Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 119 of 259
Found at i:38559262 original size:49 final size:49
Alignment explanation
Indices: 38559185--38559531 Score: 289
Period size: 50 Copynumber: 6.8 Consensus size: 49
38559175 GTAGCCGAAG
* * * *
38559185 CTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAA
* * *
38559234 CTGTCTGGTACACGTAGTAGCCTCCACTTAGTACTTCGTACTACACACGTGACCTCA
1 CTATCTGGTACACGTAGTAGCCTGCAC-T--TA----GTACTACACACGTGACC-AA
* ** *
38559291 CCATCTAATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCA-A
* * * * * * *
38559341 GTTTTTGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
1 CTATCT-GGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAA
* * *
38559391 TTATCCGGTACACGTAATAGCCTGCACTTAGTACTACACACGTGACCTAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC-AA
* * * * *
38559441 CCATCTGATACATGTAGTAGCCTACACTTAGTACTACACACGTGATCATA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCA-A
* * * * * *
38559491 GTTTTCGGGTACGCATAGTAGCCTGCACTTAGAACTACACA
1 -CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA
38559532 TGCGACCTCA
Statistics
Matches: 233, Mismatches: 52, Indels: 24
0.75 0.17 0.08
Matches are distributed among these distances:
49 60 0.26
50 65 0.28
51 65 0.28
52 2 0.01
54 2 0.01
56 16 0.07
57 23 0.10
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.27
Consensus pattern (49 bp):
CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAA
Found at i:38559370 original size:51 final size:51
Alignment explanation
Indices: 38559299--38559531 Score: 231
Period size: 51 Copynumber: 4.6 Consensus size: 51
38559289 CACCATCTAA
* *
38559299 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTTGGG
1 TACACATAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGGG
* * * * * *
38559350 TACGCATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAATTATCCGG
1 TACACATAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGGG
* * **** * *
38559399 TACACGTAATAGCCTGCACTTAGTACTACACACGTGA-C-CTAACCATCTGA
1 TACACATAGTAGCCTGCACTTAGTACTACACACGTGATCAC-AGTTTTCGGG
** * *
38559449 TACATGTAGTAGCCTACACTTAGTACTACACACGTGATCATAGTTTTCGGG
1 TACACATAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGGG
* *
38559500 TACGCATAGTAGCCTGCACTTAGAACTACACA
1 TACACATAGTAGCCTGCACTTAGTACTACACA
38559532 TGCGACCTCA
Statistics
Matches: 147, Mismatches: 32, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
49 41 0.28
50 41 0.28
51 65 0.44
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (51 bp):
TACACATAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGGG
Found at i:38559495 original size:150 final size:153
Alignment explanation
Indices: 38559191--38559538 Score: 531
Period size: 150 Copynumber: 2.3 Consensus size: 153
38559181 GAAGCTATCT
* * *
38559191 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTGTCTGGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGGTACACGTAATAGCC
* *
38559256 TCCACTTAGTACTTCGTACTACACACGTGACCTCACCATCTAATACACGTAGTAGCCTGCACTTA
66 TCCACTTA-TA---CGTACTACACACGTGACCTAACCATCTAATACACGTAGTAGCCTACACTTA
*
38559321 GTACTACACACGTGATCACAGTTTTTG
127 GTACTACACACGTGATCACAGTTTTCG
*
38559348 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAATAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGGTACACGTAATAGCC
* * *
38559413 TGCAC-T-TA-GTACTACACACGTGACCTAACCATCTGATACATGTAGTAGCCTACACTTAGTAC
66 TCCACTTATACGTACTACACACGTGACCTAACCATCTAATACACGTAGTAGCCTACACTTAGTAC
*
38559475 TACACACGTGATCATAGTTTTCG
131 TACACACGTGATCACAGTTTTCG
*
38559498 GGTACGCATAGTAGCCTGCACTTAGAACTACACATGCGACC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
38559539 TCACAATAGA
Statistics
Matches: 179, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
150 111 0.62
154 2 0.01
156 1 0.01
157 65 0.36
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (153 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGGTACACGTAATAGCC
TCCACTTATACGTACTACACACGTGACCTAACCATCTAATACACGTAGTAGCCTACACTTAGTAC
TACACACGTGATCACAGTTTTCG
Found at i:38559539 original size:101 final size:99
Alignment explanation
Indices: 38559356--38559539 Score: 242
Period size: 101 Copynumber: 1.8 Consensus size: 99
38559346 TGGGTACGCA
* * *
38559356 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAATAGCCTGCACTTA
1 TAGTAGCCTACACTTAGTACTACACACGCGACCAATTATCCGGTACACATAATAGCCTGCACTTA
* *
38559421 GTACTACACACGTGACCTAACCATCTGATACATG
66 GAACTACACACGCGACCTAACCATCTGATACATG
* * * * * *
38559455 TAGTAGCCTACACTTAGTACTACACACGTGATCATAGTTTTCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTACACTTAGTACTACACACGCGACCA-A-TTATCCGGTACACATAATAGCCTGCACT
*
38559520 TAGAACTACACATGCGACCT
64 TAGAACTACACACGCGACCT
38559540 CACAATAGAT
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
99 30 0.42
100 1 0.01
101 40 0.56
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTACACTTAGTACTACACACGCGACCAATTATCCGGTACACATAATAGCCTGCACTTA
GAACTACACACGCGACCTAACCATCTGATACATG
Found at i:38561713 original size:15 final size:15
Alignment explanation
Indices: 38561661--38561714 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
38561651 TAAAGATAAC
*
38561661 AAGAAAACC-GAATA
1 AAGAAACCCAGAATA
*
38561675 AAGAAATCCA-AGATA
1 AAGAAACCCAGA-ATA
38561690 GAA-AAACCCAGAATA
1 -AAGAAACCCAGAATA
38561705 AAGAAACCCA
1 AAGAAACCCA
38561715 AGATACGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
14 11 0.33
15 19 0.58
16 3 0.09
ACGTcount: A:0.61, C:0.19, G:0.13, T:0.07
Consensus pattern (15 bp):
AAGAAACCCAGAATA
Found at i:38564352 original size:30 final size:30
Alignment explanation
Indices: 38564318--38564414 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
38564308 TAAACTAAAA
* *
38564318 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAA-C
* * * * *
38564348 TGAGCTGAGATTAAACTCCTAAGCTGAAAC
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAAC
*
38564378 TGAGCTAAGGTTTAGCTCGTGAGCTGAATA-
1 TGAGCTAAGATTTAGCTCGTGAGCTGAA-AC
38564408 TGAGCTA
1 TGAGCTA
38564415 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
30 48 0.92
31 4 0.08
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAAC
Found at i:38566521 original size:51 final size:51
Alignment explanation
Indices: 38566343--38566675 Score: 274
Period size: 50 Copynumber: 6.6 Consensus size: 51
38566333 AAGCTATCTG
* * * ** *
38566343 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAACTGTCTG-
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTC-GA
* * * * **** *
38566392 GTACACGTAGTAGCCTCCACTTAGTACTACACACATGATCTCA-CCAACTA
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGA
* * *
38566442 ATATACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGA
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGA
** * * * *
38566493 GTATGCATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAATTATCCG-
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTT-TTCGA
* * *
38566542 GTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCA--TCT-GA
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGTGA--TCA-CAGTTTTCGA
* *
38566593 -TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGG
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGA
*
38566643 GTACGCATAGTAGCCTGCACTTAGTACTACACA
1 GTACACATAGTAGCCTGCACTTAGTACTACACA
38566676 TGCGACCTCA
Statistics
Matches: 229, Mismatches: 40, Indels: 28
0.77 0.13 0.09
Matches are distributed among these distances:
47 2 0.01
48 2 0.01
49 71 0.31
50 84 0.37
51 67 0.29
52 1 0.00
54 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.26
Consensus pattern (51 bp):
GTACACATAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGA
Found at i:38566618 original size:150 final size:150
Alignment explanation
Indices: 38566343--38566682 Score: 572
Period size: 150 Copynumber: 2.3 Consensus size: 150
38566333 AAGCTATCTG
* *
38566343 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTGTCTGGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGGTACACGTAGTAGCCT
* * *
38566408 CCACTTAGTACTACACACATGATCTCACCAACTAATATACGTAGTAGCCTGCACTTAGTACTACA
66 CCACTTAGTACTACACACATGACCTAACCAACTAATACACGTAGTAGCCTGCACTTAGTACTACA
38566473 CACGTGATCACAGTTTTCGA
131 CACGTGATCACAGTTTTCGA
* *
38566493 GTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGGTACACGTAGTAGCCT
* * * *
38566558 GCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTACA
66 CCACTTAGTACTACACACATGACCTAACCAACTAATACACGTAGTAGCCTGCACTTAGTACTACA
*
38566623 CACGTGATCACAGTTTTCGG
131 CACGTGATCACAGTTTTCGA
38566643 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
38566683 TCACAATAGA
Statistics
Matches: 177, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
150 177 1.00
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.26
Consensus pattern (150 bp):
GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGGTACACGTAGTAGCCT
CCACTTAGTACTACACACATGACCTAACCAACTAATACACGTAGTAGCCTGCACTTAGTACTACA
CACGTGATCACAGTTTTCGA
Found at i:38566683 original size:101 final size:100
Alignment explanation
Indices: 38566337--38566683 Score: 321
Period size: 101 Copynumber: 3.5 Consensus size: 100
38566327 TAGCCGAAGC
* * ** *
38566337 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-AACTGTCTGGTACACGTA
1 TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCTGATACACGTA
* * **
38566401 GTAGCCTCCACTTAGTACTACACACATGATCTCACC
66 GTAGCCTGCACTTAGTACTACACACGTGATC-CAAT
* * ** * * * *
38566437 AACTAATATACG--TAGTAGCCTGCACTTAGTACTACACACGTGA--TCA-CAGTTTTCGAGTAT
1 TA-TCAGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCA--TCT-GA-TAC
* * * *
38566497 GCATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAAT
61 ACGTAGTAGCCTGCACTTAGTACTACACACGTGATCCAAT
* * * *
38566536 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTA
1 TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCTGATACACGTA
*
38566601 GTAGCCTGCACTTAGTACTACACACGTGATCACAGT
66 GTAGCCTGCACTTAGTACTACACACGTGATC-CAAT
* * *
38566637 TTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCT
1 TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCT
38566684 CACAATAGAT
Statistics
Matches: 193, Mismatches: 41, Indels: 25
0.75 0.16 0.10
Matches are distributed among these distances:
98 5 0.03
99 66 0.34
100 37 0.19
101 81 0.42
102 2 0.01
103 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (100 bp):
TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCTGATACACGTA
GTAGCCTGCACTTAGTACTACACACGTGATCCAAT
Found at i:38578702 original size:13 final size:12
Alignment explanation
Indices: 38578683--38578729 Score: 60
Period size: 11 Copynumber: 3.8 Consensus size: 12
38578673 AGACCGTATG
38578683 CAATTTTTTTTT
1 CAATTTTTTTTT
38578695 CAAATTTTTTTTTT
1 C-AA-TTTTTTTTT
38578709 CAA-TTTTTTTT
1 CAATTTTTTTTT
*
38578720 CGATTTTTTT
1 CAATTTTTTT
38578730 GAATCTACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 10 0.32
12 7 0.23
13 4 0.13
14 10 0.32
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:38578729 original size:14 final size:14
Alignment explanation
Indices: 38578686--38578719 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
38578676 CCGTATGCAA
38578686 TTTTTTTTTCAAAT
1 TTTTTTTTTCAAAT
38578700 TTTTTTTTTC-AAT
1 TTTTTTTTTCAAAT
38578713 TTTTTTT
1 TTTTTTT
38578720 CGATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTCAAAT
Found at i:38580838 original size:10 final size:11
Alignment explanation
Indices: 38580816--38580852 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
38580806 AAAAGAGAAG
38580816 AAATTCAAAAA
1 AAATTCAAAAA
38580827 AAATTCAAAAA
1 AAATTCAAAAA
*
38580838 AAAATCGAAAAA
1 AAATTC-AAAAA
38580850 AAA
1 AAA
38580853 GAAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.14
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:38580839 original size:12 final size:12
Alignment explanation
Indices: 38580816--38580852 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
38580806 AAAAGAGAAG
38580816 AAATTC-AAAAA
1 AAATTCAAAAAA
38580827 AAATTCAAAAAA
1 AAATTCAAAAAA
38580839 AAA-TCGAAAAAA
1 AAATTC-AAAAAA
38580851 AA
1 AA
38580853 GAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.14
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:38581916 original size:24 final size:24
Alignment explanation
Indices: 38581889--38581968 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
38581879 CCATTGAGCG
38581889 AGAAAAGGAGAAAGAGATTGAAAA
1 AGAAAAGGAGAAAGAGATTGAAAA
** * * **
38581913 AGAAATCGAAAAAGTGAGAGAAAA
1 AGAAAAGGAGAAAGAGATTGAAAA
* *
38581937 AGAAAATGAAGAAAAGAAAATTGAAAA
1 AGAAAA-GGAG-AAAG-AGATTGAAAA
38581964 AGAAA
1 AGAAA
38581969 TTGAGAATGA
Statistics
Matches: 39, Mismatches: 14, Indels: 3
0.70 0.25 0.05
Matches are distributed among these distances:
24 23 0.59
25 1 0.03
26 4 0.10
27 11 0.28
ACGTcount: A:0.66, C:0.01, G:0.24, T:0.09
Consensus pattern (24 bp):
AGAAAAGGAGAAAGAGATTGAAAA
Found at i:38581969 original size:12 final size:12
Alignment explanation
Indices: 38581899--38581998 Score: 59
Period size: 12 Copynumber: 8.6 Consensus size: 12
38581889 AGAAAAGGAG
*
38581899 AAAGAGATTGAA
1 AAAGAAATTGAA
*
38581911 AAAGAAATCGAA
1 AAAGAAATTGAA
** **
38581923 AAAGTGAGAGAA
1 AAAGAAATTGAA
*
38581935 AAAGAAAATGAAGA
1 AAAGAAATTG-A-A
38581949 AAAGAAAATTGAA
1 AAAG-AAATTGAA
38581962 AAAGAAATTG--
1 AAAGAAATTGAA
38581972 --AG-AA-TGAA
1 AAAGAAATTGAA
*
38581980 AAAAAAATTGAA
1 AAAGAAATTGAA
38581992 AAAGAAA
1 AAAGAAA
38581999 AAGCGAAAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
6 2 0.03
7 2 0.03
8 2 0.03
10 1 0.02
11 2 0.03
12 40 0.61
13 6 0.09
14 6 0.09
15 5 0.08
ACGTcount: A:0.67, C:0.01, G:0.20, T:0.12
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:38581979 original size:18 final size:18
Alignment explanation
Indices: 38581952--38582001 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
38581942 ATGAAGAAAA
38581952 GAAAATTGAAAAAGAAATT
1 GAAAA-TGAAAAAGAAATT
* *
38581971 GAGAATGAAAAAAAAATT
1 GAAAATGAAAAAGAAATT
*
38581989 GAAAAAGAAAAAG
1 GAAAATGAAAAAG
38582002 CGAAAAAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.14
Consensus pattern (18 bp):
GAAAATGAAAAAGAAATT
Found at i:38581987 original size:30 final size:27
Alignment explanation
Indices: 38581932--38582019 Score: 97
Period size: 30 Copynumber: 3.1 Consensus size: 27
38581922 AAAAGTGAGA
*
38581932 GAAAAAGAAAATGAAGAAAAGAAAATT
1 GAAAAAGAAAATGAAGAAAAAAAAATT
*
38581959 GAAAAAGAAATTGAGAATGAAAAAAAAATT
1 GAAAAAGAAAAT--GAA-GAAAAAAAAATT
* *
38581989 GAAAAAGAAAAAG-CGAAAAAAGAAATT
1 GAAAAAGAAAATGAAGAAAAAA-AAATT
38582016 GAAA
1 GAAA
38582020 GAGAGCTTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
26 7 0.13
27 20 0.38
28 1 0.02
29 3 0.06
30 21 0.40
ACGTcount: A:0.69, C:0.01, G:0.18, T:0.11
Consensus pattern (27 bp):
GAAAAAGAAAATGAAGAAAAAAAAATT
Found at i:38582053 original size:33 final size:33
Alignment explanation
Indices: 38582016--38582078 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
38582006 AAAAGAAATT
38582016 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
38582049 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
38582079 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:38583885 original size:20 final size:20
Alignment explanation
Indices: 38583862--38583907 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
38583852 CCAGCTCGAA
*
38583862 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
38583882 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
38583902 TTAGCT
1 TTAGCT
38583908 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:38583889 original size:30 final size:30
Alignment explanation
Indices: 38583854--38583927 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
38583844 AGTTTTTCCC
38583854 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
38583884 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
38583914 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
38583928 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:38586208 original size:25 final size:25
Alignment explanation
Indices: 38586180--38586227 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
38586170 GATCTCAAAA
*
38586180 CTAAATTCTAGAATTTAGAAATGAG
1 CTAAATTCTAGAATTTACAAATGAG
*
38586205 CTAAATTTTAGAATTTACAAATG
1 CTAAATTCTAGAATTTACAAATG
38586228 GTCACTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.35
Consensus pattern (25 bp):
CTAAATTCTAGAATTTACAAATGAG
Found at i:38586275 original size:11 final size:11
Alignment explanation
Indices: 38586256--38586289 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
38586246 TAAATGAGCT
*
38586256 AAAATTTCTAG
1 AAAAATTCTAG
38586267 AAAAATTCTAG
1 AAAAATTCTAG
38586278 -AAAATTCTAG
1 AAAAATTCTAG
38586288 AA
1 AA
38586290 TGCTTCCTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (11 bp):
AAAAATTCTAG
Found at i:38586283 original size:10 final size:10
Alignment explanation
Indices: 38586256--38586289 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
38586246 TAAATGAGCT
38586256 AAAATTTCTAG
1 AAAA-TTCTAG
38586267 AAAAATTCTAG
1 -AAAATTCTAG
38586278 AAAATTCTAG
1 AAAATTCTAG
38586288 AA
1 AA
38586290 TGCTTCCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 6 0.27
12 4 0.18
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (10 bp):
AAAATTCTAG
Found at i:38593134 original size:21 final size:21
Alignment explanation
Indices: 38593105--38593144 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
38593095 GCTGGAACCT
38593105 TCCTTGAAGCTT-CTTGAACG
1 TCCTTGAAGCTTCCTTGAACG
38593125 TCCTTGGAAGCTTCCTTGAA
1 TCCTT-GAAGCTTCCTTGAA
38593145 GTTTCCAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (21 bp):
TCCTTGAAGCTTCCTTGAACG
Found at i:38593150 original size:11 final size:11
Alignment explanation
Indices: 38593103--38593150 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
38593093 GGGCTGGAAC
38593103 CTTCCTTGAAG
1 CTTCCTTGAAG
38593114 CTT-CTTGAA-
1 CTTCCTTGAAG
*
38593123 CGTCCTTGGAAG
1 CTTCCTT-GAAG
38593135 CTTCCTTGAAG
1 CTTCCTTGAAG
*
38593146 TTTCC
1 CTTCC
38593151 AAGCATGAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 2 0.06
10 9 0.29
11 14 0.45
12 6 0.19
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.38
Consensus pattern (11 bp):
CTTCCTTGAAG
Found at i:38593964 original size:32 final size:32
Alignment explanation
Indices: 38593919--38593983 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
38593909 CAAATTAATT
*
38593919 AGCAGCAGCTAATAAATTTGTCCTAAAACTAG
1 AGCAGCAGCTAATAAATTAGTCCTAAAACTAG
* *
38593951 AGCAGCAGTTAATAAATTAGTCCTAAGACTAG
1 AGCAGCAGCTAATAAATTAGTCCTAAAACTAG
38593983 A
1 A
38593984 CACTTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (32 bp):
AGCAGCAGCTAATAAATTAGTCCTAAAACTAG
Found at i:38594003 original size:29 final size:33
Alignment explanation
Indices: 38593919--38594003 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 33
38593909 CAAATTAATT
*
38593919 AGCAGCAGCTAATAAATT-TGTCCTAAAACTAG
1 AGCAGCAGTTAATAAATTATGTCCTAAAACTAG
*
38593951 AGCAGCAGTTAATAAATTA-GTCCTAAGACTAG
1 AGCAGCAGTTAATAAATTATGTCCTAAAACTAG
*
38593983 A-CA-C-TTTAA-AAATTATGTCCT
1 AGCAGCAGTTAATAAATTATGTCCT
38594004 CAACTAAAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
28 6 0.12
29 9 0.19
30 1 0.02
31 2 0.04
32 30 0.62
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (33 bp):
AGCAGCAGTTAATAAATTATGTCCTAAAACTAG
Found at i:38594009 original size:28 final size:29
Alignment explanation
Indices: 38593932--38594023 Score: 73
Period size: 32 Copynumber: 3.1 Consensus size: 29
38593922 AGCAGCTAAT
* *
38593932 AAATTTGTCCTAAAACT-AGAGCAGCAGTTAA
1 AAATTAGTCCTAAGACTAAGA-CA-CA-TTAA
*
38593963 TAAATTAGTCCTAAGACT-AGACACTTTAA
1 -AAATTAGTCCTAAGACTAAGACACATTAA
*
38593992 AAATTATGTCCTCA-ACTAAAGACACATTAA
1 AAATTA-GTCCTAAGACT-AAGACACATTAA
38594022 AA
1 AA
38594024 CTTTAATTAG
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
28 9 0.17
29 10 0.19
30 13 0.25
31 2 0.04
32 18 0.35
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (29 bp):
AAATTAGTCCTAAGACTAAGACACATTAA
Found at i:38595710 original size:13 final size:13
Alignment explanation
Indices: 38595692--38595716 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38595682 TGGTCATCAT
38595692 GGTGTGAACACAA
1 GGTGTGAACACAA
38595705 GGTGTGAACACA
1 GGTGTGAACACA
38595717 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:38596273 original size:30 final size:30
Alignment explanation
Indices: 38596187--38596273 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 30
38596177 TAAATTAAAA
* * *
38596187 TGAGTTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * *
38596217 TGAGCTGAGATTAAACTC-TAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
38596246 TGAGCTAAGGTTTAGCTCGTGAGCTGAA
1 TGAGCTAAGATTTAGCTCGTGAGCTGAA
38596274 TAAGAGCTAG
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 23 0.52
30 21 0.48
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:38601209 original size:18 final size:18
Alignment explanation
Indices: 38601188--38601222 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
38601178 TTTTTCTTTT
38601188 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
38601206 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
38601223 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:38602162 original size:14 final size:13
Alignment explanation
Indices: 38602145--38602178 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
38602135 TTTTGCTCGA
38602145 TTTTTTTT-AACTT
1 TTTTTTTTGAA-TT
38602158 TTTTTTTTGAATT
1 TTTTTTTTGAATT
38602171 TTTTTTTT
1 TTTTTTTT
38602179 CAATCAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 18 0.90
14 2 0.10
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:38602189 original size:16 final size:16
Alignment explanation
Indices: 38602170--38602209 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
38602160 TTTTTTGAAT
38602170 TTTTTTTTTCAATCAA
1 TTTTTTTTTCAATCAA
38602186 TTTTTTTTTCAATCAA
1 TTTTTTTTTCAATCAA
38602202 TTTTTTTT
1 TTTTTTTT
38602210 ATTTTTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTTTTTCAATCAA
Found at i:38606654 original size:20 final size:20
Alignment explanation
Indices: 38606631--38606673 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
38606621 AAAAAGTTGT
* *
38606631 AAAAAAAGTAAAAGAAAAGA
1 AAAAAAAGAAAAAGAAAACA
*
38606651 AAAATAAGAAAAAGAAAACA
1 AAAAAAAGAAAAAGAAAACA
38606671 AAA
1 AAA
38606674 GAGAGTGACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.05
Consensus pattern (20 bp):
AAAAAAAGAAAAAGAAAACA
Found at i:38615116 original size:63 final size:64
Alignment explanation
Indices: 38615036--38615219 Score: 192
Period size: 67 Copynumber: 2.8 Consensus size: 64
38615026 CATGTAGTTC
* * * * *
38615036 GCTCTCTTGTAC-ACATGGTGAACACTTAGTACCACCCATGTGACCTAGCCA-ATTTATCTCGTA
1 GCTCTCTTGT-CTACATGGTGTACACATAGTACCACCCATGCGACCTAGCCACATATATCCCGTA
* * * * * *
38615099 GCTCTCTTGTCTACATGGTGTCCTTCACCTGGAACCACGCATGCGACCTAGCTACATATATCCCG
1 GCTCTCTTGTCTACATGGTG---TACACATAGTACCACCCATGCGACCTAGCCACATATATCCCG
38615164 TA
63 TA
* * *
38615166 GCTCTCCTGTCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACAT
1 GCTCTCTTGTCTACATGGTGTACACATAGTACCACCCATGCGACCTAGCCACAT
38615220 CATAATGTCT
Statistics
Matches: 99, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
62 1 0.01
63 18 0.18
64 28 0.28
66 23 0.23
67 29 0.29
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (64 bp):
GCTCTCTTGTCTACATGGTGTACACATAGTACCACCCATGCGACCTAGCCACATATATCCCGTA
Found at i:38615985 original size:30 final size:30
Alignment explanation
Indices: 38615951--38616011 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
38615941 TCCTTAACTC
38615951 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
38615981 AAACTTTTGCATACTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
38616011 A
1 A
38616012 GGCTTGGGAA
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:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:38617238 original size:30 final size:30
Alignment explanation
Indices: 38617204--38617300 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
38617194 AGCTCACTCC
38617204 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
38617234 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * * *
38617264 CAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
38617294 TAGCTCA
1 TAGCTCA
38617301 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:38618188 original size:22 final size:20
Alignment explanation
Indices: 38618156--38618204 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
38618146 GCCGAATTTA
38618156 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
38618179 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
38618199 TGAACA
1 TGAACA
38618205 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:38623943 original size:93 final size:93
Alignment explanation
Indices: 38623779--38623949 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
38623769 GGATGGTTGA
* * *
38623779 GCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGGATGCAAACGTCCGAACTCGTTGAGT
38623844 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
38623872 GCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTAGGGATGCGAACG-CCTAAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGGATGCAAACGTCCGAA-CTCGTTGAG
38623936 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
38623950 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 4 0.06
93 67 0.94
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGGATGCAAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:38623957 original size:46 final size:46
Alignment explanation
Indices: 38623784--38623957 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 46
38623774 GTTGAGCATT
* *
38623784 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGGATGCAAACGTC
* * * *
38623830 CGAACTCGTTGAGTTGAGTCCGAGTT--CGT-GAGATGTAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGGATGCAA--A--CGTC
* *
38623877 CGAACTTGTTGAGTTGAGTCCGAGTTCACTTAGGGATGCGAACG-C
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGGATGCAAACGTC
*
38623922 CTAAGCTCGTTGAGTTGAGTCCGAGTTCACTTAGGG
1 CGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTAGGG
38623958 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 5 0.05
46 57 0.54
47 27 0.25
48 1 0.01
49 2 0.02
50 6 0.06
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGGATGCAAACGTC
Found at i:38628629 original size:20 final size:21
Alignment explanation
Indices: 38628601--38628639 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
38628591 CAAAATGAGC
*
38628601 AAACAAGCT-TATTGAGCTGG
1 AAACAAGCTAAATTGAGCTGG
*
38628621 AAACGAGCTAAATTGAGCT
1 AAACAAGCTAAATTGAGCT
38628640 CAACGAGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (21 bp):
AAACAAGCTAAATTGAGCTGG
Found at i:38632258 original size:48 final size:47
Alignment explanation
Indices: 38632179--38632284 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
38632169 GAGTGTCATG
*
38632179 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
38632227 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
38632275 GAAAAAGAAA
1 GAAAAAGAAA
38632285 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:38634000 original size:20 final size:20
Alignment explanation
Indices: 38633954--38634000 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
38633944 AGCTCGTTTC
*
38633954 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
38633974 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
38633994 CAGCTCA
1 CAGCTCA
38634001 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:38642893 original size:55 final size:52
Alignment explanation
Indices: 38642805--38643060 Score: 222
Period size: 55 Copynumber: 4.9 Consensus size: 52
38642795 CATTAGGGTT
*
38642805 TAAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAA
1 TAAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAA-GTTTCTAA
* * * * *
38642858 GGTAAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATTGATAAGTTACT-A
1 --TAAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAA
* * *
38642910 TAAGGCAAAGGTCCCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGAG-TTCATAA
1 TAAGG---A--TACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTC-TAA
* * *
38642966 GGCAAGGATACCATGTAAGACCATGTCAAGACATGG-AAATGGTAAGTTTC-AA
1 --TAAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAA
* * *
38643018 -AAGGATACCACGTAAGACCATGACAAGTCATGGCAA-TGGTAAG
1 TAAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAG
38643061 GTACCCGCGT
Statistics
Matches: 166, Mismatches: 23, Indels: 30
0.76 0.11 0.14
Matches are distributed among these distances:
49 37 0.22
50 7 0.04
52 3 0.02
53 38 0.23
54 12 0.07
55 64 0.39
56 1 0.01
58 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (52 bp):
TAAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAA
Found at i:38643012 original size:108 final size:110
Alignment explanation
Indices: 38642813--38643013 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 110
38642803 TTTAAGGATA
* *
38642813 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGTAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
* *
38642878 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGAAATGATAAGTTACTATAAGGCAAAGGTC
* *
38642923 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
38642985 ACCATGTCAAGACATGGAAATGGTAAGTT
65 ACCATGTCAAGACATGGAAATGATAAGTT
38643014 TCAAAAGGAT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
107 3 0.04
108 46 0.55
109 7 0.08
110 27 0.33
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGAAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:38643273 original size:16 final size:16
Alignment explanation
Indices: 38643252--38643282 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38643242 ATAAATTTGA
38643252 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
38643268 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
38643283 AGTGAAGAAG
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:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:38649864 original size:11 final size:12
Alignment explanation
Indices: 38649836--38649870 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
38649826 ATGCAATTTT
38649836 TTTTTCTTTTCAA
1 TTTTT-TTTTCAA
38649849 TTTTTTTTTCAA
1 TTTTTTTTTCAA
38649861 TTTTTTTTTC
1 TTTTTTTTTC
38649871 GAACTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:38649865 original size:13 final size:13
Alignment explanation
Indices: 38649835--38649869 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
38649825 TATGCAATTT
38649835 TTTTTTCTTTTCAA
1 TTTTTT-TTTTCAA
38649849 -TTTTTTTTTCAA
1 TTTTTTTTTTCAA
38649861 TTTTTTTTT
1 TTTTTTTTT
38649870 CGAACTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTTTTCAA
Found at i:38661012 original size:20 final size:20
Alignment explanation
Indices: 38660959--38661012 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
38660949 GCTGAAAGTA
*
38660959 AGCTCAGTTGAGCTCAAACG
1 AGCTGAGTTGAGCTCAAACG
**** *
38660979 AGCTGAAACAAGCTCAAATG
1 AGCTGAGTTGAGCTCAAACG
38660999 AGCTGAGTTGAGCT
1 AGCTGAGTTGAGCT
38661013 GGACGGTGCT
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.20
Consensus pattern (20 bp):
AGCTGAGTTGAGCTCAAACG
Found at i:38666119 original size:30 final size:30
Alignment explanation
Indices: 38666085--38666181 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
38666075 TAAACTAAAA
*
38666085 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
38666115 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
38666145 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
38666174 ATGAGCTA
1 -TGAGCTA
38666182 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:38668377 original size:12 final size:12
Alignment explanation
Indices: 38668362--38668392 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
38668352 TTCTTTTTGC
38668362 TTTTCAAAGGCT
1 TTTTCAAAGGCT
38668374 TTTTCAAAGGCT
1 TTTTCAAAGGCT
38668386 TTTTCAA
1 TTTTCAA
38668393 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:38668469 original size:6 final size:6
Alignment explanation
Indices: 38668453--38668502 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
38668443 TTTCTTTTTA
*
38668453 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
38668502 T
1 T
38668503 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:38668485 original size:37 final size:37
Alignment explanation
Indices: 38668442--38668512 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
38668432 CTTGCCTCTC
38668442 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
38668479 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
38668513 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:38668513 original size:16 final size:16
Alignment explanation
Indices: 38668438--38668498 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
38668428 GCCTCTTGCC
*
38668438 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
38668454 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
38668470 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
38668486 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
38668499 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:38671234 original size:30 final size:30
Alignment explanation
Indices: 38671200--38671296 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
38671190 TAAACTAAAA
*
38671200 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
38671230 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
38671260 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
38671289 ATGAGCTA
1 -TGAGCTA
38671297 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:38674362 original size:21 final size:21
Alignment explanation
Indices: 38674335--38674395 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
38674325 TATAGTGAGT
38674335 ATATCATAGCATATCATGTGC
1 ATATCATAGCATATCATGTGC
* *
38674356 ATCTCATAACATATCATGTGC
1 ATATCATAGCATATCATGTGC
*
38674377 ATATTAT-GTCATATCATGT
1 ATATCATAG-CATATCATGT
38674396 ATAACAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (21 bp):
ATATCATAGCATATCATGTGC
Found at i:38674389 original size:10 final size:11
Alignment explanation
Indices: 38674343--38674395 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
38674333 GTATATCATA
38674343 GCATATCATGT
1 GCATATCATGT
* *
38674354 GCATCTCAT-A
1 GCATATCATGT
*
38674364 ACATATCATGT
1 GCATATCATGT
*
38674375 GCATATTATGT
1 GCATATCATGT
38674386 -CATATCATGT
1 GCATATCATGT
38674396 ATAACAATAT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (11 bp):
GCATATCATGT
Found at i:38674476 original size:25 final size:26
Alignment explanation
Indices: 38674432--38674481 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
38674422 ATAATTAAAC
* *
38674432 CCTAGGGGGTATAATGGTCATTTTTA
1 CCTAGGGGGTAAAATAGTCATTTTTA
38674458 CCTA-GGGGTAAAATAGTCATTTTT
1 CCTAGGGGGTAAAATAGTCATTTTT
38674482 CATATTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (26 bp):
CCTAGGGGGTAAAATAGTCATTTTTA
Found at i:38676105 original size:11 final size:11
Alignment explanation
Indices: 38676089--38676118 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
38676079 CTTGGACCCA
38676089 TGAGCTGGTAG
1 TGAGCTGGTAG
38676100 TGAGCTGGTAG
1 TGAGCTGGTAG
38676111 TGAGCTGG
1 TGAGCTGG
38676119 ACCCGAGCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.17, C:0.10, G:0.47, T:0.27
Consensus pattern (11 bp):
TGAGCTGGTAG
Found at i:38685775 original size:33 final size:33
Alignment explanation
Indices: 38685737--38685799 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
38685727 GATTACTCAC
38685737 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
38685770 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
38685800 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:38685823 original size:6 final size:6
Alignment explanation
Indices: 38685814--38685921 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
38685804 TCTTTTTTCG
* * * **
38685814 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * *
38685865 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTCTT CATTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
38685913 -GTTTT CTTT
1 CTTTTT CTTT
38685922 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 27, Indels: 6
0.69 0.26 0.06
Matches are distributed among these distances:
5 4 0.06
6 56 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.07, C:0.19, G:0.03, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:38685826 original size:21 final size:21
Alignment explanation
Indices: 38685797--38685912 Score: 52
Period size: 18 Copynumber: 5.7 Consensus size: 21
38685787 CAAGCTCTCT
*
38685797 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
38685818 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
38685839 TTCATTTTCTTTTTCTCTCACTTT-
1 TTCATTTTC-TTTT-T-TC-CTTTC
38685863 TTCGA-TTTC-TTTTT-CTTT-
1 TTC-ATTTTCTTTTTTCCTTTC
* *
38685881 TGCAATTTC-TTTTT-C-TTC
1 TTCATTTTCTTTTTTCCTTTC
38685899 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
38685913 GTTTTCTTTC
Statistics
Matches: 74, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
17 3 0.04
18 23 0.31
19 4 0.05
20 4 0.05
21 21 0.28
22 5 0.07
23 1 0.01
24 9 0.12
25 4 0.05
ACGTcount: A:0.09, C:0.20, G:0.03, T:0.69
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:38685845 original size:14 final size:14
Alignment explanation
Indices: 38685796--38685852 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
38685786 TCAAGCTCTC
38685796 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
38685809 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
38685823 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
38685837 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
38685851 TT
1 TT
38685853 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:38685928 original size:57 final size:55
Alignment explanation
Indices: 38685814--38685932 Score: 134
Period size: 57 Copynumber: 2.1 Consensus size: 55
38685804 TCTTTTTTCG
* *
38685814 CTTTTTCTTTTTCAATTTTCTTTTCTTCATTTTCTTTTTCTCTCACTTTTTCGATTT
1 CTTTTTCTTTTGCAATTTTCTTTTCTTCATTTTCTTTTTCTCT--CTTTTTCAATTT
* *
38685871 CTTTTTCTTTTGCAATTTCTTTTTCTTCTTCATTTTCTTTTTGT-T-TTCTTTCAATTT
1 CTTTTTCTTTTGCAA-TT-TTCTT-TTCTTCATTTTCTTTTTCTCTCTT-TTTCAATTT
38685928 CTTTT
1 CTTTT
38685933 CAATCTCTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
56 2 0.04
57 27 0.50
58 2 0.04
59 5 0.09
60 18 0.33
ACGTcount: A:0.08, C:0.19, G:0.03, T:0.70
Consensus pattern (55 bp):
CTTTTTCTTTTGCAATTTTCTTTTCTTCATTTTCTTTTTCTCTCTTTTTCAATTT
Found at i:38687013 original size:12 final size:12
Alignment explanation
Indices: 38686998--38687069 Score: 56
Period size: 12 Copynumber: 5.6 Consensus size: 12
38686988 TTTTGCTCGA
*
38686998 TTTTTTTTCACT
1 TTTTTTTTCAAT
*
38687010 TTTTTTTTGAAT
1 TTTTTTTTCAAT
38687022 TTTTTTTCAATCAAAAT
1 TTTTTTT---TC--AAT
38687039 TTTTTTTTCGAAT
1 TTTTTTTTC-AAT
*
38687052 TTTTTTTT-GAT
1 TTTTTTTTCAAT
38687063 TTTTTTT
1 TTTTTTT
38687070 GTTACTCCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
11 9 0.18
12 17 0.34
13 11 0.22
14 2 0.04
15 1 0.02
17 10 0.20
ACGTcount: A:0.17, C:0.07, G:0.04, T:0.72
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:38687015 original size:28 final size:28
Alignment explanation
Indices: 38686956--38687017 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
38686946 TTAAACTTGA
*
38686956 TTTTTTTTGCTCACCTTTTTTTCTTTTC
1 TTTTTTTTGCTCACCTTTTTTTCCTTTC
*
38686984 TTTTTTTTGCTCGA-TTTTTTTTCACTTT-
1 TTTTTTTTGCTC-ACCTTTTTTTC-CTTTC
38687012 TTTTTT
1 TTTTTT
38687018 GAATTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.74
Consensus pattern (28 bp):
TTTTTTTTGCTCACCTTTTTTTCCTTTC
Found at i:38690180 original size:10 final size:10
Alignment explanation
Indices: 38690165--38690202 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
38690155 TTGTTGCTAA
38690165 ATTGAGCTCG
1 ATTGAGCTCG
38690175 ATTGAGCT-G
1 ATTGAGCTCG
38690184 ACTTGAGCTCG
1 A-TTGAGCTCG
*
38690195 AGTGAGCT
1 ATTGAGCT
38690203 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:38690191 original size:20 final size:20
Alignment explanation
Indices: 38690166--38690203 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38690156 TGTTGCTAAA
*
38690166 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
38690186 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
38690204 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:38692862 original size:12 final size:11
Alignment explanation
Indices: 38692838--38692890 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 11
38692828 ACGGTATTGT
38692838 AAAAAAAA-T-
1 AAAAAAAATTC
*
38692847 AAAAAAAACTTG
1 AAAAAAAA-TTC
38692859 AAAAAAAATTC
1 AAAAAAAATTC
38692870 AAAAAAAAAATTC
1 --AAAAAAAATTC
38692883 AAAAAAAA
1 AAAAAAAA
38692891 GTTTGTATTC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
9 8 0.21
11 11 0.29
12 8 0.21
13 11 0.29
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:38692863 original size:13 final size:12
Alignment explanation
Indices: 38692838--38692890 Score: 58
Period size: 13 Copynumber: 4.6 Consensus size: 12
38692828 ACGGTATTGT
38692838 AAAAAAAA-T-A
1 AAAAAAAATTCA
* *
38692848 AAAAAAACTT-G
1 AAAAAAAATTCA
38692859 AAAAAAAATTCAA
1 AAAAAAAATTC-A
38692872 AAAAAAAATTCA
1 AAAAAAAATTCA
38692884 AAAAAAA
1 AAAAAAA
38692891 GTTTGTATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
10 7 0.19
11 10 0.28
12 8 0.22
13 11 0.31
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.13
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:38692986 original size:24 final size:25
Alignment explanation
Indices: 38692938--38692994 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
38692928 ATTGAAGAAA
*
38692938 AAAAAGAAGAAAAAAATTCAGAATT-
1 AAAAA-AAGAAAAAAAATCAGAATTG
38692963 AAAAAAAGAAAAAAAATC-GAAATTG
1 AAAAAAAGAAAAAAAATCAG-AATTG
38692988 AAAAAAA
1 AAAAAAA
38692995 AAGAGTGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 1 0.03
24 16 0.55
25 12 0.41
ACGTcount: A:0.74, C:0.04, G:0.11, T:0.12
Consensus pattern (25 bp):
AAAAAAAGAAAAAAAATCAGAATTG
Found at i:38693865 original size:17 final size:15
Alignment explanation
Indices: 38693845--38693883 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
38693835 GCGAGCGAGA
38693845 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
38693862 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
38693877 AAGATGA
1 AA-ATGA
38693884 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:38695389 original size:20 final size:20
Alignment explanation
Indices: 38695364--38695418 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
38695354 TGTGGTTCAA
*
38695364 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
* *
38695384 CTCATTTGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
38695404 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
38695419 TTTAACTCGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:38702240 original size:33 final size:33
Alignment explanation
Indices: 38702202--38702264 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
38702192 GATTACTCAC
38702202 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
38702235 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
38702265 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:38702291 original size:27 final size:27
Alignment explanation
Indices: 38702261--38702347 Score: 97
Period size: 27 Copynumber: 3.1 Consensus size: 27
38702251 TCAAGCTCTC
*
38702261 TTTCAATTTCTTTT-TTCGCTTTTTCTT
1 TTTCAATTTCTTTTCTTC-CATTTTCTT
* *
38702288 TTTCAATTTTTTTTCATTCTCAATTTCTT
1 TTTCAATTTCTTTTC-TTC-CATTTTCTT
38702317 TTTCAATTTTCTTTTCTT-CATTTTCTT
1 TTTCAA-TTTCTTTTCTTCCATTTTCTT
38702344 TTTC
1 TTTC
38702348 TCTCACTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
27 25 0.49
29 18 0.35
30 8 0.16
ACGTcount: A:0.11, C:0.18, G:0.01, T:0.69
Consensus pattern (27 bp):
TTTCAATTTCTTTTCTTCCATTTTCTT
Found at i:38702302 original size:17 final size:18
Alignment explanation
Indices: 38702279--38702321 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
38702269 TCTTTTTTCG
* *
38702279 CTTTTTCTTTTTCAATTT
1 CTTTTTCATTCTCAATTT
38702297 -TTTTTCATTCTCAATTT
1 CTTTTTCATTCTCAATTT
38702314 CTTTTTCA
1 CTTTTTCA
38702322 ATTTTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (18 bp):
CTTTTTCATTCTCAATTT
Found at i:38702323 original size:29 final size:27
Alignment explanation
Indices: 38702282--38702347 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 27
38702272 TTTTTCGCTT
38702282 TTTCTTTTTCAATTTT-TTTTCATTCTCAA
1 TTTCTTTTTCAATTTTCTTTTC--T-TCAA
*
38702311 TTTCTTTTTCAATTTTCTTTTCTTCAT
1 TTTCTTTTTCAATTTTCTTTTCTTCAA
38702338 TTTCTTTTTC
1 TTTCTTTTTC
38702348 TCTCACTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 13 0.37
28 1 0.03
29 16 0.46
30 5 0.14
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTCTTTTTCAATTTTCTTTTCTTCAA
Found at i:38702331 original size:12 final size:12
Alignment explanation
Indices: 38702282--38702380 Score: 59
Period size: 12 Copynumber: 8.6 Consensus size: 12
38702272 TTTTTCGCTT
38702282 TTTCTTTTTCAA
1 TTTCTTTTTCAA
38702294 TTT-TTTTTC-A
1 TTTCTTTTTCAA
38702304 -TTC----TCAA
1 TTTCTTTTTCAA
38702311 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
38702323 TTTTCTTTTCTTCAT
1 -TTTC-TTT-TTCAA
**
38702338 TTTCTTTTTCTC
1 TTTCTTTTTCAA
** *
38702350 TCACTTTTTCGA
1 TTTCTTTTTCAA
38702362 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
38702374 TCTCTTT
1 TTTCTTT
38702381 CTCCTTTTCT
Statistics
Matches: 66, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
6 2 0.03
7 1 0.02
8 3 0.05
9 2 0.03
10 1 0.02
11 6 0.09
12 33 0.50
13 7 0.11
14 7 0.11
15 4 0.06
ACGTcount: A:0.12, C:0.20, G:0.01, T:0.67
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:38702389 original size:24 final size:24
Alignment explanation
Indices: 38702304--38702390 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 24
38702294 TTTTTTTTCA
* *
38702304 TTCTCAATTTCTTTTTCAATTTTCTT
1 TTCTCATTTTCTTTTTCAA-TCTC-T
** *
38702330 TTCTTCATTTTCTTTTTCTCTCACT
1 TTC-TCATTTTCTTTTTCAATCTCT
*
38702355 TTTTCGA-TTTCTTTTTCAATCTCT
1 TTCTC-ATTTTCTTTTTCAATCTCT
*
38702379 TTCTCCTTTTCT
1 TTCTCATTTTCT
38702391 CGCTCAATGG
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
24 25 0.53
25 4 0.09
26 5 0.11
27 13 0.28
ACGTcount: A:0.10, C:0.24, G:0.01, T:0.64
Consensus pattern (24 bp):
TTCTCATTTTCTTTTTCAATCTCT
Found at i:38703451 original size:23 final size:23
Alignment explanation
Indices: 38703425--38703469 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
38703415 TCTTTTCTTT
38703425 TTTTTGCTCG-ATTTTTTTTTCAC
1 TTTTT-CTCGAATTTTTTTTTCAC
* *
38703448 TTTTTTTTGAATTTTTTTTTCA
1 TTTTTCTCGAATTTTTTTTTCA
38703470 ATCAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.71
Consensus pattern (23 bp):
TTTTTCTCGAATTTTTTTTTCAC
Found at i:38703452 original size:13 final size:13
Alignment explanation
Indices: 38703369--38703455 Score: 57
Period size: 15 Copynumber: 6.2 Consensus size: 13
38703359 CTCGCAAGAC
38703369 TTTTCACTTTTTT
1 TTTTCACTTTTTT
*
38703382 TTTTAACTTGATTTT
1 TTTTCACTT--TTTT
*
38703397 TTTGCTCACCTTTTT
1 TTT--TCACTTTTTT
**
38703412 TTTTCTTTTCTTTT
1 TTTTCACTT-TTTT
* *
38703426 TTTTGCTCGATTTTT
1 TTTT-CAC-TTTTTT
38703441 TTTTCACTTTTTT
1 TTTTCACTTTTTT
38703454 TT
1 TT
38703456 GAATTTTTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
13 18 0.32
14 10 0.18
15 24 0.42
16 1 0.02
17 4 0.07
ACGTcount: A:0.08, C:0.15, G:0.05, T:0.72
Consensus pattern (13 bp):
TTTTCACTTTTTT
Found at i:38708233 original size:17 final size:18
Alignment explanation
Indices: 38708201--38708234 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38708191 AAAAGAGAGT
*
38708201 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
38708219 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
38708235 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:38716750 original size:39 final size:40
Alignment explanation
Indices: 38716655--38716877 Score: 248
Period size: 39 Copynumber: 5.7 Consensus size: 40
38716645 TTGAATGATG
*
38716655 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
38716693 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
38716734 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
38716773 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
38716812 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
38716851 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
38716878 AACGAGGAGC
Statistics
Matches: 161, Mismatches: 14, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
39 91 0.57
40 58 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:38716858 original size:79 final size:80
Alignment explanation
Indices: 38716655--38716877 Score: 253
Period size: 79 Copynumber: 2.8 Consensus size: 80
38716645 TTGAATGATG
* * * *
38716655 TCCGGGCTAAGTCCCGAAGGC--TTGTGCT-AAGTGACAATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTG-TGAA-TTACTATATCCGGGCTAAGACCCGAAGGCAT
*
38716717 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
* *
38716734 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-TACTA-ATTTCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGTGA-ATTACTATA-TCCGGGCTAAGACCCGAAGGCAT
*
38716795 TTGTGCGAGTTACTAAA
64 TTGTGCGAGATACTAAA
* * * *
38716812 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAATTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGTGAATTACTATATCCGGGCTAAGACCCGAAGGCATTT
38716877 G
66 G
38716878 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 13, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
78 46 0.38
79 54 0.44
80 21 0.17
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGTGAATTACTATATCCGGGCTAAGACCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:38716899 original size:79 final size:79
Alignment explanation
Indices: 38716655--38716910 Score: 199
Period size: 79 Copynumber: 3.3 Consensus size: 79
38716645 TTGAATGATG
* * * *
38716655 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
38716716 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* **
38716734 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTTCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
38716798 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
* *
38716812 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
38716875 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
38716892 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
38716911 TACGTGATTT
Statistics
Matches: 150, Mismatches: 17, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
77 1 0.01
78 46 0.31
79 66 0.44
80 36 0.24
81 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:38718641 original size:24 final size:25
Alignment explanation
Indices: 38718614--38718665 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
38718604 GCCTAGCCTC
38718614 TTTTAAT-AACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
**
38718638 TTTTGGTAAACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
38718663 TTT
1 TTT
38718666 CGCACTTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (25 bp):
TTTTAATAAACTGGGGCAAAGCCCT
Found at i:38718740 original size:21 final size:21
Alignment explanation
Indices: 38718713--38718773 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
38718703 TATAGTGAGT
38718713 ATATCATAGCATATCATGTGC
1 ATATCATAGCATATCATGTGC
* **
38718734 ATCTCATAAAATATCATGTGC
1 ATATCATAGCATATCATGTGC
*
38718755 ATATTAT-GTCATATCATGT
1 ATATCATAG-CATATCATGT
38718774 ATAACAATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.38
Consensus pattern (21 bp):
ATATCATAGCATATCATGTGC
Found at i:38720812 original size:20 final size:19
Alignment explanation
Indices: 38720787--38720825 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
38720777 AAAGCGGCAA
38720787 TAAAGGAGCTGCTGGTGCAT
1 TAAAGG-GCTGCTGGTGCAT
*
38720807 TAAAGGGTTGCTGGTGCAT
1 TAAAGGGCTGCTGGTGCAT
38720826 AGAACGGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.23, C:0.13, G:0.36, T:0.28
Consensus pattern (19 bp):
TAAAGGGCTGCTGGTGCAT
Found at i:38725228 original size:20 final size:20
Alignment explanation
Indices: 38725205--38725251 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
38725195 AGGTTAAGAT
*
38725205 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
38725225 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
38725245 TGAGCTG
1 TGAGCTG
38725252 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:38726977 original size:48 final size:48
Alignment explanation
Indices: 38726922--38727027 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
38726912 TTGTCTTTTC
*
38726922 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
38726970 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
38727018 TTTCTTTTTC
1 TTTCTTTTTC
38727028 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:38728082 original size:15 final size:15
Alignment explanation
Indices: 38728049--38728086 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
38728039 TTTAACTTGA
38728049 TTTTTTTTGCTCACCT
1 TTTTTTTTGCTCA-CT
38728065 TTTTTTTTGCTCGA-T
1 TTTTTTTTGCTC-ACT
38728080 TTTTTTT
1 TTTTTTT
38728087 CACTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 12 0.57
17 1 0.05
ACGTcount: A:0.05, C:0.16, G:0.08, T:0.71
Consensus pattern (15 bp):
TTTTTTTTGCTCACT
Found at i:38728094 original size:12 final size:12
Alignment explanation
Indices: 38728079--38728148 Score: 54
Period size: 13 Copynumber: 5.6 Consensus size: 12
38728069 TTTTGCTCGA
*
38728079 TTTTTTTTCACT
1 TTTTTTTTCAAT
**
38728091 TTTTTTTAAAATT
1 TTTTTTTTCAA-T
38728104 TTTTTTTCAATCAAT
1 TTTTTTT---TCAAT
38728119 TTTTTTTTCGAAT
1 TTTTTTTTC-AAT
38728132 TTTTTTTT--AT
1 TTTTTTTTCAAT
38728142 TTTTTTT
1 TTTTTTT
38728149 GTTACTCCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
10 9 0.19
12 10 0.21
13 19 0.40
15 8 0.17
16 2 0.04
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:38728106 original size:13 final size:13
Alignment explanation
Indices: 38728090--38728140 Score: 57
Period size: 13 Copynumber: 3.7 Consensus size: 13
38728080 TTTTTTTCAC
38728090 TTTTTTTTAAAAT
1 TTTTTTTTAAAAT
38728103 TTTTTTTTCAATCAAT
1 TTTTTTTT-AA--AAT
**
38728119 TTTTTTTTCGAAT
1 TTTTTTTTAAAAT
38728132 TTTTTTTTA
1 TTTTTTTTA
38728141 TTTTTTTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 19 0.59
14 2 0.06
16 11 0.34
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.71
Consensus pattern (13 bp):
TTTTTTTTAAAAT
Found at i:38729660 original size:20 final size:20
Alignment explanation
Indices: 38729637--38729683 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
38729627 AGGTTAAGAT
*
38729637 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
38729657 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
38729677 TGAGCTG
1 TGAGCTG
38729684 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:38730877 original size:10 final size:10
Alignment explanation
Indices: 38730862--38730889 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
38730852 GAAATTTGAA
38730862 AAAAAAATTC
1 AAAAAAATTC
38730872 AAAAAAATTC
1 AAAAAAATTC
38730882 AAAAAAAT
1 AAAAAAAT
38730890 CGAAGTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:38736845 original size:12 final size:12
Alignment explanation
Indices: 38736813--38736846 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
38736803 TATTGACTTT
38736813 TTAATTAATAAG
1 TTAATTAATAAG
38736825 TTCAA-TAATAAG
1 TT-AATTAATAAG
38736837 TTAATTAATA
1 TTAATTAATA
38736847 TCCTACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.10
12 16 0.80
13 2 0.10
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (12 bp):
TTAATTAATAAG
Found at i:38738715 original size:33 final size:33
Alignment explanation
Indices: 38738678--38738743 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
38738668 AAATTTGATA
*
38738678 GACAACAACACAGGGGGAATATGAAACAATTGT
1 GACAACAACACAGGGGAAATATGAAACAATTGT
38738711 GACAACAACACAGGGGAAATATGAAACAATTGT
1 GACAACAACACAGGGGAAATATGAAACAATTGT
38738744 AAGTTAAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.47, C:0.15, G:0.23, T:0.15
Consensus pattern (33 bp):
GACAACAACACAGGGGAAATATGAAACAATTGT
Found at i:38740221 original size:10 final size:10
Alignment explanation
Indices: 38740208--38740245 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
38740198 TTGTAGCTAA
38740208 ATTGAGCTCG
1 ATTGAGCTCG
38740218 ATTGAGCT-G
1 ATTGAGCTCG
38740227 ACTTGAGCTCG
1 A-TTGAGCTCG
*
38740238 AGTGAGCT
1 ATTGAGCT
38740246 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:38740225 original size:20 final size:20
Alignment explanation
Indices: 38740185--38740245 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
38740175 ACCAATAAAA
38740185 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
38740205 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
38740225 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
38740245 T
1 T
38740246 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:38740246 original size:20 final size:20
Alignment explanation
Indices: 38740209--38740246 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38740199 TGTAGCTAAA
*
38740209 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
38740229 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
38740247 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:38742765 original size:21 final size:21
Alignment explanation
Indices: 38742720--38742782 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
38742710 TTTTAACCAT
* *
38742720 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
38742742 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
*
38742763 TACCATTTCGTACTAATTCC
1 TACCATTTCGTACCAATTCC
38742783 CAAATACCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 24 0.67
22 12 0.33
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.32
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:38746419 original size:30 final size:30
Alignment explanation
Indices: 38746385--38746481 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
38746375 TAAACTAAAA
**
38746385 TGAGCTAAATTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
38746415 TGAGCTGAGGCTAAACTCTTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
38746445 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
38746474 ATGAGCTA
1 -TGAGCTA
38746482 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:38747279 original size:20 final size:20
Alignment explanation
Indices: 38747256--38747309 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
38747246 AGTTTTTCCC
*
38747256 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
38747276 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
38747296 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
38747310 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:38747291 original size:30 final size:30
Alignment explanation
Indices: 38747256--38747329 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
38747246 AGTTTTTCCC
38747256 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
38747286 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
38747316 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
38747330 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:38747319 original size:20 final size:20
Alignment explanation
Indices: 38747256--38747320 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
38747246 AGTTTTTCCC
* * * *
38747256 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
38747276 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
38747295 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
38747316 AGCTC
1 AGCTC
38747321 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:38765991 original size:135 final size:135
Alignment explanation
Indices: 38765742--38765998 Score: 327
Period size: 135 Copynumber: 1.9 Consensus size: 135
38765732 AGCAAGTCTC
* *
38765742 ATCTCCCTAAAGTTACAGTGCAACAGACTAAAGTTAGCAGATCTTGTCTCCCTGAAGTTGCAGCG
1 ATCTCCCTAAAGTTACAGTGCAACAGACTAAAGATAGCAGATCTTATCTCCCTGAAGTTGCAGCG
* * * ** *
38765807 GAGTAGATCGAAGCCATAATCCTTATTTCACTGGAGTTGTAGTATAGCAGGATAAAATTACCCAA
66 GAGTAGATCGAAACCATAATCCTTATTTCACTGAACTTACAGTAGAGCAGGATAAAATTACCCAA
38765872 ATATT
131 ATATT
* * * * * * * *
38765877 ATCTCTCTGAAGTTACAGTGGAGCAGACTGAAGATGGCAGATCTTATCTCCCTGAAGTTGTAGTG
1 ATCTCCCTAAAGTTACAGTGCAACAGACTAAAGATAGCAGATCTTATCTCCCTGAAGTTGCAGCG
* * *
38765942 GAGTAGATTGAAACTATAATCCTTATCTT-TCTGAACTTACAGTAGAGCAGGATAAAA
66 GAGTAGATCGAAACCATAATCCTTAT-TTCACTGAACTTACAGTAGAGCAGGATAAAA
38765999 AAATACGCAA
Statistics
Matches: 102, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
135 100 0.98
136 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (135 bp):
ATCTCCCTAAAGTTACAGTGCAACAGACTAAAGATAGCAGATCTTATCTCCCTGAAGTTGCAGCG
GAGTAGATCGAAACCATAATCCTTATTTCACTGAACTTACAGTAGAGCAGGATAAAATTACCCAA
ATATT
Found at i:38769887 original size:29 final size:28
Alignment explanation
Indices: 38769852--38769942 Score: 121
Period size: 29 Copynumber: 3.1 Consensus size: 28
38769842 GTTATTTCTG
*
38769852 AAAGAAAGTC-TTTATAGTGATCTCTGTTA
1 AAAGAAAG-CATTTAT-GCGATCTCTGTTA
38769881 AAAGAAAGCATTTATGGCGATCTCTGTTA
1 AAAGAAAGCATTTAT-GCGATCTCTGTTA
*
38769910 AAAGAAAGCATTTGTGACGATCTCTGTTA
1 AAAGAAAGCATTTATG-CGATCTCTGTTA
38769939 AAAG
1 AAAG
38769943 GATCCCTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
28 2 0.04
29 55 0.96
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (28 bp):
AAAGAAAGCATTTATGCGATCTCTGTTA
Found at i:38769961 original size:29 final size:29
Alignment explanation
Indices: 38769870--38769942 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
38769860 TCTTTATAGT
*
38769870 GATCTCTGTTAAAAGAAAGCATTTATGGC
1 GATCTCTGTTAAAAGAAAGCATTTGTGGC
*
38769899 GATCTCTGTTAAAAGAAAGCATTTGTGAC
1 GATCTCTGTTAAAAGAAAGCATTTGTGGC
38769928 GATCTCTGTTAAAAG
1 GATCTCTGTTAAAAG
38769943 GATCCCTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.32
Consensus pattern (29 bp):
GATCTCTGTTAAAAGAAAGCATTTGTGGC
Found at i:38770703 original size:27 final size:27
Alignment explanation
Indices: 38770673--38770732 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
38770663 AATGAGTCTT
38770673 GGGTGTCTTATAAACAACTTTTGTGAA
1 GGGTGTCTTATAAACAACTTTTGTGAA
38770700 GGGTGTCTTATAAACAACTTTTGTGAA
1 GGGTGTCTTATAAACAACTTTTGTGAA
*
38770727 AGGTGT
1 GGGTGT
38770733 TAGCATGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (27 bp):
GGGTGTCTTATAAACAACTTTTGTGAA
Found at i:38771435 original size:46 final size:44
Alignment explanation
Indices: 38771327--38771455 Score: 132
Period size: 46 Copynumber: 2.8 Consensus size: 44
38771317 ACATTATTAG
* *
38771327 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACA
1 AGCCAGTATAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGACA
* *
38771373 AGGGCTAGTATAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTA
1 A--GCCAGTATAAGACATGTCTGGGACATGCATCGGCATCGAGAC--A
* * * *
38771421 AGCCAGTTTCAGACATGTTTGAGACATGCATCGGC
1 AGCCAGTATAAGACATGTCTGGGACATGCATCGGC
38771456 TACGAGATTA
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
46 44 0.63
47 14 0.20
48 12 0.17
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (44 bp):
AGCCAGTATAAGACATGTCTGGGACATGCATCGGCATCGAGACA
Found at i:38772634 original size:21 final size:21
Alignment explanation
Indices: 38772609--38772648 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
38772599 TTGAATTGGC
38772609 CACACGGGCGTGTGCCCCTTT
1 CACACGGGCGTGTGCCCCTTT
38772630 CACACGGGCGTGTGCCCCT
1 CACACGGGCGTGTGCCCCT
38772649 ATGTCAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.40, G:0.30, T:0.20
Consensus pattern (21 bp):
CACACGGGCGTGTGCCCCTTT
Found at i:38774613 original size:46 final size:46
Alignment explanation
Indices: 38774560--38774650 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
38774550 TATATATACA
* * *
38774560 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATATC
* * *
38774606 CATCTCATACACATTTCGCATTAACCATTCGGCTTTCCCACATAT
1 CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATAT
38774651 ATACACTTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.27, C:0.32, G:0.07, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATATC
Found at i:38774693 original size:22 final size:22
Alignment explanation
Indices: 38774667--38774742 Score: 68
Period size: 22 Copynumber: 3.3 Consensus size: 22
38774657 TTCCACGTTC
38774667 ATCACATTGGCCATTCTGCCTT
1 ATCACATTGGCCATTCTGCCTT
*
38774689 ATCACATATATG-CATGT-T-CACATTT
1 ATCACAT-T-GGCCAT-TCTGC-C--TT
38774714 ATCACATTGGCCATTCTGCCTT
1 ATCACATTGGCCATTCTGCCTT
38774736 ATCACAT
1 ATCACAT
38774743 ATATGCATGT
Statistics
Matches: 43, Mismatches: 2, Indels: 18
0.68 0.03 0.29
Matches are distributed among these distances:
22 17 0.40
23 8 0.19
24 8 0.19
25 10 0.23
ACGTcount: A:0.25, C:0.28, G:0.11, T:0.37
Consensus pattern (22 bp):
ATCACATTGGCCATTCTGCCTT
Found at i:38774695 original size:47 final size:47
Alignment explanation
Indices: 38774664--38775002 Score: 507
Period size: 47 Copynumber: 7.2 Consensus size: 47
38774654 CACTTCCACG
*
38774664 TTCATCACATTGGCCATTCTGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* *
38774711 TTTATCACATTGGCCATTCTGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* * * *
38774758 TTTATCACATTGGTCATTCGGCCTTATCACATATGTGCATGTTCATA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
38774805 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* *
38774852 TTCATCACATTGGCCATTCGGCCTTATCACATATGTACATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* *
38774899 TTCATCACATTGGCCATTCGGCCTTATCACACAAATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* * * * **
38774946 TTCATCACATTTGCCATTCGGCCTTAGCTCATATATACACATTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
38774993 TCCATCACAT
1 TTCATCACAT
38775003 AAAATCCTAA
Statistics
Matches: 266, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 266 1.00
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.35
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
Found at i:38774882 original size:22 final size:22
Alignment explanation
Indices: 38774759--38774929 Score: 75
Period size: 22 Copynumber: 7.4 Consensus size: 22
38774749 ATGTTCACAT
*
38774759 TTATCACATTGGTCATTCGGCC
1 TTATCACATTGGCCATTCGGCC
***
38774781 TTATCACATATGTG-CATGTTC-ATA
1 TTATCACAT-TG-GCCA--TTCGGCC
38774805 TTCATCACATTGGCCATTCGGCC
1 TT-ATCACATTGGCCATTCGGCC
* *
38774828 TTATCACACATAT-G-CATGTTC-ACA
1 TTAT--CACAT-TGGCCA--TTCGGCC
38774852 TTCATCACATTGGCCATTCGGCC
1 TT-ATCACATTGGCCATTCGGCC
** * *
38774875 TTATCACATATGTACATGTTC-ACA
1 TTATCACAT-TGGCCA--TTCGGCC
38774899 TTCATCACATTGGCCATTCGGCC
1 TT-ATCACATTGGCCATTCGGCC
38774922 TTATCACA
1 TTATCACA
38774930 CAAATGCATG
Statistics
Matches: 110, Mismatches: 18, Indels: 42
0.65 0.11 0.25
Matches are distributed among these distances:
22 34 0.31
23 25 0.23
24 25 0.23
25 26 0.24
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (22 bp):
TTATCACATTGGCCATTCGGCC
Found at i:38778939 original size:12 final size:12
Alignment explanation
Indices: 38778924--38778948 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38778914 ACACTTGTAC
38778924 CAACACCAATGT
1 CAACACCAATGT
38778936 CAACACCAATGT
1 CAACACCAATGT
38778948 C
1 C
38778949 GTCATCAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (12 bp):
CAACACCAATGT
Found at i:38790306 original size:96 final size:96
Alignment explanation
Indices: 38790128--38790321 Score: 237
Period size: 96 Copynumber: 2.0 Consensus size: 96
38790118 TCGCTTCTTT
* *
38790128 TTGCTCCTCTTAGCCCTCCTGGCTTCAGCTTTACCCTTGCTCAAACCAAGCTTCTTGAGCTCCTT
1 TTGCTCCTCTTAGCCCTCCTGGCTTCAGCTTTACCCTTGCTCAAACCAAGCTTCCTGAGCTCCGT
* * * *
38790193 GTCTACTCCATCGTTCCCTTCGATGACAGAC
66 ATCTACTCCATCATTCCCATCGATAACAGAC
* ** * * *
38790224 TTGCTCCTCTTTA-CCCTCTTGGCTTTGGCTTTTCCCTTGCTCGAACCAAGCTTCCTGGGCTCCG
1 TTGCTCCTC-TTAGCCCTCCTGGCTTCAGCTTTACCCTTGCTCAAACCAAGCTTCCTGAGCTCCG
* * *
38790288 TATCTGCTCGATTATTCCCATCGATAACAGAC
65 TATCTACTCCATCATTCCCATCGATAACAGAC
38790320 TT
1 TT
38790322 CCTCAGACAC
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
96 79 0.96
97 3 0.04
ACGTcount: A:0.15, C:0.35, G:0.15, T:0.35
Consensus pattern (96 bp):
TTGCTCCTCTTAGCCCTCCTGGCTTCAGCTTTACCCTTGCTCAAACCAAGCTTCCTGAGCTCCGT
ATCTACTCCATCATTCCCATCGATAACAGAC
Found at i:38792820 original size:39 final size:39
Alignment explanation
Indices: 38792762--38792901 Score: 210
Period size: 39 Copynumber: 3.5 Consensus size: 39
38792752 TAATGGAGAA
38792762 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
38792801 TTATATCCGGGCTAGGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
38792840 TTATATCCGGGCTAAAGTCCCGCAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTG
38792879 TTATATCCGGGCTTAAAGTCCCG
1 TTATATCCGGGC-T-AAGTCCCG
38792902 CATGCTTTGT
Statistics
Matches: 94, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
39 73 0.78
40 21 0.22
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:38801429 original size:7 final size:7
Alignment explanation
Indices: 38801417--38801445 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
38801407 ATGAAAGCCA
38801417 CTTGCTT
1 CTTGCTT
38801424 CTTGCTT
1 CTTGCTT
38801431 CTTGCTT
1 CTTGCTT
38801438 CTTGCTT
1 CTTGCTT
38801445 C
1 C
38801446 CTAAAGTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.31, G:0.14, T:0.55
Consensus pattern (7 bp):
CTTGCTT
Found at i:38804416 original size:17 final size:18
Alignment explanation
Indices: 38804383--38804416 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38804373 ATCAAGTCAA
*
38804383 CCATTCCTCCCACAACCT
1 CCATTCCTCCAACAACCT
38804401 CCATTCC-CCAACAACC
1 CCATTCCTCCAACAACC
38804417 ATCCTCAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.56, G:0.00, T:0.18
Consensus pattern (18 bp):
CCATTCCTCCAACAACCT
Done.