Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 16 of 325
Found at i:6300767 original size:25 final size:25
Alignment explanation
Indices: 6300720--6300767 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
6300710 TTTGGTGGTC
* * *
6300720 AAATCATGTTTTTAACGCCAAAAGG
1 AAATCACGTTTTTAACACAAAAAGG
6300745 AAATCACGTTTTTAACACAAAAA
1 AAATCACGTTTTTAACACAAAAA
6300768 CCCTCGTCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (25 bp):
AAATCACGTTTTTAACACAAAAAGG
Found at i:6304047 original size:28 final size:29
Alignment explanation
Indices: 6303975--6304050 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
6303965 TTTTACCATT
* *
6303975 TTAACTTATATTTTTATAATTTTTAAAAGA
1 TTAAATTAAATTTTTATAATTTTT-AAAGA
*
6304005 TTAAATTAAATTTTTATTATTTTT-AAGA
1 TTAAATTAAATTTTTATAATTTTTAAAGA
6304033 TTAAAATGT-AATTTTTAT
1 TT-AAAT-TAAATTTTTAT
6304051 CATTATAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 6 0.15
29 13 0.32
30 22 0.54
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (29 bp):
TTAAATTAAATTTTTATAATTTTTAAAGA
Found at i:6321045 original size:20 final size:21
Alignment explanation
Indices: 6321000--6321047 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
6320990 TCAATCAAAC
*
6321000 AAAA-GAAATCCTAAAAAGGA
1 AAAATGAAATCCTAAAAAAGA
* *
6321020 ATAATGAAATCC-AAAAAATA
1 AAAATGAAATCCTAAAAAAGA
6321040 AAAATGAA
1 AAAATGAA
6321048 GATGAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.67, C:0.08, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATGAAATCCTAAAAAAGA
Found at i:6324782 original size:3 final size:3
Alignment explanation
Indices: 6324776--6324842 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
6324766 ACTCCTCCTG
6324776 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
6324824 CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT C
6324843 CTTACCTCCC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:6326161 original size:38 final size:38
Alignment explanation
Indices: 6326110--6326187 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
6326100 GTTGAGGAAC
6326110 TTACTTCAAGTTCTTCTTTGCAAAGGTTAGTGAAATCA
1 TTACTTCAAGTTCTTCTTTGCAAAGGTTAGTGAAATCA
6326148 TTACTTCAAGTTCTTCTTTGCAAAGGTTAGTGAAATCA
1 TTACTTCAAGTTCTTCTTTGCAAAGGTTAGTGAAATCA
6326186 TT
1 TT
6326188 CTTTCTAAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (38 bp):
TTACTTCAAGTTCTTCTTTGCAAAGGTTAGTGAAATCA
Found at i:6333742 original size:6 final size:6
Alignment explanation
Indices: 6333731--6333776 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
6333721 TGTTCACATG
6333731 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATA
6333777 TATCATTTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
TATACA
Found at i:6337810 original size:34 final size:34
Alignment explanation
Indices: 6337772--6337840 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
6337762 AGAAAACAAA
*
6337772 GATCATATCAATGATTATATCAATGTACCAAGAT
1 GATCATATCAATGATTATATCAATGCACCAAGAT
6337806 GATCATATCAATGATTATATCAATGCACCAAGAT
1 GATCATATCAATGATTATATCAATGCACCAAGAT
6337840 G
1 G
6337841 GTAATGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (34 bp):
GATCATATCAATGATTATATCAATGCACCAAGAT
Found at i:6340500 original size:29 final size:29
Alignment explanation
Indices: 6340450--6340505 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
6340440 ACTCACTACA
*
6340450 TTGTATTTAAACAAATCTTTAACTTATTT
1 TTGTAGTTAAACAAATCTTTAACTTATTT
*
6340479 TTGTAGTTAAATAAA-CTCTTAACTTAT
1 TTGTAGTTAAACAAATCT-TTAACTTAT
6340506 GATTTTCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (29 bp):
TTGTAGTTAAACAAATCTTTAACTTATTT
Found at i:6341699 original size:19 final size:19
Alignment explanation
Indices: 6341677--6341731 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 19
6341667 AAAGATAAAA
6341677 TATAATTAATGTAATAATT
1 TATAATTAATGTAATAATT
*
6341696 TATAA--AAGGTAA-AA--
1 TATAATTAATGTAATAATT
6341710 TATAATTAATGTAATAATT
1 TATAATTAATGTAATAATT
6341729 TAT
1 TAT
6341732 TCCTTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 5 0.17
16 8 0.28
17 8 0.28
19 8 0.28
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (19 bp):
TATAATTAATGTAATAATT
Found at i:6341709 original size:33 final size:33
Alignment explanation
Indices: 6341664--6341731 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
6341654 AAATTTTAAC
6341664 ATAAAAGATAAAATATAATTAATGTAATAATTT
1 ATAAAAGATAAAATATAATTAATGTAATAATTT
*
6341697 ATAAAAGGTAAAATATAATTAATGTAATAATTT
1 ATAAAAGATAAAATATAATTAATGTAATAATTT
6341730 AT
1 AT
6341732 TCCTTTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (33 bp):
ATAAAAGATAAAATATAATTAATGTAATAATTT
Found at i:6363355 original size:15 final size:15
Alignment explanation
Indices: 6363335--6363367 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
6363325 ATAATAAATA
6363335 ATTATTTAAATTTAT
1 ATTATTTAAATTTAT
*
6363350 ATTATTTATATTTAT
1 ATTATTTAAATTTAT
6363365 ATT
1 ATT
6363368 TATATTTGCC
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTATTTAAATTTAT
Found at i:6363536 original size:11 final size:11
Alignment explanation
Indices: 6363520--6363560 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
6363510 GAATATATCA
6363520 CATACCTTGCC
1 CATACCTTGCC
*
6363531 CATACCTTTCC
1 CATACCTTGCC
*
6363542 CATACC-TACC
1 CATACCTTGCC
6363552 CATACCTTG
1 CATACCTTG
6363561 GAAAGGTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.22, C:0.44, G:0.05, T:0.29
Consensus pattern (11 bp):
CATACCTTGCC
Found at i:6364115 original size:18 final size:18
Alignment explanation
Indices: 6364092--6364130 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6364082 TACGACCGTT
* *
6364092 TACGGTATTATTCGCGTA
1 TACGGTACTATTCACGTA
*
6364110 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
6364128 TAC
1 TAC
6364131 AGTAGTTGGG
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:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:6368187 original size:11 final size:11
Alignment explanation
Indices: 6368171--6368213 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
6368161 TATTGAATAT
6368171 CCCATACCTTG
1 CCCATACCTTG
*
6368182 CCCATACCTTT
1 CCCATACCTTG
*
6368193 CCCATACC-TA
1 CCCATACCTTG
6368203 CCCATACCTTG
1 CCCATACCTTG
6368214 GAAAGGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.21, C:0.47, G:0.05, T:0.28
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:6368198 original size:22 final size:21
Alignment explanation
Indices: 6368170--6368212 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
6368160 TTATTGAATA
*
6368170 TCCCATACCTTGCCCATACCTT
1 TCCCATACC-TACCCATACCTT
6368192 TCCCATACCTACCCATACCTT
1 TCCCATACCTACCCATACCTT
6368213 GGAAAGGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.21, C:0.47, G:0.02, T:0.30
Consensus pattern (21 bp):
TCCCATACCTACCCATACCTT
Found at i:6370076 original size:8 final size:8
Alignment explanation
Indices: 6370063--6370139 Score: 57
Period size: 8 Copynumber: 9.5 Consensus size: 8
6370053 TTATTTTAGA
6370063 AAAATTTT
1 AAAATTTT
6370071 AAAATTTT
1 AAAATTTT
*
6370079 -AATTTTT
1 AAAATTTT
** *
6370086 TTATTTTT
1 AAAATTTT
6370094 AAAATTTT
1 AAAATTTT
*
6370102 AAAATTTG
1 AAAATTTT
*
6370110 AAATTTTT
1 AAAATTTT
6370118 ATAAATATTT
1 A-AAAT-TTT
**
6370128 TGAATTTT
1 AAAATTTT
6370136 AAAA
1 AAAA
6370140 ATAATTTTGA
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
7 6 0.11
8 38 0.72
9 6 0.11
10 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (8 bp):
AAAATTTT
Found at i:6370133 original size:19 final size:20
Alignment explanation
Indices: 6370106--6370153 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
6370096 AATTTTAAAA
*
6370106 TTTGAAATTTTTATAAAT-AT
1 TTTG-AATTTTTAAAAATAAT
6370126 TTTGAA-TTTTAAAAATAAT
1 TTTGAATTTTTAAAAATAAT
6370145 TTTGAATTT
1 TTTGAATTT
6370154 ATTTTGTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 9 0.36
19 10 0.40
20 6 0.24
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (20 bp):
TTTGAATTTTTAAAAATAAT
Found at i:6372857 original size:19 final size:19
Alignment explanation
Indices: 6372829--6372865 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6372819 TAACTATTCA
6372829 TAAAAAATTGAAAAAAATT
1 TAAAAAATTGAAAAAAATT
* *
6372848 TAAAACATTGTAAAAAAT
1 TAAAAAATTGAAAAAAAT
6372866 ATAAGAAATA
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:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (19 bp):
TAAAAAATTGAAAAAAATT
Found at i:6373564 original size:5 final size:5
Alignment explanation
Indices: 6373556--6373580 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6373546 ATATATATTA
6373556 TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT
6373581 AAAACATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:6375647 original size:6 final size:6
Alignment explanation
Indices: 6375638--6375662 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6375628 CCGAAGCCGG
6375638 AACAGT AACAGT AACAGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT A
6375663 CGGTACACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:6377581 original size:39 final size:37
Alignment explanation
Indices: 6377514--6377606 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
6377504 ACCAGAATGG
* *
6377514 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
6377553 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
6377590 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
6377607 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:6377969 original size:3 final size:3
Alignment explanation
Indices: 6377961--6378008 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
6377951 ATTCCCACTC
* * * *
6377961 ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA CTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6378009 CTTACCTCAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:6378009 original size:18 final size:18
Alignment explanation
Indices: 6377962--6378010 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
6377952 TTCCCACTCA
*
6377962 TAATAATAATAATAATAC
1 TAATAATAATACTAATAC
6377980 TAATAATAATACTAATAC
1 TAATAATAATACTAATAC
*
6377998 TAATATTAATACT
1 TAATAATAATACT
6378011 TACCTCATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATAATAATACTAATAC
Found at i:6378010 original size:12 final size:12
Alignment explanation
Indices: 6377961--6378008 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
6377951 ATTCCCACTC
*
6377961 ATAATAATAATA
1 ATAATACTAATA
6377973 ATAATACTAATA
1 ATAATACTAATA
6377985 ATAATACTAATA
1 ATAATACTAATA
* *
6377997 CTAATATTAATA
1 ATAATACTAATA
6378009 CTTACCTCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATACTAATA
Found at i:6378749 original size:20 final size:20
Alignment explanation
Indices: 6378715--6378754 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6378705 TTCTATTCTG
*
6378715 TTTCTTTTCTGTTTTGTTTC
1 TTTCTTTTCTGTTTTATTTC
6378735 TTTCTTTTTCT-TTTTATTTC
1 TTTC-TTTTCTGTTTTATTTC
6378755 CTTTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTCTTTTCTGTTTTATTTC
Found at i:6378921 original size:31 final size:28
Alignment explanation
Indices: 6378885--6378952 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
6378875 TTGTCTTTAT
**
6378885 TTAATTTATTTCTTAATATAATATTTATAA
1 TTAATTTATTTAATAATAT-A-ATTTATAA
* *
6378915 TGTAATTAATTTAATAATATACTTTATAA
1 T-TAATTTATTTAATAATATAATTTATAA
6378944 TTAATTTAT
1 TTAATTTAT
6378953 ATATTTATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 8 0.25
30 2 0.06
31 15 0.47
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (28 bp):
TTAATTTATTTAATAATATAATTTATAA
Found at i:6378969 original size:21 final size:20
Alignment explanation
Indices: 6378931--6378969 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
6378921 TAATTTAATA
*
6378931 ATATACTTTATAATTAATTT
1 ATATACTTTATAAATAATTT
*
6378951 ATATATTTATATAAATAAT
1 ATATACTT-TATAAATAAT
6378970 AATATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATACTTTATAAATAATTT
Found at i:6379511 original size:5 final size:5
Alignment explanation
Indices: 6379501--6379561 Score: 88
Period size: 5 Copynumber: 12.0 Consensus size: 5
6379491 TGTTTCTTTT
*
6379501 ATATA ATATA ATATA ATATA ATATA ATATA ATA-A TATAAGA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA -AT-ATA ATATA ATATA
6379552 ATATA ATATA
1 ATATA ATATA
6379562 CTTAATTATT
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
4 1 0.02
5 47 0.90
6 3 0.06
7 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:6381853 original size:26 final size:26
Alignment explanation
Indices: 6381806--6381858 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
6381796 TTGAAAGGAA
* *
6381806 ATTTTAAAAATGTTCTAAATATATTTT
1 ATTTAAAAAATATTCTAAATAT-TTTT
*
6381833 ATTTAAAAAATATTC-ATATATTTTT
1 ATTTAAAAAATATTCTAAATATTTTT
6381858 A
1 A
6381859 ATAATTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 5 0.22
27 13 0.57
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (26 bp):
ATTTAAAAAATATTCTAAATATTTTT
Found at i:6381948 original size:11 final size:11
Alignment explanation
Indices: 6381932--6381961 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6381922 TTCACTTTCA
6381932 ATTATTTTAAC
1 ATTATTTTAAC
*
6381943 ATTATTTTAAT
1 ATTATTTTAAC
6381954 ATTATTTT
1 ATTATTTT
6381962 TTCGTACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTATTTTAAC
Found at i:6385396 original size:16 final size:17
Alignment explanation
Indices: 6385364--6385399 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
6385354 AACTTATTGA
6385364 TCATTTCTGCTCTCTGTT
1 TCATTTCTGC-CTCTGTT
6385382 TCATTTCTG-CTCTGTT
1 TCATTTCTGCCTCTGTT
6385398 TC
1 TC
6385400 GGATTCTGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.06, C:0.28, G:0.11, T:0.56
Consensus pattern (17 bp):
TCATTTCTGCCTCTGTT
Found at i:6398164 original size:52 final size:51
Alignment explanation
Indices: 6398093--6398301 Score: 293
Period size: 52 Copynumber: 4.1 Consensus size: 51
6398083 ATCAAGTGAT
*
6398093 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGT-G
* *
6398145 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
* *
6398196 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC-----
1 -AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
*
6398243 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC-AAGTG
6398295 ATAAGTG
1 A-AAGTG
6398302 GCTACACTTA
Statistics
Matches: 143, Mismatches: 6, Indels: 15
0.87 0.04 0.09
Matches are distributed among these distances:
46 43 0.30
51 1 0.01
52 94 0.66
53 5 0.03
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
Found at i:6398269 original size:98 final size:99
Alignment explanation
Indices: 6398085--6398301 Score: 301
Period size: 98 Copynumber: 2.1 Consensus size: 99
6398075 TACTTCTGAT
*
6398085 CAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGT
1 CAAGTGA-AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC-----GAAAGT
* *
6398150 GATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
60 GATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGA
* *
6398190 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC-AAAGTGATAAG
1 CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACGAAAGTGATAAG
*
6398254 TGATAGCTTTAGCTACACTTATCTGATCAAGAGA
66 TGATAGCTTCAGCTACACTTATCTGATCAAGAGA
*
6398288 CAAAGTGATAAGTG
1 C-AAGTGAAAAGTG
6398302 GCTACACTTA
Statistics
Matches: 104, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
98 43 0.41
99 11 0.11
104 43 0.41
105 7 0.07
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (99 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACGAAAGTGATAAG
TGATAGCTTCAGCTACACTTATCTGATCAAGAGA
Found at i:6398274 original size:46 final size:44
Alignment explanation
Indices: 6398197--6398412 Score: 190
Period size: 37 Copynumber: 5.3 Consensus size: 44
6398187 TGACAAGTGA
*
6398197 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTT--GCTACACTTATCTGATCAAGAGAC
6398243 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGC-TT-GCTACACTTATCTGATCAAGAGAC
*
6398289 AAAGTGATAA--G-T-G---GCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
* *
6398326 AAAGTGATAA--G-T-G---GCTACACTTATGTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
*
6398363 AAAGTGAT-AG-G-T-G---GCTACACTTATCTGATC-AGGGAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
6398399 -AAGTGATAAGTGAT
1 AAAGTGATAAGTGAT
6398413 CATACGTAAG
Statistics
Matches: 158, Mismatches: 7, Indels: 18
0.86 0.04 0.10
Matches are distributed among these distances:
35 7 0.04
36 7 0.04
37 87 0.55
38 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 51 0.32
47 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.26
Consensus pattern (44 bp):
AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
Found at i:6398309 original size:37 final size:37
Alignment explanation
Indices: 6398265--6398410 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
6398255 GATAGCTTTA
*
6398265 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
6398302 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
* *
6398339 GCTACACTTATGTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
6398376 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
6398411 ATCATACGTA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 87 0.85
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:6402918 original size:8 final size:8
Alignment explanation
Indices: 6402905--6402929 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6402895 TTACAAATAA
6402905 TAATAAAC
1 TAATAAAC
6402913 TAATAAAC
1 TAATAAAC
6402921 TAATAAAC
1 TAATAAAC
6402929 T
1 T
6402930 CATTTTCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (8 bp):
TAATAAAC
Found at i:6410854 original size:21 final size:22
Alignment explanation
Indices: 6410812--6410856 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
6410802 AGCTGAAATT
6410812 GAGAGTGCAAGAGCAGCAGTTCA
1 GAGAGTGCAAGAG-AGCAGTTCA
* *
6410835 GAGAGTGGAAGAG-GCCGTTCA
1 GAGAGTGCAAGAGAGCAGTTCA
6410856 G
1 G
6410857 GAGCAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
23 12 0.60
ACGTcount: A:0.31, C:0.16, G:0.40, T:0.13
Consensus pattern (22 bp):
GAGAGTGCAAGAGAGCAGTTCA
Found at i:6414471 original size:4 final size:4
Alignment explanation
Indices: 6414462--6414488 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
6414452 TGCTTCTAAT
6414462 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
6414489 TTCAGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:6424819 original size:22 final size:22
Alignment explanation
Indices: 6424794--6424844 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
6424784 TGTTTTCTCC
* *
6424794 TTATTTTGCTA-TAATTTTATTT
1 TTATTTTGCAACT-ATTTTATTG
*
6424816 TTATGTTGCAACTATTTTATTG
1 TTATTTTGCAACTATTTTATTG
6424838 TTATTTT
1 TTATTTT
6424845 TTAAATATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.22, C:0.06, G:0.08, T:0.65
Consensus pattern (22 bp):
TTATTTTGCAACTATTTTATTG
Found at i:6424909 original size:30 final size:30
Alignment explanation
Indices: 6424875--6424933 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
6424865 ATTTTATTGC
* *
6424875 TAATTTTGTTATTATTTTAAAGGTATTTGT
1 TAATTTTATTATTATTTTAAACGTATTTGT
*
6424905 TAATTTTATTATTATTTTATACGTATTTG
1 TAATTTTATTATTATTTTAAACGTATTTG
6424934 CTTGTTAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (30 bp):
TAATTTTATTATTATTTTAAACGTATTTGT
Found at i:6429792 original size:19 final size:21
Alignment explanation
Indices: 6429760--6429804 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
6429750 GATTTCTAAT
6429760 TATTTTTATCTTGAAA-TAAA
1 TATTTTTATCTTGAAATTAAA
*
6429780 TATTTTT-TTTTGAAATTAAA
1 TATTTTTATCTTGAAATTAAA
6429800 -ATTTT
1 TATTTT
6429805 ACTCATCCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (21 bp):
TATTTTTATCTTGAAATTAAA
Found at i:6430134 original size:12 final size:13
Alignment explanation
Indices: 6430109--6430140 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
6430099 TGCTCTTATT
6430109 AAAAATTAGAAAA
1 AAAAATTAGAAAA
*
6430122 AAAAATTATAAAA
1 AAAAATTAGAAAA
6430135 AAAAAT
1 AAAAAT
6430141 AAATTTTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (13 bp):
AAAAATTAGAAAA
Found at i:6430396 original size:10 final size:10
Alignment explanation
Indices: 6430381--6430510 Score: 69
Period size: 10 Copynumber: 13.4 Consensus size: 10
6430371 TGTACGATAT
6430381 TTTTTTATAA
1 TTTTTTATAA
6430391 TTTTTTATAA
1 TTTTTTATAA
**
6430401 -AATTTAT-A
1 TTTTTTATAA
6430409 TTTCTTTAT-A
1 TTT-TTTATAA
*
6430419 TTTTGTATAA
1 TTTTTTATAA
*
6430429 TTTTCTTACAA
1 TTTT-TTATAA
*
6430440 --CTTTATAA
1 TTTTTTATAA
**
6430448 AATTTTATAA
1 TTTTTTATAA
6430458 TTTTTT-T-A
1 TTTTTTATAA
*
6430466 TATTTCTAT-A
1 T-TTTTTATAA
*
6430476 TATTTTATAA
1 TTTTTTATAA
*
6430486 TTTTTTATGA
1 TTTTTTATAA
*
6430496 TTTTTATAAAA
1 TTTTT-TATAA
6430507 TTTT
1 TTTT
6430511 ACAATTTATA
Statistics
Matches: 91, Mismatches: 19, Indels: 19
0.71 0.15 0.15
Matches are distributed among these distances:
8 8 0.09
9 20 0.22
10 52 0.57
11 11 0.12
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:6430454 original size:57 final size:56
Alignment explanation
Indices: 6430384--6430511 Score: 134
Period size: 57 Copynumber: 2.2 Consensus size: 56
6430374 ACGATATTTT
** *
6430384 TTTATAATTTTTTATAA-AATTTATATTTCTTTATATTTTGTATAATTTTCTTA-CAAC
1 TTTATAAAATTTTATAATAATTTATATTTCTATATA-TTT-TATAATTTT-TTATCAAC
** * **
6430441 TTTATAAAATTTTATAATTTTTTTATATTTCTATATATTTTATAATTTTTTATGATT
1 TTTATAAAATTTTATAA-TAATTTATATTTCTATATATTTTATAATTTTTTATCAAC
6430498 TTTATAAAATTTTA
1 TTTATAAAATTTTA
6430512 CAATTTATAT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
56 3 0.05
57 39 0.65
58 3 0.05
59 15 0.25
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (56 bp):
TTTATAAAATTTTATAATAATTTATATTTCTATATATTTTATAATTTTTTATCAAC
Found at i:6430517 original size:19 final size:19
Alignment explanation
Indices: 6430441--6430522 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 19
6430431 TTCTTACAAC
6430441 TTTATAAAATTTTATAATT
1 TTTATAAAATTTTATAATT
* *
6430460 TTT-TTATATTTCTAT-ATAT
1 TTTATAAAATTT-TATAAT-T
** *
6430479 TTTATAATTTTTTATGATT
1 TTTATAAAATTTTATAATT
*
6430498 TTTATAAAATTTTACAATT
1 TTTATAAAATTTTATAATT
*
6430517 TATATA
1 TTTATA
6430523 TATTTTTTCT
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
18 8 0.16
19 34 0.68
20 8 0.16
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (19 bp):
TTTATAAAATTTTATAATT
Found at i:6430517 original size:57 final size:59
Alignment explanation
Indices: 6430402--6430527 Score: 159
Period size: 57 Copynumber: 2.2 Consensus size: 59
6430392 TTTTTATAAA
* *
6430402 ATTTATATTTCTTTATATTTTGTATAATTTTCTTACAACTTTATAAAATTTTATAATTT
1 ATTTATATTTCTATATATTTTGTATAATTTTCTTACAACTTTATAAAATTTTACAATTT
* * **
6430461 TTTTATATTTCTATATA-TTT-TATAATTTT-TTATGATTTTTATAAAATTTTACAATTT
1 ATTTATATTTCTATATATTTTGTATAATTTTCTTA-CAACTTTATAAAATTTTACAATTT
*
6430518 ATATATATTT
1 ATTTATATTT
6430528 TTTCTATTTG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
56 3 0.05
57 37 0.64
58 3 0.05
59 15 0.26
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (59 bp):
ATTTATATTTCTATATATTTTGTATAATTTTCTTACAACTTTATAAAATTTTACAATTT
Found at i:6433967 original size:21 final size:21
Alignment explanation
Indices: 6433943--6433985 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
6433933 AAGTTTGCTT
6433943 TCATGAGTTAATTGAAACAAA
1 TCATGAGTTAATTGAAACAAA
6433964 TCATGAGTTAATTGAAACAAA
1 TCATGAGTTAATTGAAACAAA
6433985 T
1 T
6433986 GCTTATTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (21 bp):
TCATGAGTTAATTGAAACAAA
Found at i:6442868 original size:135 final size:134
Alignment explanation
Indices: 6442627--6442899 Score: 492
Period size: 135 Copynumber: 2.0 Consensus size: 134
6442617 TGTCTGCTGA
6442627 AGAGTTGAAACTCAATAATCTTAGTATGAGTTCTTTTCCTTGTGCTTAAAATGTGTATATTTCTG
1 AGAGTTGAAACTCAATAATCTTAGTATGAGTTCTTTTCCTTGTGCTTAAAATGTGTATATTTCTG
* *
6442692 TAGGAGGTTTCTTCTGCAAGATTTTGATACAACCCTTGCTTTTGTTAATCATGAAAGGAAACAAA
66 TAGGAGATTTCTTCAGCAAGATTTTGATACAACCCTTGCTTTTGTTAATCATGAAAGGAAACAAA
6442757 GAAC
131 GAAC
* * *
6442761 AGAGTTGAAACTCAATAATTTTATTATTGAGTTCTTTTCCTTGTGCTTAAAATGTGTATATTTTT
1 AGAGTTGAAACTCAATAATCTTAGTA-TGAGTTCTTTTCCTTGTGCTTAAAATGTGTATATTTCT
6442826 GTAGGAGATTTCTTCAGCAAGATTTTGATACAACCCTTGCTTTTGTTAATCATGAAAGGAAACAA
65 GTAGGAGATTTCTTCAGCAAGATTTTGATACAACCCTTGCTTTTGTTAATCATGAAAGGAAACAA
6442891 AGAAC
130 AGAAC
6442896 AGAG
1 AGAG
6442900 GTACGTCTTC
Statistics
Matches: 133, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
134 24 0.18
135 109 0.82
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.38
Consensus pattern (134 bp):
AGAGTTGAAACTCAATAATCTTAGTATGAGTTCTTTTCCTTGTGCTTAAAATGTGTATATTTCTG
TAGGAGATTTCTTCAGCAAGATTTTGATACAACCCTTGCTTTTGTTAATCATGAAAGGAAACAAA
GAAC
Found at i:6459984 original size:19 final size:19
Alignment explanation
Indices: 6459960--6460003 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
6459950 ACTAAATATT
*
6459960 TTAATATTTTATTATCTT-A
1 TTAATATATTATTA-CTTAA
6459979 TTAATATATTATTACTTAA
1 TTAATATATTATTACTTAA
6459998 TTAATA
1 TTAATA
6460004 ATAAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
TTAATATATTATTACTTAA
Found at i:6471172 original size:43 final size:43
Alignment explanation
Indices: 6471111--6471199 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
6471101 GTCACCTATA
6471111 GAATTAATAAAATAATTCCGGATTTTTTGTGGGAACATAATTG
1 GAATTAATAAAATAATTCCGGATTTTTTGTGGGAACATAATTG
6471154 GAATTAATAAAATAATTCCGGATTTTTTGTGGGAACATAATTG
1 GAATTAATAAAATAATTCCGGATTTTTTGTGGGAACATAATTG
6471197 GAA
1 GAA
6471200 GGAGCAGAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (43 bp):
GAATTAATAAAATAATTCCGGATTTTTTGTGGGAACATAATTG
Found at i:6475298 original size:17 final size:18
Alignment explanation
Indices: 6475276--6475315 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
6475266 AATTTGTAGC
6475276 AAAAATATT-TTAAATTA
1 AAAAATATTGTTAAATTA
* *
6475293 AAAAATGTTGTTGAATTA
1 AAAAATATTGTTAAATTA
6475311 AAAAA
1 AAAAA
6475316 AAGAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (18 bp):
AAAAATATTGTTAAATTA
Found at i:6475719 original size:21 final size:21
Alignment explanation
Indices: 6475693--6475747 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
6475683 AACAGCGGTG
* *
6475693 GCGGTGAGATTAGTTCCTGTA
1 GCGGTGAGATTAGGTACTGTA
*
6475714 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
6475735 GCGGTGAGATTAG
1 GCGGTGAGATTAG
6475748 AAACAATGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.11, G:0.40, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:6477187 original size:2 final size:2
Alignment explanation
Indices: 6477180--6477213 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
6477170 TCAACTTCCA
*
6477180 TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6477214 CCTTCCACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:6480180 original size:25 final size:25
Alignment explanation
Indices: 6480152--6480201 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
6480142 ATCCACATAG
6480152 TAATTTATACAAATTGAATAAAGAA
1 TAATTTATACAAATTGAATAAAGAA
6480177 TAATTTATACAAATTGAATAAAGAA
1 TAATTTATACAAATTGAATAAAGAA
6480202 AATCCGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (25 bp):
TAATTTATACAAATTGAATAAAGAA
Found at i:6489726 original size:27 final size:27
Alignment explanation
Indices: 6489687--6489741 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
6489677 AGAGGGAAAA
6489687 ATTAAAAAGAAAAGAAAAAATGAAACC
1 ATTAAAAAGAAAAGAAAAAATGAAACC
* *
6489714 ATTAAAAATAAAAGAAAAACTGAAACC
1 ATTAAAAAGAAAAGAAAAAATGAAACC
6489741 A
1 A
6489742 ACAATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (27 bp):
ATTAAAAAGAAAAGAAAAAATGAAACC
Found at i:6502799 original size:16 final size:14
Alignment explanation
Indices: 6502778--6502812 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
6502768 CAACTCTAAT
6502778 ATAAAATTATATATA
1 ATAAAATTA-ATATA
6502793 CATAAAATTAATATA
1 -ATAAAATTAATATA
6502808 ATAAA
1 ATAAA
6502813 TTCAGTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 5 0.26
16 9 0.47
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAAATTAATATA
Found at i:6508030 original size:20 final size:20
Alignment explanation
Indices: 6508005--6508042 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6507995 ATGTATTTTA
*
6508005 AATTTTTTAATTTTTTTAAT
1 AATTTTTTAATTTATTTAAT
6508025 AATTTTTTAATTTATTTA
1 AATTTTTTAATTTATTTA
6508043 TTCTAATAAG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
AATTTTTTAATTTATTTAAT
Found at i:6508042 original size:9 final size:9
Alignment explanation
Indices: 6508000--6508042 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
6507990 GAATTATGTA
*
6508000 TTTTAAATT
1 TTTTAATTT
6508009 TTTTAATTT
1 TTTTAATTT
6508018 TTTTAATAATT
1 TTTTAAT--TT
6508029 TTTTAATTT
1 TTTTAATTT
*
6508038 ATTTA
1 TTTTA
6508043 TTCTAATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 21 0.70
11 9 0.30
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTAATTT
Found at i:6508358 original size:21 final size:21
Alignment explanation
Indices: 6508333--6508385 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
6508323 AGCGGTGGTT
* *
6508333 GTGAGATTAGTTACTGTAGCG
1 GTGAGATTAGATACTGTAGCA
* *
6508354 GTGAGATTGGATATTGTAGCA
1 GTGAGATTAGATACTGTAGCA
6508375 GTGAGATTAGA
1 GTGAGATTAGA
6508386 AACAATGGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.06, G:0.34, T:0.32
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCA
Found at i:6514003 original size:20 final size:20
Alignment explanation
Indices: 6513978--6514027 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
6513968 TGGCTTAAAA
6513978 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
6513998 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
6514015 GTGGTAGTGGATT
1 TTGGTAGTGGATT
6514028 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:6518632 original size:20 final size:20
Alignment explanation
Indices: 6518607--6518656 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
6518597 TGGCTTAAAA
6518607 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
6518627 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
6518644 GTGGTAGTGGATT
1 TTGGTAGTGGATT
6518657 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:6524503 original size:26 final size:26
Alignment explanation
Indices: 6524473--6524526 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
6524463 ATTTTCAGAA
6524473 TTTTTGGTTTACCCAATAAGTACAGT
1 TTTTTGGTTTACCCAATAAGTACAGT
6524499 TTTTTGGTTTACCCAATAAGTACAGT
1 TTTTTGGTTTACCCAATAAGTACAGT
6524525 TT
1 TT
6524527 ATTCTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (26 bp):
TTTTTGGTTTACCCAATAAGTACAGT
Found at i:6525497 original size:8 final size:9
Alignment explanation
Indices: 6525468--6525501 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
6525458 TCCCATTTTT
6525468 ATTTTGCCA
1 ATTTTGCCA
*
6525477 ATTTTGGCA
1 ATTTTGCCA
6525486 ATTTT-CCA
1 ATTTTGCCA
6525494 ATTTTGCC
1 ATTTTGCC
6525502 CTTATTTCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.47
Consensus pattern (9 bp):
ATTTTGCCA
Found at i:6530130 original size:12 final size:12
Alignment explanation
Indices: 6530115--6530145 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6530105 TTCTCTTTTA
6530115 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
6530127 TTTTTCTTTCTC
1 TTTTTCTTTCCC
6530139 TTTTTCT
1 TTTTTCT
6530146 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:6530246 original size:16 final size:16
Alignment explanation
Indices: 6530225--6530255 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6530215 TTTATTATTT
6530225 TATTAACATAATATAA
1 TATTAACATAATATAA
*
6530241 TATTAATATAATATA
1 TATTAACATAATATA
6530256 TTAAAATATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAACATAATATAA
Found at i:6531298 original size:22 final size:22
Alignment explanation
Indices: 6531236--6531288 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
6531226 ACTAATGAAC
6531236 AGAGAGCACTGAAGTGCTATAG
1 AGAGAGCACTGAAGTGCTATAG
6531258 AGAGAGCACTGAAGTGCTATAG
1 AGAGAGCACTGAAGTGCTATAG
6531280 AGAGAGCAC
1 AGAGAGCAC
6531289 AAATGTGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.15, G:0.32, T:0.15
Consensus pattern (22 bp):
AGAGAGCACTGAAGTGCTATAG
Found at i:6531331 original size:25 final size:25
Alignment explanation
Indices: 6531297--6531434 Score: 213
Period size: 25 Copynumber: 5.5 Consensus size: 25
6531287 ACAAATGTGC
* *
6531297 TAATCAGAGAGCATTGGCATGCTAA
1 TAATCAGAGAGCACTGGCGTGCTAA
*
6531322 TAATCAGAGAGCACTGGCTTGCTAA
1 TAATCAGAGAGCACTGGCGTGCTAA
*
6531347 TATTCAGAGAGCACTGGCGTGCTAA
1 TAATCAGAGAGCACTGGCGTGCTAA
*
6531372 TAATCAGAGAGCACTGACGTGCTAA
1 TAATCAGAGAGCACTGGCGTGCTAA
*
6531397 TATTCAGAGAGCACTGGCGTGCTAA
1 TAATCAGAGAGCACTGGCGTGCTAA
*
6531422 TAATTAGAGAGCA
1 TAATCAGAGAGCA
6531435 TGCTGAGGTC
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 103 1.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.23
Consensus pattern (25 bp):
TAATCAGAGAGCACTGGCGTGCTAA
Found at i:6534725 original size:25 final size:24
Alignment explanation
Indices: 6534697--6534793 Score: 113
Period size: 25 Copynumber: 3.8 Consensus size: 24
6534687 TTTTTTTGGG
6534697 GGGGTTAGGTTTTTCTTTTTTTTTT
1 GGGGTTAGGTTTTT-TTTTTTTTTT
*
6534722 GGGGTTAGGTTTTTTCTTTTTTTTGGGG
1 GGGGTTAGGTTTTTT-TTTTTTTT---T
6534750 GGGGTTAGGTTTTTTTCTTCTTTTTT
1 GGGGTTAGGTTTTTTT-TT-TTTTTT
*
6534776 TGGGTTAGGTTTTTTTTT
1 GGGGTTAGGTTTTTTTTT
6534794 GGGAGGGCTT
Statistics
Matches: 63, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
24 1 0.02
25 24 0.38
26 15 0.24
27 1 0.02
28 17 0.27
29 5 0.08
ACGTcount: A:0.04, C:0.04, G:0.28, T:0.64
Consensus pattern (24 bp):
GGGGTTAGGTTTTTTTTTTTTTTT
Found at i:6534725 original size:26 final size:24
Alignment explanation
Indices: 6534687--6534793 Score: 97
Period size: 26 Copynumber: 4.2 Consensus size: 24
6534677 GGTTTCTTGA
*
6534687 TTTTTTTGGGGGGGTTAGGTTTTT
1 TTTTTTTTGGGGGGTTAGGTTTTT
**
6534711 CTTTTTTTTTTGGGGTTAGGTTTTTT
1 -TTTTTTTTGGGGGGTTAGG-TTTTT
6534737 CTTTTTTTTGGGGGGGGTTAGGTTTTT
1 -TTTTTTTT--GGGGGGTTAGGTTTTT
***
6534764 TTCTTCTTTTTTTGGGTTAGGTTTTT
1 TT-TT-TTTTGGGGGGTTAGGTTTTT
6534790 TTTT
1 TTTT
6534794 GGGAGGGCTT
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
25 18 0.26
26 31 0.45
27 7 0.10
28 13 0.19
ACGTcount: A:0.04, C:0.04, G:0.28, T:0.64
Consensus pattern (24 bp):
TTTTTTTTGGGGGGTTAGGTTTTT
Found at i:6535219 original size:27 final size:28
Alignment explanation
Indices: 6535181--6535300 Score: 126
Period size: 27 Copynumber: 4.2 Consensus size: 28
6535171 AACTTGACAC
6535181 TTTT-TCCTAATTTGGTACCTAAACTTT
1 TTTTGTCCTAATTTGGTACCTAAACTTT
6535208 TTTTGTCC-AATTTGGTATCC-AAACTTGACACT
1 TTTTGTCCTAATTTGGTA-CCTAAACTT-----T
6535240 TTTT-TCCTAATTTGGTACCTAAACTTTT
1 TTTTGTCCTAATTTGGTACCTAAAC-TTT
6535268 TTTTGTCC-AATTTGGTACCTAATA-TTT
1 TTTTGTCCTAATTTGGTACCTAA-ACTTT
6535295 TTTTGT
1 TTTTGT
6535301 TTGATTTGGT
Statistics
Matches: 81, Mismatches: 0, Indels: 24
0.77 0.00 0.23
Matches are distributed among these distances:
27 28 0.35
28 24 0.30
29 4 0.05
31 5 0.06
32 18 0.22
33 2 0.02
ACGTcount: A:0.22, C:0.17, G:0.10, T:0.51
Consensus pattern (28 bp):
TTTTGTCCTAATTTGGTACCTAAACTTT
Found at i:6535252 original size:32 final size:32
Alignment explanation
Indices: 6535171--6535265 Score: 116
Period size: 32 Copynumber: 3.2 Consensus size: 32
6535161 TTGATACTTG
6535171 AACTTGACAC-TTTTTCCTAATTTGGTACCTA
1 AACTTGACACTTTTTTCCTAATTTGGTACCTA
6535202 AACTT-----TTTTTGTCC-AATTTGGTATCC-A
1 AACTTGACACTTTTT-TCCTAATTTGGTA-CCTA
6535229 AACTTGACACTTTTTTCCTAATTTGGTACCTA
1 AACTTGACACTTTTTTCCTAATTTGGTACCTA
6535261 AACTT
1 AACTT
6535266 TTTTTTGTCC
Statistics
Matches: 54, Mismatches: 0, Indels: 19
0.74 0.00 0.26
Matches are distributed among these distances:
27 19 0.35
28 5 0.09
31 10 0.19
32 20 0.37
ACGTcount: A:0.25, C:0.21, G:0.09, T:0.44
Consensus pattern (32 bp):
AACTTGACACTTTTTTCCTAATTTGGTACCTA
Found at i:6535259 original size:59 final size:59
Alignment explanation
Indices: 6535171--6535284 Score: 212
Period size: 59 Copynumber: 1.9 Consensus size: 59
6535161 TTGATACTTG
6535171 AACTTGACACTTTTTCCTAATTTGGTACCTAAAC-TTTTTTTGTCCAATTTGGTATCCA
1 AACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTTGTCCAATTTGGTATCCA
6535229 AACTTGACACTTTTTTCCTAATTTGGTACCTAAACTTTTTTTTGTCCAATTTGGTA
1 AACTTGACAC-TTTTTCCTAATTTGGTACCTAAACTTTTTTTTGTCCAATTTGGTA
6535285 CCTAATATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
58 10 0.19
59 24 0.44
60 20 0.37
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46
Consensus pattern (59 bp):
AACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTTGTCCAATTTGGTATCCA
Found at i:6535279 original size:28 final size:28
Alignment explanation
Indices: 6535181--6535298 Score: 127
Period size: 28 Copynumber: 4.1 Consensus size: 28
6535171 AACTTGACAC
6535181 TTTTTCCTAATTTGGTACCTAAACTTTT
1 TTTTTCCTAATTTGGTACCTAAACTTTT
* *
6535209 TTTGTCC-AATTTGGTATCC-AAACTTGACACT
1 TTTTTCCTAATTTGGTA-CCTAAACTT----TT
6535240 TTTTTCCTAATTTGGTACCTAAACTTTT
1 TTTTTCCTAATTTGGTACCTAAACTTTT
6535268 TTTTGTCC-AATTTGGTACCTAATA-TTTT
1 TTTT-TCCTAATTTGGTACCTAA-ACTTTT
6535296 TTT
1 TTT
6535299 GTTTGATTTG
Statistics
Matches: 77, Mismatches: 4, Indels: 18
0.78 0.04 0.18
Matches are distributed among these distances:
27 15 0.19
28 34 0.44
29 4 0.05
31 9 0.12
32 15 0.19
ACGTcount: A:0.22, C:0.18, G:0.09, T:0.51
Consensus pattern (28 bp):
TTTTTCCTAATTTGGTACCTAAACTTTT
Found at i:6537184 original size:16 final size:17
Alignment explanation
Indices: 6537150--6537187 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
6537140 AAATTTCATT
6537150 TAAAGTATAAAACAAAA
1 TAAAGTATAAAACAAAA
*
6537167 TAAATTATAAAA-AAAA
1 TAAAGTATAAAACAAAA
6537183 TAAAG
1 TAAAG
6537188 ATGAAAGGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (17 bp):
TAAAGTATAAAACAAAA
Found at i:6545672 original size:21 final size:21
Alignment explanation
Indices: 6545648--6545689 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6545638 TCCATTGTTC
*
6545648 AATAAGTCTTTAGTTATAGAT
1 AATAAGTCTTCAGTTATAGAT
*
6545669 AATAAGTCTTCAGTTTTAGAT
1 AATAAGTCTTCAGTTATAGAT
6545690 TTTTTTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (21 bp):
AATAAGTCTTCAGTTATAGAT
Found at i:6546623 original size:14 final size:14
Alignment explanation
Indices: 6546604--6546631 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6546594 CATTATTTAT
6546604 TTAATAATTGTAGA
1 TTAATAATTGTAGA
6546618 TTAATAATTGTAGA
1 TTAATAATTGTAGA
6546632 ATATATAAAA
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:0.14, T:0.43
Consensus pattern (14 bp):
TTAATAATTGTAGA
Found at i:6547075 original size:6 final size:6
Alignment explanation
Indices: 6547042--6547073 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
6547032 ATGACATGTT
*
6547042 GAGACA GAGACA GAGACA GAGACA GAAACA GA
1 GAGACA GAGACA GAGACA GAGACA GAGACA GA
6547074 AAAGGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.53, C:0.16, G:0.31, T:0.00
Consensus pattern (6 bp):
GAGACA
Found at i:6548126 original size:6 final size:6
Alignment explanation
Indices: 6548115--6548144 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
6548105 TGATTAATGC
*
6548115 ATTCAT ATTCAT ATTCAT ATTCTT ATTCAT
1 ATTCAT ATTCAT ATTCAT ATTCAT ATTCAT
6548145 GTTATATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (6 bp):
ATTCAT
Found at i:6548900 original size:21 final size:21
Alignment explanation
Indices: 6548874--6548925 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
6548864 AATTAGTTGT
* *
6548874 TTTAGGGTTTACGGTTAGTGG
1 TTTAGGATTTACAGTTAGTGG
**
6548895 TTTAGGATTTGTAGTTAGTGG
1 TTTAGGATTTACAGTTAGTGG
6548916 TTTAGGATTT
1 TTTAGGATTT
6548926 TAGGGTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.17, C:0.02, G:0.33, T:0.48
Consensus pattern (21 bp):
TTTAGGATTTACAGTTAGTGG
Found at i:6549408 original size:126 final size:126
Alignment explanation
Indices: 6549183--6549554 Score: 681
Period size: 126 Copynumber: 3.0 Consensus size: 126
6549173 TTAGGTTAAT
6549183 TGAGTAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAAT
1 TGAGTAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAAT
* *
6549248 TTTGGAAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAATAGTTCGTAGAAAAATAATTC
66 TTCGGAAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGTTCGTAGAAAAATAATTC
*
6549309 TGAGTAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTATCAGCAAAAT
1 TGAGTAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAAT
*
6549374 TTCGGAAAAAAGCTCCCACGTGAACGCGCTTTTGCTACAGTAGTTCGTAGAAAAATAATTC
66 TTCGGAAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGTTCGTAGAAAAATAATTC
*
6549435 TGAGTAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGCACTGTCAGCAAAAT
1 TGAGTAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAAT
* *
6549500 TTCAGAAAAAAGCTCCCACATGGACGCGCTTTTGCTACAGTAGTTCGTAGAAAAA
66 TTCGGAAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGTTCGTAGAAAAA
6549555 CTGAGGCTAT
Statistics
Matches: 237, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
126 237 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (126 bp):
TGAGTAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAAT
TTCGGAAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGTTCGTAGAAAAATAATTC
Found at i:6551957 original size:13 final size:14
Alignment explanation
Indices: 6551941--6551976 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
6551931 CAATCTCATA
6551941 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
6551954 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
6551967 TCTC-ATTTCA
1 TCTCAATTTCA
6551977 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:6551966 original size:18 final size:19
Alignment explanation
Indices: 6551928--6551968 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
6551918 TGGTTCATGT
6551928 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
6551947 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
6551965 TTTC
1 TTTC
6551969 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:6552627 original size:15 final size:15
Alignment explanation
Indices: 6552603--6552655 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
6552593 ATATATATAT
*
6552603 TATAATTTCAATCAA
1 TATAAATTCAATCAA
6552618 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* * *
6552633 AATGATTTCAATCAA
1 TATAAATTCAATCAA
6552648 TATAAATT
1 TATAAATT
6552656 TGATAAATTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:6553527 original size:19 final size:19
Alignment explanation
Indices: 6553503--6553541 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
6553493 AATACTTATT
*
6553503 TATTATTTATACATGTGTA
1 TATTATTAATACATGTGTA
6553522 TATTATTAATACATGTGTA
1 TATTATTAATACATGTGTA
6553541 T
1 T
6553542 CTATTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (19 bp):
TATTATTAATACATGTGTA
Found at i:6553549 original size:19 final size:19
Alignment explanation
Indices: 6553506--6553549 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
6553496 ACTTATTTAT
6553506 TATTT-ATACATGTGTATA
1 TATTTAATACATGTGTATA
*
6553524 T-TATTAATACATGTGTATC
1 TAT-TTAATACATGTGTATA
6553543 TATTTAA
1 TATTTAA
6553550 AATCATACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 1 0.05
18 3 0.14
19 17 0.77
20 1 0.05
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (19 bp):
TATTTAATACATGTGTATA
Found at i:6555337 original size:512 final size:513
Alignment explanation
Indices: 6554372--6555403 Score: 2021
Period size: 512 Copynumber: 2.0 Consensus size: 513
6554362 AAATTGACGG
*
6554372 TACCTTTATGTACGGTAGATATACCCATCAGCTATTGCTAGCTGTGGCACAGGATGGCAGTGGAA
1 TACCTTTATGTACGGTAGATATACCCATCAGCTATTGCTAGCTGTGGCACAGGATGACAGTGGAA
*
6554437 GAATCCTTCCAATTGCGTTTGCAATAACACCAGGGGAGTCAGCTGATGATTGAGATTTCTTTTTT
66 GAATCCTTCCAATTGCGTTTGCAATAACACCAGGGGAGTCAGCTGATGATTGAGATTTCTTTTTG
6554502 TCTAGGCTAAGGAGGCATGTTTGCCCCCAACCTAATATCTGTGTCATATCAGATCGGGGCACCGA
131 TCTAGGCTAAGGAGGCATGTTTGCCCCCAACCTAATATCTGTGTCATATCAGATCGGGGCACCGA
*
6554567 AATACTAGCCGCAATTGCGCGACAGGGAAGCATGTGGCATCACACACACCATCGGTATTGCCTAA
196 AATACTAGCCGCAATTGCGCAACAGGGAAGCATGTGGCATCACACACACCATCGGTATTGCCTAA
6554632 GGTACGTTGCGTCCAACTACCACGGGCAATTTAATTCTACAACTGAAAAATGACAAGTAACCAAC
261 GGTACGTTGCGTCCAACTACCACGGGCAATTTAATTCTACAACTGAAAAATGACAAGTAACCAAC
6554697 ATAGGTATGTAATATCTATTAATATAATTTCGTTTGTAATACTGAATTTATTTTAACTGGAAATG
326 ATAGGTATGTAATATCTATTAATATAATTTCGTTTGTAATACTGAATTTATTTTAACTGGAAATG
*
6554762 TGGTATGTAATTTTCGCTATCAACTTATATTGGTAGGGTATGAGATAAGTAAGGATCATTTCCAT
391 TGGTATGTAATTTTCGCTATCAACTTATATTGGTAGGGTATGAGATAAGTAAAGATCATTTCCAT
6554827 GAAATGTTGGCGATTCTGCGTTCGGATAACGAAGAAGGAGCAAACTACCTATGTAATA
456 GAAATGTTGGCGATTCTGCGTTCGGATAACGAAGAAGGAGCAAACTACCTATGTAATA
6554885 TACCTTTATGTACGGTAGATATACCCATCAGCTATTGCTAGCTGTGGCACAGGATGACAGTGGAA
1 TACCTTTATGTACGGTAGATATACCCATCAGCTATTGCTAGCTGTGGCACAGGATGACAGTGGAA
6554950 GAATCCTTCCAATTGCGTTTGCAATAACACCAGGGGAGTCAGCTGATGATTGAGATTTC-TTTTG
66 GAATCCTTCCAATTGCGTTTGCAATAACACCAGGGGAGTCAGCTGATGATTGAGATTTCTTTTTG
6555014 TCTAGGCTAAGGAGGCATGTTTGCCCCCAACCTAATATCTGTGTCATATCAGATCGGGGCACCGA
131 TCTAGGCTAAGGAGGCATGTTTGCCCCCAACCTAATATCTGTGTCATATCAGATCGGGGCACCGA
6555079 AATACTAGCCGCAATTGCGCAACAGGGAAGCATGTGGCATCACACACACCATCGGTATTGCCTAA
196 AATACTAGCCGCAATTGCGCAACAGGGAAGCATGTGGCATCACACACACCATCGGTATTGCCTAA
6555144 GGTACGTTGCGTCCAACTACCACGGGCAATTTAATTCTACAACTGAAAAATGACAAGTAACCAAC
261 GGTACGTTGCGTCCAACTACCACGGGCAATTTAATTCTACAACTGAAAAATGACAAGTAACCAAC
6555209 ATAGGTATGTAATATCTATTAATATAATTTCGTTTGTAATACTGAATTTATTTTAACTGGAAATG
326 ATAGGTATGTAATATCTATTAATATAATTTCGTTTGTAATACTGAATTTATTTTAACTGGAAATG
6555274 TGGTATGTAATTTTCGCTATCAACTTATATTGGTAGGGTATGAGATAAGTAAAGATCATTTCCAT
391 TGGTATGTAATTTTCGCTATCAACTTATATTGGTAGGGTATGAGATAAGTAAAGATCATTTCCAT
6555339 GAAATGTTGGCGATTCTGCGTTCGGATAACGAAGAAGGAGCAAACTACCTATGTAATA
456 GAAATGTTGGCGATTCTGCGTTCGGATAACGAAGAAGGAGCAAACTACCTATGTAATA
6555397 TACCTTT
1 TACCTTT
6555404 CGAACAGTGG
Statistics
Matches: 515, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
512 392 0.76
513 123 0.24
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (513 bp):
TACCTTTATGTACGGTAGATATACCCATCAGCTATTGCTAGCTGTGGCACAGGATGACAGTGGAA
GAATCCTTCCAATTGCGTTTGCAATAACACCAGGGGAGTCAGCTGATGATTGAGATTTCTTTTTG
TCTAGGCTAAGGAGGCATGTTTGCCCCCAACCTAATATCTGTGTCATATCAGATCGGGGCACCGA
AATACTAGCCGCAATTGCGCAACAGGGAAGCATGTGGCATCACACACACCATCGGTATTGCCTAA
GGTACGTTGCGTCCAACTACCACGGGCAATTTAATTCTACAACTGAAAAATGACAAGTAACCAAC
ATAGGTATGTAATATCTATTAATATAATTTCGTTTGTAATACTGAATTTATTTTAACTGGAAATG
TGGTATGTAATTTTCGCTATCAACTTATATTGGTAGGGTATGAGATAAGTAAAGATCATTTCCAT
GAAATGTTGGCGATTCTGCGTTCGGATAACGAAGAAGGAGCAAACTACCTATGTAATA
Found at i:6557360 original size:18 final size:18
Alignment explanation
Indices: 6557334--6557376 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
6557324 GATTAGGAAA
* *
6557334 AGGAAACATAAAAGGGTT
1 AGGATACATAAAAGGGAT
*
6557352 AGGATACATATAAGGGAT
1 AGGATACATAAAAGGGAT
6557370 AGGATAC
1 AGGATAC
6557377 GTACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.47, C:0.07, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGAT
Found at i:6557477 original size:30 final size:29
Alignment explanation
Indices: 6557442--6557531 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 29
6557432 TTGGGCCCGG
*
6557442 TGATTGTGGCGGCGCTGTTGATGAGCTTGC
1 TGATTGTGG-GGCGCTGTTGATGAGCCTGC
* *
6557472 TGATTGTATGGGCGCTGTTGATGGGCCTGC
1 TGATTGT-GGGGCGCTGTTGATGAGCCTGC
6557502 TGATTGTGTGGGCGCTGTTGAT-AGGCCTGC
1 TGATTGTG-GGGCGCTGTTGATGA-GCCTGC
6557532 GTCGTCGTCC
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
30 51 0.98
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.40, T:0.33
Consensus pattern (29 bp):
TGATTGTGGGGCGCTGTTGATGAGCCTGC
Found at i:6557488 original size:15 final size:15
Alignment explanation
Indices: 6557470--6557518 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
6557460 TGATGAGCTT
6557470 GCTGATTGTATGGGC
1 GCTGATTGTATGGGC
6557485 GCTG-TTG-ATGGGCC
1 GCTGATTGTATGGG-C
*
6557499 TGCTGATTGTGTGGGC
1 -GCTGATTGTATGGGC
6557515 GCTG
1 GCTG
6557519 TTGATAGGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
13 5 0.17
14 4 0.14
15 12 0.41
16 4 0.14
17 4 0.14
ACGTcount: A:0.08, C:0.16, G:0.43, T:0.33
Consensus pattern (15 bp):
GCTGATTGTATGGGC
Found at i:6559827 original size:103 final size:104
Alignment explanation
Indices: 6559583--6559848 Score: 419
Period size: 103 Copynumber: 2.6 Consensus size: 104
6559573 GTTGTACATA
** *
6559583 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* **
6559648 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
*
6559687 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
6559751 TCTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
65 TCTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* * *
6559790 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
6559849 AATAACGGTT
Statistics
Matches: 149, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
103 83 0.56
104 66 0.44
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (104 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
Found at i:6567306 original size:103 final size:104
Alignment explanation
Indices: 6567062--6567327 Score: 419
Period size: 103 Copynumber: 2.6 Consensus size: 104
6567052 GTTGTACATA
** *
6567062 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* **
6567127 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
*
6567166 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
6567230 TCTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
65 TCTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* * *
6567269 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
6567328 AATAACGGTT
Statistics
Matches: 149, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
103 83 0.56
104 66 0.44
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (104 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
Found at i:6569427 original size:13 final size:13
Alignment explanation
Indices: 6569409--6569434 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6569399 GCAGGGGAGA
6569409 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
6569422 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
6569435 GGAGAAAAGG
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:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:6571510 original size:21 final size:21
Alignment explanation
Indices: 6571485--6571541 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
6571475 ATGCAAACAT
*
6571485 CATAACTGAAAATTAAATTTG
1 CATAAATGAAAATTAAATTTG
6571506 CATAAATGAAAATTAAATTTG
1 CATAAATGAAAATTAAATTTG
*
6571527 AATAAAT--AAATTAAA
1 CATAAATGAAAATTAAA
6571542 GTATCACTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.24
21 26 0.76
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (21 bp):
CATAAATGAAAATTAAATTTG
Found at i:6572582 original size:30 final size:30
Alignment explanation
Indices: 6572548--6572605 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
6572538 TAATAGAAAT
*
6572548 AATATAGTGACATATA-TTTTAATTTTTTTA
1 AATAT-GTGACATATAGTTATAATTTTTTTA
* *
6572578 AATATGTTAGATATAGTTATAATTTTTT
1 AATATGTGACATATAGTTATAATTTTTT
6572606 CAATAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (30 bp):
AATATGTGACATATAGTTATAATTTTTTTA
Found at i:6575406 original size:12 final size:12
Alignment explanation
Indices: 6575389--6575414 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6575379 GTCGTCGTCG
6575389 TCGTCATCATCA
1 TCGTCATCATCA
6575401 TCGTCATCATCA
1 TCGTCATCATCA
6575413 TC
1 TC
6575415 TTCTTCTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.35, G:0.08, T:0.35
Consensus pattern (12 bp):
TCGTCATCATCA
Found at i:6583479 original size:23 final size:23
Alignment explanation
Indices: 6583453--6583511 Score: 118
Period size: 23 Copynumber: 2.6 Consensus size: 23
6583443 TGAATTTACT
6583453 TGTTATGAACATAAACACTCTCG
1 TGTTATGAACATAAACACTCTCG
6583476 TGTTATGAACATAAACACTCTCG
1 TGTTATGAACATAAACACTCTCG
6583499 TGTTATGAACATA
1 TGTTATGAACATA
6583512 TGTTTATTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.32
Consensus pattern (23 bp):
TGTTATGAACATAAACACTCTCG
Found at i:6594750 original size:2 final size:2
Alignment explanation
Indices: 6594743--6594808 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
6594733 TTTGATAGTA
6594743 AG AG AG AG AG 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 AG AG AG AG AG
6594785 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
6594809 GAGCCTGTTG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6599793 original size:15 final size:15
Alignment explanation
Indices: 6599767--6599820 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
6599757 ATTAAGGTTT
*
6599767 TAAAATTCAAAA-AA
1 TAAAATTAAAAATAA
6599781 TAAGAATTAAAAATAA
1 TAA-AATTAAAAATAA
*
6599797 TCAAATT-AAAAT-A
1 TAAAATTAAAAATAA
6599810 TAAATATTAAA
1 TAAA-ATTAAA
6599821 TTTATAACTC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 4 0.12
14 11 0.33
15 14 0.42
16 4 0.12
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (15 bp):
TAAAATTAAAAATAA
Found at i:6605672 original size:16 final size:16
Alignment explanation
Indices: 6605641--6605680 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
6605631 TTTTATAAAT
*
6605641 TTAAAAAT-AATTATA
1 TTAAAAATAAATAATA
6605656 TTAAAAATAAATAATA
1 TTAAAAATAAATAATA
*
6605672 TAAAAAATA
1 TTAAAAATA
6605681 TTCAATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAAAAATAAATAATA
Found at i:6617794 original size:3 final size:3
Alignment explanation
Indices: 6617786--6617816 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
6617776 GGCTTCTCTT
6617786 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
6617817 CTTTTGTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:6625486 original size:47 final size:47
Alignment explanation
Indices: 6625353--6625559 Score: 177
Period size: 47 Copynumber: 4.3 Consensus size: 47
6625343 ATAGTAAAAT
** * *
6625353 TATGGTCTTGCACA-TAGTCACATATCACATACCGAGGCCATAGCCCAGC
1 TATGGTCTTATACAGTAG-CACATATCAC--ACCGATGCCATAGCCCAGA
* * * *
6625402 CATGGTCTTATAC-GGATG-ACATATCACACTGATGCCATATCCCAGA
1 TATGGTCTTATACAGTA-GCACATATCACACCGATGCCATAGCCCAGA
* *
6625448 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATATCCCGGA
1 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
* * * * *
6625495 TATGGTCTTATACGGAAGCACAAATCACATTTCTCCGAAGCCATAGCCCAGC
1 TATGGTCTTATACAGTAGCACATATCACA-----CCGATGCCATAGCCCAGA
6625547 TATGGTCTTATAC
1 TATGGTCTTATAC
6625560 GGAAATCACA
Statistics
Matches: 130, Mismatches: 19, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
46 28 0.22
47 54 0.42
48 9 0.07
49 11 0.08
50 1 0.01
52 27 0.21
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (47 bp):
TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
Found at i:6626434 original size:54 final size:54
Alignment explanation
Indices: 6626372--6626481 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
6626362 CTAATTCAAA
6626372 ATTCTTCTAAATTCACACTTGACTCATAATTATTAATTTATTAAAATTTTAAAC
1 ATTCTTCTAAATTCACACTTGACTCATAATTATTAATTTATTAAAATTTTAAAC
6626426 ATTCTTCTAAATTCACACTTGACTCATAATTATTAATTTATTAAAATTTTAAAC
1 ATTCTTCTAAATTCACACTTGACTCATAATTATTAATTTATTAAAATTTTAAAC
6626480 AT
1 AT
6626482 ACTTGTCGGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.39, C:0.15, G:0.02, T:0.45
Consensus pattern (54 bp):
ATTCTTCTAAATTCACACTTGACTCATAATTATTAATTTATTAAAATTTTAAAC
Found at i:6630800 original size:19 final size:18
Alignment explanation
Indices: 6630776--6630811 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6630766 AGGTTTCCAC
*
6630776 AACATATTGTTATTTTTTA
1 AACATAATGTT-TTTTTTA
6630795 AACATAATGTTTTTTTT
1 AACATAATGTTTTTTTT
6630812 CCTATCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (18 bp):
AACATAATGTTTTTTTTA
Found at i:6631016 original size:11 final size:11
Alignment explanation
Indices: 6630986--6631015 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
6630976 TTTAATTGAT
6630986 TTTTTAAAATA
1 TTTTTAAAATA
6630997 TTTTTAAAATA
1 TTTTTAAAATA
6631008 -TTTTAAAA
1 TTTTTAAAA
6631016 AATTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTTTAAAATA
Found at i:6631558 original size:25 final size:25
Alignment explanation
Indices: 6631529--6631579 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
6631519 AGTTTATAGG
*
6631529 TACGATACTCTTGGATTATAAAAAA
1 TACGATACTCTAGGATTATAAAAAA
6631554 TACGATACTCTAGGATTATAAAAAA
1 TACGATACTCTAGGATTATAAAAAA
6631579 T
1 T
6631580 GGAAAATATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (25 bp):
TACGATACTCTAGGATTATAAAAAA
Found at i:6640116 original size:20 final size:20
Alignment explanation
Indices: 6640091--6640140 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
6640081 TGGCTTAAAA
6640091 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
6640111 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
6640128 GTGGTAGTGGATT
1 TTGGTAGTGGATT
6640141 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:6644746 original size:20 final size:20
Alignment explanation
Indices: 6644721--6644770 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
6644711 TGGCTTAAAA
6644721 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
6644741 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
6644758 GTGGTAGTGGATT
1 TTGGTAGTGGATT
6644771 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:6647390 original size:21 final size:21
Alignment explanation
Indices: 6647366--6647457 Score: 66
Period size: 21 Copynumber: 4.4 Consensus size: 21
6647356 AGTTCATTCT
6647366 ATTATTTTAATCGATTTGACA
1 ATTATTTTAATCGATTTGACA
** * *
6647387 ATTATTTTTAAATTTAATTGATTA
1 ATTA-TTTT-AATCGATTTGA-CA
* *
6647411 ATTTTTTTAATTC-A-TT--CT
1 ATTATTTTAA-TCGATTTGACA
6647429 ATTATTTTAATCGATTTGACA
1 ATTATTTTAATCGATTTGACA
6647450 ATTATTTT
1 ATTATTTT
6647458 TAAATTTAAC
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
17 2 0.04
18 10 0.19
19 2 0.04
21 15 0.28
22 7 0.13
23 13 0.25
24 4 0.08
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTATTTTAATCGATTTGACA
Found at i:6647425 original size:63 final size:63
Alignment explanation
Indices: 6647349--6647475 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
6647339 ATCAGAGTTT
* *
6647349 TTTTTTTAGTTCATTCTATTATTTTAATCGATTTGACAATTATTTTTAAATTTAATTGATTAA
1 TTTTTTTAATTCATTCTATTATTTTAATCGATTTGACAATTATTTTTAAATTTAACTGATTAA
6647412 TTTTTTTAATTCATTCTATTATTTTAATCGATTTGACAATTATTTTTAAATTTAACTGATTAA
1 TTTTTTTAATTCATTCTATTATTTTAATCGATTTGACAATTATTTTTAAATTTAACTGATTAA
6647475 T
1 T
6647476 CAATTAACAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.31, C:0.07, G:0.06, T:0.57
Consensus pattern (63 bp):
TTTTTTTAATTCATTCTATTATTTTAATCGATTTGACAATTATTTTTAAATTTAACTGATTAA
Found at i:6653956 original size:21 final size:21
Alignment explanation
Indices: 6653930--6653970 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6653920 AGACGAGCAA
* *
6653930 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
6653951 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
6653971 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:6656921 original size:37 final size:38
Alignment explanation
Indices: 6656880--6656969 Score: 93
Period size: 33 Copynumber: 2.5 Consensus size: 38
6656870 TATTACAAAT
* *
6656880 TAAAATACATAATTTATATATTTGAA-ATAAATTTTA-A
1 TAAAATACATAATTTATATA-TTCAATATAAATATTATA
6656917 T-AAA-A-ATAATTT-TATATTCAATATAAATATTATA
1 TAAAATACATAATTTATATATTCAATATAAATATTATA
*
6656951 TAAAATACATTAAATTATA
1 TAAAATACA-TAATTTATA
6656970 AATAAAGGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
32 4 0.09
33 13 0.30
34 9 0.21
35 4 0.09
36 4 0.09
37 2 0.05
38 5 0.12
39 2 0.05
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (38 bp):
TAAAATACATAATTTATATATTCAATATAAATATTATA
Found at i:6656957 original size:18 final size:18
Alignment explanation
Indices: 6656906--6656957 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
6656896 TATATTTGAA
6656906 ATAAATTTTA-ATAAAA-
1 ATAAATTTTATATAAAAT
**
6656922 AT-AATTTTATATTCAAT
1 ATAAATTTTATATAAAAT
*
6656939 ATAAATATTATATAAAAT
1 ATAAATTTTATATAAAAT
6656957 A
1 A
6656958 CATTAAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 7 0.25
16 6 0.21
17 2 0.07
18 13 0.46
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAAATTTTATATAAAAT
Found at i:6672489 original size:33 final size:33
Alignment explanation
Indices: 6672447--6672512 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
6672437 CTCCTTGGAC
6672447 CTTTAATAGTCATCTCTTGATTTTACATAGGAT
1 CTTTAATAGTCATCTCTTGATTTTACATAGGAT
6672480 CTTTAATAGTCATCTCTTGATTTTACATAGGAT
1 CTTTAATAGTCATCTCTTGATTTTACATAGGAT
6672513 TGGGGAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45
Consensus pattern (33 bp):
CTTTAATAGTCATCTCTTGATTTTACATAGGAT
Found at i:6686730 original size:25 final size:25
Alignment explanation
Indices: 6686702--6686749 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
6686692 TTGCATAATT
*
6686702 ATGTCATGATT-CTATCACTACAATC
1 ATGTCA-GATTACTATCACAACAATC
6686727 ATGTCAGATTACTATCACAACAA
1 ATGTCAGATTACTATCACAACAA
6686750 CCTTCATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (25 bp):
ATGTCAGATTACTATCACAACAATC
Found at i:6687032 original size:24 final size:24
Alignment explanation
Indices: 6687005--6687052 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
6686995 TGGATATAGA
6687005 GATTTCCCTTTTGGTTCTATTTAT
1 GATTTCCCTTTTGGTTCTATTTAT
6687029 GATTTCCCTTTTGGTTCTATTTAT
1 GATTTCCCTTTTGGTTCTATTTAT
6687053 TCTCACTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.17, G:0.12, T:0.58
Consensus pattern (24 bp):
GATTTCCCTTTTGGTTCTATTTAT
Found at i:6694206 original size:16 final size:16
Alignment explanation
Indices: 6694173--6694206 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6694163 GGTGGTTGTT
* *
6694173 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
6694189 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
6694205 AA
1 AA
6694207 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:6696582 original size:16 final size:16
Alignment explanation
Indices: 6696549--6696582 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6696539 GGAGATTGTT
* *
6696549 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
6696565 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
6696581 AA
1 AA
6696583 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:6703974 original size:21 final size:22
Alignment explanation
Indices: 6703950--6703990 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
6703940 ATTCAGATGT
6703950 CATAACCGCCACTT-CATTTTA
1 CATAACCGCCACTTACATTTTA
* *
6703971 CATATCCTCCACTTACATTT
1 CATAACCGCCACTTACATTT
6703991 ATTTCTAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.27, C:0.34, G:0.02, T:0.37
Consensus pattern (22 bp):
CATAACCGCCACTTACATTTTA
Found at i:6708249 original size:12 final size:13
Alignment explanation
Indices: 6708227--6708264 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
6708217 TGTCCTATAA
6708227 ATATAATAAAATAT
1 ATATAA-AAAATAT
6708241 AT-TAAAAAATAT
1 ATATAAAAAATAT
6708253 ATATAAATAAAT
1 ATATAAA-AAAT
6708265 TGAGACACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.41
13 7 0.32
14 6 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATATAAAAAATAT
Found at i:6723050 original size:11 final size:11
Alignment explanation
Indices: 6723034--6723103 Score: 59
Period size: 11 Copynumber: 6.3 Consensus size: 11
6723024 CGTCTCGAAT
*
6723034 TATATATTAAA
1 TATATATTTAA
**
6723045 TATATATTTTT
1 TATATATTTAA
* * *
6723056 TATTTTAATCAA
1 TA-TATATTTAA
*
6723068 TATATATTTTA
1 TATATATTTAA
*
6723079 TATATATTAAA
1 TATATATTTAA
6723090 TATATATTTAA
1 TATATATTTAA
6723101 TAT
1 TAT
6723104 GAGTCGGGCC
Statistics
Matches: 43, Mismatches: 15, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
11 37 0.86
12 6 0.14
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATATTTAA
Done.