Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 3 of 204
Found at i:870683 original size:113 final size:113
Alignment explanation
Indices: 870484--871196 Score: 924
Period size: 113 Copynumber: 6.3 Consensus size: 113
870474 AGATAAAATG
* * * * * *
870484 TTTTTGCGGCGC-TTTACAAAAAACGCCGCTAAAGGCATCAACATTAGCGGCGCTTATTCA-GAA
1 TTTTTGCGGCGCATTTA-AAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTT-TACATAAA
* * *
870547 ACGCCGCTAAAGTCCCCAAAAACTCAGAAAACGGTGACGTTAGGCTTAGGC
64 ACGCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTT-GGCTTAGGC
*
870598 -TTTTGCGGCGCATTTAAAAAAACGCCACTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
1 TTTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
870662 GCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
66 GCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTT-GGCTTAGGC
870711 -TTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
1 TTTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
*
870775 GCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGCGTTTAGGC
66 GCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTG-GCTTAGGC
* * * * *
870824 TTTTTGCGGCGCTTTTGAGAAAACGCCGCTAAAGACCTCAGCATTAGCGGCGCTTT--ATAAATG
1 TTTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAA-A
* *
870887 CGCCGCTAAAGACCCCCAAAAACTCAGAAAATGGTGCCGTTGAGCTTAGGC
65 CGCCACTAAAGA-CCCCAAAAACTCAGAAAACGGTGCCGTTG-GCTTAGGC
* * * *
870938 TTTTTTGCGGCGC-TTTAAAAAAAATGCCGCTAAAGACATGATCATTAGCGGCACTTTACAT-AA
1 -TTTTTGCGGCGCATTT-AAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAA
* *
871001 ACGCCACTAAAGACCCC-AAAACTCAGAAAACGGTGCCGTTGGGTTTAGAC
64 ACGCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTT-GGCTTAGGC
* * *
871051 TTTTTGTGGCGCATTTAAAACAACGCCGCTAAAGACCTGA-CATTAGCGGCGCTTTTACAGAAAA
1 TTTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGC-TTTACATAAAA
* * * * *
871115 CGCCGCTAAAGACCCCAAAAAATCAGAAAACAGTGCCGTTTGTCTTTGGC
65 CGCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCG-TTGGCTTAGGC
* * *
871165 TTTTTGCGGCGCTTTTATAAAAATGCCGCTAA
1 TTTTTGCGGCGCATTTAAAAAAACGCCGCTAA
871197 TGCTTATTTT
Statistics
Matches: 531, Mismatches: 52, Indels: 32
0.86 0.08 0.05
Matches are distributed among these distances:
111 11 0.02
112 47 0.09
113 262 0.49
114 149 0.28
115 58 0.11
116 2 0.00
117 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (113 bp):
TTTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
GCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGCTTAGGC
Found at i:871024 original size:227 final size:222
Alignment explanation
Indices: 870484--871196 Score: 932
Period size: 227 Copynumber: 3.1 Consensus size: 222
870474 AGATAAAATG
* * * * *
870484 TTTTTGCGGCGCTTTACAAAAAACGCCGCTAAAGGCATCAACATTAGCGGCGCTTATTCAGAAAC
1 TTTTTGCGGCGCTTTAAAAAAAACGCCGCTAAAGACATGAACATTAGCGGCGCTT-TACATAAAC
* * * *
870549 GCCGCTAAAGTCCCCAAAAACTCAGAAAACGGTGACGTTAGGCTTAGGC-TTTTGCGGCGCATTT
65 GCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTT-GGTTTAGGCTTTTTGCGGCGCATTT
* *
870613 AAAAAAACGCCACTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAACGCCACTAAAGACCCCA
129 -AAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTT--ATAAAACGCCGCTAAAGACCCCA
870678 AAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
191 AAAACTCAGAAAACGGTGCCGTT-GGCTTAGGC
* *
870711 -TTTTGCGGCGCATTT-AAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAA
1 TTTTTGCGGCGC-TTTAAAAAAAACGCCGCTAAAGACATGAACATTAGCGGCGCTTTACAT-AAA
*
870774 CGCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGCGTTTAGGCTTTTTGCGGCGCTTT
64 CGCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTG-GTTTAGGCTTTTTGCGGCGCATT
* * *
870839 TGAGAAAACGCCGCTAAAGACCTCAGCATTAGCGGCGCTTTATAAATGCGCCGCTAAAGACCCCC
128 T-AAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTATAAA-ACGCCGCTAAAGA-CCCC
*
870904 AAAAACTCAGAAAATGGTGCCGTTGAGCTTAGGC
190 AAAAACTCAGAAAACGGTGCCGTTG-GCTTAGGC
* * *
870938 TTTTTTGCGGCGCTTTAAAAAAAATGCCGCTAAAGACATGATCATTAGCGGCACTTTACATAAAC
1 -TTTTTGCGGCGCTTTAAAAAAAACGCCGCTAAAGACATGAACATTAGCGGCGCTTTACATAAAC
* *
871003 GCCACTAAAGACCCC-AAAACTCAGAAAACGGTGCCGTTGGGTTTAGACTTTTTGTGGCGCATTT
65 GCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTT-GGTTTAGGCTTTTTGCGGCGCATTT
*
871067 AAAACAACGCCGCTAAAGACCTGA-CATTAGCGGCGCTTTTACAGAAAACGCCGCTAAAGACCCC
129 AAAA-AACGCCGCTAAAGACCTGAGCATTAGCGGCGC-TTT--ATAAAACGCCGCTAAAGACCCC
* * * *
871131 AAAAAATCAGAAAACAGTGCCGTTTGTCTTTGGC
190 AAAAACTCAGAAAACGGTGCCG-TTGGCTTAGGC
* * *
871165 TTTTTGCGGCGCTTTTATAAAAATGCCGCTAA
1 TTTTTGCGGCGCTTTAAAAAAAACGCCGCTAA
871197 TGCTTATTTT
Statistics
Matches: 433, Mismatches: 37, Indels: 33
0.86 0.07 0.07
Matches are distributed among these distances:
225 9 0.02
226 149 0.34
227 182 0.42
228 38 0.09
229 55 0.13
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (222 bp):
TTTTTGCGGCGCTTTAAAAAAAACGCCGCTAAAGACATGAACATTAGCGGCGCTTTACATAAACG
CCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGTTTAGGCTTTTTGCGGCGCATTTAA
AAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTATAAAACGCCGCTAAAGACCCCAAAAAC
TCAGAAAACGGTGCCGTTGGCTTAGGC
Found at i:874552 original size:2 final size:2
Alignment explanation
Indices: 874545--874574 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
874535 ATTTATTCTC
*
874545 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
874575 GTATGAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:875726 original size:3 final size:3
Alignment explanation
Indices: 875718--875750 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
875708 AACCGTAGGT
875718 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
875751 GCAGAGCTCT
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:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:876891 original size:16 final size:16
Alignment explanation
Indices: 876847--876894 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
876837 AACTACAATT
876847 TATTAAATAAAA-ATTA
1 TATT-AATAAAATATTA
876863 TATTAATTAAAATATTA
1 TATTAA-TAAAATATTA
*
876880 TTTTAATAAAATATT
1 TATTAATAAAATATT
876895 TAATTTCATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 2 0.07
16 18 0.62
17 9 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATTAATAAAATATTA
Found at i:876948 original size:18 final size:18
Alignment explanation
Indices: 876925--876963 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
876915 TATTAATAAT
*
876925 ATTTTATTAAATAAAAAA
1 ATTTTAATAAATAAAAAA
* *
876943 ATTTTAATAATTAAAATA
1 ATTTTAATAAATAAAAAA
876961 ATT
1 ATT
876964 AACTATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTTAATAAATAAAAAA
Found at i:881741 original size:24 final size:24
Alignment explanation
Indices: 881712--881765 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
881702 TTGATGAAAG
* *
881712 ATGAACTGTTAAATACATGCAGAA
1 ATGAACTGTTAAACACATACAGAA
* *
881736 ATGAACCGTTCAACACATACAGAA
1 ATGAACTGTTAAACACATACAGAA
881760 A-GAACT
1 ATGAACT
881766 TACTTTTCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (24 bp):
ATGAACTGTTAAACACATACAGAA
Found at i:886105 original size:24 final size:26
Alignment explanation
Indices: 886047--886105 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 26
886037 AGCAATTGGC
* *
886047 AAATGGTTAACTCAACAATATTAGTA
1 AAATTGTTAACTCAACAATATTACTA
* *
886073 AAAAT-TTAACT-AACAATTTTACT-
1 AAATTGTTAACTCAACAATATTACTA
886096 AAATTGTTAA
1 AAATTGTTAA
886106 AATTACTCTC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
23 4 0.15
24 14 0.52
25 6 0.22
26 3 0.11
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (26 bp):
AAATTGTTAACTCAACAATATTACTA
Found at i:887176 original size:21 final size:20
Alignment explanation
Indices: 887146--887185 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
887136 TATAAAGCTT
*
887146 ATTGAAGAGTGTTTTTATATA
1 ATTGAAGAGT-ATTTTATATA
*
887167 ATTGATGAGTATTTTATAT
1 ATTGAAGAGTATTTTATAT
887186 TTAAAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (20 bp):
ATTGAAGAGTATTTTATATA
Found at i:887858 original size:3 final size:3
Alignment explanation
Indices: 887850--887886 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
887840 TTCTCCGTCA
*
887850 CTC CTC CT- CTC CT- CTG CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
887887 TTTCTCCTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.00, C:0.62, G:0.03, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:887860 original size:16 final size:14
Alignment explanation
Indices: 887850--887887 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
887840 TTCTCCGTCA
887850 CTCCTCCTCTCCT-
1 CTCCTCCTCTCCTC
*
887863 CTGCTCCTCCTCCTC
1 CTCCTCCT-CTCCTC
887878 CTCCTCCTCT
1 CTCCTCCTCT
887888 TTCTCCTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 7 0.33
14 7 0.33
15 7 0.33
ACGTcount: A:0.00, C:0.61, G:0.03, T:0.37
Consensus pattern (14 bp):
CTCCTCCTCTCCTC
Found at i:896720 original size:13 final size:13
Alignment explanation
Indices: 896702--896727 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
896692 ATAATACTGG
896702 GTTTTTGTTTTTT
1 GTTTTTGTTTTTT
896715 GTTTTTGTTTTTT
1 GTTTTTGTTTTTT
896728 TACCTTTCTT
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:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (13 bp):
GTTTTTGTTTTTT
Found at i:903363 original size:28 final size:28
Alignment explanation
Indices: 903331--903391 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
903321 TAGTAATGAT
* * *
903331 AAAAATTAAACTTAAATTT-TGAAATTTA
1 AAAAATAAAAC-TAAATTTCTGAAAATAA
903359 AAAAATAAAACTAAATTTCTGAAAATAA
1 AAAAATAAAACTAAATTTCTGAAAATAA
903387 AAAAA
1 AAAAA
903392 AACTGTGGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (28 bp):
AAAAATAAAACTAAATTTCTGAAAATAA
Found at i:906236 original size:21 final size:21
Alignment explanation
Indices: 906212--906255 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
906202 ACATAAAAAG
*
906212 ATAAAAATA-CCTTTAAATAAT
1 ATAAAAATATCC-TAAAATAAT
906233 ATAAAAATATCCTAAAATAAT
1 ATAAAAATATCCTAAAATAAT
906254 AT
1 AT
906256 TTAATCTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAAAAATATCCTAAAATAAT
Found at i:907032 original size:26 final size:26
Alignment explanation
Indices: 906996--907047 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
906986 AAAATATAGA
906996 GAGAGAATTCCTCTAAGAGTAATTTG
1 GAGAGAATTCCTCTAAGAGTAATTTG
907022 GAGAGAATTCCTCTAAGAGTAATTTG
1 GAGAGAATTCCTCTAAGAGTAATTTG
907048 AACTTAAAAT
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:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (26 bp):
GAGAGAATTCCTCTAAGAGTAATTTG
Found at i:910005 original size:17 final size:18
Alignment explanation
Indices: 909994--910026 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
909984 TTTATATATG
909994 GATATT-AATTATA-AAA
1 GATATTGAATTATATAAA
910010 GATATTGAATTATATAA
1 GATATTGAATTATATAA
910027 TTTTACATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 7 0.47
18 2 0.13
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (18 bp):
GATATTGAATTATATAAA
Found at i:913966 original size:7 final size:7
Alignment explanation
Indices: 913954--913983 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
913944 GAGGGGTTTT
913954 AAAATTA
1 AAAATTA
913961 AAAATTA
1 AAAATTA
913968 AAAATT-
1 AAAATTA
913974 AAAATTA
1 AAAATTA
913981 AAA
1 AAA
913984 CCATGTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTA
Found at i:913970 original size:13 final size:14
Alignment explanation
Indices: 913954--913983 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
913944 GAGGGGTTTT
913954 AAAATTAAAAATTA
1 AAAATTAAAAATTA
913968 AAAATT-AAAATTA
1 AAAATTAAAAATTA
913981 AAA
1 AAA
913984 CCATGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATTAAAAATTA
Found at i:918653 original size:83 final size:83
Alignment explanation
Indices: 918562--918729 Score: 327
Period size: 83 Copynumber: 2.0 Consensus size: 83
918552 AATTGATTTT
*
918562 AACCTCATTTTAATCTGTTAATTTAGTTGATTATTAGTTTTTGAATAAATCGATTTATTTTATAT
1 AACCTCATTTTAATCTGTTAATTTAGTTGATTATTAGTTTTTAAATAAATCGATTTATTTTATAT
918627 TATTTTTAAATGAATTAA
66 TATTTTTAAATGAATTAA
918645 AACCTCATTTTAATCTGTTAATTTAGTTGATTATTAGTTTTTAAATAAATCGATTTATTTTATAT
1 AACCTCATTTTAATCTGTTAATTTAGTTGATTATTAGTTTTTAAATAAATCGATTTATTTTATAT
918710 TATTTTTAAATGAATTAA
66 TATTTTTAAATGAATTAA
918728 AA
1 AA
918730 TATATTTATA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (83 bp):
AACCTCATTTTAATCTGTTAATTTAGTTGATTATTAGTTTTTAAATAAATCGATTTATTTTATAT
TATTTTTAAATGAATTAA
Found at i:926112 original size:7 final size:7
Alignment explanation
Indices: 926100--926124 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
926090 GTATAGGGAC
926100 TAAATTT
1 TAAATTT
926107 TAAATTT
1 TAAATTT
926114 TAAATTT
1 TAAATTT
926121 TAAA
1 TAAA
926125 AGAGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TAAATTT
Found at i:926622 original size:31 final size:31
Alignment explanation
Indices: 926587--926652 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
926577 TTAATATGCC
* * *
926587 ATTTGGTACTTGCATTTGACTTTAATGTTTA
1 ATTTGGTACTTGAATTTAACTTTAATGTTAA
926618 ATTTGGTACTTGAATTTAACTTTAATGTTAA
1 ATTTGGTACTTGAATTTAACTTTAATGTTAA
926649 ATTT
1 ATTT
926653 AATACCCGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.52
Consensus pattern (31 bp):
ATTTGGTACTTGAATTTAACTTTAATGTTAA
Found at i:930761 original size:23 final size:24
Alignment explanation
Indices: 930727--930786 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
930717 ATCAGCTCAT
*
930727 AAATATATTTGTT-TTATTATTAG
1 AAATATATTTGTTATTATAATTAG
*
930750 AAATAT-TCTTGTTATTATAATTTG
1 AAATATAT-TTGTTATTATAATTAG
*
930774 AAAAAATATTTGT
1 -AAATATATTTGT
930787 AGGAAAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 1 0.03
23 11 0.37
24 8 0.27
25 9 0.30
26 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
AAATATATTTGTTATTATAATTAG
Found at i:935958 original size:19 final size:19
Alignment explanation
Indices: 935934--935970 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
935924 TTGTGTTTGT
*
935934 TTAATGAAAAATGATTTAA
1 TTAATGAAAAATAATTTAA
*
935953 TTAATGGAAAATAATTTA
1 TTAATGAAAAATAATTTA
935971 TTGGTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
TTAATGAAAAATAATTTAA
Found at i:936271 original size:32 final size:36
Alignment explanation
Indices: 936198--936278 Score: 84
Period size: 35 Copynumber: 2.4 Consensus size: 36
936188 TATTAATATA
* * *
936198 ATTAAAATAATTATTTATTTTAATGAAATTAATGAAT
1 ATTAAAATAATTATTTATCTTAATAAAATT-ATGAAC
936235 ATTAAAAT-ATTATTT-TCTTAATAAAATT-T-AAC
1 ATTAAAATAATTATTTATCTTAATAAAATTATGAAC
936267 ATT--AATAATTAT
1 ATTAAAATAATTAT
936279 AAAATGGAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 3 0.08
31 5 0.12
32 5 0.12
33 1 0.03
35 11 0.28
36 7 0.17
37 8 0.20
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (36 bp):
ATTAAAATAATTATTTATCTTAATAAAATTATGAAC
Found at i:943844 original size:27 final size:27
Alignment explanation
Indices: 943801--943854 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
943791 TAGGCCCACC
*
943801 TTTATTATTATTATTTAAAATATTTTAT
1 TTTATTATTAATATTTAAAA-ATTTTAT
*
943829 TTTATT-TTAATATTTAATAATTTTAT
1 TTTATTATTAATATTTAAAAATTTTAT
943855 ACATTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.29
27 11 0.46
28 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTATTATTAATATTTAAAAATTTTAT
Found at i:947258 original size:2 final size:2
Alignment explanation
Indices: 947253--947295 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
947243 CCTTACATGC
* * * *
947253 AT AT AT AT AT AC AT AT AT AC AT AC AT AC 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
947295 A
1 A
947296 AAGAAAAGTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (2 bp):
AT
Found at i:947270 original size:8 final size:8
Alignment explanation
Indices: 947257--947295 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
947247 ACATGCATAT
947257 ATATATAC
1 ATATATAC
947265 ATATATAC
1 ATATATAC
*
947273 ATACATAC
1 ATATATAC
*
947281 ATATATAT
1 ATATATAC
947289 ATATATA
1 ATATATA
947296 AAGAAAAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATATAC
Found at i:954561 original size:19 final size:19
Alignment explanation
Indices: 954537--954575 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
954527 ACTGATAAGC
*
954537 TGAAGCTTAAT-TTAATATT
1 TGAAGCTCAATATT-ATATT
954556 TGAAGCTCAATATTATATT
1 TGAAGCTCAATATTATATT
954575 T
1 T
954576 AAACTTGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (19 bp):
TGAAGCTCAATATTATATT
Found at i:959306 original size:15 final size:16
Alignment explanation
Indices: 959274--959306 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
959264 ATATATATTT
*
959274 TTAATTTTTTATACAA
1 TTAATATTTTATACAA
959290 TTAATATTTTA-ACAA
1 TTAATATTTTATACAA
959305 TT
1 TT
959307 CAACCGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATATTTTATACAA
Found at i:965042 original size:29 final size:28
Alignment explanation
Indices: 964980--965042 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
964970 TTGAGAGTTT
*
964980 AGTTTTTATTTTTATTTCATGAAATTTAG
1 AGTTTTTATTTTTATTTCA-GAAAATTAG
965009 AGTTTTTATTTTTCATATTTCA-AAAATTAG
1 AGTTTTTA-TTTT--TATTTCAGAAAATTAG
965039 -GTTT
1 AGTTT
965043 GATTATTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
29 12 0.40
30 11 0.37
32 7 0.23
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.57
Consensus pattern (28 bp):
AGTTTTTATTTTTATTTCAGAAAATTAG
Found at i:973458 original size:24 final size:24
Alignment explanation
Indices: 973431--973482 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
973421 TTAGTAAGTC
*
973431 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
973455 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
973479 AAAT
1 AAAT
973483 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:975427 original size:24 final size:24
Alignment explanation
Indices: 975400--975451 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
975390 TTAGTAAGTC
*
975400 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
975424 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
975448 AAAT
1 AAAT
975452 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:982153 original size:18 final size:18
Alignment explanation
Indices: 982130--982171 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
982120 TTCAAGGTGT
982130 AATTAATTTAAA-ATATTC
1 AATTAA-TTAAATATATTC
*
982148 AATTAATTAAATATATTT
1 AATTAATTAAATATATTC
982166 AATTAA
1 AATTAA
982172 AAATCTATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTAATTAAATATATTC
Found at i:989391 original size:20 final size:21
Alignment explanation
Indices: 989368--989410 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
989358 TTTAACTTCC
*
989368 TTTAT-ATATTTTTTAGAATT
1 TTTATAATATTTTTTAAAATT
989388 TTTATAAATATTTTTTAAAATT
1 TTTAT-AATATTTTTTAAAATT
989410 T
1 T
989411 AAAAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
22 15 0.75
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTATAATATTTTTTAAAATT
Found at i:989418 original size:22 final size:22
Alignment explanation
Indices: 989373--989418 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
989363 CTTCCTTTAT
* ** *
989373 ATATTTTTTAGAATTTTTATAA
1 ATATTTTTTAAAATTTAAAAAA
989395 ATATTTTTTAAAATTTAAAAAA
1 ATATTTTTTAAAATTTAAAAAA
989417 AT
1 AT
989419 TTTAATTTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATTTTTTAAAATTTAAAAAA
Found at i:1006587 original size:141 final size:141
Alignment explanation
Indices: 1006385--1007089 Score: 1031
Period size: 142 Copynumber: 5.0 Consensus size: 141
1006375 CAAAAGTCTC
*
1006385 GAAGAACGTGAA-TTTGAATTCAAATCTAGAATTACAAAAGCATTCGCATTGGAATCGGACTCAT
1 GAAGAACGT-AATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCAT
* *
1006449 GAATTCAAATTTCAACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACA
65 GAATTCAAATTTCCACGTAATTTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACA
1006514 CACAGATCAAAA
130 CACAGATCAAAA
* *
1006526 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGAAATCGGACTCATG
1 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
* *
1006591 AATTCAAATTTCCGCGTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAACTCAATTACA
66 AATTCAAATTTCCACGTAATTTTGAAGAACTTTG-ATGAAAAATGAGGTAAAGAACTCAATTACA
1006656 CACAGATCAAAA
130 CACAGATCAAAA
* * * * *
1006668 GAAGAACGCAATTTCGAATTCAAATCTAAAATTACAAAAGCGTTCCCATTGGAACCGGACTCATG
1 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
* * * * *
1006733 AATTCAAATTTCCACGTAAATTTGAAGAATTTTGATGAAAACTGAGGCAAAGCACTCAATTACAC
66 AATTCAAATTTCCACGTAATTTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACAC
1006798 ACAGATC--AA
131 ACAGATCAAAA
* * * * *
1006807 -AAGAACGTAATTTTGAATTCAAATCTAAACTTACAAAAGCATTCGCATTGAAACCAGACTCGTG
1 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
* * * *
1006871 AATTCAAATTTCGACGTAATTTTGAAGAACTTGGAATCAAAAATGAGCTAAAGAACTCAAATTAC
66 AATTCAAATTTCCACGTAATTTTGAAGAACTTTG-ATGAAAAATGAGGTAAAGAACTC-AATTAC
1006936 ACACAGATCAAAA
129 ACACAGATCAAAA
* * * * * * *
1006949 CAAGAACGTGACTTTAAATTCAAATCTAAAGTTACAAATGCATTCGCATTGGAATCCGACTCATG
1 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
* *
1007014 AATTCAAATTTCCACGTAATTTTGAAGAACTATAATGAAAAATGAGGTAAAGAACTCAATTACAC
66 AATTCAAATTTCCACGTAATTTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACAC
1007079 ACAGATCAAAA
131 ACAGATCAAAA
1007090 AGGAGAAAAC
Statistics
Matches: 505, Mismatches: 52, Indels: 14
0.88 0.09 0.02
Matches are distributed among these distances:
138 86 0.17
139 20 0.04
140 17 0.03
141 143 0.28
142 154 0.30
143 85 0.17
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (141 bp):
GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
AATTCAAATTTCCACGTAATTTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACAC
ACAGATCAAAA
Found at i:1007077 original size:281 final size:279
Alignment explanation
Indices: 1006386--1007089 Score: 1090
Period size: 281 Copynumber: 2.5 Consensus size: 279
1006376 AAAAGTCTCG
*
1006386 AAGAACGTGAATTTGAATTCAAATCTAGAATTACAAAAGCATTCGCATTGGAATCGGACTCATGA
1 AAGAACGTGAATTTGAATTCAAATCTA-AATTACAAAAGCATTCGCATTGGAATCCGACTCATGA
*
1006451 ATTCAAATTTCAACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACACA
65 ATTCAAATTTCCACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACACA
*
1006516 CAGATCAAAAGAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGAAAT
130 CAGATC--AA-AAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGAAAC
* * *
1006581 CGGACTCATGAATTCAAATTTCCGCGTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAA
192 CAGACTCATGAATTCAAATTTCCGCGTAATTTTGAAGAACTTGGAATCAAAAATGAGCTAAAGAA
*
1006646 CTCAATTACACACAGATCAAAAG
257 CTCAATTACACACAGATCAAAAC
* * *
1006669 AAGAACG-CAATTTCGAATTCAAATCTAAAATTACAAAAGCGTTCCCATTGGAA-CCGGACTCAT
1 AAGAACGTGAATTT-GAATTCAAATCT-AAATTACAAAAGCATTCGCATTGGAATCC-GACTCAT
* * * *
1006732 GAATTCAAATTTCCACGTAAATTTGAAGAATTTTGATGAAAACTGAGGCAAAGCACTCAATTACA
63 GAATTCAAATTTCCACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACA
* *
1006797 CACAGATCAAAAGAACGTAATTTTGAATTCAAATCTAAACTTACAAAAGCATTCGCATTGAAACC
128 CACAGATCAAAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGAAACC
*
1006862 AGACTCGTGAATTCAAATTT-CGACGTAATTTTGAAGAACTTGGAATCAAAAATGAGCTAAAGAA
193 AGACTCATGAATTCAAATTTCCG-CGTAATTTTGAAGAACTTGGAATCAAAAATGAGCTAAAGAA
1006926 CTCAAATTACACACAGATCAAAAC
257 CTC-AATTACACACAGATCAAAAC
* * *
1006950 AAGAACGTGACTTTAAATTCAAATCTAAAGTTACAAATGCATTCGCATTGGAATCCGACTCATGA
1 AAGAACGTGAATTTGAATTCAAATCTAAA-TTACAAAAGCATTCGCATTGGAATCCGACTCATGA
* * *
1007015 ATTCAAATTTCCACGTAATTTTGAAGAACTATAATGAAAAATGAGGTAAAGAACTCAATTACACA
65 ATTCAAATTTCCACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACACA
1007080 CAGATCAAAA
130 CAGATCAAAA
1007090 AGGAGAAAAC
Statistics
Matches: 383, Mismatches: 30, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
279 2 0.01
280 115 0.30
281 136 0.36
282 12 0.03
283 117 0.31
284 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.26
Consensus pattern (279 bp):
AAGAACGTGAATTTGAATTCAAATCTAAATTACAAAAGCATTCGCATTGGAATCCGACTCATGAA
TTCAAATTTCCACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACACAC
AGATCAAAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGAAACCAGA
CTCATGAATTCAAATTTCCGCGTAATTTTGAAGAACTTGGAATCAAAAATGAGCTAAAGAACTCA
ATTACACACAGATCAAAAC
Found at i:1007159 original size:10 final size:10
Alignment explanation
Indices: 1007144--1007170 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1007134 AAAAAATGAG
1007144 CAGATCCGAA
1 CAGATCCGAA
1007154 CAGATCCGAA
1 CAGATCCGAA
1007164 CAGATCC
1 CAGATCC
1007171 AATTCATAAG
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:0.37, C:0.33, G:0.19, T:0.11
Consensus pattern (10 bp):
CAGATCCGAA
Found at i:1008093 original size:29 final size:28
Alignment explanation
Indices: 1008060--1008125 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
1008050 ATAATTAGAT
1008060 TTAAATT-TTAAAATTTAAAAA-ATAAAAAA
1 TTAAATTCTTAAAA--TAAAAATAT-AAAAA
*
1008089 TTAAATTCGTTAAAATAAAAATATATAAA
1 TTAAATTC-TTAAAATAAAAATATAAAAA
1008118 TTAAATTC
1 TTAAATTC
1008126 AAAAATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 25 0.76
30 2 0.06
31 6 0.18
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (28 bp):
TTAAATTCTTAAAATAAAAATATAAAAA
Found at i:1017264 original size:14 final size:14
Alignment explanation
Indices: 1017245--1017277 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1017235 ATAATAATTA
1017245 ATAAAT-TAAAATAT
1 ATAAATATAAAA-AT
1017259 ATAAATATAAAAAT
1 ATAAATATAAAAAT
1017273 ATAAA
1 ATAAA
1017278 ATTGATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAATATAAAAAT
Found at i:1022712 original size:22 final size:21
Alignment explanation
Indices: 1022661--1022712 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
1022651 GAGCAAGCTA
*
1022661 GTCCTTTTTATTAAAAATGTT
1 GTCCTTTTTATTAAAAATCTT
*
1022682 ATCCATTTTTATGTTAAAAA-CTT
1 GTCC-TTTTTA--TTAAAAATCTT
1022705 GTCCTTTT
1 GTCCTTTT
1022713 AAGTCATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 3 0.12
22 10 0.40
23 5 0.20
24 7 0.28
ACGTcount: A:0.27, C:0.13, G:0.08, T:0.52
Consensus pattern (21 bp):
GTCCTTTTTATTAAAAATCTT
Found at i:1023456 original size:24 final size:24
Alignment explanation
Indices: 1023411--1023457 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1023401 TTATTGAATA
*
1023411 TTAAAATAAAATCAAATAAATATT
1 TTAAAATAAAATCAAAAAAATATT
*
1023435 TTAAAA-AAAATTAAAAATAATAT
1 TTAAAATAAAATCAAAAA-AATAT
1023458 GGGCGGGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
TTAAAATAAAATCAAAAAAATATT
Found at i:1038909 original size:8 final size:7
Alignment explanation
Indices: 1038869--1038900 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1038859 ATTAATCTTT
1038869 AAATTTA
1 AAATTTA
1038876 AAATTTA
1 AAATTTA
1038883 AAATTTA
1 AAATTTA
1038890 AAATTTTA
1 AAA-TTTA
1038898 AAA
1 AAA
1038901 ATTTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATTTA
Found at i:1040362 original size:25 final size:25
Alignment explanation
Indices: 1040304--1040365 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
1040294 AAATTTCAAT
** *
1040304 AAATAAAAAAT-GTATAAAATTATT
1 AAATAAAAAATAAAATAAAATTATA
*
1040328 AAATATAAAATAAAATAAAATTA-A
1 AAATAAAAAATAAAATAAAATTATA
1040352 AAATTAAAAAATAA
1 AAA-TAAAAAATAA
1040366 TATGAGCGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 13 0.42
25 18 0.58
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (25 bp):
AAATAAAAAATAAAATAAAATTATA
Found at i:1041281 original size:27 final size:27
Alignment explanation
Indices: 1041243--1041294 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1041233 TTGAAAAACA
1041243 AATTTCCTTGTAGAAGGTGTAAAGACT
1 AATTTCCTTGTAGAAGGTGTAAAGACT
*
1041270 AATTTTCTTGTAGAAGGTGTAAAGA
1 AATTTCCTTGTAGAAGGTGTAAAGA
1041295 TAAACTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (27 bp):
AATTTCCTTGTAGAAGGTGTAAAGACT
Found at i:1041501 original size:36 final size:36
Alignment explanation
Indices: 1041453--1041525 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
1041443 AGTTTCACAA
1041453 AGATACTATTAATGATCTTGAAATATTATATCAATG
1 AGATACTATTAATGATCTTGAAATATTATATCAATG
* *
1041489 AGATACTCTTAATGATCTTGAAATATTGTATCAATG
1 AGATACTATTAATGATCTTGAAATATTATATCAATG
1041525 A
1 A
1041526 CTATGACATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (36 bp):
AGATACTATTAATGATCTTGAAATATTATATCAATG
Found at i:1047600 original size:14 final size:14
Alignment explanation
Indices: 1047571--1047622 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
1047561 ATATGAGATT
* *
1047571 AGTAGAAACCAGAA
1 AGTAGAAAGCAAAA
*
1047585 AGCAGAAAGCAAAA
1 AGTAGAAAGCAAAA
* *
1047599 AGTAAAAAGTAAAA
1 AGTAGAAAGCAAAA
1047613 AGTAGAAAGC
1 AGTAGAAAGC
1047623 GGGATCAAAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.62, C:0.10, G:0.21, T:0.08
Consensus pattern (14 bp):
AGTAGAAAGCAAAA
Found at i:1051276 original size:14 final size:14
Alignment explanation
Indices: 1051257--1051286 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1051247 ATAAGTTTGG
1051257 AATAAATAATATAT
1 AATAAATAATATAT
1051271 AATAAATAATATAT
1 AATAAATAATATAT
1051285 AA
1 AA
1051287 ATGAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAAATAATATAT
Found at i:1052568 original size:17 final size:18
Alignment explanation
Indices: 1052534--1052575 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
1052524 GATCCATACC
*
1052534 TTTTTTAAAAGTACATAAT
1 TTTTTTAAAAG-AAATAAT
1052553 TTTTTTAAAA-AAATAAT
1 TTTTTTAAAAGAAATAAT
1052570 TTTTTT
1 TTTTTT
1052576 CTTATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.55
19 10 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTTTTAAAAGAAATAAT
Found at i:1052618 original size:36 final size:36
Alignment explanation
Indices: 1052578--1052650 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 36
1052568 ATTTTTTTCT
1052578 TATTTTAAACAAAAAACAAAAAAAAA-TTTAAAATTA
1 TATTTTAAA-AAAAAACAAAAAAAAACTTTAAAATTA
* **
1052614 TATTTTAAAAAATATGAAAAAAAAATCTTTAAAATTA
1 TATTTTAAAAAAAAACAAAAAAAAA-CTTTAAAATTA
1052651 AAAAATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 13 0.41
36 9 0.28
37 10 0.31
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (36 bp):
TATTTTAAAAAAAAACAAAAAAAAACTTTAAAATTA
Found at i:1052654 original size:30 final size:32
Alignment explanation
Indices: 1052618--1052687 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
1052608 AAATTATATT
**
1052618 TTAAAAAATATGAAAA-AAAAA-TCTTTAAAA
1 TTAAAAAATAAAAAAATAAAAAGTCTTTAAAA
*
1052648 TTAAAAAATAAAAAAATAAAAAGTTTTTAAAA
1 TTAAAAAATAAAAAAATAAAAAGTCTTTAAAA
*
1052680 TAAAAAAA
1 TTAAAAAA
1052688 ATCTAAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 14 0.41
31 5 0.15
32 15 0.44
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (32 bp):
TTAAAAAATAAAAAAATAAAAAGTCTTTAAAA
Found at i:1053187 original size:16 final size:17
Alignment explanation
Indices: 1053149--1053187 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
1053139 AAGAGTTTCT
1053149 ATTTTTAAAAAATTATA
1 ATTTTTAAAAAATTATA
1053166 ATTTTT-AAAAATTATA
1 ATTTTTAAAAAATTATA
*
1053182 GTTTTT
1 ATTTTT
1053188 TATTTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTTAAAAAATTATA
Found at i:1056429 original size:35 final size:35
Alignment explanation
Indices: 1056384--1056451 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
1056374 TTAATTATAT
* *
1056384 AATTAATGATATTTAAA-TATAATTTATATTATACG
1 AATTAATGATAATTAAATTATAA-TGATATTATACG
*
1056419 AATTTATGATAATTAAATTATAATGATATTATA
1 AATTAATGATAATTAAATTATAATGATATTATA
1056452 TTATTAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 24 0.83
36 5 0.17
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (35 bp):
AATTAATGATAATTAAATTATAATGATATTATACG
Found at i:1082823 original size:12 final size:12
Alignment explanation
Indices: 1082806--1082830 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1082796 AACAATTGTC
1082806 ATTTGCATTAAG
1 ATTTGCATTAAG
1082818 ATTTGCATTAAG
1 ATTTGCATTAAG
1082830 A
1 A
1082831 CTTAAATTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATTTGCATTAAG
Found at i:1086193 original size:39 final size:37
Alignment explanation
Indices: 1086126--1086218 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
1086116 ACCAGAATGG
* *
1086126 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
1086165 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
1086202 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
1086219 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:1087345 original size:17 final size:16
Alignment explanation
Indices: 1087313--1087346 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1087303 TTGGCTATTC
*
1087313 TGTTTCTTTCTTCTTT
1 TGTTTCTTTATTCTTT
1087329 TGTTTCTTTTATTCTTT
1 TGTTTC-TTTATTCTTT
1087346 T
1 T
1087347 ATTTTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTATTCTTT
Found at i:1087394 original size:14 final size:14
Alignment explanation
Indices: 1087335--1087385 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1087325 CTTTTGTTTC
*
1087335 TTTTA-TTCTTTTA
1 TTTTATTTCCTTTA
* *
1087348 TTTTAACTTACTTTA
1 TTTT-ATTTCCTTTA
*
1087363 CTTTATTTCCTTTA
1 TTTTATTTCCTTTA
1087377 TTTTATTTC
1 TTTTATTTC
1087386 TTTTGTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 4 0.13
14 17 0.57
15 9 0.30
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTCCTTTA
Found at i:1087554 original size:14 final size:17
Alignment explanation
Indices: 1087535--1087571 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
1087525 ATTTATTTCT
1087535 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
1087549 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
1087566 TAATAT
1 TAATAT
1087572 CCTTTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 4 0.20
17 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:1093463 original size:18 final size:18
Alignment explanation
Indices: 1093434--1093507 Score: 112
Period size: 18 Copynumber: 4.1 Consensus size: 18
1093424 TACGACCGTT
1093434 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*** *
1093452 TACAACACTATTCACATA
1 TACGGTACTATTCACGTA
1093470 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
1093488 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
1093506 TA
1 TA
1093508 TAGTAGTTGG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:1102391 original size:14 final size:14
Alignment explanation
Indices: 1102370--1102403 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1102360 TGGTATGGGT
1102370 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
1102383 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
1102397 TTATAGG
1 TTATAGG
1102404 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:1102560 original size:24 final size:25
Alignment explanation
Indices: 1102533--1102580 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
1102523 AGAAGAAAGT
1102533 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
** *
1102557 TTAAATTACTTAAAACGAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
1102581 TATGGGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (25 bp):
TTAAAGAACATAAAACGAAAAAAAA
Found at i:1106658 original size:21 final size:21
Alignment explanation
Indices: 1106632--1106687 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
1106622 AATAGCGGTG
*
1106632 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
1106653 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
1106674 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
1106688 AACAATGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:1106919 original size:30 final size:30
Alignment explanation
Indices: 1106857--1107037 Score: 257
Period size: 30 Copynumber: 6.2 Consensus size: 30
1106847 ATTCATTTAA
*
1106857 TAAAATACACTACATATA----TATA-TTT
1 TAAAATACACTACATATATTTTTTTATTTT
*
1106882 TAAAATACACTACATATATTTTTTTATTTC
1 TAAAATACACTACATATATTTTTTTATTTT
*
1106912 TAGAATACACTACATATA-TTTTTTATTTT
1 TAAAATACACTACATATATTTTTTTATTTT
1106941 TAAAATACACTACATATATTTTTTTTATTTT
1 TAAAATACACTACATATA-TTTTTTTATTTT
*
1106972 TAAAATACACTACATGTATTTTTTTATTTT
1 TAAAATACACTACATATATTTTTTTATTTT
* *
1107002 TAAAATCCATTACATATATTTTTTTATTTT
1 TAAAATACACTACATATATTTTTTTATTTT
1107032 TAAAAT
1 TAAAAT
1107038 TTTAAATACA
Statistics
Matches: 140, Mismatches: 9, Indels: 9
0.89 0.06 0.06
Matches are distributed among these distances:
25 18 0.13
29 30 0.21
30 64 0.46
31 28 0.20
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.51
Consensus pattern (30 bp):
TAAAATACACTACATATATTTTTTTATTTT
Found at i:1107143 original size:13 final size:13
Alignment explanation
Indices: 1107125--1107226 Score: 54
Period size: 13 Copynumber: 7.8 Consensus size: 13
1107115 CCATGCAATA
*
1107125 CCCATTCCCATTT
1 CCCATTCCCATCT
1107138 CCCATTCCCATCT
1 CCCATTCCCATCT
* *
1107151 CCCCTCTTCCA--T
1 CCCAT-TCCCATCT
* *
1107163 -CGATTCCCCTCTT
1 CCCATTCCCATC-T
*
1107176 CCACCGTTCCC-TCCT
1 -C-CCATTCCCAT-CT
1107191 CCCATTCCCAT-T
1 CCCATTCCCATCT
1107203 CCCATTTCCCAT-T
1 CCCA-TTCCCATCT
1107216 CCCATTCCCAT
1 CCCATTCCCAT
1107227 TATCAACAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
10 3 0.04
11 2 0.03
12 13 0.19
13 36 0.52
14 6 0.09
15 2 0.03
16 7 0.10
ACGTcount: A:0.13, C:0.52, G:0.02, T:0.33
Consensus pattern (13 bp):
CCCATTCCCATCT
Found at i:1107201 original size:6 final size:6
Alignment explanation
Indices: 1107190--1107227 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
1107180 CGTTCCCTCC
1107190 TCCCAT TCCCAT TCCCATT TCCCAT TCCCAT TCCCAT T
1 TCCCAT TCCCAT TCCCA-T TCCCAT TCCCAT TCCCAT T
1107228 ATCAACAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.16, C:0.47, G:0.00, T:0.37
Consensus pattern (6 bp):
TCCCAT
Found at i:1107212 original size:19 final size:19
Alignment explanation
Indices: 1107190--1107227 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1107180 CGTTCCCTCC
1107190 TCCCATTCCCATTCCCATT
1 TCCCATTCCCATTCCCATT
1107209 TCCCATTCCCATTCCCATT
1 TCCCATTCCCATTCCCATT
1107228 ATCAACAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.47, G:0.00, T:0.37
Consensus pattern (19 bp):
TCCCATTCCCATTCCCATT
Found at i:1111439 original size:31 final size:31
Alignment explanation
Indices: 1111371--1111454 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
1111361 GGTTTGAGTG
* * *
1111371 ACTGATTTGTTACTTTCCGAAAACGTTAGTA
1 ACTGATTTGTCACTTTTCGAAAACGTTAATA
* * * *
1111402 ATTGATTTGTCACTTTTCGTAAATGTTAATT
1 ACTGATTTGTCACTTTTCGAAAACGTTAATA
1111433 ACTGATTTGTCACTTTT-GAAAA
1 ACTGATTTGTCACTTTTCGAAAA
1111455 TTTAGTGACT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 4 0.09
31 40 0.91
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (31 bp):
ACTGATTTGTCACTTTTCGAAAACGTTAATA
Found at i:1117446 original size:25 final size:26
Alignment explanation
Indices: 1117401--1117458 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
1117391 GGTCCTTCTG
1117401 TTAAAAATTTCATCCATTTTCTACTA
1 TTAAAAATTTCATCCATTTTCTACTA
* * * *
1117427 TTAAAATTTTCATTCA-TTTCTATTG
1 TTAAAAATTTCATCCATTTTCTACTA
1117452 TTAAAAA
1 TTAAAAA
1117459 CTGGTCTCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (26 bp):
TTAAAAATTTCATCCATTTTCTACTA
Found at i:1126601 original size:21 final size:21
Alignment explanation
Indices: 1126575--1126618 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1126565 TCAATCAAAA
1126575 CAACCTAGAGCTTAATTCTTT
1 CAACCTAGAGCTTAATTCTTT
1126596 CAACCTAGAGCTTAATTCTTT
1 CAACCTAGAGCTTAATTCTTT
1126617 CA
1 CA
1126619 TACATTTTCT
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:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (21 bp):
CAACCTAGAGCTTAATTCTTT
Found at i:1132857 original size:17 final size:19
Alignment explanation
Indices: 1132823--1132859 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
1132813 ACTACTCTTC
1132823 ATTTTCTAATCGAAAATAA
1 ATTTTCTAATCGAAAATAA
1132842 ATTTTCT-ATC-AAAATAA
1 ATTTTCTAATCGAAAATAA
1132859 A
1 A
1132860 CACAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 3 0.17
19 7 0.39
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.38
Consensus pattern (19 bp):
ATTTTCTAATCGAAAATAA
Found at i:1134902 original size:24 final size:27
Alignment explanation
Indices: 1134844--1134904 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 27
1134834 TAATATTTTT
*
1134844 AAAAAT-TAATGATTAAATTTAACTTAA
1 AAAAATATAAGGATTAAATTTAAC-TAA
1134871 AAAAATATAAGGATTAAA-TTAA-T-A
1 AAAAATATAAGGATTAAATTTAACTAA
1134895 AAAAATATAA
1 AAAAATATAA
1134905 ACTGAGAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
24 11 0.34
25 1 0.03
27 10 0.31
28 10 0.31
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (27 bp):
AAAAATATAAGGATTAAATTTAACTAA
Found at i:1140171 original size:22 final size:22
Alignment explanation
Indices: 1140141--1140203 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
1140131 GCAACCATGA
1140141 AGCAGCCCCATACCTCCACTAC
1 AGCAGCCCCATACCTCCACTAC
*
1140163 AGC-GACCCCATACCCCCACTAC
1 AGCAG-CCCCATACCTCCACTAC
*
1140185 AGCAGTCCCATACCTCCAC
1 AGCAGCCCCATACCTCCAC
1140204 AGCCCTCGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.27, C:0.51, G:0.10, T:0.13
Consensus pattern (22 bp):
AGCAGCCCCATACCTCCACTAC
Found at i:1165891 original size:32 final size:31
Alignment explanation
Indices: 1165841--1165907 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
1165831 GGGTGTGTGA
* *
1165841 CACACGGCCTAGGTCATTTTGGGCGTGTAGGC
1 CACACGGCCAAGGCCA-TTTGGGCGTGTAGGC
* * *
1165873 CACACGGGCAAGGCCATTTGGGTGTGTGGGC
1 CACACGGCCAAGGCCATTTGGGCGTGTAGGC
1165904 CACA
1 CACA
1165908 GGAGAATGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.18, C:0.25, G:0.36, T:0.21
Consensus pattern (31 bp):
CACACGGCCAAGGCCATTTGGGCGTGTAGGC
Found at i:1166493 original size:216 final size:216
Alignment explanation
Indices: 1166119--1166552 Score: 868
Period size: 216 Copynumber: 2.0 Consensus size: 216
1166109 GCATGTCTAT
1166119 TGTCTGTTATTCGAGCATGTTTCATATAATAATTTTGGTATCTAGGATTTGATAATTCTATTTTA
1 TGTCTGTTATTCGAGCATGTTTCATATAATAATTTTGGTATCTAGGATTTGATAATTCTATTTTA
1166184 TCTGGTATGCTATTGTATCTGACTATGGGGCGGGATATGTGACATGTGGAGGAAGTATTTTGTGA
66 TCTGGTATGCTATTGTATCTGACTATGGGGCGGGATATGTGACATGTGGAGGAAGTATTTTGTGA
1166249 GGCGATATCTCGCCAATATGTTGGCAGCACAGCTGCGATTATTCTGAAAAGTGTCGTATGGATGT
131 GGCGATATCTCGCCAATATGTTGGCAGCACAGCTGCGATTATTCTGAAAAGTGTCGTATGGATGT
1166314 TAAGTGATGTGTAGGGCTGGG
196 TAAGTGATGTGTAGGGCTGGG
1166335 TGTCTGTTATTCGAGCATGTTTCATATAATAATTTTGGTATCTAGGATTTGATAATTCTATTTTA
1 TGTCTGTTATTCGAGCATGTTTCATATAATAATTTTGGTATCTAGGATTTGATAATTCTATTTTA
1166400 TCTGGTATGCTATTGTATCTGACTATGGGGCGGGATATGTGACATGTGGAGGAAGTATTTTGTGA
66 TCTGGTATGCTATTGTATCTGACTATGGGGCGGGATATGTGACATGTGGAGGAAGTATTTTGTGA
1166465 GGCGATATCTCGCCAATATGTTGGCAGCACAGCTGCGATTATTCTGAAAAGTGTCGTATGGATGT
131 GGCGATATCTCGCCAATATGTTGGCAGCACAGCTGCGATTATTCTGAAAAGTGTCGTATGGATGT
1166530 TAAGTGATGTGTAGGGCTGGG
196 TAAGTGATGTGTAGGGCTGGG
1166551 TG
1 TG
1166553 GGTATTTTAT
Statistics
Matches: 218, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
216 218 1.00
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.37
Consensus pattern (216 bp):
TGTCTGTTATTCGAGCATGTTTCATATAATAATTTTGGTATCTAGGATTTGATAATTCTATTTTA
TCTGGTATGCTATTGTATCTGACTATGGGGCGGGATATGTGACATGTGGAGGAAGTATTTTGTGA
GGCGATATCTCGCCAATATGTTGGCAGCACAGCTGCGATTATTCTGAAAAGTGTCGTATGGATGT
TAAGTGATGTGTAGGGCTGGG
Found at i:1166956 original size:18 final size:18
Alignment explanation
Indices: 1166920--1166958 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1166910 CTCTGGACAT
*
1166920 TTTGGTTTAATTTTTGAA
1 TTTGGTTTAATTTTGGAA
1166938 TTTGGATTTAA-TTTGGAA
1 TTTGG-TTTAATTTTGGAA
1166956 TTT
1 TTT
1166959 TTGGCACGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.23, C:0.00, G:0.18, T:0.59
Consensus pattern (18 bp):
TTTGGTTTAATTTTGGAA
Found at i:1167914 original size:7 final size:7
Alignment explanation
Indices: 1167902--1167943 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
1167892 TTGAGTTATT
1167902 TTTTTTA
1 TTTTTTA
1167909 TTTTTTA
1 TTTTTTA
1167916 TTTTTTA
1 TTTTTTA
*
1167923 ATTTTTA
1 TTTTTTA
*
1167930 ATTTTTA
1 TTTTTTA
1167937 TTCTTTT
1 TT-TTTT
1167944 TCCCAAAGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 28 0.88
8 4 0.12
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTA
Found at i:1167919 original size:15 final size:15
Alignment explanation
Indices: 1167901--1167935 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1167891 TTTGAGTTAT
* *
1167901 TTTTTTTATTTTTTA
1 TTTTTTAATTTTTAA
1167916 TTTTTTAATTTTTAA
1 TTTTTTAATTTTTAA
1167931 TTTTT
1 TTTTT
1167936 ATTCTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTAATTTTTAA
Found at i:1167929 original size:21 final size:22
Alignment explanation
Indices: 1167903--1167943 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1167893 TGAGTTATTT
*
1167903 TTTTTATTTTTTATT-TTTTAA
1 TTTTTAATTTTTATTCTTTTAA
1167924 TTTTTAATTTTTATTCTTTT
1 TTTTTAATTTTTATTCTTTT
1167944 TCCCAAAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTAATTTTTATTCTTTTAA
Found at i:1181351 original size:23 final size:23
Alignment explanation
Indices: 1181321--1181364 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1181311 TACGAACTCT
*
1181321 AAATATAGACTGTAAAATAGACC
1 AAATATAGACCGTAAAATAGACC
1181344 AAATATAGACCGTAAAATAGA
1 AAATATAGACCGTAAAATAGA
1181365 TATGGAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.55, C:0.11, G:0.14, T:0.20
Consensus pattern (23 bp):
AAATATAGACCGTAAAATAGACC
Found at i:1183422 original size:29 final size:30
Alignment explanation
Indices: 1183368--1183447 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 30
1183358 ATATCAAAAT
* *
1183368 TATACATGAATTATGGTTTAATGTGTAATTG
1 TATACATGAATTTTGATTT-ATGTGTAATTG
*
1183399 TATACATGAATTTTGATTT-TGTGTAATTT
1 TATACATGAATTTTGATTTATGTGTAATTG
*
1183428 TATACATAAAATTTTGATTT
1 TATACAT-GAATTTTGATTT
1183448 GATCCAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 16 0.36
30 11 0.25
31 17 0.39
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.50
Consensus pattern (30 bp):
TATACATGAATTTTGATTTATGTGTAATTG
Found at i:1183448 original size:29 final size:29
Alignment explanation
Indices: 1183389--1183447 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
1183379 TATGGTTTAA
*
1183389 TGTGTAATTGTATACATGAATTTTGATTT
1 TGTGTAATTGTATACATAAATTTTGATTT
*
1183418 TGTGTAATTTTATACATAAAATTTTGATTT
1 TGTGTAATTGTATACAT-AAATTTTGATTT
1183448 GATCCAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (29 bp):
TGTGTAATTGTATACATAAATTTTGATTT
Found at i:1187561 original size:21 final size:22
Alignment explanation
Indices: 1187525--1187569 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 22
1187515 GTCACGAATG
1187525 AATTTTATAATTTAT-ATTAGCTT
1 AATTTTAT-ATTTATAATTA-CTT
1187548 AATTTTAT-TTTATAATTACTT
1 AATTTTATATTTATAATTACTT
1187569 A
1 A
1187570 GACATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 9 0.43
22 4 0.19
23 8 0.38
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (22 bp):
AATTTTATATTTATAATTACTT
Found at i:1189064 original size:19 final size:19
Alignment explanation
Indices: 1189040--1189417 Score: 134
Period size: 19 Copynumber: 18.3 Consensus size: 19
1189030 GTGCCAATGG
*
1189040 GTAATTTTGTATGTATATT
1 GTAATTTTGTATGAATATT
1189059 GTAATTTTTTGTATGAATATT
1 GTAA--TTTTGTATGAATATT
*
1189080 ATAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
1189099 GTAATTATTTTAT-AATTAATTTT
1 GTAATT-TTGTATGAA-T-A--TT
* * *
1189122 GT-ATTTATAGTTTTGGAT-TA
1 GTAATTT-T-G-TATGAATATT
*
1189142 GT-ATTTTGTACGAATATT
1 GTAATTTTGTATGAATATT
1189160 GTAATTTTGTAATTTTGCATGAATATT
1 GTAATTTTG------T--ATGAATATT
1189187 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
1189206 GTAATTTTGTAATTTTATATGAATATT
1 GTAATTTTG--------TATGAATATT
*
1189233 ATAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
1189252 GTAATTATTTTAT-AATTAATT
1 GTAATT-TTGTATGAA-T-ATT
* * *
1189273 TTATATTTATAGTTTTTG-AT-TA
1 GTA-ATTT-T-G--TATGAATATT
1189295 GT-ATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
1189313 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
1189332 GTAATTATT-T-T--ATAAT
1 GTAATT-TTGTATGAATATT
* *
1189348 -TAATTTTGTATTTATAGTTTTT
1 GTAATTTTGTA-TGA-A--TATT
*
1189370 GATTAGTATTTTGTATGAATGTT
1 G--TA--ATTTTGTATGAATATT
1189393 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
1189412 GTAATT
1 GTAATT
1189418 ATTTTATAAT
Statistics
Matches: 275, Mismatches: 29, Indels: 110
0.66 0.07 0.27
Matches are distributed among these distances:
14 2 0.01
15 6 0.02
16 7 0.03
17 7 0.03
18 9 0.03
19 113 0.41
20 26 0.09
21 28 0.10
22 12 0.04
23 8 0.03
24 4 0.01
25 8 0.03
26 2 0.01
27 43 0.16
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.56
Consensus pattern (19 bp):
GTAATTTTGTATGAATATT
Found at i:1189171 original size:8 final size:8
Alignment explanation
Indices: 1189158--1189221 Score: 56
Period size: 8 Copynumber: 7.2 Consensus size: 8
1189148 TGTACGAATA
1189158 TTGTAATT
1 TTGTAATT
1189166 TTGTAATT
1 TTGTAATT
*
1189174 TTGCATGAATA
1 TTG--T-AATT
1189185 TTGTAATT
1 TTGTAATT
*
1189193 TTGTATGAATA
1 TTG--T-AATT
1189204 TTGTAATT
1 TTGTAATT
1189212 TTGTAATT
1 TTGTAATT
1189220 TT
1 TT
1189222 ATATGAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
8 30 0.65
9 2 0.04
10 2 0.04
11 12 0.26
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (8 bp):
TTGTAATT
Found at i:1189174 original size:27 final size:27
Alignment explanation
Indices: 1189144--1189243 Score: 99
Period size: 27 Copynumber: 4.0 Consensus size: 27
1189134 TTGGATTAGT
1189144 ATTTTGTACGAATATTGTAATTTTGTA
1 ATTTTGTACGAATATTGTAATTTTGTA
*
1189171 ATTTTG--C----A-TG-AATATTGTA
1 ATTTTGTACGAATATTGTAATTTTGTA
*
1189190 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTACGAATATTGTAATTTTGTA
* * *
1189217 ATTTTATATGAATATTATAATTTTGTA
1 ATTTTGTACGAATATTGTAATTTTGTA
1189244 TGAATATTGT
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
19 14 0.23
20 2 0.03
21 1 0.02
25 2 0.03
26 2 0.03
27 39 0.65
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (27 bp):
ATTTTGTACGAATATTGTAATTTTGTA
Found at i:1189194 original size:46 final size:46
Alignment explanation
Indices: 1189144--1189257 Score: 192
Period size: 46 Copynumber: 2.5 Consensus size: 46
1189134 TTGGATTAGT
* * *
1189144 ATTTTGTACGAATATTGTAATTTTGTAATTTTGCATGAATATTGTA
1 ATTTTGTATGAATATTGTAATTTTGTAATTTTACATGAATATTATA
*
1189190 ATTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATATTATA
1 ATTTTGTATGAATATTGTAATTTTGTAATTTTACATGAATATTATA
1189236 ATTTTGTATGAATATTGTAATT
1 ATTTTGTATGAATATTGTAATT
1189258 ATTTTATAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (46 bp):
ATTTTGTATGAATATTGTAATTTTGTAATTTTACATGAATATTATA
Found at i:1189307 original size:80 final size:80
Alignment explanation
Indices: 1189217--1189566 Score: 556
Period size: 80 Copynumber: 4.3 Consensus size: 80
1189207 TAATTTTGTA
* * *
1189217 ATTTTATATGAATATTATAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTA
1 ATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTA
1189282 TAGTTTTTGATTAGT
66 TAGTTTTTGATTAGT
1189297 ATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTA
1 ATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTA
1189362 TAGTTTTTGATTAGT
66 TAGTTTTTGATTAGT
* *
1189377 ATTTTGTATGAATGTTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTTTATTTA
1 ATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTA
*
1189442 TATTTTTTGATTAGT
66 TAGTTTTTGATTAGT
*
1189457 ATTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATAGTGTAATTATTTTATAATTAATTT
1 ATTTTGTATG-A-A---T-A--TTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTT
1189522 TGTATTTATAGTTTTTGATTAGT
58 TGTATTTATAGTTTTTGATTAGT
*
1189545 ATTTTGTATAAATATTGTAATT
1 ATTTTGTATGAATATTGTAATT
1189567 ATTTTATAAT
Statistics
Matches: 251, Mismatches: 11, Indels: 16
0.90 0.04 0.06
Matches are distributed among these distances:
80 172 0.69
81 1 0.00
82 2 0.01
83 1 0.00
85 1 0.00
86 1 0.00
87 1 0.00
88 72 0.29
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (80 bp):
ATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTA
TAGTTTTTGATTAGT
Found at i:1189489 original size:88 final size:88
Alignment explanation
Indices: 1189391--1189566 Score: 316
Period size: 88 Copynumber: 2.0 Consensus size: 88
1189381 TGTATGAATG
* * *
1189391 TTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTTTATTTATATTTTTTGATTAG
1 TTGTAATTTTGTATGAATAGTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAG
*
1189456 TATTTTGTATGAATATTGTAATT
66 TATTTTGTATAAATATTGTAATT
1189479 TTGTAATTTTGTATGAATAGTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAG
1 TTGTAATTTTGTATGAATAGTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAG
1189544 TATTTTGTATAAATATTGTAATT
66 TATTTTGTATAAATATTGTAATT
1189567 ATTTTATAAT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (88 bp):
TTGTAATTTTGTATGAATAGTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAG
TATTTTGTATAAATATTGTAATT
Found at i:1189521 original size:34 final size:32
Alignment explanation
Indices: 1189482--1189587 Score: 96
Period size: 34 Copynumber: 3.3 Consensus size: 32
1189472 TGTAATTTTG
1189482 TAATTTTGTATGAATAGTGTAATTATTTTATAAT
1 TAATTTTGTAT-AATA-TGTAATTATTTTATAAT
* * * * *
1189516 TAATTTTGTAT--T-TATAGTT-TTTGATTAG
1 TAATTTTGTATAATATGTAATTATTTTATAAT
1189544 T-ATTTTGTATAAATATTGTAATTATTTTATAAT
1 TAATTTTGTAT-AATA-TGTAATTATTTTATAAT
1189577 TAATTTTGTAT
1 TAATTTTGTAT
1189588 TTATAGTTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
27 9 0.16
28 7 0.13
29 5 0.09
30 1 0.02
31 1 0.02
32 5 0.09
33 7 0.13
34 20 0.36
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (32 bp):
TAATTTTGTATAATATGTAATTATTTTATAAT
Found at i:1189522 original size:61 final size:55
Alignment explanation
Indices: 1189457--1189787 Score: 272
Period size: 61 Copynumber: 5.9 Consensus size: 55
1189447 TTTGATTAGT
*
1189457 ATTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATAGTGTAATTATTTTATAATTA
1 ATTTTGTATGAATATTGTAATTTTGT-ATTTTGTATGAATATTGT-A--ATTTT-TAA-TA
** * * * *
1189518 ATTTTGTATTTATAGTTTTTGA-TTAGTATTTTGTATAAATATTGTAATTATTTTATAATTA
1 ATTTTGTATGAATA--TTGTAATTTTGTATTTTGTATGAATATTGT-A--ATTTT-TAA-TA
** * * *
1189579 ATTTTGTATTTATAGTTTTGGA-TTAGTATTTTGTATGAATATTGTAA-TTTT-ATA
1 ATTTTGTATGAATA-TTGT-AATTTTGTATTTTGTATGAATATTGTAATTTTTAATA
*
1189633 ATTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATATTGTAATTTTGTAAT-
1 ATTTTGTATGAATATTGTAATTTTGT-ATTTTGTATGAATATTGTAATTTT-TAATA
* *
1189689 -TTTT-TATGAATATTGTAATATTG---TTTGTATGAATATTGTAA-TTTT-GTA
1 ATTTTGTATGAATATTGTAATTTTGTATTTTGTATGAATATTGTAATTTTTAATA
*
1189737 ATTTTATATGAATATTGTAATTTTGTAATTTTGTATGAATATTGTAATTTT
1 ATTTTGTATGAATATTGTAATTTTGT-ATTTTGTATGAATATTGTAATTTT
1189788 GTATGAATAT
Statistics
Matches: 235, Mismatches: 19, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
47 1 0.00
48 1 0.00
49 7 0.03
50 35 0.15
52 1 0.00
53 7 0.03
54 69 0.29
55 11 0.05
56 2 0.01
57 5 0.02
58 1 0.00
60 5 0.02
61 82 0.35
62 4 0.02
63 4 0.02
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (55 bp):
ATTTTGTATGAATATTGTAATTTTGTATTTTGTATGAATATTGTAATTTTTAATA
Found at i:1189548 original size:27 final size:27
Alignment explanation
Indices: 1189518--1189614 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 27
1189508 TTTATAATTA
1189518 ATTTTGTATTTATAGTTTTTGATTAGT
1 ATTTTGTATTTATAGTTTTTGATTAGT
* * * * *
1189545 ATTTTGTATAAATATTGTAATTATTTTATAATT
1 ATTTTG--T--AT-TTATAGTT-TTTGATTAGT
*
1189578 AATTTTGTATTTATAGTTTTGGATTAGT
1 -ATTTTGTATTTATAGTTTTTGATTAGT
1189606 ATTTTGTAT
1 ATTTTGTAT
1189615 GAATATTGTA
Statistics
Matches: 52, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
27 15 0.29
28 6 0.12
29 7 0.13
30 2 0.04
31 2 0.04
32 7 0.13
33 7 0.13
34 6 0.12
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (27 bp):
ATTTTGTATTTATAGTTTTTGATTAGT
Found at i:1189636 original size:27 final size:27
Alignment explanation
Indices: 1189606--1189790 Score: 297
Period size: 27 Copynumber: 7.0 Consensus size: 27
1189596 TTGGATTAGT
*
1189606 ATTTTGTATGAATATTGTAATTTTATA
1 ATTTTGTATGAATATTGTAATTTTGTA
1189633 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
1189660 ATTTTATATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
* *
1189687 ATTTTTTATGAATATTGTAATATTG--
1 ATTTTGTATGAATATTGTAATTTTGTA
1189712 --TTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
1189737 ATTTTATATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
1189764 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
1189791 TGAATATTGT
Statistics
Matches: 146, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
23 21 0.14
27 125 0.86
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (27 bp):
ATTTTGTATGAATATTGTAATTTTGTA
Found at i:1189655 original size:19 final size:19
Alignment explanation
Indices: 1189631--1189827 Score: 135
Period size: 19 Copynumber: 10.3 Consensus size: 19
1189621 TGTAATTTTA
1189631 TAATTTTGTATGAATATTG
1 TAATTTTGTATGAATATTG
**
1189650 TAATTTTGTAAT-TTTATATG
1 TAATTTTGT-ATGAATAT-TG
* *
1189670 -AATATTG--T-AATTTTG
1 TAATTTTGTATGAATATTG
*
1189685 TAATTTTTTATGAATATTG
1 TAATTTTGTATGAATATTG
1189704 TAATATTGTTTGTATGAATATTG
1 T-A-A-T-TTTGTATGAATATTG
**
1189727 TAATTTTGTAAT-TTTATATG
1 TAATTTTGT-ATGAATAT-TG
* *
1189747 -AATATTG--T-AATTTTG
1 TAATTTTGTATGAATATTG
1189762 TAATTTTGTATGAATATTG
1 TAATTTTGTATGAATATTG
1189781 TAATTTTGTATGAATATTG
1 TAATTTTGTATGAATATTG
1189800 TAATATTGTTTGTATGAATATTG
1 T-A-A-T-TTTGTATGAATATTG
1189823 TAATT
1 TAATT
1189828 ATTTTATAAT
Statistics
Matches: 140, Mismatches: 18, Indels: 40
0.71 0.09 0.20
Matches are distributed among these distances:
15 4 0.03
16 17 0.12
18 2 0.01
19 66 0.47
20 12 0.09
21 4 0.03
22 4 0.03
23 31 0.22
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATGAATATTG
Found at i:1189687 original size:8 final size:8
Alignment explanation
Indices: 1189620--1189790 Score: 69
Period size: 8 Copynumber: 19.6 Consensus size: 8
1189610 TGTATGAATA
1189620 TTGTAATT
1 TTGTAATT
*
1189628 TTATAATT
1 TTGTAATT
*
1189636 TTGTATGAATA
1 TTG--T-AATT
1189647 TTGTAATT
1 TTGTAATT
1189655 TTGTAATTT
1 TTGTAA-TT
* *
1189664 TATATGAATA
1 T-TGT-AATT
1189674 TTGTAATT
1 TTGTAATT
1189682 TTGTAATTTT
1 TTGTAA--TT
* *
1189692 TTATGAATA
1 TTGT-AATT
*
1189701 TTGTAATA
1 TTGTAATT
1189709 TTGT--TT
1 TTGTAATT
*
1189715 GTATG-AATA
1 -T-TGTAATT
1189724 TTGTAATT
1 TTGTAATT
1189732 TTGTAATTT
1 TTGTAA-TT
* *
1189741 TATATGAATA
1 T-TGT-AATT
1189751 TTGTAATT
1 TTGTAATT
1189759 TTGTAATT
1 TTGTAATT
*
1189767 TTGTATGAATA
1 TTG--T-AATT
1189778 TTGTAATT
1 TTGTAATT
1189786 TTGTA
1 TTGTA
1189791 TGAATATTGT
Statistics
Matches: 123, Mismatches: 20, Indels: 40
0.67 0.11 0.22
Matches are distributed among these distances:
6 1 0.01
7 3 0.02
8 69 0.56
9 17 0.14
10 15 0.12
11 18 0.15
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (8 bp):
TTGTAATT
Found at i:1189738 original size:77 final size:73
Alignment explanation
Indices: 1189631--1189827 Score: 303
Period size: 77 Copynumber: 2.7 Consensus size: 73
1189621 TGTAATTTTA
*
1189631 TAATTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATATTGTAATTTTGTAATTTTTTAT
1 TAATTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATATTGTAATTTTGTAATTTTGTAT
1189696 GAATATTG
66 GAATATTG
1189704 TAATATTGTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATATTGTAATTTTGTAATTTT
1 T-A-A-T-TTTGTATGAATATTGTAATTTTGTAATTTTATATGAATATTGTAATTTTGTAATTTT
1189769 GTATGAATATTG
62 GTATGAATATTG
* *
1189781 TAATTTTGTATGAATATTGTAATATTG----TTTGTATGAATATTGTAATT
1 TAATTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATATTGTAATT
1189828 ATTTTATAAT
Statistics
Matches: 117, Mismatches: 3, Indels: 12
0.89 0.02 0.09
Matches are distributed among these distances:
69 19 0.16
73 23 0.20
74 2 0.02
75 2 0.02
76 2 0.02
77 69 0.59
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (73 bp):
TAATTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATATTGTAATTTTGTAATTTTGTAT
GAATATTG
Found at i:1189804 original size:27 final size:27
Alignment explanation
Indices: 1189778--1189827 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 27
1189768 TGTATGAATA
*
1189778 TTGTAATTTTGTATGAATATTGTAATA
1 TTGTAATTTTGTATGAATATTGTAATT
1189805 TTG----TTTGTATGAATATTGTAATT
1 TTGTAATTTTGTATGAATATTGTAATT
1189828 ATTTTATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 19 0.86
27 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (27 bp):
TTGTAATTTTGTATGAATATTGTAATT
Found at i:1190087 original size:15 final size:16
Alignment explanation
Indices: 1190051--1190087 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1190041 CTCATTTAAT
1190051 TTTTATATAATGTAAC
1 TTTTATATAATGTAAC
1190067 TTTTATAGT-ATGTAA-
1 TTTTATA-TAATGTAAC
1190082 TTTTAT
1 TTTTAT
1190088 TTGATTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 13 0.65
17 1 0.05
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.57
Consensus pattern (16 bp):
TTTTATATAATGTAAC
Found at i:1190418 original size:14 final size:14
Alignment explanation
Indices: 1190399--1190425 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1190389 AATGAAAAAA
1190399 GTAAATACTTTTTG
1 GTAAATACTTTTTG
1190413 GTAAATACTTTTT
1 GTAAATACTTTTT
1190426 CTGACACCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (14 bp):
GTAAATACTTTTTG
Found at i:1193117 original size:2 final size:2
Alignment explanation
Indices: 1193110--1193144 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1193100 AAATGCCCCA
1193110 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1193145 TCCATCACCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1197159 original size:19 final size:19
Alignment explanation
Indices: 1197121--1197160 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1197111 GATTTTTATT
*
1197121 TTATTTAATATTATTATAA
1 TTATTAAATATTATTATAA
1197140 TTATTAAAT-TTATTATTAA
1 TTATTAAATATTATTA-TAA
1197159 TT
1 TT
1197161 TTTTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATTAAATATTATTATAA
Found at i:1198184 original size:31 final size:31
Alignment explanation
Indices: 1198125--1198184 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
1198115 ATTTGGTCAC
*
1198125 TGAACTATTTCAATATTTTCATTCAAGTCGT
1 TGAACTATTTCAAAATTTTCATTCAAGTCGT
* *
1198156 TGAACTA-TTCAAAAGTTTTTATTTAAGTC
1 TGAACTATTTCAAAA-TTTTCATTCAAGTC
1198185 ACTAGTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (31 bp):
TGAACTATTTCAAAATTTTCATTCAAGTCGT
Found at i:1199407 original size:60 final size:60
Alignment explanation
Indices: 1199308--1199430 Score: 158
Period size: 60 Copynumber: 2.0 Consensus size: 60
1199298 TAACAGCCCA
* * *
1199308 TTTTTGGGTCAAACCGGAATAGTGATTTCAGGACCACAAATCCGAAGTTAAAATAATAAT
1 TTTTTGGGTCAAACCAGAATACTGATTTCAGGACCACAAATCCAAAGTTAAAATAATAAT
* * * * *
1199368 TTTTTGGGTCAAATCAGAATACTGGTTTC-GAGACTACAAATCTAAAGTTAAAATATTAAT
1 TTTTTGGGTCAAACCAGAATACTGATTTCAG-GACCACAAATCCAAAGTTAAAATAATAAT
1199428 TTT
1 TTT
1199431 ATTATTATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
59 1 0.02
60 53 0.98
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (60 bp):
TTTTTGGGTCAAACCAGAATACTGATTTCAGGACCACAAATCCAAAGTTAAAATAATAAT
Found at i:1200036 original size:61 final size:61
Alignment explanation
Indices: 1199959--1200347 Score: 539
Period size: 61 Copynumber: 6.4 Consensus size: 61
1199949 GTATATGTTT
* *
1199959 TATACATTGCCGAATTGGTTTGTATAAAGATATACATTGCCGAATTTGATTTGCT-TATAGA
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTG-TATATAGA
* * *
1200020 TATACATTGCCAAATTGATTTGTATATAGATATACATTGCCGAATTTGAATTGTTTATAGA
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * * * *
1200081 TGTACATTGCCGAATTGATTTGTTTATAGATATACATTGTCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * *
1200142 TATACATTACCGAATTTGATTTGTATATGGATATACATTGCTGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAA-TTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * * * *
1200203 TATACATTGCTGAATTTGATTTGTATATGGTTATACATTGCCGAAGTTGATTTGTATATGGA
1 TATACATTGCCGAA-TTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * *
1200265 TATACATTGCCGAATTGATTTGTATATAGATATTCATTGCCGAATTTGATTCGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
*
1200326 TATATATTGCCGAATTGATTTG
1 TATACATTGCCGAATTGATTTG
1200348 AGCATTGGAT
Statistics
Matches: 293, Mismatches: 32, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
60 1 0.00
61 238 0.81
62 54 0.18
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (61 bp):
TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
Found at i:1200357 original size:31 final size:31
Alignment explanation
Indices: 1199959--1200347 Score: 504
Period size: 31 Copynumber: 12.7 Consensus size: 31
1199949 GTATATGTTT
* **
1199959 TATACATTGCCGAA-TTGGTTTGTATAAAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
*
1199989 TATACATTGCCGAATTTGATTTGCT-TATAGA
1 TATACATTGCCGAATTTGATTTG-TATATGGA
* *
1200020 TATACATTGCC-AAATTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* * *
1200050 TATACATTGCCGAATTTGAATTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* * *
1200081 TGTACATTGCCGAA-TTGATTTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* *
1200111 TATACATTGTCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATGGA
*
1200142 TATACATTACCGAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* *
1200173 TATACATTGCTGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* *
1200203 TATACATTGCTGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATGGA
*
1200234 TATACATTGCCGAAGTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
*
1200265 TATACATTGCCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* *
1200295 TATTCATTGCCGAATTTGATTCGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
*
1200326 TATATATTGCCGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
1200348 AGCATTGGAT
Statistics
Matches: 321, Mismatches: 31, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
29 1 0.00
30 132 0.41
31 187 0.58
32 1 0.00
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (31 bp):
TATACATTGCCGAATTTGATTTGTATATGGA
Found at i:1200357 original size:92 final size:92
Alignment explanation
Indices: 1199959--1200347 Score: 552
Period size: 92 Copynumber: 4.2 Consensus size: 92
1199949 GTATATGTTT
* **
1199959 TATACATTGCCGAA-TTGGTTTGTATAAAGATATACATTGCCGAATTTGATTTGCT-TATAGATA
1 TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAA-TTGATTTG-TATATAGATA
* *
1200022 TACATTGCC-AAATTGATTTGTATATAGA
64 TACATTGCCGAATTTGATTTGTATATGGA
* * * * *
1200050 TATACATTGCCGAATTTGAATTGTTTATAGATGTACATTGCCGAATTGATTTGTTTATAGATATA
1 TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGATATA
* *
1200115 CATTGTCGAATTTGATTTGTATATGGT
66 CATTGCCGAATTTGATTTGTATATGGA
* *
1200142 TATACATTACCGAATTTGATTTGTATATGGATATACATTGCTGAATTGATTTGTATATAGATATA
1 TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGATATA
* *
1200207 CATTGCTGAATTTGATTTGTATATGGT
66 CATTGCCGAATTTGATTTGTATATGGA
* *
1200234 TATACATTGCCGAAGTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGATATT
1 TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGATATA
*
1200299 CATTGCCGAATTTGATTCGTATATGGA
66 CATTGCCGAATTTGATTTGTATATGGA
*
1200326 TATATATTGCCGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
1200348 AGCATTGGAT
Statistics
Matches: 269, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
90 1 0.00
91 46 0.17
92 222 0.83
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (92 bp):
TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGATATA
CATTGCCGAATTTGATTTGTATATGGA
Found at i:1201716 original size:19 final size:19
Alignment explanation
Indices: 1201692--1201728 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1201682 TTAAAATATT
1201692 ATTTTA-ATAAAATATTTAA
1 ATTTTATATAAAA-ATTTAA
1201711 ATTTTATATAAAAATTTA
1 ATTTTATATAAAAATTTA
1201729 TTAATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTATATAAAAATTTAA
Found at i:1201767 original size:20 final size:19
Alignment explanation
Indices: 1201739--1201780 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1201729 TTAATTATAT
*
1201739 TTTATTGAATGAATATAATA
1 TTTAATGAATGAA-ATAATA
*
1201759 TTTAATGAATGAAATTATA
1 TTTAATGAATGAAATAATA
1201778 TTT
1 TTT
1201781 GTAAATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (19 bp):
TTTAATGAATGAAATAATA
Found at i:1213974 original size:18 final size:17
Alignment explanation
Indices: 1213941--1213994 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
1213931 AATTTTTATG
*
1213941 ATTT-TTTTTATAATTT
1 ATTTATTTTTAAAATTT
1213957 ATTTATTTTTAAATATTT
1 ATTTATTTTTAAA-ATTT
*
1213975 -TATAATTTTTAAAA-TT
1 AT-TTATTTTTAAAATTT
1213991 ATTT
1 ATTT
1213995 GTTAACGAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 7 0.23
17 10 0.32
18 14 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTATTTTTAAAATTT
Found at i:1215140 original size:31 final size:31
Alignment explanation
Indices: 1215102--1215166 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
1215092 TTCCTTCAAG
1215102 TATGTTTTCAAATCAAAGTTAAAAGTATATC
1 TATGTTTTCAAATCAAAGTTAAAAGTATATC
1215133 TATGTTTTCAAATCAAAGTTAAAAGTATATC
1 TATGTTTTCAAATCAAAGTTAAAAGTATATC
1215164 TAT
1 TAT
1215167 TTTGTTGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (31 bp):
TATGTTTTCAAATCAAAGTTAAAAGTATATC
Found at i:1217211 original size:31 final size:31
Alignment explanation
Indices: 1217163--1217229 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1217153 GAAAATCCTA
* *
1217163 AAGTTTAGGCTCTAATGTGGGAACAACTGCC
1 AAGTTCAGGCTCTAATGTAGGAACAACTGCC
* *
1217194 AAGTTCAGGACTC-AATGTAGGAGCAATTGCC
1 AAGTTCAGG-CTCTAATGTAGGAACAACTGCC
1217225 AAGTT
1 AAGTT
1217230 TAGGGACTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (31 bp):
AAGTTCAGGCTCTAATGTAGGAACAACTGCC
Found at i:1235293 original size:19 final size:20
Alignment explanation
Indices: 1235250--1235296 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1235240 ATATCACTTC
*
1235250 TGATTTAGGTACCACCTTGA
1 TGATTTAAGTACCACCTTGA
* *
1235270 TGATTTAAGTACCA-TTTTA
1 TGATTTAAGTACCACCTTGA
1235289 TGATTTAA
1 TGATTTAA
1235297 ACCTTATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (20 bp):
TGATTTAAGTACCACCTTGA
Found at i:1241989 original size:31 final size:31
Alignment explanation
Indices: 1241954--1242040 Score: 81
Period size: 29 Copynumber: 2.9 Consensus size: 31
1241944 TTGGTACGTA
1241954 AGTTTGGTTTTAATGTTCAATTTGATACTTG
1 AGTTTGGTTTTAATGTTCAATTTGATACTTG
* * * *
1241985 AGTTT-CTTTT--TGTCCCAATTTGGTACTTT
1 AGTTTGGTTTTAATGT-TCAATTTGATACTTG
* * *
1242014 AGTTTGGCTTCAATGTTTAATTTGATA
1 AGTTTGGTTTTAATGTTCAATTTGATA
1242041 TCCAGACCAT
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
28 3 0.07
29 17 0.40
30 6 0.14
31 13 0.31
32 3 0.07
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.52
Consensus pattern (31 bp):
AGTTTGGTTTTAATGTTCAATTTGATACTTG
Found at i:1250024 original size:25 final size:25
Alignment explanation
Indices: 1249977--1250025 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1249967 TAGGTTAATC
*
1249977 AGAGTTTAAATGGAGAACTAAAAAT
1 AGAGTTTAAATGGAGAACGAAAAAT
*
1250002 AGAGTTTAATTGGGAGAA-GAAAAA
1 AGAGTTTAAAT-GGAGAACGAAAAA
1250026 AACCAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.51, C:0.02, G:0.24, T:0.22
Consensus pattern (25 bp):
AGAGTTTAAATGGAGAACGAAAAAT
Found at i:1250025 original size:26 final size:25
Alignment explanation
Indices: 1249977--1250026 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
1249967 TAGGTTAATC
*
1249977 AGAGTTTAAATGGAGAACTAAAAAT
1 AGAGTTTAAATGGAGAACAAAAAAT
* *
1250002 AGAGTTTAATTGGGAGAAGAAAAAA
1 AGAGTTTAAAT-GGAGAACAAAAAA
1250027 ACCAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.52, C:0.02, G:0.24, T:0.22
Consensus pattern (25 bp):
AGAGTTTAAATGGAGAACAAAAAAT
Found at i:1255514 original size:14 final size:13
Alignment explanation
Indices: 1255479--1255508 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1255469 ATAAGCAAAC
1255479 AAAA-ATATTTTA
1 AAAATATATTTTA
1255491 AAAATATATTTTA
1 AAAATATATTTTA
1255504 AAAAT
1 AAAAT
1255509 TGTATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATATATTTTA
Found at i:1258399 original size:2 final size:2
Alignment explanation
Indices: 1258394--1258425 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1258384 ATATATAAAT
1258394 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1258426 CAGAAGGTTG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1262015 original size:6 final size:6
Alignment explanation
Indices: 1262006--1262057 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
1261996 CGGATTTTCT
1262006 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1262054 TTTT
1 TTTT
1262058 ATTACATGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:1262470 original size:31 final size:31
Alignment explanation
Indices: 1262425--1262498 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
1262415 TGTACGTTAG
*
1262425 TTAGTT-GATGACCAAAAAGACAAAATT-TAA
1 TTAGTTGGGTGACCAAAAA-ACAAAATTATAA
* *
1262455 TTAGTTGGGTGACCAAAAAATAAATTTATAA
1 TTAGTTGGGTGACCAAAAAACAAAATTATAA
*
1262486 ATAGTTGGGTGAC
1 TTAGTTGGGTGAC
1262499 TACTAATGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 12 0.32
31 26 0.68
ACGTcount: A:0.43, C:0.08, G:0.19, T:0.30
Consensus pattern (31 bp):
TTAGTTGGGTGACCAAAAAACAAAATTATAA
Found at i:1265759 original size:22 final size:22
Alignment explanation
Indices: 1265729--1265772 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1265719 AACACTCCTT
*
1265729 TAAATAATAAATAAGAAATAAG
1 TAAACAATAAATAAGAAATAAG
1265751 TAAACAATAAATAAGAAATAAG
1 TAAACAATAAATAAGAAATAAG
1265773 GGGTTCTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.68, C:0.02, G:0.09, T:0.20
Consensus pattern (22 bp):
TAAACAATAAATAAGAAATAAG
Found at i:1265770 original size:11 final size:11
Alignment explanation
Indices: 1265734--1265771 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1265724 TCCTTTAAAT
1265734 AATAAATAAGA
1 AATAAATAAGA
*
1265745 AATAAGTAA-A
1 AATAAATAAGA
1265755 CAATAAATAAGA
1 -AATAAATAAGA
1265767 AATAA
1 AATAA
1265772 GGGGTTCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 1 0.04
11 21 0.91
12 1 0.04
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (11 bp):
AATAAATAAGA
Done.