Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 114 of 230
Found at i:33149784 original size:20 final size:20
Alignment explanation
Indices: 33149761--33149814 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
33149751 AGTTTTTCCC
*
33149761 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
33149781 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
33149801 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
33149815 TACTTTAGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:33155345 original size:17 final size:18
Alignment explanation
Indices: 33155306--33155347 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
33155296 AAGAAGAAAA
33155306 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
33155323 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
33155340 TCAAAAGA
1 ACAAAAGA
33155348 AAAAGAAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:33162606 original size:19 final size:19
Alignment explanation
Indices: 33162582--33162620 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
33162572 AATAAATTAC
*
33162582 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTAAGT
33162601 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
33162620 T
1 T
33162621 GCTGGAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:33162645 original size:35 final size:35
Alignment explanation
Indices: 33162601--33162690 Score: 162
Period size: 35 Copynumber: 2.6 Consensus size: 35
33162591 TTAATTGAGT
* *
33162601 TCATCTTAGTTAATTAAGTTGCTGGAATAATTTAC
1 TCATCTTAGTTAATTAAGTTACTGGAATAAATTAC
33162636 TCATCTTAGTTAATTAAGTTACTGGAATAAATTAC
1 TCATCTTAGTTAATTAAGTTACTGGAATAAATTAC
33162671 TCATCTTAGTTAATTAAGTT
1 TCATCTTAGTTAATTAAGTT
33162691 CAACTTAGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.43
Consensus pattern (35 bp):
TCATCTTAGTTAATTAAGTTACTGGAATAAATTAC
Found at i:33162975 original size:20 final size:20
Alignment explanation
Indices: 33162938--33162975 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
33162928 GTTACGAAGA
**
33162938 TTGAATTAAAGGTTAACAAG
1 TTGAATTAAAGGCCAACAAG
33162958 TTGAATTAAAGGCCAACA
1 TTGAATTAAAGGCCAACA
33162976 GCTGTTATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (20 bp):
TTGAATTAAAGGCCAACAAG
Found at i:33164844 original size:20 final size:20
Alignment explanation
Indices: 33164821--33164867 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33164811 GGGTTAAGAT
*
33164821 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
33164841 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
33164861 TGAGCTG
1 TGAGCTG
33164868 GAAACGAGCT
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:33168348 original size:12 final size:13
Alignment explanation
Indices: 33168331--33168405 Score: 71
Period size: 13 Copynumber: 5.5 Consensus size: 13
33168321 TTGGAGTAAC
33168331 AAAAAAAA-TCAA
1 AAAAAAAATTCAA
33168343 AAAAAAAATTCGAAA
1 AAAAAAAATTC--AA
*
33168358 AAAAAAAATTGATTGA
1 AAAAAAAATTCA---A
33168374 AAAAAAAATTCAA
1 AAAAAAAATTCAA
* *
33168387 AAAAAAAAGTGAA
1 AAAAAAAATTCAA
33168400 AAAAAA
1 AAAAAA
33168406 TCGAGCAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
12 8 0.15
13 21 0.40
15 12 0.23
16 12 0.23
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:33168402 original size:14 final size:14
Alignment explanation
Indices: 33168341--33168405 Score: 69
Period size: 15 Copynumber: 4.5 Consensus size: 14
33168331 AAAAAAAATC
33168341 AAAAAAAAAATTCGA
1 AAAAAAAAAATT-GA
33168356 AAAAAAAAAATTGA
1 AAAAAAAAAATTGA
* *
33168370 TTGAAAAAAAAATT-C
1 --AAAAAAAAAATTGA
*
33168385 AAAAAAAAAAGTGA
1 AAAAAAAAAATTGA
33168399 AAAAAAA
1 AAAAAAA
33168406 TCGAGCAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
13 10 0.24
14 9 0.21
15 12 0.29
16 11 0.26
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAATTGA
Found at i:33168416 original size:15 final size:15
Alignment explanation
Indices: 33168398--33168438 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
33168388 AAAAAAAGTG
33168398 AAAAAAAATCGAGCA
1 AAAAAAAATCGAGCA
33168413 AAAAAAAAGGT-GAGCA
1 AAAAAAAA--TCGAGCA
33168429 AAAAAAAATC
1 AAAAAAAATC
33168439 AAGTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.04
15 8 0.35
16 13 0.57
17 1 0.04
ACGTcount: A:0.68, C:0.10, G:0.15, T:0.07
Consensus pattern (15 bp):
AAAAAAAATCGAGCA
Found at i:33169506 original size:17 final size:18
Alignment explanation
Indices: 33169473--33169507 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
33169463 AAAAAGAGAG
*
33169473 TGAGATTGAAGGAAGAAA
1 TGAGAGTGAAGGAAGAAA
33169491 TGAGAGTGAA-GAAGAAA
1 TGAGAGTGAAGGAAGAAA
33169508 GGAGTGTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.51, C:0.00, G:0.34, T:0.14
Consensus pattern (18 bp):
TGAGAGTGAAGGAAGAAA
Found at i:33173540 original size:48 final size:48
Alignment explanation
Indices: 33173484--33173588 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
33173474 TTGTCTTTTC
*
33173484 TTTC-TTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
33173531 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
33173579 TTTCTTTTTC
1 TTTCTTTTTC
33173589 CATGACACTC
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
47 4 0.08
48 35 0.69
49 8 0.16
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:33176235 original size:20 final size:20
Alignment explanation
Indices: 33176212--33176258 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
33176202 GGGTTAAGAT
**
33176212 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCAAG
* *
33176232 TGAGTTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
33176252 TGAGCTG
1 TGAGCTG
33176259 GAAACGAGCT
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:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:33181501 original size:34 final size:33
Alignment explanation
Indices: 33181437--33181502 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
33181427 TTAAAGATGT
* *
33181437 TGTTCTACATGAATGGAACGGCAATTAATGAGA
1 TGTTCCACATGAATGGAACGACAATTAATGAGA
*
33181470 TGTTCCACATGCAATGG-ACGACATTTAAATGAG
1 TGTTCCACATG-AATGGAACGACAATT-AATGAG
33181503 GGAGAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 17 0.61
34 11 0.39
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (33 bp):
TGTTCCACATGAATGGAACGACAATTAATGAGA
Found at i:33187026 original size:30 final size:30
Alignment explanation
Indices: 33186940--33187027 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
33186930 CTACCTCATA
33186940 TTTAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTTAGCTCACGAGCTAAACCTTAGCTCAAC
* * * * * * *
33186970 TTCAGCTTAGGAGTTTAGCCTCAGCTCAAC
1 TTTAGCTCACGAGCTAAACCTTAGCTCAAC
*
33187000 TTTAGCTCACGAGCTAAAACTTAGCTCA
1 TTTAGCTCACGAGCTAAACCTTAGCTCA
33187028 TTTTAGTTTA
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.28
Consensus pattern (30 bp):
TTTAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:33188647 original size:13 final size:12
Alignment explanation
Indices: 33188629--33188662 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
33188619 GTTCGTAACG
*
33188629 AAAAAAAACAGTC
1 AAAAAAAA-AATC
33188642 AAAAAAAAAATC
1 AAAAAAAAAATC
33188654 AAAAAAAAA
1 AAAAAAAAA
33188663 TTTTGAGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.82, C:0.09, G:0.03, T:0.06
Consensus pattern (12 bp):
AAAAAAAAAATC
Found at i:33188776 original size:11 final size:11
Alignment explanation
Indices: 33188752--33188789 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
33188742 GAAATTCAGA
*
33188752 AAAAAAAAT-A
1 AAAAAAAATCG
33188762 AAAAAAAATCG
1 AAAAAAAATCG
33188773 AAAAAAAA-CG
1 AAAAAAAATCG
33188783 AAAAAAA
1 AAAAAAA
33188790 GTGACAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 18 0.69
11 8 0.31
ACGTcount: A:0.84, C:0.05, G:0.05, T:0.05
Consensus pattern (11 bp):
AAAAAAAATCG
Found at i:33189770 original size:37 final size:37
Alignment explanation
Indices: 33189719--33189789 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
33189709 CATTCTTGTA
33189719 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
33189756 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
33189790 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:33189789 original size:6 final size:6
Alignment explanation
Indices: 33189729--33189778 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
33189719 AAGAGAAAAC
*
33189729 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
33189778 A
1 A
33189779 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:33189871 original size:11 final size:12
Alignment explanation
Indices: 33189839--33189869 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
33189829 TTGAGAGAAC
33189839 TTGAAAAAGCCT
1 TTGAAAAAGCCT
33189851 TTGAAAAAGCCT
1 TTGAAAAAGCCT
33189863 TTGAAAA
1 TTGAAAA
33189870 GCAAAAAGAA
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:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:33189896 original size:30 final size:32
Alignment explanation
Indices: 33189862--33189928 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 32
33189852 TGAAAAAGCC
33189862 TTTGAAAAG-CAAAAAGAAAATG-AAAAGAAA
1 TTTGAAAAGTCAAAAAGAAAATGAAAAAGAAA
* * *
33189892 TTTG-AGAGTGAAAAAGAAGATGAAAAAGAAA
1 TTTGAAAAGTCAAAAAGAAAATGAAAAAGAAA
33189923 -TTGAAA
1 TTTGAAA
33189929 CAAAAGAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
29 3 0.10
30 18 0.60
31 9 0.30
ACGTcount: A:0.61, C:0.01, G:0.21, T:0.16
Consensus pattern (32 bp):
TTTGAAAAGTCAAAAAGAAAATGAAAAAGAAA
Found at i:33192133 original size:30 final size:30
Alignment explanation
Indices: 33192047--33192134 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
33192037 CTACCTCATA
33192047 TTTAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTTAGCTCACGAGCTAAACCTTAGCTCAAC
* * * * * * *
33192077 TTCAGCTTAGGAGTTTAGCCTCAGCTCAAC
1 TTTAGCTCACGAGCTAAACCTTAGCTCAAC
*
33192107 TTTAGCTCACGAGCTAAAACTTAGCTCA
1 TTTAGCTCACGAGCTAAACCTTAGCTCA
33192135 TTTTAGTTTA
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.28
Consensus pattern (30 bp):
TTTAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:33194014 original size:4 final size:4
Alignment explanation
Indices: 33194005--33194032 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
33193995 TATTTTTATT
33194005 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
33194033 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:33196414 original size:18 final size:18
Alignment explanation
Indices: 33196393--33196431 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
33196383 GATTGAGAGT
* *
33196393 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
33196411 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
33196429 GAA
1 GAA
33196432 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:33197846 original size:4 final size:4
Alignment explanation
Indices: 33197837--33197864 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
33197827 TATTTTTATT
33197837 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
33197865 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:33200145 original size:20 final size:20
Alignment explanation
Indices: 33200122--33200168 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
33200112 GGGTTAAGAT
*
33200122 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
33200142 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
33200162 TGAGCTG
1 TGAGCTG
33200169 GAAACGAGCT
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:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:33203014 original size:12 final size:11
Alignment explanation
Indices: 33202990--33203042 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
33202980 CTCGCAAGAC
*
33202990 TTTTCACTTTT
1 TTTTCTCTTTT
33203001 TTTTCTCATTTT
1 TTTTCTC-TTTT
33203013 TTTTCACTTCTTTT
1 TTTT--C-TCTTTT
*
33203027 TTTTTTCTTTT
1 TTTTCTCTTTT
33203038 TTTTC
1 TTTTC
33203043 GAATTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
11 16 0.46
12 8 0.23
14 9 0.26
15 2 0.06
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTCTCTTTT
Found at i:33203026 original size:11 final size:11
Alignment explanation
Indices: 33202990--33203028 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
33202980 CTCGCAAGAC
33202990 TTTTCACTTTT
1 TTTTCACTTTT
*
33203001 TTTTCTCATTTT
1 TTTTCAC-TTTT
33203013 TTTTCACTTCTT
1 TTTTCACTT-TT
33203025 TTTT
1 TTTT
33203029 TTTTCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTCACTTTT
Found at i:33203049 original size:12 final size:12
Alignment explanation
Indices: 33203034--33203060 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
33203024 TTTTTTTTTC
33203034 TTTTTTTTCGAA
1 TTTTTTTTCGAA
33203046 TTTTTTTTCGAA
1 TTTTTTTTCGAA
33203058 TTT
1 TTT
33203061 CTTCTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:33204588 original size:20 final size:20
Alignment explanation
Indices: 33204565--33204611 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
33204555 GGGTTAAGAT
*
33204565 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
33204585 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
33204605 TGAGCTG
1 TGAGCTG
33204612 GAAACAAGCT
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:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:33207502 original size:10 final size:10
Alignment explanation
Indices: 33207489--33207526 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
33207479 TTGTAGCTAA
33207489 ATTGAGCTCG
1 ATTGAGCTCG
33207499 ATTGAGCT-G
1 ATTGAGCTCG
33207508 ACTTGAGCTCG
1 A-TTGAGCTCG
*
33207519 AGTGAGCT
1 ATTGAGCT
33207527 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:33207506 original size:20 final size:20
Alignment explanation
Indices: 33207466--33207526 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
33207456 ACCAATAAGA
33207466 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
33207486 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
33207506 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
33207526 T
1 T
33207527 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:33207527 original size:20 final size:20
Alignment explanation
Indices: 33207490--33207527 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
33207480 TGTAGCTAAA
*
33207490 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
33207510 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
33207528 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:33208600 original size:13 final size:13
Alignment explanation
Indices: 33208579--33208613 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
33208569 ATAAGTTGCT
* *
33208579 GTTAGTTAAATTA
1 GTTAATTAAATAA
33208592 GTTAATTAAATAA
1 GTTAATTAAATAA
33208605 GTTAATTAA
1 GTTAATTAA
33208614 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:33208865 original size:23 final size:23
Alignment explanation
Indices: 33208835--33208898 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
33208825 ATTTTCCAGA
33208835 CGAATTTAATGTATGTCTT-TGGC
1 CGAATTTAATGTATGT-TTCTGGC
33208858 CGAATTTAATGTATGTTTCTGGC
1 CGAATTTAATGTATGTTTCTGGC
*
33208881 TGAATTTAATGTATGTTT
1 CGAATTTAATGTATGTTT
33208899 TAAATGGTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 2 0.05
23 37 0.95
ACGTcount: A:0.23, C:0.09, G:0.20, T:0.47
Consensus pattern (23 bp):
CGAATTTAATGTATGTTTCTGGC
Found at i:33210469 original size:13 final size:12
Alignment explanation
Indices: 33210451--33210506 Score: 60
Period size: 13 Copynumber: 4.5 Consensus size: 12
33210441 ACGGTATTGT
33210451 AAAAAAATCGAA
1 AAAAAAATCGAA
*
33210463 CAAAAAAATTGAA
1 -AAAAAAATCGAA
*
33210476 AAAAAATTTCGAA
1 AAAAAA-ATCGAA
33210489 AAAAAAATTC-AA
1 AAAAAAA-TCGAA
33210501 AAAAAA
1 AAAAAA
33210507 TTGTATTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
12 14 0.38
13 23 0.62
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.14
Consensus pattern (12 bp):
AAAAAAATCGAA
Found at i:33210478 original size:11 final size:11
Alignment explanation
Indices: 33210464--33210509 Score: 56
Period size: 11 Copynumber: 3.9 Consensus size: 11
33210454 AAAATCGAAC
33210464 AAAAAAATTGA
1 AAAAAAATTGA
33210475 AAAAAAATTTCGAA
1 AAAAAAA-TT-G-A
*
33210489 AAAAAAATTCA
1 AAAAAAATTGA
33210500 AAAAAAATTG
1 AAAAAAATTG
33210510 TATTCAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 17 0.57
12 2 0.07
13 3 0.10
14 8 0.27
ACGTcount: A:0.70, C:0.04, G:0.07, T:0.20
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:33210478 original size:24 final size:23
Alignment explanation
Indices: 33210446--33210507 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 23
33210436 TCATTACGGT
*
33210446 ATTGTAAAAAAATCGAACAAAAAA
1 ATTGAAAAAAAATCGAA-AAAAAA
33210470 ATTGAAAAAAAATTTCGAAAAAAAA
1 ATTGAAAAAAAA--TCGAAAAAAAA
*
33210495 ATTCAAAAAAAAT
1 ATTGAAAAAAAAT
33210508 TGTATTCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 1 0.03
24 11 0.32
25 17 0.50
26 5 0.15
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (23 bp):
ATTGAAAAAAAATCGAAAAAAAA
Found at i:33210599 original size:27 final size:26
Alignment explanation
Indices: 33210549--33210610 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
33210539 AGTATTGAAG
33210549 AAAAAAAAGAAAAAAATCAGAATT-A
1 AAAAAAAAGAAAAAAATCAGAATTGA
*
33210574 AAAAAAGAAGAAAAAAAAT-TGAAATTGA
1 AAAAAA-AAG-AAAAAAATCAG-AATTGA
33210602 AAAAAAAAG
1 AAAAAAAAG
33210611 TGTGATTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 6 0.19
26 4 0.12
27 15 0.47
28 7 0.22
ACGTcount: A:0.76, C:0.02, G:0.11, T:0.11
Consensus pattern (26 bp):
AAAAAAAAGAAAAAAATCAGAATTGA
Found at i:33213095 original size:13 final size:12
Alignment explanation
Indices: 33213064--33213092 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
33213054 GTGTGAGATA
33213064 GAAAAGAAAATT
1 GAAAAGAAAATT
33213076 GAAAAGAAAATT
1 GAAAAGAAAATT
33213088 GAAAA
1 GAAAA
33213093 AGAGAGTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (12 bp):
GAAAAGAAAATT
Found at i:33222825 original size:23 final size:22
Alignment explanation
Indices: 33222774--33222825 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
33222764 CCTCGTCTTT
*
33222774 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
33222796 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
33222819 TTCTTTT
1 TTCTTTT
33222826 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:33226861 original size:23 final size:22
Alignment explanation
Indices: 33226810--33226861 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
33226800 CCTCGTCTTT
*
33226810 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
33226832 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
33226855 TTCTTTT
1 TTCTTTT
33226862 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:33232338 original size:13 final size:13
Alignment explanation
Indices: 33232317--33232351 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
33232307 ATAAGTTGCT
* *
33232317 GTTATTTAAATTA
1 GTTAATTAAATAA
33232330 GTTAATTAAATAA
1 GTTAATTAAATAA
33232343 GTTAATTAA
1 GTTAATTAA
33232352 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:33232634 original size:23 final size:22
Alignment explanation
Indices: 33232573--33232637 Score: 94
Period size: 23 Copynumber: 2.9 Consensus size: 22
33232563 ATTTTCCAGA
*
33232573 CGAATTTAATGTATATCTTTGGC
1 CGAATTTAATGTATGT-TTTGGC
33232596 CGAATTTAATGTATGTTTCTGGC
1 CGAATTTAATGTATGTTT-TGGC
*
33232619 CGAATTTAATGCATGTTTT
1 CGAATTTAATGTATGTTTT
33232638 AAATGGTGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
22 3 0.08
23 36 0.92
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (22 bp):
CGAATTTAATGTATGTTTTGGC
Found at i:33235565 original size:10 final size:10
Alignment explanation
Indices: 33235549--33235606 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
33235539 CAACTCCGAC
33235549 CAGCTCAATT
1 CAGCTCAATT
* *
33235559 GAGCTCATTT
1 CAGCTCAATT
33235569 CAGCTCAA-T
1 CAGCTCAATT
33235578 CGAGCTCAATT
1 C-AGCTCAATT
*
33235589 TAGCTACAATT
1 CAGCT-CAATT
33235600 CAGCTCA
1 CAGCTCA
33235607 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:33235572 original size:20 final size:20
Alignment explanation
Indices: 33235549--33235609 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
33235539 CAACTCCGAC
33235549 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
33235569 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
33235590 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
33235610 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:33237334 original size:20 final size:20
Alignment explanation
Indices: 33237309--33237363 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
33237299 TGTGGTTCAA
*
33237309 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
* *
33237329 CTCATTTGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
33237349 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
33237364 TTTAACTCGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:33242995 original size:13 final size:12
Alignment explanation
Indices: 33242978--33243033 Score: 69
Period size: 12 Copynumber: 4.7 Consensus size: 12
33242968 ACGGTATTGT
33242978 AAAAAAATCGAA
1 AAAAAAATCGAA
33242990 TAAAAAAATCGAA
1 -AAAAAAATCGAA
**
33243003 AAAAATTTCGAA
1 AAAAAAATCGAA
*
33243015 AAAAAATTC-AA
1 AAAAAAATCGAA
33243026 AAAAAAAT
1 AAAAAAAT
33243034 TTGTATTCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
11 9 0.23
12 18 0.46
13 12 0.31
ACGTcount: A:0.71, C:0.07, G:0.05, T:0.16
Consensus pattern (12 bp):
AAAAAAATCGAA
Found at i:33243125 original size:28 final size:27
Alignment explanation
Indices: 33243076--33243137 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
33243066 AGTATTGAAG
33243076 AAAAAAAAG-AAAAAAATCGAAATT-A
1 AAAAAAAAGAAAAAAAATCGAAATTGA
*
33243101 AAAAAAGAAGAAAAAAAATTTGAAATTGA
1 AAAAAA-AAGAAAAAAAA-TCGAAATTGA
33243130 AAAAAAAA
1 AAAAAAAA
33243138 AGAGTGATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 6 0.19
26 3 0.09
27 7 0.22
28 9 0.28
29 7 0.22
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.13
Consensus pattern (27 bp):
AAAAAAAAGAAAAAAAATCGAAATTGA
Found at i:33248971 original size:34 final size:33
Alignment explanation
Indices: 33248907--33248972 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
33248897 TTAAAGATGT
* *
33248907 TGTTCTACATGCATGGAACGGCAATTAATGAGA
1 TGTTCCACATGCATGGAACGACAATTAATGAGA
*
33248940 TGTTCCACATGCAATGG-ACGACATTTAAATGAG
1 TGTTCCACATGC-ATGGAACGACAATT-AATGAG
33248973 GGAGAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
TGTTCCACATGCATGGAACGACAATTAATGAGA
Found at i:33250106 original size:12 final size:12
Alignment explanation
Indices: 33250089--33250122 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
33250079 AGGAAATTTG
33250089 AAAAAAAAATTC
1 AAAAAAAAATTC
33250101 -AAAAAAAATTC
1 AAAAAAAAATTC
33250112 AAAAAAAAATT
1 AAAAAAAAATT
33250123 TTTGAAGTAT
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:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:33251104 original size:18 final size:18
Alignment explanation
Indices: 33251048--33251107 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
33251038 AGTGCGAGGG
33251048 AGAAAAAGAAATCAAAAGAAA
1 AGAAAAAGAAATC--AA-AAA
* **
33251069 AGAAAAAGAGATTGAAAA
1 AGAAAAAGAAATCAAAAA
33251087 AGAAAAAGAAATCAAAAA
1 AGAAAAAGAAATCAAAAA
33251105 AGA
1 AGA
33251108 GAGTGAGGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 21 0.64
19 1 0.03
21 11 0.33
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCAAAAA
Found at i:33253342 original size:34 final size:33
Alignment explanation
Indices: 33253278--33253343 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
33253268 TTAAAGATGT
* *
33253278 TGTTCTACATGCATGGAACGGCAATTAATGAGA
1 TGTTCCACATGCATGGAACGACAATTAATGAGA
*
33253311 TGTTCCACATGCAATGG-ACGACATTTAAATGAG
1 TGTTCCACATGC-ATGGAACGACAATT-AATGAG
33253344 GGAGAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
TGTTCCACATGCATGGAACGACAATTAATGAGA
Found at i:33258615 original size:20 final size:20
Alignment explanation
Indices: 33258569--33258615 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33258559 AGCTCGTTTC
*
33258569 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
33258589 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
33258609 CAGCTCA
1 CAGCTCA
33258616 ATTTTAACCC
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:33261875 original size:15 final size:14
Alignment explanation
Indices: 33261855--33261902 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
33261845 CTCATTTTCA
33261855 TCTTTTTCTTTTATT
1 TCTTTTTCTTTT-TT
*
33261870 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTT
*
33261884 TCTCATTTCTTTTTT
1 TCT-TTTTCTTTTTT
33261899 TCTT
1 TCTT
33261903 CTCTCAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:33261907 original size:22 final size:21
Alignment explanation
Indices: 33261855--33261913 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
33261845 CTCATTTTCA
* *
33261855 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
33261876 TCTTTTTCTCTCATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
*
33261897 T-TTCTTCTCTCAATTTC
1 TCTTTTTCTCTC-ATTTC
33261914 ATTCAAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTCTCATTTCTTTT
Found at i:33263328 original size:30 final size:30
Alignment explanation
Indices: 33263294--33263390 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
33263284 AGCTCACTCC
33263294 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
33263324 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
33263354 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
33263384 TAGCTCA
1 TAGCTCA
33263391 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:33265137 original size:14 final size:13
Alignment explanation
Indices: 33265118--33265157 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
33265108 AAGGGAGAAG
33265118 AAATTCAGAAAAAA
1 AAATTC-GAAAAAA
33265132 AAATTC-AAAAAA
1 AAATTCGAAAAAA
33265144 AAA-TCGAAAAAA
1 AAATTCGAAAAAA
33265156 AA
1 AA
33265158 GGAAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 17 0.68
14 6 0.24
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.12
Consensus pattern (13 bp):
AAATTCGAAAAAA
Found at i:33276410 original size:20 final size:20
Alignment explanation
Indices: 33276385--33276428 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
33276375 TCGTTTCCAG
*
33276385 CTCACTCGAGCTCAAGTCAA
1 CTCACTCAAGCTCAAGTCAA
*
33276405 CTCACTCAAGCTCAATTCAA
1 CTCACTCAAGCTCAAGTCAA
33276425 CTCA
1 CTCA
33276429 ATTTTAACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.09, T:0.23
Consensus pattern (20 bp):
CTCACTCAAGCTCAAGTCAA
Found at i:33279893 original size:31 final size:29
Alignment explanation
Indices: 33279814--33279897 Score: 80
Period size: 31 Copynumber: 2.8 Consensus size: 29
33279804 ACAAGACTTT
* **
33279814 TCACTTTTTTTTAACTTGATTTTTTTTGC
1 TCACTTTTTTTTCACTTTTTTTTTTTTGC
**
33279843 TCACCTTTTTTTTTTCTTTTCTTTTTTTTGC
1 TCA-CTTTTTTTTCACTTTT-TTTTTTTTGC
33279874 TCGA-TTTCTTTTTCACTTTTTTTT
1 TC-ACTTT-TTTTTCACTTTTTTTT
33279898 GAATTTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
29 3 0.07
30 19 0.42
31 22 0.49
32 1 0.02
ACGTcount: A:0.08, C:0.17, G:0.05, T:0.70
Consensus pattern (29 bp):
TCACTTTTTTTTCACTTTTTTTTTTTTGC
Found at i:33282261 original size:20 final size:19
Alignment explanation
Indices: 33282238--33282302 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
33282228 AAGCTCAAAC
33282238 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
33282258 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
33282278 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
33282298 GAGCT
1 GAGCT
33282303 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:33285794 original size:10 final size:10
Alignment explanation
Indices: 33285779--33285840 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
33285769 TTTGAACCAT
*
33285779 TACCAATTCG
1 TACCAATTCA
*
33285789 TACCAAATACCA
1 TACC-AAT-TCA
*
33285801 TACCATTTCA
1 TACCAATTCA
33285811 TACCAATTCCA
1 TACCAATT-CA
* *
33285822 TACCATTTCG
1 TACCAATTCA
33285832 TACCAATTC
1 TACCAATTC
33285841 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:33285824 original size:21 final size:21
Alignment explanation
Indices: 33285779--33285841 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
33285769 TTTGAACCAT
* *
33285779 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
33285801 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
33285822 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
33285842 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:33286458 original size:11 final size:12
Alignment explanation
Indices: 33286429--33286461 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
33286419 AAAAAACTCG
33286429 AAAAAAATTCAA
1 AAAAAAATTCAA
*
33286441 AAAAAAATTAAA
1 AAAAAAATTCAA
33286453 AAAAAAATT
1 AAAAAAATT
33286462 GGTTTCCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:33286520 original size:13 final size:15
Alignment explanation
Indices: 33286497--33286548 Score: 69
Period size: 13 Copynumber: 3.8 Consensus size: 15
33286487 GGATATCAAG
33286497 TTGTG-AAAAAAAAA
1 TTGTGAAAAAAAAAA
33286511 TT-T-AAAAAAAAAA
1 TTGTGAAAAAAAAAA
33286524 TTGTG--AAAAAAAA
1 TTGTGAAAAAAAAAA
33286537 TTGTGAAAAAAA
1 TTGTGAAAAAAA
33286549 GAGAGAGCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 25 0.76
14 3 0.09
15 5 0.15
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (15 bp):
TTGTGAAAAAAAAAA
Found at i:33291450 original size:13 final size:13
Alignment explanation
Indices: 33291429--33291463 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
33291419 ATAAGTTGCT
* *
33291429 GTTAGTTAAATTA
1 GTTAATTAAATAA
33291442 GTTAATTAAATAA
1 GTTAATTAAATAA
33291455 GTTAATTAA
1 GTTAATTAA
33291464 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:33291715 original size:23 final size:23
Alignment explanation
Indices: 33291685--33291748 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
33291675 ATTTTCCAGA
33291685 CGAATTTAATGTATGTCTT-TGGC
1 CGAATTTAATGTATGT-TTCTGGC
33291708 CGAATTTAATGTATGTTTCTGGC
1 CGAATTTAATGTATGTTTCTGGC
*
33291731 CGAATTTAATGCATGTTT
1 CGAATTTAATGTATGTTT
33291749 TAAATGGTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 2 0.05
23 37 0.95
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.44
Consensus pattern (23 bp):
CGAATTTAATGTATGTTTCTGGC
Found at i:33296211 original size:20 final size:20
Alignment explanation
Indices: 33296165--33296211 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33296155 AGCTCGTTTC
*
33296165 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
33296185 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
33296205 CAGCTCA
1 CAGCTCA
33296212 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:33300653 original size:20 final size:20
Alignment explanation
Indices: 33300607--33300653 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33300597 AGCTCGTTTC
*
33300607 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
33300627 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
33300647 CAGCTCA
1 CAGCTCA
33300654 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:33307048 original size:20 final size:20
Alignment explanation
Indices: 33307025--33307071 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
33307015 AGGTTAAGAT
*
33307025 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
33307045 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
33307065 TGAGCTG
1 TGAGCTG
33307072 GAAACAAGCT
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:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:33309757 original size:20 final size:20
Alignment explanation
Indices: 33309728--33309781 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
33309718 GTTTTTTCCC
*
33309728 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
33309748 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
33309768 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
33309782 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:33309763 original size:30 final size:30
Alignment explanation
Indices: 33309728--33309801 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
33309718 GTTTTTTCCC
33309728 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
33309758 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
33309788 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
33309802 TGGCTTAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:33309791 original size:20 final size:20
Alignment explanation
Indices: 33309728--33309792 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
33309718 GTTTTTTCCC
* * * *
33309728 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
33309748 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
33309767 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
33309788 AGCTC
1 AGCTC
33309793 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:33311925 original size:22 final size:22
Alignment explanation
Indices: 33311895--33311938 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33311885 TTTGGTATTT
33311895 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
33311917 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
33311939 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:33315204 original size:22 final size:22
Alignment explanation
Indices: 33315176--33315219 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33315166 TTTTGAACCA
33315176 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
33315198 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
33315220 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:33317819 original size:20 final size:20
Alignment explanation
Indices: 33317772--33317819 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
33317762 AGTAAGCTCG
33317772 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
33317792 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
33317812 GTTGAGCT
1 GTTGAGCT
33317820 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:33319253 original size:30 final size:27
Alignment explanation
Indices: 33319217--33319283 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 27
33319207 TTTTTCGCTT
*
33319217 TTTCTTTTTCAATTTTTTTTTCATTCTCAA
1 TTTCTTTTTCAATTTTCTTTTC--T-TCAA
*
33319247 TTTCTTTTTCAATTTTCTTTTCTTCAT
1 TTTCTTTTTCAATTTTCTTTTCTTCAA
33319274 TTTCTTTTTC
1 TTTCTTTTTC
33319284 TCTCACTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
27 13 0.37
28 1 0.03
30 21 0.60
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTCTTTTTCAATTTTCTTTTCTTCAA
Found at i:33319257 original size:57 final size:52
Alignment explanation
Indices: 33319196--33319367 Score: 159
Period size: 57 Copynumber: 3.1 Consensus size: 52
33319186 TCAAGCTCTC
33319196 TTTCAATTTCTTTTTTCGCTTTTTCTTTTTCAATTTTTTTTTCATTCTCAATTTCTT
1 TTTCAATTTCTTTTTT--CTTTTTCTTTTTC--TTTTTTTTTCATT-TCAATTTCTT
* ** **
33319253 TTTCAATTTTCTTTTCTTCATTTTCTTTTTCTCTCACTTTTTCGATTTCTTTTTCTT
1 TTTCAA-TTTCTTTT-TTCTTTTTCTTTTTCT-T-TTTTTTTC-ATTTCAATTTCTT
** *
33319310 TTGAAATTTC-TTTTTCTTTTTCGTTTTCTTTTTGTTTTCA-TTCAATTTCTT
1 TTTCAATTTCTTTTTTCTTTTTCTTTTTCTTTTT-TTTTCATTTCAATTTCTT
33319361 TTTCAAT
1 TTTCAAT
33319368 CCCTTTCTCC
Statistics
Matches: 94, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
51 14 0.15
52 2 0.02
53 6 0.06
54 14 0.15
55 4 0.04
56 5 0.05
57 36 0.38
58 11 0.12
59 2 0.02
ACGTcount: A:0.12, C:0.17, G:0.03, T:0.68
Consensus pattern (52 bp):
TTTCAATTTCTTTTTTCTTTTTCTTTTTCTTTTTTTTTCATTTCAATTTCTT
Found at i:33319310 original size:18 final size:18
Alignment explanation
Indices: 33319289--33319347 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
33319279 TTTTCTCTCA
33319289 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
***
33319307 CTTTTGAAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
33319325 CTTTTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
33319343 GTTTT
1 CTTTT
33319348 CATTCAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.07, C:0.14, G:0.07, T:0.73
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:33319364 original size:6 final size:6
Alignment explanation
Indices: 33319214--33319347 Score: 63
Period size: 6 Copynumber: 21.8 Consensus size: 6
33319204 TCTTTTTTCG
* * * ** *
33319214 CTTTTT CTTTTT CAATTTT -TTTTT CATTCT CAATTT CTTTTT CAATTTT
1 CTTTTT CTTTTT C-TTTTT CTTTTT CTTTTT CTTTTT CTTTTT C-TTTTT
* * ** ** *
33319263 CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT CGATTT CTTTTT CTTTTG
1 C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*** * *
33319313 AAATTT CTTTTT CTTTTT CGTTTT CTTTTT GTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT
33319348 CATTCAATTT
Statistics
Matches: 90, Mismatches: 34, Indels: 8
0.68 0.26 0.06
Matches are distributed among these distances:
5 4 0.04
6 70 0.78
7 13 0.14
8 3 0.03
ACGTcount: A:0.10, C:0.17, G:0.03, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:33324983 original size:9 final size:9
Alignment explanation
Indices: 33324969--33325002 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
33324959 GAATTTCGTA
*
33324969 TTTTTTGAT
1 TTTTTTGAC
33324978 TTTTTTGAC
1 TTTTTTGAC
33324987 TTTTTTGAC
1 TTTTTTGAC
33324996 TATTTTT
1 T-TTTTT
33325003 TTGCGGGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.12, C:0.06, G:0.09, T:0.74
Consensus pattern (9 bp):
TTTTTTGAC
Found at i:33330732 original size:24 final size:25
Alignment explanation
Indices: 33330679--33330732 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
33330669 AACAAATTCT
* *
33330679 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
33330704 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
33330727 TTTTTT
1 TTTTTT
33330733 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:33339906 original size:62 final size:62
Alignment explanation
Indices: 33339834--33339957 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
33339824 TTAATGGCTT
33339834 GGACGGCATTAAAGGAGGTAGATGATGCCGAATTTAATATGTACATGGACATGGGACAAGCA
1 GGACGGCATTAAAGGAGGTAGATGATGCCGAATTTAATATGTACATGGACATGGGACAAGCA
33339896 GGACGGCATTAAAGGAGGTAGATGATGCCGAATTTAATATGTACATGGACATGGGACAAGCA
1 GGACGGCATTAAAGGAGGTAGATGATGCCGAATTTAATATGTACATGGACATGGGACAAGCA
33339958 TTTAAATGAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.21
Consensus pattern (62 bp):
GGACGGCATTAAAGGAGGTAGATGATGCCGAATTTAATATGTACATGGACATGGGACAAGCA
Found at i:33340079 original size:34 final size:33
Alignment explanation
Indices: 33340015--33340080 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
33340005 TTAAAGATGT
* *
33340015 TGTTCTACATGCATGGAACGGCAATTAATGAGA
1 TGTTCCACATGCATGGAACGACAATTAATGAGA
*
33340048 TGTTCCACATGCAATGG-ACGACATTTAAATGAG
1 TGTTCCACATGC-ATGGAACGACAATT-AATGAG
33340081 GGAGAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
TGTTCCACATGCATGGAACGACAATTAATGAGA
Found at i:33342202 original size:18 final size:18
Alignment explanation
Indices: 33342149--33342205 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
33342139 TGCGAGCGAG
33342149 AAAAGAAATCAAAAGAAAAGA
1 AAAAGAAATC--AA-AAAAGA
* **
33342170 AAAAGAGATTGAAAAAGA
1 AAAAGAAATCAAAAAAGA
33342188 AAAAGAAATCAAAAAAGA
1 AAAAGAAATCAAAAAAGA
33342206 GAGTGAGGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 21 0.70
19 1 0.03
21 8 0.27
ACGTcount: A:0.74, C:0.04, G:0.16, T:0.07
Consensus pattern (18 bp):
AAAAGAAATCAAAAAAGA
Found at i:33344582 original size:17 final size:16
Alignment explanation
Indices: 33344550--33344581 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
33344540 AAAAAGAAGT
33344550 TTCAGAAGTAAAAAAA
1 TTCAGAAGTAAAAAAA
*
33344566 TTCAGAATTAAAAAAA
1 TTCAGAAGTAAAAAAA
33344582 AAAAGAAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.62, C:0.06, G:0.09, T:0.22
Consensus pattern (16 bp):
TTCAGAAGTAAAAAAA
Found at i:33346399 original size:30 final size:30
Alignment explanation
Indices: 33346364--33346437 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
33346354 AGTTTTTTCC
33346364 AGCTCGATTT-AGCTCACATGAGCTTAATTT
1 AGCTCG-TTTGAGCTCACATGAGCTTAATTT
** * *
33346394 AGCTCGTTTGAGCTCAGTTTAGCTTACTTT
1 AGCTCGTTTGAGCTCACATGAGCTTAATTT
33346424 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
33346438 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCACATGAGCTTAATTT
Found at i:33348105 original size:12 final size:12
Alignment explanation
Indices: 33348090--33348123 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
33348080 AATTTGATTG
33348090 AAAAAAAAATTC
1 AAAAAAAAATTC
* *
33348102 AAAAAAAAAGTG
1 AAAAAAAAATTC
33348114 AAAAAAAAAT
1 AAAAAAAAAT
33348124 CGAGCAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.79, C:0.03, G:0.06, T:0.12
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:33348165 original size:31 final size:28
Alignment explanation
Indices: 33348102--33348175 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 28
33348092 AAAAAAATTC
*
33348102 AAAAAAAAAGTGAAAAAAAAATCGAGCA
1 AAAAAAAAAGTGAAAAAAAAATCAAGCA
*
33348130 AAAAAAAAAGGTGACCAAAAAAAATCAAG-T
1 AAAAAAAAA-GTGA--AAAAAAAATCAAGCA
*
33348160 TAAAAAAAAGTGAAAA
1 AAAAAAAAAGTGAAAA
33348176 GTCTTGCGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 3 0.08
28 9 0.22
29 8 0.20
30 8 0.20
31 12 0.30
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09
Consensus pattern (28 bp):
AAAAAAAAAGTGAAAAAAAAATCAAGCA
Found at i:33350582 original size:15 final size:16
Alignment explanation
Indices: 33350562--33350593 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
33350552 AGAAAATGAA
33350562 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
33350577 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
33350593 A
1 A
33350594 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:33350708 original size:17 final size:18
Alignment explanation
Indices: 33350676--33350709 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33350666 AAAAGAGAGT
*
33350676 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
33350694 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
33350710 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:33351998 original size:20 final size:20
Alignment explanation
Indices: 33351975--33352028 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
33351965 AGTTTTTTCC
*
33351975 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
33351995 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
33352015 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
33352029 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:33352010 original size:30 final size:30
Alignment explanation
Indices: 33351975--33352048 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
33351965 AGTTTTTTCC
33351975 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
33352005 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
33352035 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
33352049 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:33352038 original size:20 final size:20
Alignment explanation
Indices: 33351975--33352039 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
33351965 AGTTTTTTCC
* * * *
33351975 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
33351995 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
33352014 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
33352035 AGCTC
1 AGCTC
33352040 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:33355209 original size:11 final size:13
Alignment explanation
Indices: 33355193--33355281 Score: 60
Period size: 14 Copynumber: 6.6 Consensus size: 13
33355183 TTGGAGTAAT
33355193 AAAAAAAA-TC-A
1 AAAAAAAATTCGA
33355204 AAAAAAAATTCGAA
1 AAAAAAAATTCG-A
*
33355218 AAAAAAAATTGATTGA
1 AAAAAAAA-T--TCGA
*
33355234 AAAAAAAATTCAAA
1 AAAAAAAATTC-GA
*
33355248 AAAAAAAAGT-GA
1 AAAAAAAATTCGA
33355260 AAAAAAAA-TCGA
1 AAAAAAAATTCGA
33355272 GCAAAAAAAA
1 --AAAAAAAA
33355282 AAGGTGAGCA
Statistics
Matches: 63, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
11 9 0.14
12 13 0.21
13 1 0.02
14 27 0.43
15 2 0.03
16 9 0.14
17 2 0.03
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.12
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:33355210 original size:12 final size:13
Alignment explanation
Indices: 33355193--33355254 Score: 65
Period size: 16 Copynumber: 4.6 Consensus size: 13
33355183 TTGGAGTAAT
33355193 AAAAAAAA-TC-A
1 AAAAAAAATTCAA
33355204 AAAAAAAATTCGAA
1 AAAAAAAATTC-AA
*
33355218 AAAAAAAATTGATTGA
1 AAAAAAAATTCA---A
33355234 AAAAAAAATTCAA
1 AAAAAAAATTCAA
33355247 AAAAAAAA
1 AAAAAAAA
33355255 AGTGAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
11 8 0.19
12 2 0.05
13 10 0.23
14 11 0.26
16 12 0.28
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:33355220 original size:14 final size:13
Alignment explanation
Indices: 33355203--33355267 Score: 67
Period size: 14 Copynumber: 4.6 Consensus size: 13
33355193 AAAAAAAATC
33355203 AAAAAAAAATTCGA
1 AAAAAAAAATT-GA
33355217 AAAAAAAAATTGA
1 AAAAAAAAATTGA
*
33355230 TTGAAAAAAAAATTCAA
1 ---AAAAAAAAATT-GA
*
33355247 AAAAAAAAAGTGA
1 AAAAAAAAATTGA
33355260 AAAAAAAA
1 AAAAAAAA
33355268 TCGAGCAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
13 11 0.25
14 21 0.48
16 11 0.25
17 1 0.02
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:33355239 original size:30 final size:27
Alignment explanation
Indices: 33355193--33355298 Score: 101
Period size: 26 Copynumber: 3.7 Consensus size: 27
33355183 TTGGAGTAAT
*
33355193 AAAAAAAA-TCAAAAAAAAATTCGAAA
1 AAAAAAAAGTGAAAAAAAAATTCGAAA
*
33355219 AAAAAAATTGATTGAAAAAAAAATTC-AAA
1 AAAAAAA---AGTGAAAAAAAAATTCGAAA
33355248 AAAAAAAAGTGAAAAAAAAA-TCGAGCAA
1 AAAAAAAAGTGAAAAAAAAATTCGA--AA
33355276 AAAAAAAAGGTGAGCAAAAAAAA
1 AAAAAAAA-GTGA--AAAAAAAA
33355299 AATCAAGTTA
Statistics
Matches: 68, Mismatches: 2, Indels: 15
0.80 0.02 0.18
Matches are distributed among these distances:
25 2 0.03
26 20 0.29
28 10 0.15
29 15 0.22
30 13 0.19
31 8 0.12
ACGTcount: A:0.73, C:0.06, G:0.10, T:0.11
Consensus pattern (27 bp):
AAAAAAAAGTGAAAAAAAAATTCGAAA
Found at i:33355278 original size:16 final size:16
Alignment explanation
Indices: 33355259--33355302 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
33355249 AAAAAAAGTG
33355259 AAAAAAAAATCGAGCA
1 AAAAAAAAATCGAGCA
33355275 AAAAAAAAAGGT-GAGCA
1 AAAAAAAAA--TCGAGCA
33355292 AAAAAAAAATC
1 AAAAAAAAATC
33355303 AAGTTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 9 0.36
17 14 0.56
18 1 0.04
ACGTcount: A:0.70, C:0.09, G:0.14, T:0.07
Consensus pattern (16 bp):
AAAAAAAAATCGAGCA
Found at i:33356247 original size:15 final size:16
Alignment explanation
Indices: 33356227--33356258 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
33356217 AGAAAATGAA
33356227 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
33356242 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
33356258 A
1 A
33356259 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:33356373 original size:17 final size:18
Alignment explanation
Indices: 33356341--33356374 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33356331 AAAAGAGAGT
*
33356341 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
33356359 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
33356375 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:33357663 original size:20 final size:20
Alignment explanation
Indices: 33357640--33357693 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
33357630 AGTTTTTCCC
*
33357640 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
33357660 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
33357680 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
33357694 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:33357675 original size:30 final size:30
Alignment explanation
Indices: 33357640--33357713 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
33357630 AGTTTTTCCC
33357640 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
33357670 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
33357700 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
33357714 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:33357703 original size:20 final size:20
Alignment explanation
Indices: 33357640--33357704 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
33357630 AGTTTTTCCC
* * * *
33357640 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
33357660 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
33357679 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
33357700 AGCTC
1 AGCTC
33357705 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:33362634 original size:22 final size:22
Alignment explanation
Indices: 33362604--33362647 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33362594 TTTGGTATCT
33362604 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
33362626 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
33362648 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:33374363 original size:30 final size:30
Alignment explanation
Indices: 33374329--33374423 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 30
33374319 AGCTCACTCC
*
33374329 TAGCTCATA-TTTAGCTCATGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
33374359 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
33374389 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
33374419 TAGCT
1 TAGCT
33374424 TATTTTAGTT
Statistics
Matches: 49, Mismatches: 15, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
29 1 0.02
30 48 0.98
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:33376585 original size:14 final size:14
Alignment explanation
Indices: 33376568--33376602 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
33376558 AAATTGATTG
*
33376568 AAAAAAAAATTCAA
1 AAAAAAAAAGTCAA
*
33376582 AAAAAAAAAGTGAA
1 AAAAAAAAAGTCAA
33376596 AAAAAAA
1 AAAAAAA
33376603 TCGAGTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.83, C:0.03, G:0.06, T:0.09
Consensus pattern (14 bp):
AAAAAAAAAGTCAA
Found at i:33377707 original size:17 final size:18
Alignment explanation
Indices: 33377675--33377708 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33377665 AAAAGAGAGT
*
33377675 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
33377693 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
33377709 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:33383634 original size:23 final size:22
Alignment explanation
Indices: 33383582--33383634 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
33383572 TCCACGTCTT
*
33383582 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
33383604 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
33383627 TTTCTTTT
1 TTTCTTTT
33383635 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:33396018 original size:13 final size:13
Alignment explanation
Indices: 33395992--33396080 Score: 60
Period size: 13 Copynumber: 6.6 Consensus size: 13
33395982 TTGGAGTAAC
33395992 AAAAAAAA-TC-A
1 AAAAAAAATTCGA
33396003 AAAAAAAATTCGA
1 AAAAAAAATTCGA
33396016 AAAAAAATTTGATT-GAA
1 AAAAAAA----ATTCG-A
*
33396033 AAAAAAAATTCAA
1 AAAAAAAATTCGA
*
33396046 AAAAAAAAGT-GA
1 AAAAAAAATTCGA
*
33396058 AAAAAAAAATCGA
1 AAAAAAAATTCGA
33396071 GCAAAAAAAA
1 --AAAAAAAA
33396081 AAAAGGTGAC
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
11 8 0.13
12 12 0.19
13 23 0.37
15 8 0.13
16 1 0.02
17 11 0.17
ACGTcount: A:0.73, C:0.06, G:0.08, T:0.13
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:33396063 original size:16 final size:17
Alignment explanation
Indices: 33396044--33396115 Score: 51
Period size: 16 Copynumber: 4.3 Consensus size: 17
33396034 AAAAAAATTC
33396044 AAAAAAA-AAAGTGAAA
1 AAAAAAATAAAGTGAAA
** *
33396060 AAAAAAATCGAG-CAAA
1 AAAAAAATAAAGTGAAA
*
33396076 AAAAAAA-AAGGTGACCAA
1 AAAAAAATAAAGTGA--AA
* *
33396094 AAAAAAATCAAGTTAAA
1 AAAAAAATAAAGTGAAA
33396111 AAAAA
1 AAAAA
33396116 GTGAAAAGTC
Statistics
Matches: 41, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
15 1 0.02
16 18 0.44
17 9 0.22
18 9 0.22
19 4 0.10
ACGTcount: A:0.74, C:0.07, G:0.11, T:0.08
Consensus pattern (17 bp):
AAAAAAATAAAGTGAAA
Found at i:33396065 original size:30 final size:30
Alignment explanation
Indices: 33396002--33396066 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
33395992 AAAAAAAATC
* ** ***
33396002 AAAAAAAAATTCGAAAAAAAATTTGATTGA
1 AAAAAAAAATTCAAAAAAAAAAGTGAAAAA
33396032 AAAAAAAAATTCAAAAAAAAAAGTGAAAAA
1 AAAAAAAAATTCAAAAAAAAAAGTGAAAAA
33396062 AAAAA
1 AAAAA
33396067 TCGAGCAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (30 bp):
AAAAAAAAATTCAAAAAAAAAAGTGAAAAA
Found at i:33396079 original size:26 final size:26
Alignment explanation
Indices: 33396002--33396067 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 26
33395992 AAAAAAAATC
* *
33396002 AAAAAAAAATTCGAAAAAAAATTTGATTGA
1 AAAAAAAAATTC-AAAAAAAA---AAGTGA
33396032 AAAAAAAAATTCAAAAAAAAAAGTGA
1 AAAAAAAAATTCAAAAAAAAAAGTGA
33396058 AAAAAAAAAT
1 AAAAAAAAAT
33396068 CGAGCAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 14 0.41
29 8 0.24
30 12 0.35
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.17
Consensus pattern (26 bp):
AAAAAAAAATTCAAAAAAAAAAGTGA
Found at i:33396112 original size:34 final size:31
Alignment explanation
Indices: 33396044--33396115 Score: 90
Period size: 34 Copynumber: 2.2 Consensus size: 31
33396034 AAAAAAATTC
*
33396044 AAAAAAAAAAGTGAAAAAAAAAATCGAGCAA
1 AAAAAAAAAAGTGAAAAAAAAAATCAAGCAA
**
33396075 AAAAAAAAAAGGTGACCAAAAAAAAATCAAGTTA
1 AAAAAAAAAA-GTGA--AAAAAAAAATCAAGCAA
33396109 AAAAAAA
1 AAAAAAA
33396116 GTGAAAAGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 10 0.29
32 4 0.11
34 21 0.60
ACGTcount: A:0.74, C:0.07, G:0.11, T:0.08
Consensus pattern (31 bp):
AAAAAAAAAAGTGAAAAAAAAAATCAAGCAA
Found at i:33397057 original size:15 final size:16
Alignment explanation
Indices: 33397037--33397068 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
33397027 AGAAAATGAA
33397037 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
33397052 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
33397068 A
1 A
33397069 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:33397183 original size:17 final size:18
Alignment explanation
Indices: 33397151--33397184 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33397141 AAAAGAGAGT
*
33397151 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
33397169 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
33397185 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:33401417 original size:13 final size:12
Alignment explanation
Indices: 33401401--33401434 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
33401391 AAAGAGTTCG
33401401 AAAAAAAATTGAA
1 AAAAAAAATT-AA
33401414 AAAAAAAATTAA
1 AAAAAAAATTAA
33401426 AAAGAAAAA
1 AAA-AAAAA
33401435 AAAATTGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTAA
Found at i:33404196 original size:20 final size:20
Alignment explanation
Indices: 33404173--33404219 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
33404163 GGGTTAAGAT
* *
33404173 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGATCGAG
* *
33404193 TGAGTTGACTTGAGATCGAG
1 TGAGCTGAATTGAGATCGAG
33404213 TGAGCTG
1 TGAGCTG
33404220 GAAACGAGCT
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:0.23, C:0.11, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGATCGAG
Found at i:33407120 original size:20 final size:20
Alignment explanation
Indices: 33407097--33407143 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
33407087 GGGTTAAGAT
*
33407097 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
33407117 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
33407137 TGAGCTG
1 TGAGCTG
33407144 GAAACGAGCT
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:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:33409939 original size:12 final size:12
Alignment explanation
Indices: 33409918--33409979 Score: 58
Period size: 13 Copynumber: 5.2 Consensus size: 12
33409908 CTCGCAAGAC
*
33409918 TTTTCACTTTTT
1 TTTTCTCTTTTT
33409930 TTTTCTC--TTT
1 TTTTCTCTTTTT
33409940 TTTTCTCATTTTT
1 TTTTCTC-TTTTT
* *
33409953 ATTTCACTTCTTT
1 TTTTCTCTT-TTT
33409966 TTTT-TCTTTTT
1 TTTTCTCTTTTT
33409977 TTT
1 TTT
33409980 CGAATTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
10 10 0.24
11 6 0.15
12 11 0.27
13 14 0.34
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTCTCTTTTT
Found at i:33409987 original size:11 final size:11
Alignment explanation
Indices: 33409973--33409997 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33409963 TTTTTTTTCT
33409973 TTTTTTTCGAA
1 TTTTTTTCGAA
33409984 TTTTTTTCGAA
1 TTTTTTTCGAA
33409995 TTT
1 TTT
33409998 CTTCTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTTTTCGAA
Done.