Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008269.1 Hibiscus syriacus cultivar Beakdansim tig00110926_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 799769
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:351140 original size:30 final size:30
Alignment explanation
Indices: 351104--351167 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
351094 AAGGAACATA
* *
351104 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
351134 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
351164 TGGA
1 TGGA
351168 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:353308 original size:43 final size:43
Alignment explanation
Indices: 353247--353361 Score: 157
Period size: 39 Copynumber: 2.8 Consensus size: 43
353237 GTGGTCCAAT
*
353247 TGATAAAGTGTTAGTTGTTTACATATTACTACTCGTGAATTAA
1 TGATAAAGTGTTAGTTGTTTACATATTACTACTAGTGAATTAA
* * **
353290 TGATAAAGTGTTAGTTGTTTA-A-A--GCAAGGAGTGAATTAA
1 TGATAAAGTGTTAGTTGTTTACATATTACTACTAGTGAATTAA
353329 TGATAAAGTGTTAGTTGTTTACATATTACTACT
1 TGATAAAGTGTTAGTTGTTTACATATTACTACT
353362 TGCGATTTGG
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
39 32 0.54
40 1 0.02
41 2 0.03
42 1 0.02
43 23 0.39
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (43 bp):
TGATAAAGTGTTAGTTGTTTACATATTACTACTAGTGAATTAA
Found at i:356655 original size:21 final size:21
Alignment explanation
Indices: 356629--356674 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
356619 TGATTTATTA
356629 TTATGGATTTCAAGTTGGTTG
1 TTATGGATTTCAAGTTGGTTG
*
356650 TTATGGATTTCAAGTTTGTTG
1 TTATGGATTTCAAGTTGGTTG
356671 TTAT
1 TTAT
356675 ATATGTCATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.04, G:0.24, T:0.52
Consensus pattern (21 bp):
TTATGGATTTCAAGTTGGTTG
Found at i:357416 original size:20 final size:20
Alignment explanation
Indices: 357391--357464 Score: 148
Period size: 20 Copynumber: 3.7 Consensus size: 20
357381 AACATTCTCA
357391 GTAATCTTACATTCTCACTG
1 GTAATCTTACATTCTCACTG
357411 GTAATCTTACATTCTCACTG
1 GTAATCTTACATTCTCACTG
357431 GTAATCTTACATTCTCACTG
1 GTAATCTTACATTCTCACTG
357451 GTAATCTTACATTC
1 GTAATCTTACATTC
357465 CGTGAACTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (20 bp):
GTAATCTTACATTCTCACTG
Found at i:358479 original size:21 final size:21
Alignment explanation
Indices: 358426--358466 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
358416 TTTATTTTAG
358426 CTCTTAAAATTTTAATTCATC
1 CTCTTAAAATTTTAATTCATC
358447 CTCTTAAAATTTTAATTCAT
1 CTCTTAAAATTTTAATTCAT
358467 TCACCTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (21 bp):
CTCTTAAAATTTTAATTCATC
Found at i:365914 original size:19 final size:18
Alignment explanation
Indices: 365881--365916 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
365871 TTTCACTAAT
*
365881 AGAGAAAATAGTACAAAG
1 AGAGAAAAGAGTACAAAG
365899 AGAGAGAAAGAGTACAAA
1 AGAGA-AAAGAGTACAAA
365917 TAGCCTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.61, C:0.06, G:0.25, T:0.08
Consensus pattern (18 bp):
AGAGAAAAGAGTACAAAG
Found at i:369022 original size:67 final size:67
Alignment explanation
Indices: 368924--369086 Score: 227
Period size: 67 Copynumber: 2.4 Consensus size: 67
368914 AGCAACGAAC
* * * * *
368924 TTAATGAGCTTAACGAGTAACGAATCGAGCAACAAATTATCTTAATGAGCACAAGTCGAACAAAA
1 TTAACGAGCTTAACGAGCAACGAGTCAAGCAACAAATTATCTTAACGAGCACAAGTCGAACAAAA
368989 TT
66 TT
* * * * *
368991 TTAACGAGCTTAATGAGCAACGAGTTAAGCAACAAATTTTCTTAACGAGCACGAGTCGAGCAAAA
1 TTAACGAGCTTAACGAGCAACGAGTCAAGCAACAAATTATCTTAACGAGCACAAGTCGAACAAAA
369056 TT
66 TT
*
369058 TTAACGAGCTTAACAAGCAACGAGTCAAG
1 TTAACGAGCTTAACGAGCAACGAGTCAAG
369087 TCGAGCAACA
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
67 83 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (67 bp):
TTAACGAGCTTAACGAGCAACGAGTCAAGCAACAAATTATCTTAACGAGCACAAGTCGAACAAAA
TT
Found at i:369082 original size:36 final size:36
Alignment explanation
Indices: 368964--369083 Score: 103
Period size: 35 Copynumber: 3.5 Consensus size: 36
368954 AACAAATTAT
* * *
368964 CTTAATGAGC-ACAAGTCGAACAAAATTTTAACGAG
1 CTTAACGAGCAACGAGTCGAGCAAAATTTTAACGAG
* **
368999 CTTAATGAGCAACGAGTTAAGCAACAAATTTT------
1 CTTAACGAGCAACGAGTCGAGC-A-AAATTTTAACGAG
369031 CTTAACGAGC-ACGAGTCGAGCAAAATTTTAACGAG
1 CTTAACGAGCAACGAGTCGAGCAAAATTTTAACGAG
*
369066 CTTAACAAGCAACGAGTC
1 CTTAACGAGCAACGAGTC
369084 AAGTCGAGCA
Statistics
Matches: 67, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
29 7 0.10
30 1 0.01
31 9 0.13
32 9 0.13
35 19 0.28
36 14 0.21
37 1 0.01
38 7 0.10
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (36 bp):
CTTAACGAGCAACGAGTCGAGCAAAATTTTAACGAG
Found at i:370690 original size:20 final size:21
Alignment explanation
Indices: 370665--370757 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
370655 TTTTCCCAAT
*
370665 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
370685 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
370706 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* * **
370726 TCGTAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
370747 TCGCAATGCGA
1 TCGCAATGCGA
370758 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:370710 original size:41 final size:41
Alignment explanation
Indices: 370665--370757 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
370655 TTTTCCCAAT
370665 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
370706 TCGCAATGCGAATAAGTAAATCGTAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
370747 TCGCAATGCGA
1 TCGCAATGCGA
370758 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:370771 original size:20 final size:20
Alignment explanation
Indices: 370746--370860 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
370736 AATTGGGAAA
*
370746 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
370766 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
370787 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
370807 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
370827 TTCGCAACGCAATACTGACT
1 ATCGCAACGCGATACTGACT
*
370847 TTCGCAACGCGATA
1 ATCGCAACGCGATA
370861 ATACATAATC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 65 0.82
21 14 0.18
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:371076 original size:22 final size:22
Alignment explanation
Indices: 371048--371091 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
371038 CACTCTCTCA
371048 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
371070 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
371092 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:371364 original size:20 final size:20
Alignment explanation
Indices: 371335--371378 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
371325 GCGATTTTAG
371335 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
371355 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
371375 TTTC
1 TTTC
371379 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:372719 original size:18 final size:18
Alignment explanation
Indices: 372698--372742 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
372688 TCCACTTCGG
*
372698 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
372716 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
372734 GAGCCATCA
1 GAGCCATCA
372743 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:373278 original size:19 final size:20
Alignment explanation
Indices: 373224--373290 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
373214 TAGTTTACTT
* *
373224 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
373244 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
373264 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
373283 TCGCAACG
1 TCGCAACG
373291 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:373298 original size:14 final size:14
Alignment explanation
Indices: 373279--373336 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
373269 ATGCGAAATG
373279 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
373293 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
373309 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
373325 AAAATCGCAACG
1 AAAATCGCAACG
373337 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:373321 original size:32 final size:33
Alignment explanation
Indices: 373263--373353 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
373253 GGAAATGGCT
*
373263 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
373296 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
373328 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
373354 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:373347 original size:19 final size:19
Alignment explanation
Indices: 373224--373358 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
373214 TAGTTTACTT
* **
373224 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
373244 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
373264 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
373283 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
373297 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
373315 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
373329 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
373348 TCGCAATGCGA
1 TCGCAACGCGA
373359 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:373389 original size:14 final size:14
Alignment explanation
Indices: 373370--373427 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
373360 TTGTGTTTCG
373370 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
373384 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
373400 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
373416 CGTTGCGATTTT
1 CGTTGCGATTTT
373428 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:373404 original size:32 final size:33
Alignment explanation
Indices: 373365--373435 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 33
373355 GCGATTTGTG
373365 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
373397 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
373430 TTTCGC
1 TTTCGC
373436 ATTGTGATAG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 27 0.71
33 11 0.29
ACGTcount: A:0.08, C:0.20, G:0.24, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:373452 original size:19 final size:19
Alignment explanation
Indices: 373428--373481 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
373418 TTGCGATTTT
*
373428 CATTTCGCATTGTGATAGC
1 CATTTCGCATTGCGATAGC
* *
373447 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCATTGCGATAGC
*
373467 CATTTCGCGTTGCGA
1 CATTTCGCATTGCGA
373482 ATTTAAGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:373470 original size:20 final size:19
Alignment explanation
Indices: 373416--373481 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
373406 GCGATTTTGT
**
373416 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* * *
373435 CATTGTGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
373455 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
373474 CGTTGCGA
1 CGTTGCGA
373482 ATTTAAGTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 22 0.58
20 16 0.42
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:375366 original size:14 final size:14
Alignment explanation
Indices: 375347--375382 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
375337 ATTGTTTAAT
375347 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
375361 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
375375 TGATTTGT
1 TGATTTGT
375383 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:375521 original size:19 final size:19
Alignment explanation
Indices: 375499--375602 Score: 159
Period size: 18 Copynumber: 5.8 Consensus size: 19
375489 ATCGCAACGA
375499 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
375518 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
375536 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
375554 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
375573 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
375587 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
375603 TTTTCTCATT
Statistics
Matches: 81, Mismatches: 0, Indels: 10
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.14
15 1 0.01
16 2 0.02
17 2 0.02
18 36 0.44
19 29 0.36
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:375568 original size:55 final size:52
Alignment explanation
Indices: 375499--375602 Score: 156
Period size: 55 Copynumber: 1.9 Consensus size: 52
375489 ATCGCAACGA
375499 GAAAATCGCAATGCGAAATG-AAATCGCAATGCGAAATGAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA--AAATCGCAATGCGAAAT
*
375554 GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAACGAAAAAATCGCAATGCGA
375603 TTTTCTCATT
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
52 14 0.30
54 4 0.09
55 20 0.43
56 9 0.19
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAACGAAAAAATCGCAATGCGAAAT
Found at i:375659 original size:20 final size:20
Alignment explanation
Indices: 375611--375659 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
375601 GATTTTCTCA
*
375611 TTGCGATAACCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
375631 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
375651 TTGCGATAG
1 TTGCGATAG
375660 TCAAATGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.35
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCG
Found at i:376772 original size:24 final size:24
Alignment explanation
Indices: 376716--376774 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
376706 AGTCAGTATT
* *
376716 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
376740 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
376764 CGAATTTTGAT
1 CGAAATTTGAT
376775 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:376966 original size:12 final size:12
Alignment explanation
Indices: 376949--376973 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
376939 ATATAATCCT
376949 GAAGAAGAAAAA
1 GAAGAAGAAAAA
376961 GAAGAAGAAAAA
1 GAAGAAGAAAAA
376973 G
1 G
376974 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:379307 original size:33 final size:33
Alignment explanation
Indices: 379265--379391 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
379255 GGAAATTACT
*
379265 ATCGCAATGCGAAATGAAAATCGTAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
379298 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
379330 TTTCGTAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
379364 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
379392 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
32 1 0.01
33 80 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:379376 original size:66 final size:66
Alignment explanation
Indices: 379270--379398 Score: 231
Period size: 66 Copynumber: 2.0 Consensus size: 66
379260 TTACTATCGC
* *
379270 AATGCGAAATGAAAATCGTAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTCG
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
379335 T
66 T
*
379336 AATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
379399 AATTTCTCGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.18
Consensus pattern (66 bp):
AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
T
Found at i:379430 original size:19 final size:19
Alignment explanation
Indices: 379408--379466 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
379398 TAATTTCTCG
379408 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
**
379427 TTGCGA--TTC-CCTCG--
1 TTGCGATTTTCATTTCGCA
379441 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
379460 TTGCGAT
1 TTGCGAT
379467 AGTACTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 6 0.19
16 6 0.19
17 6 0.19
19 13 0.42
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:379446 original size:33 final size:33
Alignment explanation
Indices: 379404--379466 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
379394 AATTTAATTT
379404 CTCGTTGCGATTTTCATTTCGCATTGCGATTCC
1 CTCGTTGCGATTTTCATTTCGCATTGCGATTCC
379437 CTCGTTGCGATTTTCATTTCGCATTGCGAT
1 CTCGTTGCGATTTTCATTTCGCATTGCGAT
379467 AGTACTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.43
Consensus pattern (33 bp):
CTCGTTGCGATTTTCATTTCGCATTGCGATTCC
Found at i:379592 original size:14 final size:14
Alignment explanation
Indices: 379573--379609 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
379563 CATCAATTAA
379573 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
379587 ACAAATCACCTTTT
1 ACAAATCAACTTTT
379601 ACAAATCAA
1 ACAAATCAA
379610 TTAAACAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:380994 original size:21 final size:20
Alignment explanation
Indices: 380970--381029 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
380960 TGAATCGGGA
*
380970 TCTTGAATGGTGGGAGGGACC
1 TCTTGAACGGTGGGAGGG-CC
* * **
380991 TCTTCAACGATGACAGTGGCC
1 TCTTGAACGGTGGGAG-GGCC
381012 TCTTGAACGGTGGGAGGG
1 TCTTGAACGGTGGGAGGG
381030 GACTCTCGAG
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.20, C:0.18, G:0.38, T:0.23
Consensus pattern (20 bp):
TCTTGAACGGTGGGAGGGCC
Found at i:381035 original size:21 final size:21
Alignment explanation
Indices: 380966--381035 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 21
380956 CATGTGAATC
*
380966 GGGA-TCTTGAATGGTGGGA-
1 GGGACTCTTGAACGGTGGGAG
* * **
380985 GGGACCTCTTCAACGATGACAG
1 GGGA-CTCTTGAACGGTGGGAG
* *
381007 TGGCCTCTTGAACGGTGGGAG
1 GGGACTCTTGAACGGTGGGAG
381028 GGGACTCT
1 GGGACTCT
381036 CGAGGAATGA
Statistics
Matches: 35, Mismatches: 13, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
19 4 0.11
21 29 0.83
22 2 0.06
ACGTcount: A:0.20, C:0.19, G:0.39, T:0.23
Consensus pattern (21 bp):
GGGACTCTTGAACGGTGGGAG
Found at i:381054 original size:42 final size:42
Alignment explanation
Indices: 381008--381091 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
380998 CGATGACAGT
* * *
381008 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
381050 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
381092 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:383156 original size:19 final size:19
Alignment explanation
Indices: 383092--383243 Score: 161
Period size: 19 Copynumber: 8.1 Consensus size: 19
383082 TCTTTTGGTT
*
383092 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
383111 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
383131 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
** *
383151 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
383169 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
383184 GAAATGAAAATCGCAACTGC
1 GAAATGAAAATCGCAAC-GC
383204 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
383223 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
383242 GA
1 GA
383244 TTTTGGTTTC
Statistics
Matches: 116, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
14 10 0.09
15 2 0.02
18 2 0.02
19 51 0.44
20 49 0.42
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:383227 original size:39 final size:38
Alignment explanation
Indices: 383092--383243 Score: 161
Period size: 39 Copynumber: 4.1 Consensus size: 38
383082 TCTTTTGGTT
* *
383092 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
** ** *
383131 GGAAATGACTATCGCAACGCGAAATGACTATCGCGAC-C
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
*
383169 ---A-GACAATCGCAACGCGAAATGAAAATCGCAACTGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAAC-GC
*
383204 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
383242 GA
1 GA
383244 TTTTGGTTTC
Statistics
Matches: 94, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
33 27 0.29
34 1 0.01
35 1 0.01
38 6 0.06
39 41 0.44
40 18 0.19
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:383273 original size:20 final size:19
Alignment explanation
Indices: 383239--383306 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
383229 AAAATCGCAA
**
383239 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
383258 TGCGAATTTTTATTTCGCGT
1 TGCG-ATTTTTATTTCGCGT
**
383278 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
383298 TGCGATTTT
1 TGCGATTTT
383307 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.29
20 29 0.71
ACGTcount: A:0.12, C:0.16, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:383910 original size:20 final size:20
Alignment explanation
Indices: 383825--383938 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
383815 CGCTATGTAA
* * * *
383825 ATCGCGTTGCGAAAGTAAGA
1 ATCGCATTGCGATAGTCAGT
* *
383845 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
383865 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
383886 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
383906 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
383926 ATCGCATTGCGAT
1 ATCGCATTGCGAT
383939 TTTCCCAGTT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 3 0.04
20 64 0.79
21 12 0.15
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:383923 original size:61 final size:61
Alignment explanation
Indices: 383825--383941 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
383815 CGCTATGTAA
* * * *
383825 ATCGCGTTGCGAAAGTAAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * * *
383886 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
383942 CCCAGTTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:383952 original size:61 final size:61
Alignment explanation
Indices: 383825--383959 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
383815 CGCTATGTAA
* * * * * ** *
383825 ATCGCGTTGCGAAAGTAAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAGT
* * *
383886 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAGT
1 ATCGCATTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAGT
383948 -TCGCATTGCGAT
1 ATCGCATTGCGAT
383960 TTACTTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
61 60 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAGT
Found at i:383972 original size:20 final size:21
Alignment explanation
Indices: 383922--383978 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
383912 TTGCGATAGT
*
383922 CAGTATCGCATTGCGATTTTCC
1 CAGT-TCGCATTGCGATTTACC
*
383944 CAGTTCGCATTGCGATTTACT
1 CAGTTCGCATTGCGATTTACC
*
383965 TA-TTCGCATTGCGA
1 CAGTTCGCATTGCGA
383979 ATTGGGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 12 0.38
21 16 0.50
22 4 0.12
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (21 bp):
CAGTTCGCATTGCGATTTACC
Found at i:386146 original size:17 final size:17
Alignment explanation
Indices: 386126--386162 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
386116 ATGTGAACGG
386126 AACTCGTTTGCGAACCA
1 AACTCGTTTGCGAACCA
386143 AACTCGTTTGCGAACCA
1 AACTCGTTTGCGAACCA
386160 AAC
1 AAC
386163 AAATTGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (17 bp):
AACTCGTTTGCGAACCA
Found at i:396175 original size:39 final size:39
Alignment explanation
Indices: 396119--396297 Score: 277
Period size: 39 Copynumber: 4.6 Consensus size: 39
396109 TTGTTTTTAA
* *
396119 AGAAGATTGTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
396158 ACAAGATTTTGTCTCGCTTGAGATATTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
396197 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCAAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
396236 AGAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
396275 AGAAAATTTTGTCTCACTTGAGA
1 AGAAGATTTTGTCTCGCTTGAGA
396298 CATTTTTCTT
Statistics
Matches: 128, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 128 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (39 bp):
AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:398825 original size:21 final size:21
Alignment explanation
Indices: 398799--398939 Score: 123
Period size: 21 Copynumber: 6.8 Consensus size: 21
398789 CGCGGTCTCC
398799 AGAATCGCAACGCGATTATGA
1 AGAATCGCAACGCGATTATGA
398820 AGAATCGCAACGCGATTATGA
1 AGAATCGCAACGCGATTATGA
*
398841 AGAATCGCAATGCGA-TA-GTA
1 AGAATCGCAACGCGATTATG-A
** * **
398861 CA-AATTCGCATTGCGATTTTCC
1 -AGAA-TCGCAACGCGATTATGA
*
398883 AGAATCGCAACGCGAATATGA
1 AGAATCGCAACGCGATTATGA
**
398904 A-AATCGCAACGCGAACAT-A
1 AGAATCGCAACGCGATTATGA
398923 TA-AATCGCAACGCGATT
1 -AGAATCGCAACGCGATT
398940 CTGACTATCA
Statistics
Matches: 99, Mismatches: 14, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
19 2 0.02
20 35 0.35
21 59 0.60
22 3 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (21 bp):
AGAATCGCAACGCGATTATGA
Found at i:398856 original size:42 final size:40
Alignment explanation
Indices: 398762--398938 Score: 137
Period size: 42 Copynumber: 4.3 Consensus size: 40
398752 TGACCAACAA
* * * * * *
398762 AATCGCAATGCGAAATAAAAATCGCAACGCG-GTCTCCAG
1 AATCGCAACGCGATATGAAAATCGCAACGCGATTATCAAG
*
398801 AATCGCAACGCGATTATGAAGAATCGCAACGCGATTATGAAG
1 AATCGCAACGCGA-TATGAA-AATCGCAACGCGATTATCAAG
* ** * *
398843 AATCGCAATGCGATA-GTACAAATTCGCATTGCGATTTTCCAG
1 AATCGCAACGCGATATG-A-AAA-TCGCAACGCGATTATCAAG
**
398885 AATCGCAACGCGAATATGAAAATCGCAACGCGAACAT-ATA-
1 AATCGCAACGCG-ATATGAAAATCGCAACGCGATTATCA-AG
398925 AATCGCAACGCGAT
1 AATCGCAACGCGAT
398939 TCTGACTATC
Statistics
Matches: 109, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
39 14 0.13
40 17 0.16
41 28 0.26
42 45 0.41
43 4 0.04
44 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGATATGAAAATCGCAACGCGATTATCAAG
Found at i:398910 original size:20 final size:20
Alignment explanation
Indices: 398760--399160 Score: 113
Period size: 20 Copynumber: 19.8 Consensus size: 20
398750 AATGACCAAC
* *
398760 AAAATCGCAATGCGAA-ATA
1 AAAATCGCAACGCGAATATG
* * *
398779 AAAATCGCAACGCG-GTCTCC
1 AAAATCGCAACGCGAATAT-G
* *
398799 AGAATCGCAACGCGATTATG
1 AAAATCGCAACGCGAATATG
*
398819 AAGAATCGCAACGCGATTATG
1 AA-AATCGCAACGCGAATATG
*
398840 AAGAATCGCAATGCG-ATA-G
1 AA-AATCGCAACGCGAATATG
** * * *
398859 TACAAATTCGCATTGCGATTTTCC
1 -A-AAA-TCGCAACGCGAATAT-G
*
398883 AGAATCGCAACGCGAATATG
1 AAAATCGCAACGCGAATATG
*
398903 AAAATCGCAACGCGAACAT-
1 AAAATCGCAACGCGAATATG
* *
398922 ATAAATCGCAACGCGATTCTG
1 A-AAATCGCAACGCGAATATG
** * * * **
398943 ACTATCACAACGAGTATCCG
1 AAAATCGCAACGCGAATATG
* * **
398963 TAAAATCACAACGCGTATCCG
1 -AAAATCGCAACGCGAATATG
* *
398984 TAAATCGCAACGAC-AATACG
1 AAAATCGCAACG-CGAATATG
* * **
399004 TAAAATCGCAATGCGTATCCG
1 -AAAATCGCAACGCGAATATG
* * * *
399025 TAAATCGCAATGAGAATACG
1 AAAATCGCAACGCGAATATG
* * * *
399045 TAAATCGCAATGCGTATCTG
1 AAAATCGCAACGCGAATATG
* * *
399065 TAAATCGCAACGAGAATACG
1 AAAATCGCAACGCGAATATG
* *
399085 TAAATCGCAATGC--ATATCCG
1 AAAATCGCAACGCGAATAT--G
* *
399105 TAAATCGCAACGAC-AATACG
1 AAAATCGCAACG-CGAATATG
*
399125 TAAAATCGCAACGCG--TATCC
1 -AAAATCGCAACGCGAATAT-G
399145 ATAAATCGCAACGCGA
1 A-AAATCGCAACGCGA
399161 TTTTTAAAGC
Statistics
Matches: 292, Mismatches: 65, Indels: 48
0.72 0.16 0.12
Matches are distributed among these distances:
18 3 0.01
19 19 0.07
20 163 0.56
21 100 0.34
22 6 0.02
23 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATG
Found at i:398995 original size:41 final size:41
Alignment explanation
Indices: 398950--399157 Score: 303
Period size: 41 Copynumber: 5.1 Consensus size: 41
398940 CTGACTATCA
* * * *
398950 CAACGAGTATCCGTAAAATCACAACGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAATGCGTATCCGTAAATCG
*
398991 CAACGACAATACGTAAAATCGCAATGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAATGCGTATCCGTAAATCG
* *
399032 CAATGAGAATACGT-AAATCGCAATGCGTATCTGTAAATCG
1 CAACGAGAATACGTAAAATCGCAATGCGTATCCGTAAATCG
*
399072 CAACGAGAATACGT-AAATCGCAATGCATATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAATGCGTATCCGTAAATCG
* * *
399112 CAACGACAATACGTAAAATCGCAACGCGTATCCATAAATCG
1 CAACGAGAATACGTAAAATCGCAATGCGTATCCGTAAATCG
399153 CAACG
1 CAACG
399158 CGATTTTTAA
Statistics
Matches: 151, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 75 0.50
41 76 0.50
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (41 bp):
CAACGAGAATACGTAAAATCGCAATGCGTATCCGTAAATCG
Found at i:399061 original size:40 final size:41
Alignment explanation
Indices: 398961--399157 Score: 299
Period size: 40 Copynumber: 4.9 Consensus size: 41
398951 AACGAGTATC
* *
398961 CGTAAAATCACAACGCGTATCCGTAAATCGCAACGACAATA
1 CGTAAAATCGCAATGCGTATCCGTAAATCGCAACGACAATA
* *
399002 CGTAAAATCGCAATGCGTATCCGTAAATCGCAATGAGAATA
1 CGTAAAATCGCAATGCGTATCCGTAAATCGCAACGACAATA
* *
399043 CGT-AAATCGCAATGCGTATCTGTAAATCGCAACGAGAATA
1 CGTAAAATCGCAATGCGTATCCGTAAATCGCAACGACAATA
*
399083 CGT-AAATCGCAATGCATATCCGTAAATCGCAACGACAATA
1 CGTAAAATCGCAATGCGTATCCGTAAATCGCAACGACAATA
* *
399123 CGTAAAATCGCAACGCGTATCCATAAATCGCAACG
1 CGTAAAATCGCAATGCGTATCCGTAAATCGCAACG
399158 CGATTTTTAA
Statistics
Matches: 143, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 75 0.52
41 68 0.48
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (41 bp):
CGTAAAATCGCAATGCGTATCCGTAAATCGCAACGACAATA
Found at i:399758 original size:21 final size:20
Alignment explanation
Indices: 399717--399794 Score: 88
Period size: 21 Copynumber: 3.9 Consensus size: 20
399707 TTCTAAACTT
399717 AAAATCGCAACATGA-AAATG
1 AAAATCGCAACA-GAGAAATG
**
399737 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGAGAAATG
*
399758 AAAATCGCAAC-GCGAAATG
1 AAAATCGCAACAGAGAAATG
399777 AAAATCGCAACGAGAGAA
1 AAAATCGCAAC-AGAGAA
399795 TCGCAACGCG
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
19 18 0.38
20 11 0.23
21 19 0.40
ACGTcount: A:0.50, C:0.18, G:0.21, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACAGAGAAATG
Found at i:399776 original size:19 final size:19
Alignment explanation
Indices: 399752--399788 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
399742 CGCAACGAGA
399752 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
399771 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
399789 AGAGAATCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.19, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:399784 original size:40 final size:41
Alignment explanation
Indices: 399717--399794 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 41
399707 TTCTAAACTT
* **
399717 AAAATCGCAACATGAAAATGACTATCGCAACGAGAGAAATG
1 AAAATCGCAACACGAAAATGAAAATCGCAACGAGAGAAATG
*
399758 AAAATCGCAACGCG-AAATGAAAATCGCAACGAGAGAA
1 AAAATCGCAACACGAAAATGAAAATCGCAACGAGAGAA
399795 TCGCAACGCG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
40 21 0.64
41 12 0.36
ACGTcount: A:0.50, C:0.18, G:0.21, T:0.12
Consensus pattern (41 bp):
AAAATCGCAACACGAAAATGAAAATCGCAACGAGAGAAATG
Found at i:399899 original size:20 final size:19
Alignment explanation
Indices: 399822--399911 Score: 117
Period size: 19 Copynumber: 4.7 Consensus size: 19
399812 AATCGTATTA
399822 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
* *
399841 CGATTTTAATTTCGCATTG
1 CGATTTTCATTTCGCGTTG
* **
399860 CAATAGTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
*
399879 CGATTTTCATTCTCTCGTTG
1 CGATTTTCATT-TCGCGTTG
399899 CGATTTTCATTTC
1 CGATTTTCATTTC
399912 AACCAAAAGA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
19 41 0.69
20 18 0.31
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
CGATTTTCATTTCGCGTTG
Found at i:401762 original size:94 final size:94
Alignment explanation
Indices: 401601--401911 Score: 552
Period size: 94 Copynumber: 3.3 Consensus size: 94
401591 TAGATTGCTT
* * *
401601 AGTAAATTTATTCGGTTGCTGCCAATACTACTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
401666 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
401695 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
401760 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
401789 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
401854 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
401883 AGTAAATTTGTTCGATTGCTGCCAATTCT
1 AGTAAATTTATTCGGTTGCTGCCAATTCT
401912 TCTTCTGCAA
Statistics
Matches: 211, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
93 20 0.09
94 191 0.91
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:402464 original size:21 final size:21
Alignment explanation
Indices: 402373--402469 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
402363 GACTCACCTG
*
402373 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
402395 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
402415 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
402436 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
*
402457 TCATCGTTGAAGA
1 TCATCGTTCAAGA
402470 AGTCCCTCCC
Statistics
Matches: 58, Mismatches: 16, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
20 3 0.05
21 54 0.93
22 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:403194 original size:17 final size:17
Alignment explanation
Indices: 403172--403205 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
403162 TGTTTATCCT
403172 TGTTTTGGACTGTACTC
1 TGTTTTGGACTGTACTC
403189 TGTTTTGGACTGTACTC
1 TGTTTTGGACTGTACTC
403206 ATTGGCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (17 bp):
TGTTTTGGACTGTACTC
Found at i:403871 original size:14 final size:14
Alignment explanation
Indices: 403852--403887 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
403842 ATTGTTTAAT
403852 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
403866 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
403880 TGATTTGT
1 TGATTTGT
403888 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:404159 original size:20 final size:20
Alignment explanation
Indices: 404134--404303 Score: 214
Period size: 20 Copynumber: 8.4 Consensus size: 20
404124 TACGTATTGT
*
404134 CGTTGCGATTTATGGATACG
1 CGTTGCGATTTACGGATACG
* * * *
404154 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACG
* * *
404174 CATTGTGATTTACAGATACG
1 CGTTGCGATTTACGGATACG
* * *
404194 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACG
404214 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
404234 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
404254 CATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
404274 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGGATACG
404295 CGTTGCGAT
1 CGTTGCGAT
404304 AGTCAGAATC
Statistics
Matches: 127, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
20 108 0.85
21 19 0.15
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:404166 original size:40 final size:40
Alignment explanation
Indices: 404115--404303 Score: 252
Period size: 40 Copynumber: 4.7 Consensus size: 40
404105 TCATTTCGCA
* * *
404115 TTGCGATTTTACGTATTGTCGTTGCGATTTATGGATACGCA
1 TTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCG
* * *
404156 TTGCGATTTACGTATTCTCATTGTGATTTACAGATACGCG
1 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCG
404196 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCG
1 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCG
* * * *
404236 TTGCGATTTACGGATACGCATTGCGATTTACGGATACGCG
1 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCG
* *
404276 TTGCGATTTTACGGATACTCGTTGCGAT
1 TTGCGA-TTTACGTATTCTCGTTGCGAT
404304 AGTCAGAATC
Statistics
Matches: 132, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 107 0.81
41 25 0.19
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (40 bp):
TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCG
Found at i:404217 original size:80 final size:81
Alignment explanation
Indices: 404115--404303 Score: 281
Period size: 80 Copynumber: 2.3 Consensus size: 81
404105 TCATTTCGCA
* * * * * *
404115 TTGCGATTTTACGTATTGTCGTTGCGATTTATGGATACGCATTGCGATTTACGTATTCTCATTGT
1 TTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCATTGCGATTTACGGATACGCATTGC
404180 GATTTACAGATACGCG
66 GATTTACAGATACGCG
*
404196 TTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCATTGC
1 TTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCATTGCGATTTACGGATACGCATTGC
*
404260 GATTTACGGATACGCG
66 GATTTACAGATACGCG
* *
404276 TTGCGATTTTACGGATACTCGTTGCGAT
1 TTGCGATTTTACGTATTCTCGTTGCGAT
404304 AGTCAGAATC
Statistics
Matches: 97, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 72 0.74
81 25 0.26
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (81 bp):
TTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCATTGCGATTTACGGATACGCATTGC
GATTTACAGATACGCG
Found at i:404443 original size:20 final size:20
Alignment explanation
Indices: 404396--404447 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
404386 TCTTCATAAT
404396 CGCGTTGCGATTCTGGGAAC
1 CGCGTTGCGATTCTGGGAAC
* **
404416 TGATTTGCGATTCT-GGAGAC
1 CGCGTTGCGATTCTGGGA-AC
404436 CGCGTTGCGATT
1 CGCGTTGCGATT
404448 TTTATTTCGC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.31
Consensus pattern (20 bp):
CGCGTTGCGATTCTGGGAAC
Found at i:408918 original size:63 final size:61
Alignment explanation
Indices: 408802--408929 Score: 161
Period size: 63 Copynumber: 2.1 Consensus size: 61
408792 TTAAACAAAT
*
408802 AATAATATCTTTTAATTTGAAATATTCAAAAGATATAGACATATTTCACTATTCAAACTTA
1 AATAATATCTTTTAATTTGAAATATTCAAAAGATATAGACATATTTCAATATTCAAACTTA
* * * *
408863 AATATATATCATTTTAATTTGAAATATTCGAAAGTATATA-A-TTATCTTTAATATTCAAAGTTA
1 AATA-ATATC-TTTTAATTTGAAATATTCAAAAG-ATATAGACATAT-TTCAATATTCAAACTTA
408926 AATA
1 AATA
408930 GATAATAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
61 4 0.07
62 8 0.14
63 41 0.71
64 5 0.09
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (61 bp):
AATAATATCTTTTAATTTGAAATATTCAAAAGATATAGACATATTTCAATATTCAAACTTA
Found at i:410410 original size:28 final size:30
Alignment explanation
Indices: 410349--410412 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
410339 ACAACCCATC
* *
410349 ATTTTCCAAAAATTACCAATTTGGTCCCTA
1 ATTTTTCAAAAATTACCAATATGGTCCCTA
**
410379 ATTTTTCAAAAATTA-CAA-ATGGTCTTTA
1 ATTTTTCAAAAATTACCAATATGGTCCCTA
410407 ATTTTT
1 ATTTTT
410413 TTTTCTAAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 13 0.43
29 3 0.10
30 14 0.47
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (30 bp):
ATTTTTCAAAAATTACCAATATGGTCCCTA
Found at i:416821 original size:18 final size:18
Alignment explanation
Indices: 416798--416848 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
416788 ATGGATAATC
* *
416798 GTCCTTCGGGATATAGTG
1 GTCCTTCGGGACAAAGTG
*
416816 GTCCTTTGGGACAAAGTG
1 GTCCTTCGGGACAAAGTG
*
416834 GTCATTCGGGACAAA
1 GTCCTTCGGGACAAA
416849 TTCTAAGTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (18 bp):
GTCCTTCGGGACAAAGTG
Found at i:423658 original size:21 final size:20
Alignment explanation
Indices: 423586--423658 Score: 51
Period size: 22 Copynumber: 3.4 Consensus size: 20
423576 TAAAATATAA
*
423586 AAATATTCTAAAACTT-AAAT
1 AAATATTC-AAAAATTAAAAT
423606 ATAATAATATCAAAAA-TAAAAGTT
1 A-AAT-AT-TCAAAAATTAAAA--T
423630 AAACTATTCAAAAATTTAAAAT
1 AAA-TATTCAAAAA-TTAAAAT
423652 AAATATT
1 AAATATT
423659 ATTATTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 17
0.70 0.02 0.28
Matches are distributed among these distances:
20 1 0.02
21 8 0.19
22 20 0.47
23 6 0.14
24 8 0.19
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.33
Consensus pattern (20 bp):
AAATATTCAAAAATTAAAAT
Found at i:423661 original size:24 final size:25
Alignment explanation
Indices: 423571--423661 Score: 79
Period size: 24 Copynumber: 3.9 Consensus size: 25
423561 TATATATTTC
* *
423571 AAATTTAAAATATAAAAATATTCTA
1 AAATTTAAAATATAATAATATTCAA
*
423596 AAACTT-AAATATAATAATA-TCAA
1 AAATTTAAAATATAATAATATTCAA
*
423619 AAA--TAAAAGT-TAA-ACTATTCAA
1 AAATTTAAAA-TATAATAATATTCAA
*
423641 AAATTTAAAATA-AATATTATT
1 AAATTTAAAATATAATAATATT
423662 ATTTTTTCCT
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
21 4 0.07
22 13 0.24
23 10 0.19
24 22 0.41
25 5 0.09
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.34
Consensus pattern (25 bp):
AAATTTAAAATATAATAATATTCAA
Found at i:425346 original size:13 final size:13
Alignment explanation
Indices: 425302--425348 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
425292 CTTTTCTTTG
*
425302 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
425316 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
425328 TTTATTTAAAATAA
1 -ATATTTAAAATAA
425342 ATATTTA
1 ATATTTA
425349 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:426827 original size:3 final size:3
Alignment explanation
Indices: 426819--426874 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
426809 AATATATATT
* *
426819 TAA TAA TAA TAA TAA TGA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
426867 TAA TAA TA
1 TAA TAA TA
426875 TGGGTAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:427385 original size:113 final size:113
Alignment explanation
Indices: 427126--428380 Score: 1318
Period size: 113 Copynumber: 10.8 Consensus size: 113
427116 TTTTGATGAG
* *
427126 TTCTTCTCATTATGAACTT-TCTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCT
** * * *
427190 GAAAAAAAATAACCCATCAAGTAAT-AGATT-TGATCAAAAAGGTTGAACAAA
65 G-GCAAAAATAATCCATCAAGTGATGA-ATTCAGA-C-AAAAGGTTGAACAAA
*
427241 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
427306 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
66 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
* *** **
427354 TTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGATGAATTC-AAACAAAAGGTTGAACAA
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-G--TTCTTCTCATTA---TGAAC--
* ** * *
427418 ATTCTTCT--C-ATTATGAACTTCTTCTTCCTTATTCAGATGATGAATTCAAACAAAAGGTTGAA
58 CTTC-TCTGGCAAAAAT-AA--TC--CAT-C--A---AG-TGATGAATTCAGACAAAAGGTTGAA
427480 CAAA
110 CAAA
*
427484 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
* *
427549 GCAAAAATAATCCATCATGTGATGAATTCGGAC-AAAGGTTGAACAAA
66 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
427596 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
* * * * *
427661 GCAATATTGATCCATCAAATGATGAATTCAGACAAAAGGTTGAACAAG
66 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
*** **
427709 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAATTC-AAACAAAAGGTTGAACAA
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-G--TTCTTCTCATTA---TGAAC--
* * ** * * *
427773 ATTCTTCT--CATTATGAACTTCTTCTTCCTTCTTCAGATGATGAATTCAAACAAAAGGTTGAAC
58 CTTC-TCTGGCA--A--AA----ATAATCCATC--AAG-TGATGAATTCAGACAAAAGGTTGAAC
427836 AAA
111 AAA
*
427839 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
* *
427904 GCAAAAATAATCCATCATGTGATGAATTCGGACAAAAGGTTGAACAAA
66 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
427952 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
* * * * *
428017 GCAATATTGATCCATCAAATGATGAATTCAGACAAAAGGTTGAACAAG
66 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
428065 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
* ** * *
428129 G-AAAAGCTGCTCCATCAAGTGATAGATTTGAG-CAAAAGGTTGAACAAA
66 GCAAAA-ATAATCCATCAAGTGAT-GAATTCAGACAAAAGGTTGAACAAA
* *
428177 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTTC
*** * * * *
428242 -CTGGCAATGTTGATCCATCAAATGATGAATTCAGACAAAAAGTTGAACAAG
62 TCTGGCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
* *
428293 TTCTTTTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
* *** *
428357 TCAATGTTGATCCATCAAGTGATG
66 GCAAAAATAATCCATCAAGTGATG
428381 GATTTGAATC
Statistics
Matches: 978, Mismatches: 100, Indels: 127
0.81 0.08 0.11
Matches are distributed among these distances:
111 6 0.01
112 204 0.21
113 330 0.34
114 27 0.03
115 96 0.10
116 79 0.08
117 6 0.01
118 13 0.01
119 6 0.01
120 10 0.01
121 9 0.01
122 9 0.01
123 9 0.01
124 6 0.01
125 13 0.01
126 1 0.00
127 13 0.01
128 6 0.01
129 5 0.01
130 130 0.13
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
Found at i:427429 original size:65 final size:65
Alignment explanation
Indices: 427325--427877 Score: 410
Period size: 65 Copynumber: 8.0 Consensus size: 65
427315 ATCCATCAAG
* *
427325 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGA
1 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
427390 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTATTCAGA
1 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
427455 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATA
1 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*** ** **** ** * **
427520 TGAGTTCTTCTCATTATGAACCTTCTCTGGCAA-AAATAATCCATCATGTGATGAA-TTCGGACA
1 TGA-TGAAT-TCA--AACAA-AAGGT-T-G-AACAAATTCTTC-TCAT-T-ATGAACTTC-TTC-
* **
427583 AAGGTTGAACAAATTCTTCTCA
53 ----TT---C--CTTCTTCAGA
* ** ****** * ** *
427605 TTATGAACTTC-TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATATT
1 TGATGAA-TTCAAAC-AAAAGGTTGA-ACAAATTCTTCTCATTATGAA-CTTCT-T--C----TT
** * * *
427669 GATCCATCAAA
55 CCTTCTTCAGA
* *
427680 TGATGAATTCAGACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
427745 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
427810 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATA
1 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
427875 TGA
1 TGA
427878 GTTCTTCTCA
Statistics
Matches: 391, Mismatches: 65, Indels: 64
0.75 0.12 0.12
Matches are distributed among these distances:
65 266 0.68
66 2 0.01
67 3 0.01
69 4 0.01
70 1 0.00
71 2 0.01
72 12 0.03
73 25 0.06
74 10 0.03
75 19 0.05
77 5 0.01
78 2 0.01
79 8 0.02
80 11 0.03
81 7 0.02
83 1 0.00
84 3 0.01
85 10 0.03
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (65 bp):
TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
Found at i:427521 original size:24 final size:23
Alignment explanation
Indices: 427486--427530 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
427476 TGAACAAATT
427486 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
427510 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
427531 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:427780 original size:355 final size:356
Alignment explanation
Indices: 427126--428380 Score: 1797
Period size: 355 Copynumber: 3.6 Consensus size: 356
427116 TTTTGATGAG
* * *
427126 TTCTTCTCATTATGAACTT-TCTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACCTTCTCT
** * * *
427190 GAAAAAAAATAACCCATCAAGTAAT-AGATT-TGATCAAAAAGGTTGAACAAATTCTTCTCATTA
65 G-GCAAAAATAATCCATCAAGTGATGA-ATTCGGA-C-AAAAGGTTGAACAAATTCTTCTCATTA
* * * *
427253 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAAATAATC
126 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATATTGATC
* * *
427318 CATCAAGTGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATT
191 CATCAAATGATGAATTCAGACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTT
427383 CTTCAGATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTT
256 CTTCAGATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTT
427448 ATTCAGATGATGAATTCAAACAAAAGGTTGAACAAA
321 ATTCAGATGATGAATTCAAACAAAAGGTTGAACAAA
427484 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACCTTCTCTG
*
427549 GCAAAAATAATCCATCATGTGATGAATTCGGAC-AAAGGTTGAACAAATTCTTCTCATTATGAAC
66 GCAAAAATAATCCATCAAGTGATGAATTCGGACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
427613 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATATTGATCCATCA
131 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATATTGATCCATCA
427678 AATGATGAATTCAGACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
196 AATGATGAATTCAGACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
*
427743 GATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
261 GATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTATTCA
427808 GATGATGAATTCAAACAAAAGGTTGAACAAA
326 GATGATGAATTCAAACAAAAGGTTGAACAAA
427839 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACCTTCTCTG
*
427904 GCAAAAATAATCCATCATGTGATGAATTCGGACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 GCAAAAATAATCCATCAAGTGATGAATTCGGACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
427969 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATATTGATCCATCA
131 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATATTGATCCATCA
428034 AATGATGAATTCAGACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
196 AATGATGAATTCAGACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
** ** ** * *** *
428099 GATGA-G--TTC-TTC-TCA--TT--ATGAA--CTTCTC--T-GGAAAAGCTGC-TCC--A-TCA
261 GATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTATTCA
** *
428146 -AGTGAT-AGATTTGAGCAAAAGGTTGAACAAA
326 GA-TGATGA-ATTCAAACAAAAGGTTGAACAAA
* * *
428177 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--AT-ATGAGTTCTTCTCATTATGAAC-CTTC
*** * * * * * * *
428242 -CTGGCAATGTTGATCCATCAAATGATGAATTCAGACAAAAAGTTGAACAAGTTCTTTTTATTAT
62 TCTGGCAAAAATAATCCATCAAGTGATGAATTCGGACAAAAGGTTGAACAAATTCTTCTCATTAT
* *
428306 GAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTCTCTGTCAATGTTGATCC
127 GAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATATTGATCC
*
428370 ATCAAGTGATG
192 ATCAAATGATG
428381 GATTTGAATC
Statistics
Matches: 838, Mismatches: 49, Indels: 38
0.91 0.05 0.04
Matches are distributed among these distances:
337 2 0.00
338 59 0.07
340 31 0.04
341 120 0.14
342 9 0.01
343 1 0.00
345 6 0.01
347 3 0.00
349 2 0.00
351 1 0.00
352 1 0.00
353 3 0.00
355 348 0.42
356 166 0.20
357 22 0.03
358 63 0.08
359 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (356 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACCTTCTCTG
GCAAAAATAATCCATCAAGTGATGAATTCGGACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATATTGATCCATCA
AATGATGAATTCAGACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
GATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTATTCA
GATGATGAATTCAAACAAAAGGTTGAACAAA
Found at i:427876 original size:24 final size:23
Alignment explanation
Indices: 427841--427885 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
427831 TGAACAAATT
427841 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
427865 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
427886 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:428289 original size:228 final size:225
Alignment explanation
Indices: 427809--428387 Score: 887
Period size: 228 Copynumber: 2.6 Consensus size: 225
427799 CCTTCTTCAG
* * *
427809 ATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAT
1 ATGATGAATTCAGACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * *
427874 ATGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAA-ATAATCCATCATGTGATGAATTCG-GAC
66 ATGAGTTCTTCTCATTATGAA-CTTCTCTGG-AAAAGATGATCCATCAAGTGATG-ATTTGAGAC
427937 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
128 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
428002 TATGAACCTTCTCTGGCAATATTGATCCATCAA
193 TATGAACCTACTCTGGCAATATTGATCCATCAA
428035 ATGATGAATTCAGACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
1 ATGATGAATTCAGACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* *
428100 ATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATAGATTTGAG-CAA
66 ATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAGTGAT-GATTTGAGACAA
*
428164 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCA
130 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCA
*
428229 TTATGAACTCTAC-CTGGCAATGTTGATCCATCAA
192 TTATGAAC-CTACTCTGGCAATATTGATCCATCAA
* * *
428263 ATGATGAATTCAGACAAAAAGTTGAACAAGTTCTTTTTATTATGAACTTCTTCTTCCTTCTTCAG
1 ATGATGAATTCAGACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
** * *
428328 ATGAGTTCTTCTCATTATGAACTTCTCTGTCAATGTTGATCCATCAAGTGATGGATTTGA
66 ATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAGTGAT-GATTTGA
428388 ATCTTTGCTA
Statistics
Matches: 326, Mismatches: 20, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
224 4 0.01
225 78 0.24
226 85 0.26
228 156 0.48
229 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (225 bp):
ATGATGAATTCAGACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAGTGATGATTTGAGACAAA
AGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
GAACCTACTCTGGCAATATTGATCCATCAA
Found at i:429328 original size:83 final size:83
Alignment explanation
Indices: 429180--429759 Score: 1063
Period size: 83 Copynumber: 7.0 Consensus size: 83
429170 TTTATTATGA
* * * * *
429180 GCAAATTCATCTTCCAAATTCAATGATTGG-TCTGCCCAACCAGATTAGCTAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
429244 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
* *
429262 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATTAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
429327 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
429345 GCAAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
429410 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
*
429428 GCAAATTTATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
*
429493 TTCCAGAAGATGCTATTA
66 TTCCAGAAGATGCTATTG
429511 GCAAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
429576 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
429594 GCAAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
429659 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
*
429677 GCAAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAG
1 GCAAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
429742 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
429760 AGTCTCTTTC
Statistics
Matches: 487, Mismatches: 10, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
82 29 0.06
83 458 0.94
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
GCAAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATTG
Found at i:430551 original size:19 final size:17
Alignment explanation
Indices: 430527--430573 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
430517 TCATATATAA
*
430527 AAATAAATTGAATTTCTAC
1 AAATAAATTGAA-ATCT-C
430546 AAATAAATT-AAATCTC
1 AAATAAATTGAAATCTC
430562 AAATAAATTGAA
1 AAATAAATTGAA
430574 CTTGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 10 0.38
17 5 0.19
18 2 0.08
19 9 0.35
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (17 bp):
AAATAAATTGAAATCTC
Found at i:430911 original size:6 final size:6
Alignment explanation
Indices: 430902--430941 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
430892 CTTGACCTTC
*
430902 CTTTTT CTTTTT -TTTTT CTTTTT TTTTTCT CTTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTT-T CTTTTT CTTT
430942 CTTTTCTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.17
6 20 0.67
7 5 0.17
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
CTTTTT
Found at i:430924 original size:12 final size:11
Alignment explanation
Indices: 430903--430946 Score: 70
Period size: 11 Copynumber: 3.9 Consensus size: 11
430893 TTGACCTTCC
430903 TTTTTCTTTTT
1 TTTTTCTTTTT
430914 TTTTTCTTTTT
1 TTTTTCTTTTT
430925 TTTTTCTCTTTT
1 TTTTTCT-TTTT
*
430937 TCTTTCTTTT
1 TTTTTCTTTT
430947 CTTCAAGCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 21 0.68
12 10 0.32
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:441518 original size:17 final size:17
Alignment explanation
Indices: 441496--441530 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
441486 AAAATAAAAC
*
441496 ATATAAATATTATGAAA
1 ATATAAAAATTATGAAA
*
441513 ATATAAAAATTTTGAAA
1 ATATAAAAATTATGAAA
441530 A
1 A
441531 GAAAAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
ATATAAAAATTATGAAA
Found at i:442800 original size:28 final size:29
Alignment explanation
Indices: 442746--442802 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
442736 TTTTTTTTTC
* *
442746 TTTCTCTCTCTCTTCTCTTAGAGAGAGAA
1 TTTCGCTCTCTCTTCTCTTAGACAGAGAA
442775 TTTCGCTCTCT-TTCTC-TAGAACAGAGAA
1 TTTCGCTCTCTCTTCTCTTAG-ACAGAGAA
442803 GCCAGCCGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 3 0.12
28 12 0.48
29 10 0.40
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.39
Consensus pattern (29 bp):
TTTCGCTCTCTCTTCTCTTAGACAGAGAA
Found at i:443457 original size:20 final size:20
Alignment explanation
Indices: 443429--443469 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
443419 TAATTGGGCC
443429 TGTAATTAAT-TATTTATATA
1 TGTAATTAATATATTTA-ATA
*
443449 TGTATTTAATATATTTAATA
1 TGTAATTAATATATTTAATA
443469 T
1 T
443470 AATAATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TGTAATTAATATATTTAATA
Found at i:443483 original size:3 final size:3
Alignment explanation
Indices: 443464--443509 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
443454 TTAATATATT
*
443464 TAA T-A TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
443510 TGGGTAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:445873 original size:15 final size:15
Alignment explanation
Indices: 445853--445882 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
445843 ACAAGAGACC
*
445853 CTTTGATTAATCAAA
1 CTTTGAATAATCAAA
445868 CTTTGAATAATCAAA
1 CTTTGAATAATCAAA
445883 AGCCTTTCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (15 bp):
CTTTGAATAATCAAA
Found at i:449011 original size:22 final size:23
Alignment explanation
Indices: 448977--449019 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
448967 ATATAATAAA
448977 TAATATTATTTATTATAAAAACT
1 TAATATTATTTATTATAAAAACT
*
449000 TAATATTA-TTATTTTAAAAA
1 TAATATTATTTATTATAAAAA
449020 TATTAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATATTATTTATTATAAAAACT
Found at i:449101 original size:29 final size:33
Alignment explanation
Indices: 449068--449169 Score: 101
Period size: 30 Copynumber: 3.3 Consensus size: 33
449058 TATTATTATT
*
449068 AAAATATTATTTCTA-TA-ATTTTA-T-AAATA
1 AAAATATTATTTCTAGTATATTCTATTAAAATA
**
449097 AAAATATTAACTCTAGTATATTCTATTAAAATA
1 AAAATATTATTTCTAGTATATTCTATTAAAATA
* * *
449130 AAAATATGATTT-T-GAATA-TCTATAAAAATA
1 AAAATATTATTTCTAGTATATTCTATTAAAATA
449160 AAAATATTAT
1 AAAATATTAT
449170 ATTTTAAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
29 13 0.22
30 22 0.37
31 9 0.15
32 2 0.03
33 14 0.23
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (33 bp):
AAAATATTATTTCTAGTATATTCTATTAAAATA
Found at i:449321 original size:22 final size:22
Alignment explanation
Indices: 449295--449356 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
449285 TTTTTAAGAA
*
449295 ATTAATAAATAATATAATTTTT
1 ATTAATAAATAATATAATTATT
*
449317 ATTAATAAATTATTATATATTATT
1 ATTAATAAA-TAATATA-ATTATT
*
449341 A-AAATAAA-AATATAAT
1 ATTAATAAATAATATAAT
449357 AGTATCATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 2 0.06
21 5 0.15
22 9 0.26
23 12 0.35
24 6 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTAATAAATAATATAATTATT
Found at i:449419 original size:5 final size:5
Alignment explanation
Indices: 449402--449434 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
449392 TATTGTAATA
449402 ATATT ATTATT ATATT ATATT ATATT ATATT AT
1 ATATT A-TATT ATATT ATATT ATATT ATATT AT
449435 TAAAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATATT
Found at i:449445 original size:12 final size:12
Alignment explanation
Indices: 449428--449461 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
449418 ATATTATATT
449428 ATATTATTAAAA
1 ATATTATTAAAA
*
449440 ATATTAATAAAA
1 ATATTATTAAAA
449452 ATATT-TTAAA
1 ATATTATTAAA
449462 TATGTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATTATTAAAA
Found at i:449469 original size:23 final size:24
Alignment explanation
Indices: 449428--449482 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
449418 ATATTATATT
449428 ATATTATTAAAAATATTAATAA-AA
1 ATATT-TTAAAAATATTAATAATAA
* * *
449452 ATATTTTAAATATGTTAATAATTA
1 ATATTTTAAAAATATTAATAATAA
449476 ATATTTT
1 ATATTTT
449483 TATTAAATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
ATATTTTAAAAATATTAATAATAA
Found at i:449728 original size:14 final size:14
Alignment explanation
Indices: 449695--449728 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
449685 TTAAAAGTGA
*
449695 GGAAAATGTTTTCC
1 GGAAAATGTTTTAC
449709 GGAAAATGTTTTAC
1 GGAAAATGTTTTAC
*
449723 GTAAAA
1 GGAAAA
449729 CAAACGGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (14 bp):
GGAAAATGTTTTAC
Found at i:449927 original size:23 final size:23
Alignment explanation
Indices: 449897--449941 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
449887 CATATTTGAA
*
449897 TTTGAGTTTGAACTTGAATCGAG
1 TTTGAGTTTGAACTTCAATCGAG
*
449920 TTTGAGTTTGAGCTTCAATCGA
1 TTTGAGTTTGAACTTCAATCGA
449942 AATGTTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.40
Consensus pattern (23 bp):
TTTGAGTTTGAACTTCAATCGAG
Found at i:450285 original size:2 final size:2
Alignment explanation
Indices: 450278--450343 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
450268 ATCGTTCTCA
450278 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
450320 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
450344 TAAAATTAAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:452382 original size:13 final size:13
Alignment explanation
Indices: 452364--452389 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
452354 AAATATTAGA
452364 AGTTATAAAATAT
1 AGTTATAAAATAT
452377 AGTTATAAAATAT
1 AGTTATAAAATAT
452390 TCACGTGATT
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
AGTTATAAAATAT
Found at i:458756 original size:8 final size:8
Alignment explanation
Indices: 458743--458775 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
458733 AAGAAACACA
458743 TGAATTTG
1 TGAATTTG
458751 TGAATTTG
1 TGAATTTG
458759 TGAATTTG
1 TGAATTTG
*
458767 TGAGTTTG
1 TGAATTTG
458775 T
1 T
458776 AAACACGGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (8 bp):
TGAATTTG
Found at i:459165 original size:27 final size:25
Alignment explanation
Indices: 459099--459165 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 25
459089 ATATTTCTTT
* *
459099 AAATAAAATAAAATAAAATATTTTA
1 AAATTAAATATAATAAAATATTTTA
459124 AAATTAAATTAATAATAAAATATATTTA
1 AAATTAAA-T-ATAATAAAATAT-TTTA
459152 ATAAGTT-AATATAA
1 A-AA-TTAAATATAA
459166 AATTATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
25 7 0.20
26 1 0.03
27 15 0.43
28 6 0.17
29 4 0.11
30 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (25 bp):
AAATTAAATATAATAAAATATTTTA
Found at i:459197 original size:25 final size:24
Alignment explanation
Indices: 459133--459197 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
459123 AAAATTAAAT
* *
459133 TAATAATAAAATATATTTAATAAGT
1 TAAT-ATAAAATATTTTTAATAAGG
**
459158 TAATATAAAATTATTTTTAATTTGG
1 TAATATAAAA-TATTTTTAATAAGG
459183 TATATATAAAATATT
1 TA-ATATAAAATATT
459198 ATGAATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
24 6 0.18
25 20 0.59
26 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (24 bp):
TAATATAAAATATTTTTAATAAGG
Found at i:459211 original size:26 final size:26
Alignment explanation
Indices: 459160--459216 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
459150 TAATAAGTTA
* * *
459160 ATATAAAATTATTTTTAATTTGGTAT
1 ATATAAAATTATTATGAATTTAGTAT
459186 ATATAAAA-TATTATGAATTTAAGTAT
1 ATATAAAATTATTATGAATTT-AGTAT
*
459212 TTATA
1 ATATA
459217 TACTAAGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (26 bp):
ATATAAAATTATTATGAATTTAGTAT
Found at i:462569 original size:29 final size:28
Alignment explanation
Indices: 462537--462608 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
462527 TAACATAAAA
462537 TTAAAGGACTAAATTGAA-AAAATAGAAAG
1 TTAAAGGACTAAATT-AACAAAA-AGAAAG
* * *
462566 TTAAAGGACCAAAATAACTAAAAATAAAG
1 TTAAAGGACTAAATTAAC-AAAAAGAAAG
*
462595 TTAAAGAACTAAAT
1 TTAAAGGACTAAAT
462609 AGCAAATACA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 2 0.06
29 29 0.83
30 4 0.11
ACGTcount: A:0.60, C:0.07, G:0.12, T:0.21
Consensus pattern (28 bp):
TTAAAGGACTAAATTAACAAAAAGAAAG
Found at i:463478 original size:7 final size:8
Alignment explanation
Indices: 463461--463485 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
463451 CCTTTTCTCC
463461 TTTATTTT
1 TTTATTTT
463469 TTTATTTT
1 TTTATTTT
463477 TTTATTTT
1 TTTATTTT
463485 T
1 T
463486 CTCTGGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTATTTT
Found at i:464126 original size:18 final size:18
Alignment explanation
Indices: 464103--464158 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
464093 ATTGATATTC
464103 AAACATTCATAGAAACCA
1 AAACATTCATAGAAACCA
* **
464121 AAACATTGAT---ATTC-
1 AAACATTCATAGAAACCA
464135 AAACATTCATAGAAACCA
1 AAACATTCATAGAAACCA
464153 AAACAT
1 AAACAT
464159 GAACAATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 9 0.32
15 2 0.07
17 2 0.07
18 15 0.54
ACGTcount: A:0.54, C:0.20, G:0.05, T:0.21
Consensus pattern (18 bp):
AAACATTCATAGAAACCA
Found at i:464130 original size:32 final size:32
Alignment explanation
Indices: 464073--464158 Score: 165
Period size: 32 Copynumber: 2.7 Consensus size: 32
464063 AAATTCTTCT
464073 AACATTCATAGAAACC-AAACATTGATATTCA
1 AACATTCATAGAAACCAAAACATTGATATTCA
464104 AACATTCATAGAAACCAAAACATTGATATTCA
1 AACATTCATAGAAACCAAAACATTGATATTCA
464136 AACATTCATAGAAACCAAAACAT
1 AACATTCATAGAAACCAAAACAT
464159 GAACAATAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 16 0.30
32 38 0.70
ACGTcount: A:0.51, C:0.20, G:0.06, T:0.23
Consensus pattern (32 bp):
AACATTCATAGAAACCAAAACATTGATATTCA
Found at i:467348 original size:92 final size:92
Alignment explanation
Indices: 467217--467403 Score: 338
Period size: 92 Copynumber: 2.0 Consensus size: 92
467207 AAACTTCTAA
*
467217 AATTCAAACACAAGAACAAAATGTTACAGATTTCGAAACCAAGAATGTAATACTTCGTATAGTAG
1 AATTCAAACACAAGAACAAAATGTTACAGACTTCGAAACCAAGAATGTAATACTTCGTATAGTAG
467282 TTCAACTAGAAGCTTGACATCTCTATC
66 TTCAACTAGAAGCTTGACATCTCTATC
* *
467309 AATTCAAACACAATAACAAAATGTTGCAGACTTCGAAACCAAGAATGTAATACTTCGTATAGTAG
1 AATTCAAACACAAGAACAAAATGTTACAGACTTCGAAACCAAGAATGTAATACTTCGTATAGTAG
*
467374 TTCAACTAGAAGTTTGACATCTCTATC
66 TTCAACTAGAAGCTTGACATCTCTATC
467401 AAT
1 AAT
467404 GCAGATCAAT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (92 bp):
AATTCAAACACAAGAACAAAATGTTACAGACTTCGAAACCAAGAATGTAATACTTCGTATAGTAG
TTCAACTAGAAGCTTGACATCTCTATC
Found at i:468300 original size:6 final size:6
Alignment explanation
Indices: 468289--468313 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
468279 CCTGCGTAGG
468289 AAATGA AAATGA AAATGA AAATGA A
1 AAATGA AAATGA AAATGA AAATGA A
468314 GTAATATAAA
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:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAATGA
Found at i:469371 original size:16 final size:17
Alignment explanation
Indices: 469342--469374 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
469332 AATTAACCTT
469342 TTTTTTTAATATTTATC
1 TTTTTTTAATATTTATC
*
469359 TTTTTTTCA-ATTTATC
1 TTTTTTTAATATTTATC
469375 GGGAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTTTAATATTTATC
Found at i:470622 original size:3 final size:3
Alignment explanation
Indices: 470614--470645 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
470604 ACTCTTTGTA
470614 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
470646 AGTTTATAAT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:470879 original size:15 final size:16
Alignment explanation
Indices: 470859--470891 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
470849 AATCAAATAT
470859 AAAAATATAATT-CCA
1 AAAAATATAATTACCA
*
470874 AAAAATATCATTACCA
1 AAAAATATAATTACCA
470890 AA
1 AA
470892 CGCTCCTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAATATAATTACCA
Found at i:472334 original size:3 final size:3
Alignment explanation
Indices: 472326--472381 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
472316 CATTTTTAAA
** * * *
472326 ATT ATT ATT ATT ATT ACA ATT ATT ATT ATT AAT ATT AAT ATA ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
472372 ATT ATT ATT A
1 ATT ATT ATT A
472382 ATTAACAGGC
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
3 40 0.95
4 2 0.05
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (3 bp):
ATT
Found at i:473133 original size:13 final size:13
Alignment explanation
Indices: 473117--473141 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
473107 AGAGAGGTGA
473117 GAGAGAAATGAAC
1 GAGAGAAATGAAC
473130 GAGAGAAATGAA
1 GAGAGAAATGAA
473142 TAAAACGGCC
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:0.56, C:0.04, G:0.32, T:0.08
Consensus pattern (13 bp):
GAGAGAAATGAAC
Found at i:473673 original size:18 final size:20
Alignment explanation
Indices: 473639--473678 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
473629 CTTATTCATA
*
473639 TAAATATATATATATTTGTT
1 TAAATATATATATATTTATT
473659 TAAATA-ATA-ATATTTATT
1 TAAATATATATATATTTATT
473677 TA
1 TA
473679 TTTTTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 3 0.16
20 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TAAATATATATATATTTATT
Found at i:473936 original size:2 final size:2
Alignment explanation
Indices: 473929--473964 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
473919 ACAAAACCAC
473929 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
473965 TTAATATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:474490 original size:20 final size:20
Alignment explanation
Indices: 474449--474500 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
474439 GAGAATTAAA
*
474449 TTTTATTTAATTTATGATTC
1 TTTTATTTAATTTATGACTC
*
474469 TTTTAATTTATTTTAT-ACTC
1 TTTT-ATTTAATTTATGACTC
*
474489 TTGTATATTAAT
1 TTTTAT-TTAAT
474501 ATTTAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.08
20 14 0.54
21 10 0.38
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTTATTTAATTTATGACTC
Found at i:476637 original size:42 final size:41
Alignment explanation
Indices: 476591--476878 Score: 176
Period size: 40 Copynumber: 7.1 Consensus size: 41
476581 TAGCGGTATT
*
476591 TTTAGTGGTGTTTTTTGAACAAACGCCGGTAAATACTCGTAC
1 TTTAGTGGTG-TTTTTGAACAAACGCCGCTAAATACTCGTAC
* * * * ** *
476633 TTTAGTGGCGTTTAT-AA-AAACACCACTAAATA-TTATAG
1 TTTAGTGGTGTTTTTGAACAAACGCCGCTAAATACTCGTAC
* * * * *
476671 TTTAGTGGTG-TTTTCATATAAACGCCGCTAATTAAT-ATAC
1 TTTAGTGGTGTTTTTGA-ACAAACGCCGCTAAATACTCGTAC
* ** * * *
476711 TTTAGCGGCATTTTTGTACAAACACCGCTAAAGACTCGTAC
1 TTTAGTGGTGTTTTTGAACAAACGCCGCTAAATACTCGTAC
* * * * ** *
476752 TCTAGTGGTGTTTTAAGCACAAACACCGCTAAAGGCCCGTAC
1 TTTAGTGGTGTTTT-TGAACAAACGCCGCTAAATACTCGTAC
* * * * * *
476794 ATTAGTGGCG-TTTTCATATAAACGCCGCTAATTACT-ATAC
1 TTTAGTGGTGTTTTTGA-ACAAACGCCGCTAAATACTCGTAC
* * *
476834 TTTAGCGGTGTTTTTGTACAAACGCCGCTAAAAACTCGTAC
1 TTTAGTGGTGTTTTTGAACAAACGCCGCTAAATACTCGTAC
476875 TTTA
1 TTTA
476879 ACAGCGTTTT
Statistics
Matches: 181, Mismatches: 55, Indels: 21
0.70 0.21 0.08
Matches are distributed among these distances:
37 3 0.02
38 13 0.07
39 13 0.07
40 64 0.35
41 49 0.27
42 39 0.22
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (41 bp):
TTTAGTGGTGTTTTTGAACAAACGCCGCTAAATACTCGTAC
Found at i:476822 original size:123 final size:123
Alignment explanation
Indices: 476602--477011 Score: 384
Period size: 123 Copynumber: 3.3 Consensus size: 123
476592 TTAGTGGTGT
* * *
476602 TTTTTGAACAAACGCCGGTAAATACTCGTACTTTAGTGGCG-TTTATA--A-AAACACCACTAAA
1 TTTTTGTACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTA-AGCACAAACACCACTAAA
***** ** *
476663 -TATTATAGTTTAGTGGTGTTTTCATATAAACGCCGCTAATTAATATACTTTAGCGGCA
65 GGCCCGTACATTAGTGGAGTTTTCATATAAACGCCGCTAATTAATATACTTTAGCGGCA
* * * *
476721 TTTTTGTACAAACACCGCTAAAGACTCGTACTCTAGTGGTGTTTTAAGCACAAACACCGCTAAAG
1 TTTTTGTACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTAAGCACAAACACCACTAAAG
* * **
476786 GCCCGTACATTAGTGGCGTTTTCATATAAACGCCGCTAATTACTATACTTTAGCGGTG
66 GCCCGTACATTAGTGGAGTTTTCATATAAACGCCGCTAATTAATATACTTTAGCGGCA
* *** * * * *
476844 TTTTTGTACAAACGCCGCTAAAAACTCGTACTTTAACAGCGTTTTAAGCATAATCGCTACTAAAG
1 TTTTTGTACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTAAGCACAAACACCACTAAAG
* * * * * * *
476909 TCTCGTACATTAGCGGAGTTTTAAGTACAAACGCCGCTAAAGTACATGTA-TTTAGCGGCA
66 GCCCGTACATTAGTGGAGTTTTCA-TATAAACGCCGCT-AATTA-ATATACTTTAGCGGCA
* * * *
476969 TTTTTATATAAACGCTAG-TAAAGACTCGTACTTTAGTGTCGTT
1 TTTTTGTACAAACGC-CGCTAAAGACTCGTACTTTAGTGGCGTT
477012 GTTGAAAACA
Statistics
Matches: 233, Mismatches: 49, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
119 36 0.15
120 4 0.02
121 1 0.00
122 12 0.05
123 119 0.51
124 12 0.05
125 45 0.19
126 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (123 bp):
TTTTTGTACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTAAGCACAAACACCACTAAAG
GCCCGTACATTAGTGGAGTTTTCATATAAACGCCGCTAATTAATATACTTTAGCGGCA
Found at i:476949 original size:42 final size:42
Alignment explanation
Indices: 476712--476951 Score: 159
Period size: 42 Copynumber: 5.8 Consensus size: 42
476702 TTAATATACT
* * * *
476712 TTAGCGGCATTTT-TGTACAAACACCGCTAAAGACTCGTAC-
1 TTAGCGGCGTTTTAAGTACAAACGCCGCTAAAGTCTCGTACA
* * * * * *
476752 TCTAGTGGTGTTTTAAGCACAAACACCGCTAAAGGCCCGTACA
1 T-TAGCGGCGTTTTAAGTACAAACGCCGCTAAAGTCTCGTACA
* * * * * *
476795 TTAGTGGCGTTTTCA-TATAAACGCCGCT-AATTACT-ATACT
1 TTAGCGGCGTTTTAAGTACAAACGCCGCTAAAGT-CTCGTACA
* * ** *
476835 TTAGCGGTGTTTT-TGTACAAACGCCGCTAAAAACTCGTACT
1 TTAGCGGCGTTTTAAGTACAAACGCCGCTAAAGTCTCGTACA
* * * * * **
476876 TTAACAGCGTTTTAAGCATAATCGCTACTAAAGTCTCGTACA
1 TTAGCGGCGTTTTAAGTACAAACGCCGCTAAAGTCTCGTACA
*
476918 TTAGCGGAGTTTTAAGTACAAACGCCGCTAAAGT
1 TTAGCGGCGTTTTAAGTACAAACGCCGCTAAAGT
476952 ACATGTATTT
Statistics
Matches: 148, Mismatches: 44, Indels: 14
0.72 0.21 0.07
Matches are distributed among these distances:
40 31 0.21
41 36 0.24
42 80 0.54
43 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (42 bp):
TTAGCGGCGTTTTAAGTACAAACGCCGCTAAAGTCTCGTACA
Found at i:483144 original size:20 final size:20
Alignment explanation
Indices: 483119--483156 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
483109 TTTCGGTGCA
*
483119 GAGGGAATCGATACCCCCAT
1 GAGGGAAACGATACCCCCAT
*
483139 GAGGGAAACGATTCCCCC
1 GAGGGAAACGATACCCCC
483157 TTCGAAGGGG
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:0.29, C:0.32, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAAACGATACCCCCAT
Found at i:484858 original size:12 final size:12
Alignment explanation
Indices: 484841--484867 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
484831 TGAGCCTGAA
484841 CAACCTGAGGAG
1 CAACCTGAGGAG
484853 CAACCTGAGGAG
1 CAACCTGAGGAG
484865 CAA
1 CAA
484868 GCACAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.26, G:0.30, T:0.07
Consensus pattern (12 bp):
CAACCTGAGGAG
Found at i:489794 original size:43 final size:43
Alignment explanation
Indices: 489734--490122 Score: 564
Period size: 43 Copynumber: 9.0 Consensus size: 43
489724 TAAATGACAT
* * * *
489734 TAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACGTCGT
1 TAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGC
* * *
489777 TAAATACACAGTCAATAGCGGCGTTTGTAAAGATAAACGCCAC
1 TAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGC
* *
489820 TAAATACACAGTCAATTGCGGCGTTTATAAAGACAAACACCGC
1 TAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGC
* *
489863 TAAATACACAGTCAATAGCAGCG-TTATTAAAGAAAAACGCCGC
1 TAAATACACAGTCAATAGCGGCGTTTA-TAAAGACAAACGCCGC
* * * * *
489906 TAAATGCACAGTCAATAACGGCGTTTATAAAGAAAAAAGTCGC
1 TAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGC
* *
489949 TAAATACATAGTCAATAGCGGCGTTTATAAAGACAAATGCCGC
1 TAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGC
489992 TAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGC
1 TAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGC
*
490035 TAAATACACAGTCAATAGCGGCGTTTATAAAGACAACCGCCGC
1 TAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGC
* * *
490078 TAAATACACAGTTAATAGCGGCGTTTGTAAAGACAAATGCCGC
1 TAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGC
490121 TA
1 TA
490123 TATGTCTCAA
Statistics
Matches: 313, Mismatches: 31, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
42 3 0.01
43 307 0.98
44 3 0.01
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (43 bp):
TAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGC
Found at i:492984 original size:136 final size:136
Alignment explanation
Indices: 492635--493045 Score: 625
Period size: 136 Copynumber: 3.1 Consensus size: 136
492625 AAGTTCTTCT
* * * * *
492635 AAAAAAAAGAGTCATACATTCAAAACATGACCTTGATCGGATATTTGGCAATTCGATGTTTGTTC
1 AAAAAAAAGAGTCATATATTCAAAGCATGACCTTGATCGGATATTTGGCAGTTCGGTGTTTGATC
* * *
492700 CAATGTGATTGTCAAGTAAAAGACATTGTGATGAGTTGAACCCTTTAATTAGTCCAATAAAGGCT
66 CACTGTGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCCTTTAATTAGTCCAATGAAGGCT
492765 AATGT-
131 AATGTC
* *
492770 --AAAAAA-AGTCATATATTCAAAGCATGACCTTGATTGGATATTTGGTAGTTCGGTGTTTGATC
1 AAAAAAAAGAGTCATATATTCAAAGCATGACCTTGATCGGATATTTGGCAGTTCGGTGTTTGATC
* *
492832 TACTGTGATTGCCAAGTCAAAGACATTGTGATGAGTTGAACCCTTTAATTAGTCCAATGAAGGCT
66 CACTGTGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCCTTTAATTAGTCCAATGAAGGCT
492897 AATGTC
131 AATGTC
* *
492903 AAAAAAAAGAGTTATATATTCAAAGCATGACCTTGATCAGG-TATTTGGCAGTTCGGTGTTTGCT
1 AAAAAAAAGAGTCATATATTCAAAGCATGACCTTGATC-GGATATTTGGCAGTTCGGTGTTTGAT
* *
492967 CCACTATGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCATTTAATTAGTCCAATGAAGGC
65 CCACTGTGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCCTTTAATTAGTCCAATGAAGGC
493032 TAATGTC
130 TAATGTC
*
493039 AATAAAA
1 AAAAAAA
493046 TTGAATTCAG
Statistics
Matches: 250, Mismatches: 21, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
132 114 0.46
133 6 0.02
135 6 0.02
136 122 0.49
137 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (136 bp):
AAAAAAAAGAGTCATATATTCAAAGCATGACCTTGATCGGATATTTGGCAGTTCGGTGTTTGATC
CACTGTGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCCTTTAATTAGTCCAATGAAGGCT
AATGTC
Found at i:494989 original size:75 final size:75
Alignment explanation
Indices: 494902--495071 Score: 250
Period size: 75 Copynumber: 2.3 Consensus size: 75
494892 AACAAGAAGA
* * * * * *
494902 AAATGTTGGGGCATGCTGAAAGCCCATTTTAATTATAATCAGTAATGTTGATGTATTTTGAATGT
1 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGATATATTTTGAACGT
**
494967 TTGTATCAGC
66 TCATATCAGC
494977 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGATATATTTTGAACGT
1 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGATATATTTTGAACGT
495042 TCATATCAGC
66 TCATATCAGC
* *
495052 AAATGCTGGGACATGCTGAA
1 AAATGTTGGGGCATGCTGAA
495072 GATCCACATC
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 85 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (75 bp):
AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGATATATTTTGAACGT
TCATATCAGC
Done.