Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 46 of 175
Found at i:13269239 original size:11 final size:9
Alignment explanation
Indices: 13269198--13269232 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
13269188 TTTTATTGAA
*
13269198 TTTTGTCTT
1 TTTTGACTT
*
13269207 TTTTGATTT
1 TTTTGACTT
13269216 TTTTGACTT
1 TTTTGACTT
13269225 TTTTGACT
1 TTTTGACT
13269233 GATTTTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.09, C:0.09, G:0.11, T:0.71
Consensus pattern (9 bp):
TTTTGACTT
Found at i:13271060 original size:52 final size:52
Alignment explanation
Indices: 13271001--13271101 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 52
13270991 TCGCATCATA
*
13271001 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTATTG
13271053 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTA
13271102 CTTTTCCTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTATTG
Found at i:13274228 original size:20 final size:20
Alignment explanation
Indices: 13274182--13274228 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
13274172 AGCTTGTTTC
*
13274182 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
13274202 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
13274222 CAGCTCA
1 CAGCTCA
13274229 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:13285210 original size:20 final size:20
Alignment explanation
Indices: 13285187--13285233 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
13285177 GGGTTAAGAT
*
13285187 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
13285207 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
13285227 TGAGCTG
1 TGAGCTG
13285234 GAAACGAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:13286752 original size:17 final size:18
Alignment explanation
Indices: 13286730--13286770 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
13286720 CGTTTCTTTT
13286730 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
13286747 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
13286765 T-TTTTG
1 TCTTTTG
13286771 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:13286754 original size:24 final size:25
Alignment explanation
Indices: 13286701--13286754 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
13286691 AACAAATTCT
* *
13286701 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
13286726 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
13286749 TTTTTT
1 TTTTTT
13286755 ATCACTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:13289020 original size:15 final size:15
Alignment explanation
Indices: 13289002--13289030 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13288992 CTAGACCGTA
13289002 TGCAATTTTTTTTTT
1 TGCAATTTTTTTTTT
13289017 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
13289031 CCTTCTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TGCAATTTTTTTTTT
Found at i:13294157 original size:18 final size:17
Alignment explanation
Indices: 13294074--13294202 Score: 61
Period size: 18 Copynumber: 7.4 Consensus size: 17
13294064 GGAACAAGAA
*
13294074 ATTGAAAAAGAGAGTGAG
1 ATTGAAAAAGA-AATGAG
*
13294092 ATTGAAGAAAGAAACGAG
1 ATTGAA-AAAGAAATGAG
* * *
13294110 AGTGTAAAAGAAACGAGTG
1 ATTGAAAAAGAAATGA--G
*
13294129 TCATGGAAAAAGAAATTGAG
1 --ATTGAAAAAGAAA-TGAG
*
13294149 ATTGAAAAAG-GAT--G
1 ATTGAAAAAGAAATGAG
* *
13294163 --TGAAAAAGAGAAAGAA
1 ATTGAAAAAGA-AATGAG
13294179 ATTGAAAAAGAAATTGAG
1 ATTGAAAAAGAAA-TGAG
13294197 ATTGAA
1 ATTGAA
13294203 CAAAAGTGTG
Statistics
Matches: 83, Mismatches: 15, Indels: 26
0.67 0.12 0.21
Matches are distributed among these distances:
12 8 0.10
14 2 0.02
16 1 0.01
17 13 0.16
18 40 0.48
19 6 0.07
20 1 0.01
21 10 0.12
22 2 0.02
ACGTcount: A:0.53, C:0.02, G:0.27, T:0.17
Consensus pattern (17 bp):
ATTGAAAAAGAAATGAG
Found at i:13294213 original size:48 final size:47
Alignment explanation
Indices: 13294134--13294239 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
13294124 GAGTGTCATG
*
13294134 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATT
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATT
*
13294182 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATT
*
13294230 GAAAATGAAA
1 GAAAAAGAAA
13294240 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.58, C:0.01, G:0.25, T:0.16
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATT
Found at i:13295956 original size:20 final size:20
Alignment explanation
Indices: 13295910--13295956 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
13295900 AGCTTGTTTC
*
13295910 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
13295930 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
13295950 CAGCTCA
1 CAGCTCA
13295957 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:13303609 original size:21 final size:23
Alignment explanation
Indices: 13303564--13303610 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
13303554 TCACCTGCAA
* *
13303564 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
13303587 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
13303608 TAA
1 TAA
13303611 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:13306369 original size:12 final size:12
Alignment explanation
Indices: 13306352--13306379 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
13306342 CTCAAATTTC
13306352 TTTTCATTTCCT
1 TTTTCATTTCCT
13306364 TTTTCATTTCCT
1 TTTTCATTTCCT
13306376 TTTT
1 TTTT
13306380 GCTTTTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTCATTTCCT
Found at i:13306397 original size:12 final size:12
Alignment explanation
Indices: 13306382--13306412 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
13306372 TCCTTTTTGC
13306382 TTTTCAAAGGCT
1 TTTTCAAAGGCT
13306394 TTTTCAAAGGCT
1 TTTTCAAAGGCT
13306406 TTTTCAA
1 TTTTCAA
13306413 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:13306485 original size:21 final size:22
Alignment explanation
Indices: 13306460--13306518 Score: 57
Period size: 27 Copynumber: 2.5 Consensus size: 22
13306450 CTCTTGCCTC
13306460 TCTTTTCTTTTTA-TTTCATTT
1 TCTTTTCTTTTTATTTTCATTT
*
13306481 TCTTTTTCTTCTCTTACTTTTTCTTTT
1 TC-TTTTCTT-T-TTA--TTTTCATTT
13306508 TCTTTTCTTTT
1 TCTTTTCTTTT
13306519 CTTTGTTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
21 2 0.06
22 7 0.23
23 1 0.03
24 4 0.13
25 1 0.03
26 7 0.23
27 9 0.29
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (22 bp):
TCTTTTCTTTTTATTTTCATTT
Found at i:13306489 original size:6 final size:6
Alignment explanation
Indices: 13306473--13306522 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
13306463 TTTCTTTTTA
*
13306473 TTTCAT TTTCTT TTTCTT CTCTTACTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
13306522 T
1 T
13306523 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:13306519 original size:37 final size:37
Alignment explanation
Indices: 13306462--13306532 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
13306452 CTTGCCTCTC
13306462 TTTTCTTTTTATTTCATTTTCTTT-TTCTTCTCTTACT
1 TTTTCTTTTTATTTCATTTTCTTTGTT-TTCTCTTACT
*
13306499 TTTTCTTTTTCTTTTC-TTTTCTTTGTTTTCTCTT
1 TTTTCTTTTT-ATTTCATTTTCTTTGTTTTCTCTT
13306533 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTATTTCATTTTCTTTGTTTTCTCTTACT
Found at i:13306533 original size:16 final size:16
Alignment explanation
Indices: 13306458--13306518 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
13306448 GCCTCTTGCC
*
13306458 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
13306474 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
13306490 TCTC-TTACTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
13306506 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
13306519 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:13307480 original size:12 final size:13
Alignment explanation
Indices: 13307449--13307480 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
13307439 TTTAACTCGA
13307449 TTTTTTTTGTCAC
1 TTTTTTTTGTCAC
13307462 TTTTTTTT-TC-C
1 TTTTTTTTGTCAC
13307473 TTTTTTTT
1 TTTTTTTT
13307481 CGATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 2 0.11
13 8 0.42
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.81
Consensus pattern (13 bp):
TTTTTTTTGTCAC
Found at i:13307487 original size:22 final size:21
Alignment explanation
Indices: 13307462--13307524 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
13307452 TTTTTGTCAC
13307462 TTTTTTTTTCCTTTTTTTTCGA
1 TTTTTTTTTCCTTTTTTTT-GA
**
13307484 TTTTTTTTTGAATTTTTTTTGA
1 TTTTTTTTT-CCTTTTTTTTGA
* * *
13307506 ATTTCTTCTCCTTTTTTTT
1 TTTTTTTTTCCTTTTTTTT
13307525 TAAATCCAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
21 8 0.24
22 17 0.52
23 8 0.24
ACGTcount: A:0.08, C:0.11, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTTTTTTTCCTTTTTTTTGA
Found at i:13307488 original size:12 final size:12
Alignment explanation
Indices: 13307445--13307503 Score: 54
Period size: 12 Copynumber: 5.0 Consensus size: 12
13307435 TTTTTTTAAC
13307445 TCGATTTTTTTT
1 TCGATTTTTTTT
13307457 GTC-ACTTTTTTTT
1 -TCGA-TTTTTTTT
*
13307470 TC--CTTTTTTT
1 TCGATTTTTTTT
13307480 TCGATTTTTTTT
1 TCGATTTTTTTT
13307492 T-GAATTTTTTTT
1 TCG-ATTTTTTTT
13307504 GAATTTCTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 9 0.22
11 1 0.03
12 20 0.50
13 10 0.25
ACGTcount: A:0.08, C:0.10, G:0.07, T:0.75
Consensus pattern (12 bp):
TCGATTTTTTTT
Found at i:13307504 original size:11 final size:11
Alignment explanation
Indices: 13307473--13307509 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
13307463 TTTTTTTTCC
*
13307473 TTTTTTTTCGAT
1 TTTTTTTT-GAA
13307485 TTTTTTTTGAA
1 TTTTTTTTGAA
13307496 TTTTTTTTGAA
1 TTTTTTTTGAA
13307507 TTT
1 TTT
13307510 CTTCTCCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.14, C:0.03, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:13312395 original size:20 final size:20
Alignment explanation
Indices: 13312350--13312396 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
13312340 TTAGCTTGGC
* *
13312350 TCAGCTCACCGAATCTTATT
1 TCAGCTCACCGAAGCTTAAT
*
13312370 TTAGCTCACACG-AGCTTAAT
1 TCAGCTCAC-CGAAGCTTAAT
13312390 TCAGCTC
1 TCAGCTC
13312397 GTTTGAGCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.32
Consensus pattern (20 bp):
TCAGCTCACCGAAGCTTAAT
Found at i:13315573 original size:15 final size:14
Alignment explanation
Indices: 13315547--13315599 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
13315537 TGAAATCTCA
13315547 TTTTCATCTTTTTCT
1 TTTTC-TCTTTTTCT
*
13315562 TTTATTTCTTTTTCT
1 TTT-TCTCTTTTTCT
13315577 TTTTCTCTTATTTCT
1 TTTTCTCTT-TTTCT
13315592 TTTT-TCTT
1 TTTTCTCTT
13315600 CTCTCAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 9 0.26
15 24 0.71
16 1 0.03
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTCTCTTTTTCT
Found at i:13315577 original size:21 final size:21
Alignment explanation
Indices: 13315553--13315595 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
13315543 CTCATTTTCA
*
13315553 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTTATTTCTTTT
13315574 TCTTTTTCTCTTATTTCTTTT
1 TCTTTTTCTCTTATTTCTTTT
13315595 T
1 T
13315596 TCTTCTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (21 bp):
TCTTTTTCTCTTATTTCTTTT
Found at i:13315604 original size:21 final size:21
Alignment explanation
Indices: 13315553--13315604 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
13315543 CTCATTTTCA
* *
13315553 TCTTTTTCTTTTATTTCTTTT
1 TCTTTCTCTCTTATTTCTTTT
*
13315574 TCTTTTTCTCTTATTTCTTTT
1 TCTTTCTCTCTTATTTCTTTT
13315595 T-TCTTCTCTC
1 TCT-TTCTCTC
13315605 AATTTCATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (21 bp):
TCTTTCTCTCTTATTTCTTTT
Found at i:13318396 original size:13 final size:13
Alignment explanation
Indices: 13318366--13318400 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
13318356 GTATGCAATT
13318366 TTTTTTCTTTTCAA
1 TTTTTT-TTTTCAA
13318380 -TTTTTTTTTCAA
1 TTTTTTTTTTCAA
13318392 TTTTTTTTT
1 TTTTTTTTT
13318401 GAACTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTTTTCAA
Found at i:13318408 original size:13 final size:12
Alignment explanation
Indices: 13318367--13318412 Score: 65
Period size: 12 Copynumber: 3.7 Consensus size: 12
13318357 TATGCAATTT
13318367 TTTTTCTTTTCAA
1 TTTTT-TTTTCAA
13318380 TTTTTTTTTCAA
1 TTTTTTTTTCAA
*
13318392 TTTTTTTTTGAA
1 TTTTTTTTTCAA
13318404 CTTTTTTTT
1 -TTTTTTTT
13318413 ACGTACCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 18 0.58
13 13 0.42
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:13321714 original size:15 final size:15
Alignment explanation
Indices: 13321694--13321745 Score: 86
Period size: 15 Copynumber: 3.4 Consensus size: 15
13321684 CTTCTTCTTC
13321694 TTTTTTCACGAAATTT
1 TTTTTTCACGAAA-TT
*
13321710 TTTTTTCACGAATTT
1 TTTTTTCACGAAATT
13321725 TTTTTTCACGAAATT
1 TTTTTTCACGAAATT
13321740 TTTTTT
1 TTTTTT
13321746 TTCAACTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
15 22 0.65
16 12 0.35
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.62
Consensus pattern (15 bp):
TTTTTTCACGAAATT
Found at i:13321715 original size:16 final size:16
Alignment explanation
Indices: 13321694--13321746 Score: 99
Period size: 16 Copynumber: 3.4 Consensus size: 16
13321684 CTTCTTCTTC
13321694 TTTTTTCACGAAATTT
1 TTTTTTCACGAAATTT
13321710 TTTTTTCACG-AATTT
1 TTTTTTCACGAAATTT
13321725 TTTTTTCACGAAATTT
1 TTTTTTCACGAAATTT
13321741 TTTTTT
1 TTTTTT
13321747 TCAACTTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.42
16 21 0.58
ACGTcount: A:0.21, C:0.11, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTTTTCACGAAATTT
Found at i:13321800 original size:11 final size:12
Alignment explanation
Indices: 13321781--13321827 Score: 76
Period size: 12 Copynumber: 3.8 Consensus size: 12
13321771 ATGGAAACCA
13321781 AATTTTTTTTTG
1 AATTTTTTTTTG
13321793 AATTTTTTTTTG
1 AATTTTTTTTTG
13321805 AATTTTTTTTTTG
1 AA-TTTTTTTTTG
*
13321818 AAATTTTTTT
1 AATTTTTTTT
13321828 GAAGAAACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
12 21 0.64
13 12 0.36
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:13321830 original size:11 final size:12
Alignment explanation
Indices: 13321781--13321827 Score: 76
Period size: 13 Copynumber: 3.8 Consensus size: 12
13321771 ATGGAAACCA
13321781 AATTTTTTTTTG
1 AATTTTTTTTTG
13321793 AATTTTTTTTTG
1 AATTTTTTTTTG
13321805 AATTTTTTTTTTG
1 AA-TTTTTTTTTG
13321818 AAATTTTTTT
1 -AATTTTTTT
13321828 GAAGAAACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
12 14 0.42
13 17 0.52
14 2 0.06
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:13325642 original size:13 final size:13
Alignment explanation
Indices: 13325624--13325676 Score: 88
Period size: 13 Copynumber: 4.0 Consensus size: 13
13325614 AAACTAGCTC
13325624 TTTTTTTTCACAA
1 TTTTTTTTCACAA
13325637 TTTTTTTTCACAA
1 TTTTTTTTCACAA
*
13325650 TTTTTTTTCAAAA
1 TTTTTTTTCACAA
13325663 TTTTTTTTTCACAA
1 -TTTTTTTTCACAA
13325677 CTTGATATCC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
13 25 0.68
14 12 0.32
ACGTcount: A:0.25, C:0.13, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTTTTCACAA
Found at i:13325667 original size:27 final size:26
Alignment explanation
Indices: 13325624--13325676 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
13325614 AAACTAGCTC
*
13325624 TTTTTTTTCACAATTTTTTTTCACAA
1 TTTTTTTTCAAAATTTTTTTTCACAA
13325650 TTTTTTTTCAAAATTTTTTTTTCACAA
1 TTTTTTTTCAAAA-TTTTTTTTCACAA
13325677 CTTGATATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.25, C:0.13, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTTTTTCAAAATTTTTTTTCACAA
Found at i:13325744 original size:11 final size:12
Alignment explanation
Indices: 13325714--13325747 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
13325704 TGGAAACTAG
13325714 TTTTTTTTCGAA
1 TTTTTTTTCGAA
13325726 TTTTTTTT-GAA
1 TTTTTTTTCGAA
13325737 TTTTTTTTCGA
1 TTTTTTTTCGA
13325748 GAAACTACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.15, C:0.06, G:0.09, T:0.71
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:13328055 original size:22 final size:23
Alignment explanation
Indices: 13328024--13328066 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
13328014 ACCTTTTTGA
13328024 ACCATTACCAATTCGTACCAAAT
1 ACCATTACCAATTCGTACCAAAT
*
13328047 ACCA-TACCATTTCGTACCAA
1 ACCATTACCAATTCGTACCAA
13328067 TTCCTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.37, C:0.33, G:0.05, T:0.26
Consensus pattern (23 bp):
ACCATTACCAATTCGTACCAAAT
Found at i:13333429 original size:12 final size:12
Alignment explanation
Indices: 13333395--13333429 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
13333385 TTGTAGATTC
**
13333395 AAAAAAAAATCG
1 AAAAAAAAATTA
13333407 AAAAAAAAATTA
1 AAAAAAAAATTA
13333419 AAAAAAAAATT
1 AAAAAAAAATT
13333430 GCATACGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (12 bp):
AAAAAAAAATTA
Found at i:13353135 original size:10 final size:10
Alignment explanation
Indices: 13353119--13353176 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
13353109 CAACTTCGAC
13353119 CAGCTCAATT
1 CAGCTCAATT
* *
13353129 GAGCTCATTT
1 CAGCTCAATT
13353139 CAGCTCAA-T
1 CAGCTCAATT
13353148 CGAGCTCAATT
1 C-AGCTCAATT
*
13353159 TAGCTACAATT
1 CAGCT-CAATT
13353170 CAGCTCA
1 CAGCTCA
13353177 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:13353142 original size:20 final size:20
Alignment explanation
Indices: 13353119--13353179 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
13353109 CAACTTCGAC
13353119 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
13353139 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
13353160 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
13353180 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:13354549 original size:12 final size:11
Alignment explanation
Indices: 13354522--13354555 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
13354512 ATTGGAGTAA
*
13354522 CAAAAAAAAAT
1 CAAAAAAAATT
13354533 CAAAAAAAATT
1 CAAAAAAAATT
13354544 CGAAAAAAAATT
1 C-AAAAAAAATT
13354556 GATTGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.15
Consensus pattern (11 bp):
CAAAAAAAATT
Found at i:13354592 original size:28 final size:28
Alignment explanation
Indices: 13354534--13354593 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
13354524 AAAAAAAATC
* **
13354534 AAAAAAAATTCGAAAAAAAATTGATTGAA
1 AAAAAAAATTCGAAAAAAAAGTGA-AAAA
*
13354563 AAAAAAATTTC-AAAAAAAAGTGAAAAA
1 AAAAAAAATTCGAAAAAAAAGTGAAAAA
13354590 AAAA
1 AAAA
13354594 TCGAGCAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 6 0.22
28 11 0.41
29 10 0.37
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (28 bp):
AAAAAAAATTCGAAAAAAAAGTGAAAAA
Found at i:13354603 original size:14 final size:14
Alignment explanation
Indices: 13354586--13354624 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
13354576 AAAAAAGTGA
13354586 AAAAAAAATCGAGC
1 AAAAAAAATCGAGC
13354600 AAAAAAAAGGT-GAGC
1 AAAAAAAA--TCGAGC
13354615 AAAAAAAATC
1 AAAAAAAATC
13354625 AAGTTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.05
14 8 0.36
15 12 0.55
16 1 0.05
ACGTcount: A:0.67, C:0.10, G:0.15, T:0.08
Consensus pattern (14 bp):
AAAAAAAATCGAGC
Found at i:13354605 original size:40 final size:38
Alignment explanation
Indices: 13354523--13354607 Score: 93
Period size: 40 Copynumber: 2.2 Consensus size: 38
13354513 TTGGAGTAAC
* *
13354523 AAAAAAAAATCAAAAAAAATTCGAAAAAAAATTGATTG-A
1 AAAAAAAAATCAAAAAAAAGTCGAAAAAAAATCGA--GCA
*
13354562 AAAAAAAATTTCAAAAAAAAGT-GAAAAAAAAATCGAGCA
1 AAAAAAAA-ATCAAAAAAAAGTCG-AAAAAAAATCGAGCA
13354601 AAAAAAA
1 AAAAAAA
13354608 GGTGAGCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
38 1 0.03
39 17 0.43
40 22 0.55
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.14
Consensus pattern (38 bp):
AAAAAAAAATCAAAAAAAAGTCGAAAAAAAATCGAGCA
Found at i:13354641 original size:29 final size:26
Alignment explanation
Indices: 13354573--13354644 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 26
13354563 AAAAAAATTT
*
13354573 CAAAAAAAAGTGAAAAAAAAATCGAG
1 CAAAAAAAAGTGAAAAAAAAATCAAG
13354599 CAAAAAAAAGGTGAGCAAAAAAAATCAAG
1 CAAAAAAAA-GTGA--AAAAAAAATCAAG
*
13354628 TTAAAAAAAAGTGAAAA
1 -CAAAAAAAAGTGAAAA
13354645 GTCTTGCAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 9 0.22
27 7 0.17
29 16 0.40
30 8 0.20
ACGTcount: A:0.68, C:0.07, G:0.15, T:0.10
Consensus pattern (26 bp):
CAAAAAAAAGTGAAAAAAAAATCAAG
Found at i:13355516 original size:30 final size:29
Alignment explanation
Indices: 13355456--13355516 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 29
13355446 CGCACATTGT
*
13355456 AGTGAAAAAGAAAAAGAAATCAAAATAATG
1 AGTGAAAAAGAAAAAGAAA-CAAAAAAATG
*
13355486 AGTGAAAAAGAAAATGAAGA-AAAGAAAATG
1 AGTGAAAAAGAAAAAGAA-ACAAA-AAAATG
13355516 A
1 A
13355517 AGAAAATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 3 0.11
30 23 0.85
31 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.20, T:0.11
Consensus pattern (29 bp):
AGTGAAAAAGAAAAAGAAACAAAAAAATG
Found at i:13355533 original size:14 final size:14
Alignment explanation
Indices: 13355491--13355522 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
13355481 TAATGAGTGA
13355491 AAAAGAAAATGAAG
1 AAAAGAAAATGAAG
13355505 AAAAGAAAATGAAG
1 AAAAGAAAATGAAG
13355519 AAAA
1 AAAA
13355523 TGAATAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (14 bp):
AAAAGAAAATGAAG
Found at i:13356005 original size:21 final size:21
Alignment explanation
Indices: 13355979--13356041 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
13355969 TTGGTATTTG
13355979 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
13356000 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
13356021 GGCATTTGGTAC-AAATTGGTA
1 GG-AATTGGTACGAAA-TGGTA
13356042 ACGGTTCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.32
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:13356010 original size:11 final size:11
Alignment explanation
Indices: 13355990--13356022 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
13355980 GAATTGGTAC
13355990 GAAATGGTATG
1 GAAATGGTATG
*
13356001 GAATTGGTAT-
1 GAAATGGTATG
13356011 GAAATGGTATG
1 GAAATGGTATG
13356022 G
1 G
13356023 CATTTGGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (11 bp):
GAAATGGTATG
Found at i:13360863 original size:21 final size:21
Alignment explanation
Indices: 13360837--13360893 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
13360827 TTGGTATTTG
13360837 GGAATTGGTACGAAATGATAT
1 GGAATTGGTACGAAATGATAT
* *
13360858 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGATAT
*
13360879 GGTATTTGGTACGAA
1 GG-AATTGGTACGAA
13360894 TTGGTAACGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 21 0.68
22 10 0.32
ACGTcount: A:0.33, C:0.04, G:0.32, T:0.32
Consensus pattern (21 bp):
GGAATTGGTACGAAATGATAT
Found at i:13362777 original size:20 final size:20
Alignment explanation
Indices: 13362731--13362777 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
13362721 AGCTCGTTTC
*
13362731 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
13362751 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
13362771 CAGCTCA
1 CAGCTCA
13362778 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:13364212 original size:20 final size:20
Alignment explanation
Indices: 13364166--13364212 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
13364156 AGCTCGTTTC
*
13364166 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
13364186 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
13364206 CAGCTCA
1 CAGCTCA
13364213 AGTGAAATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:13369871 original size:24 final size:25
Alignment explanation
Indices: 13369818--13369871 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
13369808 AACAAATTCT
* *
13369818 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
13369843 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
13369866 TTTTTT
1 TTTTTT
13369872 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:13377611 original size:12 final size:12
Alignment explanation
Indices: 13377594--13377639 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
13377584 AGTTTCTTGA
13377594 AAAAAAAACTCG
1 AAAAAAAACTCG
* *
13377606 AAAAAAAATTCA
1 AAAAAAAACTCG
*
13377618 AAAAAAAATTCG
1 AAAAAAAACTCG
13377630 AAAAAAAACT
1 AAAAAAAACT
13377640 AGTTTCCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.72, C:0.11, G:0.04, T:0.13
Consensus pattern (12 bp):
AAAAAAAACTCG
Found at i:13377696 original size:13 final size:13
Alignment explanation
Indices: 13377675--13377727 Score: 88
Period size: 13 Copynumber: 4.0 Consensus size: 13
13377665 GGATATCAAG
13377675 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
*
13377688 TTTTGAAAAAAAAA
1 TTGTG-AAAAAAAA
13377702 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
13377715 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
13377728 AGAGCTAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
13 25 0.68
14 12 0.32
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.25
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:13377699 original size:14 final size:14
Alignment explanation
Indices: 13377675--13377728 Score: 85
Period size: 14 Copynumber: 4.0 Consensus size: 14
13377665 GGATATCAAG
13377675 TTGTG-AAAAAAAA
1 TTGTGAAAAAAAAA
*
13377688 TTTTGAAAAAAAAA
1 TTGTGAAAAAAAAA
13377702 TTGTG-AAAAAAAA
1 TTGTGAAAAAAAAA
13377715 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
13377729 GAGCTAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
13 17 0.46
14 20 0.54
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:13377705 original size:27 final size:27
Alignment explanation
Indices: 13377675--13377728 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
13377665 GGATATCAAG
*
13377675 TTGTGAAAAAAAATTTTGAAAAAAAAA
1 TTGTGAAAAAAAATTGTGAAAAAAAAA
13377702 TTGTGAAAAAAAATTGTGAAAAAAAAA
1 TTGTGAAAAAAAATTGTGAAAAAAAAA
13377729 GAGCTAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (27 bp):
TTGTGAAAAAAAATTGTGAAAAAAAAA
Found at i:13382755 original size:30 final size:30
Alignment explanation
Indices: 13382721--13382817 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
13382711 AGCTCACTCC
13382721 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
13382751 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
13382781 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
13382811 TAGCTCA
1 TAGCTCA
13382818 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:13387365 original size:21 final size:22
Alignment explanation
Indices: 13387322--13387370 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
13387312 TCTTTTTGGA
13387322 TTTCTTTTTCTTTTCAATCTCTT
1 TTTC-TTTTCTTTTCAATCTCTT
* *
13387345 TTTCTTTTC-TTTCGATTTCTT
1 TTTCTTTTCTTTTCAATCTCTT
13387366 TTTCT
1 TTTCT
13387371 CGCTCGTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 15 0.62
22 5 0.21
23 4 0.17
ACGTcount: A:0.06, C:0.20, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTCTTTTCTTTTCAATCTCTT
Found at i:13387833 original size:20 final size:20
Alignment explanation
Indices: 13387787--13387833 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
13387777 AGCTCGTTTC
*
13387787 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
13387807 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
13387827 CAGCTCA
1 CAGCTCA
13387834 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:13390591 original size:48 final size:47
Alignment explanation
Indices: 13390512--13390617 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
13390502 GAGTGTCATG
*
13390512 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
13390560 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
13390608 GAAAAAGAAA
1 GAAAAAGAAA
13390618 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:13392331 original size:20 final size:20
Alignment explanation
Indices: 13392285--13392331 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
13392275 AGCTCGTTTC
*
13392285 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
13392305 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
13392325 CAGCTCA
1 CAGCTCA
13392332 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:13394445 original size:13 final size:14
Alignment explanation
Indices: 13394415--13394452 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 14
13394405 TATGCAATTT
13394415 TTTTTTCTTTTCAAAA
1 TTTTTT-TTTTC-AAA
13394431 TTTTTTTTTTC-AA
1 TTTTTTTTTTCAAA
13394444 TTTTTTTTT
1 TTTTTTTTT
13394453 CGAACTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.50
15 5 0.23
16 6 0.27
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTTTTTTCAAA
Found at i:13394447 original size:12 final size:14
Alignment explanation
Indices: 13394432--13394464 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
13394422 TTTTCAAAAT
13394432 TTTTTTTTTC-AA-
1 TTTTTTTTTCGAAC
13394444 TTTTTTTTTCGAAC
1 TTTTTTTTTCGAAC
13394458 TTTTTTT
1 TTTTTTT
13394465 ACGTACCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 2 0.11
14 7 0.37
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTTTTTTTCGAAC
Found at i:13395783 original size:10 final size:10
Alignment explanation
Indices: 13395770--13395807 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
13395760 TTGTAGCTAA
13395770 ATTGAGCTCG
1 ATTGAGCTCG
13395780 ATTGAGCT-G
1 ATTGAGCTCG
13395789 ACTTGAGCTCG
1 A-TTGAGCTCG
*
13395800 AGTGAGCT
1 ATTGAGCT
13395808 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:13395787 original size:20 final size:20
Alignment explanation
Indices: 13395747--13395807 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
13395737 ACCAATAAAA
13395747 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
13395767 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
13395787 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
13395807 T
1 T
13395808 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:13395808 original size:20 final size:20
Alignment explanation
Indices: 13395771--13395808 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13395761 TGTAGCTAAA
*
13395771 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
13395791 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
13395809 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:13397050 original size:40 final size:41
Alignment explanation
Indices: 13396981--13397061 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 41
13396971 AAATTCAAAG
13396981 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
1 GGATAAGAACAAGAG-TCAAATGTTTGAATTTCAAACGTTTT
13397023 GGATAAGAACAAGA-TCAAATGTTTGAATTTCAAACGTTT
1 GGATAAGAACAAGAGTCAAATGTTTGAATTTCAAACGTTT
13397062 CACACATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 25 0.64
42 14 0.36
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.32
Consensus pattern (41 bp):
GGATAAGAACAAGAGTCAAATGTTTGAATTTCAAACGTTTT
Found at i:13404430 original size:10 final size:10
Alignment explanation
Indices: 13404415--13404476 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
13404405 TTTGAACCAT
*
13404415 TACCAATTCG
1 TACCAATTCA
*
13404425 TACCAAATACCA
1 TACC-AAT-TCA
*
13404437 TACCATTTCA
1 TACCAATTCA
13404447 TACCAATTCCA
1 TACCAATT-CA
* *
13404458 TACCATTTCG
1 TACCAATTCA
13404468 TACCAATTC
1 TACCAATTC
13404477 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:13404460 original size:21 final size:21
Alignment explanation
Indices: 13404415--13404477 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
13404405 TTTGAACCAT
* *
13404415 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
13404437 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
13404458 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
13404478 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:13407072 original size:23 final size:22
Alignment explanation
Indices: 13407020--13407072 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
13407010 TCCACGTCTT
*
13407020 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
13407042 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
13407065 TTTCTTTT
1 TTTCTTTT
13407073 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:13412508 original size:21 final size:21
Alignment explanation
Indices: 13412463--13412525 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
13412453 TTTCAACCAT
* *
13412463 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
13412485 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
13412506 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
13412526 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:13414705 original size:8 final size:9
Alignment explanation
Indices: 13414669--13414704 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
13414659 CAAAAAAATC
13414669 AGTCAAAAA
1 AGTCAAAAA
13414678 AGTCAAAAA
1 AGTCAAAAA
13414687 AGTCAAAAA
1 AGTCAAAAA
13414696 A-TCAAAAA
1 AGTCAAAAA
13414704 A
1 A
13414705 TACGAAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.69, C:0.11, G:0.08, T:0.11
Consensus pattern (9 bp):
AGTCAAAAA
Found at i:13415971 original size:27 final size:27
Alignment explanation
Indices: 13415941--13415992 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
13415931 AAAAGTGAGG
13415941 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
13415968 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
13415993 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:13418691 original size:11 final size:11
Alignment explanation
Indices: 13418675--13418708 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
13418665 AATTGTAGAT
13418675 TCAAAAAAAAA
1 TCAAAAAAAAA
*
13418686 TCAAAAAAAAT
1 TCAAAAAAAAA
*
13418697 TGAAAAAAAAA
1 TCAAAAAAAAA
13418708 T
1 T
13418709 TGCATACGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (11 bp):
TCAAAAAAAAA
Found at i:13425064 original size:30 final size:30
Alignment explanation
Indices: 13425029--13425102 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
13425019 AGTTTTTCCC
13425029 AGCTCGATTT-AGCTCACAT-GAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATCGAGCTTAATTT
* *
13425059 AGCTCGTTTGAGCTCAATCTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATCGAGCTTAATTT
13425089 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
13425103 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 5 0.12
30 35 0.88
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATCGAGCTTAATTT
Found at i:13427350 original size:10 final size:10
Alignment explanation
Indices: 13427335--13427372 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
13427325 TTGGGTTAAG
13427335 ATTGAGCTGA
1 ATTGAGCTGA
13427345 ATTGAGCTCGA
1 ATTGAGCT-GA
13427356 A-TGAGCTGA
1 ATTGAGCTGA
*
13427365 CTTGAGCT
1 ATTGAGCT
13427373 CGAGTGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.80
11 3 0.12
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:13427360 original size:20 final size:20
Alignment explanation
Indices: 13427337--13427383 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
13427327 GGGTTAAGAT
13427337 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAGCTCGAA
* *
13427357 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
13427377 TGAGCTG
1 TGAGCTG
13427384 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:13428914 original size:12 final size:12
Alignment explanation
Indices: 13428897--13428921 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13428887 TTTCACTCTT
13428897 CTCTTTTTCAAA
1 CTCTTTTTCAAA
13428909 CTCTTTTTCAAA
1 CTCTTTTTCAAA
13428921 C
1 C
13428922 CCTCTCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:13429949 original size:12 final size:12
Alignment explanation
Indices: 13429933--13430004 Score: 58
Period size: 11 Copynumber: 5.8 Consensus size: 12
13429923 TTTTTGCTCG
13429933 ATTTTTTTTTC-
1 ATTTTTTTTTCA
* *
13429944 ACTTTTTTTTGA
1 ATTTTTTTTTCA
13429956 ATTTTTTTTTCAATCA
1 A-TTTTTTTT---TCA
13429972 ATTTTTTTTTCGA
1 ATTTTTTTTTC-A
*
13429985 ATTTTTTTTT-G
1 ATTTTTTTTTCA
13429996 ATTTTTTTT
1 ATTTTTTTT
13430005 GTTACTCCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
11 18 0.36
12 3 0.06
13 18 0.36
15 8 0.16
16 3 0.06
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:13429949 original size:23 final size:23
Alignment explanation
Indices: 13429923--13429967 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
13429913 CTTTTCTTTT
13429923 TTTTTGCTCG-ATTTTTTTTTCAC
1 TTTTT-CTCGAATTTTTTTTTCAC
* *
13429946 TTTTTTTTGAATTTTTTTTTCA
1 TTTTTCTCGAATTTTTTTTTCA
13429968 ATCAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.71
Consensus pattern (23 bp):
TTTTTCTCGAATTTTTTTTTCAC
Found at i:13429962 original size:13 final size:13
Alignment explanation
Indices: 13429946--13430004 Score: 59
Period size: 12 Copynumber: 4.5 Consensus size: 13
13429936 TTTTTTTCAC
13429946 TTTTTTTTGAATT
1 TTTTTTTTGAATT
*
13429959 TTTTTTTCAATCAATT
1 TTTTTTT---TGAATT
*
13429975 TTTTTTTCGAA-T
1 TTTTTTTTGAATT
13429987 TTTTTTTTG-ATT
1 TTTTTTTTGAATT
13429999 TTTTTT
1 TTTTTT
13430005 GTTACTCCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
11 1 0.03
12 16 0.42
13 9 0.24
16 12 0.32
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.75
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:13431505 original size:20 final size:20
Alignment explanation
Indices: 13431482--13431528 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
13431472 GGGTTAAGAT
13431482 TGAGCTGAATTGAGCTCAAA
1 TGAGCTGAATTGAGCTCAAA
* * *
13431502 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCAAA
13431522 TGAGCTG
1 TGAGCTG
13431529 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAA
Found at i:13432278 original size:11 final size:11
Alignment explanation
Indices: 13432247--13432279 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
13432237 GTTCGTAATG
*
13432247 TAAAAAAAAAG
1 TAAAAAAAAAT
13432258 T-AAAAAAAAT
1 TAAAAAAAAAT
13432268 TAAAAAAAAAT
1 TAAAAAAAAAT
13432279 T
1 T
13432280 TGAGTTGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (11 bp):
TAAAAAAAAAT
Found at i:13432377 original size:10 final size:11
Alignment explanation
Indices: 13432355--13432391 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
13432345 AAAAGAGAAG
13432355 AAATTCAAAAA
1 AAATTCAAAAA
13432366 AAATTCAAAAA
1 AAATTCAAAAA
*
13432377 AAAATCGAAAAA
1 AAATTC-AAAAA
13432389 AAA
1 AAA
13432392 AGAAGTGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.14
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:13432378 original size:12 final size:12
Alignment explanation
Indices: 13432355--13432392 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
13432345 AAAAGAGAAG
13432355 AAATTC-AAAAA
1 AAATTCAAAAAA
13432366 AAATTCAAAAAA
1 AAATTCAAAAAA
13432378 AAA-TCGAAAAAA
1 AAATTC-AAAAAA
13432390 AAA
1 AAA
13432393 GAAGTGACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.13
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:13433450 original size:18 final size:18
Alignment explanation
Indices: 13433410--13433496 Score: 75
Period size: 18 Copynumber: 4.7 Consensus size: 18
13433400 GAGAGAAAAC
13433410 AAAAAGAAAAAGAAATTG
1 AAAAAGAAAAAGAAATTG
* *
13433428 CAAAAGAAAAAGAAATTT
1 AAAAAGAAAAAGAAATTG
** * **
13433446 AAAAAGTGAGAGAAAAAG
1 AAAAAGAAAAAGAAATTG
*
13433464 AAAATGAAGAAAAGAAAATTG
1 AAAAAG-A-AAAAG-AAATTG
13433485 AAAAAGAAAAAG
1 AAAAAGAAAAAG
13433497 CGAAAAAAGA
Statistics
Matches: 50, Mismatches: 16, Indels: 5
0.70 0.23 0.07
Matches are distributed among these distances:
18 32 0.64
19 5 0.10
20 4 0.08
21 9 0.18
ACGTcount: A:0.70, C:0.01, G:0.18, T:0.10
Consensus pattern (18 bp):
AAAAAGAAAAAGAAATTG
Found at i:13433478 original size:14 final size:13
Alignment explanation
Indices: 13433457--13433494 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
13433447 AAAAGTGAGA
13433457 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
13433469 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
13433484 GAAAAAGAAAA
1 GAAAAAGAAAA
13433495 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:13433508 original size:21 final size:21
Alignment explanation
Indices: 13433458--13433508 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
13433448 AAAGTGAGAG
*
13433458 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
13433479 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
13433500 AAAAAGAAA
1 AAAAAGAAA
13433509 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:13433548 original size:33 final size:33
Alignment explanation
Indices: 13433511--13433573 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
13433501 AAAAGAAATT
13433511 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
13433544 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
13433574 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:13447907 original size:90 final size:90
Alignment explanation
Indices: 13447801--13448006 Score: 274
Period size: 91 Copynumber: 2.3 Consensus size: 90
13447791 TCAGTAATAT
* * * * **
13447801 AATAATACACAGATTGATAGTTTAAGTACCACATT-GATATTTTTAAATTATAAGTATTACATTA
1 AATAATACACAAATTGATAGTTTAAGTACCACATTAGACATTTTTAAAGTACAAGTACCACATTA
*
13447865 GACATTTTATGAAAGTACAGGTACC
66 GACATTTTATGAAAGTACAAGTACC
* * *
13447890 GAATAATACTCAAATTGATAGTTTAGGTATCACATTAGACATTTTTAAAGTACAAGTACCACATT
1 -AATAATACACAAATTGATAGTTTAAGTACCACATTAGACATTTTTAAAGTACAAGTACCACATT
13447955 AGACATTTTATGAAAGTACAAGTACC
65 AGACATTTTATGAAAGTACAAGTACC
*
13447981 AA-AA-ACACAAATTGATTAGTTCAAGT
1 AATAATACACAAATTGA-TAGTTTAAGT
13448007 TAGAGGTGTT
Statistics
Matches: 101, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
88 10 0.10
89 10 0.10
90 33 0.33
91 48 0.48
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (90 bp):
AATAATACACAAATTGATAGTTTAAGTACCACATTAGACATTTTTAAAGTACAAGTACCACATTA
GACATTTTATGAAAGTACAAGTACC
Found at i:13447962 original size:29 final size:31
Alignment explanation
Indices: 13447920--13447981 Score: 110
Period size: 29 Copynumber: 2.1 Consensus size: 31
13447910 GTTTAGGTAT
13447920 CACATTAGACATTTT-T-AAAGTACAAGTAC
1 CACATTAGACATTTTATGAAAGTACAAGTAC
13447949 CACATTAGACATTTTATGAAAGTACAAGTAC
1 CACATTAGACATTTTATGAAAGTACAAGTAC
13447980 CA
1 CA
13447982 AAAACACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 15 0.48
30 1 0.03
31 15 0.48
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (31 bp):
CACATTAGACATTTTATGAAAGTACAAGTAC
Found at i:13448237 original size:32 final size:32
Alignment explanation
Indices: 13448201--13448263 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
13448191 CCAATATAAT
*
13448201 AAATATATTTTTTTTATTT-TAAAAATATTTTA
1 AAATA-ATTTTTTTAATTTCTAAAAATATTTTA
* *
13448233 AAATACTTTTTTTAATTTCTAAAAATTTTTT
1 AAATAATTTTTTTAATTTCTAAAAATATTTT
13448264 TGGTGTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (32 bp):
AAATAATTTTTTTAATTTCTAAAAATATTTTA
Found at i:13448243 original size:31 final size:32
Alignment explanation
Indices: 13448200--13448263 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
13448190 GCCAATATAA
*
13448200 TAAATATATTTTTTTTATTT-TAAAAATATTT
1 TAAATATATTTTTTTAATTTCTAAAAATATTT
*
13448231 TAAA-ATACTTTTTTTAATTTCTAAAAATTTTT
1 TAAATATA-TTTTTTTAATTTCTAAAAATATTT
13448263 T
1 T
13448264 TGGTGTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 3 0.10
31 15 0.52
32 11 0.38
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (32 bp):
TAAATATATTTTTTTAATTTCTAAAAATATTT
Found at i:13449356 original size:3 final size:3
Alignment explanation
Indices: 13449348--13449372 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13449338 AAATCGTGAT
13449348 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
13449373 GCTTAAGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:13449749 original size:21 final size:22
Alignment explanation
Indices: 13449725--13449770 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
13449715 AAATTAGAAT
*
13449725 TTTTTTGTAAAA-ATTGTAAAA
1 TTTTTTATAAAATATTGTAAAA
13449746 TTTTTTATAAAATATTGTAAAA
1 TTTTTTATAAAATATTGTAAAA
13449768 TTT
1 TTT
13449771 AATAAAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
TTTTTTATAAAATATTGTAAAA
Found at i:13449750 original size:22 final size:23
Alignment explanation
Indices: 13449722--13449770 Score: 75
Period size: 21 Copynumber: 2.2 Consensus size: 23
13449712 TAAAAATTAG
*
13449722 AATTTTTTTGTAAAA-ATTGTAA
1 AATTTTTTTATAAAATATTGTAA
13449744 AA-TTTTTTATAAAATATTGTAA
1 AATTTTTTTATAAAATATTGTAA
13449766 AATTT
1 AATTT
13449771 AATAAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 11 0.46
22 11 0.46
23 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (23 bp):
AATTTTTTTATAAAATATTGTAA
Found at i:13450165 original size:20 final size:20
Alignment explanation
Indices: 13450114--13450155 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
13450104 TTTAGAAAAA
13450114 TTACAATTTTTATAATTTTT
1 TTACAATTTTTATAATTTTT
13450134 TTACAATTTTTATAATTTTT
1 TTACAATTTTTATAATTTTT
13450154 TT
1 TT
13450156 CTAGTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TTACAATTTTTATAATTTTT
Found at i:13450508 original size:92 final size:90
Alignment explanation
Indices: 13450354--13450520 Score: 221
Period size: 92 Copynumber: 1.8 Consensus size: 90
13450344 AATTAATTGC
* *
13450354 TTTTTGAAAAAGTTTGAAGGCCTTTTGATGCATTTCAAAAGTCCAAGTACCCAATTGGATGCAAA
1 TTTTTGAAAAAGTTTGAAGGCCTTTTGATGCATTTCAAAAGTCCAAGTACCCAAGTGAATGCAAA
13450419 AAAAAGTGGGGGATTAAGTGCTTTTT
66 AAAAAG-GGGGGATTAAGTGCTTTTT
* * * *
13450445 TTTTTGAAAAAGTTT-TAGGACCTTTTTGATGTATTGTGAAAA-TTCAAGTACCCAAGTGAATGC
1 TTTTTGAAAAAGTTTGAAGG-CC-TTTTGATGCATT-TCAAAAGTCCAAGTACCCAAGTGAATGC
*
13450508 AAAAAGAAGGGGG
63 AAAAAAAAGGGGG
13450521 TTTAATTACT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
90 3 0.05
91 21 0.32
92 37 0.56
93 5 0.08
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (90 bp):
TTTTTGAAAAAGTTTGAAGGCCTTTTGATGCATTTCAAAAGTCCAAGTACCCAAGTGAATGCAAA
AAAAAGGGGGGATTAAGTGCTTTTT
Found at i:13452206 original size:25 final size:24
Alignment explanation
Indices: 13452177--13452223 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
13452167 AAAATGTCAT
*
13452177 TAAAATAATAATAGTAGTCATTTAA
1 TAAAAGAAT-ATAGTAGTCATTTAA
* *
13452202 TAAAAGGATATATTAGTCATTT
1 TAAAAGAATATAGTAGTCATTT
13452224 CCTAACTGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (24 bp):
TAAAAGAATATAGTAGTCATTTAA
Found at i:13454479 original size:31 final size:31
Alignment explanation
Indices: 13454435--13454571 Score: 111
Period size: 31 Copynumber: 4.5 Consensus size: 31
13454425 GAACATTTTC
*
13454435 AAAGTATAAGTACCACATTAGACATTTTATG
1 AAAGTACAAGTACCACATTAGACATTTTATG
* * * * **
13454466 AAAGTACATGTACCAAATAATACA-TAAATTG
1 AAAGTACAAGTACCACATTAGACATTTTA-TG
* * * *
13454497 ATAGTTCAAGTATCACATTAGACATTTT-TT
1 AAAGTACAAGTACCACATTAGACATTTTATG
* *
13454527 AAA-TACAAATACCACATCA-AGCATTTTATG
1 AAAGTACAAGTACCACATTAGA-CATTTTATG
13454557 AAAGTACAAGTACCA
1 AAAGTACAAGTACCA
13454572 AATAAAACAC
Statistics
Matches: 77, Mismatches: 24, Indels: 10
0.69 0.22 0.09
Matches are distributed among these distances:
28 1 0.01
29 18 0.23
30 9 0.12
31 48 0.62
32 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (31 bp):
AAAGTACAAGTACCACATTAGACATTTTATG
Found at i:13454487 original size:91 final size:91
Alignment explanation
Indices: 13454383--13454614 Score: 254
Period size: 91 Copynumber: 2.5 Consensus size: 91
13454373 TTAACTTTAG
* * * * *
13454383 GTACCATAATAATACACAAATTGATAGTTTAGGCACCCCATT-GAACA-TTTTCAAAGTATAAGT
1 GTACCA-AATAATACACAAATTGATAGTTCAAGCACCACATTAG-ACATTTTTCAAA-TACAAAT
* *
13454446 ACCACAT-TAGACATTTTATGAAAGTACAT
63 ACCACATCAAG-CATTTTATGAAAGTACAA
* * * *
13454475 GTACCAAATAATACATAAATTGATAGTTCAAGTATCACATTAGACATTTTTTAAATACAAATACC
1 GTACCAAATAATACACAAATTGATAGTTCAAGCACCACATTAGACATTTTTCAAATACAAATACC
13454540 ACATCAAGCATTTTATGAAAGTACAA
66 ACATCAAGCATTTTATGAAAGTACAA
* ** * * *
13454566 GTACCAAATAAAACACAAATAAATAGTTCAAGTATCACATTAGATATTT
1 GTACCAAATAATACACAAATTGATAGTTCAAGCACCACATTAGACATTT
13454615 CAATATTTTA
Statistics
Matches: 121, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
91 105 0.87
92 16 0.13
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (91 bp):
GTACCAAATAATACACAAATTGATAGTTCAAGCACCACATTAGACATTTTTCAAATACAAATACC
ACATCAAGCATTTTATGAAAGTACAA
Found at i:13455772 original size:18 final size:17
Alignment explanation
Indices: 13455751--13455796 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
13455741 AGTAGAATCA
13455751 TATTATTTGTTCCAACGT
1 TATTATTT-TTCCAACGT
13455769 TATTA-TTTTCTCAACGT
1 TATTATTTTTC-CAACGT
13455786 TA-TATTTTTCC
1 TATTATTTTTCC
13455797 TATTTTTGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.23
17 15 0.58
18 5 0.19
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.54
Consensus pattern (17 bp):
TATTATTTTTCCAACGT
Found at i:13456163 original size:358 final size:357
Alignment explanation
Indices: 13455679--13456326 Score: 809
Period size: 358 Copynumber: 1.8 Consensus size: 357
13455669 TTTTTTTTAA
*
13455679 TTTTTTACTATTTTAGTCAAACAAACTTCCTGAATTTTCTCAGGTTTCTAACGTTATTAACCAGT
1 TTTTTTACTATTTTAGTCAAACAAACTTCCTGAATTTTCTCAGGTTTCTAACGTTATTAACCAGC
* * * *
13455744 AGAATCATATTATTTGTTCCAACGTTATTATTTTCTCAACGTTATATTTTTCCTATTTTTGGCAT
66 AGAATCAAATTATTTATTCCAACGTTATTAGTTTCTCAACGTTATACTTTTCCTATTTTTGGCAT
** * * * * * * *
13455809 GCATTGTACCTGTAAATACTATGCATGACTGTACTTCAGAATCACACAACTTGTAAATTATTCAT
131 GCACGGTACATATAAAAACCATGCATGACTGCACTTCAGAATCACACAACCTATAAATTATTCAT
* ** * *
13455874 CTTCACTCTCAAAGCTTTCTACCTTCTCAAATCTTTC-TCCCTCAATTCCAGTTGAGTATTTTAT
196 CTTCACTCCCAAAGCTTTCTACCTTCTCAAAGATTTCTTCCC-CAATTCCAGCTGAGTATTTAAT
* *
13455938 T-GCTTTGTTCTTCCTTGTTTCTTGTTTTCCTTCAGTTAATAAATCTGCTTGTTGAATCCTTGAG
260 TAG-TTTGTTCTTCCTT-TTCCATGTTTTCCTTCAGTTAATAAATCTGCTTGTTGAATCCTTGAG
13456002 GATAAGCGGATTTGTTTTTTTTTTCTGTATTATTT
323 GATAAGCGGATTTGTTTTTTTTTTCTGTATTATTT
* ** * * * *
13456037 TTTTTTCCTATTTTAGTCAAACAAGGTTCCTTAATTTTCTTAGATTTTCTAACGTTATTAACTAG
1 TTTTTTACTATTTTAGTCAAACAAACTTCCTGAATTTTCTCAG-GTTTCTAACGTTATTAACCAG
* **
13456102 CAGAATCAAATT-TTCTATTCCAACGTTATT-GTTTCTTATTGTTATACTTTTCCTATTTTTGGC
65 CAGAATCAAATTATT-TATTCCAACGTTATTAGTTTCTCAACGTTATACTTTTCCTATTTTTGGC
* * * * * * * *
13456165 ATGGACGGTATATATAAAAACCATGCATGATTGCATTTCAGAATTACTCAACCTATGAATTGTTC
129 ATGCACGGTACATATAAAAACCATGCATGACTGCACTTCAGAATCACACAACCTATAAATTATTC
* * * * ***
13456230 ATCTTCTCTCCCAACGCTTTTTGCCTTCTCAAAGATTTCTTCCCCAATTTTGGCTGAGTATTTAA
194 ATCTTCACTCCCAAAGCTTTCTACCTTCTCAAAGATTTCTTCCCCAATTCCAGCTGAGTATTTAA
13456295 TTAGTTTGTTCTTCCTTTTCCATGTTTTCCTT
259 TTAGTTTGTTCTTCCTTTTCCATGTTTTCCTT
13456327 AAATTAACAA
Statistics
Matches: 240, Mismatches: 46, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
357 13 0.05
358 179 0.75
359 48 0.20
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46
Consensus pattern (357 bp):
TTTTTTACTATTTTAGTCAAACAAACTTCCTGAATTTTCTCAGGTTTCTAACGTTATTAACCAGC
AGAATCAAATTATTTATTCCAACGTTATTAGTTTCTCAACGTTATACTTTTCCTATTTTTGGCAT
GCACGGTACATATAAAAACCATGCATGACTGCACTTCAGAATCACACAACCTATAAATTATTCAT
CTTCACTCCCAAAGCTTTCTACCTTCTCAAAGATTTCTTCCCCAATTCCAGCTGAGTATTTAATT
AGTTTGTTCTTCCTTTTCCATGTTTTCCTTCAGTTAATAAATCTGCTTGTTGAATCCTTGAGGAT
AAGCGGATTTGTTTTTTTTTTCTGTATTATTT
Found at i:13462575 original size:213 final size:213
Alignment explanation
Indices: 13462208--13462629 Score: 729
Period size: 213 Copynumber: 2.0 Consensus size: 213
13462198 ATTTAGCTGG
* *
13462208 CAAAACAGTATTAAGTGAGATGTCGAGGACTAATCCATAATTTTTCCTTTTCCTCAATTAACTTC
1 CAAAACAGTATTAAGCGAGATGTCGAGGACTAATCCACAATTTTTCCTTTTCCTCAATTAACTTC
** * *
13462273 TGATTGATTCAAATATTGATCTAAATGTTAATCCATTTCAATTTATCCGTTTTAAATACCTTATA
66 TGATTGATTCAAATATTGATCTAAACATTAATCCATTTCAATTTATCAGTTTCAAATACCTTATA
13462338 ACAGTTTATTTTATGATTATGAAAATTTCACAAATTAATCCTTAGGCTAACTAAATCAAGCTCCC
131 ACAGTTTATTTTATGATTATGAAAATTTCACAAATTAATCCTTAGGCTAACTAAATCAAGCTCCC
13462403 AAGGTCTCAAAAATTTCA
196 AAGGTCTCAAAAATTTCA
* ** *
13462421 CAAAACAGTATTAAGCGAGATGTTGAGGACTAATCCACAATTTTTCCTTTTCCTTGATTAACTTT
1 CAAAACAGTATTAAGCGAGATGTCGAGGACTAATCCACAATTTTTCCTTTTCCTCAATTAACTTC
13462486 TGATTGATTCAAATATTGATCTAAACATTAATCCATTTCAATTTATCAGTTTCAAATACCTTATA
66 TGATTGATTCAAATATTGATCTAAACATTAATCCATTTCAATTTATCAGTTTCAAATACCTTATA
*
13462551 ACAGTTTATTTTATGCA-TATGAAAATTTCACAAATTAATCCTTAGGCTAACTAAATCAAGCTTC
131 ACAGTTTATTTTATG-ATTATGAAAATTTCACAAATTAATCCTTAGGCTAACTAAATCAAGCTCC
13462615 CAAGGTCTCAAAAAT
195 CAAGGTCTCAAAAAT
13462630 ATAAAAATTA
Statistics
Matches: 197, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
213 196 0.99
214 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (213 bp):
CAAAACAGTATTAAGCGAGATGTCGAGGACTAATCCACAATTTTTCCTTTTCCTCAATTAACTTC
TGATTGATTCAAATATTGATCTAAACATTAATCCATTTCAATTTATCAGTTTCAAATACCTTATA
ACAGTTTATTTTATGATTATGAAAATTTCACAAATTAATCCTTAGGCTAACTAAATCAAGCTCCC
AAGGTCTCAAAAATTTCA
Found at i:13464652 original size:17 final size:16
Alignment explanation
Indices: 13464625--13464658 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
13464615 TCTGAAAAAA
*
13464625 ACAAAAGAAATATCTC
1 ACAAAAGAAATAACTC
13464641 ACAAAGAGAAATAACTC
1 ACAAA-AGAAATAACTC
13464658 A
1 A
13464659 AAGAGTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.59, C:0.18, G:0.09, T:0.15
Consensus pattern (16 bp):
ACAAAAGAAATAACTC
Found at i:13469221 original size:55 final size:55
Alignment explanation
Indices: 13469137--13469246 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
13469127 TGTTTTTCTT
13469137 ATTTTTATAAAATAGCTTTTCTCATCACCTTAGGATTAATCGTAATATAATTTAA
1 ATTTTTATAAAATAGCTTTTCTCATCACCTTAGGATTAATCGTAATATAATTTAA
*
13469192 ATTTTTATAAAATATCTTTTCTCATCACCTTAGGATTAATCGTAATATAATTTAA
1 ATTTTTATAAAATAGCTTTTCTCATCACCTTAGGATTAATCGTAATATAATTTAA
13469247 TTAAATTATT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (55 bp):
ATTTTTATAAAATAGCTTTTCTCATCACCTTAGGATTAATCGTAATATAATTTAA
Found at i:13475554 original size:27 final size:26
Alignment explanation
Indices: 13475496--13475556 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
13475486 CCTAAATATT
* *
13475496 AGATAGTCTTCACAAACTTCCACTAA
1 AGATAGTCTTCAAAAACTTCCACCAA
* * *
13475522 AAATAGTCTTGATAAAATTTCCACCAA
1 AGATAGTCTTCA-AAAACTTCCACCAA
13475549 AGATAGTC
1 AGATAGTC
13475557 CTGACGGATT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (26 bp):
AGATAGTCTTCAAAAACTTCCACCAA
Found at i:13479138 original size:11 final size:11
Alignment explanation
Indices: 13479097--13479138 Score: 66
Period size: 12 Copynumber: 3.6 Consensus size: 11
13479087 TCCCAGCATT
13479097 AAAAAAATCAA
1 AAAAAAATCAA
13479108 GAAAAAAATTCAA
1 -AAAAAAA-TCAA
13479121 AAAAAAATCAA
1 AAAAAAATCAA
13479132 AAAAAAA
1 AAAAAAA
13479139 GTGGGAGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.38
12 14 0.48
13 4 0.14
ACGTcount: A:0.81, C:0.07, G:0.02, T:0.10
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:13479515 original size:19 final size:19
Alignment explanation
Indices: 13479491--13479528 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
13479481 TTTTGAATTG
13479491 GTGAGATTCATTTACTATT
1 GTGAGATTCATTTACTATT
13479510 GTGAGATTCATTTACTATT
1 GTGAGATTCATTTACTATT
13479529 TATTCTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (19 bp):
GTGAGATTCATTTACTATT
Found at i:13480196 original size:13 final size:12
Alignment explanation
Indices: 13480178--13480219 Score: 54
Period size: 10 Copynumber: 3.7 Consensus size: 12
13480168 TGTGAGCGAG
13480178 AAAAGAACATTGA
1 AAAAGAA-ATTGA
13480191 AAAAGAAATTG-
1 AAAAGAAATTGA
13480202 -AAAGAAA-TGA
1 AAAAGAAATTGA
13480212 AAAAGAAA
1 AAAAGAAA
13480220 AAGATGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.07
10 7 0.26
11 7 0.26
12 4 0.15
13 7 0.26
ACGTcount: A:0.69, C:0.02, G:0.17, T:0.12
Consensus pattern (12 bp):
AAAAGAAATTGA
Found at i:13480279 original size:12 final size:12
Alignment explanation
Indices: 13480262--13480339 Score: 54
Period size: 12 Copynumber: 6.4 Consensus size: 12
13480252 AGTGAAAAGC
13480262 AAAAAGAGATTG
1 AAAAAGAGATTG
*
13480274 AAAAAGAAATTG
1 AAAAAGAGATTG
*
13480286 --AAAGAGA-AG
1 AAAAAGAGATTG
*
13480295 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
13480310 AAAAAGAAATTG
1 AAAAAGAGATTG
*
13480322 AAAAAGAGTTTG
1 AAAAAGAGATTG
13480334 TAAAAA
1 -AAAAA
13480340 AAACGAGTGA
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
9 1 0.02
10 6 0.12
11 4 0.08
12 23 0.45
13 10 0.20
15 7 0.14
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.14
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:13480303 original size:15 final size:15
Alignment explanation
Indices: 13480285--13480318 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
13480275 AAAAGAAATT
13480285 GAAAGAGAAGAAAAA
1 GAAAGAGAAGAAAAA
**
13480300 GAAAGAGTGGAAAAA
1 GAAAGAGAAGAAAAA
13480315 GAAA
1 GAAA
13480319 TTGAAAAAGA
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:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
GAAAGAGAAGAAAAA
Found at i:13480324 original size:21 final size:20
Alignment explanation
Indices: 13480272--13480324 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 20
13480262 AAAAAGAGAT
13480272 TGAAAAAGAAATTGAAAGA-
1 TGAAAAAGAAATTGAAAGAG
*
13480291 -GAAGAA-AAA--GAAAGAG
1 TGAAAAAGAAATTGAAAGAG
13480307 TGGAAAAAGAAATTGAAA
1 T-GAAAAAGAAATTGAAA
13480325 AAGAGTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
15 6 0.23
17 3 0.12
18 10 0.38
19 3 0.12
21 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11
Consensus pattern (20 bp):
TGAAAAAGAAATTGAAAGAG
Found at i:13488650 original size:9 final size:9
Alignment explanation
Indices: 13488633--13488669 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
13488623 TGAGTTTTCG
13488633 AATTCGAAT
1 AATTCGAAT
*
13488642 AACTCGAAT
1 AATTCGAAT
*
13488651 AATTTGAAT
1 AATTCGAAT
13488660 AATTCGAAT
1 AATTCGAAT
13488669 A
1 A
13488670 TCACACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:13488915 original size:30 final size:31
Alignment explanation
Indices: 13488881--13488940 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
13488871 AAACCTTTTA
*
13488881 TTTTCCCCCAAAATTTTTACT-CCTTCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
13488911 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
13488941 TCCCATCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:13489598 original size:5 final size:5
Alignment explanation
Indices: 13489588--13489613 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
13489578 GAACAAATAT
13489588 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
13489614 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:13490252 original size:25 final size:25
Alignment explanation
Indices: 13490211--13490388 Score: 164
Period size: 25 Copynumber: 7.1 Consensus size: 25
13490201 TCATTAGGGT
*
13490211 TACCAATTTATAA-CTCGTAAGAGCA
1 TACCGATTTA-AAGCTCGTAAGAGCA
**
13490236 TATTGATTTAAAGCTCGTAAGAGCA
1 TACCGATTTAAAGCTCGTAAGAGCA
* *
13490261 TAACGATTTAAAGATCGTAAGAGCA
1 TACCGATTTAAAGCTCGTAAGAGCA
*
13490286 TACCGATTTATAGCTCGTAAGAGCA
1 TACCGATTTAAAGCTCGTAAGAGCA
* * * *
13490311 TACTGGTTTATAGCTCGTGAGAGCA
1 TACCGATTTAAAGCTCGTAAGAGCA
* * *
13490336 TACCGATCTT-CAGCTC-AAATGGGCA
1 TACCGAT-TTAAAGCTCGTAA-GAGCA
* * *
13490361 TACCGATTCATAGCTCGTATGAGCA
1 TACCGATTTAAAGCTCGTAAGAGCA
13490386 TAC
1 TAC
13490389 ATGTACATGA
Statistics
Matches: 125, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
24 4 0.03
25 118 0.94
26 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (25 bp):
TACCGATTTAAAGCTCGTAAGAGCA
Found at i:13490362 original size:75 final size:75
Alignment explanation
Indices: 13490211--13490388 Score: 207
Period size: 75 Copynumber: 2.4 Consensus size: 75
13490201 TCATTAGGGT
* * *
13490211 TACCAATTTATAACTCGTAAGAGCATATTGATTTAAAGCTCGTAAGAGCATAACGATTTAAAGAT
1 TACCGATTTATAGCTCGTAAGAGCATACTGATTTAAAGCTCGTAAGAGCATAACGATTTAAAGAT
*
13490276 CGTAAGAGCA
66 CGAAAGAGCA
* * * * * *
13490286 TACCGATTTATAGCTCGTAAGAGCATACTGGTTTATAGCTCGTGAGAGCATACCGATCTT-CAGC
1 TACCGATTTATAGCTCGTAAGAGCATACTGATTTAAAGCTCGTAAGAGCATAACGAT-TTAAAGA
*
13490350 TC-AAATGGGCA
65 TCGAAA-GAGCA
* *
13490361 TACCGATTCATAGCTCGTATGAGCATAC
1 TACCGATTTATAGCTCGTAAGAGCATAC
13490389 ATGTACATGA
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
74 2 0.02
75 84 0.95
76 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (75 bp):
TACCGATTTATAGCTCGTAAGAGCATACTGATTTAAAGCTCGTAAGAGCATAACGATTTAAAGAT
CGAAAGAGCA
Found at i:13491983 original size:21 final size:21
Alignment explanation
Indices: 13491944--13491984 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13491934 TGTTTTAAGG
*
13491944 TTATTTTGATATCTTTAAAAT
1 TTATTTTGATATCTCTAAAAT
13491965 TTATATTTGATAT-TCTAAAA
1 TTAT-TTTGATATCTCTAAAA
13491985 AGTCATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (21 bp):
TTATTTTGATATCTCTAAAAT
Found at i:13491985 original size:22 final size:21
Alignment explanation
Indices: 13491944--13491985 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
13491934 TGTTTTAAGG
*
13491944 TTATTTTGATATCTTTAAAAT
1 TTATTTTGATATCTTAAAAAT
13491965 TTATATTTGATAT-TCTAAAAA
1 TTAT-TTTGATATCT-TAAAAA
13491986 GTCATTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (21 bp):
TTATTTTGATATCTTAAAAAT
Found at i:13494839 original size:20 final size:20
Alignment explanation
Indices: 13494771--13494841 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
13494761 ATTGCACTTT
* *
13494771 GGTGCATCTGCTTGCACTAC
1 GGTGCCTCTGTTTGCACTAC
* * ** *
13494791 AGTGCCTCTATTCACACTTC
1 GGTGCCTCTGTTTGCACTAC
* *
13494811 GATGTCTCTGTTTGCACTAC
1 GGTGCCTCTGTTTGCACTAC
13494831 GGTGCCTCTGT
1 GGTGCCTCTGT
13494842 ACAGGATTAC
Statistics
Matches: 35, Mismatches: 16, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.14, C:0.30, G:0.21, T:0.35
Consensus pattern (20 bp):
GGTGCCTCTGTTTGCACTAC
Done.