Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 197 of 208
Found at i:61062919 original size:33 final size:33
Alignment explanation
Indices: 61062840--61063010 Score: 147
Period size: 34 Copynumber: 5.1 Consensus size: 33
61062830 AGAGGGGAAG
61062840 AAGAA-GAAAG-AAAGGA-AGG-AAGAAAGAAA
1 AAGAAGGAAAGAAAAGGAGAGGAAAGAAAGAAA
*
61062869 AAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAA
1 AAGAAGG-AAAGAAAAGGAGAGGAAAGAAAGAAA
61062903 AAGAAGGAAAGAAAAGGAAAGGGGAGGAAAGAAAGAAA
1 AAGAAGGAAAGAAAAGG--A---GAGGAAAGAAAGAAA
* *
61062941 AATAAGGAAAGAAAAGGAAAGGAGAAGAGAA-AAA
1 AAGAAGGAAAGAAAAGGAGAGGA-AAGA-AAGAAA
* * * *
61062975 AA-AAAGAAAGAAGAAGAAGAGGGAAGGAAGGAAA
1 AAGAAGGAAAGAA-AAGGAGA-GGAAAGAAAGAAA
61063009 AA
1 AA
61063011 AAAAGAAAAT
Statistics
Matches: 119, Mismatches: 8, Indels: 25
0.78 0.05 0.16
Matches are distributed among these distances:
29 5 0.04
30 1 0.01
31 4 0.03
32 6 0.05
33 26 0.22
34 39 0.33
35 6 0.05
36 1 0.01
38 31 0.26
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (33 bp):
AAGAAGGAAAGAAAAGGAGAGGAAAGAAAGAAA
Found at i:61063746 original size:19 final size:19
Alignment explanation
Indices: 61063698--61063749 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
61063688 AAAAAATATA
** *
61063698 TAATATTTTGGTATTTTTT
1 TAATATTTTATTATTTTTG
61063717 TAATATTTTATTATTTTTG
1 TAATATTTTATTATTTTTG
*
61063736 TAATGTTTTATTAT
1 TAATATTTTATTAT
61063750 GGGTTTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (19 bp):
TAATATTTTATTATTTTTG
Found at i:61063822 original size:27 final size:27
Alignment explanation
Indices: 61063785--61063852 Score: 120
Period size: 27 Copynumber: 2.5 Consensus size: 27
61063775 AAATAAAAAA
61063785 TTACCAAAATAT-TATAACTTTTTTTAT
1 TTACCAAAATATATATAA-TTTTTTTAT
61063812 TTACCAAAATATATATAATTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTAT
61063839 TTACCAAAATATAT
1 TTACCAAAATATAT
61063853 CAAAAAAGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 35 0.88
28 5 0.12
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (27 bp):
TTACCAAAATATATATAATTTTTTTAT
Found at i:61068592 original size:18 final size:18
Alignment explanation
Indices: 61068566--61068603 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
61068556 ATCCCAATGA
*
61068566 TCGCCACCACCTTCTTCT
1 TCGCAACCACCTTCTTCT
61068584 TCGCAACCACCTTCTTCT
1 TCGCAACCACCTTCTTCT
61068602 TC
1 TC
61068604 ACCACCAACA
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:0.13, C:0.47, G:0.05, T:0.34
Consensus pattern (18 bp):
TCGCAACCACCTTCTTCT
Found at i:61068610 original size:18 final size:18
Alignment explanation
Indices: 61068569--61068610 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
61068559 CCAATGATCG
*
61068569 CCACCACCTTCTTCTTCG
1 CCACCACCTTCTTCTTCA
*
61068587 CAACCACCTTCTTCTTCA
1 CCACCACCTTCTTCTTCA
61068605 CCACCA
1 CCACCA
61068611 ACAATATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.50, G:0.02, T:0.29
Consensus pattern (18 bp):
CCACCACCTTCTTCTTCA
Found at i:61069290 original size:26 final size:26
Alignment explanation
Indices: 61069261--61069312 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
61069251 TAGTTAGTAT
61069261 TATTTTGTATATAAAATTATTAATAA
1 TATTTTGTATATAAAATTATTAATAA
61069287 TATTTTGTATATAAAATTATTAATAA
1 TATTTTGTATATAAAATTATTAATAA
61069313 CTAACTACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (26 bp):
TATTTTGTATATAAAATTATTAATAA
Found at i:61069375 original size:3 final size:3
Alignment explanation
Indices: 61069367--61069416 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
61069357 AGTAACATCT
61069367 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
61069415 TA
1 TA
61069417 CTATAAAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:61069604 original size:8 final size:8
Alignment explanation
Indices: 61069591--61069616 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
61069581 GATTTTTCTC
61069591 TTCTCTTT
1 TTCTCTTT
61069599 TTCTCTTT
1 TTCTCTTT
61069607 TTCTCTTT
1 TTCTCTTT
61069615 TT
1 TT
61069617 TTCCGCAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTCTCTTT
Found at i:61069802 original size:17 final size:17
Alignment explanation
Indices: 61069780--61069812 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
61069770 AGTCCAGGTT
61069780 TTTTTTTCTGTTTTTTA
1 TTTTTTTCTGTTTTTTA
61069797 TTTTTTTCTGTTTTTT
1 TTTTTTTCTGTTTTTT
61069813 TGATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.06, G:0.06, T:0.85
Consensus pattern (17 bp):
TTTTTTTCTGTTTTTTA
Found at i:61069846 original size:28 final size:27
Alignment explanation
Indices: 61069815--61069881 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 27
61069805 TGTTTTTTTG
*
61069815 ATATATTTTGGTAAATAAAAAACATTAT
1 ATATATTTTGGTAAATAAAAAAAATT-T
* *
61069843 ATATTTTTTGATAAATAAAAAAAATTT
1 ATATATTTTGGTAAATAAAAAAAATTT
*
61069870 ATAACATTTTGG
1 AT-ATATTTTGG
61069882 ATATTTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 3 0.09
28 29 0.91
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (27 bp):
ATATATTTTGGTAAATAAAAAAAATTT
Found at i:61072641 original size:16 final size:16
Alignment explanation
Indices: 61072611--61072644 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61072601 CTTTCTCTTA
**
61072611 TTTGTTGATGGAACTT
1 TTTGTTGATCCAACTT
61072627 TTTGTTGATCCAACTT
1 TTTGTTGATCCAACTT
61072643 TT
1 TT
61072645 CTCTGTCAGA
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:0.18, C:0.12, G:0.18, T:0.53
Consensus pattern (16 bp):
TTTGTTGATCCAACTT
Found at i:61080945 original size:18 final size:18
Alignment explanation
Indices: 61080922--61080992 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 18
61080912 CCCAACTACT
*
61080922 ATATACGTGAACAGTACC
1 ATATACGTGAATAGTACC
* *
61080940 ATATACGTGAATAGTGCT
1 ATATACGTGAATAGTACC
* * *
61080958 GTATACATGAATAGTGCC
1 ATATACGTGAATAGTACC
*
61080976 GTATACGTGAATAGTAC
1 ATATACGTGAATAGTAC
61080993 TGTAAACGGT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.28
Consensus pattern (18 bp):
ATATACGTGAATAGTACC
Found at i:61080981 original size:36 final size:36
Alignment explanation
Indices: 61080918--61080996 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
61080908 CAATCCCAAC
* *
61080918 TACTATATACGTGAACAGTACCATATACGTGAATAG
1 TACTGTATACATGAACAGTACCATATACGTGAATAG
* * * *
61080954 TGCTGTATACATGAATAGTGCCGTATACGTGAATAG
1 TACTGTATACATGAACAGTACCATATACGTGAATAG
61080990 TACTGTA
1 TACTGTA
61080997 AACGGTCGTA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30
Consensus pattern (36 bp):
TACTGTATACATGAACAGTACCATATACGTGAATAG
Found at i:61082707 original size:25 final size:25
Alignment explanation
Indices: 61082673--61082724 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
61082663 TAACATGGCT
61082673 TTGAAAGCTGCTCTAAAATCATCCA
1 TTGAAAGCTGCTCTAAAATCATCCA
61082698 TTGAAAGCTGCTCTAAAATCATCCA
1 TTGAAAGCTGCTCTAAAATCATCCA
61082723 TT
1 TT
61082725 CTTTCATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.31
Consensus pattern (25 bp):
TTGAAAGCTGCTCTAAAATCATCCA
Found at i:61085276 original size:21 final size:21
Alignment explanation
Indices: 61085251--61085306 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
61085241 AATAGTGGTG
*
61085251 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
61085272 GCGGTGAGATTAGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
61085293 GCGGTGAAATTAGA
1 GCGGTGAGATTAGA
61085307 AACAATGGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:61086292 original size:25 final size:25
Alignment explanation
Indices: 61086258--61086307 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
61086248 CGGTTGATGT
*
61086258 TAGCCAATGAGCAAAATCTCGAACC
1 TAGCCAATGAGCAAAATCTCAAACC
61086283 TAGCCAATGAGCAAAATCTCAAACC
1 TAGCCAATGAGCAAAATCTCAAACC
61086308 ACATCATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.28, G:0.14, T:0.16
Consensus pattern (25 bp):
TAGCCAATGAGCAAAATCTCAAACC
Found at i:61091977 original size:30 final size:30
Alignment explanation
Indices: 61091931--61092054 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
61091921 TTTTATTATG
*
61091931 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
61091962 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
61091992 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * * *
61092022 CTATTATTTGATACCCATATTTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
61092052 CCA
1 CCA
61092055 TAAATATGGA
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 80 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:61091986 original size:15 final size:15
Alignment explanation
Indices: 61091941--61092048 Score: 69
Period size: 15 Copynumber: 7.2 Consensus size: 15
61091931 CCAATATCTC
*
61091941 GATACCCATATCTTT
1 GATACCCATATATTT
**
61091956 GACTTTCCA-ATATTT
1 GA-TACCCATATATTT
*
61091971 GATACCCATATCTTT
1 GATACCCATATATTT
**
61091986 GACTTTCCA-ATATTT
1 GA-TACCCATATATTT
*
61092001 GATACCCATATCTTT
1 GATACCCATATATTT
** *
61092016 GACTTTCTAT-TATTT
1 GA-TACCCATATATTT
*
61092031 GATACCCATATTTTT
1 GATACCCATATATTT
61092046 GAT
1 GAT
61092049 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.45
Consensus pattern (15 bp):
GATACCCATATATTT
Found at i:61096669 original size:30 final size:30
Alignment explanation
Indices: 61096625--61096748 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
61096615 TTTTATTATG
61096625 CCAATATCTTGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
61096656 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
61096686 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
61096716 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
61096746 CCA
1 CCA
61096749 TAAATATGGA
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
30 82 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:61096710 original size:15 final size:15
Alignment explanation
Indices: 61096628--61096742 Score: 85
Period size: 15 Copynumber: 7.7 Consensus size: 15
61096618 TATTATGCCA
61096628 ATATC-TTGATACCC
1 ATATCTTTGATACCC
**
61096642 ATATCTTTGACTTTCC
1 ATATCTTTGA-TACCC
*
61096658 A-ATATTTGATACCC
1 ATATCTTTGATACCC
**
61096672 ATATCTTTGACTTTCC
1 ATATCTTTGA-TACCC
*
61096688 A-ATATTTGATACCC
1 ATATCTTTGATACCC
** *
61096702 ATATCTTTGACTTTCT
1 ATATCTTTGA-TACCC
*
61096718 AT-TATTTGATACCC
1 ATATCTTTGATACCC
61096732 ATATCTTTGAT
1 ATATCTTTGAT
61096743 TTTCCATAAA
Statistics
Matches: 74, Mismatches: 20, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
14 17 0.23
15 45 0.61
16 12 0.16
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.45
Consensus pattern (15 bp):
ATATCTTTGATACCC
Found at i:61099278 original size:18 final size:18
Alignment explanation
Indices: 61099251--61099285 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
61099241 TTAAAAAATA
*
61099251 AATTTCTAGTTAATTCGG
1 AATTTCTAGTCAATTCGG
*
61099269 AATTTTTAGTCAATTCG
1 AATTTCTAGTCAATTCG
61099286 AATATGTAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (18 bp):
AATTTCTAGTCAATTCGG
Found at i:61099368 original size:18 final size:18
Alignment explanation
Indices: 61099333--61099369 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
61099323 AACTTTTTCC
**
61099333 ATTTGAATAACTTGAATA
1 ATTTGAATAACTCAAATA
61099351 ATTTGAATAACTCAAATA
1 ATTTGAATAACTCAAATA
61099369 A
1 A
61099370 CAGATGGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (18 bp):
ATTTGAATAACTCAAATA
Found at i:61099636 original size:16 final size:16
Alignment explanation
Indices: 61099617--61099647 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61099607 TTGAAAAAGT
61099617 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
61099633 TTTCAAATTTATATG
1 TTTCAAATATATATG
61099648 CAGTAAAATA
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:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:61100505 original size:34 final size:34
Alignment explanation
Indices: 61100462--61100537 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 34
61100452 AATACATGTA
* *
61100462 AAGCATGTTTATTGCTACCGTATTAA-TCTGTTTT
1 AAGCATGTTTATTGCTACCATATTAATTC-GTTAT
* *
61100496 AAGCATGTTTATTGTTACCATATTGATTCGTTAT
1 AAGCATGTTTATTGCTACCATATTAATTCGTTAT
61100530 AAGCATGT
1 AAGCATGT
61100538 CATATTGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 35 0.95
35 2 0.05
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (34 bp):
AAGCATGTTTATTGCTACCATATTAATTCGTTAT
Found at i:61104088 original size:33 final size:33
Alignment explanation
Indices: 61104033--61104181 Score: 124
Period size: 33 Copynumber: 4.5 Consensus size: 33
61104023 TTTCACACAG
* * * *
61104033 CATATAGGCTCACATGTACCTAGGGTTCGCATA
1 CATATAGGCTCGCTTATTCCTAGGGTTCGCATA
* * * *
61104066 CATATTGACTCGCTTATTCCTAGGGTTTGTATA
1 CATATAGGCTCGCTTATTCCTAGGGTTCGCATA
*
61104099 CATATAGGCTCGCATGTA-T-C-AGGGGTTCGTATA
1 CATATAGGCTCGC-T-TATTCCTA-GGGTTCGCATA
* * * *
61104132 CATATAGGCTCACTTATTCATAGGGTTCCCATG
1 CATATAGGCTCGCTTATTCCTAGGGTTCGCATA
*
61104165 CATATAGGCTCACTTAT
1 CATATAGGCTCGCTTAT
61104182 AATAAACACA
Statistics
Matches: 94, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
31 2 0.02
32 3 0.03
33 84 0.89
34 3 0.03
35 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (33 bp):
CATATAGGCTCGCTTATTCCTAGGGTTCGCATA
Found at i:61104115 original size:66 final size:66
Alignment explanation
Indices: 61104033--61104177 Score: 175
Period size: 66 Copynumber: 2.2 Consensus size: 66
61104023 TTTCACACAG
* * *
61104033 CATATAGGCTCACATGTACCTA-GGGTTCGCATACATATTGACTCGCTTATTCCTAGGGTTTGTA
1 CATATAGGCTCACATGTACC-AGGGGTTCGCATACATATAGACTCACTTATTCATAGGGTTTGTA
61104097 TA
65 TA
* * * * ***
61104099 CATATAGGCTCGCATGTATCAGGGGTTCGTATACATATAGGCTCACTTATTCATAGGGTTCCCAT
1 CATATAGGCTCACATGTACCAGGGGTTCGCATACATATAGACTCACTTATTCATAGGGTTTGTAT
*
61104164 G
66 A
61104165 CATATAGGCTCAC
1 CATATAGGCTCAC
61104178 TTATAATAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 1 0.02
66 65 0.98
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (66 bp):
CATATAGGCTCACATGTACCAGGGGTTCGCATACATATAGACTCACTTATTCATAGGGTTTGTAT
A
Found at i:61104219 original size:36 final size:36
Alignment explanation
Indices: 61104171--61104257 Score: 129
Period size: 36 Copynumber: 2.4 Consensus size: 36
61104161 CATGCATATA
* *
61104171 GGCTCACTTATAATAAACACATGGTTTGCATAACAT
1 GGCTCACATATAATAAACACATGGTTCGCATAACAT
*
61104207 GGCTCACATATAATAAACACATGGTTCGCGTAACAT
1 GGCTCACATATAATAAACACATGGTTCGCATAACAT
* *
61104243 GGCTCGCACATAATA
1 GGCTCACATATAATA
61104258 TCATATAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (36 bp):
GGCTCACATATAATAAACACATGGTTCGCATAACAT
Found at i:61105047 original size:11 final size:11
Alignment explanation
Indices: 61105031--61105056 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
61105021 GAAAAAAAAT
61105031 AAAAATTCTTA
1 AAAAATTCTTA
61105042 AAAAATTCTTA
1 AAAAATTCTTA
61105053 AAAA
1 AAAA
61105057 TATATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAATTCTTA
Found at i:61105181 original size:16 final size:16
Alignment explanation
Indices: 61105160--61105190 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61105150 ATTGAAAAAG
61105160 ATTTCAAATATATATA
1 ATTTCAAATATATATA
*
61105176 ATTTCAAATTTATAT
1 ATTTCAAATATATAT
61105191 GCAGTAAAAT
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:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTCAAATATATATA
Found at i:61106022 original size:34 final size:34
Alignment explanation
Indices: 61105949--61106024 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 34
61105939 GAAATACATG
* * *
61105949 TTAAGCATGTTTATTGATACCGTATTAATCTGGT
1 TTAAGCATATTTATTGATACCATATTAATCTCGT
* *
61105983 TTAAGCATATTTATTGTTACCATATTGATC-CGT
1 TTAAGCATATTTATTGATACCATATTAATCTCGT
61106016 TATAAGCAT
1 T-TAAGCAT
61106025 GTCATATTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
33 3 0.08
34 33 0.92
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.43
Consensus pattern (34 bp):
TTAAGCATATTTATTGATACCATATTAATCTCGT
Found at i:61109297 original size:34 final size:34
Alignment explanation
Indices: 61109250--61109325 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
61109240 CACATTTACA
* * **
61109250 GGTTCGCATAACATACAGGCTTGCATGCACCTAG
1 GGTTCACACAACATACAGGCTCACATGCACCTAG
* * *
61109284 GTTTCACACAACATATAGGCTCACATGTACCTAG
1 GGTTCACACAACATACAGGCTCACATGCACCTAG
61109318 GGTTCACA
1 GGTTCACA
61109326 TACATATTGA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (34 bp):
GGTTCACACAACATACAGGCTCACATGCACCTAG
Found at i:61109373 original size:33 final size:33
Alignment explanation
Indices: 61109294--61109410 Score: 103
Period size: 33 Copynumber: 3.5 Consensus size: 33
61109284 GTTTCACACA
* * * *
61109294 ACATATAGGCTCACATGTACCTAGGGTTCACAT
1 ACATATAGGCTCACTTATTCCTAGGGTTCGCAT
* * * *
61109327 ACATATTGACTCGCTTATTCCTAGGGTTCGTAT
1 ACATATAGGCTCACTTATTCCTAGGGTTCGCAT
* **
61109360 ACATATAGGCTCGCATGTA-T-CGGGGGTTCGCAT
1 ACATATAGGCTCAC-T-TATTCCTAGGGTTCGCAT
61109393 ACATATAGGCTCACTTAT
1 ACATATAGGCTCACTTAT
61109411 AACAAAAACA
Statistics
Matches: 67, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
31 2 0.03
32 1 0.01
33 60 0.90
34 2 0.03
35 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (33 bp):
ACATATAGGCTCACTTATTCCTAGGGTTCGCAT
Found at i:61112234 original size:7 final size:7
Alignment explanation
Indices: 61112224--61112274 Score: 79
Period size: 7 Copynumber: 7.6 Consensus size: 7
61112214 TTTAAATTTT
61112224 AACCCTA
1 AACCCTA
61112231 AACCCTA
1 AACCCTA
61112238 AACCCTA
1 AACCCTA
*
61112245 AACCTTA
1 AACCCTA
61112252 AA-CCTA
1 AACCCTA
61112258 AA-CCTA
1 AACCCTA
61112264 AACCCTA
1 AACCCTA
61112271 AACC
1 AACC
61112275 TAGAAACAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 11 0.27
7 30 0.73
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (7 bp):
AACCCTA
Found at i:61112276 original size:13 final size:13
Alignment explanation
Indices: 61112224--61112276 Score: 81
Period size: 13 Copynumber: 4.0 Consensus size: 13
61112214 TTTAAATTTT
61112224 AACCCTAAACCCTA
1 AACCCTAAA-CCTA
61112238 AACCCTAAACCTTA
1 AACCCTAAACC-TA
61112252 AA-CCTAAACCTA
1 AACCCTAAACCTA
61112264 AACCCTAAACCTA
1 AACCCTAAACCTA
61112277 GAAACAGGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.11
13 20 0.54
14 13 0.35
ACGTcount: A:0.45, C:0.38, G:0.00, T:0.17
Consensus pattern (13 bp):
AACCCTAAACCTA
Found at i:61112559 original size:18 final size:18
Alignment explanation
Indices: 61112500--61112567 Score: 65
Period size: 16 Copynumber: 4.1 Consensus size: 18
61112490 ATGCCTTATG
61112500 TAATAAAAAATA-AAA-A
1 TAATAAAAAATATAAATA
* *
61112516 -AATAAAAAATTTATATA
1 TAATAAAAAATATAAATA
*
61112533 -AAT-ATAAATATAAATA
1 TAATAAAAAATATAAATA
*
61112549 TAATAAAAAATAAAAATA
1 TAATAAAAAATATAAATA
61112567 T
1 T
61112568 CAACATGGAC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
15 10 0.24
16 12 0.29
17 7 0.17
18 12 0.29
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
TAATAAAAAATATAAATA
Found at i:61114839 original size:21 final size:22
Alignment explanation
Indices: 61114813--61114859 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
61114803 CTCTGCTCAA
*
61114813 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
61114834 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
61114856 ACTC
1 ACTC
61114860 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:61125019 original size:3 final size:3
Alignment explanation
Indices: 61125011--61125054 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
61125001 AAAGTTGTCT
61125011 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
61125055 TACTATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:61133050 original size:30 final size:30
Alignment explanation
Indices: 61133016--61133076 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
61133006 CGGTCTATAA
61133016 TAGACCATACGGCTTGGACACACGGGCGTG
1 TAGACCATACGGCTTGGACACACGGGCGTG
* *
61133046 TAGACTATACGGCTTGGACACACGGGTGTG
1 TAGACCATACGGCTTGGACACACGGGCGTG
61133076 T
1 T
61133077 CCTAGGCCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.21
Consensus pattern (30 bp):
TAGACCATACGGCTTGGACACACGGGCGTG
Found at i:61133683 original size:6 final size:6
Alignment explanation
Indices: 61133674--61133701 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
61133664 CTCTTGCCCA
61133674 TTTTAC TTTTAC TTTTAC TTTTAC TTTT
1 TTTTAC TTTTAC TTTTAC TTTTAC TTTT
61133702 TATGTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAC
Found at i:61135584 original size:30 final size:30
Alignment explanation
Indices: 61135544--61135600 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
61135534 CAGCATTTTT
* *
61135544 CACACGGGCTGGGCACAAGCCCATGTGAGA
1 CACACAGGCTGGCCACAAGCCCATGTGAGA
*
61135574 CACACAGGCTGGCCACACGCCCATGTG
1 CACACAGGCTGGCCACAAGCCCATGTG
61135601 CTAGCCCGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.25, C:0.35, G:0.30, T:0.11
Consensus pattern (30 bp):
CACACAGGCTGGCCACAAGCCCATGTGAGA
Found at i:61137928 original size:37 final size:37
Alignment explanation
Indices: 61137877--61137967 Score: 155
Period size: 37 Copynumber: 2.5 Consensus size: 37
61137867 TAGACACTAT
* *
61137877 ATGGTGTATAGGGATGGGTGGGTGTTTTATACCCCAC
1 ATGGTGTGTTGGGATGGGTGGGTGTTTTATACCCCAC
61137914 ATGGTGTGTTGGGATGGGTGGGTGTTTTATACCCCAC
1 ATGGTGTGTTGGGATGGGTGGGTGTTTTATACCCCAC
*
61137951 ATGGTGAGTTGGGATGG
1 ATGGTGTGTTGGGATGG
61137968 TTGGAGTTGG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.16, C:0.11, G:0.40, T:0.33
Consensus pattern (37 bp):
ATGGTGTGTTGGGATGGGTGGGTGTTTTATACCCCAC
Found at i:61141983 original size:26 final size:23
Alignment explanation
Indices: 61141946--61142005 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 23
61141936 ACTGATGCCC
*
61141946 GAATAGACATGAAAAGATGTCTCTAT
1 GAATAGAAATGAAAA-AT-TC-CTAT
61141972 GAATAGAAATG-AAAATTCCTAT
1 GAATAGAAATGAAAAATTCCTAT
*
61141994 AAATAGAAATGA
1 GAATAGAAATGA
61142006 GATTTCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 14 0.45
23 2 0.06
24 2 0.06
25 3 0.10
26 10 0.32
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (23 bp):
GAATAGAAATGAAAAATTCCTAT
Found at i:61149552 original size:21 final size:21
Alignment explanation
Indices: 61149527--61149572 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
61149517 TCTTCCTATC
*
61149527 TATTATTTCCACATTTTGTGT
1 TATTATTTCCACATTTTATGT
61149548 TATTATTTCCACATTTTATGT
1 TATTATTTCCACATTTTATGT
61149569 TATT
1 TATT
61149573 TTCAGAACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.59
Consensus pattern (21 bp):
TATTATTTCCACATTTTATGT
Found at i:61150871 original size:30 final size:29
Alignment explanation
Indices: 61150813--61150876 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
61150803 TGTACAATTG
* *
61150813 AAATTTAGTCTTTAATTTTTAATTTTTAA
1 AAATTTAGTCTTCAATTTTTAATATTTAA
*
61150842 GAATTTAGTCCTTCAATTTTTCAA-ATTTAA
1 AAATTTAGT-CTTCAATTTTT-AATATTTAA
61150872 AAATT
1 AAATT
61150877 CAAATATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 8 0.28
30 19 0.66
31 2 0.07
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.52
Consensus pattern (29 bp):
AAATTTAGTCTTCAATTTTTAATATTTAA
Found at i:61151267 original size:17 final size:17
Alignment explanation
Indices: 61151224--61151269 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
61151214 TAACATAGGA
61151224 ACTAAAATTGAAACTTT
1 ACTAAAATTGAAACTTT
* ** *
61151241 ACCATTATTGAAATTTT
1 ACTAAAATTGAAACTTT
61151258 ACTAAAATTGAA
1 ACTAAAATTGAA
61151270 GTTTGCCTTA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (17 bp):
ACTAAAATTGAAACTTT
Found at i:61157275 original size:15 final size:15
Alignment explanation
Indices: 61157255--61157284 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61157245 AGTATATAAT
61157255 TTAAAATTTAAACCA
1 TTAAAATTTAAACCA
*
61157270 TTAAAATTTCAACCA
1 TTAAAATTTAAACCA
61157285 AATTATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAAATTTAAACCA
Found at i:61160824 original size:22 final size:23
Alignment explanation
Indices: 61160799--61160848 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
61160789 CGTGGAACTC
61160799 TCCACA-TTTTGAACAATTGTCT
1 TCCACAGTTTTGAACAATTGTCT
*
61160821 TCCATATGTTTTGAACAATTGTCT
1 TCCACA-GTTTTGAACAATTGTCT
61160845 TCCA
1 TCCA
61160849 TATTCTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 5 0.20
24 20 0.80
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (23 bp):
TCCACAGTTTTGAACAATTGTCT
Found at i:61160832 original size:24 final size:24
Alignment explanation
Indices: 61160805--61160851 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
61160795 ACTCTCCACA
61160805 TTTTGAACAATTGTCTTCCATATG
1 TTTTGAACAATTGTCTTCCATATG
61160829 TTTTGAACAATTGTCTTCCATAT
1 TTTTGAACAATTGTCTTCCATAT
61160852 TCTAACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.47
Consensus pattern (24 bp):
TTTTGAACAATTGTCTTCCATATG
Found at i:61161001 original size:41 final size:41
Alignment explanation
Indices: 61160912--61161001 Score: 92
Period size: 42 Copynumber: 2.2 Consensus size: 41
61160902 ACTTCTTTTG
* * * *
61160912 AATCGATTATTTTTTGTTTAAATTGATTCTTCTCTATTTTG
1 AATCGATTATTTTTTATTTAAATTGATTCATCTCTAGTTTA
* * * *
61160953 AACCGATTGTTTTTTTATTTGAATTGATTCATCT-TGGTTTA
1 AATCGATT-ATTTTTTATTTAAATTGATTCATCTCTAGTTTA
61160994 AATCGATT
1 AATCGATT
61161002 CTTTGTGGAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
41 18 0.46
42 21 0.54
ACGTcount: A:0.23, C:0.10, G:0.12, T:0.54
Consensus pattern (41 bp):
AATCGATTATTTTTTATTTAAATTGATTCATCTCTAGTTTA
Found at i:61164771 original size:23 final size:23
Alignment explanation
Indices: 61164715--61164778 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 23
61164705 AAATTAGAAT
*
61164715 AAAATTAA-CATTTATTATTTCA
1 AAAATAAATCATTTATTATTTCA
*
61164737 ATTTAAAAAAATCATTTATTATTTCA
1 A---AAATAAATCATTTATTATTTCA
61164763 AAAATAAATCAATTTA
1 AAAATAAATC-ATTTA
61164779 ATTTTTGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
22 1 0.03
23 8 0.24
24 5 0.15
25 5 0.15
26 15 0.44
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (23 bp):
AAAATAAATCATTTATTATTTCA
Found at i:61181038 original size:27 final size:29
Alignment explanation
Indices: 61180966--61181027 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
61180956 ATTGAAATTT
* *
61180966 TAAAATTTAAAATTTAAAAATGAAAATAAA
1 TAAAA-TTAAAGTATAAAAATGAAAATAAA
*
61180996 TTAAATTAAAGTATAAAAAT-AAAA-AAA
1 TAAAATTAAAGTATAAAAATGAAAATAAA
61181023 TAAAA
1 TAAAA
61181028 CTTACATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 7 0.25
28 4 0.14
29 13 0.46
30 4 0.14
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (29 bp):
TAAAATTAAAGTATAAAAATGAAAATAAA
Found at i:61183578 original size:18 final size:18
Alignment explanation
Indices: 61183552--61183595 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
61183542 GACTCGAAAA
* * *
61183552 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
61183570 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
61183588 AGGATACA
1 AGGATACA
61183596 CACTTGGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.09, G:0.27, T:0.18
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:61184252 original size:7 final size:7
Alignment explanation
Indices: 61184242--61184267 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
61184232 TTATATACAT
61184242 AATACTA
1 AATACTA
61184249 AATACTA
1 AATACTA
61184256 AATACTA
1 AATACTA
61184263 AATAC
1 AATAC
61184268 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:61185460 original size:11 final size:11
Alignment explanation
Indices: 61185444--61185489 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
61185434 AAATAGGGAT
61185444 TTGAGAGAAAA
1 TTGAGAGAAAA
*
61185455 TTGAGAGGAAA
1 TTGAGAGAAAA
* *
61185466 TTGATAGCAAA
1 TTGAGAGAAAA
61185477 TTGAGAGAAAA
1 TTGAGAGAAAA
61185488 TT
1 TT
61185490 AGGGAAATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.48, C:0.02, G:0.26, T:0.24
Consensus pattern (11 bp):
TTGAGAGAAAA
Found at i:61186291 original size:18 final size:20
Alignment explanation
Indices: 61186251--61186293 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
61186241 AAAGAATTTC
**
61186251 AAAAATTCAGAAAAATCTTA
1 AAAAATTCAGAAAAATCAGA
61186271 AAAAATT-A-AAAAATCAGA
1 AAAAATTCAGAAAAATCAGA
61186289 AAAAA
1 AAAAA
61186294 CTTGCCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 13 0.62
19 1 0.05
20 7 0.33
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.19
Consensus pattern (20 bp):
AAAAATTCAGAAAAATCAGA
Found at i:61188724 original size:41 final size:41
Alignment explanation
Indices: 61188641--61188725 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
61188631 TATAGCGGCA
* **
61188641 TTTATGAGAAAAATGATGCAAAAGATCAAGCAGTAGTGGCG
1 TTTATGAGAAAAACGATGCAAAAGATCAAGCAGTAGCAGCG
* *
61188682 TTTATGAGAAAAACGCTGCAAAA-AGTCAAGCATTAGCAGCG
1 TTTATGAGAAAAACGATGCAAAAGA-TCAAGCAGTAGCAGCG
61188723 TTT
1 TTT
61188726 TTGCAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.24
Consensus pattern (41 bp):
TTTATGAGAAAAACGATGCAAAAGATCAAGCAGTAGCAGCG
Found at i:61207306 original size:19 final size:19
Alignment explanation
Indices: 61207282--61207326 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
61207272 AAATAATATA
61207282 TATAAAA-TAAGAAAAAAAT
1 TATAAAAGTAA-AAAAAAAT
*
61207301 TATAAAAGTAAAATAAAAT
1 TATAAAAGTAAAAAAAAAT
61207320 TATAAAA
1 TATAAAA
61207327 AATATTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (19 bp):
TATAAAAGTAAAAAAAAAT
Found at i:61207346 original size:31 final size:30
Alignment explanation
Indices: 61207249--61207346 Score: 72
Period size: 30 Copynumber: 3.1 Consensus size: 30
61207239 ATTTTTTCTC
* *
61207249 TAAATATTATAAAAAATATTGAAAAATAATATATA
1 TAAA-ATTATAAAAAATATT--AAAAT-GT-TAAA
* * * *
61207284 TAAAATAAGAAAAAA-ATTATAAAAGTAAAA
1 TAAAATTATAAAAAATATTA-AAATGTTAAA
61207314 TAAAATTATAAAAAATATTCAAAATGTTAAA
1 TAAAATTATAAAAAATATT-AAAATGTTAAA
61207345 TA
1 TA
61207347 TTAAAAATAT
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
30 15 0.30
31 15 0.30
32 4 0.08
33 3 0.06
34 9 0.18
35 4 0.08
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (30 bp):
TAAAATTATAAAAAATATTAAAATGTTAAA
Found at i:61207607 original size:16 final size:18
Alignment explanation
Indices: 61207578--61207615 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
61207568 TTGAACAGAT
61207578 TTTTTTAATATTTTAATA
1 TTTTTTAATATTTTAATA
61207596 TTTTTT-AT-TTTTAATA
1 TTTTTTAATATTTTAATA
61207612 TTTT
1 TTTT
61207616 ATTTAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.60
17 2 0.10
18 6 0.30
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTAATATTTTAATA
Found at i:61207917 original size:28 final size:27
Alignment explanation
Indices: 61207885--61207963 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
61207875 ATGCTAATAC
61207885 TATTTTTCAATTTTATATATTTTTATAA
1 TATTTTT-AATTTTATATATTTTTATAA
* * * *
61207913 TATTTATAAATTTTTTA-ATTTTTCTGA
1 TATTT-TTAATTTTATATATTTTTATAA
*
61207940 TATTTTATATTTTTAT-TATTTTTA
1 TATTTT-TAATTTTATATATTTTTA
61207964 ATCATTTTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
26 1 0.03
27 25 0.62
28 13 0.32
29 1 0.03
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (27 bp):
TATTTTTAATTTTATATATTTTTATAA
Found at i:61207935 original size:9 final size:9
Alignment explanation
Indices: 61207895--61207974 Score: 65
Period size: 10 Copynumber: 8.7 Consensus size: 9
61207885 TATTTTTCAA
61207895 TTTTATATAT
1 TTTTATA-AT
61207905 TTTTATAAT
1 TTTTATAAT
*
61207914 ATTTATAAAT
1 TTTTAT-AAT
61207924 TTTT-TAAT
1 TTTTATAAT
* *
61207932 TTTTCTGAT
1 TTTTATAAT
61207941 ATTTTAT-AT
1 -TTTTATAAT
*
61207950 TTTTATTAT
1 TTTTATAAT
*
61207959 TTTTAATCAT
1 TTTT-ATAAT
61207969 TTTTAT
1 TTTTAT
61207975 GAAAAAAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
8 13 0.22
9 21 0.35
10 26 0.43
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.68
Consensus pattern (9 bp):
TTTTATAAT
Found at i:61208896 original size:21 final size:21
Alignment explanation
Indices: 61208872--61208924 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
61208862 CATTGCTTCT
* *
61208872 AATCTCACCGTTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
61208893 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
61208914 AATCTCACCGC
1 AATCTCACCGC
61208925 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:61214525 original size:218 final size:218
Alignment explanation
Indices: 61214139--61214800 Score: 1184
Period size: 218 Copynumber: 3.0 Consensus size: 218
61214129 TCTAATACTC
* * *
61214139 TATA-GCTGTCACCACCTAGTTCGAATAGGACGTTGATATTGTATCTAACGGTGTTTGATAATTC
1 TATATGCT-TCACCACCTAGTTCGAATAGGATGCTGATACTGTATCTAACGGTGTTTGATAATTC
*
61214203 CATAGGGTGTGTGCTAGGTCAACATGATGAAACGGGAAAGAAAGAAAGGGCGATATATTATCTCA
65 CATGGGGTGTGTGCTAGGTCAACATGATGAAACGGGAAAGAAAGAAAGGGCGATATATTATCTCA
*
61214268 GCAAGAAATTCACTGACTGTGAAATGAGATACTCGTCTGTCGAAAAGTTGTGTTGTGCATTGATT
130 GCAAGAAATTCACTGACTGTGAAATGAGATACTCGTCTGTCGAAAAGTTGTGTTGTGCCTTGATT
61214333 TGGACAACCCGGAGATTAAGGCAG
195 TGGACAACCCGGAGATTAAGGCAG
* ** * *
61214357 TATATGCTTCACCACCTAGTTCGAATAAGATGCTGATACCATATCTAATGGTTTTTGATAATTCC
1 TATATGCTTCACCACCTAGTTCGAATAGGATGCTGATACTGTATCTAACGGTGTTTGATAATTCC
61214422 ATGGGGTGTGTGCTAGGTCAACATGATGAAACGGGAAAGAAAGAAAGGGCGATATATTATCTCAG
66 ATGGGGTGTGTGCTAGGTCAACATGATGAAACGGGAAAGAAAGAAAGGGCGATATATTATCTCAG
61214487 CAAGAAATTCACTGACTGTGAAATGAGATACTCGTCTGTCGAAAAGTTGTGTTGTGCCTTGATTT
131 CAAGAAATTCACTGACTGTGAAATGAGATACTCGTCTGTCGAAAAGTTGTGTTGTGCCTTGATTT
61214552 GGACAACCCGGAGATTAAGGCAG
196 GGACAACCCGGAGATTAAGGCAG
*
61214575 TATATGTTTCACCACCTAGTTCGAATAGGATGCTGATACTGTATCTAACGGTGTTTGATAATTCC
1 TATATGCTTCACCACCTAGTTCGAATAGGATGCTGATACTGTATCTAACGGTGTTTGATAATTCC
*
61214640 ATGGGGTGTGTGCTAGGTCAACATGATGAAACGAGAAA-AGAAGAAAGGGCGATATATTATCTCA
66 ATGGGGTGTGTGCTAGGTCAACATGATGAAACGGGAAAGA-AAGAAAGGGCGATATATTATCTCA
61214704 GCAAGAAATTCACTGACTGTGAAATGAGATACTCGTCTGTCGAAAAGTTGTGTTGTGCCTTGATT
130 GCAAGAAATTCACTGACTGTGAAATGAGATACTCGTCTGTCGAAAAGTTGTGTTGTGCCTTGATT
61214769 TGGACAACCCGGAGATTAAGGCAG
195 TGGACAACCCGGAGATTAAGGCAG
61214793 TATATGCT
1 TATATGCT
61214801 ATACCATACG
Statistics
Matches: 424, Mismatches: 18, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
217 1 0.00
218 420 0.99
219 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (218 bp):
TATATGCTTCACCACCTAGTTCGAATAGGATGCTGATACTGTATCTAACGGTGTTTGATAATTCC
ATGGGGTGTGTGCTAGGTCAACATGATGAAACGGGAAAGAAAGAAAGGGCGATATATTATCTCAG
CAAGAAATTCACTGACTGTGAAATGAGATACTCGTCTGTCGAAAAGTTGTGTTGTGCCTTGATTT
GGACAACCCGGAGATTAAGGCAG
Found at i:61217771 original size:89 final size:89
Alignment explanation
Indices: 61217620--61218245 Score: 941
Period size: 89 Copynumber: 7.0 Consensus size: 89
61217610 GCAGGTTGAG
* *
61217620 AGAAAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAGAGATAACAAATCTTGTCTTCC
1 AGAAAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCC
61217685 CATACTGGTGGCGAAGTAGATCGA
66 CATACTGGTGGCGAAGTAGATCGA
* *
61217709 AGAAAGTAGATATTGTCTTCATGTACTGGCATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCC
1 AGAAAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCC
*
61217774 CATACTGGTGGTGAAGTAGATCGA
66 CATACTGGTGGCGAAGTAGATCGA
* *
61217798 AGAAAGTAGATCTTGTCTTCATGTACTGGCATGAAATAGATCAGAGATAGCAGATCTTGTCTTCC
1 AGAAAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCC
*
61217863 CATACCGGTGGCGAAGTAGATCGA
66 CATACTGGTGGCGAAGTAGATCGA
* * ** *
61217887 AGAAAGCAGATCTTATCTTCATGTACTGGCATGAAGTAGATCAAAGATAATAGATCTTATCTTCC
1 AGAAAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCC
* *
61217952 TATATTGGTGGCGAAGTAGATCGA
66 CATACTGGTGGCGAAGTAGATCGA
* *
61217976 AGAAAACAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAGAGATAGTAGATCTTGTCTTCC
1 AGAAAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCC
*
61218041 CATACTGGTGGCGAAGTAGATTGA
66 CATACTGGTGGCGAAGTAGATCGA
* * * * *
61218065 AGAAAGTAGATCTTGTCTTTATGTATTGGCATGAAGTAGATCAGAGATAGCAAATCTTGTTTTCC
1 AGAAAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCC
61218130 CATACTGGTGGCGAAGTAGATCGA
66 CATACTGGTGGCGAAGTAGATCGA
* * *
61218154 AGAAAGCAGATCTTGTCTTCATGTA-TCAGCATGAAGTAGATCA-AGGACAGCAGATCTTGTTTT
1 AGAAAGCAGATCTTGTCTTCATGTACT-GGCATGAAGTAGATCAGA-GATAGCAGATCTTGTCTT
* * * * *
61218217 CCTATATTGGTGGTGAAATAGATCAA
64 CCCATACTGGTGGCGAAGTAGATCGA
61218243 AGA
1 AGA
61218246 TACAAGTCTT
Statistics
Matches: 490, Mismatches: 45, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
88 2 0.00
89 488 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.29
Consensus pattern (89 bp):
AGAAAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCC
CATACTGGTGGCGAAGTAGATCGA
Found at i:61247593 original size:17 final size:19
Alignment explanation
Indices: 61247568--61247613 Score: 71
Period size: 17 Copynumber: 2.6 Consensus size: 19
61247558 TCTTTTATGC
61247568 AATTGAAAACTAAAATT-A
1 AATTGAAAACTAAAATTGA
61247586 AA-TGAAAAC-AAAATTGA
1 AATTGAAAACTAAAATTGA
61247603 AATTGAAAACT
1 AATTGAAAACT
61247614 CAAGTCCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.24
17 10 0.40
18 9 0.36
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.24
Consensus pattern (19 bp):
AATTGAAAACTAAAATTGA
Found at i:61248641 original size:29 final size:30
Alignment explanation
Indices: 61248599--61248673 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 30
61248589 TATATGAACT
*
61248599 TAAAGAAATCATTAAAATAT-T-TAAAATTTTA
1 TAAA-AAAT-ATTAAAATATCTATAAAA-GTTA
61248630 TAAAAAATATTAAAA-ATCTATAAAAGTTA
1 TAAAAAATATTAAAATATCTATAAAAGTTA
61248659 T-AAAAATATTAAAAT
1 TAAAAAATATTAAAAT
61248674 TGATATAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
28 15 0.38
29 12 0.30
30 9 0.22
31 4 0.10
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (30 bp):
TAAAAAATATTAAAATATCTATAAAAGTTA
Found at i:61248642 original size:20 final size:21
Alignment explanation
Indices: 61248612--61248654 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
61248602 AGAAATCATT
* *
61248612 AAAATATTTAAAATTTTATAA
1 AAAATATTTAAAAATCTATAA
61248633 AAAATA-TTAAAAATCTATAA
1 AAAATATTTAAAAATCTATAA
61248653 AA
1 AA
61248655 GTTATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATATTTAAAAATCTATAA
Found at i:61248653 original size:10 final size:9
Alignment explanation
Indices: 61248627--61248692 Score: 53
Period size: 10 Copynumber: 7.0 Consensus size: 9
61248617 ATTTAAAATT
61248627 TTATAAAAA
1 TTATAAAAA
*
61248636 ATATTAAAAA
1 TTA-TAAAAA
*
61248646 TCTATAAAAG
1 T-TATAAAAA
61248656 TTATAAAAA
1 TTATAAAAA
*
61248665 -TATTAAAA
1 TTATAAAAA
*
61248673 TTGATATAAAC
1 TT-ATA-AAAA
61248684 TTATAAAAA
1 TTATAAAAA
61248693 CTTGAACTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
8 7 0.16
9 13 0.30
10 17 0.39
11 7 0.16
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (9 bp):
TTATAAAAA
Found at i:61248695 original size:10 final size:9
Alignment explanation
Indices: 61248493--61248692 Score: 67
Period size: 9 Copynumber: 21.7 Consensus size: 9
61248483 ATTTTTTCCC
61248493 TAAAAATTA
1 TAAAAATTA
61248502 TAAAAATTA
1 TAAAAATTA
*
61248511 TAAAAAATA
1 TAAAAATTA
* *
61248520 TATATATATA
1 TAAAAAT-TA
* *
61248530 TAATAA-GA
1 TAAAAATTA
61248538 -AAAAATTA
1 TAAAAATTA
61248546 TAAAAA-TA
1 TAAAAATTA
*
61248554 TTCAAAATGT-
1 -TAAAAAT-TA
*
61248564 TAAATA-T-
1 TAAAAATTA
61248571 TAAAAATATA
1 TAAAAAT-TA
*
61248581 TGAAAATTTA
1 T-AAAAATTA
* *
61248591 TATGAACTTA
1 TA-AAAATTA
*
61248601 -AAGAAATCA
1 TAA-AAATTA
61248610 TTAAAATATT-
1 -TAAAA-ATTA
*
61248620 TAAAATTTTA
1 TAAAA-ATTA
*
61248630 TAAAAAATA
1 TAAAAATTA
61248639 TTAAAAATCTA
1 -TAAAAAT-TA
*
61248650 TAAAAGTTA
1 TAAAAATTA
61248659 TAAAAA-TA
1 TAAAAATTA
*
61248667 TTAAAATTGA
1 TAAAAATT-A
*
61248677 TATAAACTTA
1 TA-AAAATTA
61248687 TAAAAA
1 TAAAAA
61248693 CTTGAACTGA
Statistics
Matches: 139, Mismatches: 31, Indels: 42
0.66 0.15 0.20
Matches are distributed among these distances:
7 10 0.07
8 11 0.08
9 63 0.45
10 38 0.27
11 17 0.12
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Found at i:61248804 original size:17 final size:18
Alignment explanation
Indices: 61248782--61248816 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
61248772 TGAACAGATT
61248782 TTTTTAATATTTT-TTTA
1 TTTTTAATATTTTATTTA
61248799 TTTTTAATATTTTATTTA
1 TTTTTAATATTTTATTTA
61248817 ATTAAATTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTAATATTTTATTTA
Found at i:61249114 original size:9 final size:9
Alignment explanation
Indices: 61249091--61249211 Score: 67
Period size: 9 Copynumber: 13.6 Consensus size: 9
61249081 TATTTTTCAA
61249091 TTTTATATAT
1 TTTTATA-AT
61249101 TTTTATAAT
1 TTTTATAAT
*
61249110 ATTTATAAGT
1 TTTTATAA-T
61249120 TTTTATAAT
1 TTTTATAAT
*
61249129 TTTAATAAGT
1 TTTTATAA-T
*
61249139 TTATATCAAT
1 TTTTAT-AAT
*
61249149 TTTAAT-A-
1 TTTTATAAT
*
61249156 TTTAAT-AT
1 TTTTATAAT
*
61249164 CTTTAT--T
1 TTTTATAAT
61249171 TTTTATAAT
1 TTTTATAAT
* *
61249180 TTTTCTGAT
1 TTTTATAAT
61249189 ATTTTAT-AT
1 -TTTTATAAT
61249198 ATTTTAT-AT
1 -TTTTATAAT
61249207 TTTTA
1 TTTTA
61249212 ATTATTTTCA
Statistics
Matches: 91, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
7 13 0.14
8 10 0.11
9 36 0.40
10 30 0.33
11 2 0.02
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:61249116 original size:19 final size:19
Alignment explanation
Indices: 61249092--61249211 Score: 61
Period size: 19 Copynumber: 6.7 Consensus size: 19
61249082 ATTTTTCAAT
61249092 TTTATATATTTTTATAATA
1 TTTATATATTTTTATAATA
61249111 TTTATA-AGTTTTTATAAT-
1 TTTATATA-TTTTTATAATA
*
61249129 TTTA-ATAAGTTTATATCAAT-
1 TTTATAT-A-TTTTTAT-AATA
61249149 TTTA-ATA---TT-TAATA
1 TTTATATATTTTTATAATA
*
61249163 TCTT-TAT-TTTTTATAATT
1 T-TTATATATTTTTATAATA
*
61249181 TTTCTGATA-TTTTAT-ATA
1 TTTAT-ATATTTTTATAATA
61249199 TTT-TATATTTTTA
1 TTTATATATTTTTA
61249212 ATTATTTTCA
Statistics
Matches: 82, Mismatches: 4, Indels: 32
0.69 0.03 0.27
Matches are distributed among these distances:
13 3 0.04
14 2 0.02
15 5 0.06
16 3 0.04
17 11 0.13
18 16 0.20
19 33 0.40
20 9 0.11
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTATATATTTTTATAATA
Found at i:61249151 original size:20 final size:19
Alignment explanation
Indices: 61249104--61249155 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
61249094 TATATATTTT
*
61249104 TATAATATTT-ATAAGTTTT
1 TATAAT-TTTAATAAGTTTA
61249123 TATAATTTTAATAAGTTTA
1 TATAATTTTAATAAGTTTA
61249142 TATCAATTTTAATA
1 TAT-AATTTTAATA
61249156 TTTAATATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 3 0.10
19 17 0.57
20 10 0.33
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (19 bp):
TATAATTTTAATAAGTTTA
Found at i:61250694 original size:96 final size:95
Alignment explanation
Indices: 61250592--61250908 Score: 465
Period size: 96 Copynumber: 3.3 Consensus size: 95
61250582 AACAACTAGT
* * * * *
61250592 TTTATTTGATTTTTCCTTAAAAACCCTAAATATTAAACCCCAATCTAATTTTTTTAAAATTTAAA
1 TTTATTTAATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAA-TTTTTTAAAATTTATA
61250657 ATTAATTTACTCAAGTAACCCTAAACCCTAA
65 ATTAATTTACTCAAGTAACCCTAAACCCTAA
** *
61250688 TTTATTTAATTTTTTATATAAAAACCCTAAACACTAAACCCTAATCTAATTTTTAAAAATTTATA
1 TTTATTTAATTTTTCCT-TAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTAAAATTTATA
*
61250753 ATTAATTTACTCAAGTAACCCTAAACTCTAA
65 ATTAATTTACTCAAGTAACCCTAAACCCTAA
* *
61250784 TTTATTTAATTTTTTCCTTAAAAACCATAAACACTAAACCCTAATCTAATTTTTTAATATTTATA
1 TTTATTTAA-TTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTAAAATTTATA
* * * *
61250849 ATTAATTTAATTAAGAAACCCTAAACCCTTA
65 ATTAATTTACTCAAGTAACCCTAAACCCTAA
61250880 TTTATTTAATTTTTCCTT-AAAACCCTAAA
1 TTTATTTAATTTTTCCTTAAAAACCCTAAA
61250909 ATCTAAAAAT
Statistics
Matches: 199, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
94 10 0.05
95 9 0.05
96 146 0.73
97 34 0.17
ACGTcount: A:0.40, C:0.17, G:0.01, T:0.41
Consensus pattern (95 bp):
TTTATTTAATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTAAAATTTATAA
TTAATTTACTCAAGTAACCCTAAACCCTAA
Found at i:61258257 original size:4 final size:4
Alignment explanation
Indices: 61258248--61258277 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
61258238 TTGATAAAGA
61258248 AAAT AAAT AAAT AAAT AAAT AAAT -AAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
61258278 ATAATAACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:61261120 original size:7 final size:7
Alignment explanation
Indices: 61261108--61261138 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
61261098 TTAATTTGAT
61261108 TTAGTGG
1 TTAGTGG
61261115 TTAGTGG
1 TTAGTGG
61261122 TTAGTGG
1 TTAGTGG
61261129 TTAGTGG
1 TTAGTGG
61261136 TTA
1 TTA
61261139 AGTGTCTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (7 bp):
TTAGTGG
Found at i:61264542 original size:30 final size:31
Alignment explanation
Indices: 61264462--61264526 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
61264452 AACAGCTCAG
*
61264462 TGACTTAAATAAAAACTTTTGAATAGTTCAA
1 TGACTTAAATGAAAACTTTTGAATAGTTCAA
61264493 TGACTTAAATGAAAACTTTTGAATAGTTCAA
1 TGACTTAAATGAAAACTTTTGAATAGTTCAA
61264524 TGA
1 TGA
61264527 TTGAATTGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.35
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTTGAATAGTTCAA
Found at i:61266291 original size:193 final size:193
Alignment explanation
Indices: 61265955--61266349 Score: 720
Period size: 193 Copynumber: 2.0 Consensus size: 193
61265945 TGCGTAAATG
* * *
61265955 TTGATAAAATATGTAAATTTTGCAGACTAAATTTGTTAAATCAAGATCAAATTGATAGAATGTGT
1 TTGATGAAATATGTAAATTTTACAGACTAAATTTGTTAAATCAAGATCAAATTGATAGAATGTAT
61266020 AAAAGTTGTGGACTAAATTTTTAAATTAGAATAAAACTGACATAATATGTAAATGTTGAGATGAA
66 AAAAGTTGTGGACTAAATTTTTAAATTAGAATAAAACTGACATAATATGTAAATGTTGAGATGAA
61266085 ATTGATCAAATGTTTAAACTTAGAAGGCTAAATTTGATATGTTACCAAAAAAAATATGTATAA
131 ATTGATCAAATGTTTAAACTTAGAAGGCTAAATTTGATATGTTACCAAAAAAAATATGTATAA
61266148 TTGATGAAATATGTAAATTTTACAGACTAAATTTGTTAAATCAAGATCAAATTGATAGAATGTAT
1 TTGATGAAATATGTAAATTTTACAGACTAAATTTGTTAAATCAAGATCAAATTGATAGAATGTAT
*
61266213 AAAAGTTGTGGACTAAATTTTTAAATTAGAATAAAATTGACATAATATGTAAATGTTGAGATGAA
66 AAAAGTTGTGGACTAAATTTTTAAATTAGAATAAAACTGACATAATATGTAAATGTTGAGATGAA
* *
61266278 ATTGA-CAAAATGTTTAAACTTAGAGGGCTAAATTTGATATGTTACCAATAAAAATATGTATAA
131 ATTGATC-AAATGTTTAAACTTAGAAGGCTAAATTTGATATGTTACCAAAAAAAATATGTATAA
61266341 TTGATGAAA
1 TTGATGAAA
61266350 AATATTAACA
Statistics
Matches: 195, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
192 1 0.01
193 194 0.99
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (193 bp):
TTGATGAAATATGTAAATTTTACAGACTAAATTTGTTAAATCAAGATCAAATTGATAGAATGTAT
AAAAGTTGTGGACTAAATTTTTAAATTAGAATAAAACTGACATAATATGTAAATGTTGAGATGAA
ATTGATCAAATGTTTAAACTTAGAAGGCTAAATTTGATATGTTACCAAAAAAAATATGTATAA
Found at i:61267163 original size:13 final size:13
Alignment explanation
Indices: 61267145--61267170 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61267135 GTATTAACCT
61267145 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
61267158 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
61267171 TGCTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGAAGA
Found at i:61268032 original size:4 final size:4
Alignment explanation
Indices: 61268023--61268063 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
61268013 TTATAGAAGT
61268023 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
61268064 AAAAACCGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:61268607 original size:13 final size:14
Alignment explanation
Indices: 61268589--61268620 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
61268579 ACAAAAATAC
61268589 TAAATTTAAA-AAA
1 TAAATTTAAATAAA
61268602 TAAATTTAAATAAA
1 TAAATTTAAATAAA
61268616 -AAATT
1 TAAATT
61268621 AGACTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAATTTAAATAAA
Found at i:61268941 original size:18 final size:18
Alignment explanation
Indices: 61268914--61268952 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
61268904 ATTAAAAATT
*
61268914 AATTTATTTAACCCTCCA
1 AATTTATTTAAACCTCCA
* *
61268932 AATTTTTTTAAACCTTCA
1 AATTTATTTAAACCTCCA
61268950 AAT
1 AAT
61268953 AAACATGTTT
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:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTATTTAAACCTCCA
Found at i:61270034 original size:20 final size:20
Alignment explanation
Indices: 61269996--61270034 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
61269986 GGTAGAATTC
*
61269996 ACATCATGCTATTATATATG
1 ACATCATGCTATTACATATG
61270016 ACATACATGCTA-TACATAT
1 ACAT-CATGCTATTACATAT
61270035 CATGCTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (20 bp):
ACATCATGCTATTACATATG
Found at i:61278074 original size:4 final size:4
Alignment explanation
Indices: 61278057--61278111 Score: 92
Period size: 4 Copynumber: 13.5 Consensus size: 4
61278047 TTACAGAAGT
*
61278057 TGTA TGTA GAGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA -TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
61278106 TGTA TG
1 TGTA TG
61278112 ATGAGCAACA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
4 45 0.94
5 3 0.06
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.47
Consensus pattern (4 bp):
TGTA
Found at i:61279626 original size:7 final size:7
Alignment explanation
Indices: 61279614--61279638 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
61279604 CAAGGTTCTT
61279614 GATTCGG
1 GATTCGG
61279621 GATTCGG
1 GATTCGG
61279628 GATTCGG
1 GATTCGG
61279635 GATT
1 GATT
61279639 TAGAGTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.12, G:0.40, T:0.32
Consensus pattern (7 bp):
GATTCGG
Found at i:61281922 original size:21 final size:20
Alignment explanation
Indices: 61281894--61281932 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
61281884 AAAGCTGAGC
61281894 TTAGTTTAATTAATTTTTCT
1 TTAGTTTAATTAATTTTTCT
*
61281914 TTAGATTTATTTAATTTTT
1 TTAG-TTTAATTAATTTTT
61281933 TTATTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (20 bp):
TTAGTTTAATTAATTTTTCT
Found at i:61287185 original size:15 final size:15
Alignment explanation
Indices: 61287165--61287195 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
61287155 TTTGAAGTAT
61287165 ATCTTTAAGAAAATA
1 ATCTTTAAGAAAATA
61287180 ATCTTTAAGAAAATA
1 ATCTTTAAGAAAATA
61287195 A
1 A
61287196 AATAAGGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (15 bp):
ATCTTTAAGAAAATA
Found at i:61287653 original size:25 final size:27
Alignment explanation
Indices: 61287609--61287664 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
61287599 TCAATTGAAT
* *
61287609 TTAACAAATAAATTGCATAAA-TTTAA
1 TTAAAAAATAAATTACATAAAGTTTAA
*
61287635 TTAAAAAAT-AATTACATAAAGTTTAT
1 TTAAAAAATAAATTACATAAAGTTTAA
61287661 TTAA
1 TTAA
61287665 TTAAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.38
Consensus pattern (27 bp):
TTAAAAAATAAATTACATAAAGTTTAA
Found at i:61293206 original size:15 final size:14
Alignment explanation
Indices: 61293153--61293208 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
61293143 AAAGTAGAGT
61293153 TTAAAATACAAAGA
1 TTAAAATACAAAGA
61293167 TTAAAATTGATC-AA-A
1 TTAAAA-T-A-CAAAGA
61293182 TTAAAATACAAAGA
1 TTAAAATACAAAGA
61293196 TTAAAACTACAAA
1 TTAAAA-TACAAA
61293209 TTTCATAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
12 1 0.03
13 3 0.08
14 14 0.39
15 14 0.39
16 3 0.08
17 1 0.03
ACGTcount: A:0.61, C:0.09, G:0.05, T:0.25
Consensus pattern (14 bp):
TTAAAATACAAAGA
Found at i:61296802 original size:30 final size:30
Alignment explanation
Indices: 61296768--61296830 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
61296758 ACTTATTTTA
*
61296768 TTGTTAATTTTGTTACTATTTTA-AAGACAT
1 TTGTTAATTTTATTACTATTTTAGAAG-CAT
*
61296798 TTGTTAATTTTATTATTATTTTAGAAGCAT
1 TTGTTAATTTTATTACTATTTTAGAAGCAT
61296828 TTG
1 TTG
61296831 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTATTACTATTTTAGAAGCAT
Found at i:61298658 original size:30 final size:30
Alignment explanation
Indices: 61298622--61298681 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
61298612 TTTATGGGAG
*
61298622 TTCTTTTATTTTTGAATTTGGTGCTTTTGT
1 TTCTTTTATTTTTGAATTGGGTGCTTTTGT
61298652 TTCTTTTATTTTTGAATTGGGTGCTTTTGT
1 TTCTTTTATTTTTGAATTGGGTGCTTTTGT
61298682 GGTAAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.10, C:0.07, G:0.18, T:0.65
Consensus pattern (30 bp):
TTCTTTTATTTTTGAATTGGGTGCTTTTGT
Found at i:61301175 original size:29 final size:29
Alignment explanation
Indices: 61301084--61301193 Score: 87
Period size: 29 Copynumber: 3.8 Consensus size: 29
61301074 CAAAAATAAA
* *
61301084 AAATTATATTTTGACCCCCTAAACCTT-TTG
1 AAATTACATTTTGA-CCCATAAA-CTTCTTG
* * * * *
61301114 AAATTGCATTTTCACCCCTAAACTTCCTA
1 AAATTACATTTTGACCCATAAACTTCTTG
* *
61301143 AAATTACATTTTGGCCCATCAACTTCTTG
1 AAATTACATTTTGACCCATAAACTTCTTG
* * *
61301172 AAATAATATTTTGACCCCTAAA
1 AAATTACATTTTGACCCATAAA
61301194 TTTTCTCAAA
Statistics
Matches: 62, Mismatches: 17, Indels: 3
0.76 0.21 0.04
Matches are distributed among these distances:
28 3 0.05
29 48 0.77
30 11 0.18
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (29 bp):
AAATTACATTTTGACCCATAAACTTCTTG
Found at i:61301754 original size:10 final size:10
Alignment explanation
Indices: 61301739--61301816 Score: 56
Period size: 10 Copynumber: 7.7 Consensus size: 10
61301729 GAAGAAAGGA
61301739 AAAAAGAAAG
1 AAAAAGAAAG
61301749 AAAAAGAAAG
1 AAAAAGAAAG
61301759 AAAAA-AAGGAG
1 AAAAAGAA--AG
*
61301770 AGAAAAAAATAG
1 A-AAAAGAA-AG
*
61301782 AAAAGGAAAG
1 AAAAAGAAAG
61301792 -AAAAGAAA-
1 AAAAAGAAAG
*
61301800 ATAAAA-AAAT
1 A-AAAAGAAAG
61301810 AAAAAGA
1 AAAAAGA
61301817 TAACAAAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
9 16 0.29
10 23 0.41
11 8 0.14
12 7 0.12
13 2 0.04
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:61301756 original size:22 final size:22
Alignment explanation
Indices: 61301730--61301799 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
61301720 TAACCCGAAG
61301730 AAGAAAGGAAAAAAGAAAGAAA
1 AAGAAAGGAAAAAAGAAAGAAA
* *
61301752 AAGAAAGAAAAAAAGGAGAGAAA
1 AAGAAAGGAAAAAA-GAAAGAAA
*
61301775 AA-AATA-G-AAAAGGAAAG-AA
1 AAGAA-AGGAAAAAAGAAAGAAA
61301794 AAGAAA
1 AAGAAA
61301800 ATAAAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 5 0.12
20 6 0.15
21 4 0.10
22 15 0.38
23 10 0.25
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (22 bp):
AAGAAAGGAAAAAAGAAAGAAA
Found at i:61301773 original size:13 final size:13
Alignment explanation
Indices: 61301741--61301808 Score: 57
Period size: 13 Copynumber: 4.9 Consensus size: 13
61301731 AGAAAGGAAA
61301741 AAAGAAAGAAAAAG
1 AAAGAAA-AAAAAG
*
61301755 AAAGAAAAAAAGG
1 AAAGAAAAAAAAG
*
61301768 AGAGAAAAAAATAG
1 AAAGAAAAAAA-AG
*
61301782 AAAAGGAAAGAAAAG
1 -AAA-GAAAAAAAAG
61301797 AAA-ATAAAAAAA
1 AAAGA-AAAAAAA
61301809 TAAAAAGATA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
12 1 0.02
13 21 0.48
14 11 0.25
15 4 0.09
16 7 0.16
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (13 bp):
AAAGAAAAAAAAG
Found at i:61302210 original size:15 final size:16
Alignment explanation
Indices: 61302192--61302221 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61302182 TAATTTAGTT
61302192 TTATTT-ATTTAAATA
1 TTATTTCATTTAAATA
61302207 TTATTTCATTTAAAT
1 TTATTTCATTTAAAT
61302222 TTAACTAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATTTCATTTAAATA
Found at i:61309481 original size:83 final size:81
Alignment explanation
Indices: 61309285--61310614 Score: 1596
Period size: 83 Copynumber: 16.5 Consensus size: 81
61309275 TTCTGTTTTC
* *
61309285 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACACTGAGGTA----TTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
*
61309346 AATTTCTATTTTTC--G
65 AATTTCTATTTTTCAAA
*
61309361 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
*
61309426 AATTTCTATGTTTCAAAAA
65 AATTTCTATTTTTC--AAA
*
61309445 AAAAATCAACTCATATTAC-AGAGGTGAGTTGAGCCTCGGGT-CACGCTGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
* ***
61309508 ATTTCTGTTTTTTTTTTCA
66 ATTTC---TATTTTTCAAA
* * *
61309527 AAAAATCAACTCATATTGCGAGAAGTGAATTGAGCCTCGGATCGCACGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
61309592 AATTTCTATTTTTCAAA
65 AATTTCTATTTTTCAAA
* *
61309609 AAAAATCAACTCATATTAC-AGAGATGAGTTGAGCCTCGGGT-CACGCTGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
***
61309672 ATTTCTATTTTTTTTCA
66 ATTTCTA-TTTTTCAAA
*
61309689 AAAAATCAACTCATATTAC-AGAGGTGAGTTGAGCCTCGGGT-CACGCTGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
*
61309752 ATTTCTGTTTTTTTTTC-AA
66 ATTTC----TATTTTTCAAA
*
61309771 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
61309836 AATTTCTATTTTTCAAA
65 AATTTCTATTTTTCAAA
* * *
61309853 AAAAATCAACTCATATTAC-AGAGATGAGTTGAGCCTCGGGT-CACGTTGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
*
61309916 ATTTCTGTTTTTTTTCAAA
66 ATTTC---TATTTTTCAAA
* ** * *
61309935 AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTC-GAACCATGCCGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
*
61309999 ATTTCTGTTTTTC---
66 ATTTCTATTTTTCAAA
*
61310012 AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGTCGCACGCTGAGGTA----TTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
61310073 AATTTCTATTTTTTC-AA
65 AATTTCTA-TTTTTCAAA
*
61310090 AAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
61310155 AATTTCTATTTTTTCAAA
65 AATTTCTA-TTTTTCAAA
*
61310173 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
61310238 AATTTCTATTTTTCAAAA
65 AATTTCTATTTTTC-AAA
* * *
61310256 AAAAATCAACTTATATTAC-AGAGGTTAGTTGAGCCTCGGGT-CACGCTGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
* *
61310319 ATTTTTGTTTTTTTC-AA
66 A--TTTCTATTTTTCAAA
** * * * *
61310336 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GAACCATGCCGAGGTATTTTTTTTAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
*
61310400 ATTTCTGTTTTT----
66 ATTTCTATTTTTCAAA
** * * * * *
61310412 TTAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC-GGACACATGCCGAGGTATTTCGTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
***
61310476 AATTTCTATTTTTTTTTCA
65 AATTTCTA--TTTTTCAAA
* *
61310495 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCT-AGGTATTTTCTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACG-CTGAGGTA-TTTCTTT
*
61310559 TAAATTTCTGTTTTTC-AA
63 TAAATTTCTATTTTTCAAA
*
61310577 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
61310615 AGGCCACACG
Statistics
Matches: 1108, Mismatches: 93, Indels: 100
0.85 0.07 0.08
Matches are distributed among these distances:
75 12 0.01
76 99 0.09
77 63 0.06
78 56 0.05
79 79 0.07
80 141 0.13
81 108 0.10
82 205 0.19
83 238 0.21
84 37 0.03
85 70 0.06
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (81 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
ATTTCTATTTTTCAAA
Found at i:61309737 original size:244 final size:243
Alignment explanation
Indices: 61309280--61310614 Score: 1704
Period size: 244 Copynumber: 5.5 Consensus size: 243
61309270 TCAATTTCTG
*
61309280 TTTTC-AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACACTGAGGTA---
1 TTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTT
*
61309341 -TTTTAAATTTCTATTTTTC-GAAAAATCAACTCATATTGC-GAGAAGTGAGTTGAGCCTCGGGT
66 CTTTTAAATTTCTATTTTTCAAAAAAATCAACTCATATTGCAGAG-A-TGAGTTGAGCCTCGGGT
**** *
61309403 CGCACGCTGAGGTATTTCTTTTAAATTTCTATGTTTCAAAAAAAAAATCAACTCATATTAC-AGA
129 --CACGCTGAGGTATTTCTTTTAAATTTCTAT-TTTTTTTAAAAAAATCAACTCATATTGCGAGA
61309467 GGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTTTTAAATTTCTGTTTTTT
191 GGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTTTTAAATTTCTG-TTTTT
* *
61309521 TTTTCAAAAAATCAACTCATATTGCGAGAAGTGAATTGAGCCTCGGATCGCACGCTGAGGTATTT
1 TTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTT
*
61309586 CTTTTAAATTTCTATTTTTCAAAAAAAATCAACTCATATTACAGAGATGAGTTGAGCCTCGGGTC
66 CTTTTAAATTTCTATTTTTC-AAAAAAATCAACTCATATTGCAGAGATGAGTTGAGCCTCGGGTC
* *
61309651 ACGCTGAGGTATTTCTTTTAAATTTCTATTTTTTTTCAAAAAATCAACTCATATTAC-AGAGGTG
130 ACGCTGAGGTATTTCTTTTAAATTTCTATTTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTG
61309715 AGTTGAGCCTCGGGTCACGCTGAGGTATTTCTTTTAAATTTCTGTTTTT
195 AGTTGAGCCTCGGGTCACGCTGAGGTATTTCTTTTAAATTTCTGTTTTT
61309764 TTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATT
1 TTTTC-AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATT
*
61309829 TCTTTTAAATTTCTATTTTTCAAAAAAAATCAACTCATATTACAGAGATGAGTTGAGCCTCGGGT
65 TCTTTTAAATTTCTATTTTTC-AAAAAAATCAACTCATATTGCAGAGATGAGTTGAGCCTCGGGT
* *
61309894 CACGTTGAGGTATTTCTTTTAAATTTCTGTTTTTTTTCAAAAAAAATCAACTCATATTGCGAGAG
129 CACGCTGAGGTATTTCTTTTAAATTTCTATTTTTTTT--AAAAAAATCAACTCATATTGCGAGAG
* *** * *
61309959 GTGAGTTAAGCCTCGAACCATGCCGAGGTATTTCTTTTAAATTTCTG----T
192 GTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTTTTAAATTTCTGTTTTT
* *
61310007 TTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGTCGCACGCTGAGGTA---
1 TTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTT
* *
61310068 -TTTTAAATTTCTATTTTTTCAAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
66 CTTTTAAATTTCTA-TTTTTCAAAAAAATCAACTCATATTGC-AGAGATGAGTTGAGCCTCGGGT
** *
61310132 CGCACGCTGAGGTATTTCTTTTAAATTTCTATTTTTTCAAAAAAAATCAACTCATATTGCGAGAA
129 --CACGCTGAGGTATTTCTTTTAAATTTCTATTTTTTTTAAAAAAATCAACTCATATTGCGAGAG
*
61310197 GTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAATTTCT-ATTTT
192 GTGAGTTGAGCCTCGGGT--CACGCTGAGGTATTTCTTTTAAATTTCTGTTTTT
**** * * * *
61310250 TCAAAAAAAAATCAACTTATATTAC-AGAGGTTAGTTGAGCCTCGGGT--CACGCTGAGGTATTT
1 TTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTT
* * * **
61310312 CTTTTAAATTTTTGTTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAA
66 CTTTTAAA--TTTCTATTTTTCAAAAAAATCAACTCATATTGC-AGAGATGAGTTGAGCCTCGGG
* * * * * *
61310377 CCATGCCGAGGTATTTTTTTTATATTTCT-GTTTTTTT----AAATCAACTCATATTGCGAGAGG
128 TCACGCTGAGGTATTTCTTTTAAATTTCTATTTTTTTTAAAAAAATCAACTCATATTGCGAGAGG
* * * * *
61310437 TGAGTTGAACCTC-GGACACATGCCGAGGTATTTCGTTTAAATTTCTATTTTT
193 TGAGTTGAGCCTCGGGTCAC--GCTGAGGTATTTCTTTTAAATTTCTGTTTTT
* * * *
61310489 TTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCT-AGGTATT
1 TTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACG-CTGAGGTA-T
*
61310553 TTCTTTTAAATTTCTGTTTTTCAAAAAAATCAACTCATATTGC-GAGAAGTGAGTTGAGCCTC
64 TTCTTTTAAATTTCTATTTTTCAAAAAAATCAACTCATATTGCAGAG-A-TGAGTTGAGCCTC
61310615 AGGCCACACG
Statistics
Matches: 978, Mismatches: 77, Indels: 78
0.86 0.07 0.07
Matches are distributed among these distances:
236 3 0.00
237 32 0.03
238 91 0.09
239 59 0.06
240 80 0.08
241 115 0.12
242 61 0.06
243 56 0.06
244 272 0.28
245 37 0.04
246 84 0.09
247 66 0.07
248 19 0.02
249 3 0.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (243 bp):
TTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTT
CTTTTAAATTTCTATTTTTCAAAAAAATCAACTCATATTGCAGAGATGAGTTGAGCCTCGGGTCA
CGCTGAGGTATTTCTTTTAAATTTCTATTTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGA
GTTGAGCCTCGGGTCACGCTGAGGTATTTCTTTTAAATTTCTGTTTTT
Found at i:61309886 original size:164 final size:161
Alignment explanation
Indices: 61309285--61310614 Score: 1487
Period size: 164 Copynumber: 8.2 Consensus size: 161
61309275 TTCTGTTTTC
* *
61309285 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACACTGAGGTA----TTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
*
61309346 AATTTCTATTTTTC-GAAAAATCAACTCATATTGC-GAGAAGTGAGTTGAGCCTCGGGTCGCACG
65 AATTTCTATTTTTCAAAAAAATCAACTCATATTGCAGAG-A-TGAGTTGAGCCTCGGGTC-CACG
* ****
61309409 CTGAGGTATTTCTTTTAAATTTCTATGTTTCAAAAA
127 CTGAGGTATTTCTTTTAAATTTCT-TTTTTTTTCAA
*
61309445 AAAAATCAACTCATATTAC-AGAGGTGAGTTGAGCCTCGGGT-CACGCTGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
* * *
61309508 ATTTCTGTTTTTTTTTTC-AAAAAATCAACTCATATTGC-GAGAAGTGAATTGAGCCTCGGATCG
66 ATTTC-----TATTTTTCAAAAAAATCAACTCATATTGCAGAG-A-TGAGTTGAGCCTCGGGTC-
*
61309571 CACGCTGAGGTATTTCTTTTAAATTTC--TATTTTTCAAA
123 CACGCTGAGGTATTTCTTTTAAATTTCTTTTTTTTTC-AA
* *
61309609 AAAAATCAACTCATATTAC-AGAGATGAGTTGAGCCTCGGGT-CACGCTGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
* *
61309672 ATTTCTATTTTTTTTC-AAAAAATCAACTCATATTACAGAGGTGAGTTGAGCCTCGGGT-CACGC
66 ATTTCTA---TTTTTCAAAAAAATCAACTCATATTGCAGAGATGAGTTGAGCCTCGGGTCCACGC
61309735 TGAGGTATTTCTTTTAAATTTCTGTTTTTTTTTCAA
128 TGAGGTATTTCTTTTAAATTTC--TTTTTTTTTCAA
*
61309771 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
* *
61309836 AATTTCTATTTTTCAAAAAAAATCAACTCATATTACAGAGATGAGTTGAGCCTCGGGT-CACGTT
65 AATTTCTATTTTTC-AAAAAAATCAACTCATATTGCAGAGATGAGTTGAGCCTCGGGTCCACGCT
61309900 GAGGTATTTCTTTTAAATTTCTGTTTTTTTTCAAA
129 GAGGTATTTCTTTTAAATTTCT-TTTTTTTTC-AA
* ** * *
61309935 AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTC-GAACCATGCCGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
* * *
61309999 ATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGTCGCACGCT
66 ATTTCTATTTTTCAAAAAAATCAACTCATATTGC-AGAGATGAGTTGAGCCTCGGGTC-CACGCT
*
61310062 GAGGTA----TTTTAAATTTC-TATTTTTTCAA
129 GAGGTATTTCTTTTAAATTTCTTTTTTTTTCAA
*
61310090 AAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
61310155 AATTTCTATTTTTTCAAAAAAAATCAACTCATATTGC-GAGAAGTGAGTTGAGCCTCGGGTCGCA
65 AATTTCTA-TTTTTC-AAAAAAATCAACTCATATTGCAGAG-A-TGAGTTGAGCCTCGGGTC-CA
* ***
61310219 CGCTGAGGTATTTCTTTTAAATTTCTATTTTTCAAAA
125 CGCTGAGGTATTTCTTTTAAATTTCTTTTTTTTTCAA
* * *
61310256 AAAAATCAACTTATATTAC-AGAGGTTAGTTGAGCCTCGGGT-CACGCTGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
* * * ** *
61310319 ATTTTTGTTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GAACCATGC
66 A--TTTCTATTTTTCAAAAAAATCAACTCATATTGC-AGAGATGAGTTGAGCCTCGGGTCCACGC
* * * *
61310383 CGAGGTATTTTTTTTATATTTCTGTTTTTTT---
128 TGAGGTATTTCTTTTAAATTTCTTTTTTTTTCAA
* * * * *
61310414 --AAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC-GGACACATGCCGAGGTATTTCGTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
* *
61310476 AATTTCTATTTTTTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
65 AATTTCTA----TTTTTCAAAAAAATCAACTCATATTGC-AGAGATGAGTTGAGCCTCGGGTC-C
* *
61310540 ATGCCT-AGGTATTTTCTTTTAAATTTC--TGTTTTTCAA
124 ACG-CTGAGGTA-TTTCTTTTAAATTTCTTTTTTTTTCAA
*
61310577 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
61310615 AGGCCACACG
Statistics
Matches: 1023, Mismatches: 86, Indels: 117
0.83 0.07 0.10
Matches are distributed among these distances:
155 38 0.04
156 31 0.03
157 53 0.05
158 37 0.04
159 108 0.11
160 52 0.05
161 113 0.11
162 111 0.11
163 100 0.10
164 180 0.18
165 102 0.10
166 98 0.10
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (161 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
ATTTCTATTTTTCAAAAAAATCAACTCATATTGCAGAGATGAGTTGAGCCTCGGGTCCACGCTGA
GGTATTTCTTTTAAATTTCTTTTTTTTTCAA
Found at i:61310801 original size:8 final size:8
Alignment explanation
Indices: 61310788--61310819 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
61310778 CGCGCTTTTT
61310788 TAAAAAAA
1 TAAAAAAA
61310796 TAAAAAAA
1 TAAAAAAA
61310804 TACAAAAAA
1 TA-AAAAAA
61310813 TAAAAAA
1 TAAAAAA
61310820 TTATATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.12
Consensus pattern (8 bp):
TAAAAAAA
Found at i:61310881 original size:30 final size:29
Alignment explanation
Indices: 61310816--61310941 Score: 83
Period size: 30 Copynumber: 4.2 Consensus size: 29
61310806 CAAAAAATAA
* * *
61310816 AAAATTATATTTTGACCCCCTAAACTTTTT
1 AAAATTACATTTTCA-CCCCTAAACTTTCT
* *
61310846 GAAATTGCATTTTCACCCCTAAACTTTCCT
1 AAAATTACATTTTCACCCCTAAACTTT-CT
** ** *
61310876 AAAATTACATTTTGGCCTATCAAC-TTCTT
1 AAAATTACATTTTCACCCCTAAACTTTC-T
* * * *
61310905 GAAATTATATTTTGACCCCTAAATTTTCT
1 AAAATTACATTTTCACCCCTAAACTTTCT
61310934 CAAAATTA
1 -AAAATTA
61310942 TGCTTGGCCG
Statistics
Matches: 72, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
28 1 0.01
29 33 0.46
30 38 0.53
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (29 bp):
AAAATTACATTTTCACCCCTAAACTTTCT
Found at i:61311475 original size:10 final size:10
Alignment explanation
Indices: 61311460--61311537 Score: 56
Period size: 10 Copynumber: 7.7 Consensus size: 10
61311450 GAAGAAAGGA
61311460 AAAAAGAAAG
1 AAAAAGAAAG
61311470 AAAAAGAAAG
1 AAAAAGAAAG
61311480 AAAAA-AATGAG
1 AAAAAGAA--AG
*
61311491 AGAAAAAAATAG
1 A-AAAAGAA-AG
*
61311503 AAAAGGAAAG
1 AAAAAGAAAG
61311513 -AAAAGAAA-
1 AAAAAGAAAG
*
61311521 ATAAAA-AAAT
1 A-AAAAGAAAG
61311531 AAAAAGA
1 AAAAAGA
61311538 TAACAAAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
9 16 0.29
10 23 0.41
11 8 0.14
12 7 0.12
13 2 0.04
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:61311477 original size:22 final size:22
Alignment explanation
Indices: 61311451--61311520 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
61311441 TAACCCGAAG
61311451 AAGAAAGGAAAAAAGAAAGAAA
1 AAGAAAGGAAAAAAGAAAGAAA
* *
61311473 AAGAAAGAAAAAAATGAGAGAAA
1 AAGAAAGGAAAAAA-GAAAGAAA
*
61311496 AA-AATA-G-AAAAGGAAAG-AA
1 AAGAA-AGGAAAAAAGAAAGAAA
61311515 AAGAAA
1 AAGAAA
61311521 ATAAAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 5 0.12
20 6 0.15
21 4 0.10
22 15 0.38
23 10 0.25
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (22 bp):
AAGAAAGGAAAAAAGAAAGAAA
Found at i:61311486 original size:12 final size:12
Alignment explanation
Indices: 61311451--61311499 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
61311441 TAACCCGAAG
*
61311451 AAGAAAGGAAAA
1 AAGAAAGAAAAA
61311463 AAGAAAG--AAA
1 AAGAAAGAAAAA
61311473 AAGAAAGAAAAA
1 AAGAAAGAAAAA
*
61311485 AATGAGAGAAAAA
1 AA-GAAAGAAAAA
61311498 AA
1 AA
61311500 TAGAAAAGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
10 10 0.30
12 12 0.36
13 11 0.33
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (12 bp):
AAGAAAGAAAAA
Found at i:61311494 original size:13 final size:13
Alignment explanation
Indices: 61311462--61311505 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
61311452 AGAAAGGAAA
*
61311462 AAAGAAAGAAAAAG
1 AAAGAAA-AAAATG
61311476 AAAGAAAAAAATG
1 AAAGAAAAAAATG
*
61311489 AGAGAAAAAAATAG
1 AAAGAAAAAAAT-G
61311503 AAA
1 AAA
61311506 AGGAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (13 bp):
AAAGAAAAAAATG
Found at i:61311930 original size:15 final size:15
Alignment explanation
Indices: 61311912--61311944 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
61311902 TAATTTAGTT
61311912 TTATTT-ATTTAAATA
1 TTATTTCATTTAAA-A
61311927 TTATTTCATTTAAAA
1 TTATTTCATTTAAAA
61311942 TTA
1 TTA
61311945 ACTAGCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATTTCATTTAAAA
Found at i:61314895 original size:42 final size:43
Alignment explanation
Indices: 61314828--61314983 Score: 157
Period size: 42 Copynumber: 3.7 Consensus size: 43
61314818 ACCCCGTACA
* *
61314828 ATGCCAA-TGTCCCAGACGTGATCTTACATGTAATCAATATCG
1 ATGCCAACTGTCCCAGACGTGGTCTTACATGAAATCAATATCG
*
61314870 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAATCAAATAT-G
1 ATGCCAACTGTCCCAGAC-GTGGTCTTACATGAAATC-AATATCG
* *
61314912 ATGCCGA-TGTCCCAGACATGGTCTTATACAT-AAATCTCAA-ATCG
1 ATGCCAACTGTCCCAGACGTGGTC-T-TACATGAAA--TCAATATCG
61314956 ATGCCAAC-GTCCCAGACGTGGTCTTACA
1 ATGCCAACTGTCCCAGACGTGGTCTTACA
61314984 CGATAAAACA
Statistics
Matches: 96, Mismatches: 7, Indels: 22
0.77 0.06 0.18
Matches are distributed among these distances:
41 1 0.01
42 52 0.54
43 14 0.15
44 27 0.28
45 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAACTGTCCCAGACGTGGTCTTACATGAAATCAATATCG
Found at i:61328596 original size:21 final size:18
Alignment explanation
Indices: 61328550--61328597 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 18
61328540 GATGAGTATC
61328550 AATATATTAATTATAAATA
1 AATAT-TTAATTATAAATA
*
61328569 AAAATTTAATTAAATAAACTA
1 AATATTTAATT--ATAAA-TA
61328590 AATATTTA
1 AATATTTA
61328598 GTGTGTCAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.25
19 4 0.17
20 5 0.21
21 9 0.38
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
AATATTTAATTATAAATA
Found at i:61329216 original size:22 final size:22
Alignment explanation
Indices: 61329188--61329229 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
61329178 AAATTATCTA
61329188 ATTTAAA-ACAAATTATAAAATT
1 ATTTAAAGACAAATTA-AAAATT
61329210 ATTTAAAGACAAATTAAAAA
1 ATTTAAAGACAAATTAAAAA
61329230 CTTTTAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (22 bp):
ATTTAAAGACAAATTAAAAATT
Found at i:61329535 original size:134 final size:137
Alignment explanation
Indices: 61329244--61329556 Score: 379
Period size: 134 Copynumber: 2.3 Consensus size: 137
61329234 TAGTATTTTA
* * * *
61329244 AACTTGTGATACTAATTCAGCTTGATCAATCGAAAAATC-AAAGCAAAAACTATTTGATTTAAAA
1 AACTTATGATACTAATTCAGCTTGATTAATCGAAAAATCAAAAGCAAAAACTATCTAATTTAAAA
* * * * * * *
61329308 ATAAATTATGAAATTATTTGATGACATAAATTAAAATATTTTAGTATTTAATCTTTTCAGTTGGT
66 ACAAATTATGAAATTATTTAAAGACA-AAATTAAAATATTCTAATATTTAAACTTTTCAGTTGAT
*
61329373 ATCAGATT
130 ATCAAATT
* *
61329381 AACTTCTGATA-TCAATTCAGCTTGATTAATCGAAAAATCAAAATC-AAAACTATCTAATTT-AA
1 AACTTATGATACT-AATTCAGCTTGATTAATCGAAAAATCAAAAGCAAAAACTATCTAATTTAAA
* *
61329443 AACAAATTAT-AATATTATTTAAAGAC-AAATTAAAA-ACTTCTAATTTTTAAACTTTTTAGTTG
65 AACAAATTATGAA-ATTATTTAAAGACAAAATTAAAATA-TTCTAATATTTAAACTTTTCAGTTG
61329505 ATATCAAATT
128 ATATCAAATT
**
61329515 AACTTATGATACTACCTCAGCTTGATTAATCGAAAAATCAAA
1 AACTTATGATACTAATTCAGCTTGATTAATCGAAAAATCAAA
61329557 GTAAATTTAA
Statistics
Matches: 153, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
133 1 0.01
134 74 0.48
135 3 0.02
136 23 0.15
137 48 0.31
138 4 0.03
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.36
Consensus pattern (137 bp):
AACTTATGATACTAATTCAGCTTGATTAATCGAAAAATCAAAAGCAAAAACTATCTAATTTAAAA
ACAAATTATGAAATTATTTAAAGACAAAATTAAAATATTCTAATATTTAAACTTTTCAGTTGATA
TCAAATT
Found at i:61335819 original size:15 final size:15
Alignment explanation
Indices: 61335781--61335823 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
61335771 TTACATATCT
61335781 TTTTATAATTTACTA
1 TTTTATAATTTACTA
61335796 TTTTAATAATTTA-TA
1 TTTT-ATAATTTACTA
61335811 TCTTTATAATTTA
1 T-TTTATAATTTA
61335824 AAGGATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTATAATTTACTA
Found at i:61335895 original size:29 final size:29
Alignment explanation
Indices: 61335858--61335913 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
61335848 TTTTTAAATC
* *
61335858 AAAGTTTAATTTAATTATTATTTATTTTG
1 AAAGTTTAATTTAATCATTATTAATTTTG
*
61335887 AAAGTTTAATTTTATCATTATTAATTT
1 AAAGTTTAATTTAATCATTATTAATTT
61335914 AAAATTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (29 bp):
AAAGTTTAATTTAATCATTATTAATTTTG
Found at i:61337262 original size:29 final size:29
Alignment explanation
Indices: 61337214--61337285 Score: 117
Period size: 29 Copynumber: 2.4 Consensus size: 29
61337204 ATTAACTACA
*
61337214 AGTCACTCAATTTTAGACTAGTTGACAAAAC
1 AGTCACT--ATTTTAAACTAGTTGACAAAAC
61337245 AGTCACTATTTTAAACTAGTTGACAAAAC
1 AGTCACTATTTTAAACTAGTTGACAAAAC
61337274 AGTCACTATTTT
1 AGTCACTATTTT
61337286 GAATTAAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 33 0.82
31 7 0.17
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (29 bp):
AGTCACTATTTTAAACTAGTTGACAAAAC
Found at i:61342502 original size:15 final size:15
Alignment explanation
Indices: 61342484--61342516 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
61342474 TTTCTTTTAT
61342484 ATTTTTTTAACTT-TC
1 ATTTTTTT-ACTTCTC
61342499 ATTTTTTTACTTCTC
1 ATTTTTTTACTTCTC
61342514 ATT
1 ATT
61342517 CTCTTCTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTTTTACTTCTC
Found at i:61342718 original size:38 final size:39
Alignment explanation
Indices: 61342660--61342733 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 39
61342650 ATAAAAAAAA
*
61342660 TATTTTAAAAATAAAAAAATAAAAAAAATATTTTTAAAG
1 TATTTTAAAAATAAAAAAATAAAAAAAATATATTTAAAG
* *
61342699 TATTTT-AAAATTAAAAAATAAAAAATATATATTTA
1 TATTTTAAAAATAAAAAAATAAAAAAAATATATTTA
61342734 TTATATTCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 26 0.81
39 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (39 bp):
TATTTTAAAAATAAAAAAATAAAAAAAATATATTTAAAG
Found at i:61343445 original size:22 final size:22
Alignment explanation
Indices: 61343410--61343461 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
61343400 TAAATTACCC
*
61343410 TAAAATA-AATTATAAAAACT-A
1 TAAAATATAAATAT-AAAACTAA
*
61343431 TAAAATATAAATATAAAGCTAA
1 TAAAATATAAATATAAAACTAA
61343453 TAAAATATA
1 TAAAATATA
61343462 CAATTTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (22 bp):
TAAAATATAAATATAAAACTAA
Found at i:61345105 original size:21 final size:21
Alignment explanation
Indices: 61345066--61345109 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
61345056 TTTAAAATGA
* *
61345066 TTTTTATAATTTTTTATAAATT
1 TTTTTATAATTCTTCAT-AATT
61345088 TTTTTAT-ATTCTTCATAATT
1 TTTTTATAATTCTTCATAATT
61345108 TT
1 TT
61345110 AATGCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 7 0.35
22 7 0.35
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTTATAATTCTTCATAATT
Found at i:61345591 original size:19 final size:20
Alignment explanation
Indices: 61345557--61345607 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
61345547 ATTACAAAAG
61345557 AAAA-TCAAAATAATTT-TCA
1 AAAATTCAAAATAATTTAT-A
61345576 AAAATTCAAAAT-ATTTATA
1 AAAATTCAAAATAATTTATA
61345595 AAAATTTCAAAAT
1 AAAA-TTCAAAAT
61345608 TTATATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATTCAAAATAATTTATA
Found at i:61345629 original size:23 final size:24
Alignment explanation
Indices: 61345586--61345632 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
61345576 AAAATTCAAA
* *
61345586 ATATTTATAAAAATTTCAAAATTT
1 ATATTTATAAAAATATAAAAATTT
61345610 ATATTTA-AAAAATATAAAAATTT
1 ATATTTATAAAAATATAAAAATTT
61345633 CTCTCTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATTTATAAAAATATAAAAATTT
Found at i:61346304 original size:27 final size:27
Alignment explanation
Indices: 61346269--61346323 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
61346259 TAGTCCATCA
61346269 ACCACGATGCTCCCGACTTTGTGAACC
1 ACCACGATGCTCCCGACTTTGTGAACC
*
61346296 ACCATGATGCTCCCGACTTTGTGAACC
1 ACCACGATGCTCCCGACTTTGTGAACC
61346323 A
1 A
61346324 GACTTATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (27 bp):
ACCACGATGCTCCCGACTTTGTGAACC
Done.