Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1149.1
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: 561462
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.33
Warning! 17900 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:385327 original size:28 final size:27
Alignment explanation
Indices: 385294--385389 Score: 99
Period size: 28 Copynumber: 3.5 Consensus size: 27
385284 GAATATATGA
385294 ACTATGTGTGCGAAATTATTAACTGAGC
1 ACTATGTGTGCGAAATTATTAAC-GAGC
* **
385322 ACTATG-GTGCGAGATCGGGTGTAA-G-GC
1 ACTATGTGTGCGAAAT--TAT-TAACGAGC
385349 ACTATGTGTGCGAAATTATTAACCGAGC
1 ACTATGTGTGCGAAATTATTAA-CGAGC
385377 ACTATGTGTGCGA
1 ACTATGTGTGCGA
385390 GATCGGGTGT
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
25 3 0.05
26 1 0.02
27 17 0.31
28 30 0.55
29 1 0.02
30 3 0.05
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (27 bp):
ACTATGTGTGCGAAATTATTAACGAGC
Found at i:385378 original size:55 final size:56
Alignment explanation
Indices: 385294--385426 Score: 223
Period size: 55 Copynumber: 2.4 Consensus size: 56
385284 GAATATATGA
*
385294 ACTATGTGTGCGAAATTATTAACTGAGCACTATG-GTGCGAGATCGGGTGTAAGGC
1 ACTATGTGTGCGAAATTATTAACCGAGCACTATGTGTGCGAGATCGGGTGTAAGGC
385349 ACTATGTGTGCGAAATTATTAACCGAGCACTATGTGTGCGAGATCGGGTGTAAGGC
1 ACTATGTGTGCGAAATTATTAACCGAGCACTATGTGTGCGAGATCGGGTGTAAGGC
*
385405 ACTGCGTGTGTGCGAAATTATT
1 ACT--ATGTGTGCGAAATTATT
385427 TAAGGAATAT
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
55 33 0.45
56 24 0.33
58 16 0.22
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (56 bp):
ACTATGTGTGCGAAATTATTAACCGAGCACTATGTGTGCGAGATCGGGTGTAAGGC
Found at i:385406 original size:28 final size:28
Alignment explanation
Indices: 385320--385407 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
385310 TATTAACTGA
385320 GCACTATG-GTGCGAGATCGGGTGTAAG
1 GCACTATGTGTGCGAGATCGGGTGTAAG
* **
385347 GCACTATGTGTGCGAAAT--TAT-TAACCG
1 GCACTATGTGTGCGAGATCGGGTGTAA--G
385374 AGCACTATGTGTGCGAGATCGGGTGTAAG
1 -GCACTATGTGTGCGAGATCGGGTGTAAG
385403 GCACT
1 GCACT
385408 GCGTGTGTGC
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
25 3 0.06
26 1 0.02
27 9 0.19
28 30 0.62
29 1 0.02
30 1 0.02
31 3 0.06
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGGGTGTAAG
Found at i:393504 original size:14 final size:14
Alignment explanation
Indices: 393485--393514 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
393475 AACAATTATC
*
393485 TTTAATTTTGGGTT
1 TTTAATTCTGGGTT
393499 TTTAATTCTGGGTT
1 TTTAATTCTGGGTT
393513 TT
1 TT
393515 ATTTGAATTT
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:0.13, C:0.03, G:0.20, T:0.63
Consensus pattern (14 bp):
TTTAATTCTGGGTT
Found at i:404069 original size:32 final size:27
Alignment explanation
Indices: 403999--404053 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
403989 GAAATCAACA
*
403999 TACCCTTTTTATTTTGGTATTGTTATG
1 TACCTTTTTTATTTTGGTATTGTTATG
404026 TACCTTTTTTATTTTGGTATTGTTATG
1 TACCTTTTTTATTTTGGTATTGTTATG
404053 T
1 T
404054 GATGTTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.09, G:0.15, T:0.62
Consensus pattern (27 bp):
TACCTTTTTTATTTTGGTATTGTTATG
Found at i:404470 original size:80 final size:80
Alignment explanation
Indices: 404365--404520 Score: 276
Period size: 80 Copynumber: 1.9 Consensus size: 80
404355 AAAAGGATTC
*
404365 ATCCACACATTAAAATCATGCTTTAATTTTGTTATAATATTATTGTTTTTGTATGCTTTAAAAAT
1 ATCCACACATTAAAATCATGCTTTAATTTTGTTATAATATTATTATTTTTGTATGCTTTAAAAAT
404430 ATAAATTTCAAATTG
66 ATAAATTTCAAATTG
* * *
404445 ATCCGCACATTAAAATCGTGTTTTAATTTTGTTATAATATTATTATTTTTGTATGCTTTAAAAAT
1 ATCCACACATTAAAATCATGCTTTAATTTTGTTATAATATTATTATTTTTGTATGCTTTAAAAAT
404510 ATAAATTTCAA
66 ATAAATTTCAA
404521 CAATAATGTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.47
Consensus pattern (80 bp):
ATCCACACATTAAAATCATGCTTTAATTTTGTTATAATATTATTATTTTTGTATGCTTTAAAAAT
ATAAATTTCAAATTG
Found at i:405007 original size:16 final size:16
Alignment explanation
Indices: 404988--405051 Score: 51
Period size: 16 Copynumber: 4.0 Consensus size: 16
404978 TTGTAAGTTC
404988 AATTATTTTAGATTTT
1 AATTATTTTAGATTTT
*
405004 AATTATTTT-GAATTTG
1 AATTATTTTAG-ATTTT
* *
405020 AGTTACTTGTA-ATTTT
1 AATTA-TTTTAGATTTT
* *
405036 AATTAATTTAAATTTT
1 AATTATTTTAGATTTT
405052 CAAGGTCAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
15 4 0.11
16 30 0.81
17 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.58
Consensus pattern (16 bp):
AATTATTTTAGATTTT
Found at i:412000 original size:30 final size:31
Alignment explanation
Indices: 411960--412028 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
411950 AACTCAACAT
411960 TTTAATGACTTAGATAAA-ACTTTTGAATAA
1 TTTAATGACTTAGATAAATACTTTTGAATAA
* * **
411990 TTTACTGACTTATATAAATTTTTTTGAATAA
1 TTTAATGACTTAGATAAATACTTTTGAATAA
412021 TTTAATGA
1 TTTAATGA
412029 TAATTTTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 16 0.48
31 17 0.52
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (31 bp):
TTTAATGACTTAGATAAATACTTTTGAATAA
Found at i:412500 original size:21 final size:22
Alignment explanation
Indices: 412474--412514 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
412464 TTCAAAGTTT
412474 TTTTAAT-A-ATTTTATTATAGA
1 TTTTAATCATATTTT-TTATAGA
412495 TTTTAATCATATTTTTTATA
1 TTTTAATCATATTTTTTATA
412515 TAATATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTAATCATATTTTTTATAGA
Found at i:413298 original size:22 final size:21
Alignment explanation
Indices: 413265--413305 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
413255 TATTTCGTCT
413265 TTGAATTATATTATTTTTTATA
1 TTGAATTATATT-TTTTTTATA
413287 TTGATATT-TATTTTTTTTA
1 TTGA-ATTATATTTTTTTTA
413306 ATTTAGTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 8 0.44
23 3 0.17
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
TTGAATTATATTTTTTTTATA
Found at i:413493 original size:9 final size:9
Alignment explanation
Indices: 413472--413621 Score: 52
Period size: 9 Copynumber: 15.6 Consensus size: 9
413462 AAGGTTGTAA
413472 AAAAATTATT
1 AAAAATTA-T
413482 AAAAATTAT
1 AAAAATTAT
***
413491 AAAAAAGCT
1 AAAAATTAT
*
413500 GAAAATTAT
1 AAAAATTAT
*
413509 AAAAAAATTGT
1 --AAAAATTAT
413520 AAAAA-TAGT
1 AAAAATTA-T
*
413529 AAAAA-AATT
1 AAAAATTA-T
* *
413538 AAAATTTGT
1 AAAAATTAT
413547 AAATAATTAT
1 AAA-AATTAT
* *
413557 CAAATATTTT
1 -AAAAATTAT
*
413567 AAAAATATTTT
1 -AAAA-ATTAT
* *
413578 AAAATTGTAA
1 AAAAAT-TAT
413588 AAAAAGTTATT
1 AAAAA-TTA-T
413599 AAAAATTAT
1 AAAAATTAT
*
413608 AAAAATTGT
1 AAAAATTAT
413617 AAAAA
1 AAAAA
413622 AATTAACAAA
Statistics
Matches: 103, Mismatches: 27, Indels: 21
0.68 0.18 0.14
Matches are distributed among these distances:
8 1 0.01
9 48 0.47
10 33 0.32
11 21 0.20
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:413549 original size:18 final size:20
Alignment explanation
Indices: 413468--413537 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 20
413458 AAGAAAGGTT
*
413468 GTAAAAAAATTATTAAAAATTA
1 GTAAAAAAATT-GTAAAAA-TA
** *
413490 -TAAAAAAGCTG-AAAATTA
1 GTAAAAAAATTGTAAAAATA
413508 -TAAAAAAATTGTAAAAATA
1 GTAAAAAAATTGTAAAAATA
413527 GTAAAAAAATT
1 GTAAAAAAATT
413538 AAAATTTGTA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
18 11 0.28
19 10 0.26
20 10 0.26
21 8 0.21
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.27
Consensus pattern (20 bp):
GTAAAAAAATTGTAAAAATA
Found at i:413626 original size:20 final size:20
Alignment explanation
Indices: 413466--413612 Score: 90
Period size: 20 Copynumber: 7.5 Consensus size: 20
413456 TAAAGAAAGG
413466 TTGTAAAAAAATTATTAAAAA
1 TTGTAAAAAAATTA-TAAAAA
* ** *
413487 TTAT-AAAAAA-GCTGAAAA
1 TTGTAAAAAAATTATAAAAA
* *
413505 TTATAAAAAAATTGTAAAAA
1 TTGTAAAAAAATTATAAAAA
* *
413525 TAGTAAAAAAA-T-TAAAAT
1 TTGTAAAAAAATTATAAAAA
* *
413543 TTGT-AAATAATTATCAAATA
1 TTGTAAAAAAATTAT-AAAAA
* * *
413563 TTTTAAAAATATT-TTAAAA
1 TTGTAAAAAAATTATAAAAA
413582 TTGTAAAAAAAGTTATTAAAAA
1 TTGTAAAAAAA-TTA-TAAAAA
*
413604 TTATAAAAA
1 TTGTAAAAA
413613 TTGTAAAAAA
Statistics
Matches: 94, Mismatches: 23, Indels: 17
0.70 0.17 0.13
Matches are distributed among these distances:
17 5 0.05
18 18 0.19
19 20 0.21
20 29 0.31
21 9 0.10
22 13 0.14
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.33
Consensus pattern (20 bp):
TTGTAAAAAAATTATAAAAA
Found at i:419305 original size:22 final size:22
Alignment explanation
Indices: 419280--419332 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
419270 TTAAATTTTT
419280 TACTTAAATAATGGGTA-TTTGG
1 TACTTAAATAATGGGTACTTT-G
*
419302 TACTTAAATAATGGGTACTTTT
1 TACTTAAATAATGGGTACTTTG
419324 TACTTAAAT
1 TACTTAAAT
419333 TTAAAAATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (22 bp):
TACTTAAATAATGGGTACTTTG
Found at i:423133 original size:14 final size:14
Alignment explanation
Indices: 423114--423145 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
423104 TAACTAATTT
423114 TATAGTTATATATA
1 TATAGTTATATATA
*
423128 TATAGTTATATATT
1 TATAGTTATATATA
423142 TATA
1 TATA
423146 TTAAGGATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (14 bp):
TATAGTTATATATA
Found at i:427671 original size:29 final size:30
Alignment explanation
Indices: 427620--427688 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
427610 TGAATATAAG
*
427620 TTTGATTTAATGTGTAATATTATATATAAAAT
1 TTTGATTT--TGTGTAATATTATAAATAAAAT
* *
427652 TTT-ATTTTGTGTGATTTTATAAATAAAAT
1 TTTGATTTTGTGTAATATTATAAATAAAAT
427681 TTTGATTT
1 TTTGATTT
427689 GATTTAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 22 0.67
30 4 0.12
31 4 0.12
32 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (30 bp):
TTTGATTTTGTGTAATATTATAAATAAAAT
Found at i:436290 original size:17 final size:17
Alignment explanation
Indices: 436270--436303 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
436260 ATTTTGATCT
436270 AAGATACGTTCTTTTAC
1 AAGATACGTTCTTTTAC
*
436287 AAGATATGTTCTTTTAC
1 AAGATACGTTCTTTTAC
436304 TCGTCGATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (17 bp):
AAGATACGTTCTTTTAC
Found at i:436727 original size:31 final size:31
Alignment explanation
Indices: 436689--436764 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
436679 GAAAAAATTT
*
436689 AATAATTCGATAACT-TAAATGAAAAT-TTTTA
1 AATAATTCAATAA-TGTAAAT-AAAATCTTTTA
*
436720 AATAATTCAATAATGTAAATAAATTCTTTTA
1 AATAATTCAATAATGTAAATAAAATCTTTTA
*
436751 AATAATTTAATAAT
1 AATAATTCAATAAT
436765 TATCTTATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
30 5 0.12
31 35 0.88
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (31 bp):
AATAATTCAATAATGTAAATAAAATCTTTTA
Found at i:437760 original size:20 final size:20
Alignment explanation
Indices: 437716--437754 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
437706 TATGTACATA
* *
437716 GATTAATTTATTTATTTATG
1 GATTAATTAATTAATTTATG
437736 GATTAATTAATTAATTTAT
1 GATTAATTAATTAATTTAT
437755 TTATTAGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (20 bp):
GATTAATTAATTAATTTATG
Found at i:439273 original size:14 final size:14
Alignment explanation
Indices: 439248--439287 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
439238 ATTTTATCTC
439248 AAATTT-TAATTTA
1 AAATTTATAATTTA
439261 AAATTTATAATTTA
1 AAATTTATAATTTA
* *
439275 AGATTTAAAATTT
1 AAATTTATAATTT
439288 TAGAGTACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
AAATTTATAATTTA
Found at i:440023 original size:12 final size:12
Alignment explanation
Indices: 440006--440031 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
439996 CAAAACAGGC
440006 TTTTAGCGGCGT
1 TTTTAGCGGCGT
440018 TTTTAGCGGCGT
1 TTTTAGCGGCGT
440030 TT
1 TT
440032 GGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:440401 original size:114 final size:114
Alignment explanation
Indices: 440100--440466 Score: 524
Period size: 114 Copynumber: 3.2 Consensus size: 114
440090 AAAATAAGCA
* * * * *
440100 TTAGCGGCGTATTTGAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGTCGTTTCTCGAGCTT
1 TTAGCGGCATTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTTTGAGCTT
* * *
440164 TCGGGGATTTAGAGGCGTTTATAAGAAAGCGCCGCTAATGCTCAAGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
*
440213 TTAGCGGCATTTTTGGG-AAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCTT
1 TTAGCGGCATTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTTTGAGCTT
* * * *
440277 TCGGGGATTTAGCGGCATTTTTAAGAAAGCACCGCTAATGCTCGGGGTT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * *
440326 TTAGCGGCATTTTGGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTTAAGCTT
1 TTAGCGGCATTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTTTGAGCTT
* *
440391 TCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGC-CTAGGACT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTC-AGGGCT
* *
440440 TTAGCGGCGTTTTTGGTAAAGCGCCGC
1 TTAGCGGCATTTTTGGGAAAGCGCCGC
440467 TAATGCCCAG
Statistics
Matches: 225, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
112 9 0.04
113 107 0.48
114 109 0.48
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (114 bp):
TTAGCGGCATTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTTTGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:440462 original size:41 final size:40
Alignment explanation
Indices: 440398--440507 Score: 150
Period size: 41 Copynumber: 2.7 Consensus size: 40
440388 CTTTCGGGGA
*
440398 TTTAGCGGCGTTTTTAAGG-AAGCGCCGCTAATGCCTAGGAC
1 TTTAGCGGCGTTTTT--GGAAAGCGCCGCTAATGCCCAGGAC
*
440439 TTTAGCGGCGTTTTTGGTAAAGCGCCGCTAATGCCCAGGGC
1 TTTAGCGGCGTTTTTGG-AAAGCGCCGCTAATGCCCAGGAC
*
440480 TTTAGCGGCATTTTTGGAAAAGCGCCGC
1 TTTAGCGGCGTTTTTGG-AAAGCGCCGC
440508 AAAAAAACCT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
39 2 0.03
41 61 0.97
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.27
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTGGAAAGCGCCGCTAATGCCCAGGAC
Found at i:440502 original size:155 final size:155
Alignment explanation
Indices: 440284--440583 Score: 444
Period size: 155 Copynumber: 1.9 Consensus size: 155
440274 CTTTCGGGGA
* * * *
440284 TTTAGCGGCATTTTTAAGAAAGCACCGCTAATGCTCGGGGTTTTAGCGGCATTTTGGGGAAAGCG
1 TTTAGCGGCATTTTTAAGAAAGCACCGCTAATGCCCAGGGCTTTAGCGGCATTTTGGGAAAAGCG
*
440349 CCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTTAAGCTTTCGGGGATTTAGCGGCG-TTTTT
66 CCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGGGGATTTAGCGGCGTTTTTT
440413 -AAGGAAGCGCCGCTAATGCCTAGGAC
131 GAA--AAGCGCCGCTAATGCCTAGGAC
* * * *
440439 TTTAGCGGCGTTTTT-GGTAAAGCGCCGCTAATGCCCAGGGCTTTAGCGGCATTTTTGGAAAAGC
1 TTTAGCGGCATTTTTAAG-AAAGCACCGCTAATGCCCAGGGCTTTAGCGGCATTTTGGGAAAAGC
* * *
440503 GCCGCAAAAAAACCTAAGCTCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTTGCGGCGTTTTT
65 GCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGGGGATTTAGCGGCGTTTTT
440568 TGAAAAGCGCCGCTAA
130 TGAAAAGCGCCGCTAA
440584 ATTTTTTTTA
Statistics
Matches: 130, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
154 1 0.01
155 122 0.94
156 5 0.04
157 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (155 bp):
TTTAGCGGCATTTTTAAGAAAGCACCGCTAATGCCCAGGGCTTTAGCGGCATTTTGGGAAAAGCG
CCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGGGGATTTAGCGGCGTTTTTT
GAAAAGCGCCGCTAATGCCTAGGAC
Found at i:440851 original size:15 final size:14
Alignment explanation
Indices: 440827--440867 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
440817 GTTCATATTT
440827 TATGGTTTAGGGAG
1 TATGGTTTAGGGAG
*
440841 TATGAGTTTAGGGAT
1 TATG-GTTTAGGGAG
*
440856 TATGGATTAGGG
1 TATGGTTTAGGG
440868 GTTGGGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.37
Consensus pattern (14 bp):
TATGGTTTAGGGAG
Found at i:441160 original size:7 final size:7
Alignment explanation
Indices: 441150--441198 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
441140 GATTTAAGGT
441150 TTAGGGG
1 TTAGGGG
441157 TTAGGGG
1 TTAGGGG
441164 TTTAGGGG
1 -TTAGGGG
**
441172 TTAGATG
1 TTAGGGG
441179 TTAGGGG
1 TTAGGGG
* *
441186 TTAAGAG
1 TTAGGGG
441193 TTAGGG
1 TTAGGG
441199 ATTTAAGGTT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:441167 original size:15 final size:15
Alignment explanation
Indices: 441146--441213 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
441136 TTGAGATTTA
441146 AGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
441161 GGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
441176 ATG-TTAGGGGTTA-
1 AGGTTTAGGGGTTAG
*
441189 AGAG-TTAGGGATTTA-
1 AG-GTTTAGGG-GTTAG
441204 AGGTTTAGGG
1 AGGTTTAGGG
441214 ATTCAGGGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
13 1 0.02
14 18 0.40
15 26 0.58
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.34
Consensus pattern (15 bp):
AGGTTTAGGGGTTAG
Found at i:441167 original size:36 final size:36
Alignment explanation
Indices: 441126--441211 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
441116 TAGGGATTAT
* * *
441126 GGTTTAAGGGTTGAGAT-TTAAGGTTTAGGGGTTAGG
1 GGTTTAAGGGTT-AGATGTTAAGGGTTAAGAGTTAGG
* *
441162 GGTTTAGGGGTTAGATGTTAGGGGTTAAGAGTTAGG
1 GGTTTAAGGGTTAGATGTTAAGGGTTAAGAGTTAGG
* *
441198 GATTTAAGGTTTAG
1 GGTTTAAGGGTTAG
441212 GGATTCAGGG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
35 4 0.10
36 37 0.90
ACGTcount: A:0.23, C:0.00, G:0.41, T:0.36
Consensus pattern (36 bp):
GGTTTAAGGGTTAGATGTTAAGGGTTAAGAGTTAGG
Found at i:441893 original size:19 final size:20
Alignment explanation
Indices: 441859--441899 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
441849 AAAACGCCGC
**
441859 AAAAAATAAATCAA-TTTAT
1 AAAAAATAAAAAAATTTTAT
441878 AAAAAATAAAAAAATTTTAT
1 AAAAAATAAAAAAATTTTAT
441898 AA
1 AA
441900 TAGCAAAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAAATAAAAAAATTTTAT
Found at i:442145 original size:147 final size:146
Alignment explanation
Indices: 441700--442153 Score: 788
Period size: 145 Copynumber: 3.1 Consensus size: 146
441690 TGAAATAGCT
* *
441700 TAAAAAACGCCGCAAAAAATAAATCAACTTATAAAAAAATAAAAAAAATTTATAATAGCAAAACG
1 TAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAATTTTATAATAGCAAAACG
* * *
441765 GCGCCGTTTTGTTCAAAATGAAAAAAAATTGCGGCGCATTATAAGAAGCGCCGCTAAAGGTAAGC
66 GCGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGC
441830 AATAGCGGCGTTTTCTA
131 AATAGCGGCGTTTT-TA
441847 T-AAAAACGCCGCAAAAAATAAATCAATTTAT-AAAAAATAAAAAAATTTTATAATAGCAAAACG
1 TAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAATTTTATAATAGCAAAACG
441910 GCGTCGTTTTGTTCAAAATG-AAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGC
66 GCGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGC
441974 AATAGCGGCGTTTTTTA
131 AATAGCGGCG-TTTTTA
* * *
441991 TAGAAAACGCTGCAAAAAATAAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAAC
1 TAAAAAACGCCGCAAAAAATAAATCAATTTAT-AAAAAAATAAAAAAATTTTATAATAGCAAAAC
442056 GGCGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAG
65 GGCGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAG
442121 CAATAGCGGCGTTTTTA
130 CAATAGCGGCGTTTTTA
442138 TAAAAAACGCCGCAAA
1 TAAAAAACGCCGCAAA
442154 GCAAAACGGC
Statistics
Matches: 292, Mismatches: 10, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
144 55 0.19
145 82 0.28
146 29 0.10
147 72 0.25
148 54 0.18
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.24
Consensus pattern (146 bp):
TAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAATTTTATAATAGCAAAACG
GCGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGC
AATAGCGGCGTTTTTA
Found at i:442164 original size:105 final size:106
Alignment explanation
Indices: 442048--442259 Score: 390
Period size: 105 Copynumber: 2.0 Consensus size: 106
442038 ATTTTAGAAT
442048 AGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTA
1 AGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTA
442113 AAGGTAAGCAATAGCGGCG-TTTTTATAAAAAACGCCGCAA
66 AAGGTAAGCAATAGCGGCGTTTTTTATAAAAAACGCCGCAA
**
442153 AGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAATTTTTGCGGCGCTTTATAAGAAGCGCCGCTA
1 AGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTA
*
442218 AAGGTAAGCAATAGCGGCGTTTTTTATAGAAAACGCCGCAA
66 AAGGTAAGCAATAGCGGCGTTTTTTATAAAAAACGCCGCAA
442259 A
1 A
442260 AAATAAATCA
Statistics
Matches: 103, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
105 82 0.80
106 21 0.20
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (106 bp):
AGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTA
AAGGTAAGCAATAGCGGCGTTTTTTATAAAAAACGCCGCAA
Found at i:442285 original size:105 final size:102
Alignment explanation
Indices: 442071--442283 Score: 259
Period size: 105 Copynumber: 2.0 Consensus size: 102
442061 CGTTTTGTTC
442071 AAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTT
1 AAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTT
** * ****
442136 TATAAAAAACGCCGCAAAGCAAAACGGCGTCGTTTTGTTC
66 TATAAAAAACGCCGCAAA-CAAAA--GAATCATTTTAAAA
**
442176 AAAATGAAAAATTTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTT
1 AAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCG-TTT
*
442241 TTATAGAAAACGCCGCAAA-AAATA-AATCAATTTATAAAA
65 TTATAAAAAACGCCGCAAACAAA-AGAATC-ATTT-TAAAA
442280 AAAA
1 AAAA
442284 ATTTAGAATA
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
102 2 0.02
103 3 0.03
104 8 0.09
105 60 0.64
106 21 0.22
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.23
Consensus pattern (102 bp):
AAAATGAAAAAAATTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTT
TATAAAAAACGCCGCAAACAAAAGAATCATTTTAAAA
Found at i:442389 original size:117 final size:119
Alignment explanation
Indices: 442218--442455 Score: 365
Period size: 124 Copynumber: 2.0 Consensus size: 119
442208 AGCGCCGCTA
*
442218 AAGGTAAGCAATAGCGGCGTTTTTTATAGAAAACGCCGCAAAAAATAAATCAATTTAT-A-AAAA
1 AAGGTAAGCAATAGCGGCGTTTTCTATAGAAAACGCCGCAAAAAATAAATCAATTTATAATAAAA
442281 AAAATTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAAATTTTGCGG
66 AAAATTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAAT-AAAAAATTTTGCGG
* *
442336 AAGGTAATCAATAGTGGCGTTTTCTATA-AAAACGCCGCAAAAAATAAATCAATTTATAAAAAAA
1 AAGGTAAGCAATAGCGGCGTTTTCTATAGAAAACGCCGCAAAAAATAAATCAATTTAT-----AA
*
442400 TAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATAAAAAATTTTG
61 TAAAAAAAATTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAATAAAAAATTTTG
442456 TGGCGCTTCT
Statistics
Matches: 109, Mismatches: 4, Indels: 9
0.89 0.03 0.07
Matches are distributed among these distances:
117 29 0.27
118 25 0.23
123 12 0.11
124 43 0.39
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (119 bp):
AAGGTAAGCAATAGCGGCGTTTTCTATAGAAAACGCCGCAAAAAATAAATCAATTTATAATAAAA
AAAATTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAATAAAAAATTTTGCGG
Found at i:444662 original size:25 final size:26
Alignment explanation
Indices: 444614--444662 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
444604 TTTCAGTTTG
*
444614 ATTATTTTTAGTTTTATATTTTTAGT
1 ATTATTTTTAGTTTTATATATTTAGT
444640 ATTA-TTTTAGTTTCTATA-ATTTA
1 ATTATTTTTAGTTT-TATATATTTA
444663 ACATATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (26 bp):
ATTATTTTTAGTTTTATATATTTAGT
Found at i:446353 original size:43 final size:43
Alignment explanation
Indices: 446320--446544 Score: 292
Period size: 43 Copynumber: 5.2 Consensus size: 43
446310 GAATCATACT
*
446320 TTTAGTGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
* * *
446363 TTTAGTGGCGTTTGTGATGAAAGCGCCACTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
* *
446406 TTTAGTGGCGTTTGTGATAAAAGCGCTGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
* *
446449 TTTAGCGGCGTTTATGAGT-AAAGCGCCGCTAAAGAACATGTTC
1 TTTAGCGGCGTTTGTGA-TAAAAGCGCCGCTAAAGATCATGTTC
* ** * **
446492 TTTAGCGGCGTTT-TGTTTTTAAGCGCCGCTAAAGAACATGACC
1 TTTAGCGGCGTTTGTG-ATAAAAGCGCCGCTAAAGATCATGTTC
446535 TTTAGCGGCG
1 TTTAGCGGCG
446545 CTTATTTCTG
Statistics
Matches: 166, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
42 3 0.02
43 162 0.98
44 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
Found at i:452226 original size:129 final size:130
Alignment explanation
Indices: 452007--452328 Score: 481
Period size: 129 Copynumber: 2.5 Consensus size: 130
451997 ATTCTAATGT
* * *
452007 TATGTTTAAGAACGTGAACTTGAAA-ATTTG-GATTTAGGTTTCAATTACTATATAAATCGTGAG
1 TATGATTAAGAACGTGAACTTGAAAGATTTGAG-TTTAGATTTCAATTACTCTATAAATCGTGAG
* *
452070 GAGAATGGAATTTATACTTAAAATTAGTTGAGTTTCAGTATGATTATATATCTCGAATTCAATTA
65 GAGAATGAAATTTATACTTAAAATTAGTTGAGTTTCAGTATGATTACATATCTCGAATTCAATTA
452135 G
130 G
*
452136 TATGATTAAGAACGTGAATTTGAAAGATTTGAGTTTAGATTTCAATTAC-CTATAAATC-TCGAG
1 TATGATTAAGAACGTGAACTTGAAAGATTTGAGTTTAGATTTCAATTACTCTATAAATCGT-GAG
* *
452199 GAGAATGAAATTTCTACTTAAAATTAGTTGAGTTTCAGTATGATTACATATTTCGAATTCAATTA
65 GAGAATGAAATTTATACTTAAAATTAGTTGAGTTTCAGTATGATTACATATCTCGAATTCAATTA
452264 G
130 G
* * * * *
452265 CATGATTAAGAACATGAACTTGAAAGCTCTGAGTTTAGATTTCAAGTACTCTATAAATCGTGAG
1 TATGATTAAGAACGTGAACTTGAAAGATTTGAGTTTAGATTTCAATTACTCTATAAATCGTGAG
452329 AAGAGTAAAA
Statistics
Matches: 174, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
128 1 0.01
129 139 0.80
130 32 0.18
131 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (130 bp):
TATGATTAAGAACGTGAACTTGAAAGATTTGAGTTTAGATTTCAATTACTCTATAAATCGTGAGG
AGAATGAAATTTATACTTAAAATTAGTTGAGTTTCAGTATGATTACATATCTCGAATTCAATTAG
Found at i:452423 original size:85 final size:85
Alignment explanation
Indices: 452261--452424 Score: 215
Period size: 85 Copynumber: 1.9 Consensus size: 85
452251 TCGAATTCAA
**
452261 TTAGCATGATTAAGAACATGAACTTGAAAGCTCTGAGTTTAGATTTCAAGTACTCTATAAATCGT
1 TTAGCATGATTAAGAACATGAACTTGAAAGCTCTGAGTTTAGATTTCAAGTACTCTATAAATCAC
*
452326 GAGAAGAGTAAAATCTATAG
66 GAGAAGAATAAAATCTATAG
* * * * *
452346 TTAGTATGATTAAGAATATGAACTTGAAA-CATTTGAGTTTGGATTTC-AGTTACTCTATAAGTC
1 TTAGCATGATTAAGAACATGAACTTGAAAGC-TCTGAGTTTAGATTTCAAG-TACTCTATAAATC
*
452409 ACGAGGAGAATAAAAT
64 ACGAGAAGAATAAAAT
452425 GTTTACTTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 3 0.04
85 65 0.96
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.32
Consensus pattern (85 bp):
TTAGCATGATTAAGAACATGAACTTGAAAGCTCTGAGTTTAGATTTCAAGTACTCTATAAATCAC
GAGAAGAATAAAATCTATAG
Found at i:452501 original size:214 final size:214
Alignment explanation
Indices: 452132--452553 Score: 591
Period size: 214 Copynumber: 2.0 Consensus size: 214
452122 TCGAATTCAA
* * * *
452132 TTAGTATGATTAAGAACGTGAATTTGAAAGATTTGAGTTTAGATTTCAATTACCTATAAATCTCG
1 TTAGTATGATTAAGAACATGAACTTGAAACATTTGAGTTTAGATTTCAATTACCTATAAATCACG
* *
452197 AGGAGAATGAAATTTCTACTTAAAATTAGTTGAGTTTCAGTATGATTACATATTTCGAATTCAAT
66 AGGAGAATAAAATTTCTACTTAAAATTAGTTAAGTTTCAGTATGATTACATATTTCGAATTCAAT
*
452262 TAGCATGATTAAGAACATGAACTTGAAAGCTCTGAGTTTAGATTTCAAGTACTCTATAAATCGTG
131 TAGCATGATTAAGAACAGGAACTTGAAAGCTCTGAGTTTAGATTTCAAGTACTCTATAAATCGTG
452327 AGAAGAGTAAAATCTATAG
196 AGAAGAGTAAAATCTATAG
* * * *
452346 TTAGTATGATTAAGAATATGAACTTGAAACATTTGAGTTTGGATTTCAGTTACTCTATAAGTCAC
1 TTAGTATGATTAAGAACATGAACTTGAAACATTTGAGTTTAGATTTCAATTAC-CTATAAATCAC
* * *
452411 GAGGAGAATAAAATGTT-TACTT-AAATTA-TTCAAGTTTCTGTTTGATTATATATTTCGAATT-
65 GAGGAGAATAAAAT-TTCTACTTAAAATTAGTT-AAGTTTCAGTATGATTACATATTTCGAATTC
* * * * *
452472 TATATAGTATGATTAAGAACAGGAACTTGAAAGCTTTGAGTTTAGTTTTCAATTACTCTATAAAT
128 AAT-TAGCATGATTAAGAACAGGAACTTGAAAGCTCTGAGTTTAGATTTCAAGTACTCTATAAAT
**
452537 CGTGAGGGGAGTAAAAT
192 CGTGAGAAGAGTAAAAT
452554 GCATATTTAA
Statistics
Matches: 183, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
213 4 0.02
214 150 0.82
215 27 0.15
216 2 0.01
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (214 bp):
TTAGTATGATTAAGAACATGAACTTGAAACATTTGAGTTTAGATTTCAATTACCTATAAATCACG
AGGAGAATAAAATTTCTACTTAAAATTAGTTAAGTTTCAGTATGATTACATATTTCGAATTCAAT
TAGCATGATTAAGAACAGGAACTTGAAAGCTCTGAGTTTAGATTTCAAGTACTCTATAAATCGTG
AGAAGAGTAAAATCTATAG
Found at i:452586 original size:129 final size:129
Alignment explanation
Indices: 452344--452723 Score: 480
Period size: 129 Copynumber: 2.9 Consensus size: 129
452334 TAAAATCTAT
* * * *
452344 AGTTAGTATGATTAAGAATATGAACTTGAAACATTTGAGTTTGGATTTCAGTTACTCTATAAGTC
1 AGTTAGTATGATTAAGAACATGAACTTGAAACATTTGAGTTTAGATTTCAATTACTCTATAAATC
** * * *
452409 ACGAGGAGAATAAAATGTTTACTTAAATTA-TTCAAGTTTCT-GTTTGATTATATATTTCGAATT
66 GTGAGGAGAATAAAATGTATACTTAAATTAGTT-GAGTTT-TAGTATGATTATATATTTCGAATT
*
452472 T
129 C
* *
452473 A-TATAGTATGATTAAGAACAGGAACTTGAAAGC-TTTGAGTTTAGTTTTCAATTACTCTATAAA
1 AGT-TAGTATGATTAAGAACATGAACTTGAAA-CATTTGAGTTTAGATTTCAATTACTCTATAAA
* * * * * *
452536 TCGTGAGGGGAGTAAAATGCATATTTAAATTAGTTGAGTTTTAGCATGATTATATATTCCGAATT
64 TCGTGAGGAGAATAAAATGTATACTTAAATTAGTTGAGTTTTAGTATGATTATATATTTCGAATT
452601 C
129 C
* * *
452602 AGTTAGTACGATTAAGAACATGAATTTGAGACATTTGAGTTTAGATTTCAATTACTCTATAAATC
1 AGTTAGTATGATTAAGAACATGAACTTGAAACATTTGAGTTTAGATTTCAATTACTCTATAAATC
* * *
452667 GTGAGGAGAAAAAAATGTATACTTAAATTAGTTGAGATTTAGTGTGATTATATATTT
66 GTGAGGAGAATAAAATGTATACTTAAATTAGTTGAGTTTTAGTATGATTATATATTT
452724 AAGATATAAA
Statistics
Matches: 213, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
128 3 0.01
129 206 0.97
130 4 0.02
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.39
Consensus pattern (129 bp):
AGTTAGTATGATTAAGAACATGAACTTGAAACATTTGAGTTTAGATTTCAATTACTCTATAAATC
GTGAGGAGAATAAAATGTATACTTAAATTAGTTGAGTTTTAGTATGATTATATATTTCGAATTC
Found at i:452643 original size:343 final size:343
Alignment explanation
Indices: 452007--452671 Score: 848
Period size: 343 Copynumber: 1.9 Consensus size: 343
451997 ATTCTAATGT
* * **
452007 TATGTTTAAGAACGTGAACTTGAAAATTTGGATTTAGGTTTCAATTACTATATAAATCGTGAGGA
1 TATGATTAAGAACATGAACTTGAAAATTTGGATTTAGGTTTCAATTACTATATAAATCACGAGGA
** *
452072 GAATGGAATTTATACTTAAAATTAGTTGAGTTTCAGTATGATTATATATCTCGAATTCAATTAGT
66 GAATAAAATTTATACTTAAAATTAGTTAAGTTTCAGTATGATTATATATCTCGAATTCAATTAGT
*
452137 ATGATTAAGAACGTGAATTTGAAAGATTTGAGTTTAGATTTCAATTACCTATAAATCTCGAGGAG
131 ATGATTAAGAACGTGAACTTGAAAGATTTGAGTTTAGATTTCAATTACCTATAAATCTCGAGGAG
* * * *
452202 AATGAAATTTCTACTTAAAATTAGTTGAGTTTCAGTATGATTACATATTTCGAATTCAATTAGCA
196 AATGAAAATGCTACTTAAAATTAGTTGAGTTTCAGCATGATTACATATTCCGAATTCAATTAGCA
*
452267 TGATTAAGAACATGAACTTGAAAGCTCTGAGTTTAGATTTCAAGTACTCTATAAATCGTGAGAAG
261 CGATTAAGAACATGAACTTGAAAGCTCTGAGTTTAGATTTCAAGTACTCTATAAATCGTGAGAAG
452332 AGTAAAATCTATAGTTAG
326 AGTAAAATCTATAGTTAG
* * * *
452350 TATGATTAAGAATATGAACTTGAAACATTT-GAGTTT-GGATTTCAGTTACTCTATAAGTCACGA
1 TATGATTAAGAACATGAACTTGAAA-ATTTGGA-TTTAGG-TTTCAATTACTATATAAATCACGA
* * * *
452413 GGAGAATAAAATGTT-TACTT-AAATTA-TTCAAGTTTCTGTTTGATTATATATTTCGAATT-TA
63 GGAGAATAAAAT-TTATACTTAAAATTAGTT-AAGTTTCAGTATGATTATATATCTCGAATTCAA
* *
452474 TATAGTATGATTAAGAACAG-GAACTTGAAAGCTTTGAGTTTAGTTTTCAATTACTCTATAAATC
126 T-TAGTATGATTAAGAAC-GTGAACTTGAAAGATTTGAGTTTAGATTTCAATTAC-CTATAAATC
* * * * *
452538 GT-GAGGGGAGT-AAAATGCATA-TTTAAATTAGTTGAGTTTTAGCATGATTATATATTCCGAAT
188 -TCGAGGAGAATGAAAATGC-TACTTAAAATTAGTTGAGTTTCAGCATGATTACATATTCCGAAT
* * * * * *
452600 TCAGTTAGTACGATTAAGAACATGAATTTGAGA-CATTTGAGTTTAGATTTCAATTACTCTATAA
251 TCAATTAGCACGATTAAGAACATGAACTTGAAAGC-TCTGAGTTTAGATTTCAAGTACTCTATAA
452664 ATCGTGAG
315 ATCGTGAG
452672 GAGAAAAAAA
Statistics
Matches: 277, Mismatches: 34, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
342 5 0.02
343 209 0.75
344 60 0.22
345 3 0.01
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.37
Consensus pattern (343 bp):
TATGATTAAGAACATGAACTTGAAAATTTGGATTTAGGTTTCAATTACTATATAAATCACGAGGA
GAATAAAATTTATACTTAAAATTAGTTAAGTTTCAGTATGATTATATATCTCGAATTCAATTAGT
ATGATTAAGAACGTGAACTTGAAAGATTTGAGTTTAGATTTCAATTACCTATAAATCTCGAGGAG
AATGAAAATGCTACTTAAAATTAGTTGAGTTTCAGCATGATTACATATTCCGAATTCAATTAGCA
CGATTAAGAACATGAACTTGAAAGCTCTGAGTTTAGATTTCAAGTACTCTATAAATCGTGAGAAG
AGTAAAATCTATAGTTAG
Found at i:457606 original size:20 final size:20
Alignment explanation
Indices: 457581--457620 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
457571 AAATAAATAT
457581 TTATTTTTCTTATTTTCTAA
1 TTATTTTTCTTATTTTCTAA
457601 TTATTTTTCTTATTTTCTAA
1 TTATTTTTCTTATTTTCTAA
457621 CATAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTTTTCTTATTTTCTAA
Found at i:488684 original size:31 final size:30
Alignment explanation
Indices: 488629--488708 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 30
488619 ATCTCAAAAT
*
488629 TATACATAAACTATGA-TTGAATGTACAATT-
1 TATACATAAACTTTGATTTGAATGT--AATTA
488659 TGATACATAAACTTTGATTTG-ATGTAATTA
1 T-ATACATAAACTTTGATTTGAATGTAATTA
*
488689 TACACATGAAACTTTGATTT
1 TATACAT-AAACTTTGATTT
488709 ATTTTTATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
29 9 0.20
30 14 0.32
31 18 0.41
32 3 0.07
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (30 bp):
TATACATAAACTTTGATTTGAATGTAATTA
Found at i:489129 original size:24 final size:24
Alignment explanation
Indices: 489102--489153 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
489092 TTAGTAAGTC
*
489102 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
489126 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
489150 AAAT
1 AAAT
489154 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:497050 original size:17 final size:17
Alignment explanation
Indices: 497028--497061 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
497018 TAGAAAGGAA
497028 TGTCCAATTCTTAACGT
1 TGTCCAATTCTTAACGT
497045 TGTCCAATTCTTAACGT
1 TGTCCAATTCTTAACGT
497062 CGTTAAAATT
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:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (17 bp):
TGTCCAATTCTTAACGT
Found at i:500304 original size:186 final size:178
Alignment explanation
Indices: 499978--500306 Score: 419
Period size: 186 Copynumber: 1.8 Consensus size: 178
499968 TATAAGTTAC
* * *
499978 ATTTGAGTTGTCACTTAACACTAAAAATTTAATGACTAAACTAATGAAAGGACATGATTGATACG
1 ATTTGAGTTGTCACTTAACACTAAAAAATTAATGACTAAACTAATGAAAGGACATAATTGATACC
* * * * * *
500043 TTACTTGTTATACTCCAAGGTATTACTTTCATCGCAATGAAATAGCCTACGTTGTTATTGACATT
66 TTACTTGTTATACTCCAAGGCATTACTTGCACCACAAAGAAAGAGCCTACGTTGTTATTGACATT
500108 TAGTAGGCAACGCAATGATACCATTGTCGCAAATCTACCGTGGACATG
131 TAGTAGGCAACGCAATGATACCATTGTCGCAAATCTACCGTGGACATG
* * *
500156 ATTTGAGTTGTCACTTAACACTCAAAAAATT-ATGGCTAAGCTAATGAAATGACATAATTGATAC
1 ATTTGAGTTGTCACTTAACACT-AAAAAATTAATGACTAAACTAATGAAAGGACATAATTGATAC
**
500220 AATACTTACGATCCTTGTTATAC-CTTAGGCATTACTTGCACCACAAAGAAAGAGCCTACGTTGT
65 ----CTT---A--CTTGTTATACTCCAAGGCATTACTTGCACCACAAAGAAAGAGCCTACGTTGT
*
500284 TGTTGACATTTAGTAGGCAACGC
121 TATTGACATTTAGTAGGCAACGC
500307 CACAATGCAA
Statistics
Matches: 126, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
178 51 0.40
179 7 0.06
182 2 0.02
185 1 0.01
186 55 0.44
187 10 0.08
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (178 bp):
ATTTGAGTTGTCACTTAACACTAAAAAATTAATGACTAAACTAATGAAAGGACATAATTGATACC
TTACTTGTTATACTCCAAGGCATTACTTGCACCACAAAGAAAGAGCCTACGTTGTTATTGACATT
TAGTAGGCAACGCAATGATACCATTGTCGCAAATCTACCGTGGACATG
Found at i:504772 original size:29 final size:29
Alignment explanation
Indices: 504739--504808 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
504729 CACATTTAAA
* *
504739 AAATAAATA-CATCAATTTATTTTTATATT
1 AAATAAATATAAT-AATTTATTTTTATAAT
*
504768 AAATAAATATAATTATTTATTTTTATAAT
1 AAATAAATATAATAATTTATTTTTATAAT
*
504797 ATATAAATATAA
1 AAATAAATATAA
504809 AATGATGTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 34 0.94
30 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
AAATAAATATAATAATTTATTTTTATAAT
Found at i:508813 original size:16 final size:15
Alignment explanation
Indices: 508769--508851 Score: 53
Period size: 16 Copynumber: 5.3 Consensus size: 15
508759 AATTGGGTTT
* *
508769 ATTTAAAATTTAGGTT
1 ATTT-AAATTTAGATC
508785 ATTTAAA-TTAGATC
1 ATTTAAATTTAGATC
*
508799 ATTATAAATTTAGATT
1 ATT-TAAATTTAGATC
*
508815 ATTTCATATTTAGAT-
1 ATTT-AAATTTAGATC
*
508830 AGTTTAATATTTTGAGTC
1 A-TTTAA-ATTTAGA-TC
508848 ATTT
1 ATTT
508852 TCAAATTAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
14 8 0.15
15 10 0.19
16 31 0.57
17 4 0.07
18 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.51
Consensus pattern (15 bp):
ATTTAAATTTAGATC
Found at i:511603 original size:23 final size:22
Alignment explanation
Indices: 511558--511601 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
511548 CAATGCCAGT
511558 TTTTAACAATAAAAATGATAAA
1 TTTTAACAATAAAAATGATAAA
*
511580 TTTTAACAGTAAAAGA-GATAAA
1 TTTTAACAATAAAA-ATGATAAA
511602 ATGCAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.30
Consensus pattern (22 bp):
TTTTAACAATAAAAATGATAAA
Found at i:516503 original size:18 final size:18
Alignment explanation
Indices: 516476--516568 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
516466 TACGACCGTT
516476 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
516494 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
516512 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
516530 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
516548 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
516566 TAC
1 TAC
516569 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:527954 original size:30 final size:30
Alignment explanation
Indices: 527918--527977 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
527908 CAACACCTGT
*
527918 TTGTATCTAGACTGACATTATTATAGGTAA
1 TTGTATCTAGAATGACATTATTATAGGTAA
*
527948 TTGTATCTAGAATGATATTATTATAGGTAA
1 TTGTATCTAGAATGACATTATTATAGGTAA
527978 AAGTACCATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (30 bp):
TTGTATCTAGAATGACATTATTATAGGTAA
Found at i:534690 original size:17 final size:18
Alignment explanation
Indices: 534665--534704 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
534655 ACAATATCGA
*
534665 TAAAA-TTAAAAT-ATTT
1 TAAAATTTAAAATCAATT
534681 TAAAATTTAAAATCAATT
1 TAAAATTTAAAATCAATT
534699 TAAAAT
1 TAAAAT
534705 ATAATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.24
17 7 0.33
18 9 0.43
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAATTTAAAATCAATT
Found at i:541974 original size:110 final size:111
Alignment explanation
Indices: 541778--541993 Score: 303
Period size: 110 Copynumber: 2.0 Consensus size: 111
541768 GGACTTCCTA
* * *
541778 AAATGGTAAGTTTTCTATTTAATCCTTTAAATTTTTATGAAATTACATGTTAGTATAATGATAAG
1 AAATGGTAAGTTTTCCATTTAATCCTTTAAAATTTTATAAAATTACATGTTAGTATAATGATAAG
* **
541843 ATTTCACTTTTGCCCTCCCAATAATTAATGATTCATCTTTGCTCTC
66 ATTTCACCTTAACCCTCCCAATAATTAATGATTCATCTTTGCTCTC
* *
541889 AAATGGT-AGATTTTCCATTTAGTGC-TTAAAATTTTATAAAATTACATGTTAGTATAATGATAA
1 AAATGGTAAG-TTTTCCATTTAATCCTTTAAAATTTTATAAAATTACATGTTAGTATAATGATAA
* *
541952 -ATTTTCACCTTAACCCTTCCAATAATTTATGATTCATCTTTG
65 GA-TTTCACCTTAACCCTCCCAATAATTAATGATTCATCTTTG
541994 GTCCCCTTAA
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
109 1 0.01
110 73 0.78
111 19 0.20
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (111 bp):
AAATGGTAAGTTTTCCATTTAATCCTTTAAAATTTTATAAAATTACATGTTAGTATAATGATAAG
ATTTCACCTTAACCCTCCCAATAATTAATGATTCATCTTTGCTCTC
Found at i:549912 original size:18 final size:18
Alignment explanation
Indices: 549885--549927 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
549875 TTGAACCAGG
*
549885 TTTTTT-ATTTTTAATAT
1 TTTTTTAATTTTTAATAA
549902 TTTTTTAATTTTTAATAA
1 TTTTTTAATTTTTAATAA
549920 TTTTTTAA
1 TTTTTTAA
549928 GCGAACAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTAATTTTTAATAA
Found at i:553293 original size:13 final size:13
Alignment explanation
Indices: 553275--553299 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
553265 CCTTTGCCTT
553275 TTTTTCTTTTTAC
1 TTTTTCTTTTTAC
553288 TTTTTCTTTTTA
1 TTTTTCTTTTTA
553300 TTATACAATA
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:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTTAC
Done.