Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006076.1 Hibiscus syriacus cultivar Beakdansim tig00014385_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: 112514
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:5032 original size:19 final size:20
Alignment explanation
Indices: 5008--5047 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4998 TGAATTATAA
*
5008 TTTCGAAGCTACAA-CAGAG
1 TTTCGAAACTACAAGCAGAG
*
5027 TTTCGAAACTATAAGCAGAG
1 TTTCGAAACTACAAGCAGAG
5047 T
1 T
5048 CGAATATCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (20 bp):
TTTCGAAACTACAAGCAGAG
Found at i:7626 original size:13 final size:14
Alignment explanation
Indices: 7607--7652 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
7597 AATCTCTTAA
7607 ATTTTTAATATAAT
1 ATTTTTAATATAAT
*
7621 -TTTTTAA-ATTTAT
1 ATTTTTAATA-TAAT
*
7634 ATTTTTAATATAAA
1 ATTTTTAATATAAT
7648 ATTTT
1 ATTTT
7653 ACATCCATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
12 1 0.04
13 10 0.38
14 14 0.54
15 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTTTAATATAAT
Found at i:7653 original size:13 final size:13
Alignment explanation
Indices: 7604--7653 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
7594 TCGAATCTCT
7604 TAAATTTTTAATA
1 TAAATTTTTAATA
* *
7617 TAATTTTTTAAATT
1 TAAATTTTT-AATA
*
7631 TATATTTTTAATA
1 TAAATTTTTAATA
*
7644 TAAAATTTTA
1 TAAATTTTTA
7654 CATCCATCCT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TAAATTTTTAATA
Found at i:9352 original size:20 final size:20
Alignment explanation
Indices: 9315--9353 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9305 AAACAACTAA
*
9315 TATTAAAAGTCAATAAATAT
1 TATTAAAAGTCAAAAAATAT
* *
9335 TATTAATAGTTAAAAAATA
1 TATTAAAAGTCAAAAAATA
9354 ATCACACAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (20 bp):
TATTAAAAGTCAAAAAATAT
Found at i:9430 original size:11 final size:10
Alignment explanation
Indices: 9385--9441 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
9375 AAAGTTGACG
*
9385 TTTTTATTAA
1 TTTTTATTCA
*
9395 ATTTTATTCA
1 TTTTTATTCA
* *
9405 CTTTTAATTCT
1 -TTTTTATTCA
9416 TTTTTATTACA
1 TTTTTATT-CA
*
9427 TTTTTATTGA
1 TTTTTATTCA
9437 TTTTT
1 TTTTT
9442 TTAAAAAGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 21 0.57
11 16 0.43
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTTTATTCA
Found at i:9440 original size:21 final size:21
Alignment explanation
Indices: 9385--9441 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
9375 AAAGTTGACG
*
9385 TTTTTATTAAATTTTATTCAC
1 TTTTTATTAATTTTTATTCAC
* **
9406 TTTTAATTCTTTTTTATT-AC
1 TTTTTATTAATTTTTATTCAC
*
9426 ATTTTTATTGATTTTT
1 -TTTTTATTAATTTTT
9442 TTAAAAAGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTTATTAATTTTTATTCAC
Found at i:9552 original size:31 final size:32
Alignment explanation
Indices: 9493--9566 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
9483 TTTAAAGTAT
* * *
9493 AAAAATGCAATAAAAAAAGAATTAAAAGT-GAA
1 AAAAATTCAAT-ACAAAAGAATTAAAAGTCAAA
*
9525 TAAAATTCAATACAAAAGAA-TATAAAGTCAAA
1 AAAAATTCAATACAAAAGAATTA-AAAGTCAAA
9557 AAAAATTCAA
1 AAAAATTCAA
9567 AAATATATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 2 0.06
31 13 0.37
32 20 0.57
ACGTcount: A:0.66, C:0.07, G:0.08, T:0.19
Consensus pattern (32 bp):
AAAAATTCAATACAAAAGAATTAAAAGTCAAA
Found at i:12899 original size:22 final size:23
Alignment explanation
Indices: 12868--12914 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
12858 TAATTGCGAG
12868 TTTAGAAGATACGA-TTTTGGGC
1 TTTAGAAGATACGATTTTTGGGC
*
12890 TTTAGCAGATACGATTTTTGGGC
1 TTTAGAAGATACGATTTTTGGGC
12913 TT
1 TT
12915 GTTTAGGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (23 bp):
TTTAGAAGATACGATTTTTGGGC
Found at i:18163 original size:39 final size:39
Alignment explanation
Indices: 18120--18194 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
18110 GATTACAATT
*
18120 AAAATGTTACATTAT-TTATAATAATTTTGATTGTAATCG
1 AAAATGTTAC-TTATATTATAACAATTTTGATTGTAATCG
* * *
18159 AAAATGTTACTTTTATTATAACATTTTTTATTGTAA
1 AAAATGTTACTTATATTATAACAATTTTGATTGTAA
18195 ATTCTAGACC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.10
39 28 0.90
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.49
Consensus pattern (39 bp):
AAAATGTTACTTATATTATAACAATTTTGATTGTAATCG
Found at i:20082 original size:3 final size:3
Alignment explanation
Indices: 20067--20110 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
20057 CAAAGGAAAA
* *
20067 AAT AAT AAC AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20111 ATAGAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:27071 original size:19 final size:21
Alignment explanation
Indices: 27042--27082 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
27032 AACATATATG
27042 ATTTAATCTTAA-ATTTATCA
1 ATTTAATCTTAATATTTATCA
*
27062 ATTT-ATCTTAATTTTTATCA
1 ATTTAATCTTAATATTTATCA
27082 A
1 A
27083 AAGTTTATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTAATCTTAATATTTATCA
Found at i:27410 original size:21 final size:21
Alignment explanation
Indices: 27386--27451 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
27376 GCAAATTCGC
27386 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
27407 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* * *
27427 TTTCCATTTCGTGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
27448 GTTG
1 GTTG
27452 AAAATCACGT
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:27435 original size:41 final size:40
Alignment explanation
Indices: 27397--27536 Score: 176
Period size: 41 Copynumber: 3.5 Consensus size: 40
27387 TTGCATTTCG
*
27397 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC-ATTT
1 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAAATT
*
27436 CGTGTTGCGATAGTTGAAAATCACGTTGCGATTTTCCAAATT
1 C--GTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAAATT
* * *
27478 CGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCCAAATT
*
27519 CGTTGCGATAGTTAAAAA
1 CGTTGCGATAGTTGAAAA
27537 AAAAGATTTT
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
39 1 0.01
40 15 0.17
41 67 0.77
42 4 0.05
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (40 bp):
CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAAATT
Found at i:27465 original size:21 final size:21
Alignment explanation
Indices: 27394--27467 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
27384 GCGTTGCATT
27394 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
27415 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
27435 TCGTGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
27456 TCACGTTGCGAT
1 TCGCGTTGCGAT
27468 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 14 0.36
21 25 0.64
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:27483 original size:19 final size:19
Alignment explanation
Indices: 27459--27527 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
27449 TTGAAAATCA
27459 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
* * **
27478 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGAT--TTTCCAAAT-T
27500 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
27519 CGTTGCGAT
1 CGTTGCGAT
27528 AGTTAAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 19 0.49
20 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:27619 original size:6 final size:6
Alignment explanation
Indices: 27608--27645 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
27598 GACACGTATT
27608 ACCACG ACCACG ACCACG ACCACG ACC-CG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
27646 CGAGACGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.32, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:27640 original size:11 final size:11
Alignment explanation
Indices: 27612--27648 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
27602 CGTATTACCA
27612 CGACCACGACC
1 CGACCACGACC
27623 ACGACCACGACC
1 -CGACCACGACC
27635 CGACCACGACC
1 CGACCACGACC
27646 CGA
1 CGA
27649 GACGAGACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.30, C:0.51, G:0.19, T:0.00
Consensus pattern (11 bp):
CGACCACGACC
Found at i:28218 original size:6 final size:6
Alignment explanation
Indices: 28157--28217 Score: 99
Period size: 6 Copynumber: 10.5 Consensus size: 6
28147 TCTCGTCTCG
28157 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
*
28203 GGTCGT GGTAGT GGT
1 GGTCGT GGTCGT GGT
28218 AATACGTGTC
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
5 10 0.19
6 44 0.81
ACGTcount: A:0.02, C:0.15, G:0.52, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:28368 original size:41 final size:41
Alignment explanation
Indices: 28322--28412 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 41
28312 ACTGTAGACT
*
28322 ATCGCAACAACAACTGTAGAATATCGCAAC-GAATTTGGAAA
1 ATCGCAACAACAACTGTAGAATATCGCAACGGAA-CTGGAAA
* *
28363 ATCGCAACGACAACTGTAGACTATCGCAACGTGAACTGGAAA
1 ATCGCAACAACAACTGTAGAATATCGCAACG-GAACTGGAAA
28405 ATCGCAAC
1 ATCGCAAC
28413 GCAATTTTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
41 28 0.62
42 14 0.31
43 3 0.07
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.18
Consensus pattern (41 bp):
ATCGCAACAACAACTGTAGAATATCGCAACGGAACTGGAAA
Found at i:28400 original size:22 final size:22
Alignment explanation
Indices: 28304--28393 Score: 105
Period size: 22 Copynumber: 4.2 Consensus size: 22
28294 ACTATCACAA
*
28304 CAACGACAACTGTAGACTATCG
1 CAACGACAACTGTAGAATATCG
*
28326 CAACAACAACTGTAGAATATCG
1 CAACGACAACTGTAGAATATCG
* * *
28348 CAACG--AA-TTTGGAAAATCG
1 CAACGACAACTGTAGAATATCG
*
28367 CAACGACAACTGTAGACTATCG
1 CAACGACAACTGTAGAATATCG
28389 CAACG
1 CAACG
28394 TGAACTGGAA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
19 14 0.25
20 2 0.04
21 2 0.04
22 37 0.67
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (22 bp):
CAACGACAACTGTAGAATATCG
Found at i:28410 original size:20 final size:20
Alignment explanation
Indices: 28322--28413 Score: 69
Period size: 22 Copynumber: 4.5 Consensus size: 20
28312 ACTGTAGACT
* *
28322 ATCGCAACAACAACTGTAGAAT
1 ATCGCAACGACAACTG--GAAA
**
28344 ATCGCAACGA-ATTTGGAAA
1 ATCGCAACGACAACTGGAAA
**
28363 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTG--GAAA
**
28385 ATCGCAACGTGAACTGGAAA
1 ATCGCAACGACAACTGGAAA
28405 ATCGCAACG
1 ATCGCAACG
28414 CAATTTTCAA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
19 13 0.24
20 14 0.25
21 3 0.05
22 25 0.45
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGACAACTGGAAA
Found at i:28430 original size:63 final size:62
Alignment explanation
Indices: 28304--28434 Score: 165
Period size: 63 Copynumber: 2.1 Consensus size: 62
28294 ACTATCACAA
* *
28304 CAACGACAACTGTAGACTATCGCAACAACAACTGTAGAATATCGCAACGAATTTGGAAAATCG
1 CAACGACAACTGTAGACTATCGCAACAACAACTG-AGAAAATCGCAACGAATTTGCAAAATCG
*** * *
28367 CAACGACAACTGTAGACTATCGCAACGTGAACTG-GAAAATCGCAACGCAATTTTCAACTATCG
1 CAACGACAACTGTAGACTATCGCAACAACAACTGAGAAAATCGCAACG-AATTTGCAA-AATCG
28430 CAACG
1 CAACG
28435 CGATTTTCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
61 12 0.20
62 7 0.12
63 40 0.68
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (62 bp):
CAACGACAACTGTAGACTATCGCAACAACAACTGAGAAAATCGCAACGAATTTGCAAAATCG
Found at i:28431 original size:21 final size:21
Alignment explanation
Indices: 28405--28552 Score: 98
Period size: 21 Copynumber: 7.4 Consensus size: 21
28395 GAACTGGAAA
28405 ATCGCAACGCAATTTTCAACT
1 ATCGCAACGCAATTTTCAACT
* *
28426 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCAATTTTCAACT
* * *
28447 ATCGCAACACGAA-ATGC-A--
1 ATCGCAACGC-AATTTTCAACT
*
28465 A-CGCGACG--ATTTTCAACT
1 ATCGCAACGCAATTTTCAACT
* ** *
28483 ATCGCAACGCGAA-CTGGAA-A
1 ATCGCAACGC-AATTTTCAACT
28503 ATCGCAACGCAATTTTCAACT
1 ATCGCAACGCAATTTTCAACT
* * *
28524 ATCGCAATGCGATTTTCAATT
1 ATCGCAACGCAATTTTCAACT
28545 ATCGCAAC
1 ATCGCAAC
28553 ACGAAATGCA
Statistics
Matches: 93, Mismatches: 23, Indels: 22
0.67 0.17 0.16
Matches are distributed among these distances:
14 1 0.01
15 2 0.02
16 1 0.01
17 5 0.05
18 2 0.02
19 8 0.09
20 14 0.15
21 58 0.62
22 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (21 bp):
ATCGCAACGCAATTTTCAACT
Found at i:28497 original size:98 final size:98
Alignment explanation
Indices: 28382--28568 Score: 356
Period size: 98 Copynumber: 1.9 Consensus size: 98
28372 ACAACTGTAG
*
28382 ACTATCGCAACGTGAACTGGAAAATCGCAACGCAATTTTCAACTATCGCAACGCGATTTTCAATT
1 ACTATCGCAACGCGAACTGGAAAATCGCAACGCAATTTTCAACTATCGCAACGCGATTTTCAATT
28447 ATCGCAACACGAAATGCAACGCGACGATTTTCA
66 ATCGCAACACGAAATGCAACGCGACGATTTTCA
*
28480 ACTATCGCAACGCGAACTGGAAAATCGCAACGCAATTTTCAACTATCGCAATGCGATTTTCAATT
1 ACTATCGCAACGCGAACTGGAAAATCGCAACGCAATTTTCAACTATCGCAACGCGATTTTCAATT
28545 ATCGCAACACGAAATGCAACGCGA
66 ATCGCAACACGAAATGCAACGCGA
28569 ATTTGCGATA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 87 1.00
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (98 bp):
ACTATCGCAACGCGAACTGGAAAATCGCAACGCAATTTTCAACTATCGCAACGCGATTTTCAATT
ATCGCAACACGAAATGCAACGCGACGATTTTCA
Found at i:29141 original size:3 final size:3
Alignment explanation
Indices: 29133--29181 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
29123 TTGTTTTTAC
29133 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29181 T
1 T
29182 GAAAGATGGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:36698 original size:31 final size:31
Alignment explanation
Indices: 36660--36769 Score: 175
Period size: 31 Copynumber: 3.5 Consensus size: 31
36650 AGGGTCGAGG
*
36660 GTTTACCTATGTTCTTCGGGACATATAGATT
1 GTTTACCTATGTTCTTCGGGACATATAGACT
*
36691 GTTTACCTATGTTCTTTGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATAGACT
*
36722 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATAGACT
* *
36753 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
36770 AGAATCTATG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 73 1.00
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATAGACT
Found at i:36780 original size:31 final size:31
Alignment explanation
Indices: 36662--36784 Score: 95
Period size: 31 Copynumber: 4.0 Consensus size: 31
36652 GGTCGAGGGT
* * * * * *
36662 TTACCTATGTTCTTCGGGACATATAGATTGT
1 TTACCTAGGTTCTTCAGAACATATGGACTGA
* ** * * *
36693 TTACCTATGTTCTTTGGGACATATAGACTGT
1 TTACCTAGGTTCTTCAGAACATATGGACTGA
* * *
36724 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTAGGTTCTTCAGAACATATGGACTGA
36755 TTACCTAGGTTCTTCAGAATC-TATGGACTG
1 TTACCTAGGTTCTTCAGAA-CATATGGACTG
36785 GTTCTTCGGG
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
31 82 0.99
32 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (31 bp):
TTACCTAGGTTCTTCAGAACATATGGACTGA
Found at i:37561 original size:19 final size:20
Alignment explanation
Indices: 37515--37565 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
37505 CTGTTCACGG
37515 TACTGTTCATACGATATTGT
1 TACTGTTCATACGATATTGT
37535 TCACTGTTCATACCG-TATT-T
1 T-ACTGTTCATA-CGATATTGT
37555 TACTGTTCATA
1 TACTGTTCATA
37566 AAACATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.34
20 3 0.10
21 14 0.48
22 2 0.07
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.45
Consensus pattern (20 bp):
TACTGTTCATACGATATTGT
Found at i:38198 original size:18 final size:18
Alignment explanation
Indices: 38175--38211 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38165 TATCACTTAA
*
38175 TCTTAAATTCTATCTATT
1 TCTTAAATTCTATCAATT
*
38193 TCTTAAATTTTATCAATT
1 TCTTAAATTCTATCAATT
38211 T
1 T
38212 ACTTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.14, G:0.00, T:0.57
Consensus pattern (18 bp):
TCTTAAATTCTATCAATT
Found at i:38755 original size:16 final size:16
Alignment explanation
Indices: 38734--38768 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
38724 TTCGGTGGAT
38734 AGGGTTTGCAAATGTG
1 AGGGTTTGCAAATGTG
38750 AGGGTTTGCAAATGTG
1 AGGGTTTGCAAATGTG
38766 AGG
1 AGG
38769 AAGGATGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.40, T:0.29
Consensus pattern (16 bp):
AGGGTTTGCAAATGTG
Found at i:39801 original size:183 final size:185
Alignment explanation
Indices: 39458--39847 Score: 660
Period size: 183 Copynumber: 2.1 Consensus size: 185
39448 TTTTCTAATT
* *
39458 TATATAA-AAATTTAAATATTTTATAATTCAAAAAAACAGTTTATAATTAATTTAAATAATATAT
1 TATATAATATATTT-AATATTTTATAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATAT
*
39522 AATTATAAAATATAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
65 AATTATAAAATAAAAATTTTATATAA-TTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
*
39587 ATTAGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGACTGAGCCCATATGTTA
129 ATTAGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGACTGAGCCCATATGTTA
* *
39644 TATATAATATATTTAATATTTTTTAATT-AAATAAACAGTTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
39708 ATTATAAAATAAAAATTTTATATAA-TTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
66 ATTATAAAATAAAAATTTTATATAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
* **
39772 TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGTTGAGCCCATATGTTA
131 TAGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGACTGAGCCCATATGTTA
39827 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
39848 AAAATTTTAA
Statistics
Matches: 194, Mismatches: 9, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
183 111 0.57
185 58 0.30
186 20 0.10
187 5 0.03
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (185 bp):
TATATAATATATTTAATATTTTATAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAATTTTATATAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
TAGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGACTGAGCCCATATGTTA
Found at i:39998 original size:27 final size:29
Alignment explanation
Indices: 39931--40001 Score: 92
Period size: 27 Copynumber: 2.5 Consensus size: 29
39921 CCGTTAACCG
39931 ACCGAACTAATTCGGTAACCGATCAAATTA
1 ACCGAACTAATTCGGT-ACCGATCAAATTA
* *
39961 ACCGAACTAATTCGGT-TCGATC-AGTTA
1 ACCGAACTAATTCGGTACCGATCAAATTA
*
39988 ACCGAATTAATTCG
1 ACCGAACTAATTCG
40002 AAAATTTGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 17 0.45
28 5 0.13
30 16 0.42
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (29 bp):
ACCGAACTAATTCGGTACCGATCAAATTA
Found at i:43471 original size:2 final size:2
Alignment explanation
Indices: 43466--43490 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43456 GCGCGCGCAC
43466 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
43491 AAGAAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48224 original size:598 final size:598
Alignment explanation
Indices: 46928--48667 Score: 3317
Period size: 598 Copynumber: 2.9 Consensus size: 598
46918 TGATTCATGT
*
46928 AAAAT-AATA-TTAAATTAAAAATATAAAAATTTATTAAATATTTAATC----AAGGACCAAACT
1 AAAATAAATATTTAAATTAAAAATATAAAAATTTATTAAATATTTAATCAAGTAAGGATCAAACT
* *
46987 AAAGAAGTATAACCCGTGTTATCAAAATTTTTGGTCTAATAACAATTTAAG---TTATAAGTTT-
66 AAAGAAGGATAACCTGTGTTATCAAAATTTTTGGTCTAATAACAATTTAAGTCATTATAAGTTTA
47048 AATATTAGACAAATTAGGTGTTATC-TTTGCGAATTTTGAGA--TTTTAATAAATTTAGGGTGAA
131 AATATTAGACAAATTAGGTGTTATCTTTTGCGAATTTTGAGATTTTTTAATAAATTTAGGGTGAA
*
47110 TACAAGGTAGTATATGTACAAAGACTCTTAACTATTTGACAATGAACGCTCATACCTCTACATAC
196 TACAAGGTAGTATATGTACAAAGACTCTTAACTATTTGACAATGAACGCTCATTCCTCTACATAC
*
47175 ACAGTGCTCGAACTCGAGACCTCAAGAGTAAAAATAATCCCTTAATCACTAAGGTCGCTAGGTTC
261 ACAGTGCTCGAACTCGAGACCTCAAGAGTAAAAATAATCCCTTAATCACTAAGGTCGCTTGGTTC
*
47240 GTGCTGAATTTTGAGTTTAAATACCTAATAAATTTTTATATATTTTTTAAATAATTCAATATTTC
326 GTGCTGAATTTTGAGTTTAAATACATAATAAATTTTTATATATTTTTTAAATAATTCAATATTTC
*
47305 GGCCATATCAATATTTAGTTCTGGCTCCGTCCTTGGTTTTATCTTTAGAAATCTTAATTGCATCA
391 GGCCCTATCAATATTTAGTTCTGGCTCCGTCCTTGGTTTTATCTTTAGAAATCTTAATTGCATCA
47370 CATCTTAAATACATTAAAATAAATAAGTAAAGCATGCATGATGCAGCAATGTTTTTCAACTTCAA
456 CATCTTAAATACATTAAAATAAATAAGTAAAGCATGCATGATGCAGCAATGTTTTTCAACTTCAA
47435 TCAACGGGTTTAGAGTTCAGAATTCATATCTTCATGCGAATTTATTAATATTTTGGTTCATGTAT
521 TCAACGGGTTTAGAGTTCAGAATTCATATCTTCATGCGAATTTATTAATATTTTGGTTCATGTAT
47500 TTTGGTTAATATA
586 TTTGGTTAATATA
47513 AAAATAAATATTTAAATTAAAAATATAAAAATTTATTAAATATTTAATCAAGTAAGGATCAAACT
1 AAAATAAATATTTAAATTAAAAATATAAAAATTTATTAAATATTTAATCAAGTAAGGATCAAACT
47578 AAAGAAGGATAACCTGTGTTATCAAAATTTTTGGTCTAATAACAATTTAAGTCATTATAAGTTTA
66 AAAGAAGGATAACCTGTGTTATCAAAATTTTTGGTCTAATAACAATTTAAGTCATTATAAGTTTA
47643 AATATTAGACAAATTAGGTGTTATCTTTTGCGAATTTTGAGATTTTTTAATAAATTTAGGGTGAA
131 AATATTAGACAAATTAGGTGTTATCTTTTGCGAATTTTGAGATTTTTTAATAAATTTAGGGTGAA
47708 TACAAGGTAGTATATGTACAAAGACTCTTAACTATTTGACAATGAACGCTCATTCCTCTACATAC
196 TACAAGGTAGTATATGTACAAAGACTCTTAACTATTTGACAATGAACGCTCATTCCTCTACATAC
47773 ACAGTGCTCGAACTCGAGACCTCAAGAGTAAAAATAATCCCTTAATCACTAAGGTCGCTTGGTTC
261 ACAGTGCTCGAACTCGAGACCTCAAGAGTAAAAATAATCCCTTAATCACTAAGGTCGCTTGGTTC
47838 GTGCTGAATTTTGAGTTTAAATACATAATAAATTTTTATATATTTTTTAAATAATTCAATATTTC
326 GTGCTGAATTTTGAGTTTAAATACATAATAAATTTTTATATATTTTTTAAATAATTCAATATTTC
47903 GGCCCTATCAATATTTAGTTCTGGCTCCGTCCTTGGTTTTATCTTTAGAAATCTTAATTGCATCA
391 GGCCCTATCAATATTTAGTTCTGGCTCCGTCCTTGGTTTTATCTTTAGAAATCTTAATTGCATCA
47968 CATCTTAAATACATTAAAATAAATAAGTAAAGCATGCATGATGCAGCAATGTTTTTCAACTTCAA
456 CATCTTAAATACATTAAAATAAATAAGTAAAGCATGCATGATGCAGCAATGTTTTTCAACTTCAA
48033 TCAACGGGTTTAGAGTTCAGAATTCATATCTTCATGCGAATTTATTAATATTTTGGTTCATGTAT
521 TCAACGGGTTTAGAGTTCAGAATTCATATCTTCATGCGAATTTATTAATATTTTGGTTCATGTAT
48098 TTTGGTTAATATA
586 TTTGGTTAATATA
48111 AAAATAAATATTTAAATTAAAAATATAAAAATTTATTAAATATTTAATCAAGTAAGGATCAAACT
1 AAAATAAATATTTAAATTAAAAATATAAAAATTTATTAAATATTTAATCAAGTAAGGATCAAACT
48176 AAAGAAGGATAACCTGTGTTATCAAAATTTTTGGTCTAATAACAATTTAAGTCATTATAAGTTTA
66 AAAGAAGGATAACCTGTGTTATCAAAATTTTTGGTCTAATAACAATTTAAGTCATTATAAGTTTA
48241 AATATTAGACAAATTAGGTGTTATCTTTTGCGAATTTTGAGATTTTTTAATAAATTTAGGGTGAA
131 AATATTAGACAAATTAGGTGTTATCTTTTGCGAATTTTGAGATTTTTTAATAAATTTAGGGTGAA
48306 TACAAGGTAGTATATGTACAAAGACTCTTAACTATTTGACAATGAACGCTCATTCCTCTACATAC
196 TACAAGGTAGTATATGTACAAAGACTCTTAACTATTTGACAATGAACGCTCATTCCTCTACATAC
48371 ACAGTGCTCGAACTCGAGACCTCAAGAGTAAAAATAATCCCTTAATCACTAAGGTCGCTTGGTTC
261 ACAGTGCTCGAACTCGAGACCTCAAGAGTAAAAATAATCCCTTAATCACTAAGGTCGCTTGGTTC
48436 GTGCTGAATTTTGAGTTTAAATACATAATAAATTTTTATATATTTTTTAAATAATTCAATATTTC
326 GTGCTGAATTTTGAGTTTAAATACATAATAAATTTTTATATATTTTTTAAATAATTCAATATTTC
48501 GGCCCTATCAATATTTAGTTCTGGCTCCGTCCTTGGTTTTATCTTTAGAAATCTTAATTGCATCA
391 GGCCCTATCAATATTTAGTTCTGGCTCCGTCCTTGGTTTTATCTTTAGAAATCTTAATTGCATCA
*
48566 CATCTTAAATACATTAAAATAAATAAGTAAAGCATGCATGATGCAGCTATGTTTTTCAACTTCAA
456 CATCTTAAATACATTAAAATAAATAAGTAAAGCATGCATGATGCAGCAATGTTTTTCAACTTCAA
48631 TCAACGGGTTTAGAGTTCAGAATTCATATCTTCATGC
521 TCAACGGGTTTAGAGTTCAGAATTCATATCTTCATGC
48668 CATCAGCGAA
Statistics
Matches: 1134, Mismatches: 8, Indels: 13
0.98 0.01 0.01
Matches are distributed among these distances:
585 5 0.00
586 4 0.00
587 38 0.03
591 60 0.05
594 10 0.01
595 25 0.02
596 16 0.01
598 976 0.86
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (598 bp):
AAAATAAATATTTAAATTAAAAATATAAAAATTTATTAAATATTTAATCAAGTAAGGATCAAACT
AAAGAAGGATAACCTGTGTTATCAAAATTTTTGGTCTAATAACAATTTAAGTCATTATAAGTTTA
AATATTAGACAAATTAGGTGTTATCTTTTGCGAATTTTGAGATTTTTTAATAAATTTAGGGTGAA
TACAAGGTAGTATATGTACAAAGACTCTTAACTATTTGACAATGAACGCTCATTCCTCTACATAC
ACAGTGCTCGAACTCGAGACCTCAAGAGTAAAAATAATCCCTTAATCACTAAGGTCGCTTGGTTC
GTGCTGAATTTTGAGTTTAAATACATAATAAATTTTTATATATTTTTTAAATAATTCAATATTTC
GGCCCTATCAATATTTAGTTCTGGCTCCGTCCTTGGTTTTATCTTTAGAAATCTTAATTGCATCA
CATCTTAAATACATTAAAATAAATAAGTAAAGCATGCATGATGCAGCAATGTTTTTCAACTTCAA
TCAACGGGTTTAGAGTTCAGAATTCATATCTTCATGCGAATTTATTAATATTTTGGTTCATGTAT
TTTGGTTAATATA
Found at i:49830 original size:25 final size:25
Alignment explanation
Indices: 49800--49861 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
49790 ATTATTTGAT
49800 TTAAAAATG-AATTTGATTTAAATA
1 TTAAAAATGAAATTTGATTTAAATA
49824 TTAAAAATGAAATTTGATTTAAATA
1 TTAAAAATGAAATTTGATTTAAATA
*
49849 TTAAAAATAAAAT
1 TTAAAAATGAAAT
49862 CAAAGCTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
24 9 0.25
25 27 0.75
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (25 bp):
TTAAAAATGAAATTTGATTTAAATA
Found at i:55449 original size:4 final size:4
Alignment explanation
Indices: 55440--55473 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
55430 ATCTCTCTTC
*
55440 CCCT CCCT CCCT TCCT CCCT CCCT CCCT CCCT CC
1 CCCT CCCT CCCT CCCT CCCT CCCT CCCT CCCT CC
55474 ATCTTTCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.74, G:0.00, T:0.26
Consensus pattern (4 bp):
CCCT
Found at i:59140 original size:143 final size:143
Alignment explanation
Indices: 58882--59167 Score: 527
Period size: 143 Copynumber: 2.0 Consensus size: 143
58872 ACATTATGAC
* * * *
58882 GTCGAATTAGTGTTGGAAATATTATGTCGTGGAGTCAGTGTTTGAAATTAATGATGGTGTCAGCA
1 GTCGAACTAGTGCTGGAAATATTATGTCGTGGAGTCAATGTTTGAAAGTAATGATGGTGTCAGCA
58947 GATATCATTAAAATGTAATTAAAATTCAATACAAATAACGCAATACTAAGGATGGTCTTGAAATG
66 GATATCATTAAAATGTAATTAAAATTCAATACAAATAACGCAATACTAAGGATGGTCTTGAAATG
59012 TCAACTTAGATAA
131 TCAACTTAGATAA
59025 GTCGAACTAGTGCTGGAAATATTATGTCGTGGAGTCAATGTTTGAAAGTAATGATGGTGTCAGCA
1 GTCGAACTAGTGCTGGAAATATTATGTCGTGGAGTCAATGTTTGAAAGTAATGATGGTGTCAGCA
*
59090 GATATCATTAAAATGTAATTAAAATTCAATACAAATAACGCATTACTAAGGATGGTCTTGAAATG
66 GATATCATTAAAATGTAATTAAAATTCAATACAAATAACGCAATACTAAGGATGGTCTTGAAATG
59155 TCAACTTAGATAA
131 TCAACTTAGATAA
59168 AAATAGGATA
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
143 138 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.31
Consensus pattern (143 bp):
GTCGAACTAGTGCTGGAAATATTATGTCGTGGAGTCAATGTTTGAAAGTAATGATGGTGTCAGCA
GATATCATTAAAATGTAATTAAAATTCAATACAAATAACGCAATACTAAGGATGGTCTTGAAATG
TCAACTTAGATAA
Found at i:59448 original size:7 final size:7
Alignment explanation
Indices: 59431--59464 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
59421 ATTTACTCTA
59431 GTTCTTTT
1 GTTC-TTT
59439 GTTCTTT
1 GTTCTTT
59446 GTTCTTT
1 GTTCTTT
59453 GTTCTTT
1 GTTCTTT
*
59460 ATTCT
1 GTTCT
59465 CTTGGTGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 21 0.84
8 4 0.16
ACGTcount: A:0.03, C:0.15, G:0.12, T:0.71
Consensus pattern (7 bp):
GTTCTTT
Found at i:60457 original size:20 final size:20
Alignment explanation
Indices: 60410--60457 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
60400 ATCCGGCCTG
* * *
60410 AAATAATATATTTATTTAAA
1 AAATATTATTTTTATTCAAA
60430 AAATATTATTTTTATTCAATA
1 AAATATTATTTTTATTCAA-A
60451 AAA-ATTA
1 AAATATTA
60458 AAGTTTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATATTATTTTTATTCAAA
Found at i:63189 original size:21 final size:22
Alignment explanation
Indices: 63165--63211 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
63155 ATCAATATTT
* *
63165 AAAATGT-AGAAGATATAAGAA
1 AAAATGTAAAAAGATACAAGAA
*
63186 AAAATGTAAAAAGATACAAGGA
1 AAAATGTAAAAAGATACAAGAA
63208 AAAA
1 AAAA
63212 GGAGAAGCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.66, C:0.02, G:0.17, T:0.15
Consensus pattern (22 bp):
AAAATGTAAAAAGATACAAGAA
Found at i:69520 original size:51 final size:51
Alignment explanation
Indices: 69460--69559 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 51
69450 TTTTTTAACA
* *
69460 ACATATAATATTAGGTATAATTTTTTAATGACATATGATCAAAACGAATTC
1 ACATATAATATTAGGTATAAATTTTTAAAGACATATGATCAAAACGAATTC
69511 ACATATAATATTAGGTATAAATTTTTAAAGACATATGATCAAAACGAAT
1 ACATATAATATTAGGTATAAATTTTTAAAGACATATGATCAAAACGAAT
69560 CTAAAATATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (51 bp):
ACATATAATATTAGGTATAAATTTTTAAAGACATATGATCAAAACGAATTC
Found at i:69582 original size:52 final size:51
Alignment explanation
Indices: 69462--69582 Score: 152
Period size: 51 Copynumber: 2.4 Consensus size: 51
69452 TTTTAACAAC
* * * * * *
69462 ATATAATATTAGGTATAATTTTTTAATGACATATGATCAAAACGAATTCAC
1 ATATAACATTAGATATAAATTTTTAAAGACATATGATCAAAACGAATTAAA
* *
69513 ATATAATATTAGGTATAAATTTTTAAAGACATATGATCAAAACGAATCTAAA
1 ATATAACATTAGATATAAATTTTTAAAGACATATGATCAAAACGAAT-TAAA
*
69565 ATATAACATTTGATATAA
1 ATATAACATTAGATATAA
69583 TTAAAAAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
51 45 0.73
52 17 0.27
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (51 bp):
ATATAACATTAGATATAAATTTTTAAAGACATATGATCAAAACGAATTAAA
Found at i:70327 original size:15 final size:15
Alignment explanation
Indices: 70307--70336 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
70297 AACGTACCCT
70307 TAAAGCATCAAGAAA
1 TAAAGCATCAAGAAA
70322 TAAAGCATCAAGAAA
1 TAAAGCATCAAGAAA
70337 AGTGTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (15 bp):
TAAAGCATCAAGAAA
Found at i:70754 original size:20 final size:20
Alignment explanation
Indices: 70709--70753 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
70699 ATATTTATAT
70709 AAAAAAGTATAATAAGATAC
1 AAAAAAGTATAATAAGATAC
*
70729 TAAAAAGTATAATAA-ATAC
1 AAAAAAGTATAATAAGATAC
70748 AAAAAA
1 AAAAAA
70754 ATGGAAAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (20 bp):
AAAAAAGTATAATAAGATAC
Found at i:72564 original size:99 final size:100
Alignment explanation
Indices: 72323--72927 Score: 718
Period size: 106 Copynumber: 6.0 Consensus size: 100
72313 TGTTTGTGGG
* **
72323 CAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTTTAATATCCTTCGTTGT
1 CAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGTTGT
* *
72388 GAAGTCGAAATTGACTCTG-AA-TGA-AATTTTGTTGA
66 GAAGTTGAAATTGGCTCTGAAATTGAGAA---TGTTGA
* * * * *
72423 CAATCAGCCGCCCCTTCG-TCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCTAATATCCTTCGCTG
1 CAGTCAGCCGCCCCTTCGCT-GTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGTTG
*
72487 GGAAGTTGAAATTGGCTCTGAAATTGAGAA-GTTGA
65 TGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGA
* * *
72522 CAGTGAGCCGTCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCTTTCGTTGT
1 CAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGTTGT
** * *
72587 GAAGTTGAAATTGTTTATGAAATTGTGAAGTTGTTTGTTGA
66 GAAGTTGAAATTGGCTCTGAAATTGAGAA------TGTTGA
* *
72628 CAGTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCATTCGTTGT
1 CAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGTTGT
* * * * *
72693 GAAGTTGAATTTAGCTATAAAATTGGGAA-GTTGA
66 GAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGA
* * *
72727 CAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGT
1 CAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGTTGT
* *
72792 GAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTGTTGA
66 GAAGTTGAAATTGGCTCTGAAATTGAGAA------TGTTGA
* * *
72833 CAGTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCATTCGTTGT
1 CAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGTTGT
*
72898 GAAGTTGAAATTGGCTCTGAAATTGGGAAT
66 GAAGTTGAAATTGGCTCTGAAATTGAGAAT
72928 CCCCTTCGTC
Statistics
Matches: 441, Mismatches: 45, Indels: 38
0.84 0.09 0.07
Matches are distributed among these distances:
99 176 0.40
100 75 0.17
101 2 0.00
102 3 0.01
103 2 0.00
106 183 0.41
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (100 bp):
CAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGTTGT
GAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGA
Found at i:72699 original size:205 final size:205
Alignment explanation
Indices: 72323--72922 Score: 888
Period size: 205 Copynumber: 3.0 Consensus size: 205
72313 TGTTTGTGGG
* **
72323 CAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTTTAATATCCTTCGTTGT
1 CAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGTTGT
* * * *
72388 GAAGTCGAAATTGACTCTG-AA---TGAA-AT-TTTGTTGACAATCAGCCGCCCCTTCGTCGTGA
66 GAAGTTGAAATTGACTCTGAAATTGTGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCCGTGA
* * * * *
72447 AGTTGAGCTTGTGTTGTCTTGGGTCTAATATCCTTCGCTGGGAAGTTGAAATTGGCTCTGAAATT
131 AGTTGAGCTTGTGTTGTCTTGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
72512 GAGAAGTTGA
196 GAGAAGTTGA
* * *
72522 CAGTGAGCCGTCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCTTTCGTTGT
1 CAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGTTGT
** *
72587 GAAGTTGAAATTGTTTATGAAATTGTGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCCGTGA
66 GAAGTTGAAATTGACTCTGAAATTGTGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCCGTGA
* * * * *
72652 AGTTGAGCTTGTGCTGTCTTGAGTCCAATATCATTCGTTGTGAAGTTGAATTTAGCTATAAAATT
131 AGTTGAGCTTGTGTTGTCTTGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
*
72717 GGGAAGTTGA
196 GAGAAGTTGA
* * *
72727 CAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGT
1 CAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGTTGT
* * *
72792 GAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCCGTGA
66 GAAGTTGAAATTGACTCTGAAATTGTGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCCGTGA
72857 AGTTGAGCTTGTGTTGTCTTGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
131 AGTTGAGCTTGTGTTGTCTTGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
72922 G
196 G
72923 GGAATCCCCT
Statistics
Matches: 355, Mismatches: 40, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
199 74 0.21
200 2 0.01
203 4 0.01
204 1 0.00
205 274 0.77
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (205 bp):
CAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGTTGT
GAAGTTGAAATTGACTCTGAAATTGTGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCCGTGA
AGTTGAGCTTGTGTTGTCTTGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
GAGAAGTTGA
Found at i:74057 original size:12 final size:11
Alignment explanation
Indices: 74040--74101 Score: 79
Period size: 11 Copynumber: 5.5 Consensus size: 11
74030 ACCCACCTTA
74040 TTTTTCTTTTAT
1 TTTTTCTTTT-T
74052 TTTTTCTTTTT
1 TTTTTCTTTTT
*
74063 ATTTTTCTCTTT
1 -TTTTTCTTTTT
*
74075 TTTCTCTTTTT
1 TTTTTCTTTTT
*
74086 ATTTTCTTTTT
1 TTTTTCTTTTT
74097 TTTTT
1 TTTTT
74102 TCAATTTAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
11 23 0.53
12 20 0.47
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:74067 original size:23 final size:23
Alignment explanation
Indices: 74037--74101 Score: 96
Period size: 22 Copynumber: 2.8 Consensus size: 23
74027 TGAACCCACC
74037 TTATTTTTCTTTTATTTTTTCTTT
1 TTATTTTTCTTTT-TTTTTTCTTT
* *
74061 TTATTTTTCTCTTTTTTCTCTTT
1 TTATTTTTCTTTTTTTTTTCTTT
74084 TTA-TTTTCTTTTTTTTTT
1 TTATTTTTCTTTTTTTTTT
74102 TCAATTTAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.35
23 12 0.32
24 12 0.32
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (23 bp):
TTATTTTTCTTTTTTTTTTCTTT
Found at i:74084 original size:22 final size:21
Alignment explanation
Indices: 74051--74102 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
74041 TTTTCTTTTA
74051 TTTTTTC-TTTTTATTTTTCTC
1 TTTTTTCTTTTTTA-TTTTCTC
74072 TTTTTTCTCTTTTTATTTTCT-
1 TTTTTTCT-TTTTTATTTTCTC
74093 TTTTTT-TTTT
1 TTTTTTCTTTT
74103 CAATTTAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 3 0.10
20 1 0.03
21 13 0.45
22 6 0.21
23 6 0.21
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.85
Consensus pattern (21 bp):
TTTTTTCTTTTTTATTTTCTC
Found at i:74095 original size:34 final size:33
Alignment explanation
Indices: 74040--74103 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
74030 ACCCACCTTA
74040 TTTTTCTTTTATTTTTTCTTTTTATTTTTCTCT
1 TTTTTCTTTTATTTTTTCTTTTTATTTTTCTCT
*
74073 TTTTTCTCTTT-TTATTTTCTTTTTTTTTTTC
1 TTTTTCT-TTTATT-TTTTCTTTTTATTTTTC
74104 AATTTAGGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 9 0.32
34 19 0.68
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (33 bp):
TTTTTCTTTTATTTTTTCTTTTTATTTTTCTCT
Found at i:74102 original size:12 final size:12
Alignment explanation
Indices: 74040--74103 Score: 69
Period size: 12 Copynumber: 5.5 Consensus size: 12
74030 ACCCACCTTA
*
74040 TTTTTCTTTTAT
1 TTTTTCTTTTTT
*
74052 TTTTTCTTTTTA
1 TTTTTCTTTTTT
*
74064 TTTTTC-TCTTT
1 TTTTTCTTTTTT
*
74075 TTTCTC-TTTTT
1 TTTTTCTTTTTT
*
74086 ATTTTCTTTTTT
1 TTTTTCTTTTTT
74098 TTTTTC
1 TTTTTC
74104 AATTTAGGGA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
11 16 0.38
12 26 0.62
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:74109 original size:23 final size:23
Alignment explanation
Indices: 74041--74103 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
74031 CCCACCTTAT
*
74041 TTTTCTTTTATTTTTTCTTTTTA
1 TTTTCTTTTTTTTTTTCTTTTTA
* *
74064 TTTT-TCTCTTTTTTCTCTTTTTA
1 TTTTCT-TTTTTTTTTTCTTTTTA
74087 TTTTCTTTTTTTTTTTC
1 TTTTCTTTTTTTTTTTC
74104 AATTTAGGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 1 0.03
23 31 0.94
24 1 0.03
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.83
Consensus pattern (23 bp):
TTTTCTTTTTTTTTTTCTTTTTA
Found at i:74181 original size:11 final size:10
Alignment explanation
Indices: 74153--74179 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
74143 TTCTTTTTTG
74153 TTTTTTTCCT
1 TTTTTTTCCT
74163 TTTTTTTCCT
1 TTTTTTTCCT
74173 TTTTTTT
1 TTTTTTT
74180 TCAACTTAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTCCT
Found at i:74214 original size:78 final size:82
Alignment explanation
Indices: 74058--74214 Score: 189
Period size: 78 Copynumber: 2.0 Consensus size: 82
74048 TTATTTTTTC
* * * *
74058 TTTTTATTTTTCTCTTTTTTCTCTTTTTATTTTCTTTTTTTTTTTCAATTTAGGGAGCCCTTTCG
1 TTTTTATTTTTCTCTTTTTTCTCCTTTTATTTTCTCTTTTTTTTTCAACTTAGGGAGCCCTCTCG
74123 ACTTTTCACCCTAAACG
66 ACTTTTCACCCTAAACG
* *
74140 TTTTTCTTTTT-TGTTTTTT-TCCTTTT-TTTTC-CTTTTTTTTTCAACTTA-GGACGCCCTCTC
1 TTTTTATTTTTCTCTTTTTTCTCCTTTTATTTTCTCTTTTTTTTTCAACTTAGGGA-GCCCTCTC
** *
74200 GGGTTTTCATCCTAA
65 GACTTTTCACCCTAA
74215 GCGAAGTACT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
77 3 0.05
78 34 0.52
79 5 0.08
80 6 0.09
81 7 0.11
82 10 0.15
ACGTcount: A:0.11, C:0.20, G:0.08, T:0.60
Consensus pattern (82 bp):
TTTTTATTTTTCTCTTTTTTCTCCTTTTATTTTCTCTTTTTTTTTCAACTTAGGGAGCCCTCTCG
ACTTTTCACCCTAAACG
Found at i:83498 original size:21 final size:22
Alignment explanation
Indices: 83472--83521 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
83462 AATAAAAATA
*
83472 AAAAATAAAAA-ATGACGAAAG
1 AAAAATAAAAAGATGAAGAAAG
* *
83493 AAAAATAAAAAGATTAAGAAGG
1 AAAAATAAAAAGATGAAGAAAG
83515 AAAAATA
1 AAAAATA
83522 TGGTTAGGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.72, C:0.02, G:0.14, T:0.12
Consensus pattern (22 bp):
AAAAATAAAAAGATGAAGAAAG
Found at i:84816 original size:20 final size:20
Alignment explanation
Indices: 84771--84815 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
84761 ACATTTATAT
84771 AAAAAAGTATAATAAGATAC
1 AAAAAAGTATAATAAGATAC
*
84791 TAAAAAGTATAATAA-ATAC
1 AAAAAAGTATAATAAGATAC
84810 AAAAAA
1 AAAAAA
84816 AACGGAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (20 bp):
AAAAAAGTATAATAAGATAC
Found at i:87510 original size:2 final size:2
Alignment explanation
Indices: 87505--87546 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
87495 GTTTTTTCTG
*
87505 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
87547 AGAAAATGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:88046 original size:3 final size:3
Alignment explanation
Indices: 88040--88127 Score: 134
Period size: 3 Copynumber: 31.3 Consensus size: 3
88030 TATTTTTTAA
88040 AAT AAT AAT AAT AAT AAT -AT AAT -AT AAT AAT AAT -AT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
88084 -AT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
88128 CTGTAAGGTG
Statistics
Matches: 79, Mismatches: 0, Indels: 12
0.87 0.00 0.13
Matches are distributed among these distances:
2 12 0.15
3 67 0.85
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:89646 original size:15 final size:15
Alignment explanation
Indices: 89613--89646 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
89603 TTTATCTCAA
* *
89613 AAAATAAAAAATAAT
1 AAAATAAAAAAGAAG
89628 AAAATAAAAAAGAAG
1 AAAATAAAAAAGAAG
89643 AAAA
1 AAAA
89647 ATCCCGCGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (15 bp):
AAAATAAAAAAGAAG
Found at i:91192 original size:14 final size:14
Alignment explanation
Indices: 91142--91193 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
91132 TATTCGATTG
91142 TTTAATTATTGTTAT
1 TTTAATT-TTGTTAT
91157 TTTAATTTT-TCT-T
1 TTTAATTTTGT-TAT
91170 TTTAAAATTTTGTTAT
1 TTT--AATTTTGTTAT
91186 TTTAATTT
1 TTTAATTT
91194 CTGCTTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
13 5 0.16
14 8 0.25
15 14 0.44
16 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (14 bp):
TTTAATTTTGTTAT
Found at i:91202 original size:27 final size:29
Alignment explanation
Indices: 91145--91208 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 29
91135 TCGATTGTTT
**
91145 AATTATTGTTATTTTAATTTTTCTTTTTAA
1 AATTATTGTTATTTTAA-TTTTCTGCTTAA
91175 AATT-TTGTTATTTTAA-TTTCTGCTTAA
1 AATTATTGTTATTTTAATTTTCTGCTTAA
91202 AATTATT
1 AATTATT
91209 AATTGTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 13 0.42
28 2 0.06
29 12 0.39
30 4 0.13
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (29 bp):
AATTATTGTTATTTTAATTTTCTGCTTAA
Found at i:91335 original size:30 final size:30
Alignment explanation
Indices: 91301--91359 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
91291 TCATTTTAGT
*
91301 CATTTACTTA-ATGTTTTAATTTCAGTTTTG
1 CATTTACTTATATATTTTAATTT-AGTTTTG
* *
91331 CATTTATTTATTTATTTTAATTTAGTTTT
1 CATTTACTTATATATTTTAATTTAGTTTT
91360 TTCTGTATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.63
Consensus pattern (30 bp):
CATTTACTTATATATTTTAATTTAGTTTTG
Found at i:91777 original size:135 final size:137
Alignment explanation
Indices: 91547--91928 Score: 452
Period size: 135 Copynumber: 2.8 Consensus size: 137
91537 CCCTAAACTT
* * * * * *
91547 TTAATTTAGGAGAATTTTTTATTTGGTCCTCACTTATGCTCAAGGTTCCGAA-TTAATTATTTGA
1 TTAAATTAGGAGAATTTTTAATTTGGTCCTCGCTTTTGCT-GAGGTTCC-AATTTAATTATTCGA
* *
91611 TAGTCCATAATTGATTAAACTTAATTAGGATTAATATTAGAGTCTCCATCTTAGGCCTAATTTCA
64 -AGTCAATAATTGATTAAACTTAATTAGGATTAATATTAGAGCCTCCATCTTAGGCCTAATTTCA
91676 TA-TTTAATCC
128 -ACTTTAATCC
* * *
91686 -TAAATTAGGTGAATTTTTAATTTGGTCATCGCTTTTGCTGAGGTTCCAATTTAGTTATTCGAA-
1 TTAAATTAGGAGAATTTTTAATTTGGTCCTCGCTTTTGCTGAGGTTCCAATTTAATTATTCGAAG
* * *
91749 TCAATAATTGATTAAAGTTGATTAGGATTAATATTAGAGCCTCTATCTTAGGCCTAATTTCAACT
66 TCAATAATTGATTAAACTTAATTAGGATTAATATTAGAGCCTCCATCTTAGGCCTAATTTCAACT
*
91814 TTAGTCC
131 TTAATCC
* * * *
91821 TTAATTTAGGAGAATTTTTCATTTGGTCCTTGCTTTTGCTTGAGGTTCCACTTTAATTATTCGAA
1 TTAAATTAGGAGAATTTTTAATTTGGTCCTCGCTTTTGC-TGAGGTTCCAATTTAATTATTCGAA
* * * *
91886 TTGCAAT-ATTGATTAAAATTAATTTAAG-TTAATATTAGGGCCT
65 GT-CAATAATTGATTAAACTTAA-TTAGGATTAATATTAGAGCCT
91929 ACATTTTCAG
Statistics
Matches: 210, Mismatches: 26, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
134 1 0.00
135 64 0.30
136 36 0.17
137 40 0.19
138 61 0.29
139 8 0.04
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (137 bp):
TTAAATTAGGAGAATTTTTAATTTGGTCCTCGCTTTTGCTGAGGTTCCAATTTAATTATTCGAAG
TCAATAATTGATTAAACTTAATTAGGATTAATATTAGAGCCTCCATCTTAGGCCTAATTTCAACT
TTAATCC
Found at i:96812 original size:3 final size:3
Alignment explanation
Indices: 96804--96837 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
96794 CCCTTAATCC
96804 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
96838 TATTATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:98193 original size:19 final size:20
Alignment explanation
Indices: 98169--98211 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
98159 TATTGAAAGA
*
98169 TTAAAGG-AGAAAATCAATT
1 TTAAAGGTAGAAAATCAAAT
98188 TTAAAGGTAGAAAATCAAAT
1 TTAAAGGTAGAAAATCAAAT
98208 TTAA
1 TTAA
98212 TTACAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (20 bp):
TTAAAGGTAGAAAATCAAAT
Found at i:105324 original size:22 final size:21
Alignment explanation
Indices: 105261--105324 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
105251 TAAACAAACG
* *
105261 TAAACGAACACAAACGAACGGACA
1 TAAACAAACACAAA-AAAC-GA-A
* *
105285 TAAACAAACATAATAAACGAA
1 TAAACAAACACAAAAAACGAA
105306 TAACACAAACACAAAAAAC
1 TAA-ACAAACACAAAAAAC
105325 AAACTTATTC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 4 0.12
22 15 0.45
23 3 0.09
24 11 0.33
ACGTcount: A:0.62, C:0.22, G:0.08, T:0.08
Consensus pattern (21 bp):
TAAACAAACACAAAAAACGAA
Found at i:105601 original size:14 final size:14
Alignment explanation
Indices: 105582--105621 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
105572 ACATAAATGG
105582 ACATAAATGAACGA
1 ACATAAATGAACGA
105596 ACATAAATGAACGA
1 ACATAAATGAACGA
*
105610 ACATAAACGAAC
1 ACATAAATGAAC
105622 ATATAATCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.57, C:0.17, G:0.12, T:0.12
Consensus pattern (14 bp):
ACATAAATGAACGA
Found at i:105618 original size:24 final size:25
Alignment explanation
Indices: 105569--105634 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
105559 GCCCTCTGTT
* *
105569 CGAACATAAATGGAC-ATAAATGAA
1 CGAACATAAATGAACGATAAATAAA
*
105593 CGAACATAAATGAACGA-ACATAAA
1 CGAACATAAATGAACGATAAATAAA
105617 CGAACATATAATCGAACG
1 CGAACATA-AAT-GAACG
105635 TTCACGAACG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 27 0.75
25 4 0.11
26 5 0.14
ACGTcount: A:0.53, C:0.17, G:0.15, T:0.15
Consensus pattern (25 bp):
CGAACATAAATGAACGATAAATAAA
Found at i:105644 original size:26 final size:24
Alignment explanation
Indices: 105590--105644 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
105580 GGACATAAAT
*
105590 GAACGAACATAAATGAACGAACAT
1 GAACGAACATAAATGAACGAACAC
* **
105614 AAACGAACATATAATCGAACGTTCAC
1 GAACGAACATA-AAT-GAACGAACAC
105640 GAACG
1 GAACG
105645 TAAATGAACG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 10 0.42
25 3 0.12
26 11 0.46
ACGTcount: A:0.49, C:0.20, G:0.16, T:0.15
Consensus pattern (24 bp):
GAACGAACATAAATGAACGAACAC
Found at i:105724 original size:40 final size:40
Alignment explanation
Indices: 105680--105767 Score: 151
Period size: 40 Copynumber: 2.2 Consensus size: 40
105670 CGTGTTCTTC
105680 CATTTAATTAAAC-AAGCACAAAATCTTGTTCATATTCGTT
1 CATTTAATTAAACGAA-CACAAAATCTTGTTCATATTCGTT
*
105720 CATTTAATTAAACGAACACAAAATCTTGTTCATGTTCGTT
1 CATTTAATTAAACGAACACAAAATCTTGTTCATATTCGTT
105760 CATTTAAT
1 CATTTAAT
105768 AAATAAACGA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 44 0.96
41 2 0.04
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (40 bp):
CATTTAATTAAACGAACACAAAATCTTGTTCATATTCGTT
Done.