Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 140 of 208
Found at i:42831789 original size:7 final size:7
Alignment explanation
Indices: 42831777--42831812 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
42831767 ATAAGGATAC
42831777 TTTCCAT
1 TTTCCAT
42831784 TTTCCAT
1 TTTCCAT
42831791 TTTCCAT
1 TTTCCAT
42831798 TTTCCAT
1 TTTCCAT
42831805 TTTCCAT
1 TTTCCAT
42831812 T
1 T
42831813 AACTATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTCCAT
Found at i:42853937 original size:37 final size:37
Alignment explanation
Indices: 42853887--42853960 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
42853877 ACATTCCCAT
42853887 TGCCTATGGTTGTAGGTAAACTTGTCTGGTAATTGTA
1 TGCCTATGGTTGTAGGTAAACTTGTCTGGTAATTGTA
*
42853924 TGCCTGTGGTTGTAGGTAAACTTGTCTGGTAATTGTA
1 TGCCTATGGTTGTAGGTAAACTTGTCTGGTAATTGTA
42853961 GTGCTAAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.20, C:0.11, G:0.28, T:0.41
Consensus pattern (37 bp):
TGCCTATGGTTGTAGGTAAACTTGTCTGGTAATTGTA
Found at i:42858893 original size:19 final size:19
Alignment explanation
Indices: 42858869--42858905 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
42858859 CATGTGTCAG
42858869 GCATGTGTTACACTGATAT
1 GCATGTGTTACACTGATAT
42858888 GCATGTGTTACACTGATA
1 GCATGTGTTACACTGATA
42858906 GTATACAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (19 bp):
GCATGTGTTACACTGATAT
Found at i:42859478 original size:2 final size:2
Alignment explanation
Indices: 42859471--42859495 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42859461 GAATTGGATT
42859471 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
42859496 TCTTAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42859787 original size:27 final size:28
Alignment explanation
Indices: 42859757--42859816 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
42859747 AATTTATAAA
*
42859757 ATTTTAA-AT-TAATAATGATAAAATTAC
1 ATTTTAATATCTAA-AATAATAAAATTAC
* *
42859784 ATTTTAATCTCTAAAATAATAAAATTAT
1 ATTTTAATATCTAAAATAATAAAATTAC
42859812 ATTTT
1 ATTTT
42859817 TACAATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.25
28 18 0.64
29 3 0.11
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (28 bp):
ATTTTAATATCTAAAATAATAAAATTAC
Found at i:42865875 original size:33 final size:33
Alignment explanation
Indices: 42865833--42865905 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
42865823 AAAAGATAAT
42865833 AAATATTCTACACATATTCATCCAAACACCAGA
1 AAATATTCTACACATATTCATCCAAACACCAGA
42865866 AAATATTCTACACATATTCATCCAAACACCAGA
1 AAATATTCTACACATATTCATCCAAACACCAGA
42865899 AAATATT
1 AAATATT
42865906 ACCTTTTCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.26
Consensus pattern (33 bp):
AAATATTCTACACATATTCATCCAAACACCAGA
Found at i:42865958 original size:13 final size:14
Alignment explanation
Indices: 42865923--42865960 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
42865913 CCAGAAAAGT
42865923 AAGTCATTTTCTAG
1 AAGTCATTTTCTAG
* *
42865937 AAATCATTTTC-CG
1 AAGTCATTTTCTAG
42865950 AAGTCATTTTC
1 AAGTCATTTTC
42865961 AGTAAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (14 bp):
AAGTCATTTTCTAG
Found at i:42872089 original size:7 final size:7
Alignment explanation
Indices: 42872077--42872121 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
42872067 CCGTTGAACT
42872077 ATATACG
1 ATATACG
42872084 ATATACG
1 ATATACG
42872091 ATATACG
1 ATATACG
42872098 ATATACG
1 ATATACG
42872105 ATATACG
1 ATATACG
42872112 ATATAC-
1 ATATACG
42872118 ATAT
1 ATAT
42872122 CATTGTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.11
7 34 0.89
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.31
Consensus pattern (7 bp):
ATATACG
Found at i:42874736 original size:14 final size:14
Alignment explanation
Indices: 42874717--42874756 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
42874707 TTGTTTGGCA
42874717 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
42874731 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
42874745 GGAAAATGTTTT
1 GTAAAATGTTTT
42874757 ACTTTTCTGT
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:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:42874765 original size:20 final size:20
Alignment explanation
Indices: 42874740--42874779 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
42874730 CGTAAAATGA
*
42874740 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
42874760 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
42874780 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:42874769 original size:34 final size:35
Alignment explanation
Indices: 42874725--42874791 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
42874715 CAGTAAAATG
*
42874725 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
42874759 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
42874792 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:42874795 original size:14 final size:15
Alignment explanation
Indices: 42874719--42874795 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
42874709 GTTTGGCAGT
* *
42874719 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
42874733 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
42874747 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
42874767 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
42874782 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
42874796 TGTTTGGTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:42874850 original size:32 final size:31
Alignment explanation
Indices: 42874772--42874856 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 31
42874762 TCTGTAAAAT
* *
42874772 GATTTACTGGAAAATATTTTCTGGTGTTTGGTA
1 GATTT-CT-GAAAATATTTTCTGCTGTTTGGCA
* * *
42874805 AATCTGTGTAAAATATTTTCTGCTGTTTGGCA
1 GATTTCTG-AAAATATTTTCTGCTGTTTGGCA
42874837 GATTTCCTGAAAATATTTTC
1 GATTT-CTGAAAATATTTTC
42874857 CGGAAAAGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
31 1 0.02
32 36 0.86
33 5 0.12
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.45
Consensus pattern (31 bp):
GATTTCTGAAAATATTTTCTGCTGTTTGGCA
Found at i:42874897 original size:14 final size:14
Alignment explanation
Indices: 42874878--42874905 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42874868 TTTTTACATA
42874878 TATTAATATATATT
1 TATTAATATATATT
42874892 TATTAATATATATT
1 TATTAATATATATT
42874906 AATAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTAATATATATT
Found at i:42875193 original size:33 final size:33
Alignment explanation
Indices: 42875155--42875269 Score: 108
Period size: 33 Copynumber: 3.3 Consensus size: 33
42875145 TGCATAATAT
42875155 TACACCACATATATCCAAATACATAATTAATGG
1 TACACCACATATATCCAAATACATAATTAATGG
* * * **
42875188 TACACCACATAGTA-ACAACATTGTC-TAGTGCATAATAT
1 TACACCACATA-TATCCAA-A-T-ACATAAT---TAATGG
42875226 TACACCACATATATCCAAATACATAATTAATGG
1 TACACCACATATATCCAAATACATAATTAATGG
42875259 TACACCACATA
1 TACACCACATA
42875270 GTAAGAACAT
Statistics
Matches: 63, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
33 29 0.46
34 3 0.05
35 5 0.08
36 5 0.08
37 3 0.05
38 18 0.29
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (33 bp):
TACACCACATATATCCAAATACATAATTAATGG
Found at i:42875211 original size:71 final size:71
Alignment explanation
Indices: 42875095--42875308 Score: 401
Period size: 71 Copynumber: 3.0 Consensus size: 71
42875085 ATAATAATAT
42875095 TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCTAGTGCATAATATTACAC
1 TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCTAGTGCATAATATTACAC
42875160 CACATA
66 CACATA
42875166 TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCTAGTGCATAATATTACAC
1 TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCTAGTGCATAATATTACAC
42875231 CACATA
66 CACATA
* *
42875237 TATCCAAATACATAATTAATGGTACACCACATAGTAAGAACATTGTCCAAGTGCATAATATTACA
1 TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGT-CTAGTGCATAATATTACA
42875302 CCACATA
65 CCACATA
42875309 AATGTATCAA
Statistics
Matches: 140, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
71 116 0.83
72 24 0.17
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (71 bp):
TATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCTAGTGCATAATATTACAC
CACATA
Found at i:42876333 original size:35 final size:36
Alignment explanation
Indices: 42876287--42876355 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
42876277 ATTCAACCAT
42876287 TTCAATATCCAACAAGCTTAAAACATAAT-AATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
42876322 TTCAATATCCAACAAGCTTAAAACATAATCAATA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATA
42876356 TCTAACAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.52, C:0.19, G:0.03, T:0.26
Consensus pattern (36 bp):
TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
Found at i:42876353 original size:27 final size:28
Alignment explanation
Indices: 42876323--42876392 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
42876313 AATAATAAAT
*
42876323 TCAATATCCAACAAGCTT-AAAACATA-A
1 TCAATATCCAACAA-ATTCAAAACATATA
* *
42876350 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAACAAATTCAAAACATATA
*
42876378 TCAAAATCCAACAAA
1 TCAATATCCAACAAA
42876393 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.06
27 20 0.56
28 14 0.39
ACGTcount: A:0.53, C:0.21, G:0.03, T:0.23
Consensus pattern (28 bp):
TCAATATCCAACAAATTCAAAACATATA
Found at i:42880532 original size:25 final size:25
Alignment explanation
Indices: 42880493--42880544 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
42880483 AAAATGTCTG
42880493 CTGCTTAGAAGAGAACAGAAAATGT
1 CTGCTTAGAAGAGAACAGAAAATGT
**
42880518 CTGCTTAG-AGAAGAATGGAAAATGT
1 CTGCTTAGAAG-AGAACAGAAAATGT
42880543 CT
1 CT
42880545 TACCAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (25 bp):
CTGCTTAGAAGAGAACAGAAAATGT
Found at i:42885995 original size:18 final size:18
Alignment explanation
Indices: 42885959--42886004 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
42885949 TGCTTCTAAG
* *
42885959 AAGCGCTTTTGGGCCAAA
1 AAGCGCTTTTGAGACAAA
*
42885977 AAGCGCTTTTGAGAGAAA
1 AAGCGCTTTTGAGACAAA
*
42885995 AAGTGCTTTT
1 AAGCGCTTTT
42886005 CAAATGCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (18 bp):
AAGCGCTTTTGAGACAAA
Found at i:42898449 original size:19 final size:19
Alignment explanation
Indices: 42898425--42898478 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
42898415 GATTTTCAAG
42898425 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
42898444 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
42898463 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
42898479 AGATATGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:42898467 original size:38 final size:40
Alignment explanation
Indices: 42898425--42898501 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
42898415 GATTTTCAAG
42898425 GATATGCAATCTT-AGATATGA-TATGTAATCTTAGATAT
1 GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
*
42898463 GATATGCAATCTTAGAAGATATGATTTTGTAATCTTAGA
1 GATATGCAATCTT--AAGATATGATTATGTAATCTTAGA
42898502 GATTTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 13 0.38
41 8 0.24
42 13 0.38
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (40 bp):
GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
Found at i:42898727 original size:23 final size:23
Alignment explanation
Indices: 42898683--42898727 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
42898673 TCTTATTTTG
* *
42898683 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
42898706 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
42898728 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:42899751 original size:22 final size:21
Alignment explanation
Indices: 42899717--42899760 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
42899707 TAATTTATTT
42899717 ATTTTTAATAAAAAGGGTAAA
1 ATTTTTAATAAAAAGGGTAAA
42899738 ATTTTTAATAAAAAGGGTAAA
1 ATTTTTAATAAAAAGGGTAAA
42899759 AT
1 AT
42899761 GCAATCTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (21 bp):
ATTTTTAATAAAAAGGGTAAA
Found at i:42899995 original size:20 final size:21
Alignment explanation
Indices: 42899970--42900019 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
42899960 TAAAAGTAAC
*
42899970 ATACAAATGAA-AGTATAGAT
1 ATACAAATGAATAATATAGAT
42899990 ATACAAAT-AATAATATAGAT
1 ATACAAATGAATAATATAGAT
42900010 ATACAAATGA
1 ATACAAATGA
42900020 TGAAAGTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.26
Consensus pattern (21 bp):
ATACAAATGAATAATATAGAT
Found at i:42900904 original size:7 final size:8
Alignment explanation
Indices: 42900855--42900903 Score: 57
Period size: 8 Copynumber: 6.1 Consensus size: 8
42900845 ATATATGATC
42900855 TTAAAAAA
1 TTAAAAAA
42900863 TTAAAAAA
1 TTAAAAAA
42900871 TTAAAAACTA
1 TTAAAAA--A
42900881 TT-AAAAA
1 TTAAAAAA
*
42900888 TTATAAAA
1 TTAAAAAA
42900896 -TAAAAAA
1 TTAAAAAA
42900903 T
1 T
42900904 AGGTATGACG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
7 9 0.26
8 19 0.54
9 4 0.11
10 3 0.09
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (8 bp):
TTAAAAAA
Found at i:42906525 original size:21 final size:21
Alignment explanation
Indices: 42906480--42906527 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
42906470 CACGTTCCCA
*
42906480 TTTTCTTCTTTCTTTCATTTT
1 TTTTCTTCTTTCTTTCATTTG
42906501 TTTTCTT-TTTCTTTCATTTGG
1 TTTTCTTCTTTCTTTCATTT-G
42906522 TTTTCT
1 TTTTCT
42906528 ACTCAAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (21 bp):
TTTTCTTCTTTCTTTCATTTG
Found at i:42911076 original size:17 final size:18
Alignment explanation
Indices: 42911047--42911081 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42911037 TTTTTGCTCG
*
42911047 GTTTTTGATAATTTTTAC
1 GTTTTTGATAATTGTTAC
42911065 GTTTTTGA-AATTGTTAC
1 GTTTTTGATAATTGTTAC
42911082 TTCAAATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.23, C:0.06, G:0.14, T:0.57
Consensus pattern (18 bp):
GTTTTTGATAATTGTTAC
Found at i:42911866 original size:44 final size:44
Alignment explanation
Indices: 42911802--42911930 Score: 167
Period size: 43 Copynumber: 3.0 Consensus size: 44
42911792 ATAGAATTTT
42911802 GATA-TGAGATTTCATGTAAGACCACGTCTGGGACGATGGCATC
1 GATATTGAGATTTCATGTAAGACCACGTCTGGGACGATGGCATC
* *
42911845 GAT-TTGAGACTTTCGTGTAAGACCATGTCTGGGAC-AGTGGCATC
1 GATATTGAGA-TTTCATGTAAGACCACGTCTGGGACGA-TGGCATC
* * *
42911889 GATATT-TGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 GATATTGAGATTTCATGTAAGACCACGTCTGGGACGATGGCAT
42911931 TGTACGAGCT
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
43 37 0.50
44 35 0.47
45 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.29
Consensus pattern (44 bp):
GATATTGAGATTTCATGTAAGACCACGTCTGGGACGATGGCATC
Found at i:42911921 original size:43 final size:43
Alignment explanation
Indices: 42911806--42911930 Score: 164
Period size: 44 Copynumber: 2.9 Consensus size: 43
42911796 AATTTTGATA
42911806 TGAGATTTCATGTAAGACCACGTCTGGGACGATGGCATCGATT
1 TGAGATTTCATGTAAGACCACGTCTGGGACGATGGCATCGATT
* *
42911849 TGAGACTTTCGTGTAAGACCATGTCTGGGAC-AGTGGCATCGATAT
1 TGAGA-TTTCATGTAAGACCACGTCTGGGACGA-TGGCATCGAT-T
* * *
42911894 T-TGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 TGAGATTTCATGTAAGACCACGTCTGGGACGATGGCAT
42911931 TGTACGAGCT
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
43 34 0.48
44 35 0.49
45 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (43 bp):
TGAGATTTCATGTAAGACCACGTCTGGGACGATGGCATCGATT
Found at i:42913923 original size:38 final size:41
Alignment explanation
Indices: 42913879--42913966 Score: 101
Period size: 43 Copynumber: 2.2 Consensus size: 41
42913869 TAATATTAAT
*
42913879 TTAATAT-AATACTTA-T-CAAGATAAATATTAGATTAAAC
1 TTAATATAAATACTTACTACAAGATAAATATTAAATTAAAC
* * *
42913917 TTAATATTAAATATTTATCTACAAGATAAATATTAAATTTAAT
1 TTAATA-TAAATACTTA-CTACAAGATAAATATTAAATTAAAC
42913960 TTAATAT
1 TTAATAT
42913967 TAAGATAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
38 6 0.15
39 1 0.02
40 7 0.17
42 2 0.05
43 25 0.61
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (41 bp):
TTAATATAAATACTTACTACAAGATAAATATTAAATTAAAC
Found at i:42914008 original size:25 final size:25
Alignment explanation
Indices: 42913954--42914008 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
42913944 AAATATTAAA
*
42913954 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
42913979 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
42914003 TATTAA
1 T-TTAA
42914009 GATAAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:42922846 original size:26 final size:25
Alignment explanation
Indices: 42922788--42922847 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
42922778 ACAACCTAGA
*
42922788 TTCACATAACAAAGTAACACATGAC
1 TTCACATAACAAAGTAAAACATGAC
*
42922813 TT-AGCATAACAACA-TAAAAGCATGAG
1 TTCA-CATAACAA-AGTAAAA-CATGAC
42922839 TTCACATAA
1 TTCACATAA
42922848 AAGCAGAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
24 1 0.03
25 14 0.48
26 13 0.45
27 1 0.03
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.22
Consensus pattern (25 bp):
TTCACATAACAAAGTAAAACATGAC
Found at i:42933035 original size:27 final size:27
Alignment explanation
Indices: 42932999--42933052 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
42932989 CTCGACAAGT
42932999 ATGATGTGAAACACAAAATAGCTATTG
1 ATGATGTGAAACACAAAATAGCTATTG
42933026 ATGATGTGAAACACAAAATAGCTATTG
1 ATGATGTGAAACACAAAATAGCTATTG
42933053 CCTATCATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (27 bp):
ATGATGTGAAACACAAAATAGCTATTG
Found at i:42936013 original size:17 final size:20
Alignment explanation
Indices: 42935973--42936013 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
42935963 ACTTAAGAAG
*
42935973 TCTTCATGACTCACCTCTCT
1 TCTTTATGACTCACCTCTCT
42935993 TCTTTATGACTCACCTCTCT
1 TCTTTATGACTCACCTCTCT
42936013 T
1 T
42936014 TCCTAGTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.37, G:0.05, T:0.44
Consensus pattern (20 bp):
TCTTTATGACTCACCTCTCT
Found at i:42942916 original size:17 final size:17
Alignment explanation
Indices: 42942894--42942930 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
42942884 ATCAAAAGAT
42942894 AAACAAATTATTAGTTG
1 AAACAAATTATTAGTTG
42942911 AAACAAATTATTAGTTG
1 AAACAAATTATTAGTTG
42942928 AAA
1 AAA
42942931 ATGTGAGGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (17 bp):
AAACAAATTATTAGTTG
Found at i:42945343 original size:90 final size:90
Alignment explanation
Indices: 42945202--42945528 Score: 440
Period size: 90 Copynumber: 3.6 Consensus size: 90
42945192 ATTCTAGAAT
* * * * * *** *
42945202 ATTAATACACAAAAATATAAAATTCAAAC-AAAAATAATACACACTAAATTAAATTTAGACACCC
1 ATTAATACACGAAAATTTTAAATTCAAACTATATATAATACGGGCTAAATTAAATTTAAACACCC
42945266 AACAAACTACAAACAGATGGGTAAA
66 AACAAACTACAAACAGATGGGTAAA
* * * *
42945291 ATTAATACATGAAAATTTTAAAGTCTAACTATATATAATATGGGCTAAATTAAATTTAAACACCC
1 ATTAATACACGAAAATTTTAAATTCAAACTATATATAATACGGGCTAAATTAAATTTAAACACCC
* *
42945356 AACAAACTAAAAACAGATGGATAAA
66 AACAAACTACAAACAGATGGGTAAA
** * * * * *
42945381 ATTTGTGCACGAAATTTTTAAATTCAAACTATATATAACACAGACTAAATTAAATTTAAACACCC
1 ATTAATACACGAAAATTTTAAATTCAAACTATATATAATACGGGCTAAATTAAATTTAAACACCC
42945446 AACAAACTACAAACAGATGGGTAAA
66 AACAAACTACAAACAGATGGGTAAA
*
42945471 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACGGGCTAAATTAAATTTA
1 ATTAATACACGAAAATTTTAAATTCAAACTATATATAATACGGGCTAAATTAAATTTA
42945529 TAGATAAAAA
Statistics
Matches: 201, Mismatches: 36, Indels: 1
0.84 0.15 0.00
Matches are distributed among these distances:
89 23 0.11
90 178 0.89
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (90 bp):
ATTAATACACGAAAATTTTAAATTCAAACTATATATAATACGGGCTAAATTAAATTTAAACACCC
AACAAACTACAAACAGATGGGTAAA
Found at i:42945641 original size:21 final size:22
Alignment explanation
Indices: 42945617--42945659 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
42945607 CATTAAATTT
42945617 ACATATATAAA-AAA-AATACAA
1 ACAT-TATAAAGAAATAATACAA
*
42945638 ACATTTTAAAGAAATAATACAA
1 ACATTATAAAGAAATAATACAA
42945660 TTATTTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 7 0.37
22 7 0.37
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.23
Consensus pattern (22 bp):
ACATTATAAAGAAATAATACAA
Found at i:42952774 original size:2 final size:2
Alignment explanation
Indices: 42952767--42952797 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42952757 CAAATCTCAT
42952767 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42952798 TAAAAATTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42962439 original size:21 final size:23
Alignment explanation
Indices: 42962415--42962460 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
42962405 TTCTTTTCTA
42962415 TTTCGGCCGATTTGC-TCA-CAG
1 TTTCGGCCGATTTGCGTCATCAG
*
42962436 TTTCTGCCGATTTGCGTCATCAG
1 TTTCGGCCGATTTGCGTCATCAG
42962459 TT
1 TT
42962461 AGTCTATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.64
22 3 0.14
23 5 0.23
ACGTcount: A:0.13, C:0.26, G:0.22, T:0.39
Consensus pattern (23 bp):
TTTCGGCCGATTTGCGTCATCAG
Found at i:42965043 original size:51 final size:51
Alignment explanation
Indices: 42964979--42965081 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
42964969 AAATTAAAAG
42964979 ATTATACATACACCAACAATGTTTTTTAGGG-ACAATAACATTAAACCAACA
1 ATTATACATACACCAACAATGTTTTTTAGGGTA-AATAACATTAAACCAACA
42965030 ATTATACATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAACA
1 ATTATACATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAACA
42965081 A
1 A
42965082 GTAATTTTAG
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
51 50 0.98
52 1 0.02
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (51 bp):
ATTATACATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAACA
Found at i:42965090 original size:33 final size:34
Alignment explanation
Indices: 42965032--42965137 Score: 105
Period size: 33 Copynumber: 3.2 Consensus size: 34
42965022 AACCAACAAT
* *
42965032 TATACATACACCAACAATGT-TTTTTAGGGT-AAA
1 TATACATAAACCAACAA-GTAATTTTAGGGTCAAA
*
42965065 TA-ACATTAAACCAACAAGTAATTTTA-GGTCAAT
1 TATACA-TAAACCAACAAGTAATTTTAGGGTCAAA
* * *
42965098 TATACATACACCAACAATTAATTTTA-GGTCAAT
1 TATACATAAACCAACAAGTAATTTTAGGGTCAAA
42965131 TATACAT
1 TATACAT
42965138 GCTTTATAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
32 8 0.12
33 53 0.83
34 3 0.05
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.33
Consensus pattern (34 bp):
TATACATAAACCAACAAGTAATTTTAGGGTCAAA
Found at i:42968505 original size:18 final size:18
Alignment explanation
Indices: 42968477--42968525 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 18
42968467 AATTATAAGA
42968477 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
42968494 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
42968510 A-TTTAATTATAATTAT
1 ATTTTAATTA-AATTAT
42968526 GTTTAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 5 0.18
18 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:42968511 original size:16 final size:16
Alignment explanation
Indices: 42968477--42968531 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
42968467 AATTATAAGA
42968477 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
42968494 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
42968510 A-TTTAATTATAAT-T
1 ATTTTAATTAAAATAT
42968524 ATGTTTAA
1 AT-TTTAA
42968532 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:42968581 original size:137 final size:138
Alignment explanation
Indices: 42968329--42968594 Score: 435
Period size: 137 Copynumber: 1.9 Consensus size: 138
42968319 TAAGAATATG
* *
42968329 AATTATTAAGAATTTTATTAAATTATATACCAAAATTATAATGTATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
* * *
42968394 AATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAAA
66 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAA
42968459 TTTCTGCT
131 TTTCTGCT
**** *
42968467 AATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
42968531 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
42968595 TAATCATTTA
Statistics
Matches: 118, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
137 113 0.96
138 5 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (138 bp):
AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAA
TTTCTGCT
Found at i:42968768 original size:16 final size:16
Alignment explanation
Indices: 42968747--42968782 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
42968737 GATTAGCTAT
*
42968747 TACACCTCTAATCTAA
1 TACACCTCTAATCCAA
42968763 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
42968779 TACA
1 TACA
42968783 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:42969371 original size:2 final size:2
Alignment explanation
Indices: 42969366--42969397 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
42969356 TTTAAAAAAT
42969366 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42969398 ATAAATGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42970096 original size:17 final size:19
Alignment explanation
Indices: 42970074--42970109 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
42970064 GATATTAGTC
42970074 TAATT-AAT-TTTATTTTT
1 TAATTAAATATTTATTTTT
42970091 TAATTAAATATTTATTTTT
1 TAATTAAATATTTATTTTT
42970110 AGATAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
19 9 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TAATTAAATATTTATTTTT
Found at i:42971010 original size:71 final size:72
Alignment explanation
Indices: 42970893--42971031 Score: 235
Period size: 71 Copynumber: 1.9 Consensus size: 72
42970883 TCTCGGATTT
* *
42970893 AAAAAAGGGATCATGCACAATAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCACGCACAATAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
42970958 CTTAAGG
66 CTTAAGG
* *
42970965 AAAAAA-GGATCACGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCACGCACAATAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
42971029 CTT
66 CTT
42971032 GAGTTTGAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 57 0.90
72 6 0.10
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (72 bp):
AAAAAAGGGATCACGCACAATAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
CTTAAGG
Found at i:42974039 original size:19 final size:18
Alignment explanation
Indices: 42974002--42974038 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42973992 ATTTTTAAAA
42974002 TATAAATTTTAGAACTTT
1 TATAAATTTTAGAACTTT
42974020 TATAAATATTTAGAA-TTT
1 TATAAAT-TTTAGAACTTT
42974038 T
1 T
42974039 TGAAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
TATAAATTTTAGAACTTT
Found at i:42974049 original size:20 final size:19
Alignment explanation
Indices: 42974002--42974039 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
42973992 ATTTTTAAAA
*
42974002 TATAAAT-TTTAGAACTTT
1 TATAAATATTTAGAATTTT
42974020 TATAAATATTTAGAATTTT
1 TATAAATATTTAGAATTTT
42974039 T
1 T
42974040 GAAAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:42976063 original size:21 final size:21
Alignment explanation
Indices: 42976039--42976081 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
42976029 TTTTGCCTAA
*
42976039 AATATGAATTGGATTGAATTG
1 AATATGAATTGGATTAAATTG
*
42976060 AATATGAATTGTATTAAATTG
1 AATATGAATTGGATTAAATTG
42976081 A
1 A
42976082 GTTAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (21 bp):
AATATGAATTGGATTAAATTG
Found at i:42976891 original size:2 final size:2
Alignment explanation
Indices: 42976884--42976941 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
42976874 NNNNNNNTAC
42976884 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42976926 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
42976942 AGTTATAAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42977011 original size:11 final size:11
Alignment explanation
Indices: 42976997--42977030 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
42976987 ATACGAAAAT
42976997 AAGAAGAAAGA
1 AAGAAGAAAGA
42977008 AAGAAGAAAGAA
1 AAGAAGAAAG-A
42977020 AAGAA-AAAGA
1 AAGAAGAAAGA
42977030 A
1 A
42977031 GAAACTAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.09
11 14 0.64
12 6 0.27
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAGAAGAAAGA
Found at i:42977381 original size:22 final size:24
Alignment explanation
Indices: 42977353--42977396 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
42977343 TATGACAAGA
42977353 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGTTAGAAAAGTAAGTATG
*
42977375 AATTAAGTTGGAAAAGTAAGTA
1 AATTAAGTTAGAAAAGTAAGTA
42977397 AACTTAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.25
Consensus pattern (24 bp):
AATTAAGTTAGAAAAGTAAGTATG
Found at i:42978651 original size:43 final size:42
Alignment explanation
Indices: 42978584--42978754 Score: 197
Period size: 43 Copynumber: 4.0 Consensus size: 42
42978574 ACATAGGATT
**
42978584 TCGATATGTGTTTTTGTGTAAGACCACGTCTGGGACGTTGGCA
1 TCGAT-TGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCA
* *
42978627 TCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACATTGGCA
1 TCGA-TTGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCA
*
42978670 TCGTATT-TGATTT--GTGTAAGACCATGTCTGGGACAG-TGGCA
1 TCG-ATTGTG-TTTACGTGTAAGACCACGTCTGGGAC-GTTGGCA
* *
42978711 TCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCA
1 TCGAT-TGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCA
42978754 T
1 T
42978755 TGTACTAGTC
Statistics
Matches: 111, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
40 2 0.02
41 32 0.29
42 5 0.05
43 70 0.63
44 2 0.02
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.33
Consensus pattern (42 bp):
TCGATTGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:42978742 original size:84 final size:84
Alignment explanation
Indices: 42978596--42978754 Score: 241
Period size: 84 Copynumber: 1.9 Consensus size: 84
42978586 GATATGTGTT
* * *
42978596 TTTGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGG
1 TTTGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGG
42978661 ACATTGGCATCGTATTTGA
66 ACATTGGCATCGTATTTGA
*
42978680 TTTGTGTAAGACCATGTCTGGGACAG-TGGCATCGA-TATGTGATTACATGTAAGACCACGTCTG
1 TTTGTGTAAGACCACGTCTGGGAC-GTTGGCATCGACT-TGTGATTACATGTAAGACCACGTCTG
*
42978743 GGACGTTGGCAT
64 GGACATTGGCAT
42978755 TGTACTAGTC
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
83 1 0.01
84 66 0.97
85 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (84 bp):
TTTGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGG
ACATTGGCATCGTATTTGA
Found at i:42978944 original size:16 final size:17
Alignment explanation
Indices: 42978915--42978946 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
42978905 TGAATTGATG
42978915 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
42978932 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
42978947 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:42982814 original size:25 final size:25
Alignment explanation
Indices: 42982779--42982851 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 25
42982769 TATTGACTTG
* *
42982779 CATGAGC-TTCCTGA-ATATGGCTCT
1 CATGAGCTTTCC-GATACATGGCTCA
*
42982803 TATGAGCTTTCCGATACATGGCTCA
1 CATGAGCTTTCCGATACATGGCTCA
* * *
42982828 CATGAGCTTCCCGTTATATGGCTC
1 CATGAGCTTTCCGATACATGGCTC
42982852 GAGAGAGTGC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
24 8 0.20
25 32 0.80
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (25 bp):
CATGAGCTTTCCGATACATGGCTCA
Found at i:42985320 original size:49 final size:49
Alignment explanation
Indices: 42985267--42985396 Score: 215
Period size: 49 Copynumber: 2.7 Consensus size: 49
42985257 ATTTGGTAGC
*
42985267 AGGGTTTTGTTATTACCTTCCGTGAGTCTCCCCCTATGCATCTAGGAAA
1 AGGGTTTTGTTATTACCTTCCGTGAGCCTCCCCCTATGCATCTAGGAAA
42985316 AGGGTTTTGTTATTACCTTCCGTGAGCCTCCCCCTATGCATCTAGGAAA
1 AGGGTTTTGTTATTACCTTCCGTGAGCCTCCCCCTATGCATCTAGGAAA
* * * *
42985365 AGAGTTTTATTATTACCTTCCATAAGCCTCCC
1 AGGGTTTTGTTATTACCTTCCGTGAGCCTCCC
42985397 ATCATACGTC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 76 1.00
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.35
Consensus pattern (49 bp):
AGGGTTTTGTTATTACCTTCCGTGAGCCTCCCCCTATGCATCTAGGAAA
Found at i:42992688 original size:30 final size:30
Alignment explanation
Indices: 42992652--42993038 Score: 497
Period size: 30 Copynumber: 12.8 Consensus size: 30
42992642 ATGTATACAT
*
42992652 ATACAAATAAATTCGGCAATGTATATCCAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
* * * * *
42992682 ATACAAATCAATTCAGAAATGAATATCTAT
1 ATACAAATCAATTCGGCAATGTATATCCAA
* *
42992712 ATACAAATCAATTCGACAATGTATATCTAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
* *
42992742 ATACGAATCAATTCGACAATGTATATCCAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
*
42992772 ATACAAATCAATTCAGCAATGTATAT-CAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
*
42992801 TATACCAATCAATTCGGCAATGTATATCCAA
1 -ATACAAATCAATTCGGCAATGTATATCCAA
** * *
42992832 ATACAAATCAATTCGATAATGTATATCTAT
1 ATACAAATCAATTCGGCAATGTATATCCAA
42992862 ATACAAATCAATTCGGCAATGTATATCCAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
* *
42992892 ATACGAATCAATTTGGCAATGTATATCCAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
* * *
42992922 ATACAAATCAATTCGGCAATGTAGATCTAT
1 ATACAAATCAATTCGGCAATGTATATCCAA
* ** *
42992952 ATACCAATCAATTCGGCAATGTATATATATGT
1 ATACAAATCAATTCGGCAATGTATATCCA--A
42992984 ATACAAATCAATTCGGCAATGTATATCCAA
1 ATACAAATCAATTCGGCAATGTATATCCAA
* *
42993014 ATACGAATTAATTCGGCAATGTATA
1 ATACAAATCAATTCGGCAATGTATA
42993039 AAACATATAC
Statistics
Matches: 310, Mismatches: 43, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
29 3 0.01
30 277 0.89
31 3 0.01
32 27 0.09
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (30 bp):
ATACAAATCAATTCGGCAATGTATATCCAA
Found at i:42994144 original size:20 final size:21
Alignment explanation
Indices: 42994119--42994160 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
42994109 TGTTGAATTG
42994119 TGTATT-TTGGAATGTT-CAAA
1 TGTATTCTT-GAATGTTACAAA
42994139 TGTATTCTTGAATGTTACAAA
1 TGTATTCTTGAATGTTACAAA
42994160 T
1 T
42994161 TGGTACAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (21 bp):
TGTATTCTTGAATGTTACAAA
Found at i:43000827 original size:19 final size:18
Alignment explanation
Indices: 43000799--43000834 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
43000789 AAGTTACCTT
43000799 CTTTGTTTCTGGTTTTGA
1 CTTTGTTTCTGGTTTTGA
*
43000817 CTTTGGTTTCTGTTTTTG
1 CTTT-GTTTCTGGTTTTG
43000835 TTTGTGGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.03, C:0.11, G:0.22, T:0.64
Consensus pattern (18 bp):
CTTTGTTTCTGGTTTTGA
Found at i:43005002 original size:27 final size:27
Alignment explanation
Indices: 43004971--43005039 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
43004961 AAAACATATT
43004971 TATATTTTATAATAT-ATAAGTTGGTAAA
1 TATATTTTATAATATCATAAGTT--TAAA
* * *
43004999 -ATATTTTTATATTTTCATTAGTTTAAA
1 TATA-TTTTATAATATCATAAGTTTAAA
43005026 TATATTTTATAATA
1 TATATTTTATAATA
43005040 CATTTATTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
27 15 0.45
28 12 0.36
29 6 0.18
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (27 bp):
TATATTTTATAATATCATAAGTTTAAA
Found at i:43009004 original size:2 final size:2
Alignment explanation
Indices: 43008952--43008987 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
43008942 TAATCTGTAC
*
43008952 GA GA GA GA GA GA GA GA GA GG GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
43008988 CTTGATGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:43010471 original size:15 final size:15
Alignment explanation
Indices: 43010462--43010494 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
43010452 CAAATGCTAT
43010462 AATAATAAATACAAC
1 AATAATAAATACAAC
*
43010477 AATAATAAATACATC
1 AATAATAAATACAAC
43010492 AAT
1 AAT
43010495 GGCATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:43010974 original size:23 final size:23
Alignment explanation
Indices: 43010931--43010975 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
43010921 AATAAGTGTA
* *
43010931 TACATATAGATTATAAAAAAAAT
1 TACATATAGAATAAAAAAAAAAT
*
43010954 TACATAT-GAATAAAAATAAAAT
1 TACATATAGAATAAAAAAAAAAT
43010976 AAAAATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (23 bp):
TACATATAGAATAAAAAAAAAAT
Found at i:43011076 original size:26 final size:26
Alignment explanation
Indices: 43011034--43011093 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
43011024 AAAATATTTT
**
43011034 AAAAAAATAATTAAATATGAAAAATA
1 AAAAAAATAATTAAATAAAAAAAATA
43011060 AAAAAAACTAATT-AATAAAAAAAATA
1 AAAAAAA-TAATTAAATAAAAAAAATA
*
43011086 AAGAAAAT
1 AAAAAAAT
43011094 GAAAAAGGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 1 0.03
26 24 0.80
27 5 0.17
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (26 bp):
AAAAAAATAATTAAATAAAAAAAATA
Found at i:43011972 original size:65 final size:65
Alignment explanation
Indices: 43011903--43012101 Score: 169
Period size: 64 Copynumber: 3.1 Consensus size: 65
43011893 ATGAAGTTTT
43011903 TGTGTTTGCTGTGAAAAATATTTGCTACTTCTTTTATTGATTGTTTTTTCGGATCCCGTTTACAA
1 TGTGTTTGCTGTGAAAAATATTTGCTACTTCTTTTATTGATTGTTTTTTCGGATCCCGTTTACAA
** * * * * ** ** * ***
43011968 TGTG-TTAATG-GAAATAAAAGTAT-CAACCT-TTTTATTTCTTGATTAATCCTCTGATGAAGTT
1 TGTGTTTGCTGTGAAA-AATA-TTTGCTACTTCTTTTATTGATTG-TT--TTTTCGGATCCCGTT
*
43012029 T---T
61 TACAA
43012031 TGTGTTTGCTGTGAAAAATATTTGCTACTTCTTTTATTGATTGTTTTTTCGGATCCCGTTTACAA
1 TGTGTTTGCTGTGAAAAATATTTGCTACTTCTTTTATTGATTGTTTTTTCGGATCCCGTTTACAA
43012096 TGTGTT
1 TGTGTT
43012102 AATGGCCTTT
Statistics
Matches: 92, Mismatches: 30, Indels: 24
0.63 0.21 0.16
Matches are distributed among these distances:
62 10 0.11
63 20 0.22
64 26 0.28
65 26 0.28
66 10 0.11
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.48
Consensus pattern (65 bp):
TGTGTTTGCTGTGAAAAATATTTGCTACTTCTTTTATTGATTGTTTTTTCGGATCCCGTTTACAA
Found at i:43012043 original size:128 final size:128
Alignment explanation
Indices: 43011851--43012106 Score: 512
Period size: 128 Copynumber: 2.0 Consensus size: 128
43011841 ATAAAAACGA
43011851 AAATAAAAGTATCAACCTTTTTATTTCTTGATTAATCCTCTGATGAAGTTTTTGTGTTTGCTGTG
1 AAATAAAAGTATCAACCTTTTTATTTCTTGATTAATCCTCTGATGAAGTTTTTGTGTTTGCTGTG
43011916 AAAAATATTTGCTACTTCTTTTATTGATTGTTTTTTCGGATCCCGTTTACAATGTGTTAATGG
66 AAAAATATTTGCTACTTCTTTTATTGATTGTTTTTTCGGATCCCGTTTACAATGTGTTAATGG
43011979 AAATAAAAGTATCAACCTTTTTATTTCTTGATTAATCCTCTGATGAAGTTTTTGTGTTTGCTGTG
1 AAATAAAAGTATCAACCTTTTTATTTCTTGATTAATCCTCTGATGAAGTTTTTGTGTTTGCTGTG
43012044 AAAAATATTTGCTACTTCTTTTATTGATTGTTTTTTCGGATCCCGTTTACAATGTGTTAATGG
66 AAAAATATTTGCTACTTCTTTTATTGATTGTTTTTTCGGATCCCGTTTACAATGTGTTAATGG
43012107 CCTTTTTATA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 128 1.00
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (128 bp):
AAATAAAAGTATCAACCTTTTTATTTCTTGATTAATCCTCTGATGAAGTTTTTGTGTTTGCTGTG
AAAAATATTTGCTACTTCTTTTATTGATTGTTTTTTCGGATCCCGTTTACAATGTGTTAATGG
Found at i:43013126 original size:217 final size:217
Alignment explanation
Indices: 43012594--43013582 Score: 1540
Period size: 217 Copynumber: 4.5 Consensus size: 217
43012584 CTTCAATCTA
* * * * *
43012594 CTCCTCTGCAACTTCAGGGAGATAAGGCTAGATGTGATCTGCTCTCTGCAACTTCATAAAGATAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
* * * *
43012659 GATCCAAGATTTATGGTTCTAATCTGCTCCATTGCAACTTCAAGGAGATAGGATTATTGGTTTTA
66 GATCC---A---A-GGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGTTTTA
*
43012724 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCGCTGCAACTTC
124 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
43012789 AGGAGGATAAGA----CTTGCTTAGTCTG
189 AGGAGGATAAGACTTGCTTGCTTAGTCTG
43012814 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
* * * *
43012879 GATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAACCTGCT
66 GATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGTTTTAATCTGCT
* * * * *
43012944 CCACTGTAACTTCAGGGAAATAATATTTGCCATCTTCAGTTTGCCTCGCTGCAACTTCAGGAGGA
131 CCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGA
*
43013009 TAAGACTTGCTTG-TATAGTTTG
196 TAAGACTTGCTTGCT-TAGTCTG
*
43013031 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTTAGAGAGATAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
43013096 GATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGTTTTAATCTGCT
66 GATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGTTTTAATCTGCT
* *
43013161 CCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGTAGGA
131 CCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGA
43013226 TAAGACTTGCTTGCTTAGTCTG
196 TAAGACTTGCTTGCTTAGTCTG
*
43013248 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCCCTGCAACTTCAGAGAGATAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
*
43013313 GATCCAAGGTTTTAATCCGCTCTACTGCAACTTCAGGGAGATAGGATTATTGGTTTTAATCTGCT
66 GATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGTTTTAATCTGCT
* *
43013378 CCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTTAGTCTGCCTCACTGCAACTTCAGAAAGG
131 CCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAG-GAGG
43013443 ATAAGACTTGCTTGCTTAGTCTG
195 ATAAGACTTGCTTGCTTAGTCTG
* *
43013466 CTCCACTACAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAAAGATAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
*** * * *
43013531 GAT-CTTTGATTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATCATTGG
66 GATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGG
43013583 CTTTCGATCT
Statistics
Matches: 715, Mismatches: 47, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
213 117 0.16
214 1 0.00
216 1 0.00
217 440 0.62
218 92 0.13
220 64 0.09
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (217 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
GATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGTTTTAATCTGCT
CCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGA
TAAGACTTGCTTGCTTAGTCTG
Found at i:43013419 original size:173 final size:175
Alignment explanation
Indices: 43013029--43013572 Score: 446
Period size: 173 Copynumber: 3.1 Consensus size: 175
43013019 TTGTATAGTT
* * * * *
43013029 TGCTCCACTGCAACTTCAGGGAGATAAGACTAG-ATGC-GA-TCTG-CTCTCTGCAACTTTAGAG
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATGCTTAGTCTGCCTCACTGCAACTTCAGAA
* * * * * * * * *
43013090 A-GATAAGA-T-CCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGTTT
66 AGGATAAGACTAGC-ATG-CTGAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATCA-AGGTTT
* * * * *
43013152 TAATCTGCTCCACTGCAACTTTAGGGAGATAAGA-TTTGCCATCTTCAGTC
128 TAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTTG--GT-TTTAATC
* *
43013202 TGC-CTCACTGCAACTTCA-GTAGGATAAGACTTGCTTGCTTAGTCTG-CTCCACTGCAACTTCA
1 TGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCATGCTTAGTCTGCCT-CACTGCAACTTCA
** *
43013264 GGGA-GATAAGACTAG-ATGC-GA-TCTGCTCC-CTGCAACTTCAGAGAGATAAGATCCAAGGTT
63 GAAAGGATAAGACTAGCATGCTGAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAT-CAAGGTT
* *
43013324 TTAATCCGCTCTACTGCAACTTCAGGGAGATAGGATTATTGGTTTTAATC
127 TTAATCTGCTCTACTGCAACTTCAGGGAGATAAGATT-TTGGTTTTAATC
*
43013374 TGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCAT-CTTTAGTCTGCCTCACTGCAACTTCAG
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CATGC-TTAGTCTGCCTCACTGCAACTTCAG
* * * * * * **
43013438 AAAGGATAAGACTTGCTTGCTTAGTCTGCTCCACTACAACTTCAGGGAGATAAGA-CTA-GATGC
64 AAAGGATAAGACTAGCATGCTGAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATCAAGGTTTT
* ** *
43013501 GATCTGCTCT-CTGCAACTTCAGAAAGATAAGATCTTT-GATTTAATC
129 AATCTGCTCTACTGCAACTTCAGGGAGATAAGAT-TTTGGTTTTAATC
**
43013547 CACTCCACTGCAACTTCAGGGAGATA
1 TGCTCCACTGCAACTTCAGGGAGATA
43013573 GGATCATTGG
Statistics
Matches: 304, Mismatches: 45, Indels: 44
0.77 0.11 0.11
Matches are distributed among these distances:
172 35 0.12
173 143 0.47
174 46 0.15
175 19 0.06
176 9 0.03
177 31 0.10
178 21 0.07
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (175 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATGCTTAGTCTGCCTCACTGCAACTTCAGAA
AGGATAAGACTAGCATGCTGAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATCAAGGTTTTAA
TCTGCTCTACTGCAACTTCAGGGAGATAAGATTTTGGTTTTAATC
Found at i:43013492 original size:44 final size:44
Alignment explanation
Indices: 43012681--43013494 Score: 434
Period size: 44 Copynumber: 18.8 Consensus size: 44
43012671 ATGGTTCTAA
* * * * * *
43012681 TCTGCTCCATTGCAACTTCAAGGAGATAGGA-TT-ATTGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTT-G-CTTAG
* *
43012725 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCAT-CTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CTTGCTT-AG
*
43012770 TCTGC-CTCGCTGCAACTTCA-GGAGGATAAGA----CTTGCTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTTGCTTAG
* * *
43012810 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG-ATGC-GA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTGCTTAG
* * * * *
43012851 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTAAGGTT--TTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCTTGCTTAG
* * * * *
43012894 TCCGCTCCACTGCAACTTCAGGGAGATAGGA-TT-ATCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCT-TGC-TTAG
* * * * * *
43012938 CCTGCTCCACTGTAACTTCAGGGAAATAATATTTGCCAT-CTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CTTGCTT-AG
* *
43012983 TTTGC-CTCGCTGCAACTTCA-GGAGGATAAGACTTGCTTG-TATAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTTGCT-TAG
* * * *
43013027 TTTGCTCCACTGCAACTTCAGGGAGATAAGACTAG-ATGC-GA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTGCTTAG
* * * ** * *
43013068 TCTGCT-CTCTGCAACTTTAGAGAGATAAGATCCAAGGTT--TTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA--CTTGCTTGCTTAG
* * * * *
43013111 TCCGCTCCACTGCAACTTCAGGGAGATAGGA-TT-ATTGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTT-G-CTTAG
* * *
43013155 TCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCAT-CTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CTTGCTT-AG
*
43013200 TCTGC-CTCACTGCAACTTCA-GTAGGATAAGACTTGCTTGCTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTTGCTTAG
* * *
43013244 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG-ATGC-GA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTGCTTAG
* ** * *
43013285 TCTGCTCC-CTGCAACTTCAGAGAGATAAGATCCAAGGTT--TTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA--CTTGCTTGCTTAG
* * * * * *
43013328 TCCGCTCTACTGCAACTTCAGGGAGATAGGA-TT-ATTGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTT-G-CTTAG
* *
43013372 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCAT-CTTTAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CTTGC-TTAG
**
43013417 TCTGC-CTCACTGCAACTTCAGAAAGGATAAGACTTGCTTGCTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTTGCTTAG
*
43013462 TCTGCTCCACTACAACTTCAGGGAGATAAGACT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT
43013495 AGATGCGATC
Statistics
Matches: 599, Mismatches: 100, Indels: 142
0.71 0.12 0.17
Matches are distributed among these distances:
40 97 0.16
41 28 0.05
42 15 0.03
43 27 0.05
44 273 0.46
45 144 0.24
46 12 0.02
47 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTGCTTAG
Found at i:43026974 original size:14 final size:14
Alignment explanation
Indices: 43026955--43026999 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
43026945 GGCCACCGCG
43026955 CCGGCCGCCGATCT
1 CCGGCCGCCGATCT
* *
43026969 CCGGCCACCG--CA
1 CCGGCCGCCGATCT
43026981 CCGGCCGCCGATCT
1 CCGGCCGCCGATCT
43026995 CCGGC
1 CCGGC
43027000 GCCAGCACCA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 10 0.40
14 15 0.60
ACGTcount: A:0.09, C:0.53, G:0.29, T:0.09
Consensus pattern (14 bp):
CCGGCCGCCGATCT
Found at i:43027007 original size:26 final size:26
Alignment explanation
Indices: 43026943--43027008 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
43026933 CGGACGGTCA
* *
43026943 CCGGCCACCGCGCCGGCCGCCGATCT
1 CCGGCCACAGCACCGGCCGCCGATCT
*
43026969 CCGGCCACCGCACCGGCCGCCGATCT
1 CCGGCCACAGCACCGGCCGCCGATCT
43026995 CCGGCGC-CAGCACC
1 CCGGC-CACAGCACC
43027009 ACCGTCCGCG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 36 0.97
27 1 0.03
ACGTcount: A:0.11, C:0.55, G:0.29, T:0.06
Consensus pattern (26 bp):
CCGGCCACAGCACCGGCCGCCGATCT
Found at i:43027017 original size:29 final size:26
Alignment explanation
Indices: 43026943--43026999 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
43026933 CGGACGGTCA
*
43026943 CCGGCCACCGCGCCGGCCGCCGATCT
1 CCGGCCACCGCACCGGCCGCCGATCT
43026969 CCGGCCACCGCACCGGCCGCCGATCT
1 CCGGCCACCGCACCGGCCGCCGATCT
43026995 CCGGC
1 CCGGC
43027000 GCCAGCACCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.09, C:0.54, G:0.30, T:0.07
Consensus pattern (26 bp):
CCGGCCACCGCACCGGCCGCCGATCT
Found at i:43036131 original size:41 final size:39
Alignment explanation
Indices: 43036086--43036194 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 39
43036076 ACTTCGAGTT
* **
43036086 GATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTC
1 GATGAGACACTGGGTGTCAATTTA-TACTTCGG-TTAAGCC
* * *
43036127 GATGAGGCACTGGGTGCCAA-TT-TACTTCGGTTTAGCC
1 GATGAGACACTGGGTGTCAATTTATACTTCGGTTAAGCC
*
43036164 GATGAGACACTGGGTGTTAATTTATTACTTC
1 GATGAGACACTGGGTGTCAATTTA-TACTTC
43036195 AAATTATCCG
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
37 21 0.38
38 9 0.16
40 8 0.14
41 18 0.32
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.35
Consensus pattern (39 bp):
GATGAGACACTGGGTGTCAATTTATACTTCGGTTAAGCC
Found at i:43036206 original size:40 final size:40
Alignment explanation
Indices: 43036086--43036219 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 40
43036076 ACTTCGAGTT
* * *
43036086 GATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTC
1 GATGAGACACTGGGTGTCAATTTATTACTTCGGATT-ATCC
* * * *
43036127 GATGAGGCACTGGGTGCCAA--T-TTACTTCGGTTTAGCC
1 GATGAGACACTGGGTGTCAATTTATTACTTCGGATTATCC
* **
43036164 GATGAGACACTGGGTGTTAATTTATTACTTCAAATTATCC
1 GATGAGACACTGGGTGTCAATTTATTACTTCGGATTATCC
* *
43036204 GATGAGGCACTAGGTG
1 GATGAGACACTGGGTG
43036220 CCAAACTGGT
Statistics
Matches: 74, Mismatches: 16, Indels: 7
0.76 0.16 0.07
Matches are distributed among these distances:
37 19 0.26
38 9 0.12
39 2 0.03
40 26 0.35
41 18 0.24
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (40 bp):
GATGAGACACTGGGTGTCAATTTATTACTTCGGATTATCC
Found at i:43058546 original size:21 final size:20
Alignment explanation
Indices: 43058504--43058563 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
43058494 AGCTTATTTA
* **
43058504 TATTTTAATTAATCATGTTT
1 TATTTTAATTAATCTTAATT
43058524 TAGTTTTAATTAATCTTAATT
1 TA-TTTTAATTAATCTTAATT
* *
43058545 TA-CTTAATTAAGCTTAATT
1 TATTTTAATTAATCTTAATT
43058564 GTTAATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 15 0.44
20 2 0.06
21 17 0.50
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (20 bp):
TATTTTAATTAATCTTAATT
Found at i:43059426 original size:14 final size:14
Alignment explanation
Indices: 43059407--43059435 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43059397 TAAAACAATG
43059407 AAAATATTTTACAT
1 AAAATATTTTACAT
43059421 AAAATATTTTACAT
1 AAAATATTTTACAT
43059435 A
1 A
43059436 CAAACAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATATTTTACAT
Found at i:43063787 original size:21 final size:21
Alignment explanation
Indices: 43063763--43063809 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
43063753 AGATATTGTG
* *
43063763 ATACCCAAAGTGGATATCGCT
1 ATACCCAAAATGGATACCGCT
*
43063784 ATACCCAAAATGGATACCGTT
1 ATACCCAAAATGGATACCGCT
43063805 ATACC
1 ATACC
43063810 ACTGTAGGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (21 bp):
ATACCCAAAATGGATACCGCT
Found at i:43064844 original size:27 final size:27
Alignment explanation
Indices: 43064814--43064865 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
43064804 GAACGCCAGT
*
43064814 ACCCCTACGGCGCAGCGGAAAATTAGA
1 ACCCCTACGGCGCAGCAGAAAATTAGA
* *
43064841 ACCCCTACTGCGTAGCAGAAAATTA
1 ACCCCTACGGCGCAGCAGAAAATTA
43064866 AAACATTCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.35, C:0.29, G:0.21, T:0.15
Consensus pattern (27 bp):
ACCCCTACGGCGCAGCAGAAAATTAGA
Found at i:43065919 original size:20 final size:20
Alignment explanation
Indices: 43065868--43065910 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
43065858 CTCTTTCAAA
* *
43065868 ATTTC-TTATTTTCATTTGC
1 ATTTCATTACTTTCAATTGC
43065887 ATTTCATTACTTTCAATTGC
1 ATTTCATTACTTTCAATTGC
43065907 ATTT
1 ATTT
43065911 ACTTTCTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.21, C:0.16, G:0.05, T:0.58
Consensus pattern (20 bp):
ATTTCATTACTTTCAATTGC
Found at i:43068638 original size:134 final size:134
Alignment explanation
Indices: 43068398--43068647 Score: 500
Period size: 134 Copynumber: 1.9 Consensus size: 134
43068388 GTGTGTATTG
43068398 GTATTTAAAAATGATATATTATATGCATGTGGTAAATATTATATGATGATTGTGTGGGTCTTGCC
1 GTATTTAAAAATGATATATTATATGCATGTGGTAAATATTATATGATGATTGTGTGGGTCTTGCC
43068463 TTTGGGTGGTATATAGTTTATTGAAATGATTTTATGTGTATTTTAATCATTATATGATATATTTT
66 TTTGGGTGGTATATAGTTTATTGAAATGATTTTATGTGTATTTTAATCATTATATGATATATTTT
43068528 ATGT
131 ATGT
43068532 GTATTTAAAAATGATATATTATATGCATGTGGTAAATATTATATGATGATTGTGTGGGTCTTGCC
1 GTATTTAAAAATGATATATTATATGCATGTGGTAAATATTATATGATGATTGTGTGGGTCTTGCC
43068597 TTTGGGTGGTATATAGTTTATTGAAATGATTTTATGTGTATTTTAATCATT
66 TTTGGGTGGTATATAGTTTATTGAAATGATTTTATGTGTATTTTAATCATT
43068648 GTACATGTTG
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 116 1.00
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (134 bp):
GTATTTAAAAATGATATATTATATGCATGTGGTAAATATTATATGATGATTGTGTGGGTCTTGCC
TTTGGGTGGTATATAGTTTATTGAAATGATTTTATGTGTATTTTAATCATTATATGATATATTTT
ATGT
Found at i:43072785 original size:37 final size:35
Alignment explanation
Indices: 43072711--43072782 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 35
43072701 TAATAACAAA
*
43072711 GAAAAATAAAAACAAAAAATATTTTTGGATTTTTT
1 GAAAAATAAAAAAAAAAAATATTTTTGGATTTTTT
43072746 GAAAAATAAAAAAATAGAAAATATTTTTGGGATTTTT
1 GAAAAATAAAAAAA-A-AAAATATTTTT-GGATTTTT
43072783 GAATTTTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 13 0.39
36 1 0.03
37 11 0.33
38 8 0.24
ACGTcount: A:0.51, C:0.01, G:0.11, T:0.36
Consensus pattern (35 bp):
GAAAAATAAAAAAAAAAAATATTTTTGGATTTTTT
Found at i:43075651 original size:57 final size:57
Alignment explanation
Indices: 43075485--43075677 Score: 235
Period size: 57 Copynumber: 3.4 Consensus size: 57
43075475 TTATTGTTTG
* * ** *
43075485 CATGCTATCATAAATTGAATTAAAGCTGTTGTTTGAGTGCGTCAAATTGAGCATTTC
1 CATGCTATCATAAATTGAATTAAAGTTGTTGTTTTAGTGTATCAAATTGAGCATTTT
* * * * * *
43075542 CTTACTGTCTTAAATTGAA-TCAAGTTGTTGTTTTAGTGTTTCAAATTGAGCATTTT
1 CATGCTATCATAAATTGAATTAAAGTTGTTGTTTTAGTGTATCAAATTGAGCATTTT
* * *
43075598 CATGCTGTCATAAATTGAATTAAAGTTGCTATTTTAGTGTATCAAATTGAGCATTTT
1 CATGCTATCATAAATTGAATTAAAGTTGTTGTTTTAGTGTATCAAATTGAGCATTTT
* *
43075655 CATGCTATCTTAAATTAAATTAA
1 CATGCTATCATAAATTGAATTAA
43075678 CCTAATGTTT
Statistics
Matches: 115, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
56 47 0.41
57 68 0.59
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.42
Consensus pattern (57 bp):
CATGCTATCATAAATTGAATTAAAGTTGTTGTTTTAGTGTATCAAATTGAGCATTTT
Found at i:43075687 original size:113 final size:114
Alignment explanation
Indices: 43075485--43075736 Score: 292
Period size: 113 Copynumber: 2.2 Consensus size: 114
43075475 TTATTGTTTG
* * * * * * *
43075485 CATGCTATCATAAATTGAATTAAAGCTGTTGTTTGAGTGCGTCAAATTGAGCATTTCCTTACTGT
1 CATGCTGTCATAAATTGAATTAAAGTTGCTATTTGAGTGCATCAAATTGAGCATTTCCATACTAT
* ** ** * *
43075550 CTTAAATTGAATCAAGTTGTTGTTTTAGTGTTTCAAATTGAGCATT-TT
66 CTTAAATTAAATCAACCTAATGTTTTAATGGTTCAAATTGAGCATTATT
* * * *
43075598 CATGCTGTCATAAATTGAATTAAAGTTGCTATTTTAGTGTATCAAATTGAGCATTTTCATGCTAT
1 CATGCTGTCATAAATTGAATTAAAGTTGCTATTTGAGTGCATCAAATTGAGCATTTCCATACTAT
* *
43075663 CTTAAATTAAATTAACCTAATGTTTTAATGGTTCAAATTGAGTATTATT
66 CTTAAATTAAATCAACCTAATGTTTTAATGGTTCAAATTGAGCATTATT
* *
43075712 -ATGCTGTCCTAAATTAAATTAAAGT
1 CATGCTGTCATAAATTGAATTAAAGT
43075737 GTTTCTTCAA
Statistics
Matches: 116, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
113 114 0.98
114 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (114 bp):
CATGCTGTCATAAATTGAATTAAAGTTGCTATTTGAGTGCATCAAATTGAGCATTTCCATACTAT
CTTAAATTAAATCAACCTAATGTTTTAATGGTTCAAATTGAGCATTATT
Found at i:43075755 original size:56 final size:53
Alignment explanation
Indices: 43075485--43075772 Score: 179
Period size: 56 Copynumber: 5.1 Consensus size: 53
43075475 TTATTGTTTG
* * * * *
43075485 CATGCTATCATAAATTGAATTAAAGCTGTTGTTTGAGTGCGTCAAATTGAGCATTTC
1 CATGCTGTCATAAATTAAATTAAAG-TGTT-TTT-AATG-TTCAAATTGAGCATTTT
* * * * * *
43075542 CTTACTGTCTTAAATTGAA-TCAAGTTGTTGTTTTAGTGTTTCAAATTGAGCATTTT
1 CATGCTGTCATAAATTAAATTAAAG-TG-T-TTTTAATG-TTCAAATTGAGCATTTT
* *
43075598 CATGCTGTCATAAATTGAATTAAAGTTGCTATTTTAGTGTATCAAATTGAGCATTTT
1 CATGCTGTCATAAATTAAATTAAAG-TG-T-TTTTAATGT-TCAAATTGAGCATTTT
* * * *
43075655 CATGCTATCTTAAATTAAATTAACCTAATG-TTTTAATGGTTCAAATTGAGTATTATT
1 CATGCTGTCATAAATTAAATTAA---AGTGTTTTTAAT-GTTCAAATTGAGCATT-TT
* * *
43075712 -ATGCTGTCCTAAATTAAATTAAAGTGTTTCTTCAATGTCTCAAAGTAAGCATTATT
1 CATGCTGTCATAAATTAAATTAAAGTGTTT-TT-AATGT-TCAAATTGAGCATT-TT
43075768 -ATGCT
1 CATGCT
43075773 ATTGAAAAAT
Statistics
Matches: 191, Mismatches: 27, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
53 3 0.02
54 2 0.01
55 4 0.02
56 103 0.54
57 75 0.39
58 1 0.01
59 2 0.01
60 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (53 bp):
CATGCTGTCATAAATTAAATTAAAGTGTTTTTAATGTTCAAATTGAGCATTTT
Found at i:43075783 original size:113 final size:113
Alignment explanation
Indices: 43075570--43075774 Score: 249
Period size: 113 Copynumber: 1.8 Consensus size: 113
43075560 ATCAAGTTGT
* * * *
43075570 TGTTTTAGTGTTTCAAATTGAGCATTTTCATGCTGTCATAAATTGAATTAAAGTTGCTATTTTAG
1 TGTTTTAATGGTTCAAATTGAGCATTTTCATGCTGTCATAAATTAAATTAAAGTTGCTATTTTAA
* * *
43075635 TGTATCAAATTGAGCATTTTCATGCTATCTTAAATTAAATTAACCTAA
66 TGTATCAAAGTAAGCATTTTCATGCTATCTAAAATTAAATTAACCTAA
* *
43075683 TGTTTTAATGGTTCAAATTGAGTATTATT-ATGCTGTCCTAAATTAAATTAAAG-TG-T-TTCTT
1 TGTTTTAATGGTTCAAATTGAGCATT-TTCATGCTGTCATAAATTAAATTAAAGTTGCTATT-TT
*
43075744 CAATGTCTCAAAGTAAGCATTATT-ATGCTAT
64 -AATGTATCAAAGTAAGCATT-TTCATGCTAT
43075775 TGAAAAATTG
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
110 2 0.03
111 3 0.04
112 25 0.32
113 47 0.59
114 2 0.03
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (113 bp):
TGTTTTAATGGTTCAAATTGAGCATTTTCATGCTGTCATAAATTAAATTAAAGTTGCTATTTTAA
TGTATCAAAGTAAGCATTTTCATGCTATCTAAAATTAAATTAACCTAA
Found at i:43076628 original size:113 final size:113
Alignment explanation
Indices: 43076427--43076656 Score: 433
Period size: 113 Copynumber: 2.0 Consensus size: 113
43076417 GAAAAGTAAG
*
43076427 AATATTCATTATATTGATAAAGTACACTACATTCTCTTTTGGCTTATGTGCCTCCAATGTGATGA
1 AATATTCATTATATTGATAAAGTACACCACATTCTCTTTTGGCTTATGTGCCTCCAATGTGATGA
*
43076492 AAATTATAAGGAAATCAATAGTAAAATCTTGTTAAATGGTTTTCTTGA
66 AAATTATAAGGAAATCAAGAGTAAAATCTTGTTAAATGGTTTTCTTGA
*
43076540 AATATTCATTATATTGATAAAGTACACCACATTCTCTTTTGGCTTATGTGCCTCGAATGTGATGA
1 AATATTCATTATATTGATAAAGTACACCACATTCTCTTTTGGCTTATGTGCCTCCAATGTGATGA
43076605 AAATTATAAGGAAATCAAGAGTAAAATCTTGTTAAATGGTTTTCTTGA
66 AAATTATAAGGAAATCAAGAGTAAAATCTTGTTAAATGGTTTTCTTGA
43076653 AATA
1 AATA
43076657 CATCAATAAT
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 114 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (113 bp):
AATATTCATTATATTGATAAAGTACACCACATTCTCTTTTGGCTTATGTGCCTCCAATGTGATGA
AAATTATAAGGAAATCAAGAGTAAAATCTTGTTAAATGGTTTTCTTGA
Found at i:43102807 original size:16 final size:16
Alignment explanation
Indices: 43102786--43102819 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
43102776 TTTCTTCCCC
43102786 AACTAAAAGTATAAAG
1 AACTAAAAGTATAAAG
43102802 AACTAAAAGTATAAAG
1 AACTAAAAGTATAAAG
43102818 AA
1 AA
43102820 ACCATAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (16 bp):
AACTAAAAGTATAAAG
Found at i:43103946 original size:26 final size:29
Alignment explanation
Indices: 43103898--43103953 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 29
43103888 GATGTTGGTG
43103898 ATATTTTAAATAATATATATTAATAATAA
1 ATATTTTAAATAATATATATTAATAATAA
*
43103927 ATATTTT-GATAATAT-T-TTAATAATAA
1 ATATTTTAAATAATATATATTAATAATAA
43103953 A
1 A
43103954 ATGATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 11 0.42
27 1 0.04
28 7 0.27
29 7 0.27
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (29 bp):
ATATTTTAAATAATATATATTAATAATAA
Found at i:43109787 original size:2 final size:2
Alignment explanation
Indices: 43109780--43109826 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
43109770 CGGATATTGA
43109780 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43109822 AT AT A
1 AT AT A
43109827 AACAGAACTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43111695 original size:16 final size:16
Alignment explanation
Indices: 43111644--43111686 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
43111634 ATTAAAATGT
*
43111644 ATAATATATAACATATAA
1 ATAATATTTAA-A-ATAA
*
43111662 GTAATATTTAAAATAA
1 ATAATATTTAAAATAA
43111678 ATAATATTT
1 ATAATATTT
43111687 TATAAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 12 0.55
17 1 0.05
18 9 0.41
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
ATAATATTTAAAATAA
Found at i:43112417 original size:44 final size:46
Alignment explanation
Indices: 43112367--43112465 Score: 130
Period size: 52 Copynumber: 2.1 Consensus size: 46
43112357 TACAAGATAG
43112367 AAAATTATTTT-AAG-ACATTTGGAAATTTAAAATGACATATATAT
1 AAAATTATTTTAAAGAACATTTGGAAATTTAAAATGACATATATAT
43112411 AAAATTATTTTAAAAGAACTTAACATTTGGAAATTTAAAATGACATATATAT
1 AAAATTATTTT-AAAG-----AACATTTGGAAATTTAAAATGACATATATAT
43112463 AAA
1 AAA
43112466 TATATGATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
44 11 0.23
46 3 0.06
52 33 0.70
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (46 bp):
AAAATTATTTTAAAGAACATTTGGAAATTTAAAATGACATATATAT
Found at i:43120020 original size:40 final size:40
Alignment explanation
Indices: 43119949--43120025 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
43119939 CCTTTTTTTA
**
43119949 TTTTTTAATTTTTTAAATCTTTTTTTTAAAAAGTAAAAGT
1 TTTTTTAATTTTTTAAATCTTTTTTAAAAAAAGTAAAAGT
*
43119989 TTTTTTCAATTTTTTAAA-CTTTTTTAAAAAAATTAAA
1 TTTTTT-AATTTTTTAAATCTTTTTTAAAAAAAGTAAA
43120026 TAATAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 22 0.67
41 11 0.33
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.56
Consensus pattern (40 bp):
TTTTTTAATTTTTTAAATCTTTTTTAAAAAAAGTAAAAGT
Found at i:43129797 original size:15 final size:15
Alignment explanation
Indices: 43129777--43129807 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
43129767 AAAACAACAT
43129777 AACTCTTAACCTTTC
1 AACTCTTAACCTTTC
*
43129792 AACTCTTGACCTTTC
1 AACTCTTAACCTTTC
43129807 A
1 A
43129808 CTTACATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.39
Consensus pattern (15 bp):
AACTCTTAACCTTTC
Found at i:43131902 original size:29 final size:29
Alignment explanation
Indices: 43131860--43131915 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
43131850 AAATTTTGTT
* *
43131860 CTTTTGTTTGATG-ATTGTGATACTATTCC
1 CTTTTGGTTAATGAATT-TGATACTATTCC
*
43131889 CTTTTGGTTAATGAATTTGATTCTATT
1 CTTTTGGTTAATGAATTTGATACTATT
43131916 TTATCCCCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.20, C:0.11, G:0.16, T:0.54
Consensus pattern (29 bp):
CTTTTGGTTAATGAATTTGATACTATTCC
Found at i:43142790 original size:44 final size:43
Alignment explanation
Indices: 43142709--43142792 Score: 141
Period size: 43 Copynumber: 1.9 Consensus size: 43
43142699 ATACAGAAAG
* *
43142709 CTCACAAAAGGTCATGCTTTCAAGGAGCACGCAGAGTGAGCGA
1 CTCACAAAAGCTCATGCTCTCAAGGAGCACGCAGAGTGAGCGA
43142752 CTCACAAAAGCTCATGCTCTCAAAGGAGCACGCAGAGTGAG
1 CTCACAAAAGCTCATGCTCTC-AAGGAGCACGCAGAGTGAG
43142793 TCGTCTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 19 0.50
44 19 0.50
ACGTcount: A:0.33, C:0.25, G:0.26, T:0.15
Consensus pattern (43 bp):
CTCACAAAAGCTCATGCTCTCAAGGAGCACGCAGAGTGAGCGA
Found at i:43142823 original size:42 final size:43
Alignment explanation
Indices: 43142710--43142824 Score: 112
Period size: 42 Copynumber: 2.7 Consensus size: 43
43142700 TACAGAAAGC
* * * *
43142710 TCACAAAAGGTCATGCTTTC-AAGGAGCACGCAGAGTGAGCGA
1 TCACAAAAGCTCATACTCTCAAAAGAGCACGCAGAGTGAGCGA
* *
43142752 CTCACAAAAGCTCATGCTCTCAAAGGAGCACGCAGAGTGAGTCG-
1 -TCACAAAAGCTCATACTCTCAAAAGAGCACGCAGAGTGAG-CGA
*
43142796 TC-TAAAAGCTCATACTCGT-AAAAGAGCAC
1 TCACAAAAGCTCATACTC-TCAAAAGAGCAC
43142825 ATAGAAACAG
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
42 22 0.34
43 21 0.33
44 19 0.30
45 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.17
Consensus pattern (43 bp):
TCACAAAAGCTCATACTCTCAAAAGAGCACGCAGAGTGAGCGA
Found at i:43152126 original size:21 final size:20
Alignment explanation
Indices: 43152083--43152132 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
43152073 ATTATCAACT
43152083 AATATCAAACAATTCATACCG
1 AATATCAAACAATTCATA-CG
43152104 AATATCAAATCAAATTCAT-CG
1 AATATCAAA-C-AATTCATACG
*
43152125 AATGTCAA
1 AATATCAA
43152133 TGACATCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 18 0.69
22 1 0.04
23 7 0.27
ACGTcount: A:0.48, C:0.20, G:0.06, T:0.26
Consensus pattern (20 bp):
AATATCAAACAATTCATACG
Found at i:43164930 original size:30 final size:30
Alignment explanation
Indices: 43164896--43164952 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
43164886 AGTGTGGCCA
43164896 GGCCATGTGACTCACACGGTCAGGAGAAAC
1 GGCCATGTGACTCACACGGTCAGGAGAAAC
43164926 GGCCATGTGACTCACACGGTCAGGAGA
1 GGCCATGTGACTCACACGGTCAGGAGA
43164953 CACGCCCGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.32, T:0.14
Consensus pattern (30 bp):
GGCCATGTGACTCACACGGTCAGGAGAAAC
Found at i:43165126 original size:12 final size:12
Alignment explanation
Indices: 43165109--43165138 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
43165099 CCTCACATGC
43165109 CCATGTGCCAGG
1 CCATGTGCCAGG
*
43165121 CCATGTGCTAGG
1 CCATGTGCCAGG
43165133 CCATGT
1 CCATGT
43165139 AACAGCCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (12 bp):
CCATGTGCCAGG
Found at i:43167769 original size:20 final size:20
Alignment explanation
Indices: 43167741--43167778 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
43167731 AACTATCATG
*
43167741 TTTTCTTTATTTTATTAACC
1 TTTTATTTATTTTATTAACC
43167761 TTTTATTTATTTTATTAA
1 TTTTATTTATTTTATTAA
43167779 TAAAATAACA
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATTTATTTTATTAACC
Found at i:43173043 original size:11 final size:11
Alignment explanation
Indices: 43173027--43173067 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
43173017 ATATTTTTTT
43173027 TATTTTTAAAA
1 TATTTTTAAAA
43173038 TATTTTTAAAA
1 TATTTTTAAAA
43173049 TATTTTTAAAA
1 TATTTTTAAAA
*
43173060 TACTTTTA
1 TATTTTTA
43173068 TTTATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:43173076 original size:22 final size:21
Alignment explanation
Indices: 43173015--43173078 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
43173005 CAGATATAAT
*
43173015 AAATATTTTTTTTA-TTTTTA
1 AAATATTTTATTTATTTTTTA
**
43173035 AAATATTTT-TAAAATATTTTTA
1 AAATATTTTAT-TTAT-TTTTTA
43173057 AAATACTTTTATTTATTTTTTA
1 AAATA-TTTTATTTATTTTTTA
43173079 TTTTTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 1 0.03
20 10 0.29
22 17 0.49
23 6 0.17
24 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
AAATATTTTATTTATTTTTTA
Found at i:43173412 original size:21 final size:20
Alignment explanation
Indices: 43173361--43173413 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
43173351 TGTGTAATTA
* * *
43173361 AATTGTATTTATATGTTTTT
1 AATTGTATATATATGTTATG
*
43173381 AATTGAAATATATATGTTATG
1 AATTG-TATATATATGTTATG
43173402 AATTGTCATATA
1 AATTGT-ATATA
43173414 AAATTACCGA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (20 bp):
AATTGTATATATATGTTATG
Found at i:43173724 original size:25 final size:25
Alignment explanation
Indices: 43173623--43173724 Score: 91
Period size: 25 Copynumber: 4.1 Consensus size: 25
43173613 AGAAAGCAAA
*
43173623 ACTGATCTACAGCTCGAGTAAGCAT
1 ACTGATCTACAACTCGAGTAAGCAT
*
43173648 ACTAATCTACAGA-TCGAGTAAGCAT
1 ACTGATCTACA-ACTCGAGTAAGCAT
* * * * * *
43173673 ACTGATTTATAGCTTG-GGAGAGTAT
1 ACTGATCTACAACTCGAGTA-AGCAT
*
43173698 ACTGATCTACAACTCGAGTGAGCAT
1 ACTGATCTACAACTCGAGTAAGCAT
43173723 AC
1 AC
43173725 CGATTCACAG
Statistics
Matches: 57, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
24 2 0.04
25 54 0.95
26 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (25 bp):
ACTGATCTACAACTCGAGTAAGCAT
Found at i:43173738 original size:25 final size:25
Alignment explanation
Indices: 43173579--43173738 Score: 67
Period size: 25 Copynumber: 6.4 Consensus size: 25
43173569 GCGGATACTC
* *
43173579 CACAGCTCGTGTGAGCATACCGATT
1 CACAGCTCGAGTAAGCATACCGATT
* * * * * *
43173604 TATAGCTCAAGAAAGCAAAACTGA-T
1 CACAGCTCGAGTAAGC-ATACCGATT
* *
43173629 CTACAGCTCGAGTAAGCATA-CTAAT
1 C-ACAGCTCGAGTAAGCATACCGATT
* *
43173654 CTACAGATCGAGTAAGCATACTGATT
1 C-ACAGCTCGAGTAAGCATACCGATT
* * * * * *
43173680 TATAGCTTG-GGAGAGTATACTGA-T
1 CACAGCTCGAGTA-AGCATACCGATT
* *
43173704 CTACAACTCGAGTGAGCATACCGATT
1 C-ACAGCTCGAGTAAGCATACCGATT
43173730 CACAGCTCG
1 CACAGCTCG
43173739 TATGAGTATA
Statistics
Matches: 93, Mismatches: 34, Indels: 16
0.65 0.24 0.11
Matches are distributed among these distances:
24 4 0.04
25 67 0.72
26 22 0.24
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (25 bp):
CACAGCTCGAGTAAGCATACCGATT
Found at i:43178506 original size:21 final size:21
Alignment explanation
Indices: 43178445--43178506 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 21
43178435 CTTTCTGTTT
* * *
43178445 AGCTTTTTCGAGCTTCTGTTT
1 AGCTCTTTCGAGCTTCCGTTC
* * * * *
43178466 AACTCATACGAGTTTTCGTTC
1 AGCTCTTTCGAGCTTCCGTTC
43178487 AGCTCTTTCGAGCTTCCGTT
1 AGCTCTTTCGAGCTTCCGTT
43178507 AACCCTTATG
Statistics
Matches: 28, Mismatches: 13, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (21 bp):
AGCTCTTTCGAGCTTCCGTTC
Found at i:43178527 original size:41 final size:41
Alignment explanation
Indices: 43178436--43178562 Score: 137
Period size: 41 Copynumber: 3.1 Consensus size: 41
43178426 CGTGTTTTAC
* * * * * * *
43178436 TTTCTGTTTAGCTTTTTCGAGCTTCTGTTTAACTCATACGAG
1 TTTCCGTTCAGCTCTTTCGAGCTTCTG-TTAACCCTTATGGG
* *
43178478 TTTTCGTTCAGCTCTTTCGAGCTTCCGTTAACCCTTATGGG
1 TTTCCGTTCAGCTCTTTCGAGCTTCTGTTAACCCTTATGGG
* * *
43178519 TTTCCGTTCTGCTCTTACAAGCTTCTGTTAACCCTTATGGG
1 TTTCCGTTCAGCTCTTTCGAGCTTCTGTTAACCCTTATGGG
43178560 TTT
1 TTT
43178563 AGGTCTCATG
Statistics
Matches: 71, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 49 0.69
42 22 0.31
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (41 bp):
TTTCCGTTCAGCTCTTTCGAGCTTCTGTTAACCCTTATGGG
Found at i:43180636 original size:20 final size:20
Alignment explanation
Indices: 43180593--43180634 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
43180583 TAAAGAAAGT
43180593 AAATGCAATGGAAAGTAATG
1 AAATGCAATGGAAAGTAATG
43180613 AAATGCAAAT-GAAAGTAA-G
1 AAATGC-AATGGAAAGTAATG
43180632 AAA
1 AAA
43180635 ATTTGGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 14 0.67
21 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.17
Consensus pattern (20 bp):
AAATGCAATGGAAAGTAATG
Found at i:43181105 original size:15 final size:16
Alignment explanation
Indices: 43181085--43181114 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43181075 TGGTGCCTTG
43181085 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
43181100 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
43181115 AGCATGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:43181293 original size:32 final size:32
Alignment explanation
Indices: 43181257--43181318 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
43181247 CCAACTAGAT
* *
43181257 ATGGTTAGATTTGTGTAATTTAGATGGCCTTG
1 ATGGTTAGAGTTGTGTAATTTAGACGGCCTTG
*
43181289 ATGGTTGGAGTTGTGTAATTTAGACGGCCT
1 ATGGTTAGAGTTGTGTAATTTAGACGGCCT
43181319 GGCACACTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.21, C:0.08, G:0.31, T:0.40
Consensus pattern (32 bp):
ATGGTTAGAGTTGTGTAATTTAGACGGCCTTG
Found at i:43183894 original size:25 final size:23
Alignment explanation
Indices: 43183848--43184013 Score: 109
Period size: 23 Copynumber: 7.1 Consensus size: 23
43183838 AAAATAGTAA
* * *
43183848 GTATACTTGGTTTTGTTCGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
* *
43183871 TTATATATATGGTTGTGTATGGAGG
1 GTATA-AT-TGGTTGTGTTTGGAGG
* *
43183896 GTATACTTGGTTGGGTTTGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
* ** *
43183919 TTATAAATAAAGTTGTGTTTGAAGG
1 GTAT-AAT-TGGTTGTGTTTGGAGG
43183944 GTATAATTGGTTGTG-TTGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
** * *
43183966 GTATGTTTAGTTGTGTTTGGAAG
1 GTATAATTGGTTGTGTTTGGAGG
* ** * *
43183989 ATATGTTTGGTTATGTTTGGTGG
1 GTATAATTGGTTGTGTTTGGAGG
43184012 GT
1 GT
43184014 GATAGTTTTA
Statistics
Matches: 109, Mismatches: 29, Indels: 10
0.74 0.20 0.07
Matches are distributed among these distances:
22 18 0.17
23 52 0.48
24 7 0.06
25 32 0.29
ACGTcount: A:0.19, C:0.02, G:0.35, T:0.44
Consensus pattern (23 bp):
GTATAATTGGTTGTGTTTGGAGG
Found at i:43183919 original size:48 final size:48
Alignment explanation
Indices: 43183848--43183965 Score: 148
Period size: 48 Copynumber: 2.5 Consensus size: 48
43183838 AAAATAGTAA
* * * ** *
43183848 GTATACTTGGTTTTGTTCGGAGGTTATATATATGGTTGTGTATGGAGG
1 GTATACTTGGTTGTGTTTGGAGGTTATAAATAAAGTTGTGTATGAAGG
* *
43183896 GTATACTTGGTTGGGTTTGGAGGTTATAAATAAAGTTGTGTTTGAAGG
1 GTATACTTGGTTGTGTTTGGAGGTTATAAATAAAGTTGTGTATGAAGG
*
43183944 GTATAATTGGTTGTG-TTGGAGG
1 GTATACTTGGTTGTGTTTGGAGG
43183966 GTATGTTTAG
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
47 7 0.12
48 53 0.88
ACGTcount: A:0.21, C:0.03, G:0.35, T:0.42
Consensus pattern (48 bp):
GTATACTTGGTTGTGTTTGGAGGTTATAAATAAAGTTGTGTATGAAGG
Found at i:43188208 original size:3 final size:3
Alignment explanation
Indices: 43188200--43188232 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
43188190 ATAAGTAAAT
43188200 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
43188233 CAAAGCTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:43190115 original size:51 final size:51
Alignment explanation
Indices: 43190029--43190231 Score: 176
Period size: 51 Copynumber: 4.0 Consensus size: 51
43190019 CTTTAGTCTT
*
43190029 TAACGCC-AGAGAGATAAGATTCGCTGCCTTCAGCTTTAATCTACTCCACTG
1 TAACGCCAAGA-AGATAGGATTCGCTGCCTTCAGCTTTAATCTACTCCACTG
* * * * ** *
43190080 TAATGCCAAGAAGATTGGATTCGCTGCCTTTAGCTTTAATCTGCTCTGCTA
1 TAACGCCAAGAAGATAGGATTCGCTGCCTTCAGCTTTAATCTACTCCACTG
* * * * * * * **
43190131 TAACACCAGGGAA-ACAAGATTCTCTACCTTTAGCTTTAATCTGTTCCACTG
1 TAACGCCA-AGAAGATAGGATTCGCTGCCTTCAGCTTTAATCTACTCCACTG
* * * * *
43190182 TAAGGCCAAGCAGATAGGATTCGCTGCCTTCATCTTTAATCCATTCCACT
1 TAACGCCAAGAAGATAGGATTCGCTGCCTTCAGCTTTAATCTACTCCACT
43190232 TCAACTTTAA
Statistics
Matches: 117, Mismatches: 32, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
50 2 0.02
51 109 0.93
52 6 0.05
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.31
Consensus pattern (51 bp):
TAACGCCAAGAAGATAGGATTCGCTGCCTTCAGCTTTAATCTACTCCACTG
Found at i:43190257 original size:21 final size:21
Alignment explanation
Indices: 43190215--43190257 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
43190205 CTGCCTTCAT
*
43190215 CTTTAATCCATTCCACTTCAA
1 CTTTAATCCATTCCACTGCAA
** *
43190236 CTTTAATTTATTCCAGTGCAA
1 CTTTAATCCATTCCACTGCAA
43190257 C
1 C
43190258 GCTAGGGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.05, T:0.40
Consensus pattern (21 bp):
CTTTAATCCATTCCACTGCAA
Found at i:43190326 original size:51 final size:51
Alignment explanation
Indices: 43190236--43190395 Score: 187
Period size: 51 Copynumber: 3.1 Consensus size: 51
43190226 TCCACTTCAA
* * * * * *
43190236 CTTTAATTTATTCCAGTGCAACGCTAGGGAAATATGATTCGCTACCTTTAG
1 CTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTACCTTTAG
* *
43190287 CTTTAATCTGTTCCACTGCAACGCCAGAGAAACAAGATTCTCTACCTTTAG
1 CTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTACCTTTAG
* * * * *
43190338 CTTTAATCTGTTCTACTGTAACGCCA-AGGAGATAGGATTCGCTACCTTCAG
1 CTTTAATCTGTTCCACTGCAACGCCAGA-GAAATAAGATTCGCTACCTTTAG
43190389 CTTTAAT
1 CTTTAAT
43190396 ACGCTCCACT
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
50 1 0.01
51 92 0.99
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (51 bp):
CTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTACCTTTAG
Done.