGCCACTATAGAACAAGGCCTTT
* * * * *
568988 AGCAGCGCCTTTCCCACAAACGCCGCTATAACTCAAGACCTGGAAAAAT
66 AGCAGCGCCTTTCCCAAAAACGCCACTAAAACTCAACACCTGAAAAAAT
*
569037 CGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCACTATAGAACAA-GCCTT
1 CGCCGCTATAGATCAAGACCTTTAGCGGCGC-ATTTCCACAAACGCCACTATAGAACAAGGCCTT
*
569101 TAGC-GACG-CTTCTCGCAAAAACGCCACTAAAA
65 TAGCAG-CGCCTT-TCCCAAAAACGCCACTAAAA
569133 ACATAACATT
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
113 4 0.05
114 57 0.68
115 23 0.27
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (114 bp):
CGCCGCTATAGATCAAGACCTTTAGCGGCGCATTTCCACAAACGCCACTATAGAACAAGGCCTTT
AGCAGCGCCTTTCCCAAAAACGCCACTAAAACTCAACACCTGAAAAAAT
Found at i:570679 original size:94 final size:95
Alignment explanation
Indices: 570514--570685 Score: 274
Period size: 94 Copynumber: 1.8 Consensus size: 95
570504 AAAGTACGTG
* *
570514 CTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAAGGGAAGCGCACAGAGGCAAT
1 CTGCAAGAATGGTATCACCAACTCTAAAAATTCAAAAACAAAAAAGGGAAGCGCACAGAGGCAAT
570579 GAAAGAGGAAGCATTAGAAAAAGGTACCTA
66 GAAAGAGGAAGCATTAGAAAAAGGTACCTA
** * **
570609 CTGCAAGAATGGTATTGCCAGCTCTAAAAATTCAAAAAC-AAAAAGGGAAGCGCGTAGAGGCAAT
1 CTGCAAGAATGGTATCACCAACTCTAAAAATTCAAAAACAAAAAAGGGAAGCGCACAGAGGCAAT
570673 GAAAGAGGAAGCA
66 GAAAGAGGAAGCA
570686 CTCAGGCTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
94 36 0.51
95 34 0.49
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (95 bp):
CTGCAAGAATGGTATCACCAACTCTAAAAATTCAAAAACAAAAAAGGGAAGCGCACAGAGGCAAT
GAAAGAGGAAGCATTAGAAAAAGGTACCTA
Found at i:571569 original size:2 final size:2
Alignment explanation
Indices: 571562--571586 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
571552 TCATGAAATT
571562 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
571587 CAATGTTGTC
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:576184 original size:15 final size:14
Alignment explanation
Indices: 576166--576268 Score: 68
Period size: 15 Copynumber: 7.1 Consensus size: 14
576156 TCGACCCCTA
576166 AATCCCTAAACCTT
1 AATCCCTAAACCTT
*
576180 AAAT-CCTTAACTCTT
1 -AATCCCTAAAC-CTT
* *
576195 AACCCCT-AACATCT
1 AATCCCTAAACCT-T
* *
576209 AACCCCTAAACCCCT
1 AATCCCTAAA-CCTT
*
576224 AATCCCTAAACCCCT
1 AATCCCTAAA-CCTT
576239 AATCCCTAAACCTT
1 AATCCCTAAACCTT
*
576253 AAATCCC-AACCCTT
1 -AATCCCTAAACCTT
576267 AA
1 AA
576269 ACCATAATCC
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
13 3 0.04
14 28 0.38
15 42 0.57
16 1 0.01
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (14 bp):
AATCCCTAAACCTT
Found at i:576204 original size:7 final size:7
Alignment explanation
Indices: 576194--576247 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
576184 CCTTAACTCT
576194 TAACCCC
1 TAACCCC
**
576201 TAACATC
1 TAACCCC
576208 TAACCCC
1 TAACCCC
576215 TAAACCCC
1 T-AACCCC
*
576223 TAATCCC
1 TAACCCC
576230 TAAACCCC
1 T-AACCCC
*
576238 TAATCCC
1 TAACCCC
576245 TAA
1 TAA
576248 ACCTTAAATC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
7 25 0.66
8 13 0.34
ACGTcount: A:0.35, C:0.44, G:0.00, T:0.20
Consensus pattern (7 bp):
TAACCCC
Found at i:576222 original size:8 final size:8
Alignment explanation
Indices: 576209--576250 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
576199 CCTAACATCT
576209 AACCCCTA
1 AACCCCTA
576217 AACCCCT-
1 AACCCCTA
*
576224 AATCCCTA
1 AACCCCTA
576232 AACCCCT-
1 AACCCCTA
*
576239 AATCCCTA
1 AACCCCTA
576247 AACC
1 AACC
576251 TTAAATCCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 12 0.43
8 16 0.57
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.17
Consensus pattern (8 bp):
AACCCCTA
Found at i:576530 original size:15 final size:15
Alignment explanation
Indices: 576512--576553 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
576502 CCTAGCACGT
576512 CTAACCCTTAAACCC
1 CTAACCCTTAAACCC
*
576527 CTAACTCTCT-AACCC
1 CTAACCCT-TAAACCC
*
576542 CTAAACCTTAAA
1 CTAACCCTTAAA
576554 TCCCAATCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (15 bp):
CTAACCCTTAAACCC
Found at i:576537 original size:23 final size:23
Alignment explanation
Indices: 576476--576548 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
576466 ACCCTAACTC
* * * *
576476 AACCCCTAAATCCCTAA-CTTTT
1 AACCCCTAACTCTCTAACCCTTA
* *
576498 AACCCCTAGCACGTCTAACCCTTA
1 AACCCCTAACTC-TCTAACCCTTA
*
576522 AACCCCTAACTCTCTAACCCCTA
1 AACCCCTAACTCTCTAACCCTTA
576545 AACC
1 AACC
576549 TTAAATCCCA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
22 9 0.22
23 18 0.45
24 13 0.32
ACGTcount: A:0.32, C:0.42, G:0.03, T:0.23
Consensus pattern (23 bp):
AACCCCTAACTCTCTAACCCTTA
Found at i:576988 original size:32 final size:32
Alignment explanation
Indices: 576947--577007 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
576937 AGGTTTTTTT
576947 TGCGGCGCTTTCCCAAAAACACCGCTAAAGCC
1 TGCGGCGCTTTCCCAAAAACACCGCTAAAGCC
** *
576979 TGCGGCGCTTTCTTAAAAACGCCGCTAAA
1 TGCGGCGCTTTCCCAAAAACACCGCTAAA
577008 TCCCCGAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.20
Consensus pattern (32 bp):
TGCGGCGCTTTCCCAAAAACACCGCTAAAGCC
Found at i:577133 original size:113 final size:114
Alignment explanation
Indices: 576984--577541 Score: 764
Period size: 114 Copynumber: 4.9 Consensus size: 114
576974 AAGCCTGCGG
*
576984 CGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAGGTTT
1 CGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCATCGTTGGGCTTAGGTTT
*
577049 TTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAG-CCTGAGCAATAGCGA
66 TTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCCGAGCAATAGCGA
*
577097 CGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAACATCGTTGGGCTTAGGTTT
1 CGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCATCGTTGGGCTTAGGTTT
* * *
577162 TTTTGCGGCACTTTCCCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGG
66 TTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCCGAGCAATAGCGA
* * *
577211 CGCTTTCTT-AAAACTGTCGCTAAATCCCTGAAAGCTCAGAAAAC-GACGTCGTTGGGCTTAGG-
1 CGCTTTCTTAAAAAC-GCCGCTAAATCCCCGAAAGCTCAGAAAACAG-CATCGTTGGGCTTAGGT
* * * *
577273 TTTTTTGTGGCACTTTCCCAAAAACGCCGCTAAAGCCCCGACCAATAGCGG
64 TTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCCGAGCAATAGCGA
* * * ** * *
577324 CGCTTTCTTAGAAACGCCGCTAAATCCCTGAAAGCTTAGAAAATGGCATCGTTGGGCTTTGGTAT
1 CGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCATCGTTGGGCTTAGGTTT
* * * *
577389 TTTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGA
66 TTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCCGAGCAATAGCGA
* * * * * *
577438 CGCTTTCCTAAAGACGCCACTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTATGTTT
1 CGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCATCGTTGGGCTTAGGTTT
* * * *
577503 TTTTGCGGCGCTTTCTCAGAAACTCCGCTAAATCCCCGA
66 TTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCCGA
577542 AAGCTCGGGA
Statistics
Matches: 395, Mismatches: 44, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
113 197 0.50
114 198 0.50
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (114 bp):
CGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCATCGTTGGGCTTAGGTTT
TTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCCGAGCAATAGCGA
Found at i:577246 original size:114 final size:113
Alignment explanation
Indices: 576980--577541 Score: 768
Period size: 113 Copynumber: 4.9 Consensus size: 113
576970 GCTAAAGCCT
* *
576980 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAG
1 GCGGCGCTTTCTT-AAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAG
*
577045 GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAG-CCTGAGCAATA
65 GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCCGAGCAATA
* **
577093 GCGACGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAACATCGTTGGGCTTAG
1 GCGGCGCTTTCTT-AAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAG
* *
577158 GTTTTTTTGCGGCACTTTCCCAAAAACGCCGCTAAAGCCCCGAGCATTA
65 GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCCGAGCAATA
* * * *
577207 GCGGCGCTTTCTTAAAACTGTCGCTAAATCCCTGAAAGCTCAGAAAACGACGTCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAC-GCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAG
* * *
577272 G-TTTTTTGTGGCACTTTCCCAAAAACGCCGCTAAAGCCCCGACCAATA
65 GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCCGAGCAATA
* * * *
577320 GCGGCGCTTTCTTAGAAACGCCGCTAAATCCCTGAAAGCTTAGAAAATGGCATCGTTGGGCTTTG
1 GCGGCGCTTTCTTA-AAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAG
* * * * *
577385 GTATTTTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
65 GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCCGAGCAATA
* * * * *
577434 GCGACGCTTTCCTAAAGACGCCACTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAT
1 GCGGCGCTTTCTTAAA-ACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAG
* * * *
577499 GTTTTTTTGCGGCGCTTTCTCAGAAACTCCGCTAAATCCCCGA
65 GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCCGA
577542 AAGCTCGGGA
Statistics
Matches: 401, Mismatches: 43, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
113 204 0.51
114 197 0.49
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (113 bp):
GCGGCGCTTTCTTAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGG
TTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCCGAGCAATA
Found at i:577321 original size:227 final size:226
Alignment explanation
Indices: 576893--577541 Score: 870
Period size: 227 Copynumber: 2.9 Consensus size: 226
576883 AGCATTTTTG
*
576893 GCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTT
1 GCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGG-TTTTTTTGCGGCGCTTT
*
576958 CCCAAAAACACCGCTAAAG---C---C--T-GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCG
65 CCCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGCTTTCTT-AAAACGCCGCTAAATCCCCG
577014 AAAGCTCAGAAAAC-AGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCT
129 AAAGCTCAGAAAACGA-CGTCGTTGGGCTTAGG-TTTTTTGCGGCGCTTTCCCAAAAACGCCGCT
* *
577078 AAAG-CCTGAGCAATAGCGACGCTTTCTTAAAAAC
192 AAAGCCCCGACCAATAGCGACGCTTTCTTAAAAAC
** *
577112 GCCGCTAAATCCCCGAAAGCTCAGAAAACAACATCGTTGGGCTTAGGTTTTTTTGCGGCACTTTC
1 GCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTC
* *
577177 CCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGCTTTCTTAAAACTGTCGCTAAATCCCTGA
66 CCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGCTTTCTTAAAAC-GCCGCTAAATCCCCGA
* *
577242 AAGCTCAGAAAACGACGTCGTTGGGCTTAGGTTTTTTGTGGCACTTTCCCAAAAACGCCGCTAAA
130 AAGCTCAGAAAACGACGTCGTTGGGCTTAGGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAA
* *
577307 GCCCCGACCAATAGCGGCGCTTTCTTAGAAAC
195 GCCCCGACCAATAGCGACGCTTTCTTAAAAAC
* * * * * *
577339 GCCGCTAAATCCCTGAAAGCTTAGAAAATGGCATCGTTGGGCTTTGGTATTTTAGCGGCGCTTTC
1 GCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTC
* * * * *
577404 TCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCTTTCCTAAAGACGCCACTAAATCCCCGA
66 CCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGCTTTCTTAAA-ACGCCGCTAAATCCCCGA
* * * * * * *
577469 AAGCTCACAAAACGGCATCGTTGGGCTTATGTTTTTTTGCGGCGCTTTCTCAGAAACTCCGCTAA
130 AAGCTCAGAAAACGACGTCGTTGGGCTTA-GGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAA
*
577534 ATCCCCGA
194 AGCCCCGA
577542 AAGCTCGGGA
Statistics
Matches: 377, Mismatches: 39, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
218 34 0.09
219 44 0.12
221 1 0.00
224 1 0.00
226 39 0.10
227 219 0.58
228 39 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (226 bp):
GCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTC
CCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGCTTTCTTAAAACGCCGCTAAATCCCCGAA
AGCTCAGAAAACGACGTCGTTGGGCTTAGGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAG
CCCCGACCAATAGCGACGCTTTCTTAAAAAC
Found at i:577536 original size:73 final size:72
Alignment explanation
Indices: 577457--577592 Score: 209
Period size: 73 Copynumber: 1.9 Consensus size: 72
577447 AAAGACGCCA
*
577457 CTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTATGTTTTTTTGCGGCGCTTTCTCAG
1 CTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTA-GGTTTTTTGCGGCGCTTTCTCAG
577522 AAACTCCG
65 AAACTCCG
*** * *
577530 CTAAATCCCCGAAAGCTCGGGAAACGGCATCGTTGGGCTTAGGTTTTTTGCTGTGCTTTCTCA
1 CTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAGGTTTTTTGCGGCGCTTTCTCA
577593 AAAATGTCGC
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
72 19 0.33
73 38 0.67
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (72 bp):
CTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAGGTTTTTTGCGGCGCTTTCTCAGA
AACTCCG
Found at i:587092 original size:32 final size:31
Alignment explanation
Indices: 587045--587105 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
587035 ATTTTTGGCT
* * *
587045 TTGACTGACCTTTGATTGATTGTTGACCGATG
1 TTGACTGACCATTGA-TCAGTGTTGACCGATG
*
587077 TTGACTGATCATTGATCAGTGTTGACCGA
1 TTGACTGACCATTGATCAGTGTTGACCGA
587106 CCAAGTGGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 12 0.48
32 13 0.52
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (31 bp):
TTGACTGACCATTGATCAGTGTTGACCGATG
Found at i:590859 original size:41 final size:41
Alignment explanation
Indices: 590814--590912 Score: 121
Period size: 41 Copynumber: 2.4 Consensus size: 41
590804 ATTGATCTCG
* * *
590814 GTTTCGCACACTTAGTTCCCG-TCATTTAACATCATGATTTA
1 GTTTCGCACACTTAGTGCCCGAT-ATTCAACATCATAATTTA
* *
590855 GTTTCGCACACTTAGTGCTCGATATTCAACCTCATAATTTA
1 GTTTCGCACACTTAGTGCCCGATATTCAACATCATAATTTA
*
590896 G-TTCACACACTTAGTGC
1 GTTTCGCACACTTAGTGC
590913 TAATCAAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
40 15 0.29
41 35 0.69
42 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.36
Consensus pattern (41 bp):
GTTTCGCACACTTAGTGCCCGATATTCAACATCATAATTTA
Found at i:596840 original size:18 final size:19
Alignment explanation
Indices: 596803--596843 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
596793 GCGCGTGTTG
*
596803 CGCCTCCGTGCCAAAGCCA
1 CGCCTCCGAGCCAAAGCCA
*
596822 CGCCTCCGAGCC-GAGCCA
1 CGCCTCCGAGCCAAAGCCA
596840 CGCC
1 CGCC
596844 ACCACCAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.17, C:0.51, G:0.24, T:0.07
Consensus pattern (19 bp):
CGCCTCCGAGCCAAAGCCA
Found at i:597873 original size:16 final size:15
Alignment explanation
Indices: 597849--597878 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
597839 ATGTACCTAT
597849 TTATATATTATTTTA
1 TTATATATTATTTTA
597864 TTATACTATTATTTT
1 TTATA-TATTATTTT
597879 TTAAACTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATATTATTTTA
Found at i:601542 original size:14 final size:14
Alignment explanation
Indices: 601523--601552 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
601513 CGAGTAAATC
*
601523 ATGATGGTTTCCTT
1 ATGATGGTTTCATT
601537 ATGATGGTTTCATT
1 ATGATGGTTTCATT
601551 AT
1 AT
601553 TATACTTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.50
Consensus pattern (14 bp):
ATGATGGTTTCATT
Found at i:606542 original size:20 final size:20
Alignment explanation
Indices: 606475--606556 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 20
606465 GTAGATGCGT
*
606475 AACAAAGGCACCAAAGTGCA
1 AACAGAGGCACCAAAGTGCA
* * *
606495 AACA-ATGACACTAAAGTG-T
1 AACAGA-GGCACCAAAGTGCA
* *
606514 AATAGAGGCACGAAAGTGCA
1 AACAGAGGCACCAAAGTGCA
* *
606534 AACAGAGGCACCGATGTGCA
1 AACAGAGGCACCAAAGTGCA
606554 AAC
1 AAC
606557 CCGTACAAGC
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
19 14 0.29
20 34 0.71
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (20 bp):
AACAGAGGCACCAAAGTGCA
Found at i:614872 original size:19 final size:20
Alignment explanation
Indices: 614848--614899 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 20
614838 AACAGTTCAC
614848 CTTTTTTTTATAC-TCG-AAA
1 CTTTTTTTTA-ACTTCGTAAA
*
614867 C-TTTTTTTAACTTCGTATA
1 CTTTTTTTTAACTTCGTAAA
614886 CTTTTTTTT-ACTTC
1 CTTTTTTTTAACTTC
614900 AAATACAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 2 0.07
18 11 0.38
19 9 0.31
20 7 0.24
ACGTcount: A:0.19, C:0.17, G:0.04, T:0.60
Consensus pattern (20 bp):
CTTTTTTTTAACTTCGTAAA
Found at i:614905 original size:19 final size:19
Alignment explanation
Indices: 614866--614905 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
614856 TATACTCGAA
**
614866 ACTTTTTTTAACTTCGTAT
1 ACTTTTTTTAACTTCAAAT
*
614885 ACTTTTTTTTACTTCAAAT
1 ACTTTTTTTAACTTCAAAT
614904 AC
1 AC
614906 AATTGAATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.17, G:0.03, T:0.55
Consensus pattern (19 bp):
ACTTTTTTTAACTTCAAAT
Found at i:618942 original size:50 final size:51
Alignment explanation
Indices: 618864--619040 Score: 142
Period size: 50 Copynumber: 3.4 Consensus size: 51
618854 TGTCATATCT
* * *** * *
618864 CAGATATGGTCTTACATGGGAGTTCTCATAC-AGGTGCCCATGCCATGTCC
1 CAGACATGGTCTTACAGGGGACCGCTCATACTAGGTGCCAACGCCATGTCC
* * *
618914 CAGACATGGTCTTACGGGGGACCGCTCAT-CTTGGTTCCAACGCCATGTCC
1 CAGACATGGTCTTACAGGGGACCGCTCATACTAGGTGCCAACGCCATGTCC
* * * * * *
618964 CAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATTCCAATGCCATGTCT
1 CAGACATGGTCTTACAGGGGACCGCTCAT-A-CT--A-GGTGCCAACGCCATGTCC
*
619020 CAGACATGGTCTTACATGGGA
1 CAGACATGGTCTTACAGGGGA
619041 TCTCATCCTC
Statistics
Matches: 103, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
49 1 0.01
50 64 0.62
53 2 0.02
56 36 0.35
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (51 bp):
CAGACATGGTCTTACAGGGGACCGCTCATACTAGGTGCCAACGCCATGTCC
Found at i:619009 original size:56 final size:50
Alignment explanation
Indices: 618905--619040 Score: 164
Period size: 56 Copynumber: 2.6 Consensus size: 50
618895 AGGTGCCCAT
** *
618905 GCCATGTCCCAGACATGGTCTTACGGGGGACCGCTCATCTTGGTTCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCGCTCATCTTGATTCCAAC
* *
618955 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATTCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCGCTC---ATCT---TGATTCCAAC
*
619011 GCCATGTCTCAGACATGGTCTTACATGGGA
1 GCCATGTCCCAGACATGGTCTTACATGGGA
619041 TCTCATCCTC
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
50 33 0.45
53 4 0.05
56 37 0.50
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCGCTCATCTTGATTCCAAC
Found at i:619417 original size:30 final size:30
Alignment explanation
Indices: 619383--619440 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
619373 CCTCGGCTCT
619383 AACTTTGACAAAATTACGA-TTTTGCCCCTA
1 AACTTTGACAAAATTAC-ACTTTTGCCCCTA
* *
619413 AACTTTTACATAATTACACTTTTGCCCC
1 AACTTTGACAAAATTACACTTTTGCCCC
619441 AAAGCTCGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (30 bp):
AACTTTGACAAAATTACACTTTTGCCCCTA
Found at i:628679 original size:19 final size:19
Alignment explanation
Indices: 628655--628693 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
628645 CATTCAGCAG
628655 GACATGTGAGGGAAAATAA
1 GACATGTGAGGGAAAATAA
*
628674 GACATGTGAGGGGAAATAA
1 GACATGTGAGGGAAAATAA
628693 G
1 G
628694 GAGAGTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.36, T:0.15
Consensus pattern (19 bp):
GACATGTGAGGGAAAATAA
Found at i:635510 original size:25 final size:24
Alignment explanation
Indices: 635482--635532 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
635472 GGATGTTATC
635482 CGAAAAGGATATCAAATGAAAAGGT
1 CGAAAAGGATA-CAAATGAAAAGGT
* * *
635507 CGAAAATGATAGAAATGAAAATGT
1 CGAAAAGGATACAAATGAAAAGGT
635531 CG
1 CG
635533 GTATCTCATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.51, C:0.08, G:0.24, T:0.18
Consensus pattern (24 bp):
CGAAAAGGATACAAATGAAAAGGT
Found at i:646152 original size:17 final size:17
Alignment explanation
Indices: 646130--646162 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
646120 TTTTGTTCTA
646130 GTAGCTAAAGATATTCC
1 GTAGCTAAAGATATTCC
646147 GTAGCTAAAGATATTC
1 GTAGCTAAAGATATTC
646163 AATAGCTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (17 bp):
GTAGCTAAAGATATTCC
Found at i:646168 original size:17 final size:17
Alignment explanation
Indices: 646131--646170 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
646121 TTTGTTCTAG
**
646131 TAGCTAAAGATATTCCG
1 TAGCTAAAGATATTCAA
646148 TAGCTAAAGATATTCAA
1 TAGCTAAAGATATTCAA
646165 TAGCTA
1 TAGCTA
646171 TGGAACCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (17 bp):
TAGCTAAAGATATTCAA
Found at i:647318 original size:25 final size:27
Alignment explanation
Indices: 647257--647322 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
647247 CGTTCCGACC
*
647257 CACAGCTCGTGTGAGTATGCCCATTTG
1 CACAGCTCGTGTGAATATGCCCATTTG
* **
647284 CACAGCTCGTGTGAATATTCTGA-TT-
1 CACAGCTCGTGTGAATATGCCCATTTG
647309 CACAGCTCGTGTGA
1 CACAGCTCGTGTGA
647323 GCATACATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 14 0.40
26 2 0.06
27 19 0.54
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.30
Consensus pattern (27 bp):
CACAGCTCGTGTGAATATGCCCATTTG
Found at i:649928 original size:19 final size:18
Alignment explanation
Indices: 649904--649942 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
649894 CTCATTTCCC
649904 TTCTTCTTCTTACTATTCT
1 TTCTTCTTCTTACT-TTCT
*
649923 TTCTTCTTCTTCCTTTCT
1 TTCTTCTTCTTACTTTCT
649941 TT
1 TT
649943 TTATTTTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.67
Consensus pattern (18 bp):
TTCTTCTTCTTACTTTCT
Found at i:651207 original size:70 final size:70
Alignment explanation
Indices: 651068--651198 Score: 171
Period size: 70 Copynumber: 1.9 Consensus size: 70
651058 CGAATAAGAA
* * * * *
651068 AAGGCAAAACTATGTCGTTTTGATAAATGTTTACATCTTCTAAAGTTAAAAGTCAAAACTATTAA
1 AAGGCAAAACAATGTCGTTTTGATAAATATTTACATCGTCTAAAGTTAAAAGGCAAAACCATTAA
651133 GTTAT
66 GTTAT
*
651138 AAGGCAAAACAATGAT-GTTTTGATAATTATTTAC-TCGT-T-AAGTTAAAAGGCAAAACCATTA
1 AAGGCAAAACAATG-TCGTTTTGATAAATATTTACATCGTCTAAAGTTAAAAGGCAAAACCATTA
651199 TATTGTTATG
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
67 20 0.37
68 1 0.02
69 3 0.06
70 29 0.54
71 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (70 bp):
AAGGCAAAACAATGTCGTTTTGATAAATATTTACATCGTCTAAAGTTAAAAGGCAAAACCATTAA
GTTAT
Found at i:651305 original size:5 final size:5
Alignment explanation
Indices: 651295--651330 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
651285 GGATTCGTTA
*
651295 ACTCG ACTCG ACTCG ACTCG ACTCG ACTTG ACTCG A
1 ACTCG ACTCG ACTCG ACTCG ACTCG ACTCG ACTCG A
651331 AATTTTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.22
Consensus pattern (5 bp):
ACTCG
Found at i:653664 original size:33 final size:32
Alignment explanation
Indices: 653626--653741 Score: 121
Period size: 33 Copynumber: 3.6 Consensus size: 32
653616 AGATTAATTT
653626 ATATTTTATGTATCATTATATTAAATTATTTAA
1 ATATTTTATGTATCATTATATTAAATT-TTTAA
* *
653659 ATATTTCATGTATCATTATATTAAATTGTTTAG
1 ATATTTTATGTATCATTATATTAAATT-TTTAA
* *
653692 ATATCATTTAT-TATTA-TAT-TTAAGTTTTTAAA
1 ATAT--TTTATGTATCATTATATTAAATTTTT-AA
*
653724 ATATTTTATGTTTCATTA
1 ATATTTTATGTATCATTA
653742 ATTTTATAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
30 5 0.07
31 6 0.09
32 13 0.19
33 37 0.54
34 4 0.06
35 4 0.06
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.55
Consensus pattern (32 bp):
ATATTTTATGTATCATTATATTAAATTTTTAA
Found at i:656090 original size:32 final size:32
Alignment explanation
Indices: 656054--656122 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
656044 AACTTATTCG
* * *
656054 AAAATATTTAATTAATACTTAAATTTGTCTAA
1 AAAATACTTAACTAATACTTAAATTTGTCCAA
* *
656086 AAAATACTTAACTAGTATTTAAATTTGTCCAA
1 AAAATACTTAACTAATACTTAAATTTGTCCAA
656118 AAAAT
1 AAAAT
656123 TATAATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (32 bp):
AAAATACTTAACTAATACTTAAATTTGTCCAA
Found at i:657579 original size:36 final size:36
Alignment explanation
Indices: 657511--657685 Score: 94
Period size: 36 Copynumber: 4.9 Consensus size: 36
657501 AAAAACAAAA
** * *
657511 AATTATTTAAAAAATTAAAATTTTCCATAAATATAAAG
1 AATTATTT--AAAATTGGAATTTTTCAAAAATATAAAG
**
657549 AATTATTTATTATTGGAATTTTTCAAAAATA-AAA-
1 AATTATTTAAAATTGGAATTTTTCAAAAATATAAAG
* * *
657583 AA-TACTATTAAAATT--AAATTTT-AATAGAT-TAAAAA
1 AATTA-T-TTAAAATTGGAATTTTTCAA-AAATAT-AAAG
* ** * *
657618 AATTATTAAAAAATTAAAATTTTCCATAAATATAAAG
1 AATTATT-TAAAATTGGAATTTTTCAAAAATATAAAG
**
657655 AATTATTTATTATTGGAATTTTTCAAAAATA
1 AATTATTTAAAATTGGAATTTTTCAAAAATA
657686 AAAAATACTA
Statistics
Matches: 102, Mismatches: 23, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
32 2 0.02
33 11 0.11
34 7 0.07
35 18 0.18
36 36 0.35
37 18 0.18
38 10 0.10
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (36 bp):
AATTATTTAAAATTGGAATTTTTCAAAAATATAAAG
Found at i:657627 original size:106 final size:107
Alignment explanation
Indices: 657507--657726 Score: 424
Period size: 106 Copynumber: 2.1 Consensus size: 107
657497 TGTTAAAAAC
657507 AAAAAATTATTTAAAAAATTAAAATTTTCCATAAATATAAAGAATTATTTATTATTGGAATTTTT
1 AAAAAATTATTTAAAAAATTAAAATTTTCCATAAATATAAAGAATTATTTATTATTGGAATTTTT
*
657572 CAAAAATAAAAAATACTATTAAAATTAAATTTTAATAGATTA
66 CAAAAATAAAAAATACTATTAAAATTAAAATTTAATAGATTA
657614 AAAAAATTA-TTAAAAAATTAAAATTTTCCATAAATATAAAGAATTATTTATTATTGGAATTTTT
1 AAAAAATTATTTAAAAAATTAAAATTTTCCATAAATATAAAGAATTATTTATTATTGGAATTTTT
657678 CAAAAATAAAAAATACTATTAAAATTAAAATTTAATAGATTA
66 CAAAAATAAAAAATACTATTAAAATTAAAATTTAATAGATTA
657720 AAAAAAT
1 AAAAAAT
657727 AAAAAATAAT
Statistics
Matches: 112, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
106 103 0.92
107 9 0.08
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (107 bp):
AAAAAATTATTTAAAAAATTAAAATTTTCCATAAATATAAAGAATTATTTATTATTGGAATTTTT
CAAAAATAAAAAATACTATTAAAATTAAAATTTAATAGATTA
Found at i:657630 original size:53 final size:53
Alignment explanation
Indices: 657573--657726 Score: 134
Period size: 53 Copynumber: 2.9 Consensus size: 53
657563 GGAATTTTTC
*
657573 AAAAATAAAAAATACTATTAAAATTAAATTTTAATAGATTAAAAAAATTATTA
1 AAAAATAAAAAATACTATTAAAATTAAAATTTAATAGATTAAAAAAATTATTA
** * * * ** **** * *
657626 AAAAATTAAAATTTTCCA-T-AAATATAAAGAATT-ATTTATTATTGGAATTTTTC
1 AAAAA-TAAAAAATACTATTAAAAT-TAAA-ATTTAATAGATTAAAAAAATTATTA
657679 AAAAATAAAAAATACTATTAAAATTAAAATTTAATAGATTAAAAAAAT
1 AAAAATAAAAAATACTATTAAAATTAAAATTTAATAGATTAAAAAAAT
657727 AAAAAATAAT
Statistics
Matches: 70, Mismatches: 25, Indels: 12
0.65 0.23 0.11
Matches are distributed among these distances:
52 15 0.21
53 41 0.59
54 14 0.20
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (53 bp):
AAAAATAAAAAATACTATTAAAATTAAAATTTAATAGATTAAAAAAATTATTA
Found at i:663485 original size:16 final size:16
Alignment explanation
Indices: 663464--663506 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
663454 TTAGTTCGCT
663464 GTAATGTAATAGAAGC
1 GTAATGTAATAGAAGC
* *
663480 GTAATGGAATAGAGGC
1 GTAATGTAATAGAAGC
663496 GTAATAGTAAT
1 GTAAT-GTAAT
663507 TCAATTGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.42, C:0.05, G:0.28, T:0.26
Consensus pattern (16 bp):
GTAATGTAATAGAAGC
Found at i:663544 original size:45 final size:44
Alignment explanation
Indices: 663480--663576 Score: 151
Period size: 44 Copynumber: 2.2 Consensus size: 44
663470 TAATAGAAGC
663480 GTAATGGAATAGAGGCGTAATAGTAATTCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGT-ATTC-ATGTGTTTGGTTGAAT
*
663525 GTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGTATTCATGTGTTTGGTTGAAT
*
663569 GGAATGGA
1 GTAATGGA
663577 GGTGTAATAG
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 24 0.49
45 24 0.49
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGTATTCATGTGTTTGGTTGAAT
Found at i:663570 original size:39 final size:43
Alignment explanation
Indices: 663480--663586 Score: 125
Period size: 45 Copynumber: 2.5 Consensus size: 43
663470 TAATAGAAGC
663480 GTAATGGAATAGAGGCGTAATAGTAATTCAATTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGTAATTCAATTGTTTGGTT--AT
*
663525 GTAATGGAATAGAGGCGTAATAGT-ATTC-TTGTGTTTGG-T-T
1 GTAATGGAATAGAGGCGTAATAGTAATTCAAT-TGTTTGGTTAT
* *
663565 G-AATGGAATGGAGGTGTAATAG
1 GTAATGGAATAGAGGCGTAATAG
663587 CATAAGAGAA
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
39 19 0.33
40 2 0.03
43 2 0.03
44 11 0.19
45 24 0.41
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.35
Consensus pattern (43 bp):
GTAATGGAATAGAGGCGTAATAGTAATTCAATTGTTTGGTTAT
Found at i:665233 original size:18 final size:17
Alignment explanation
Indices: 665179--665239 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
665169 ACCTCTTCGT
665179 CTTCATCCTCGGAATCA
1 CTTCATCCTCGGAATCA
* * *
665196 TCTTCATCATCAGAACCA
1 -CTTCATCCTCGGAATCA
665214 CTTCCATCCTCGGAATCA
1 CTT-CATCCTCGGAATCA
665232 CTATCATC
1 CT-TCATC
665240 ATCATCGTCC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 3 0.09
18 31 0.89
19 1 0.03
ACGTcount: A:0.26, C:0.36, G:0.08, T:0.30
Consensus pattern (17 bp):
CTTCATCCTCGGAATCA
Found at i:670319 original size:17 final size:17
Alignment explanation
Indices: 670270--670322 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
670260 TTGCTATAAA
*
670270 ATATTTATTA-TGAAAT
1 ATATTTATTATTAAAAT
* * *
670286 ATCTATGATTTTTAAAAT
1 ATAT-TTATTATTAAAAT
670304 ATATTTATTATTAAAAT
1 ATATTTATTATTAAAAT
670321 AT
1 AT
670323 TAATAATTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
16 3 0.11
17 17 0.61
18 8 0.29
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (17 bp):
ATATTTATTATTAAAAT
Found at i:670743 original size:8 final size:8
Alignment explanation
Indices: 670730--670758 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
670720 TTATGAAATT
670730 AAAATATA
1 AAAATATA
670738 AAAATATA
1 AAAATATA
670746 AAAATATA
1 AAAATATA
670754 AAAAT
1 AAAAT
670759 TTAATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATATA
Found at i:670862 original size:19 final size:19
Alignment explanation
Indices: 670840--670878 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
670830 TTTAGATATC
*
670840 TATTTCATTT-TAAATAGTA
1 TATTTAATTTCTAAA-AGTA
670859 TATTTAATTTCTAAAAGTA
1 TATTTAATTTCTAAAAGTA
670878 T
1 T
670879 TGATGAACTT
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:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (19 bp):
TATTTAATTTCTAAAAGTA
Found at i:673245 original size:19 final size:21
Alignment explanation
Indices: 673202--673250 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
673192 TAAATTTAAA
*
673202 AAAAATTAAGGACCAATATAAT
1 AAAAATT-AGAACCAATATAAT
673224 AAAAATTAGAACCAA-A-AAT
1 AAAAATTAGAACCAATATAAT
673243 AAAAATTA
1 AAAAATTA
673251 AAAGAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.42
20 1 0.04
21 7 0.27
22 7 0.27
ACGTcount: A:0.65, C:0.08, G:0.06, T:0.20
Consensus pattern (21 bp):
AAAAATTAGAACCAATATAAT
Found at i:678584 original size:60 final size:60
Alignment explanation
Indices: 678482--678601 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 60
678472 TAACACGTGC
* * *
678482 TTATACAATGTGGGTTTGCCGTTATGATGGTGTGAACATACATCGTGCGGTCTCATAGAA
1 TTATACAATGTGGGTTTGCCGTTATGATGATGCGAACATACATCGTGCAGTCTCATAGAA
* * * *
678542 TTATACGATGTGGGTTTTCC-TATATGATGATGCGAACCTACATCGTGTAGTCTCATAGAA
1 TTATACAATGTGGGTTTGCCGT-TATGATGATGCGAACATACATCGTGCAGTCTCATAGAA
678602 GGGTATGCGA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
59 1 0.02
60 51 0.98
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (60 bp):
TTATACAATGTGGGTTTGCCGTTATGATGATGCGAACATACATCGTGCAGTCTCATAGAA
Done.