Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 66 of 222
Found at i:20179286 original size:75 final size:75
Alignment explanation
Indices: 20179180--20179338 Score: 176
Period size: 75 Copynumber: 2.1 Consensus size: 75
20179170 AGGCACTTCG
* * * * *
20179180 AATAATTCGCCACAAAGTCTCTTCAGATAATTTACTATAAAGGTTTTTTAGATAATTCACCACAA
1 AATAATTCGCCACAAAGTCTCTTCAGATAATTCACCACAAAGGATTTGTAGATAATTCACCACAA
20179245 AGGATTTTCA
66 AGGATTTTCA
* * * * * **
20179255 AATAATTCGCCACTAAGGT-TTTTTAGATAATTCACCGCAAAGGATTTGTAGTTAATTTTCCACA
1 AATAATTCGCCAC-AAAGTCTCTTCAGATAATTCACCACAAAGGATTTGTAGATAATTCACCACA
*
20179319 AAGGCTTTTCA
65 AAGGATTTTCA
*
20179330 GATAATTCG
1 AATAATTCG
20179339 AAAATAAGGC
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
75 65 0.94
76 4 0.06
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (75 bp):
AATAATTCGCCACAAAGTCTCTTCAGATAATTCACCACAAAGGATTTGTAGATAATTCACCACAA
AGGATTTTCA
Found at i:20179311 original size:50 final size:50
Alignment explanation
Indices: 20179218--20179337 Score: 152
Period size: 50 Copynumber: 2.4 Consensus size: 50
20179208 AATTTACTAT
20179218 AAAGGTTTTTTAGATAATTCACCACAAAGGATTTTCAAATAATTCGCCAC
1 AAAGGTTTTTTAGATAATTCACCACAAAGGATTTTCAAATAATTCGCCAC
* * ** **
20179268 TAAGGTTTTTTAGATAATTCACCGCAAAGGATTTGT-AGTTAATTTTCCAC
1 AAAGGTTTTTTAGATAATTCACCACAAAGGATTT-TCAAATAATTCGCCAC
* *
20179318 AAAGGCTTTTCAGATAATTC
1 AAAGGTTTTTTAGATAATTC
20179338 GAAAATAAGG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
50 59 0.98
51 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (50 bp):
AAAGGTTTTTTAGATAATTCACCACAAAGGATTTTCAAATAATTCGCCAC
Found at i:20179386 original size:25 final size:24
Alignment explanation
Indices: 20179318--20179387 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
20179308 AATTTTCCAC
20179318 AAAGGCTTTTCAGATAATTCGAAA
1 AAAGGCTTTTCAGATAATTCGAAA
* * ***
20179342 ATAAGGCTCTTAAGATAATTCGCCGT
1 A-AAGGCTTTTCAGATAATTCG-AAA
*
20179368 AAAGGCTTTTCAGAAAATTC
1 AAAGGCTTTTCAGATAATTC
20179388 ACTGAAATGG
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
24 1 0.03
25 34 0.94
26 1 0.03
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (24 bp):
AAAGGCTTTTCAGATAATTCGAAA
Found at i:20185500 original size:11 final size:11
Alignment explanation
Indices: 20185484--20185520 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
20185474 AAGAGAGAAT
*
20185484 GATGCTTGATG
1 GATGCTTGAGG
20185495 GATGCTTGAGG
1 GATGCTTGAGG
*
20185506 GATGATTGAGG
1 GATGCTTGAGG
20185517 GATG
1 GATG
20185521 ATGAATGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.22, C:0.05, G:0.43, T:0.30
Consensus pattern (11 bp):
GATGCTTGAGG
Found at i:20189469 original size:17 final size:17
Alignment explanation
Indices: 20189447--20189479 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20189437 TATAAAGAGC
*
20189447 TTTTTTTATAAGACTTT
1 TTTTTTTATAAAACTTT
20189464 TTTTTTTATAAAACTT
1 TTTTTTTATAAAACTT
20189480 CTATTAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTTTTTATAAAACTTT
Found at i:20195808 original size:25 final size:25
Alignment explanation
Indices: 20195774--20195846 Score: 89
Period size: 25 Copynumber: 2.9 Consensus size: 25
20195764 TAGACCACAA
20195774 ACAAGATTAGCCACAAAGGCTTTTC
1 ACAAGATTAGCCACAAAGGCTTTTC
*
20195799 ACAAGGTTAGCCACAAAGGC-TTTC
1 ACAAGATTAGCCACAAAGGCTTTTC
20195823 -C-AGATAATATGCCACAAAGGCTTT
1 ACAAGAT--TA-GCCACAAAGGCTTT
20195847 CTGAGTAACC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 3 0.07
23 1 0.02
24 6 0.14
25 30 0.71
26 2 0.05
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (25 bp):
ACAAGATTAGCCACAAAGGCTTTTC
Found at i:20203427 original size:35 final size:35
Alignment explanation
Indices: 20203388--20203458 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
20203378 GATTTATAGG
* * *
20203388 TATTCTGATTATGACTCCCATGTTAAGCATGTCAT
1 TATTCTAATTATGACTCACATGTTAAGCATGCCAT
* *
20203423 TATTCTAATTCTGATTCACATGTTAAGCATGCCAT
1 TATTCTAATTATGACTCACATGTTAAGCATGCCAT
20203458 T
1 T
20203459 GTGTTAAACT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.41
Consensus pattern (35 bp):
TATTCTAATTATGACTCACATGTTAAGCATGCCAT
Found at i:20208480 original size:25 final size:24
Alignment explanation
Indices: 20208452--20208540 Score: 81
Period size: 25 Copynumber: 3.6 Consensus size: 24
20208442 TATTACTTCA
20208452 CCACAAAGGCCTTTCACAACATTAG
1 CCACAAAGG-CTTTCACAACATTAG
* * * *
20208477 CCACAACGG-TTTCCCATATAATACG
1 CCACAAAGGCTTTCACA-ACATTA-G
* *
20208502 CCATAAAGGCTTTTCACAAGATTAG
1 CCACAAAGGC-TTTCACAACATTAG
20208527 CCACAAAGGCTTTC
1 CCACAAAGGCTTTC
20208541 TAGATAATAC
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
23 6 0.12
24 8 0.16
25 26 0.52
26 4 0.08
27 6 0.12
ACGTcount: A:0.34, C:0.29, G:0.13, T:0.24
Consensus pattern (24 bp):
CCACAAAGGCTTTCACAACATTAG
Found at i:20208531 original size:50 final size:50
Alignment explanation
Indices: 20208456--20208570 Score: 160
Period size: 50 Copynumber: 2.3 Consensus size: 50
20208446 ACTTCACCAC
* * *
20208456 AAAGGCCTTTCACAACATTAGCCACAACGG-TTTCCCATATAATACGCCAT
1 AAAGGCTTTTCACAACATTAGCCACAAAGGCTTT-CCAGATAATACGCCAT
* * *
20208506 AAAGGCTTTTCACAAGATTAGCCACAAAGGCTTTCTAGATAATACGCTAT
1 AAAGGCTTTTCACAACATTAGCCACAAAGGCTTTCCAGATAATACGCCAT
20208556 AAAGGCTTTTCACAA
1 AAAGGCTTTTCACAA
20208571 TGTTAGTTGT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 55 0.95
51 3 0.05
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (50 bp):
AAAGGCTTTTCACAACATTAGCCACAAAGGCTTTCCAGATAATACGCCAT
Found at i:20210434 original size:25 final size:25
Alignment explanation
Indices: 20210406--20210470 Score: 96
Period size: 26 Copynumber: 2.6 Consensus size: 25
20210396 TACATTAGCT
*
20210406 ACAAAGGCTTTCTAGATAATACGCC
1 ACAAAGGCTTTCCAGATAATACGCC
*
20210431 ACAAAAGGTTTTCCAGATAATACGCC
1 AC-AAAGGCTTTCCAGATAATACGCC
20210457 ACAAA-GCTTTCCAG
1 ACAAAGGCTTTCCAG
20210471 GTAACCTATC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.22
25 5 0.14
26 23 0.64
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (25 bp):
ACAAAGGCTTTCCAGATAATACGCC
Found at i:20212760 original size:21 final size:20
Alignment explanation
Indices: 20212717--20212759 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
20212707 CAGAAAATTA
* *
20212717 TTTCTGGAAATTGATTTGCT
1 TTTCTGGAAAATGATTTACT
20212737 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
20212757 TTT
1 TTT
20212760 TTGGTGTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.09, G:0.16, T:0.51
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:20215730 original size:50 final size:50
Alignment explanation
Indices: 20215666--20215764 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
20215656 TTTGGTGTCA
*
20215666 CCCTACTTTATCCAACTTCCAATGGACTCGGCTGGCCTTTTGATCTTTCG
1 CCCTACTTTATCCAACTTCCAATGGACTCAGCTGGCCTTTTGATCTTTCG
* *
20215716 CCCTGCTTTATCCAACTTCCAATGGACTCAGTTGGCCTTTTGATCTTTC
1 CCCTACTTTATCCAACTTCCAATGGACTCAGCTGGCCTTTTGATCTTTC
20215765 TATTATTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.16, C:0.31, G:0.15, T:0.37
Consensus pattern (50 bp):
CCCTACTTTATCCAACTTCCAATGGACTCAGCTGGCCTTTTGATCTTTCG
Found at i:20220858 original size:21 final size:21
Alignment explanation
Indices: 20220832--20220898 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
20220822 GGAGCATAAA
*
20220832 CAGGGGCACGTATGTACAATT
1 CAGGGGCACATATGTACAATT
* * *
20220853 CAGGGGTACCA-AAGTACAAAT
1 CAGGGGCA-CATATGTACAATT
*
20220874 -AGGGGCACATATGTGCAATT
1 CAGGGGCACATATGTACAATT
*
20220894 TAGGG
1 CAGGG
20220899 CTATCGAAGT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
19 2 0.06
20 13 0.37
21 19 0.54
22 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (21 bp):
CAGGGGCACATATGTACAATT
Found at i:20220893 original size:41 final size:41
Alignment explanation
Indices: 20220833--20221016 Score: 242
Period size: 41 Copynumber: 4.5 Consensus size: 41
20220823 GAGCATAAAC
* *
20220833 AGGGGCACGTATGTACAATTCAGGGGTACCAAAGTACAAAT
1 AGGGGCACATATGTGCAATTCAGGGGTACCAAAGTACAAAT
* * * *
20220874 AGGGGCACATATGTGCAATTTAGGGCTATCGAAGTACAAAT
1 AGGGGCACATATGTGCAATTCAGGGGTACCAAAGTACAAAT
* * *
20220915 AGGGGCACATATTTGTAATTCAGGGGTATCAAAGTACAAAT
1 AGGGGCACATATGTGCAATTCAGGGGTACCAAAGTACAAAT
* * * *
20220956 AAGGGCACGTATGTGCAATTCAGGAGTACCAAAGTACAAAC
1 AGGGGCACATATGTGCAATTCAGGGGTACCAAAGTACAAAT
*
20220997 AGGGGCACATATGTGTAATT
1 AGGGGCACATATGTGCAATT
20221017 TAGGTAATAA
Statistics
Matches: 122, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 122 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (41 bp):
AGGGGCACATATGTGCAATTCAGGGGTACCAAAGTACAAAT
Found at i:20223831 original size:28 final size:28
Alignment explanation
Indices: 20223786--20223856 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
20223776 GCTAATAAAC
*
20223786 AGAGTGAAAGGAGGACGACTGTTGTGATG
1 AGAGTG-AAGGAGAACGACTGTTGTGATG
*
20223815 AGAGTGAAGGAGAACGATTGTTGTGATG
1 AGAGTGAAGGAGAACGACTGTTGTGATG
*
20223843 AGATTGAAGGAGAA
1 AGAGTGAAGGAGAA
20223857 TGGAAAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.85
29 6 0.15
ACGTcount: A:0.35, C:0.04, G:0.39, T:0.21
Consensus pattern (28 bp):
AGAGTGAAGGAGAACGACTGTTGTGATG
Found at i:20224847 original size:28 final size:28
Alignment explanation
Indices: 20224814--20224876 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
20224804 GACAGAGAGA
* * *
20224814 AAGGAGAATGATTGTTGTGATGAGAATG
1 AAGGAGAACGACTGTTGTGATAAGAATG
*
20224842 AAGGAGAACGACTGTTGTGATAAGAGTG
1 AAGGAGAACGACTGTTGTGATAAGAATG
20224870 AAGGAGA
1 AAGGAGA
20224877 GTGGAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.38, C:0.03, G:0.37, T:0.22
Consensus pattern (28 bp):
AAGGAGAACGACTGTTGTGATAAGAATG
Found at i:20226413 original size:26 final size:26
Alignment explanation
Indices: 20226377--20226449 Score: 96
Period size: 26 Copynumber: 2.8 Consensus size: 26
20226367 ACGAACTTTC
20226377 TCAAAATTTTACCGAGGGTTAAA-TCG
1 TCAAAATTTTACCGAGGG-TAAATTCG
* *
20226403 TCAAAATTTTATCGAGGGTAAATTTG
1 TCAAAATTTTACCGAGGGTAAATTCG
*
20226429 TCAAAATTTTACC-ATGGTAAA
1 TCAAAATTTTACCGAGGGTAAA
20226450 ATTGGGGTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
25 11 0.26
26 31 0.74
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.34
Consensus pattern (26 bp):
TCAAAATTTTACCGAGGGTAAATTCG
Found at i:20234576 original size:39 final size:36
Alignment explanation
Indices: 20234513--20234595 Score: 87
Period size: 39 Copynumber: 2.2 Consensus size: 36
20234503 AGAAGACACT
* *
20234513 GTTGTTGAGAAGGAAATTGATGCTGCAGAAGCA-GAA
1 GTTGTTGAGAAGGAAATTGATGCTGAAGAA-AAGGAA
* *
20234549 GTTGTTGTAGAAGATGAAGTTGTTGCTGAAGAAAAGGAA
1 GTTGTTG-AGAAG--GAAATTGATGCTGAAGAAAAGGAA
20234588 GTTGTTGA
1 GTTGTTGA
20234596 AAATGAGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
36 7 0.18
37 5 0.13
38 2 0.05
39 25 0.64
ACGTcount: A:0.34, C:0.05, G:0.34, T:0.28
Consensus pattern (36 bp):
GTTGTTGAGAAGGAAATTGATGCTGAAGAAAAGGAA
Found at i:20234581 original size:21 final size:19
Alignment explanation
Indices: 20234512--20234594 Score: 64
Period size: 21 Copynumber: 4.3 Consensus size: 19
20234502 AAGAAGACAC
* *
20234512 TGTTGTTGAGAAG-GAAAT
1 TGTTGCTGAGAAGAGAAGT
*
20234530 TGATGCTGCAGAAGCAGAAGT
1 TGTTGCTG-AGAAG-AGAAGT
20234551 TGTTG-T-AGAAGATGAAGT
1 TGTTGCTGAGAAGA-GAAGT
*
20234569 TGTTGCTGAAGAAAAGGAAGT
1 TGTTGCTG-AGAAGA-GAAGT
20234590 TGTTG
1 TGTTG
20234595 AAAATGAGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
17 1 0.02
18 21 0.40
19 6 0.12
20 1 0.02
21 23 0.44
ACGTcount: A:0.33, C:0.05, G:0.34, T:0.29
Consensus pattern (19 bp):
TGTTGCTGAGAAGAGAAGT
Found at i:20244828 original size:9 final size:9
Alignment explanation
Indices: 20244814--20244931 Score: 70
Period size: 9 Copynumber: 13.6 Consensus size: 9
20244804 TGAGATATAT
20244814 TTATGTAAG
1 TTATGTAAG
*
20244823 TTATGTAAC
1 TTATGTAAG
*
20244832 TTATGATATG
1 TTATG-TAAG
* * *
20244842 ATATAT-AT
1 TTATGTAAG
20244850 TTATGT-AG
1 TTATGTAAG
20244858 -TATGTAAG
1 TTATGTAAG
20244866 TTATGTAAG
1 TTATGTAAG
*
20244875 TTATG-ACAT
1 TTATGTA-AG
*
20244884 TTATGATATG
1 TTATG-TAAG
* * *
20244894 ATATAT-AT
1 TTATGTAAG
20244902 TTATGT-A-
1 TTATGTAAG
20244909 TTATGTAAG
1 TTATGTAAG
20244918 TTATGTAAG
1 TTATGTAAG
20244927 TTATG
1 TTATG
20244932 AAATTTGAAC
Statistics
Matches: 82, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
7 11 0.13
8 14 0.17
9 48 0.59
10 8 0.10
11 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:20244849 original size:36 final size:34
Alignment explanation
Indices: 20244802--20244870 Score: 102
Period size: 36 Copynumber: 2.0 Consensus size: 34
20244792 TAAGTATAAT
20244802 TATGAGATATATTTATGTAAGTTATGTAACTTATGA
1 TATGAGATATATTTATGT-AG-TATGTAACTTATGA
* *
20244838 TATGATATATATTTATGTAGTATGTAAGTTATG
1 TATGAGATATATTTATGTAGTATGTAACTTATG
20244871 TAAGTTATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 12 0.39
35 2 0.06
36 17 0.55
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.46
Consensus pattern (34 bp):
TATGAGATATATTTATGTAGTATGTAACTTATGA
Found at i:20244853 original size:18 final size:17
Alignment explanation
Indices: 20244802--20244909 Score: 67
Period size: 18 Copynumber: 6.2 Consensus size: 17
20244792 TAAGTATAAT
*
20244802 TATGAGATATATTTATG
1 TATGATATATATTTATG
* * * *
20244819 TAAGTTATGTAACTTATG
1 TATGATATAT-ATTTATG
20244837 ATATGATATATATTTATG
1 -TATGATATATATTTATG
* *
20244855 TA-G-TATGTAAGTTATG
1 TATGATATAT-ATTTATG
* * *
20244871 TAAGTTATGACATTTATG
1 TATGATAT-ATATTTATG
20244889 ATATGATATATATTTATG
1 -TATGATATATATTTATG
20244907 TAT
1 TAT
20244910 TATGTAAGTT
Statistics
Matches: 67, Mismatches: 17, Indels: 14
0.68 0.17 0.14
Matches are distributed among these distances:
15 4 0.06
16 9 0.13
17 12 0.18
18 29 0.43
19 13 0.19
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (17 bp):
TATGATATATATTTATG
Found at i:20244876 original size:52 final size:52
Alignment explanation
Indices: 20244814--20244932 Score: 204
Period size: 52 Copynumber: 2.3 Consensus size: 52
20244804 TGAGATATAT
20244814 TTATGTAAGTTATGTA-ACTTATGATATGATATATATTTATGTAGTATGTAAG
1 TTATGTAAGTTATG-ACACTTATGATATGATATATATTTATGTAGTATGTAAG
* *
20244866 TTATGTAAGTTATGACATTTATGATATGATATATATTTATGTATTATGTAAG
1 TTATGTAAGTTATGACACTTATGATATGATATATATTTATGTAGTATGTAAG
20244918 TTATGTAAGTTATGA
1 TTATGTAAGTTATGA
20244933 AATTTGAACT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
51 1 0.02
52 63 0.98
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (52 bp):
TTATGTAAGTTATGACACTTATGATATGATATATATTTATGTAGTATGTAAG
Found at i:20255922 original size:15 final size:15
Alignment explanation
Indices: 20255891--20255936 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
20255881 TTAAAACACT
* *
20255891 AAACCATAAGCCTTA
1 AAACCATAAACCCTA
20255906 AAACCATAAACCCTA
1 AAACCATAAACCCTA
20255921 AATA-C-TAAACCCTA
1 AA-ACCATAAACCCTA
20255935 AA
1 AA
20255937 GAATAAGCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 11 0.39
15 16 0.57
16 1 0.04
ACGTcount: A:0.52, C:0.28, G:0.02, T:0.17
Consensus pattern (15 bp):
AAACCATAAACCCTA
Found at i:20255931 original size:14 final size:14
Alignment explanation
Indices: 20255911--20255950 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
20255901 CCTTAAAACC
*
20255911 ATAAACCCTAAATA
1 ATAAACCCTAAAGA
*
20255925 CTAAACCCTAAAGA
1 ATAAACCCTAAAGA
*
20255939 ATAAGCCCTAAA
1 ATAAACCCTAAA
20255951 CCTTAAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.25, G:0.05, T:0.17
Consensus pattern (14 bp):
ATAAACCCTAAAGA
Found at i:20255963 original size:21 final size:21
Alignment explanation
Indices: 20255925--20255978 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
20255915 ACCCTAAATA
* *
20255925 CTAAACCCTAAAGAATAAGCC
1 CTAAACCTTAAAGAATAAACC
**
20255946 CTAAACCTTAAATTATAAACC
1 CTAAACCTTAAAGAATAAACC
*
20255967 TTAAACCTTAAA
1 CTAAACCTTAAA
20255979 ATAAAATGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.48, C:0.24, G:0.04, T:0.24
Consensus pattern (21 bp):
CTAAACCTTAAAGAATAAACC
Found at i:20256403 original size:124 final size:123
Alignment explanation
Indices: 20256138--20256420 Score: 404
Period size: 124 Copynumber: 2.3 Consensus size: 123
20256128 AACAATGCTA
* * * * *
20256138 TTTAAGTCAAATAGGTATTGTAATTTTGCGGCGTTTATGAAAAACGCCGCTAATGTATAACCTTT
1 TTTAAGTCAAATTGGTATTGCAATTTTGCGGCATTTATGAAAAACGCCACTAATATATAACCTTT
* * * * **
20256203 GTGGCATTCCAGTCAAAACACCAATAAAAACTTCATTCCCTATAGTGAAACGACGTTG
66 GCGGCATTCCAGTCAAAACACCAACAAAAACTTAAATCCCTATAGTGAAACGACGCCG
20256261 TTTAAGTCAAATTGGTATTGCAATTTTGCGGCATTTATGAAAAACGCCACTAATATATAACCTTT
1 TTTAAGTCAAATTGGTATTGCAATTTTGCGGCATTTATGAAAAACGCCACTAATATATAACCTTT
* * * * *
20256326 GCGGCATTTTCTGTCGAAACACCACCAAAAACTTAAATCCCTGTAGTGAAACGACGCCG
66 GCGGCA-TTCCAGTCAAAACACCAACAAAAACTTAAATCCCTATAGTGAAACGACGCCG
*
20256385 TTTAAGTCAAATTGGTATTGCATTTTTGCGGCATTT
1 TTTAAGTCAAATTGGTATTGCAATTTTGCGGCATTT
20256421 TCGGTCAAAA
Statistics
Matches: 142, Mismatches: 17, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
123 65 0.46
124 77 0.54
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (123 bp):
TTTAAGTCAAATTGGTATTGCAATTTTGCGGCATTTATGAAAAACGCCACTAATATATAACCTTT
GCGGCATTCCAGTCAAAACACCAACAAAAACTTAAATCCCTATAGTGAAACGACGCCG
Found at i:20256472 original size:86 final size:86
Alignment explanation
Indices: 20256323--20256500 Score: 275
Period size: 86 Copynumber: 2.1 Consensus size: 86
20256313 ATATATAACC
* * * *
20256323 TTTGCGGCATTTTCTGTCGAAACACCACCAAAAACTTAAATCCCTGTAGTGAAACGACGCCGTTT
1 TTTGCGGCATTTTCGGTCAAAACACCACCAAAAACTTAAATCCCTATAGTGAAACGACACCGTTT
*
20256388 AAGTCAAATTGGTATTGCATT
66 AAGTCAAATTGGTATTGCAAT
* * * *
20256409 TTTGCGGCATTTTCGGTCAAAACGCCACTAAAAATTTAATTCCCTATAGTGAAACGACACCGTTT
1 TTTGCGGCATTTTCGGTCAAAACACCACCAAAAACTTAAATCCCTATAGTGAAACGACACCGTTT
20256474 AAGTCAAATTGGTATTGCAAT
66 AAGTCAAATTGGTATTGCAAT
20256495 TTTGCG
1 TTTGCG
20256501 ATGTTTATGA
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 83 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (86 bp):
TTTGCGGCATTTTCGGTCAAAACACCACCAAAAACTTAAATCCCTATAGTGAAACGACACCGTTT
AAGTCAAATTGGTATTGCAAT
Found at i:20256605 original size:98 final size:98
Alignment explanation
Indices: 20256433--20256626 Score: 291
Period size: 98 Copynumber: 2.0 Consensus size: 98
20256423 GGTCAAAACG
*
20256433 CCACTAAAAATTTAATTCCCTATAGTGAAACGACACCGTTTAAGTCAAATTGGTATTGCAATTTT
1 CCACTAAAAATTTAATGCCCTATAGTGAAACGACACCGTTTAAGTCAAATTGGTATTGCAATTTT
*
20256498 GCGATGTTTATGAAAAACACCACTAATGTATGA
66 GCGACGTTTATGAAAAACACCACTAATGTATGA
* * **
20256531 CCACTAAAAATTTAATGCTCTATAGTGAAACGACGCCGTTTAAGTTGAATTGGTATTGCAATTTT
1 CCACTAAAAATTTAATGCCCTATAGTGAAACGACACCGTTTAAGTCAAATTGGTATTGCAATTTT
* **
20256596 GTTG-CGTTTATGAAAAATGCCACTAATGTAT
66 G-CGACGTTTATGAAAAACACCACTAATGTAT
20256627 CACCTTTGTG
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
98 85 0.99
99 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (98 bp):
CCACTAAAAATTTAATGCCCTATAGTGAAACGACACCGTTTAAGTCAAATTGGTATTGCAATTTT
GCGACGTTTATGAAAAACACCACTAATGTATGA
Found at i:20260116 original size:21 final size:21
Alignment explanation
Indices: 20260084--20260124 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
20260074 AAGCTTGAGG
20260084 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
20260105 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
20260125 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:20264873 original size:11 final size:12
Alignment explanation
Indices: 20264854--20264882 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
20264844 AAAAATTAAA
20264854 AAAATATATTTT
1 AAAATATATTTT
20264866 AAAA-ATATTTT
1 AAAATATATTTT
20264877 AAAATA
1 AAAATA
20264883 AAAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAATATATTTT
Found at i:20265822 original size:11 final size:11
Alignment explanation
Indices: 20265806--20265856 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
20265796 AAGAAACTAA
*
20265806 TGTTTTCTTGT
1 TGTTTTCTTAT
20265817 TGTTTT-TTCAT
1 TGTTTTCTT-AT
*
20265828 TGTTTTCTTGT
1 TGTTTTCTTAT
* *
20265839 TGCTTTCTCAT
1 TGTTTTCTTAT
20265850 TGTTTTC
1 TGTTTTC
20265857 CTGTAATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
10 2 0.06
11 28 0.88
12 2 0.06
ACGTcount: A:0.04, C:0.14, G:0.14, T:0.69
Consensus pattern (11 bp):
TGTTTTCTTAT
Found at i:20265834 original size:22 final size:22
Alignment explanation
Indices: 20265806--20265856 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
20265796 AAGAAACTAA
* *
20265806 TGTTTTCTTGTTGTTTTTTCAT
1 TGTTTTCTTGTTGCTTTCTCAT
20265828 TGTTTTCTTGTTGCTTTCTCAT
1 TGTTTTCTTGTTGCTTTCTCAT
20265850 TGTTTTC
1 TGTTTTC
20265857 CTGTAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.04, C:0.14, G:0.14, T:0.69
Consensus pattern (22 bp):
TGTTTTCTTGTTGCTTTCTCAT
Found at i:20266384 original size:18 final size:20
Alignment explanation
Indices: 20266353--20266389 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
20266343 GTAACTTACT
*
20266353 ATTTTTTTATGATT-TTTTA
1 ATTTTTTGATGATTGTTTTA
20266372 ATTTTTTGA-GATTGTTTT
1 ATTTTTTGATGATTGTTTT
20266390 TTGAATTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.19, C:0.00, G:0.11, T:0.70
Consensus pattern (20 bp):
ATTTTTTGATGATTGTTTTA
Found at i:20266411 original size:22 final size:21
Alignment explanation
Indices: 20266365--20266412 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
20266355 TTTTTTATGA
* *
20266365 TTTTTTAATTTTTTGAGATTG
1 TTTTTTAATTTTTTGACAATG
20266386 TTTTTTGAATTTGTTTGACAAT-
1 TTTTTT-AATTT-TTTGACAATG
20266408 TTTTT
1 TTTTT
20266413 ATATTTTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 6 0.26
22 10 0.43
23 7 0.30
ACGTcount: A:0.19, C:0.02, G:0.12, T:0.67
Consensus pattern (21 bp):
TTTTTTAATTTTTTGACAATG
Found at i:20269141 original size:11 final size:11
Alignment explanation
Indices: 20269125--20269156 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
20269115 TGTTACCCCT
20269125 AAAACAAGCCA
1 AAAACAAGCCA
20269136 AAAACAAGCCA
1 AAAACAAGCCA
20269147 AAAACAAGCC
1 AAAACAAGCC
20269157 TACTTCTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.62, C:0.28, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAACAAGCCA
Found at i:20270091 original size:20 final size:19
Alignment explanation
Indices: 20270065--20270165 Score: 64
Period size: 20 Copynumber: 5.1 Consensus size: 19
20270055 ATAGATGCGT
*
20270065 AACAGAGGAACCGAAGTGT
1 AACAGAGGAACCGAAGTGC
*
20270084 AGACAGAGGCAA--AAATGTGC
1 A-ACAGAGG-AACCGAA-GTGC
* *
20270104 AATCAGAGGCACCGTAGTGC
1 AA-CAGAGGAACCGAAGTGC
* *
20270124 AA-ATAGAGACACCGAAGTGT
1 AACAGAG-GA-ACCGAAGTGC
20270144 ATACAGAGGAACCGAAGTGC
1 A-ACAGAGGAACCGAAGTGC
20270164 AA
1 AA
20270166 TCCCGTACAA
Statistics
Matches: 61, Mismatches: 11, Indels: 20
0.66 0.12 0.22
Matches are distributed among these distances:
18 3 0.05
19 7 0.11
20 42 0.69
21 6 0.10
22 3 0.05
ACGTcount: A:0.42, C:0.18, G:0.29, T:0.12
Consensus pattern (19 bp):
AACAGAGGAACCGAAGTGC
Found at i:20272305 original size:13 final size:13
Alignment explanation
Indices: 20272287--20272311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20272277 CACCCCAAAC
20272287 ACAGATACAGAAT
1 ACAGATACAGAAT
20272300 ACAGATACAGAA
1 ACAGATACAGAA
20272312 ATAACAGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.16, T:0.12
Consensus pattern (13 bp):
ACAGATACAGAAT
Found at i:20273266 original size:5 final size:5
Alignment explanation
Indices: 20273256--20273281 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20273246 GAAGAGAGAA
20273256 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
20273282 GGATTTAAGT
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:20277746 original size:13 final size:13
Alignment explanation
Indices: 20277730--20277755 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20277720 AACTAAGATA
20277730 AATAAAATCAAAT
1 AATAAAATCAAAT
20277743 AATAAAATCAAAT
1 AATAAAATCAAAT
20277756 GTTGGACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAAAATCAAAT
Found at i:20288638 original size:50 final size:50
Alignment explanation
Indices: 20288533--20288774 Score: 220
Period size: 50 Copynumber: 4.7 Consensus size: 50
20288523 GGGAATGAGA
* **
20288533 TCCCAGGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGATTACGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGC---ACCGAGA-T--GAGAGG
*
20288589 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * **
20288639 TCCTCA-GTAAGACCAAGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCC-CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * **
20288689 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAGGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGG
* * *
20288738 TCGCATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
20288775 TGTTATTATC
Statistics
Matches: 159, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
48 1 0.01
49 39 0.25
50 77 0.48
51 2 0.01
52 1 0.01
53 5 0.03
56 34 0.21
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:20288993 original size:12 final size:12
Alignment explanation
Indices: 20288976--20289003 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
20288966 ATGAGTTATT
20288976 TAAGTAAACAAG
1 TAAGTAAACAAG
20288988 TAAGTAAACAAG
1 TAAGTAAACAAG
20289000 TAAG
1 TAAG
20289004 AGAGTAAGTA
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:0.57, C:0.07, G:0.18, T:0.18
Consensus pattern (12 bp):
TAAGTAAACAAG
Found at i:20289024 original size:12 final size:12
Alignment explanation
Indices: 20289009--20289041 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
20288999 GTAAGAGAGT
20289009 AAGTAAAGAAGA
1 AAGTAAAGAAGA
20289021 AAGTAAAGAAGA
1 AAGTAAAGAAGA
20289033 AAGTAAAGA
1 AAGTAAAGA
20289042 TCATGATACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (12 bp):
AAGTAAAGAAGA
Found at i:20304619 original size:55 final size:55
Alignment explanation
Indices: 20304468--20304626 Score: 189
Period size: 55 Copynumber: 2.9 Consensus size: 55
20304458 TTTATTTTAT
* * * * *
20304468 TTCCCCACATGACGCCATAGTCCCAAACTAGTTCTTACACTATGTGGTTCTCTTA
1 TTCCCCATATGATGCCATAGTCCCAGACTAGGTCTTACACTATATGGTTCTCTTA
* *
20304523 -TCCCCATATGATGCCACAGCCACCATGACTAGGTCTTACACTATATGGTT-T-TTCA
1 TTCCCCATATGATGCCATAGTC-CCA-GACTAGGTCTTACACTATATGGTTCTCTT-A
*
20304578 CTTCCCCATATGATGCCATAGTCTCAGACTAGGTCTTACACTATATGGT
1 -TTCCCCATATGATGCCATAGTCCCAGACTAGGTCTTACACTATATGGT
20304627 CTTCTTGCCA
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
54 19 0.21
55 28 0.31
56 23 0.26
57 19 0.21
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (55 bp):
TTCCCCATATGATGCCATAGTCCCAGACTAGGTCTTACACTATATGGTTCTCTTA
Found at i:20305335 original size:34 final size:34
Alignment explanation
Indices: 20305292--20305356 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
20305282 ATATAGGCAG
20305292 AGAATACTTCCTGAGGAAGTAATGCGCAGTTCCT
1 AGAATACTTCCTGAGGAAGTAATGCGCAGTTCCT
20305326 AGAATACTTCCTGAGGAAGTAATGCGCAGTT
1 AGAATACTTCCTGAGGAAGTAATGCGCAGTT
20305357 GCCAGCACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (34 bp):
AGAATACTTCCTGAGGAAGTAATGCGCAGTTCCT
Found at i:20312470 original size:10 final size:10
Alignment explanation
Indices: 20312455--20312481 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
20312445 TATAATTTAT
20312455 ATTTTAATGA
1 ATTTTAATGA
20312465 ATTTTAATGA
1 ATTTTAATGA
20312475 ATTTTAA
1 ATTTTAA
20312482 ATTTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (10 bp):
ATTTTAATGA
Found at i:20320099 original size:84 final size:84
Alignment explanation
Indices: 20319989--20320143 Score: 226
Period size: 84 Copynumber: 1.8 Consensus size: 84
20319979 ACTTTTTCGA
* * *
20319989 AAAAAAATAATTAAGCTCCTGCTTTTTTTTGCACTCAAGT-GGATACTTAAACT-TTCAAAATTC
1 AAAAAAATAATTAAGCCCCTGATTTTTTTTGCACTCAAGTAGG-TACTTAAACTGTT--AAATGC
20320052 ATCAAAAAGACCCTCAAACTTT
63 ATCAAAAAGACCCTCAAACTTT
*
20320074 AAAAAAA-AATTAAGCCCCTGATTTTTTTTGCACTCAATTAGGTACTTAAACTGTTAAATGCATC
1 AAAAAAATAATTAAGCCCCTGATTTTTTTTGCACTCAAGTAGGTACTTAAACTGTTAAATGCATC
20320138 AAAAAG
66 AAAAAG
20320144 GTCTTTTGAC
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
83 14 0.22
84 39 0.61
85 11 0.17
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (84 bp):
AAAAAAATAATTAAGCCCCTGATTTTTTTTGCACTCAAGTAGGTACTTAAACTGTTAAATGCATC
AAAAAGACCCTCAAACTTT
Found at i:20320342 original size:19 final size:19
Alignment explanation
Indices: 20320318--20320381 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
20320308 AAATTATAAA
20320318 AAAAAACTATAAAAATCAT
1 AAAAAACTATAAAAATCAT
**
20320337 AAAAAACTATAAAAAGTTGT
1 AAAAAACTATAAAAA-TCAT
***
20320357 AAAATTTTATAAAAATCAT
1 AAAAAACTATAAAAATCAT
20320376 AAAAAA
1 AAAAAA
20320382 TCATAAAATG
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 21 0.60
20 14 0.40
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.25
Consensus pattern (19 bp):
AAAAAACTATAAAAATCAT
Found at i:20320598 original size:20 final size:19
Alignment explanation
Indices: 20320573--20320732 Score: 67
Period size: 20 Copynumber: 7.8 Consensus size: 19
20320563 TTAGTATGAT
*
20320573 AATTTTATAATTTTTTTATG
1 AATTTTATAATTTTTTTA-C
*
20320593 AATTTTAT-ATTTCTTTAC
1 AATTTTATAATTTTTTTAC
*
20320611 AATTTTTATAATTTTCTTAC
1 AA-TTTTATAATTTTTTTAC
* * *
20320631 GACTTTATAAAATTTTATATTTCTAT
1 -AATTT-TATAA--TT-T-TTT-TAC
20320657 ATATTTTATAATTTTTTTAAC
1 A-ATTTTATAATTTTTTT-AC
* **
20320678 GATTTTTATAA-AATTTTAC
1 -AATTTTATAATTTTTTTAC
*
20320697 AATTTTTATAAATTTTTATA-
1 AA-TTTTAT-AATTTTTTTAC
20320717 AATTTT-TATATTTTTT
1 AATTTTATA-ATTTTTT
20320733 ATATTTTTTA
Statistics
Matches: 105, Mismatches: 19, Indels: 34
0.66 0.12 0.22
Matches are distributed among these distances:
17 1 0.01
18 10 0.10
19 26 0.25
20 28 0.27
21 21 0.20
22 2 0.02
23 4 0.04
24 1 0.01
25 7 0.07
26 5 0.05
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (19 bp):
AATTTTATAATTTTTTTAC
Found at i:20320653 original size:48 final size:49
Alignment explanation
Indices: 20320593--20320722 Score: 151
Period size: 48 Copynumber: 2.7 Consensus size: 49
20320583 TTTTTTTATG
20320593 AATTTTATATTTCTTTACAATTTTTATAATTTTCTT-ACGA-CTTTATAA
1 AATTTTATATTTCTTTA-AATTTTTATAATTTTCTTAACGATCTTTATAA
* * * *
20320641 AATTTTATATTTCTATATA-TTTTATAATTTTTTTAACGATTTTTATAA
1 AATTTTATATTTCTTTAAATTTTTATAATTTTCTTAACGATCTTTATAA
*
20320689 AATTTTACAATTT-TTATAAATTTTTATAAATTTT
1 AATTTTA-TATTTCTT-TAAATTTTTAT-AATTTT
20320723 TATATTTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
46 14 0.20
47 5 0.07
48 31 0.45
49 7 0.10
50 6 0.09
51 6 0.09
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (49 bp):
AATTTTATATTTCTTTAAATTTTTATAATTTTCTTAACGATCTTTATAA
Found at i:20320687 original size:67 final size:66
Alignment explanation
Indices: 20320573--20320741 Score: 171
Period size: 67 Copynumber: 2.5 Consensus size: 66
20320563 TTAGTATGAT
* * * ** *
20320573 AATTTTATAATTTTTTTATGAATTTTATATTTCTTTACAATTTTTATAATTTTCTTACGA-CTTT
1 AATTTTATAATTTCTATAT--ATTTTATATTTTTTTACAATTTTTATAAAATT-TTACAATCTTT
20320637 ATAA
63 ATAA
* *
20320641 AATTTTAT-ATTTCTATATATTTTATAATTTTTTTAACGATTTTTATAAAATTTTACAATTTTTA
1 AATTTTATAATTTCTATATATTTTAT-ATTTTTTT-ACAATTTTTATAAAATTTTACAATCTTTA
20320705 TAA
64 TAA
* * *
20320708 ATTTTTATAAATTTTTATATTTTTTATATTTTTT
1 AATTTTAT-AATTTCTATATATTTTATATTTTTT
20320742 ATTAAAATTT
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
65 7 0.08
66 12 0.14
67 36 0.42
68 15 0.18
69 15 0.18
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (66 bp):
AATTTTATAATTTCTATATATTTTATATTTTTTTACAATTTTTATAAAATTTTACAATCTTTATA
A
Found at i:20320703 original size:19 final size:19
Alignment explanation
Indices: 20320679--20320766 Score: 88
Period size: 19 Copynumber: 4.5 Consensus size: 19
20320669 TTTTTTAACG
*
20320679 ATTTTTATAAAATTTTACA
1 ATTTTTATAAAATTTTATA
*
20320698 ATTTTTATAAATTTTTATAA
1 ATTTTTATAAAATTTTAT-A
**
20320718 ATTTTTAT-ATTTTTTATA
1 ATTTTTATAAAATTTTATA
* *
20320736 TTTTTTATTAAAATTTAATA
1 ATTTTTA-TAAAATTTTATA
20320756 ATTTTTTATAA
1 A-TTTTTATAA
20320767 CTTTTATTGA
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
18 7 0.12
19 25 0.44
20 19 0.33
21 6 0.11
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTTATAAAATTTTATA
Found at i:20320712 original size:29 final size:29
Alignment explanation
Indices: 20320659--20320771 Score: 120
Period size: 29 Copynumber: 3.8 Consensus size: 29
20320649 ATTTCTATAT
*
20320659 ATTTTATAATTTTTTTAACGATTTTTATAAA
1 ATTTTATAATTTTTATAA--ATTTTTATAAA
*
20320690 ATTTTACAATTTTTATAAATTTTTATAAA
1 ATTTTATAATTTTTATAAATTTTTATAAA
* * *
20320719 TTTTTATATTTTTTAT-ATTTTTTATTAAA
1 ATTTTATAATTTTTATAAATTTTTA-TAAA
* *
20320748 ATTTAATAATTTTTTATAACTTTT
1 ATTTTATAA-TTTTTATAAATTTT
20320772 ATTGATTTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
28 7 0.10
29 34 0.49
30 7 0.10
31 21 0.30
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (29 bp):
ATTTTATAATTTTTATAAATTTTTATAAA
Found at i:20320732 original size:10 final size:10
Alignment explanation
Indices: 20320634--20320771 Score: 92
Period size: 10 Copynumber: 14.2 Consensus size: 10
20320624 TTCTTACGAC
*
20320634 TTTATAAAAT
1 TTTATAAATT
20320644 TTTAT--ATT
1 TTTATAAATT
* *
20320652 TCTATATA-T
1 TTTATAAATT
20320661 TTTAT-AATT
1 TTTATAAATT
*
20320670 TTTTTAACGATT
1 TTTATAA--ATT
*
20320682 TTTATAAAAT
1 TTTATAAATT
*
20320692 TTTA-CAATT
1 TTTATAAATT
20320701 TTTATAAATT
1 TTTATAAATT
20320711 TTTATAAATT
1 TTTATAAATT
*
20320721 TTTAT-ATTT
1 TTTATAAATT
*
20320730 TTTAT-ATTT
1 TTTATAAATT
*
20320739 TTTATTAAAAT
1 TTTA-TAAATT
* *
20320750 TTAATAATTT
1 TTTATAAATT
*
20320760 TTTATAACTT
1 TTTATAAATT
20320770 TT
1 TT
20320772 ATTGATTTTT
Statistics
Matches: 101, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
8 7 0.07
9 33 0.33
10 47 0.47
11 5 0.05
12 9 0.09
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (10 bp):
TTTATAAATT
Found at i:20320788 original size:9 final size:10
Alignment explanation
Indices: 20320646--20320743 Score: 71
Period size: 9 Copynumber: 10.1 Consensus size: 10
20320636 TATAAAATTT
*
20320646 TATATTTCTA
1 TATATTTTTA
20320656 TATA-TTTTA
1 TATATTTTTA
*
20320665 TA-ATTTTTT
1 TATATTTTTA
*
20320674 TAACGATTTTTA
1 T-A-TATTTTTA
* *
20320686 TAAAATTTTA
1 TATATTTTTA
*
20320696 CA-ATTTTTA
1 TATATTTTTA
*
20320705 TAAATTTTTA
1 TATATTTTTA
*
20320715 TAAATTTTTA
1 TATATTTTTA
20320725 TAT-TTTTTA
1 TATATTTTTA
20320734 TAT-TTTTTA
1 TATATTTTTA
20320743 T
1 T
20320744 TAAAATTTAA
Statistics
Matches: 74, Mismatches: 9, Indels: 11
0.79 0.10 0.12
Matches are distributed among these distances:
8 1 0.01
9 34 0.46
10 31 0.42
11 1 0.01
12 7 0.09
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (10 bp):
TATATTTTTA
Found at i:20321224 original size:32 final size:31
Alignment explanation
Indices: 20321178--20321274 Score: 176
Period size: 31 Copynumber: 3.1 Consensus size: 31
20321168 TCTTAGATAA
20321178 CTTTAAAGAGTTTTATTAGGATTCAATTACT
1 CTTTAAAGAGTTTTATTAGGATTCAATTACT
20321209 CTTTAAAGAGTTTTTATTAGGATTCAATTACT
1 CTTTAAAGAG-TTTTATTAGGATTCAATTACT
*
20321241 CTTGAAAGAGTTTTATTAGGATTCAATTACT
1 CTTTAAAGAGTTTTATTAGGATTCAATTACT
20321272 CTT
1 CTT
20321275 GTAATTTGCC
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
31 34 0.53
32 30 0.47
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (31 bp):
CTTTAAAGAGTTTTATTAGGATTCAATTACT
Found at i:20321857 original size:9 final size:10
Alignment explanation
Indices: 20321820--20321894 Score: 91
Period size: 10 Copynumber: 7.4 Consensus size: 10
20321810 TTCTTTAAAT
20321820 AAAAGCAAAA
1 AAAAGCAAAA
20321830 AAATAGC-AAA
1 AAA-AGCAAAA
*
20321840 AACAGCAAAA
1 AAAAGCAAAA
20321850 AAAA-CAAAA
1 AAAAGCAAAA
*
20321859 AAAAGAAAAA
1 AAAAGCAAAA
20321869 AAAAGCGCAAAA
1 AAAA--GCAAAA
20321881 AAAAGCAAAA
1 AAAAGCAAAA
20321891 AAAA
1 AAAA
20321895 AGCTCAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
9 12 0.21
10 32 0.57
11 3 0.05
12 9 0.16
ACGTcount: A:0.79, C:0.11, G:0.09, T:0.01
Consensus pattern (10 bp):
AAAAGCAAAA
Found at i:20321880 original size:13 final size:13
Alignment explanation
Indices: 20321864--20321909 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
20321854 CAAAAAAAAG
20321864 AAAAAAAAAGCGC
1 AAAAAAAAAGCGC
20321877 -AAAAAAAA--GC
1 AAAAAAAAAGCGC
*
20321887 AAAAAAAAAGCTC
1 AAAAAAAAAGCGC
20321900 AAAAAAAAAG
1 AAAAAAAAAG
20321910 TTGCCTACCT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 8 0.28
12 8 0.28
13 11 0.38
ACGTcount: A:0.76, C:0.11, G:0.11, T:0.02
Consensus pattern (13 bp):
AAAAAAAAAGCGC
Found at i:20321894 original size:11 final size:11
Alignment explanation
Indices: 20321820--20321909 Score: 84
Period size: 9 Copynumber: 8.5 Consensus size: 11
20321810 TTCTTTAAAT
20321820 AAAAGCAAAAA
1 AAAAGCAAAAA
*
20321831 AATAGC--AAA
1 AAAAGCAAAAA
*
20321840 AACAGC-AAAA
1 AAAAGCAAAAA
20321850 AAAA-C-AAAA
1 AAAAGCAAAAA
20321859 AAAAG-AAAAA
1 AAAAGCAAAAA
*
20321869 AAAAGCGCAAAA
1 AAAAGC-AAAAA
20321881 AAAAGCAAAAA
1 AAAAGCAAAAA
20321892 AAAAGCTCAAAAA
1 AAAAG--CAAAAA
20321905 AAAAG
1 AAAAG
20321910 TTGCCTACCT
Statistics
Matches: 67, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
9 17 0.25
10 15 0.22
11 14 0.21
12 10 0.15
13 11 0.16
ACGTcount: A:0.77, C:0.11, G:0.10, T:0.02
Consensus pattern (11 bp):
AAAAGCAAAAA
Found at i:20326477 original size:32 final size:31
Alignment explanation
Indices: 20326432--20326527 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
20326422 CTTAGATAAT
20326432 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
20326463 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
* *
20326495 TTGAAATAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
20326526 TT
1 TT
20326528 GTAATTTGCC
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 33 0.53
32 29 0.47
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:20328529 original size:20 final size:20
Alignment explanation
Indices: 20328507--20328544 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20328497 CCAAATCCTT
*
20328507 TTTTGTTCA-TTTTTATTTA
1 TTTTATTCATTTTTTATTTA
20328526 TTTTATTCATTTTTTATTT
1 TTTTATTCATTTTTTATTT
20328545 TGTTTTGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTATTCATTTTTTATTTA
Found at i:20329369 original size:12 final size:12
Alignment explanation
Indices: 20329348--20329377 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
20329338 TTTTATATTT
20329348 TATA-ATTTTTA
1 TATACATTTTTA
20329359 TATACATTTTTA
1 TATACATTTTTA
20329371 TATACAT
1 TATACAT
20329378 ATACGTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (12 bp):
TATACATTTTTA
Found at i:20332150 original size:15 final size:15
Alignment explanation
Indices: 20332127--20332169 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
20332117 TTTAGGCATA
*
20332127 CATTTCATGCATTTG
1 CATTACATGCATTTG
20332142 CATTACATGCATTTG
1 CATTACATGCATTTG
*
20332157 CACTACATGCATT
1 CATTACATGCATT
20332170 AAAGTCCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.40
Consensus pattern (15 bp):
CATTACATGCATTTG
Found at i:20336648 original size:87 final size:87
Alignment explanation
Indices: 20336483--20336750 Score: 376
Period size: 87 Copynumber: 3.1 Consensus size: 87
20336473 AGATTGGTGA
* * * * * *
20336483 AGATTGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGTTGGTGAAAGATAACAGATCTTGT
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* * *
20336548 TTTCATGCGTTAACAACGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* *
20336570 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATTTTAC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
20336635 CTTCCTGCATTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
** * *
20336657 AGATCGAAAATGAAGCCTTGCCTCCATTGGTTGCAGTGGAGCTGGTTAAAGATAGCAGGTCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
20336722 CTT-CTGCGTTAACAGTGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
20336743 AGATCGAA
1 AGATCGAA
20336751 GATTACAAGT
Statistics
Matches: 161, Mismatches: 20, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
86 24 0.15
87 137 0.85
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (87 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCGTTAACAGCGAAGC
Found at i:20336871 original size:44 final size:44
Alignment explanation
Indices: 20336804--20337127 Score: 157
Period size: 43 Copynumber: 7.6 Consensus size: 44
20336794 AAATTACAAG
** *
20336804 TCTTATCTCCCT-AAGCAGTAGTGGAGCAGACAGAAGAAATCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAA
* * **
20336847 TCCTATCTCCCTGAAGTTGCAGTGGAGC-G-GATTA-AAATCATAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATC--A-A
* ** * *
20336891 TCTTATCTCTCTGAAGTTGCAGT--AG-AG-CAGATCACATCGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATC-AA
** * *
20336932 TCTTATCTCCCT-AAGCAGTAGTGGAGCAAACAGAAGAAATCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAA
* * * *
20336975 TCCTATCTCCCTGAAGTTGCAGTGGAG-GGATTA-AA-ACCA-CAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAGAAGA-AATCA-A
* * *
20337018 TCTTATCTCTCTGAAGTTGCAGT--AG-AG-CAGATTG-CATCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AGAAATCAA
** * *
20337058 GTCTTATCTCCCT-AAGCAGTAGTGGAGCAGAC-GAAAGAAATAAA
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAG-AAGAAATCAA
* *
20337102 TCCTATCTCCCCGAAGTTGCAGTGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGA
20337128 ATGGATAAAA
Statistics
Matches: 205, Mismatches: 50, Indels: 51
0.67 0.16 0.17
Matches are distributed among these distances:
39 1 0.00
40 18 0.09
41 32 0.16
42 14 0.07
43 70 0.34
44 70 0.34
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAA
Found at i:20337083 original size:127 final size:128
Alignment explanation
Indices: 20336800--20337127 Score: 561
Period size: 127 Copynumber: 2.6 Consensus size: 128
20336790 TTGGAAATTA
20336800 CAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
1 CAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
* *
20336865 GCAGTGGAGCGGATTAAAATCATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACAT
66 GCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACAT
* *
20336928 CGAGTCTTATCTCCCTAAGCAGTAGTGGAGCAAACAGAAGAAATCAATCCTATCTCCCTGAAGTT
1 CAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
**
20336993 GCAGTGGAG-GGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGCAT
66 GCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACAT
* *
20337055 CAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGAC-GAAAGAAATAAATCCTATCTCCCCGAAGT
1 CAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAG-AAGAAATCAATCCTATCTCCCTGAAGT
20337119 TGCAGTGGA
65 TGCAGTGGA
20337128 ATGGATAAAA
Statistics
Matches: 189, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
126 1 0.01
127 116 0.61
128 72 0.38
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (128 bp):
CAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
GCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACAT
Found at i:20337857 original size:19 final size:20
Alignment explanation
Indices: 20337835--20337879 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
20337825 CCAAATCCTT
20337835 TTTTGTTCA-TTTTTATTTA
1 TTTTGTTCATTTTTTATTTA
* *
20337854 TTTTATTCATTTTTTATTTT
1 TTTTGTTCATTTTTTATTTA
20337874 TTTTGT
1 TTTTGT
20337880 GCAAAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.78
Consensus pattern (20 bp):
TTTTGTTCATTTTTTATTTA
Found at i:20337867 original size:20 final size:18
Alignment explanation
Indices: 20337833--20337876 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
20337823 TTCCAAATCC
*
20337833 TTTTTTGTTCATTTTTAT
1 TTTTTTATTCATTTTTAT
20337851 TTATTTTATTCATTTTTTAT
1 TT-TTTTATTCA-TTTTTAT
20337871 TTTTTT
1 TTTTTT
20337877 TGTGCAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 12 0.52
20 9 0.39
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTTTATTCATTTTTAT
Found at i:20338446 original size:3 final size:3
Alignment explanation
Indices: 20338438--20338477 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
20338428 ATTTTCTTAA
20338438 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
20338478 TCCTCATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:20338587 original size:23 final size:22
Alignment explanation
Indices: 20338545--20338587 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
20338535 ATGTGCATGC
*
20338545 GTACATTTTTTTTATATTATAT
1 GTACATTTTTTTAATATTATAT
20338567 GTACATATTTTTGTAAT-TTAT
1 GTACAT-TTTTT-TAATATTAT
20338588 TTATTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 6 0.33
23 9 0.50
24 3 0.17
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (22 bp):
GTACATTTTTTTAATATTATAT
Found at i:20339488 original size:108 final size:107
Alignment explanation
Indices: 20339264--20339467 Score: 331
Period size: 108 Copynumber: 1.9 Consensus size: 107
20339254 ATAATAAAGG
*
20339264 CAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTAGGTTTCGATTTTTCTCAT
1 CAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTAGGTTTCGA-TTTTCTCAT
*
20339329 TCGACCAAATAGCCAAATATCCTTTTAAAATTTCGAAGTAAGA
65 TCGACCAAATAGCCAAATATCCTCTTAAAATTTCGAAGTAAGA
* * *
20339372 CAATATTTTGCGTTTGGAAATTCGAGGAAACGTGCCCTAATGTGCTGGGTTTCGA-TTTCTCGTT
1 CAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTAGGTTTCGATTTTCTCATT
*
20339436 TGACCAAATAGCCAAATATCCTCTT-AAATTTC
66 CGACCAAATAGCCAAATATCCTCTTAAAATTTC
20339468 AATCCATGTC
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
105 7 0.08
106 31 0.34
108 52 0.58
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (107 bp):
CAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTAGGTTTCGATTTTCTCATT
CGACCAAATAGCCAAATATCCTCTTAAAATTTCGAAGTAAGA
Found at i:20358369 original size:21 final size:23
Alignment explanation
Indices: 20358315--20358370 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 23
20358305 ACCCCATTAA
*
20358315 AATA-TAAT-TTAAGAATAATTT
1 AATAGTAATATTAAAAATAATTT
20358336 AATAGTAA-A-TAAAAATAA-TT
1 AATAGTAATATTAAAAATAATTT
20358356 -ATAGTAATATTAAAA
1 AATAGTAATATTAAAA
20358371 CAATACCTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 7 0.23
20 3 0.10
21 17 0.57
22 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (23 bp):
AATAGTAATATTAAAAATAATTT
Found at i:20363362 original size:9 final size:9
Alignment explanation
Indices: 20363348--20363390 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
20363338 GCTGTCTAAA
20363348 TTAATGAAT
1 TTAATGAAT
*
20363357 TTAATGAAA
1 TTAATGAAT
*
20363366 TT-ATTAAT
1 TTAATGAAT
20363374 TTAATGAAT
1 TTAATGAAT
20363383 TTAATGAA
1 TTAATGAA
20363391 ATTATTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 6 0.21
9 23 0.79
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (9 bp):
TTAATGAAT
Found at i:20363377 original size:26 final size:26
Alignment explanation
Indices: 20363348--20363401 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
20363338 GCTGTCTAAA
20363348 TTAATGAATTTAATGAAATTATTAAT
1 TTAATGAATTTAATGAAATTATTAAT
20363374 TTAATGAATTTAATGAAATTATTAAT
1 TTAATGAATTTAATGAAATTATTAAT
20363400 TT
1 TT
20363402 GGATTAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (26 bp):
TTAATGAATTTAATGAAATTATTAAT
Found at i:20364553 original size:20 final size:20
Alignment explanation
Indices: 20364504--20364560 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
20364494 AGTTTATCTT
* * *
20364504 AAGTAAATGAAATGGAAAGT
1 AAGTAAATGGAATGGTAAGA
20364524 AAGTAAATGGAATGGTAAGA
1 AAGTAAATGGAATGGTAAGA
*
20364544 AAGTAAATGGAGTGGTA
1 AAGTAAATGGAATGGTA
20364561 CATAGTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.30, T:0.21
Consensus pattern (20 bp):
AAGTAAATGGAATGGTAAGA
Found at i:20370200 original size:6 final size:6
Alignment explanation
Indices: 20370191--20370273 Score: 67
Period size: 6 Copynumber: 12.5 Consensus size: 6
20370181 TAAGTCTAAG
*
20370191 AAAATA AAAATA AAAATA ACACAACTAAA AAAATA AAAATA AAAATA AACATAA
1 AAAATA AAAATA AAAATA A-A-AA-T--A AAAATA AAAATA AAAATA AAAAT-A
* *
20370245 AAAATA AAACTAA AAGAAAA AAAATA AAA
1 AAAATA AAAAT-A AA-AATA AAAATA AAA
20370274 TCAAGGATCC
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
6 41 0.65
7 12 0.19
8 4 0.06
9 3 0.05
10 1 0.02
11 2 0.03
ACGTcount: A:0.80, C:0.06, G:0.01, T:0.13
Consensus pattern (6 bp):
AAAATA
Found at i:20370249 original size:19 final size:20
Alignment explanation
Indices: 20370202--20370273 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
20370192 AAATAAAAAT
20370202 AAAAATAACACAACTAAAA-AAA
1 AAAAATAA-A-AA-TAAAACAAA
*
20370224 TAAAAATAAAAAT-AAACATA
1 -AAAAATAAAAATAAAACAAA
* *
20370244 AAAAATAAAACTAAAAGAAA
1 AAAAATAAAAATAAAACAAA
20370264 AAAAATAAAA
1 AAAAATAAAA
20370274 TCAAGGATCC
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 14 0.33
20 18 0.42
21 2 0.05
22 1 0.02
23 8 0.19
ACGTcount: A:0.79, C:0.07, G:0.01, T:0.12
Consensus pattern (20 bp):
AAAAATAAAAATAAAACAAA
Found at i:20370252 original size:25 final size:29
Alignment explanation
Indices: 20370186--20370259 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
20370176 TGAAATAAGT
*
20370186 CTAAGAAAATAAAAATAAAAATAACACAA
1 CTAAAAAAATAAAAATAAAAATAACACAA
20370215 CTAAAAAAATAAAAATAAAAATAA-AC-A
1 CTAAAAAAATAAAAATAAAAATAACACAA
*
20370242 -T-AAAAAATAAAACTAAAA
1 CTAAAAAAATAAAAATAAAA
20370260 GAAAAAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.37
26 1 0.02
27 1 0.02
28 2 0.05
29 23 0.53
ACGTcount: A:0.76, C:0.08, G:0.01, T:0.15
Consensus pattern (29 bp):
CTAAAAAAATAAAAATAAAAATAACACAA
Found at i:20370299 original size:3 final size:3
Alignment explanation
Indices: 20370284--20370478 Score: 68
Period size: 3 Copynumber: 66.0 Consensus size: 3
20370274 TCAAGGATCC
* * * * * * *
20370284 TAA TAA GAA TAA TAA TAC TAA TAA TAC TAA TAC TCA TAC TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
20370332 TAA TAA CAG TAA -AA CAAA TAA TAA TTAA CTGA TGA TAA TTAA -AC GAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA -TAA -TAA TAA TAA -TAA TAA TAA
* * * * *
20370379 GAA TAA TAA GAA -AA TTA -AA TAA TAA TAA CAA T-A TAA TAA CAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* *
20370425 TAA TTA TAAA TAA -AA -AA TAA -AA TAA T-A TAA -AA AAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20370466 TAAA TAA TAA TAA
1 T-AA TAA TAA TAA
20370479 ACAAATAAAT
Statistics
Matches: 143, Mismatches: 34, Indels: 30
0.69 0.16 0.14
Matches are distributed among these distances:
2 18 0.13
3 107 0.75
4 18 0.13
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:20370437 original size:4 final size:4
Alignment explanation
Indices: 20370419--20370522 Score: 74
Period size: 4 Copynumber: 25.5 Consensus size: 4
20370409 ATATAATAAC
*
20370419 AATA AATA ATTATA AATA AA-A AATAA AATA ATATA AAAA AAT- AAT-
1 AATA AATA A--ATA AATA AATA AAT-A AATA A-ATA AATA AATA AATA
* * *
20370464 AATA AAT- AAT- AATA AACA AATA AATA ATTA GATA AATA AATAA AATAA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AAT-A AAT-A
20370512 AATAA AATA AA
1 AAT-A AATA AA
20370523 GAACAAGGGT
Statistics
Matches: 84, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
3 15 0.18
4 43 0.51
5 22 0.26
6 4 0.05
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:20370443 original size:21 final size:21
Alignment explanation
Indices: 20370419--20370512 Score: 79
Period size: 21 Copynumber: 4.3 Consensus size: 21
20370409 ATATAATAAC
20370419 AATAAATAATTATAAATAAAA
1 AATAAATAATTATAAATAAAA
20370440 AATAAAATAA-TATAAA-AAAA
1 AAT-AAATAATTATAAATAAAA
*
20370460 TAAT-AATAAATA-ATAATAAACA
1 -AATAAATAATTATA-AATAAA-A
20370482 AATAAATAATTAGATAAATAAATAA
1 AATAAATAATT--ATAAAT-AA-AA
20370507 AATAAA
1 AATAAA
20370513 ATAAAATAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 20
0.74 0.01 0.25
Matches are distributed among these distances:
19 6 0.10
20 8 0.13
21 18 0.30
22 13 0.22
24 4 0.07
25 10 0.17
26 1 0.02
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.26
Consensus pattern (21 bp):
AATAAATAATTATAAATAAAA
Found at i:20370449 original size:62 final size:66
Alignment explanation
Indices: 20370395--20370522 Score: 169
Period size: 67 Copynumber: 2.0 Consensus size: 66
20370385 TAAGAAAATT
*
20370395 AAATAATAATAACA-ATATAAT-AAC-AATAAATAATT-ATAAAT-AA-AAAATAAAATAATATA
1 AAATAATAATAA-ATA-ATAATAAACAAATAAATAATTAATAAATAAATAAAATAAAATAAGATA
20370454 AAA
64 AAA
*
20370457 AAATAATAATAAATAATAATAAACAAATAAATAATTAGATAAATAAATAAAATAAAATAAAATAA
1 AAATAATAATAAATAATAATAAACAAATAAATAATTA-ATAAATAAATAAAATAAAATAAGATAA
20370522 A
65 A
20370523 GAACAAGGGT
Statistics
Matches: 58, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
61 6 0.10
62 16 0.28
63 11 0.19
65 6 0.10
66 2 0.03
67 17 0.29
ACGTcount: A:0.72, C:0.02, G:0.01, T:0.25
Consensus pattern (66 bp):
AAATAATAATAAATAATAATAAACAAATAAATAATTAATAAATAAATAAAATAAAATAAGATAAA
A
Found at i:20370506 original size:41 final size:38
Alignment explanation
Indices: 20370380--20370518 Score: 97
Period size: 41 Copynumber: 3.5 Consensus size: 38
20370370 TTAAACGAAG
* * * * *
20370380 AATAATAAGA-AAATTAAATAATAATAACAATATAATAAC
1 AATAATAAAATAAAATAAAAAATAA-AATAATATAA-AAA
*
20370419 AATAA-ATAATTATAAATAAAAAATAAAATAATATAAAAA
1 AATAATA-AAATA-AAATAAAAAATAAAATAATATAAAAA
* *
20370458 AATAATAATAAATAATAATAAACAAAT-AAATAAT-TAGATA
1 AATAAT-A-AAATAA-AATAAA-AAATAAAATAATATAAAAA
20370498 AATAAATAAAATAAAATAAAA
1 AAT-AATAAAATAAAATAAAA
20370519 TAAAGAACAA
Statistics
Matches: 83, Mismatches: 9, Indels: 18
0.75 0.08 0.16
Matches are distributed among these distances:
37 1 0.01
38 7 0.08
39 19 0.23
40 19 0.23
41 33 0.40
42 4 0.05
ACGTcount: A:0.71, C:0.02, G:0.01, T:0.25
Consensus pattern (38 bp):
AATAATAAAATAAAATAAAAAATAAAATAATATAAAAA
Found at i:20370516 original size:10 final size:10
Alignment explanation
Indices: 20370389--20370522 Score: 64
Period size: 10 Copynumber: 12.8 Consensus size: 10
20370379 GAATAATAAG
*
20370389 AAAATTAAAT
1 AAAATAAAAT
20370399 AATAATAACAAT
1 AA-AATAA-AAT
*
20370411 ATAATAACAAT
1 AAAATAA-AAT
*
20370422 -AAATAATTAT
1 AAAATAA-AAT
*
20370432 AAATAAAAAAT
1 AAA-ATAAAAT
*
20370443 AAAATAATAT
1 AAAATAAAAT
20370453 -AAA-AAAAT
1 AAAATAAAAT
20370461 AATAAT-AAAT
1 AA-AATAAAAT
*
20370471 AATAATAAACAA
1 AA-AATAAA-AT
20370483 ATAAATAATTAGAT
1 A-AAATAA--A-AT
20370497 -AAAT-AAAT
1 AAAATAAAAT
20370505 AAAATAAAAT
1 AAAATAAAAT
20370515 AAAATAAA
1 AAAATAAA
20370523 GAACAAGGGT
Statistics
Matches: 97, Mismatches: 13, Indels: 28
0.70 0.09 0.20
Matches are distributed among these distances:
8 6 0.06
9 9 0.09
10 38 0.39
11 23 0.24
12 18 0.19
13 1 0.01
14 2 0.02
ACGTcount: A:0.72, C:0.02, G:0.01, T:0.25
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:20379948 original size:41 final size:41
Alignment explanation
Indices: 20379891--20379999 Score: 182
Period size: 41 Copynumber: 2.6 Consensus size: 41
20379881 GACTATATGT
*
20379891 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC
*
20379932 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC
*
20379973 CTAGCAGGCTAAGTGCCAGTGAATCTG
1 CTAGCAGGCTAAGTGCCGGTG-ATCTG
20380000 TTAAATTAAG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
41 59 0.92
42 5 0.08
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC
Found at i:20382854 original size:40 final size:40
Alignment explanation
Indices: 20382756--20383058 Score: 387
Period size: 40 Copynumber: 7.6 Consensus size: 40
20382746 TCCTCGTTCA
* * * * *
20382756 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
20382795 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
20382835 AATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
20382875 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
20382915 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
20382955 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
20382995 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
20383035 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
20383059 CAGCATTCAA
Statistics
Matches: 239, Mismatches: 21, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
39 37 0.15
40 194 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:20401428 original size:28 final size:27
Alignment explanation
Indices: 20401365--20401544 Score: 288
Period size: 28 Copynumber: 6.6 Consensus size: 27
20401355 ATATTAAGTC
* * *
20401365 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
20401392 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
20401420 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
20401447 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
20401475 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
20401503 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
20401530 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20401545 GCACAATTTA
Statistics
Matches: 147, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
27 66 0.45
28 81 0.55
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:20401449 original size:55 final size:55
Alignment explanation
Indices: 20401365--20401544 Score: 299
Period size: 55 Copynumber: 3.3 Consensus size: 55
20401355 ATATTAAGTC
* * * *
20401365 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
20401420 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
*
20401475 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTC-AATT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAGTCAAACT
20401530 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20401545 GCACAATTTA
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
55 92 0.77
56 27 0.23
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
Found at i:20401503 original size:83 final size:82
Alignment explanation
Indices: 20401365--20401544 Score: 306
Period size: 83 Copynumber: 2.2 Consensus size: 82
20401355 ATATTAAGTC
* *
20401365 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
20401430 GTGCTACATAGTCAACT
66 GTGCTACATAGTCAACT
* *
20401447 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTT
*
20401512 AGTGCTACATAGTCAATT
65 AGTGCTACATAGTCAACT
20401530 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20401545 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
82 20 0.22
83 72 0.78
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (82 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
GTGCTACATAGTCAACT
Found at i:20409492 original size:28 final size:27
Alignment explanation
Indices: 20409429--20409553 Score: 187
Period size: 28 Copynumber: 4.6 Consensus size: 27
20409419 ATATTAAGTC
* *
20409429 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
20409456 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
20409484 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
20409512 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
20409539 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20409554 GCACAATTTA
Statistics
Matches: 93, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
27 39 0.42
28 54 0.58
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:20409574 original size:56 final size:56
Alignment explanation
Indices: 20409429--20409553 Score: 173
Period size: 55 Copynumber: 2.3 Consensus size: 56
20409419 ATATTAAGTC
* * * *
20409429 CGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCTACATAATCAAACT
* * *
20409484 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTC-AATT
1 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCTACATAATCAAACT
20409539 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20409554 GCACAATTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
55 38 0.59
56 26 0.41
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (56 bp):
CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCTACATAATCAAACT
Found at i:20410494 original size:16 final size:16
Alignment explanation
Indices: 20410470--20410503 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
20410460 TTATTCAAAT
*
20410470 TACTTATGTTCACACA
1 TACTCATGTTCACACA
20410486 TACTCATGTTCACACA
1 TACTCATGTTCACACA
20410502 TA
1 TA
20410504 ATAAGCATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.35
Consensus pattern (16 bp):
TACTCATGTTCACACA
Found at i:20419069 original size:272 final size:272
Alignment explanation
Indices: 20418275--20419092 Score: 1186
Period size: 279 Copynumber: 3.0 Consensus size: 272
20418265 CCAAACTCGA
* * *
20418275 CCTAGATGTTATAGTCAGATTATGGAGGTCACATCACTAAATAAAAGAAAGTACTAGTGTTTTGA
1 CCTAGATGTTACAGTCGGATTATGGAGGTCACATCACTAGATAAAAGAAAGTACTAGTGTTTTGA
* * *
20418340 AGAACCAATTCCAGCAAGTTAAAACTTTATTGTCTCATTTAAAAAAAAAGAACACTTCAAACATG
66 AGAACCAATTCCAGCAGGTTAAAACTTTATTGTCTCGTTT--AAAAAAA-AACATTTCAAACATG
*
20418405 TCAAAATATTAAGTTAAATTCTCTTATAAACGTACCCACTGAAATTATTTTTAATGAAAACCTCA
128 TCAAAATATCAAGTTAAATTCTCTTATAAACGTACCCACTGAAATTATTTTTAATGAAAACCTCA
* * * * * *
20418470 TACTTAATTTGTAGCGACAATTACTTGAAAACTTAAAGTTTCGTTTTAGTCTCTTTAGGAAAAAA
193 AACTTAATTTGTAGCAACAATTACTTGAAAACTTAAAGTTTCATTTTGGTCTCTTTAGGAAGAAT
*
20418535 TATTTATAAACCCGG
258 TATTTATAAACCCAG
*
20418550 CCTAGACGTTACAGTCGGATTATGGAGGTCACATCACTAGATAAAAGAAAGTACTAGTGTTTTGA
1 CCTAGATGTTACAGTCGGATTATGGAGGTCACATCACTAGATAAAAGAAAGTACTAGTGTTTTGA
* * * *
20418615 ATAATCAATTCCAGCAGGTTAAAACTTCATTGTCTTGTTTTTTTTCTAAAAAAAAACATTTCAAA
66 AGAACCAATTCCAGCAGGTTAAAACTTTATTGTCTCG------TT-TAAAAAAAAACATTTCAAA
* * * ** * * *
20418680 CATGTTAAAATATCAAGCTAAATTCTCTTATAAATGTGTCCGCTGAATTTTTTTTTAATGAAAAC
124 CATGTCAAAATATCAAGTTAAATTCTCTTATAAACGTACCCACTGAAATTATTTTTAATGAAAAC
* *
20418745 TTCAAACTTAATTTGTAGCAACAATTACTTGAAAACTTAAAGTTTTATTTTGGTCTCTTTAGGAA
189 CTCAAACTTAATTTGTAGCAACAATTACTTGAAAACTTAAAGTTTCATTTTGGTCTCTTTAGGAA
* *
20418810 GGATTATTTATAAACCTAG
254 GAATTATTTATAAACCCAG
* * *
20418829 CCTAGATGTTACGGTCGGATTACGGAGGTTACATCACTAGATAAAAGAAAGTACTAGTGTTTTGA
1 CCTAGATGTTACAGTCGGATTATGGAGGTCACATCACTAGATAAAAGAAAGTACTAGTGTTTTGA
*
20418894 AGAACCAATTCCAGCAGGTTAAAACTTTATTTTCTCGTTTAAAAAAAAACATTTCAAACATGTCA
66 AGAACCAATTCCAGCAGGTTAAAACTTTATTGTCTCGTTTAAAAAAAAACATTTCAAACATGTCA
* *
20418959 AAATATCAAGTTATATTCTCTTATAAACGTACCCACTAAAATTATTTTTAATGAAAACCTCAAAC
131 AAATATCAAGTTAAATTCTCTTATAAACGTACCCACTGAAATTATTTTTAATGAAAACCTCAAAC
* * *
20419024 TTAATTTGCAGCTACAATTACTTGAAAACTTAAAGCTTCATTTTGGTCTCTTTAGGAAGAATTAT
196 TTAATTTGTAGCAACAATTACTTGAAAACTTAAAGTTTCATTTTGGTCTCTTTAGGAAGAATTAT
20419089 TTAT
261 TTAT
20419093 CATTTGAGCT
Statistics
Matches: 480, Mismatches: 56, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
272 144 0.30
273 2 0.00
275 92 0.19
279 232 0.48
280 7 0.01
281 2 0.00
282 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (272 bp):
CCTAGATGTTACAGTCGGATTATGGAGGTCACATCACTAGATAAAAGAAAGTACTAGTGTTTTGA
AGAACCAATTCCAGCAGGTTAAAACTTTATTGTCTCGTTTAAAAAAAAACATTTCAAACATGTCA
AAATATCAAGTTAAATTCTCTTATAAACGTACCCACTGAAATTATTTTTAATGAAAACCTCAAAC
TTAATTTGTAGCAACAATTACTTGAAAACTTAAAGTTTCATTTTGGTCTCTTTAGGAAGAATTAT
TTATAAACCCAG
Found at i:20420280 original size:29 final size:31
Alignment explanation
Indices: 20420248--20420306 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
20420238 TATGGTTTAA
20420248 TGTGCAATTGTATAAATG-AA-TTTGATTTT
1 TGTGCAATTGTATAAATGAAATTTTGATTTT
* *
20420277 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATAAATGAAATTTTGATTT
20420307 GATCCAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 16 0.62
30 2 0.08
31 8 0.31
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (31 bp):
TGTGCAATTGTATAAATGAAATTTTGATTTT
Found at i:20421595 original size:4 final size:4
Alignment explanation
Indices: 20421588--20421642 Score: 101
Period size: 4 Copynumber: 13.8 Consensus size: 4
20421578 CAAACAATAA
20421588 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
20421636 ACAC ATA
1 ATAC ATA
20421643 TATTGTTTAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:20422097 original size:19 final size:19
Alignment explanation
Indices: 20422062--20422100 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20422052 GGGTTTTTTT
20422062 TAATTTTTTAATATTAATA
1 TAATTTTTTAATATTAATA
*
20422081 TAATTATTTTTAT-TTAATA
1 TAATT-TTTTAATATTAATA
20422100 T
1 T
20422101 TAATATCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TAATTTTTTAATATTAATA
Found at i:20422121 original size:28 final size:26
Alignment explanation
Indices: 20422059--20422122 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
20422049 AGAGGGTTTT
20422059 TTTTAATTT-TTTAATATTAATATAA
1 TTTTAATTTATTTAATATTAATATAA
20422084 TTATT--TTTATTTAATATTAATATCAA
1 TT-TTAATTTATTTAATATTAATAT-AA
20422110 TTTTAAATTTATT
1 TTTT-AATTTATT
20422123 ATTATATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
24 3 0.09
25 18 0.55
26 6 0.18
28 6 0.18
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTAATTTATTTAATATTAATATAA
Found at i:20423594 original size:16 final size:16
Alignment explanation
Indices: 20423552--20423594 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
20423542 ACTCATTATT
20423552 TGACCAACACAAATAA
1 TGACCAACACAAATAA
* *
20423568 T--TCAGCACAAATAA
1 TGACCAACACAAATAA
20423582 TGACCAACACAAA
1 TGACCAACACAAA
20423595 CATTTTATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
14 12 0.57
16 9 0.43
ACGTcount: A:0.53, C:0.26, G:0.07, T:0.14
Consensus pattern (16 bp):
TGACCAACACAAATAA
Found at i:20424559 original size:25 final size:25
Alignment explanation
Indices: 20424525--20424580 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
20424515 GTGCCACTAC
20424525 TATTCCTACTCTAATCTAGAATTTA
1 TATTCCTACTCTAATCTAGAATTTA
20424550 TATTCCTACTCTAATCTAGAATTTA
1 TATTCCTACTCTAATCTAGAATTTA
*
20424575 TCTTCC
1 TATTCC
20424581 CAAATAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.45
Consensus pattern (25 bp):
TATTCCTACTCTAATCTAGAATTTA
Found at i:20426160 original size:29 final size:29
Alignment explanation
Indices: 20426128--20426252 Score: 91
Period size: 30 Copynumber: 4.1 Consensus size: 29
20426118 TTTATTATAG
20426128 ATTATTTTAAATATTTTAATATATGAAA-T
1 ATTATTTTAAATATTTTAATATAT-AAACT
*
20426157 ATTAATTTTAAATATTTTAAGTA-ATTAATATT
1 ATT-ATTTTAAATATTTTAA-TATA-TAA-ACT
*
20426189 AATTATTTATAAATTTTAATTAGAATATATAAACT
1 -ATTATTT-TAAATATT--TT--AATATATAAACT
20426224 -TTATTTTAAATA-TTTAA-ATATAAAC-
1 ATTATTTTAAATATTTTAATATATAAACT
20426249 ATTA
1 ATTA
20426253 AATATTTGTA
Statistics
Matches: 80, Mismatches: 3, Indels: 29
0.71 0.03 0.26
Matches are distributed among these distances:
26 11 0.14
27 2 0.03
29 5 0.06
30 19 0.24
31 5 0.06
32 10 0.12
33 16 0.20
35 4 0.05
36 5 0.06
37 3 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
ATTATTTTAAATATTTTAATATATAAACT
Found at i:20427645 original size:28 final size:27
Alignment explanation
Indices: 20427605--20427659 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
20427595 AAACTTTTGC
20427605 ATCGGTGCCCAAGATGTACAAGAAAAAT
1 ATCGGTGCCCAAGATGTACAA-AAAAAT
*
20427633 ATCGGTTCCCAAGATGTACAAAAAAAT
1 ATCGGTGCCCAAGATGTACAAAAAAAT
20427660 TCCCAACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (27 bp):
ATCGGTGCCCAAGATGTACAAAAAAAT
Found at i:20429043 original size:32 final size:32
Alignment explanation
Indices: 20429007--20429537 Score: 654
Period size: 32 Copynumber: 16.6 Consensus size: 32
20428997 TGTATTCTCT
* ***
20429007 AATTGAATTGTATAGGTATACACCTATTGTCG
1 AATTGAATTGTATATGTATACTTATATTGTCG
*
20429039 AATTGAATTGTATATGTATACTTATATTGCCG
1 AATTGAATTGTATATGTATACTTATATTGTCG
* *
20429071 AATTGAATTGTATGTGTATACTTATATTGCCG
1 AATTGAATTGTATATGTATACTTATATTGTCG
* *** *
20429103 AATTGAATTGTATAGGTATACACCTATTGTTG
1 AATTGAATTGTATATGTATACTTATATTGTCG
* *** *
20429135 AATTGAATTGTATAAGTATACACCTATTGTCA
1 AATTGAATTGTATATGTATACTTATATTGTCG
*
20429167 AATTGAATTGTATATGTATACTTATATTGCCG
1 AATTGAATTGTATATGTATACTTATATTGTCG
* ***
20429199 AATTGAATTGTATAGGTATACACCTATTGTCG
1 AATTGAATTGTATATGTATACTTATATTGTCG
*
20429231 AATTGAATTGTATATGTATACTTATATTGCCG
1 AATTGAATTGTATATGTATACTTATATTGTCG
20429263 AATTGAATTGTATATGTATACTTATATTGTCG
1 AATTGAATTGTATATGTATACTTATATTGTCG
20429295 AATTGAATTGTATATGTATACTTATATT-TCTG
1 AATTGAATTGTATATGTATACTTATATTGTC-G
* * *** *
20429327 AATTAAATTGTATAGGTATACACCTATTTTCG
1 AATTGAATTGTATATGTATACTTATATTGTCG
20429359 AATTGAATTGTATATGTATACTTATATTGTCG
1 AATTGAATTGTATATGTATACTTATATTGTCG
*
20429391 AATTGAATTGTA-ATAGTATACTTATATTGCCG
1 AATTGAATTGTATAT-GTATACTTATATTGTCG
* *** *
20429423 AATTGAATTGTATAGGTATACACCTATTGTCA
1 AATTGAATTGTATATGTATACTTATATTGTCG
* *
20429455 AATTGAATTGTATATATATACTTATATTGCCG
1 AATTGAATTGTATATGTATACTTATATTGTCG
* * *
20429487 AATTGAATTGTATATGTATATTTATGTTGCCG
1 AATTGAATTGTATATGTATACTTATATTGTCG
20429519 AATTG-ATTGGTATATGTAT
1 AATTGAATT-GTATATGTAT
20429538 TTATATATTG
Statistics
Matches: 433, Mismatches: 61, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
31 7 0.02
32 423 0.98
33 3 0.01
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (32 bp):
AATTGAATTGTATATGTATACTTATATTGTCG
Found at i:20430786 original size:41 final size:41
Alignment explanation
Indices: 20430741--20430822 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
20430731 TAAGGGTGTT
*
20430741 ACTTAAATAATCGGTTAAAACATTCTATGCGTTGTAAAATC
1 ACTTAAATAATCGGTTAAAACATTCTATGCATTGTAAAATC
20430782 ACTTAAATAATCGGTTAAAACATTCTATGCATTGTAAAATC
1 ACTTAAATAATCGGTTAAAACATTCTATGCATTGTAAAATC
20430823 TCTTTCTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (41 bp):
ACTTAAATAATCGGTTAAAACATTCTATGCATTGTAAAATC
Found at i:20433105 original size:41 final size:40
Alignment explanation
Indices: 20433055--20433201 Score: 188
Period size: 41 Copynumber: 3.6 Consensus size: 40
20433045 AAGTGTAAAA
*
20433055 AGGGACACATATGTGCAATTCAGGGGTATCGAAGTACAAAC
1 AGGG-CACATAAGTGCAATTCAGGGGTATCGAAGTACAAAC
* *
20433096 AGCGGCACATTAGTGCAATTCAGGGGT-TACAAAGTACAAAC
1 AG-GGCACATAAGTGCAATTCAGGGGTAT-CGAAGTACAAAC
* *
20433137 AGAGGCACATAAGTGCAATTCAGGGGTATTGAAGTACGAAC
1 AG-GGCACATAAGTGCAATTCAGGGGTATCGAAGTACAAAC
*
20433178 AGGTGCACGTAAGTGCAATTCAGG
1 AGG-GCACATAAGTGCAATTCAGG
20433202 TATAATTAAC
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
40 2 0.02
41 88 0.95
42 3 0.03
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (40 bp):
AGGGCACATAAGTGCAATTCAGGGGTATCGAAGTACAAAC
Found at i:20439882 original size:79 final size:81
Alignment explanation
Indices: 20439747--20439964 Score: 238
Period size: 79 Copynumber: 2.8 Consensus size: 81
20439737 AAATCACGTA
** * *
20439747 CCTTCGGAAT-TTAA-CCGGATATAGCT-ACTT-GTTCAAATGCCTTCGGGACATAGCCCGG-TT
1 CCTTCGG-ATCTTAACCCGGATATAG-TAACTTAGCACAAATGCCTTCGGGACTTAGCCCGGAAT
20439807 ATAGTAACTCGCACAAATG
64 -TAGTAACTCGCACAAATG
* *
20439826 CCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGAATT
1 CCTTC-GGATCTTAACCCGGATATAGTAACTTAGCACAAATGCCTTCGGGACTTAGCCCGGAATT
*
20439888 AGTATCTCGCACAAATG
65 AGTAACTCGCACAAATG
** * *
20439905 CCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 CCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAAATGCCTTCGGGACTTAGCCCGGA
20439965 CATCATTCAA
Statistics
Matches: 118, Mismatches: 12, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
78 3 0.03
79 67 0.57
80 48 0.41
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (81 bp):
CCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTA
GTAACTCGCACAAATG
Found at i:20439964 original size:40 final size:40
Alignment explanation
Indices: 20439780--20439964 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
20439770 GCTACTTGTT
* *
20439780 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
20439820 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
20439860 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
20439899 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
20439940 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
20439965 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 80 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:20443142 original size:41 final size:41
Alignment explanation
Indices: 20443060--20443232 Score: 152
Period size: 41 Copynumber: 4.2 Consensus size: 41
20443050 ACCAGAGTGT
* * **
20443060 AAACAGGGGCACGTAAGTGCAATTGT-GGTGTACCAAAGTAC
1 AAACAGGGGCATGTAAGTGCAATT-TAGGAGTACTGAAGTAC
* * * *
20443101 AAACTGGAGCATGTAAGTGCAATTTAGGGGTACTGAGGTAC
1 AAACAGGGGCATGTAAGTGCAATTTAGGAGTACTGAAGTAC
* ** * *
20443142 AAAAAGGGGCACATAAGTGCAATTTAGGAGTACCGAAGTAG
1 AAACAGGGGCATGTAAGTGCAATTTAGGAGTACTGAAGTAC
* * * *
20443183 AAACAGGGGCATGTAAATTCAATTTAAGTGTA-TAGAAGTAC
1 AAACAGGGGCATGTAAGTGCAATTTAGGAGTACT-GAAGTAC
*
20443224 AAACTGGGG
1 AAACAGGGG
20443233 TACATAAGTG
Statistics
Matches: 104, Mismatches: 26, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
40 1 0.01
41 103 0.99
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.21
Consensus pattern (41 bp):
AAACAGGGGCATGTAAGTGCAATTTAGGAGTACTGAAGTAC
Found at i:20443257 original size:82 final size:82
Alignment explanation
Indices: 20443064--20443265 Score: 201
Period size: 82 Copynumber: 2.5 Consensus size: 82
20443054 GAGTGTAAAC
* ** * * * *
20443064 AGGGGCACGTAAGTGCAATTGTGGTGTACCAAAGTACAAACTGGAGCATGTAAGTGCAATTTAGG
1 AGGGGCACATAAGTGCAATTAAGGAGTACCAAAGTACAAACAGGAGCATGTAAATGCAATTTAAG
*
20443129 GGTACTGAGGTACAAAA
66 GGTACTGAAGTACAAAA
* * * * *
20443146 AGGGGCACATAAGTGCAATTTAGGAGTACCGAAGTAGAAACAGGGGCATGTAAATTCAATTTAAG
1 AGGGGCACATAAGTGCAATTAAGGAGTACCAAAGTACAAACAGGAGCATGTAAATGCAATTTAAG
* *
20443211 TGTA-TAGAAGTACAAAC
66 GGTACT-GAAGTACAAAA
* * * *
20443228 TGGGGTACATAAGTGTAATTCAAGG-GTACCAAAATACA
1 AGGGGCACATAAGTGCAATT-AAGGAGTACCAAAGTACA
20443266 GACAAGGGCA
Statistics
Matches: 97, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
81 1 0.01
82 93 0.96
83 3 0.03
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.22
Consensus pattern (82 bp):
AGGGGCACATAAGTGCAATTAAGGAGTACCAAAGTACAAACAGGAGCATGTAAATGCAATTTAAG
GGTACTGAAGTACAAAA
Found at i:20450593 original size:15 final size:15
Alignment explanation
Indices: 20450560--20450620 Score: 77
Period size: 15 Copynumber: 3.9 Consensus size: 15
20450550 GTATCTTTAT
20450560 TAAAAATAAAATATAA
1 TAAAAATAAAA-ATAA
*
20450576 TAAAAATAAAAATTA
1 TAAAAATAAAAATAA
*
20450591 TAAACATAAAAATAA
1 TAAAAATAAAAATAA
20450606 TAAATAAATAAAAAT
1 T-AA-AAATAAAAAT
20450621 CTCAAACACT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
15 17 0.44
16 13 0.33
17 9 0.23
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAAAATAAAAATAA
Found at i:20450628 original size:32 final size:31
Alignment explanation
Indices: 20450558--20450628 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 31
20450548 AAGTATCTTT
20450558 ATTA-AAA-ATAAAATATAATAAAAATAAAA
1 ATTACAAACATAAAATATAATAAAAATAAAA
*
20450587 ATTATAAACATAAAA-ATAATAAATAAATAAAA
1 ATTACAAACATAAAATATAAT-AA-AAATAAAA
20450619 ATCT-CAAACA
1 AT-TACAAACA
20450629 CTACACTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
29 4 0.11
30 8 0.22
31 8 0.22
32 15 0.42
33 1 0.03
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (31 bp):
ATTACAAACATAAAATATAATAAAAATAAAA
Found at i:20451219 original size:31 final size:32
Alignment explanation
Indices: 20451158--20451219 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
20451148 CATATATGCC
**
20451158 ATTTTTTTTTAAAATAATTAGGGATTTAGGTCG
1 ATTTTTTTTTAAAAT-ATTAGGGAAATAGGTCG
*
20451191 ATTTTTTTTTGAAAT-TTAGGGAAATAGGT
1 ATTTTTTTTTAAAATATTAGGGAAATAGGT
20451220 TGTTCTAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 12 0.46
33 14 0.54
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (32 bp):
ATTTTTTTTTAAAATATTAGGGAAATAGGTCG
Found at i:20452499 original size:3 final size:3
Alignment explanation
Indices: 20452491--20452629 Score: 278
Period size: 3 Copynumber: 46.3 Consensus size: 3
20452481 ATACTCTTAT
20452491 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
20452539 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
20452587 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC T
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC T
20452630 GTTATTATTA
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 136 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:20461469 original size:37 final size:37
Alignment explanation
Indices: 20461419--20461497 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
20461409 TTATTACGAA
* *
20461419 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
20461456 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
20461493 GTCTT
1 GTCTT
20461498 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:20461694 original size:47 final size:47
Alignment explanation
Indices: 20461616--20462093 Score: 785
Period size: 47 Copynumber: 10.1 Consensus size: 47
20461606 CCCTTCGGGA
* * * * * * *
20461616 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
***
20461663 CCCGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20461710 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20461757 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
20461804 CTTATCACACATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20461851 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20461900 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20461947 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20461994 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20462043 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20462090 CTTA
1 CTTA
20462094 CTATCATTTC
Statistics
Matches: 406, Mismatches: 21, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
47 316 0.78
49 90 0.22
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:20461925 original size:143 final size:143
Alignment explanation
Indices: 20461616--20462093 Score: 816
Period size: 143 Copynumber: 3.4 Consensus size: 143
20461606 CCCTTCGGGA
* * * * * * * *** *
20461616 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCCGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACAC
20461681 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
20461744 TCGGCCATTAGGC
131 TCGGCCATTAGGC
20461757 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACAC
*
20461822 TTTCACATTCATCACATCGACCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
*
20461887 TCGGCTATTAGGC
131 TCGGCCATTAGGC
*
20461900 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACAC
20461965 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
20462030 TCGGCCATTAGGC
131 TCGGCCATTAGGC
20462043 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
20462094 CTATCATTTC
Statistics
Matches: 318, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
141 90 0.28
143 228 0.72
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (143 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:20467640 original size:37 final size:37
Alignment explanation
Indices: 20467599--20467774 Score: 298
Period size: 37 Copynumber: 4.8 Consensus size: 37
20467589 TTTGAGTACT
20467599 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
20467636 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
20467673 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
20467710 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
** *
20467747 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGAAACAAAGTGATAAGTGG
20467775 TAGCTTCAGC
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:20467846 original size:45 final size:46
Alignment explanation
Indices: 20467737--20467860 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
20467727 GTGATAAGTG
* *
20467737 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
20467783 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
20467828 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
20467861 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:20471505 original size:26 final size:26
Alignment explanation
Indices: 20471472--20471523 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
20471462 AAATATCTAA
20471472 GAAAAAGTCTAAATTTAGACTATCCC
1 GAAAAAGTCTAAATTTAGACTATCCC
20471498 GAAAAAGTCTAAATTTAGACTATCCC
1 GAAAAAGTCTAAATTTAGACTATCCC
20471524 TTCGAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (26 bp):
GAAAAAGTCTAAATTTAGACTATCCC
Found at i:20472253 original size:51 final size:51
Alignment explanation
Indices: 20472189--20472287 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
20472179 TAAGACTGAG
*
20472189 GGTAGTGAATCTTATTTCCCTAGCGTTGCAATGGAACAGATTAAAGCTAAA
1 GGTAGCGAATCTTATTTCCCTAGCGTTGCAATGGAACAGATTAAAGCTAAA
* * * *
20472240 GGTAGCGAATCTTATTTCTCTGGCGTTGCAGTGGAATAGATTAAAGCT
1 GGTAGCGAATCTTATTTCCCTAGCGTTGCAATGGAACAGATTAAAGCT
20472288 GAAATAGAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (51 bp):
GGTAGCGAATCTTATTTCCCTAGCGTTGCAATGGAACAGATTAAAGCTAAA
Found at i:20472437 original size:51 final size:50
Alignment explanation
Indices: 20472299--20472438 Score: 154
Period size: 51 Copynumber: 2.7 Consensus size: 50
20472289 AAATAGAGTG
* * * * *
20472299 GATTAAAGCTGAAGGCAACCAATCCTATCTCCTTGGCGTTACAGTGGAATA
1 GATTAAAGCTGAAGGTAGCGAATCTTATCTCC-TGGCGTTACAGTGGAACA
** * * * *
20472350 GATTAAAGCAAAAGGTAGCGAATCTTGTTTCCCTGGCGTTGCAGTGGAGCA
1 GATTAAAGCTGAAGGTAGCGAATCTTATCT-CCTGGCGTTACAGTGGAACA
20472401 GATTAAAGCTGAAGGTAGCGAATCTTATCTCTCTGGCG
1 GATTAAAGCTGAAGGTAGCGAATCTTATCTC-CTGGCG
20472439 CAGATTAAAG
Statistics
Matches: 72, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
50 1 0.01
51 69 0.96
52 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (50 bp):
GATTAAAGCTGAAGGTAGCGAATCTTATCTCCTGGCGTTACAGTGGAACA
Done.