Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 308 of 378
Found at i:93455730 original size:92 final size:93
Alignment explanation
Indices: 93455572--93455741 Score: 297
Period size: 92 Copynumber: 1.8 Consensus size: 93
93455562 CGCCCTAAGT
* *
93455572 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
93455637 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
93455665 GAACTCGGACTCAACTCAACGAGTTCGGACATT-GCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
93455729 CGAGTTCGGATGC
66 CGAGTTCGGATGC
93455742 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 43 0.59
93 30 0.41
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:93463280 original size:93 final size:93
Alignment explanation
Indices: 93463116--93463285 Score: 268
Period size: 93 Copynumber: 1.8 Consensus size: 93
93463106 CCCCTAAGTG
* * * *
93463116 AACTCGGACTCAACTTAATGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
93463181 GAGTTCGGATGCCTAGTTACATCTCACA
66 GAGTTCGGATGCCTAGTTACATCTCACA
* * * *
93463209 AACTTGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
93463274 GAGTTCGGATGC
66 GAGTTCGGATGC
93463286 TCAACCATCC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCACA
Found at i:93463281 original size:46 final size:46
Alignment explanation
Indices: 93463110--93463282 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 46
93463100 AACCAGCCCC
* * * * * *
93463110 TAAGTGAACTCGGACTCAACTTAATGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
93463156 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATC-CA
* *
93463207 -CA---AACTTGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
93463249 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
93463283 TGCTCAACCA
Statistics
Matches: 103, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 8 0.08
44 1 0.01
46 56 0.54
47 27 0.26
49 1 0.01
50 6 0.06
51 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:93463301 original size:46 final size:45
Alignment explanation
Indices: 93463160--93463301 Score: 114
Period size: 46 Copynumber: 3.1 Consensus size: 45
93463150 CATCCATAAA
93463160 TGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCTCA-
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT-AG
** * * * *
93463207 CAAACTTGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCAT-AAG
1 TGAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCTAG
93463253 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CTAG
93463299 TGA
1 TGA
93463302 CATGTCACTT
Statistics
Matches: 74, Mismatches: 12, Indels: 19
0.70 0.11 0.18
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 31 0.42
47 29 0.39
49 3 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCTAG
Found at i:93474053 original size:27 final size:28
Alignment explanation
Indices: 93474023--93474076 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
93474013 GGAGAAAAGG
*
93474023 GAGG-GAAGAAA-AGAGAAGGAAAAATAA
1 GAGGAGAAGAAATAGA-AAAGAAAAATAA
93474050 GAGGAGAAGAAATAGAAAAGAAAAATA
1 GAGGAGAAGAAATAGAAAAGAAAAATA
93474077 GAAAAGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 17 0.71
29 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.06
Consensus pattern (28 bp):
GAGGAGAAGAAATAGAAAAGAAAAATAA
Found at i:93474077 original size:13 final size:14
Alignment explanation
Indices: 93474054--93474087 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
93474044 AAATAAGAGG
93474054 AGAAGAAATAGAAA
1 AGAAGAAATAGAAA
93474068 AGAA-AAATAGAAA
1 AGAAGAAATAGAAA
93474081 AGAAGAA
1 AGAAGAA
93474088 GTAGGAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (14 bp):
AGAAGAAATAGAAA
Found at i:93474084 original size:27 final size:28
Alignment explanation
Indices: 93474027--93474087 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
93474017 AAAAGGGAGG
* **
93474027 GAAGAAAAGAGAAGGAAAAATAAGAGGA
1 GAAGAAAAGAGAAAGAAAAATAAGAAAA
93474055 GAAGAAATAGA-AAAGAAAAAT-AGAAAA
1 GAAGAAA-AGAGAAAGAAAAATAAGAAAA
93474082 GAAGAA
1 GAAGAA
93474088 GTAGGAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 10 0.34
28 16 0.55
29 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05
Consensus pattern (28 bp):
GAAGAAAAGAGAAAGAAAAATAAGAAAA
Found at i:93474543 original size:22 final size:22
Alignment explanation
Indices: 93474518--93474566 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
93474508 CTGTGGACAT
93474518 GCCCATGTATCTAGGCCGTGTG
1 GCCCATGTATCTAGGCCGTGTG
93474540 GCCCATGTATCTAGGCCGTGTG
1 GCCCATGTATCTAGGCCGTGTG
93474562 GCCCA
1 GCCCA
93474567 CATAGCCGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.14, C:0.31, G:0.31, T:0.24
Consensus pattern (22 bp):
GCCCATGTATCTAGGCCGTGTG
Found at i:93476559 original size:21 final size:21
Alignment explanation
Indices: 93476533--93476574 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
93476523 CTTCAGGGAA
93476533 TGATTCATTTATCTCCTGTTC
1 TGATTCATTTATCTCCTGTTC
93476554 TGATTCATTTATCTCCTGTTC
1 TGATTCATTTATCTCCTGTTC
93476575 ATCAAGTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.24, G:0.10, T:0.52
Consensus pattern (21 bp):
TGATTCATTTATCTCCTGTTC
Found at i:93487710 original size:15 final size:15
Alignment explanation
Indices: 93487677--93487749 Score: 76
Period size: 15 Copynumber: 4.9 Consensus size: 15
93487667 TATGATATTG
*
93487677 TATCTTGGATTT-TCG
1 TATCTTGGATTTCT-T
93487692 TATCTTGGATTTCTT
1 TATCTTGGATTTCTT
*
93487707 TATCTAGGATTTCTT
1 TATCTTGGATTTCTT
* *
93487722 TGTCTTGGACTTCTT
1 TATCTTGGATTTCTT
* *
93487737 TGTCTTGGTTTTC
1 TATCTTGGATTTC
93487750 ATGTCATCTC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
15 49 0.98
16 1 0.02
ACGTcount: A:0.11, C:0.15, G:0.18, T:0.56
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:93488372 original size:33 final size:33
Alignment explanation
Indices: 93488335--93488402 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
93488325 GATGTATTGG
*
93488335 TGCTCGAGTTTGGAACTCGACATTTCTGATCTT
1 TGCTCAAGTTTGGAACTCGACATTTCTGATCTT
93488368 TGCTCAAGTTTGGAACTCGACATTTCTGATCTT
1 TGCTCAAGTTTGGAACTCGACATTTCTGATCTT
93488401 TG
1 TG
93488403 TGTTTGAATA
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:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (33 bp):
TGCTCAAGTTTGGAACTCGACATTTCTGATCTT
Found at i:93489826 original size:3 final size:3
Alignment explanation
Indices: 93489818--93489842 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
93489808 ATTAAATGCT
93489818 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
93489843 ATAAATTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:93494005 original size:14 final size:14
Alignment explanation
Indices: 93493986--93494015 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
93493976 GATCCACCTG
93493986 TATTAATTTTTTTA
1 TATTAATTTTTTTA
93494000 TATTAATTTTTTTA
1 TATTAATTTTTTTA
93494014 TA
1 TA
93494016 AAATAAATTA
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTAATTTTTTTA
Found at i:93501666 original size:19 final size:19
Alignment explanation
Indices: 93501644--93501688 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
93501634 TTTTTTTAAA
93501644 AATTTTT-ATAAA-TATTTT
1 AATTTTTGA-AAATTATTTT
93501662 GAATTTTTGAAAATTATTTT
1 -AATTTTTGAAAATTATTTT
93501682 AATTTTT
1 AATTTTT
93501689 TTGTAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (19 bp):
AATTTTTGAAAATTATTTT
Found at i:93501669 original size:20 final size:19
Alignment explanation
Indices: 93501646--93501689 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
93501636 TTTTTAAAAA
93501646 TTTTTATAAA-TATTTTGAAT
1 TTTTTA-AAATTATTTT-AAT
*
93501666 TTTTGAAAATTATTTTAAT
1 TTTTTAAAATTATTTTAAT
93501685 TTTTT
1 TTTTT
93501690 TGTAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTTAAAATTATTTTAAT
Found at i:93501682 original size:31 final size:31
Alignment explanation
Indices: 93501624--93501701 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 31
93501614 CTTTCTCTAT
* *
93501624 ATATTTTTAATTTTTTTAAAAATTTTTATAA
1 ATATTTTGAATTTTTTGAAAAATTTTTATAA
93501655 ATATTTTGAA-TTTTTG-AAAATTATTT-TAA
1 ATATTTTGAATTTTTTGAAAAATT-TTTATAA
* *
93501684 TTTTTTTGTAATTTTTTG
1 ATATTTTG-AATTTTTTG
93501702 TTGAGAGAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 15 0.38
30 10 0.25
31 15 0.38
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (31 bp):
ATATTTTGAATTTTTTGAAAAATTTTTATAA
Found at i:93504903 original size:2 final size:2
Alignment explanation
Indices: 93504892--93504937 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
93504882 AGCTTTTAAA
93504892 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
93504933 AT AT A
1 AT AT A
93504938 GAATCAACAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93506909 original size:16 final size:16
Alignment explanation
Indices: 93506888--93506923 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
93506878 GTATTTTAGT
93506888 AAAAAATATGAAACAA
1 AAAAAATATGAAACAA
* *
93506904 AAAAAATGTGAAAGAA
1 AAAAAATATGAAACAA
93506920 AAAA
1 AAAA
93506924 TATTTTGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.75, C:0.03, G:0.11, T:0.11
Consensus pattern (16 bp):
AAAAAATATGAAACAA
Found at i:93510702 original size:29 final size:29
Alignment explanation
Indices: 93510614--93510714 Score: 91
Period size: 29 Copynumber: 3.6 Consensus size: 29
93510604 TGACATGTGG
* * *
93510614 AAAAAAAT-TATAAATAATAAAAAATAAT
1 AAAAAAATATAAAAATATTAAAAATTAAT
** **
93510642 -AAAAGTTATAAAAATATTAAATTTTAAT
1 AAAAAAATATAAAAATATTAAAAATTAAT
*
93510670 AAAAAAATATAAAACTATTAAAAATTAGA-
1 AAAAAAATATAAAAATATTAAAAATTA-AT
*
93510699 AAAAAATTATAAAAAT
1 AAAAAAATATAAAAAT
93510715 CGCAAAAATA
Statistics
Matches: 56, Mismatches: 14, Indels: 5
0.75 0.19 0.07
Matches are distributed among these distances:
27 5 0.09
28 15 0.27
29 35 0.62
30 1 0.02
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (29 bp):
AAAAAAATATAAAAATATTAAAAATTAAT
Found at i:93510712 original size:9 final size:9
Alignment explanation
Indices: 93510616--93510812 Score: 50
Period size: 9 Copynumber: 21.0 Consensus size: 9
93510606 ACATGTGGAA
93510616 AAAAATTAT
1 AAAAATTAT
93510625 AAATAA-TA-
1 AAA-AATTAT
*
93510633 AAAAATAAT
1 AAAAATTAT
*
93510642 AAAAGTTAT
1 AAAAATTAT
93510651 AAAAA-TATT
1 AAAAATTA-T
**
93510660 AAATTTTAAT
1 AAAAATT-AT
*
93510670 AAAAA-AAT
1 AAAAATTAT
*
93510678 ATAAAACTATT
1 A-AAAATTA-T
*
93510689 AAAAATTAGAA
1 AAAAATT--AT
93510700 AAAAATTAT
1 AAAAATTAT
***
93510709 AAAAATCGC
1 AAAAATTAT
93510718 AAAAA-TAT
1 AAAAATTAT
* *
93510726 AGAAGTT-T
1 AAAAATTAT
* *
93510734 TAAAATTTT
1 AAAAATTAT
93510743 ATAAAATTGCA-
1 A-AAAATT--AT
93510754 AGAAAATTAT
1 A-AAAATTAT
*
93510764 AAAAATTGT
1 AAAAATTAT
*
93510773 AAAGAAATAT
1 AAA-AATTAT
93510783 -AAAATTCAT
1 AAAAATT-AT
93510792 AAAAGAAATTAT
1 --AA-AAATTAT
93510804 AAAAATTAT
1 AAAAATTAT
93510813 CATGCCAAAA
Statistics
Matches: 134, Mismatches: 31, Indels: 46
0.64 0.15 0.22
Matches are distributed among these distances:
7 2 0.01
8 20 0.15
9 60 0.45
10 26 0.19
11 17 0.13
12 4 0.03
13 5 0.04
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:93510763 original size:19 final size:19
Alignment explanation
Indices: 93510741--93510807 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 19
93510731 TTTTAAAATT
93510741 TTATAAAATTGC-AAGAAAA
1 TTATAAAATTGCAAAG-AAA
*
93510760 TTATAAAAATTGTAAAGAAA
1 TTAT-AAAATTGCAAAGAAA
93510780 -TATAAAATT-CATAAAAGAAA
1 TTATAAAATTGC---AAAGAAA
93510800 TTATAAAA
1 TTATAAAA
93510808 ATTATCATGC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
18 6 0.15
19 7 0.17
20 17 0.43
21 10 0.25
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.28
Consensus pattern (19 bp):
TTATAAAATTGCAAAGAAA
Found at i:93510777 original size:21 final size:21
Alignment explanation
Indices: 93510735--93510810 Score: 63
Period size: 21 Copynumber: 3.7 Consensus size: 21
93510725 TAGAAGTTTT
* *
93510735 AAAATTTTATAAAATTG-CAAG
1 AAAATTATA-AAAATTGTAAAG
93510756 AAAATTATAAAAATTGTAAAG
1 AAAATTATAAAAATTGTAAAG
*
93510777 -AAA-TAT-AAAATTCATAAA-
1 AAAATTATAAAAATT-GTAAAG
93510795 AGAAATTATAAAAATT
1 A-AAATTATAAAAATT
93510811 ATCATGCCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
18 6 0.13
19 7 0.15
20 13 0.28
21 14 0.30
22 6 0.13
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAATTATAAAAATTGTAAAG
Found at i:93510780 original size:20 final size:22
Alignment explanation
Indices: 93510757--93510810 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
93510747 AATTGCAAGA
*
93510757 AAATTATAAAAATT-GT-AAAG
1 AAATTATAAAAATTCATAAAAG
93510777 AAA-TAT-AAAATTCATAAAAG
1 AAATTATAAAAATTCATAAAAG
93510797 AAATTATAAAAATT
1 AAATTATAAAAATT
93510811 ATCATGCCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 6 0.21
19 4 0.14
20 10 0.34
21 3 0.10
22 6 0.21
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (22 bp):
AAATTATAAAAATTCATAAAAG
Found at i:93511057 original size:29 final size:29
Alignment explanation
Indices: 93510995--93511056 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
93510985 TTTTTAATGC
93510995 ATTTTACAATCTTTAATGATTTTTATAAA
1 ATTTTACAATCTTTAATGATTTTTATAAA
* *
93511024 ATTTTACAATTTTTATAT-ATTTTT-TAAT
1 ATTTTACAATCTTTA-ATGATTTTTATAAA
93511052 ATTTT
1 ATTTT
93511057 TTCCTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 8 0.27
29 20 0.67
30 2 0.07
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.60
Consensus pattern (29 bp):
ATTTTACAATCTTTAATGATTTTTATAAA
Found at i:93511385 original size:84 final size:84
Alignment explanation
Indices: 93511229--93511388 Score: 216
Period size: 84 Copynumber: 1.9 Consensus size: 84
93511219 GATCAAATAA
* * *
93511229 CCTTTTTGATGCATTTTGAGAGTTCAAGTACCCAATTGAATGCAAAAAAAAAGGTGCTTAATTGT
1 CCTTTTTGATGCATTTTGAAAGTTAAAGTACCCAATTGAATGCAAAAAAAAAGGAGCTTAATTGT
**
93511294 TTTTTTTTTAATTTGAGGG
66 TCCTTTTTTAATTTGAGGG
* * *
93511313 CCTTTTTTATGCATTTTGAAAGTTAAAGTACTCAATTGAGTGCAAAAAAAAGTAGGAGCTTAA-T
1 CCTTTTTGATGCATTTTGAAAGTTAAAGTACCCAATTGAATGCAAAAAAAA--AGGAGCTTAATT
93511377 -TTCCTTTTTTAA
64 GTTCCTTTTTTAA
93511389 AATAAAAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
84 56 0.85
85 1 0.02
86 9 0.14
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (84 bp):
CCTTTTTGATGCATTTTGAAAGTTAAAGTACCCAATTGAATGCAAAAAAAAAGGAGCTTAATTGT
TCCTTTTTTAATTTGAGGG
Found at i:93512930 original size:49 final size:47
Alignment explanation
Indices: 93512825--93513042 Score: 176
Period size: 49 Copynumber: 4.6 Consensus size: 47
93512815 ATAAGATGTT
* * ** * * * *
93512825 GATGCCATGTCCTAGACATGGTCTTTCACTGGCTAACACATCAA-GTC
1 GATGCCATGTCCCAGACA-GGTCTTACACTGATTCATATAACAAGGTC
*
93512872 GATGCCATGTCCCAGACATGTCTTACACTGAATTTCATATAACAAGGTC
1 GATGCCATGTCCCAGACAGGTCTTACACTG-A-TTCATATAACAAGGTC
* * * * *
93512921 GATGCCATGTCCAAGACAGGTCTTACACTGGCTCTCATCTATC-AGTGTT
1 GATGCCATGTCCCAGACAGGTCTTACACT-GAT-TCATATAACAAG-GTC
* * * *
93512970 GATGCCATGTCCCACACAGGTCTTACATTGA--CACATAACAAGCT-
1 GATGCCATGTCCCAGACAGGTCTTACACTGATTCATATAACAAGGTC
*
93513014 GATGCCATGTCCCAGACAGGTTTTACACT
1 GATGCCATGTCCCAGACAGGTCTTACACT
93513043 AGCTTGTATA
Statistics
Matches: 138, Mismatches: 26, Indels: 17
0.76 0.14 0.09
Matches are distributed among these distances:
44 26 0.19
45 6 0.04
46 12 0.09
47 17 0.12
48 11 0.08
49 65 0.47
50 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (47 bp):
GATGCCATGTCCCAGACAGGTCTTACACTGATTCATATAACAAGGTC
Found at i:93513040 original size:93 final size:92
Alignment explanation
Indices: 93512824--93513042 Score: 237
Period size: 98 Copynumber: 2.3 Consensus size: 92
93512814 GATAAGATGT
* *
93512824 TGATGCCATGTCCTAGACATGGTCTTT-CACTGGCTAACACATCAAGTCGATGCCATGTCCCAGA
1 TGATGCCATGTCCAAGACA-GGT-TTTACACTGGCTAACACATCAAGTCGATGCCATGTCCCACA
* * *
93512888 CATGTCTTACACTGAATTTCATATAACAAGG
64 CAGGTCTTACACTGAA--TCACATAACAAGC
* ** * *
93512919 TCGATGCCATGTCCAAGACAGGTCTTACACTGGCTCTCATCTATCAGTGTTGATGCCATGTCCCA
1 T-GATGCCATGTCCAAGACAGGTTTTACACTGGCTAACA-C-ATCA-AGTCGATGCCATGTCCCA
*
93512984 CACAGGTCTTACATTG-A-CACATAACAAGC
62 CACAGGTCTTACACTGAATCACATAACAAGC
*
93513013 TGATGCCATGTCCCAGACAGGTTTTACACT
1 TGATGCCATGTCCAAGACAGGTTTTACACT
93513043 AGCTTGTATA
Statistics
Matches: 106, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
93 27 0.25
94 13 0.12
95 14 0.13
96 18 0.17
97 5 0.05
98 29 0.27
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (92 bp):
TGATGCCATGTCCAAGACAGGTTTTACACTGGCTAACACATCAAGTCGATGCCATGTCCCACACA
GGTCTTACACTGAATCACATAACAAGC
Found at i:93516363 original size:24 final size:25
Alignment explanation
Indices: 93516326--93516378 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
93516316 TTTAATTAGT
93516326 AAATATATATTTT-AT-AATTTATAA
1 AAATATATATTTTAATAAATTT-TAA
93516350 AAATATAT-TATTTAATAAATTTTAA
1 AAATATATAT-TTTAATAAATTTTAA
93516375 AAAT
1 AAAT
93516379 GAACACAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 1 0.04
24 11 0.42
25 9 0.35
26 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AAATATATATTTTAATAAATTTTAA
Found at i:93516365 original size:22 final size:23
Alignment explanation
Indices: 93516315--93516365 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
93516305 TTTTTCAATC
*
93516315 ATTTAA-TTAGTAAATATATATT
1 ATTTAATTTAGTAAAAATATATT
93516337 -TTATAATTTA-TAAAAATATATT
1 ATT-TAATTTAGTAAAAATATATT
93516359 ATTTAAT
1 ATTTAAT
93516366 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 2 0.08
22 18 0.72
23 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATTTAATTTAGTAAAAATATATT
Found at i:93516367 original size:25 final size:24
Alignment explanation
Indices: 93516326--93516378 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
93516316 TTTAATTAGT
*
93516326 AAATATATATTTTAT-AATTTATAA
1 AAATATATATTTAATAAATTT-TAA
93516350 AAATATATTATTTAATAAATTTTAA
1 AAATATA-TATTTAATAAATTTTAA
93516375 AAAT
1 AAAT
93516379 GAACACAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 7 0.27
25 14 0.54
26 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATATATATTTAATAAATTTTAA
Found at i:93522010 original size:12 final size:12
Alignment explanation
Indices: 93521995--93522028 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
93521985 ATGCAGAAGG
93521995 AGATGCAAGAAC
1 AGATGCAAGAAC
*
93522007 AGATGCAAGCAC
1 AGATGCAAGAAC
*
93522019 AAATGCAAGA
1 AGATGCAAGA
93522029 GTAATTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.18, G:0.24, T:0.09
Consensus pattern (12 bp):
AGATGCAAGAAC
Found at i:93529887 original size:143 final size:143
Alignment explanation
Indices: 93529706--93529994 Score: 452
Period size: 143 Copynumber: 2.0 Consensus size: 143
93529696 CAGATTGAGT
* * *
93529706 AATCATGGTGAATCTTATCTCCCAGAAGTCACAGTGGAGGAGATTGAAGCCACAAGTCTTATCTC
1 AATCATGGTGAATCTTATCTCCCAGAAGCCACAATGGAGCAGATTGAAGCCACAAGTCTTATCTC
* * * * *
93529771 CCTGAAGTTGCAGCGGAGCAGACTAAAGATAACGAATCTCATTCCCTTGAAGTTGCAGTGGGACA
66 CCTAAAATTACAGCGGAGCAGACTAAAGATAACGAATCTCATTCCCCTGAAGTTACAGTGGGACA
*
93529836 GATTAAAGTTACA
131 GATTAAAGCTACA
* * *
93529849 AATCATGGTGAATCTTATCTCCCTGAAGCCGCAATGGAGCAGATTGAATCCACAAGTCTTATCTC
1 AATCATGGTGAATCTTATCTCCCAGAAGCCACAATGGAGCAGATTGAAGCCACAAGTCTTATCTC
* *
93529914 CCTAAAATTACAGCGGAGCAGACTAAAGATAACGGATCTCATTCCCCTGAAGTTATAGTGGGACA
66 CCTAAAATTACAGCGGAGCAGACTAAAGATAACGAATCTCATTCCCCTGAAGTTACAGTGGGACA
93529979 GATTAAAGCTACA
131 GATTAAAGCTACA
93529992 AAT
1 AAT
93529995 TATGACAAAT
Statistics
Matches: 132, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
143 132 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (143 bp):
AATCATGGTGAATCTTATCTCCCAGAAGCCACAATGGAGCAGATTGAAGCCACAAGTCTTATCTC
CCTAAAATTACAGCGGAGCAGACTAAAGATAACGAATCTCATTCCCCTGAAGTTACAGTGGGACA
GATTAAAGCTACA
Found at i:93530033 original size:143 final size:143
Alignment explanation
Indices: 93529716--93530036 Score: 428
Period size: 143 Copynumber: 2.2 Consensus size: 143
93529706 AATCATGGTG
* * *
93529716 AATCTTATCTCCC-AGAAGTCACAGTGGAGGAGATTGAAGCCACAAGTCTTATCTCCCTGAAGTT
1 AATCTTATCTCCCTA-AAGTCACAGTGGAGCAGATTGAAGCCACAAGTCTTATCTCCCTAAAATT
* * * *
93529780 GCAGCGGAGCAGACTAAAGATAACGAATCTCATTCCCTTGAAGTTGCAGTGGGACAGATTAAAGT
65 ACAGCGGAGCAGACTAAAGATAACGAATCTCATTCCCCTGAAGTTACAGTGGGACAGATTAAAGC
***
93529845 TACAAATCATGGTG
130 TACAAATCATGACA
* * * * *
93529859 AATCTTATCTCCCTGAAGCCGCAATGGAGCAGATTGAATCCACAAGTCTTATCTCCCTAAAATTA
1 AATCTTATCTCCCTAAAGTCACAGTGGAGCAGATTGAAGCCACAAGTCTTATCTCCCTAAAATTA
* *
93529924 CAGCGGAGCAGACTAAAGATAACGGATCTCATTCCCCTGAAGTTATAGTGGGACAGATTAAAGCT
66 CAGCGGAGCAGACTAAAGATAACGAATCTCATTCCCCTGAAGTTACAGTGGGACAGATTAAAGCT
*
93529989 ACAAATTATGACA
131 ACAAATCATGACA
* * * *
93530002 AATCTTATCTTCTTAAAGTTACAGTGAAGCAGATT
1 AATCTTATCTCCCTAAAGTCACAGTGGAGCAGATT
93530037 AAAGGCTGCA
Statistics
Matches: 151, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
143 151 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (143 bp):
AATCTTATCTCCCTAAAGTCACAGTGGAGCAGATTGAAGCCACAAGTCTTATCTCCCTAAAATTA
CAGCGGAGCAGACTAAAGATAACGAATCTCATTCCCCTGAAGTTACAGTGGGACAGATTAAAGCT
ACAAATCATGACA
Found at i:93531898 original size:3 final size:3
Alignment explanation
Indices: 93531890--93531948 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
93531880 ACTTATGTTC
93531890 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
93531938 TAT TAT TAT TA
1 TAT TAT TAT TA
93531949 CTTTGTGTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:93533783 original size:25 final size:25
Alignment explanation
Indices: 93533750--93533802 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
93533740 GTGGAAGAAA
*
93533750 TATTATTGTACTTATATATATTTTT
1 TATTATTGTACTTAGATATATTTTT
93533775 TATTATTGTACTTAGATATATTTTT
1 TATTATTGTACTTAGATATATTTTT
93533800 TAT
1 TAT
93533803 GTTAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (25 bp):
TATTATTGTACTTAGATATATTTTT
Found at i:93534181 original size:41 final size:41
Alignment explanation
Indices: 93534114--93534336 Score: 302
Period size: 41 Copynumber: 5.4 Consensus size: 41
93534104 CGCAAAAATT
* * * *
93534114 GTAAAACGCCGCTAAAAACTAAAGCATTAGCGGCGCTTTTA
1 GTAAAACGCCGCTAAAAGCCAGAGCATTAGCGGCGCTTTTG
* * *
93534155 GTAAAACGCCGCTAGAAGCCAGAGCATTAGCGGTGCTTTTT
1 GTAAAACGCCGCTAAAAGCCAGAGCATTAGCGGCGCTTTTG
* * *
93534196 GTAAAACGCCGCTATAAGCCAGAGTACTAGCGGCGCTTTTG
1 GTAAAACGCCGCTAAAAGCCAGAGCATTAGCGGCGCTTTTG
*
93534237 GTAAAACGCCGCTAAAAGCCAGAGCATTAGCGGCGCTTTTT
1 GTAAAACGCCGCTAAAAGCCAGAGCATTAGCGGCGCTTTTG
* * * *
93534278 GTAAAACGCCACTAAAAACCAGATCATTAGCGGCACTTTTG
1 GTAAAACGCCGCTAAAAGCCAGAGCATTAGCGGCGCTTTTG
*
93534319 GTAAAACGCCACTAAAAG
1 GTAAAACGCCGCTAAAAG
93534337 TCATATAACC
Statistics
Matches: 161, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 161 1.00
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (41 bp):
GTAAAACGCCGCTAAAAGCCAGAGCATTAGCGGCGCTTTTG
Found at i:93535506 original size:23 final size:24
Alignment explanation
Indices: 93535466--93535514 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
93535456 ATCTCAACAC
* *
93535466 AAAAATTTTGAAAGAAAAAATAAA
1 AAAAATGTTGAAAAAAAAAATAAA
*
93535490 AAAAATGTT-AAAAAAAAAATTAA
1 AAAAATGTTGAAAAAAAAAATAAA
93535513 AA
1 AA
93535515 TTGAGCAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.20
Consensus pattern (24 bp):
AAAAATGTTGAAAAAAAAAATAAA
Found at i:93535862 original size:3 final size:3
Alignment explanation
Indices: 93535854--93535900 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
93535844 AGTGAACGAG
* *
93535854 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAG GAA GAA AAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
93535901 GAGTAAAGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:93540493 original size:42 final size:43
Alignment explanation
Indices: 93540391--93540493 Score: 102
Period size: 42 Copynumber: 2.4 Consensus size: 43
93540381 CGCTAGGTCG
* * * * * **
93540391 TGGTCTTTAGTGGCGCTTGCGAAGAAAGTGCCGCTAAGAGTTG
1 TGGTCTTTAGCGGCGTTTGAGAAGAAAGCGCCGCTAAAAGTCA
* *
93540434 TGGT-TTTTGGGGACGTTTGAGAA-AAAGCGCCGCTAAAAGTCA
1 TGGTCTTTAGCGG-CGTTTGAGAAGAAAGCGCCGCTAAAAGTCA
93540476 TGGTCTTTAGCGGCGTTT
1 TGGTCTTTAGCGGCGTTT
93540494 TTTAGATGTG
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
42 30 0.62
43 18 0.38
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.30
Consensus pattern (43 bp):
TGGTCTTTAGCGGCGTTTGAGAAGAAAGCGCCGCTAAAAGTCA
Found at i:93540564 original size:68 final size:68
Alignment explanation
Indices: 93540432--93540565 Score: 250
Period size: 69 Copynumber: 2.0 Consensus size: 68
93540422 CGCTAAGAGT
*
93540432 TGTGGTTTTTGGGGACGTTTGAGAAAAAGCGCCGCTAAAAGTCATGGTCTTTAGCGGCGTTTTTT
1 TGTGGTTTTTGGCGACGTTTGAGAAAAAGCGCCGCTAAAAGTCATGGTCTTTAGCGGCGTTTTTT
93540497 AGA
66 AGA
93540500 TGTGGTTTTTGGCGACGTTTGAGAAAAAAGCGCCGCTAAAAGTCATGGTCTTTAGCGGCGTTTTT
1 TGTGGTTTTTGGCGACGTTTGAG-AAAAAGCGCCGCTAAAAGTCATGGTCTTTAGCGGCGTTTTT
93540565 T
65 T
93540566 TAAAAAACGC
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
68 22 0.34
69 42 0.66
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (68 bp):
TGTGGTTTTTGGCGACGTTTGAGAAAAAGCGCCGCTAAAAGTCATGGTCTTTAGCGGCGTTTTTT
AGA
Found at i:93542526 original size:18 final size:18
Alignment explanation
Indices: 93542503--93542538 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
93542493 AATTGACTTA
93542503 TTATTTGTAATGATGAAC
1 TTATTTGTAATGATGAAC
93542521 TTATTTGTAATGATGAAC
1 TTATTTGTAATGATGAAC
93542539 AAGTAGGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (18 bp):
TTATTTGTAATGATGAAC
Found at i:93543534 original size:30 final size:29
Alignment explanation
Indices: 93543498--93543577 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 29
93543488 AGTAGGTGAA
93543498 GAGGATGGTTTATTAGAGTGTTACTTAGGT
1 GAGGATGGTTTATT-GAGTGTTACTTAGGT
**
93543528 GAGGATGGTTTATTGGAGTGTTGTTTAGGT
1 GAGGATGGTTTATT-GAGTGTTACTTAGGT
*
93543558 AAGGATGGTTTTATTGAGTG
1 GAGGATGG-TTTATTGAGTG
93543578 GCTTGTGAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 39 0.87
31 6 0.13
ACGTcount: A:0.21, C:0.01, G:0.36, T:0.41
Consensus pattern (29 bp):
GAGGATGGTTTATTGAGTGTTACTTAGGT
Found at i:93548221 original size:28 final size:28
Alignment explanation
Indices: 93548163--93548221 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
93548153 ATTCTAAAAG
* * *
93548163 AAAACTCAAAGAGAAATTTTTGAAGAGA
1 AAAACTCAAAAAGAAATTTTTGAACACA
*
93548191 AAAACTCAAAAAG-AATTTTATTAACACA
1 AAAACTCAAAAAGAAATTTT-TGAACACA
93548219 AAA
1 AAA
93548222 GAGAAAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.58, C:0.10, G:0.10, T:0.22
Consensus pattern (28 bp):
AAAACTCAAAAAGAAATTTTTGAACACA
Found at i:93551043 original size:21 final size:21
Alignment explanation
Indices: 93551002--93551045 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
93550992 GGAGTGTTTT
*
93551002 GAGGGATTAGGGGAGTAATTA
1 GAGGGATTAGGAGAGTAATTA
*
93551023 GAGGGATTTGGAGAGCT-ATTA
1 GAGGGATTAGGAGAG-TAATTA
93551044 GA
1 GA
93551046 ATCCCATTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.32, C:0.02, G:0.41, T:0.25
Consensus pattern (21 bp):
GAGGGATTAGGAGAGTAATTA
Found at i:93561420 original size:41 final size:42
Alignment explanation
Indices: 93561363--93561446 Score: 134
Period size: 41 Copynumber: 2.0 Consensus size: 42
93561353 ATAAATTCTG
* *
93561363 AAATCTACGATGAGTGCAAGTGCTGCTCATGGAC-GGGTACT
1 AAATCCACGATGAGTGCAAGTGCTACTCATGGACGGGGTACT
*
93561404 AAATCCACGATGAGTGCAAGTGGTACTCATGGACGGGGTACT
1 AAATCCACGATGAGTGCAAGTGCTACTCATGGACGGGGTACT
93561446 A
1 A
93561447 GAGGTTGTGG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 31 0.79
42 8 0.21
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.23
Consensus pattern (42 bp):
AAATCCACGATGAGTGCAAGTGCTACTCATGGACGGGGTACT
Found at i:93575094 original size:22 final size:22
Alignment explanation
Indices: 93575062--93575105 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
93575052 TGAGAAGCTT
*
93575062 AAGTCTATTCTGACTCAGGCTC
1 AAGTCTATTCTAACTCAGGCTC
*
93575084 AAGTCTGTTCTAACTCAGGCTC
1 AAGTCTATTCTAACTCAGGCTC
93575106 CTGTTCTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (22 bp):
AAGTCTATTCTAACTCAGGCTC
Found at i:93577485 original size:30 final size:30
Alignment explanation
Indices: 93577450--93577509 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
93577440 TTCCAAAAGA
93577450 AAACTCCTTATTTTCTCTGACGTTTCCACT
1 AAACTCCTTATTTTCTCTGACGTTTCCACT
93577480 AAACTCCTTATTTTCTCTGACGTTTCCACT
1 AAACTCCTTATTTTCTCTGACGTTTCCACT
93577510 CCCCCTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.30, G:0.07, T:0.43
Consensus pattern (30 bp):
AAACTCCTTATTTTCTCTGACGTTTCCACT
Found at i:93585415 original size:12 final size:11
Alignment explanation
Indices: 93585387--93585414 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
93585377 TATATATATA
93585387 TTTTTTCACTT
1 TTTTTTCACTT
93585398 TTTTTTCACTT
1 TTTTTTCACTT
93585409 TTTTTT
1 TTTTTT
93585415 TTTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTCACTT
Found at i:93586488 original size:3 final size:3
Alignment explanation
Indices: 93586436--93586477 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
93586426 AAAAAGAAAG
93586436 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
93586478 ACTCAATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:93586571 original size:21 final size:23
Alignment explanation
Indices: 93586519--93586571 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
93586509 TTGTAATGTT
93586519 AATAGTAAAAAGAAAAAAATAAG-
1 AATAG-AAAAAGAAAAAAATAAGA
*
93586542 AA-AGAAAAAAAAAAAAAT-AGA
1 AATAGAAAAAGAAAAAAATAAGA
93586563 AATAGAAAA
1 AATAGAAAA
93586572 TAATAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.07
21 15 0.56
22 8 0.30
23 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.09
Consensus pattern (23 bp):
AATAGAAAAAGAAAAAAATAAGA
Found at i:93586670 original size:22 final size:20
Alignment explanation
Indices: 93586652--93586703 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 20
93586642 AATTAATTAG
93586652 TAAAATAAAAATAAATAATA
1 TAAAATAAAAATAAATAATA
*
93586672 TAAAAATTAAAAATAAATAAAA
1 T-AAAA-TAAAAATAAATAATA
93586694 TAAAATAAAA
1 TAAAATAAAA
93586704 TTGGGGTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 6 0.21
21 8 0.28
22 15 0.52
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
TAAAATAAAAATAAATAATA
Found at i:93586676 original size:15 final size:14
Alignment explanation
Indices: 93586656--93586698 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
93586646 AATTAGTAAA
93586656 ATAAAAATAAATAAT
1 ATAAAAATAAA-AAT
93586671 ATAAAAATTAAAAAT
1 ATAAAAA-TAAAAAT
*
93586686 AAATAAAATAAAA
1 ATA-AAAATAAAA
93586699 TAAAATTGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 17 0.68
16 8 0.32
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
ATAAAAATAAAAAT
Found at i:93591091 original size:30 final size:30
Alignment explanation
Indices: 93591055--93591115 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
93591045 CATGGGCTAG
** * *
93591055 CACATGGGTGTGTGGCCTACTCGTGTGGAT
1 CACATGGGCATGTGGCATACCCGTGTGGAT
*
93591085 CACATGGGCATGTGGCATGCCCGTGTGGAT
1 CACATGGGCATGTGGCATACCCGTGTGGAT
93591115 C
1 C
93591116 CTGAAAACTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.15, C:0.23, G:0.36, T:0.26
Consensus pattern (30 bp):
CACATGGGCATGTGGCATACCCGTGTGGAT
Found at i:93599393 original size:27 final size:25
Alignment explanation
Indices: 93599363--93599415 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
93599353 CTCTTTTGAG
*
93599363 TCAATAAATTCTCTTTGAGTTTTCTTT
1 TCAAGAAATTCTC-TTGAG-TTTCTTT
*
93599390 TCAAGAATTTCTCTTGAGTTTCTTT
1 TCAAGAAATTCTCTTGAGTTTCTTT
93599415 T
1 T
93599416 AGAAGAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 5 0.21
27 11 0.46
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.55
Consensus pattern (25 bp):
TCAAGAAATTCTCTTGAGTTTCTTT
Found at i:93602711 original size:28 final size:28
Alignment explanation
Indices: 93602674--93602782 Score: 103
Period size: 28 Copynumber: 3.9 Consensus size: 28
93602664 TTAGATTGTC
*
93602674 CTGACGAACTTCCACATTTAATATCATT
1 CTGACGAACTTCCACATTTAAGATCATT
** * *
93602702 CTGACGAACTTCCATGTTTAAGATCGTC
1 CTGACGAACTTCCACATTTAAGATCATT
** * * *
93602730 CTGGTGGACTTCCACGTTTAAGATTATT
1 CTGACGAACTTCCACATTTAAGATCATT
*
93602758 CT-ACCAGACTTCCACATTTAAGATC
1 CTGACGA-ACTTCCACATTTAAGATC
93602783 GTCCCAGCAA
Statistics
Matches: 62, Mismatches: 18, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.34
Consensus pattern (28 bp):
CTGACGAACTTCCACATTTAAGATCATT
Found at i:93602741 original size:56 final size:56
Alignment explanation
Indices: 93602656--93602786 Score: 142
Period size: 56 Copynumber: 2.4 Consensus size: 56
93602646 ACCTCCCGAG
* ** * * *
93602656 CTTCCACA-TT-AGATTGTCCTGACGAACTTCCACATTTAATATCATTCTGACGA-A
1 CTTCCACATTTAAGATCGTCCTGGTGGACTTCCACATTTAAGATCATTCT-ACCAGA
** * *
93602710 CTTCCATGTTTAAGATCGTCCTGGTGGACTTCCACGTTTAAGATTATTCTACCAGA
1 CTTCCACATTTAAGATCGTCCTGGTGGACTTCCACATTTAAGATCATTCTACCAGA
93602766 CTTCCACATTTAAGATCGTCC
1 CTTCCACATTTAAGATCGTCC
93602787 CAGCAAACTT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
54 6 0.10
55 5 0.08
56 51 0.82
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (56 bp):
CTTCCACATTTAAGATCGTCCTGGTGGACTTCCACATTTAAGATCATTCTACCAGA
Found at i:93609450 original size:5 final size:5
Alignment explanation
Indices: 93609416--93609448 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
93609406 ATTTAGTGAG
93609416 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
93609449 TTATCATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTTC
Found at i:93614073 original size:81 final size:81
Alignment explanation
Indices: 93613970--93614387 Score: 683
Period size: 81 Copynumber: 5.2 Consensus size: 81
93613960 GCCTGAAGAT
* *
93613970 AAGTTTCCTTGGAGCAGAGTCCTCAACTCTACTATTTTGATCATCAGAATTTCTGTTGTCAAGAG
1 AAGTTTCGTTGGAGCAGAGTCCTCACCTCTACTATTTTGATCATCAGAATTTCTGTTGTCAAGAG
*
93614035 TTCTTTGGCAGGACTT
66 TTCTTTGGCAGGACTC
*
93614051 AAGTTTTGTTGGAGCAGAGTCCTCACCTCTACTATTTTGATCATCAGAATTTCTGTTGTCAAGAG
1 AAGTTTCGTTGGAGCAGAGTCCTCACCTCTACTATTTTGATCATCAGAATTTCTGTTGTCAAGAG
*
93614116 CTCTTTGGCAGGACTC
66 TTCTTTGGCAGGACTC
* *
93614132 AAGTTTTGTTGGAGCAGTGTCCTCACCTCTACTATTTTGATCATCAGAATTTCTGTTGTCAAGAG
1 AAGTTTCGTTGGAGCAGAGTCCTCACCTCTACTATTTTGATCATCAGAATTTCTGTTGTCAAGAG
93614197 TTCTTTGGCAGGACTC
66 TTCTTTGGCAGGACTC
**
93614213 AAGTGCCGTTGGAGCAGAGTCCTCACCTCTACTATTTTGATCATCAGAATTTCTGTTGTCAAGAG
1 AAGTTTCGTTGGAGCAGAGTCCTCACCTCTACTATTTTGATCATCAGAATTTCTGTTGTCAAGAG
* *
93614278 TTCTTCGGCAGGAATC
66 TTCTTTGGCAGGACTC
* * * *
93614294 AAATTTCGCTGGAGCAGAGTCCTCACCTCTACTATTTTGAACATCAGAATTTCTGTTGTCAAGAT
1 AAGTTTCGTTGGAGCAGAGTCCTCACCTCTACTATTTTGATCATCAGAATTTCTGTTGTCAAGAG
*
93614359 TTCTTTGGCGGGACTC
66 TTCTTTGGCAGGACTC
*
93614375 AAGTTTCCTTGGA
1 AAGTTTCGTTGGA
93614388 CTAAACTCCT
Statistics
Matches: 312, Mismatches: 25, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 312 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (81 bp):
AAGTTTCGTTGGAGCAGAGTCCTCACCTCTACTATTTTGATCATCAGAATTTCTGTTGTCAAGAG
TTCTTTGGCAGGACTC
Found at i:93614552 original size:84 final size:82
Alignment explanation
Indices: 93614429--93614678 Score: 254
Period size: 84 Copynumber: 3.0 Consensus size: 82
93614419 GATCATCTAT
* * * * * *
93614429 GTTGTCAACAATTAATTTTCGCCTGAAC-TCGTGTATCCTTGGAGTAAGTTCCTCGATTCTACTG
1 GTTGTCAACAATTACTCTTCGCC-GAACTTC-AGTCTCCTTGGAGTAA-CTCCTTGATTCTACTG
*
93614493 TTTTTGTTATCACCATTTTG
63 TTTTGGTTATCACCATTTTG
*
93614513 GTTGTCAACAATTACTCTTCGCCGAAACTTCAGTCTCCTTGGAGTACACTCCTTGACTT-TACCG
1 GTTGTCAACAATTACTCTTCGCCG-AACTTCAGTCTCCTTGGAGTA-ACTCCTTGA-TTCTACTG
*
93614577 TTTTGGTTATTACCATTTTG
63 TTTTGGTTATCACCATTTTG
* * * * *
93614597 GTTGTCAACAATTTCTCTTCGTCTGAACTTGAGTCT-CTTCGGGGTAAACTCCTTGACTCTACTG
1 GTTGTCAACAATTACTCTTCG-CCGAACTTCAGTCTCCTT-GGAGT-AACTCCTTGATTCTACTG
* *
93614661 TTTTGGTTTTCATCATTT
63 TTTTGGTTATCACCATTT
93614679 ATGCTATTAA
Statistics
Matches: 140, Mismatches: 18, Indels: 16
0.80 0.10 0.09
Matches are distributed among these distances:
83 5 0.04
84 127 0.91
85 8 0.06
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.42
Consensus pattern (82 bp):
GTTGTCAACAATTACTCTTCGCCGAACTTCAGTCTCCTTGGAGTAACTCCTTGATTCTACTGTTT
TGGTTATCACCATTTTG
Found at i:93617991 original size:15 final size:14
Alignment explanation
Indices: 93617950--93617993 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
93617940 TAAATAATTT
* *
93617950 AAAATTTTAAAATA
1 AAAATATTAAAAAA
93617964 AAAATATTAAAAAA
1 AAAATATTAAAAAA
93617978 AAAATAATTCAAAAAA
1 AAAAT-ATT-AAAAAA
93617994 TTATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 17 0.65
15 3 0.12
16 6 0.23
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAATATTAAAAAA
Found at i:93619499 original size:18 final size:18
Alignment explanation
Indices: 93619478--93619515 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
93619468 AATTATGTAA
93619478 TTAGTTTAAATTTAATTT
1 TTAGTTTAAATTTAATTT
*
93619496 TTAGTTTAAATTTGATTT
1 TTAGTTTAAATTTAATTT
93619514 TT
1 TT
93619516 TAATTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (18 bp):
TTAGTTTAAATTTAATTT
Found at i:93620964 original size:31 final size:31
Alignment explanation
Indices: 93620906--93620964 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
93620896 GCTAATAGAC
* * *
93620906 TCTTTTTAAAAAGTTGATGGTCCAATTTAAT
1 TCTTTTTAAAAAGTTGAAGATCAAATTTAAT
* *
93620937 TCTTTTTAAAAGGTTTAAGATCAAATTT
1 TCTTTTTAAAAAGTTGAAGATCAAATTT
93620965 TGCTTAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.46
Consensus pattern (31 bp):
TCTTTTTAAAAAGTTGAAGATCAAATTTAAT
Found at i:93622383 original size:24 final size:20
Alignment explanation
Indices: 93622339--93622404 Score: 66
Period size: 17 Copynumber: 3.3 Consensus size: 20
93622329 ATAATTCAAA
93622339 AAAATTAAAAATTTTAAAAAT
1 AAAA-TAAAAATTTTAAAAAT
* *
93622360 --AA-AAATATTCTAAAATAT
1 AAAATAAAAATTTTAAAA-AT
93622378 ATAAATAAAAATTTTAAAAAT
1 A-AAATAAAAATTTTAAAAAT
93622399 AAAATA
1 AAAATA
93622405 TTATATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
17 11 0.31
18 2 0.06
19 2 0.06
20 5 0.14
21 5 0.14
22 11 0.31
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAATAAAAATTTTAAAAAT
Found at i:93622411 original size:33 final size:36
Alignment explanation
Indices: 93622339--93622420 Score: 100
Period size: 39 Copynumber: 2.3 Consensus size: 36
93622329 ATAATTCAAA
93622339 AAAATTAAAAATTTTAAAAATAAAAATATTCTAAAATAT
1 AAAA-TAAAAATTTTAAAAATAAAAATATTCT--AATAT
93622378 ATAAATAAAAATTTTAAAAAT-AAAATA-T-T-ATAT
1 A-AAATAAAAATTTTAAAAATAAAAATATTCTAATAT
93622411 AAAATAAAAA
1 AAAATAAAAA
93622421 AATATTTAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
32 9 0.21
33 5 0.12
36 1 0.02
37 1 0.02
38 6 0.14
39 17 0.40
40 3 0.07
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (36 bp):
AAAATAAAAATTTTAAAAATAAAAATATTCTAATAT
Found at i:93624925 original size:20 final size:20
Alignment explanation
Indices: 93624902--93624944 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
93624892 CGTACTCTTT
93624902 CAATACTTCTTTAATTTTAC
1 CAATACTTCTTTAATTTTAC
93624922 CAATACTTCTTTAATTTTAC
1 CAATACTTCTTTAATTTTAC
93624942 CAA
1 CAA
93624945 CTCCTACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.47
Consensus pattern (20 bp):
CAATACTTCTTTAATTTTAC
Found at i:93633299 original size:2 final size:2
Alignment explanation
Indices: 93633294--93633322 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
93633284 AAAAACACTG
93633294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
93633323 ATACAGCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:93636307 original size:2 final size:2
Alignment explanation
Indices: 93636294--93636325 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
93636284 TAAGAGTAAG
*
93636294 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
93636326 AATGTATATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:93637763 original size:44 final size:44
Alignment explanation
Indices: 93637714--93637802 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
93637704 AGGACTAAAA
*
93637714 TCCATAACTTAGACATAATATGAGACTAATAGCTAAATTGGATC
1 TCCATAACTTAGACATAATATGAGACTAATAACTAAATTGGATC
*
93637758 TCCATAACTTAGACATAATATGAGACTAATAACTGAATTGGATC
1 TCCATAACTTAGACATAATATGAGACTAATAACTAAATTGGATC
93637802 T
1 T
93637803 AACAAATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.30
Consensus pattern (44 bp):
TCCATAACTTAGACATAATATGAGACTAATAACTAAATTGGATC
Found at i:93642439 original size:46 final size:48
Alignment explanation
Indices: 93642315--93642451 Score: 188
Period size: 48 Copynumber: 2.9 Consensus size: 48
93642305 GATGACTCCC
* * * *
93642315 GACTAAAATACGTTGTGGATAAACCATTGGTCGAACAAATAAACTACT
1 GACTAAAATACGTTGTGCATAAACCGTTGGTCGAGCAGATAAACTACT
* *
93642363 GACTAATATACGTTGTGCATAAACCGTTGGTCGAGCAGATAAACTGCT
1 GACTAAAATACGTTGTGCATAAACCGTTGGTCGAGCAGATAAACTACT
* *
93642411 -A-TAAAATACATTGCGCATAAACCGTTGGTCGAGCAGATAAA
1 GACTAAAATACGTTGTGCATAAACCGTTGGTCGAGCAGATAAA
93642452 TTGCCAACTA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
46 37 0.46
47 1 0.01
48 42 0.52
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (48 bp):
GACTAAAATACGTTGTGCATAAACCGTTGGTCGAGCAGATAAACTACT
Found at i:93645276 original size:16 final size:17
Alignment explanation
Indices: 93645255--93645287 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
93645245 GAATATAGTA
*
93645255 AAATATTTAAAA-AAAT
1 AAATATATAAAAGAAAT
93645271 AAATATATAAAAGAAAT
1 AAATATATAAAAGAAAT
93645288 GGGAGGCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (17 bp):
AAATATATAAAAGAAAT
Found at i:93645993 original size:20 final size:20
Alignment explanation
Indices: 93645970--93646007 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
93645960 TATTTAAAAC
*
93645970 AAAACTATAATTTTTAGTAA
1 AAAACTATAAATTTTAGTAA
*
93645990 AAAATTATAAATTTTAGT
1 AAAACTATAAATTTTAGT
93646008 GATTCAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (20 bp):
AAAACTATAAATTTTAGTAA
Found at i:93646136 original size:24 final size:25
Alignment explanation
Indices: 93646091--93646137 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
93646081 ATGTGAAAAC
** *
93646091 ATTATCATTTAATTCAATTTAAATA
1 ATTATCATTTAATAAAAGTTAAATA
93646116 ATTATCA-TTAATAAAAGTTAAA
1 ATTATCATTTAATAAAAGTTAAA
93646138 AAAATATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTATCATTTAATAAAAGTTAAATA
Found at i:93647067 original size:3 final size:3
Alignment explanation
Indices: 93647056--93647091 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
93647046 TTATTTATAG
93647056 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
93647092 ACATTTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:93647868 original size:26 final size:23
Alignment explanation
Indices: 93647838--93647904 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 23
93647828 ATACATATTT
93647838 AATTATTTATATTTAGTCATATAATA
1 AATTATTTATATTTA-T--TATAATA
*
93647864 AATTATTAATATAATTTATTTTAATA
1 AATTATT--TAT-ATTTATTATAATA
93647890 AATTATTTAATATTT
1 AATTATTT-ATATTT
93647905 TAATTTTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
24 5 0.14
25 2 0.06
26 20 0.56
28 4 0.11
29 5 0.14
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (23 bp):
AATTATTTATATTTATTATAATA
Found at i:93647910 original size:26 final size:25
Alignment explanation
Indices: 93647859--93647912 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
93647849 TTTAGTCATA
93647859 TAATAAATTATTAATATAATTTATTT
1 TAATAAATTATTAATAT-ATTTATTT
93647885 TAATAAATTATTTAATAT-TTTAATTT
1 TAATAAATTA-TTAATATATTT-ATTT
93647911 TA
1 TA
93647913 TTTTAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 3 0.12
26 16 0.62
27 7 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TAATAAATTATTAATATATTTATTT
Found at i:93647916 original size:31 final size:26
Alignment explanation
Indices: 93647859--93647921 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 26
93647849 TTTAGTCATA
93647859 TAATAAATTATTAATATAATTTATTT
1 TAATAAATTATTAATATAATTTATTT
93647885 TAATAAATTATTTAATATTTTAATTTTATTT
1 TAATAAATTA-TTAATA---TAA-TTTATTT
93647916 TAATAA
1 TAATAA
93647922 TAAATTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 10 0.31
27 6 0.19
30 3 0.09
31 13 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TAATAAATTATTAATATAATTTATTT
Found at i:93647928 original size:13 final size:14
Alignment explanation
Indices: 93647912--93647953 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
93647902 TTTTAATTTT
93647912 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
93647925 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
93647940 ATTTTAAATAATAT
1 ATTTT-AATAATAT
93647954 TCTTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:93647938 original size:16 final size:16
Alignment explanation
Indices: 93647916--93647952 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
93647906 AATTTTATTT
93647916 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
93647933 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
93647948 TAATA
1 TAATA
93647953 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:93648035 original size:15 final size:15
Alignment explanation
Indices: 93647985--93648035 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 15
93647975 ATTCAATATT
93647985 AATAT-TTAATAATA
1 AATATATTAATAATA
*
93647999 AATATTTATTAGAATTATA
1 AATA--TATT--AATAATA
93648018 AATATATTAATAATA
1 AATATATTAATAATA
93648033 AAT
1 AAT
93648036 GTTTTATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.13
15 9 0.30
16 1 0.03
17 6 0.20
19 10 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:93663444 original size:29 final size:31
Alignment explanation
Indices: 93663396--93663459 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
93663386 TTTATAGTTA
*
93663396 TTTAATTAGATAATTATTATT-TATTTAATAT
1 TTTAATAAGATAATTATTATTAT-TTTAATAT
*
93663427 TTTAATAAGAT-ATT-TTATTATTTTATTAT
1 TTTAATAAGATAATTATTATTATTTTAATAT
93663456 TTTA
1 TTTA
93663460 TTTAGTCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.53
30 4 0.13
31 10 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (31 bp):
TTTAATAAGATAATTATTATTATTTTAATAT
Found at i:93663448 original size:8 final size:8
Alignment explanation
Indices: 93663437--93663461 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
93663427 TTTAATAAGA
93663437 TATTTTAT
1 TATTTTAT
93663445 TATTTTAT
1 TATTTTAT
93663453 TATTTTAT
1 TATTTTAT
93663461 T
1 T
93663462 TAGTCTATCT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:93666432 original size:26 final size:26
Alignment explanation
Indices: 93666389--93666445 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
93666379 ACCCGTAATT
* *
93666389 ATATATTTATATAATAAGACCCA-TGC
1 ATATATGTACATAATAAGACCCACT-C
*
93666415 ATATATGTACATAGTAAGACCCACTC
1 ATATATGTACATAATAAGACCCACTC
93666441 ATATA
1 ATATA
93666446 ATATAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 26 0.96
27 1 0.04
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.32
Consensus pattern (26 bp):
ATATATGTACATAATAAGACCCACTC
Found at i:93667792 original size:3 final size:3
Alignment explanation
Indices: 93667784--93667817 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
93667774 ATTTAATTAA
93667784 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
93667818 ACTAATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:93670932 original size:19 final size:19
Alignment explanation
Indices: 93670910--93670957 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
93670900 AAAATATCAT
* *
93670910 TTTTATGAAAATCGTAAAA
1 TTTTATAAAAATAGTAAAA
93670929 TTTTATAAAAATAGTAAAA
1 TTTTATAAAAATAGTAAAA
**
93670948 AATTATAAAA
1 TTTTATAAAA
93670958 TATATAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (19 bp):
TTTTATAAAAATAGTAAAA
Found at i:93670949 original size:29 final size:30
Alignment explanation
Indices: 93670924--93671015 Score: 104
Period size: 29 Copynumber: 3.2 Consensus size: 30
93670914 ATGAAAATCG
93670924 TAAAATTTTATA-AAA-ATAGTAAAAAATTA
1 TAAAATTTTATAGAAATATAG-AAAAAATTA
*
93670953 TAAAA-TATATAGAAATATAGAAAAAATTA
1 TAAAATTTTATAGAAATATAGAAAAAATTA
* *
93670982 TAAAATTTTAT-GAAGTCATA-AGAAAATTA
1 TAAAATTTTATAGAAAT-ATAGAAAAAATTA
93671011 TAAAA
1 TAAAA
93671016 AATGTAAAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.09
29 39 0.71
30 11 0.20
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.32
Consensus pattern (30 bp):
TAAAATTTTATAGAAATATAGAAAAAATTA
Found at i:93671619 original size:89 final size:88
Alignment explanation
Indices: 93671457--93671631 Score: 226
Period size: 89 Copynumber: 2.0 Consensus size: 88
93671447 GGTCAAAGGG
* * **
93671457 CCTTTTTAATGCATTTTGACAGTTCAAGTACCCAATTGAGTGCCAAAAAAAAAAGCAAGGGTTTA
1 CCTTTTTAATGCATTTTAAAAGTTCAAGTACCCAATTGAGTG-CAAAAAAAAAAGCAAGGACTTA
*
93671522 ATTTTTTTTGAAAAAGTTTGAGTA
65 ATTATTTTTGAAAAAGTTTGAGTA
* * * *
93671546 CCTTTTTTATGCATTTTAAAAGTTGAAGTATCCAATTGAGTG-TAAAAAAAAAGCAAGGACTTAA
1 CCTTTTTAATGCATTTTAAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAAGCAAGGACTTAA
*
93671610 TTACATTTTTTAAAAAGTTTGA
66 TT--ATTTTTGAAAAAGTTTGA
93671632 AAGCTTTTTA
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 21 0.28
89 53 0.72
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (88 bp):
CCTTTTTAATGCATTTTAAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAAGCAAGGACTTAA
TTATTTTTGAAAAAGTTTGAGTA
Found at i:93671910 original size:20 final size:20
Alignment explanation
Indices: 93671872--93671910 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
93671862 TAAATATCAT
*
93671872 TGTTGAAATTGTGCGAAATA
1 TGTTGAAATTGTGCAAAATA
93671892 TGTTGAAGATT-TGCAAAAT
1 TGTTGAA-ATTGTGCAAAAT
93671911 TAAGTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (20 bp):
TGTTGAAATTGTGCAAAATA
Found at i:93677734 original size:35 final size:35
Alignment explanation
Indices: 93677681--93677767 Score: 102
Period size: 35 Copynumber: 2.5 Consensus size: 35
93677671 TACTCTATAT
* * * *
93677681 TTGACGTGTTTCGTTTGGATTAGCTCTTATGAGCA
1 TTGACGTGTTACGGTTGGATTAACTCTTATAAGCA
*
93677716 TTGATGTGTTACGGTTGGATTAACTCTTATAAGCA
1 TTGACGTGTTACGGTTGGATTAACTCTTATAAGCA
* * *
93677751 TTGGCATGATACGGTTG
1 TTGACGTGTTACGGTTG
93677768 AATTGGCTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.40
Consensus pattern (35 bp):
TTGACGTGTTACGGTTGGATTAACTCTTATAAGCA
Found at i:93680791 original size:50 final size:46
Alignment explanation
Indices: 93680681--93680807 Score: 148
Period size: 50 Copynumber: 2.7 Consensus size: 46
93680671 TTCGAGAGCT
* * *
93680681 AGTGTAAGACCATGTATGGGACATGACATCGGCTATGAGGTGTGTC
1 AGTGTAAGACCATGTATGGGACATGACATCGGCAATGACGAGTGTC
*
93680727 AGTGTAAGACCATGTCTGGGACATGACATCGGCACAAATGGACGAGAT-TC
1 AGTGTAAGACCATGTATGGGACATGACATCGG--C-AAT-GACGAG-TGTC
* *
93680777 AGTGTAAGACCATGTTTGGGACATGGCATCG
1 AGTGTAAGACCATGTATGGGACATGACATCG
93680808 ACCTCGACAT
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
46 31 0.44
48 1 0.01
49 2 0.03
50 35 0.50
51 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACCATGTATGGGACATGACATCGGCAATGACGAGTGTC
Found at i:93680831 original size:50 final size:48
Alignment explanation
Indices: 93680777--93680905 Score: 152
Period size: 48 Copynumber: 2.6 Consensus size: 48
93680767 GACGAGATTC
*
93680777 AGTGTAAGACCATGTTTGGGACATGGCATCGACCTCGACATAC-AAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACCTCG--ATACGAA-AGCT
* * * * *
93680827 AGTGTAAGACCATGTCTGGGACATTGCATTGACTTTGATACGTAAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACCTCGATACGAAAGCT
* *
93680875 AGTGTAAGACCATATCTGGGACATGACATCG
1 AGTGTAAGACCATGTCTGGGACATGGCATCG
93680906 GCTTCCTACC
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
48 35 0.51
49 1 0.01
50 32 0.47
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACCTCGATACGAAAGCT
Found at i:93684669 original size:16 final size:16
Alignment explanation
Indices: 93684650--93684683 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
93684640 ATCACCTTTG
93684650 ATGTAACCACCCTTCA
1 ATGTAACCACCCTTCA
93684666 ATGTAACCACCCTTCA
1 ATGTAACCACCCTTCA
93684682 AT
1 AT
93684684 TGAGCTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.35, G:0.06, T:0.26
Consensus pattern (16 bp):
ATGTAACCACCCTTCA
Found at i:93691707 original size:25 final size:26
Alignment explanation
Indices: 93691679--93691729 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
93691669 AAGTATTTTT
*
93691679 TTAATAATATTTAACATA-TTAAATA
1 TTAAGAATATTTAACATATTTAAATA
*
93691704 TTAAGAATATTTAGCATATTTAAATA
1 TTAAGAATATTTAACATATTTAAATA
93691730 ACATATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (26 bp):
TTAAGAATATTTAACATATTTAAATA
Found at i:93711555 original size:22 final size:22
Alignment explanation
Indices: 93711505--93711592 Score: 74
Period size: 23 Copynumber: 3.9 Consensus size: 22
93711495 TGATAAACAA
**
93711505 TAAGCTCTATTAAGCTGAAACGG
1 TAAGCTCTATCGAGCTGAAAC-G
93711528 TAAGCTCTATCGAGCTGAATA-G
1 TAAGCTCTATCGAGCTGAA-ACG
*
93711550 TAAGCT-TATACGAGCTAAAACGG
1 TAAGCTCTAT-CGAGCTGAAAC-G
*
93711573 TAAGCTCCAAT-GAGCTGAAA
1 TAAGCT-CTATCGAGCTGAAA
93711593 ACAATAAACT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
21 4 0.07
22 15 0.28
23 32 0.59
24 1 0.02
25 2 0.04
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (22 bp):
TAAGCTCTATCGAGCTGAAACG
Found at i:93714940 original size:35 final size:35
Alignment explanation
Indices: 93714896--93715062 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
93714886 TCCTCATTGA
** *
93714896 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
93714931 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
93714971 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
93715006 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
93715041 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
93715063 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:93714979 original size:75 final size:73
Alignment explanation
Indices: 93714891--93715062 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
93714881 GGTTTTCCTC
** * * **
93714891 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
93714955 TCAGTATGG
65 TCAGTATGG
*
93714964 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
93715029 CTCAGTATGG
64 CTCAGTATGG
93715039 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
93715063 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:93722432 original size:35 final size:35
Alignment explanation
Indices: 93722388--93722554 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
93722378 TCCTCATTGA
** *
93722388 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
93722423 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
93722463 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
93722498 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
93722533 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
93722555 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:93722471 original size:75 final size:73
Alignment explanation
Indices: 93722383--93722554 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
93722373 GGTTTTCCTC
** * * **
93722383 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
93722447 TCAGTATGG
65 TCAGTATGG
*
93722456 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
93722521 CTCAGTATGG
64 CTCAGTATGG
93722531 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
93722555 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:93724455 original size:10 final size:10
Alignment explanation
Indices: 93724408--93724473 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
93724398 GAGCATTTGA
93724408 GAGCAAAAAT
1 GAGCAAAAAT
*
93724418 -CGCGAAAAAT
1 GAGC-AAAAAT
93724428 GAGCAAAAAT
1 GAGCAAAAAT
*
93724438 -CGCGAAAAAT
1 GAGC-AAAAAT
93724448 GAGCAAAAAT
1 GAGCAAAAAT
* *
93724458 CAGACAAAAAA
1 GAG-CAAAAAT
93724469 GAGCA
1 GAGCA
93724474 GATTTTAGGA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
9 4 0.09
10 28 0.64
11 12 0.27
ACGTcount: A:0.58, C:0.15, G:0.20, T:0.08
Consensus pattern (10 bp):
GAGCAAAAAT
Found at i:93724466 original size:20 final size:20
Alignment explanation
Indices: 93724408--93724458 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
93724398 GAGCATTTGA
93724408 GAGCAAAAATCGCGAAAAAT
1 GAGCAAAAATCGCGAAAAAT
93724428 GAGCAAAAATCGCGAAAAAT
1 GAGCAAAAATCGCGAAAAAT
93724448 GAGCAAAAATC
1 GAGCAAAAATC
93724459 AGACAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.55, C:0.16, G:0.20, T:0.10
Consensus pattern (20 bp):
GAGCAAAAATCGCGAAAAAT
Found at i:93725699 original size:30 final size:30
Alignment explanation
Indices: 93725665--93725733 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
93725655 GAATATGTTT
* *
93725665 CTCACACAAGA-TGACAATATATCAGGATTG
1 CTCACACAA-ATTGACAATATAACAGAATTG
* *
93725695 CTCACACAAATTGACATTATAACATAATTG
1 CTCACACAAATTGACAATATAACAGAATTG
93725725 CTCACACAA
1 CTCACACAA
93725734 TCTAACATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 1 0.03
30 33 0.97
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (30 bp):
CTCACACAAATTGACAATATAACAGAATTG
Found at i:93736440 original size:21 final size:21
Alignment explanation
Indices: 93736393--93736441 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
93736383 TCCAGACGGG
93736393 CATGTGCCCCTATCACACAGC
1 CATGTGCCCCTATCACACAGC
**
93736414 TGTGTGCCCCTATCACAC-GAC
1 CATGTGCCCCTATCACACAG-C
93736435 CATGTGC
1 CATGTGC
93736442 TACCTTTCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.20, C:0.39, G:0.18, T:0.22
Consensus pattern (21 bp):
CATGTGCCCCTATCACACAGC
Found at i:93738878 original size:23 final size:23
Alignment explanation
Indices: 93738851--93738897 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
93738841 TAATTAAGTT
93738851 AAATTTTCTTTTATAGGGAGACA
1 AAATTTTCTTTTATAGGGAGACA
93738874 AAATTTTCTTTTATAGGGAGACA
1 AAATTTTCTTTTATAGGGAGACA
93738897 A
1 A
93738898 GAATATGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (23 bp):
AAATTTTCTTTTATAGGGAGACA
Found at i:93756171 original size:3 final size:3
Alignment explanation
Indices: 93756163--93756221 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
93756153 AGTTAAAGAA
93756163 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
93756211 AAT AAT AAT AA
1 AAT AAT AAT AA
93756222 CAAACTATCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:93756970 original size:20 final size:21
Alignment explanation
Indices: 93756932--93756971 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
93756922 TATATATATT
* *
93756932 TTTTGAAATGAAATTAATCTA
1 TTTTGAAATAAAATAAATCTA
93756953 TTTTG-AATAAAATAAATCT
1 TTTTGAAATAAAATAAATCT
93756972 CTAGAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (21 bp):
TTTTGAAATAAAATAAATCTA
Found at i:93765945 original size:22 final size:22
Alignment explanation
Indices: 93765917--93765963 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
93765907 TTTGACTTTG
93765917 ATTTTATTCTATTAAGGCCAAT
1 ATTTTATTCTATTAAGGCCAAT
93765939 ATTTTATTCTATTAAGGCCAAT
1 ATTTTATTCTATTAAGGCCAAT
93765961 ATT
1 ATT
93765964 CTATATTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.47
Consensus pattern (22 bp):
ATTTTATTCTATTAAGGCCAAT
Found at i:93774830 original size:23 final size:23
Alignment explanation
Indices: 93774791--93774835 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
93774781 TTTTGAATTT
93774791 TTTTCAAAGTTTTTTTCTTTTTC
1 TTTTCAAAGTTTTTTTCTTTTTC
*
93774814 TTTTC-AATTTTTCTTTCTTTTT
1 TTTTCAAAGTTTT-TTTCTTTTT
93774836 AAAAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.11, C:0.13, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTCAAAGTTTTTTTCTTTTTC
Found at i:93783875 original size:26 final size:27
Alignment explanation
Indices: 93783829--93783883 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
93783819 TAATTTTTTG
*
93783829 AAAATCAAAATATTTACAAAAGAATAA
1 AAAATCAAAATATTTACAAAAAAATAA
* *
93783856 AAAATCATAATTTTTA-AAAAAAATAA
1 AAAATCAAAATATTTACAAAAAAATAA
93783882 AA
1 AA
93783884 TTTAAGAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.25
Consensus pattern (27 bp):
AAAATCAAAATATTTACAAAAAAATAA
Found at i:93784855 original size:30 final size:30
Alignment explanation
Indices: 93784798--93784863 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
93784788 TCATTGAACC
* *
93784798 TAAATTTTTAAATTTAAAAAATTAAAAAAT
1 TAAATTTTTAAATATAAAAAATCAAAAAAT
* *
93784828 TAAATTTTTAAATAT-AAAAGTACAAAAATT
1 TAAATTTTTAAATATAAAAAAT-CAAAAAAT
93784858 TAAATT
1 TAAATT
93784864 CAAATTTACG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (30 bp):
TAAATTTTTAAATATAAAAAATCAAAAAAT
Found at i:93786231 original size:2 final size:2
Alignment explanation
Indices: 93786224--93786254 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
93786214 TTGTTCCTTT
93786224 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
93786255 GAATGATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:93788424 original size:25 final size:25
Alignment explanation
Indices: 93788395--93788442 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
93788385 ATATTATATT
93788395 GTCTGCTTCTAATAGCACGTTTTGA
1 GTCTGCTTCTAATAGCACGTTTTGA
*
93788420 GTCTGCTTCTAATAGCATGTTTT
1 GTCTGCTTCTAATAGCACGTTTT
93788443 CGAATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (25 bp):
GTCTGCTTCTAATAGCACGTTTTGA
Found at i:93790666 original size:32 final size:32
Alignment explanation
Indices: 93790630--93790690 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
93790620 TCAACATAAA
93790630 AAGAGTAAGAATATGAGTCGTTTGGAGAATGG
1 AAGAGTAAGAATATGAGTCGTTTGGAGAATGG
93790662 AAGAGTAAGAATATGAGTCGTTTGGAGAA
1 AAGAGTAAGAATATGAGTCGTTTGGAGAA
93790691 CGGGGATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.03, G:0.33, T:0.25
Consensus pattern (32 bp):
AAGAGTAAGAATATGAGTCGTTTGGAGAATGG
Found at i:93791141 original size:22 final size:22
Alignment explanation
Indices: 93791115--93791159 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
93791105 TTTTAATAAA
93791115 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
93791137 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
93791159 A
1 A
93791160 CACTCCCCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:93795728 original size:22 final size:22
Alignment explanation
Indices: 93795703--93795747 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
93795693 TTTAATAAAA
93795703 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
93795725 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
93795747 A
1 A
93795748 CAGATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:93798555 original size:2 final size:2
Alignment explanation
Indices: 93798548--93798587 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
93798538 GCAATCTATC
93798548 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
93798588 CACGATATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:93798719 original size:42 final size:41
Alignment explanation
Indices: 93798672--93798752 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 41
93798662 AACTAAAGAT
93798672 ATAAAAAATTAAATAAAGAATTAAAA-ATAATATTTTAAAAAA
1 ATAAAAAATTAAATAAAGAATTAAAACA-AAT-TTTTAAAAAA
**
93798714 ATAAAAAATTAAATAAATCATTAAAACAAATTTTTAAAA
1 ATAAAAAATTAAATAAAGAATTAAAACAAATTTTTAAAA
93798753 TCTTAAATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 8 0.22
42 27 0.75
43 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (41 bp):
ATAAAAAATTAAATAAAGAATTAAAACAAATTTTTAAAAAA
Found at i:93799372 original size:13 final size:12
Alignment explanation
Indices: 93799332--93799375 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
93799322 ATTACTGTCA
93799332 AAAAATATTTTT
1 AAAAATATTTTT
*
93799344 AAAAAT-TTATTA
1 AAAAATATT-TTT
93799356 AAAAATATTTTT
1 AAAAATATTTTT
93799368 GAAAAATA
1 -AAAAATA
93799376 AAATATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 2 0.07
12 16 0.59
13 9 0.33
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (12 bp):
AAAAATATTTTT
Found at i:93805019 original size:15 final size:15
Alignment explanation
Indices: 93804999--93805036 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
93804989 ATAAAATCTG
93804999 TTTATTCTT-TATTAT
1 TTTATT-TTATATTAT
*
93805014 TTTATTTTATTTTAT
1 TTTATTTTATATTAT
93805029 TTTATTTT
1 TTTATTTT
93805037 CACAAATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 2 0.10
15 19 0.90
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATTTTATATTAT
Found at i:93805020 original size:5 final size:5
Alignment explanation
Indices: 93805010--93805036 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
93805000 TTATTCTTTA
93805010 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
93805037 CACAAATTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:93809205 original size:16 final size:18
Alignment explanation
Indices: 93809170--93809207 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
93809160 ATCCTTATTT
93809170 AAATAAAATACAATAGTA
1 AAATAAAATACAATAGTA
93809188 AAATAAAATA-AA-AGTA
1 AAATAAAATACAATAGTA
93809204 AAAT
1 AAAT
93809208 CCATATAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAATACAATAGTA
Found at i:93811646 original size:64 final size:65
Alignment explanation
Indices: 93811568--93811698 Score: 201
Period size: 64 Copynumber: 2.0 Consensus size: 65
93811558 AAATGATTAG
* * *
93811568 TAATATATCCTTGAAATGGATATTGACTTGATTTTGTCTGATTATAGCAACA-TCTATTCTGATC
1 TAATATATCCTTGAAATGGATATTGACTTGACTATGTCTGATTATAGCAACATTCTATTCTAATC
* * *
93811632 TAATATATCTTTGAAATGGATATTGACTTGACTATGTTTGATTATAGCAACATTTTATTCTAATC
1 TAATATATCCTTGAAATGGATATTGACTTGACTATGTCTGATTATAGCAACATTCTATTCTAATC
93811697 TA
1 TA
93811699 TTTTGAATTG
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
64 48 0.80
65 12 0.20
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (65 bp):
TAATATATCCTTGAAATGGATATTGACTTGACTATGTCTGATTATAGCAACATTCTATTCTAATC
Done.