Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr8
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: 19593398
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1222752 characters in sequence are not A, C, G, or T
File 48 of 50
Found at i:19293367 original size:23 final size:23
Alignment explanation
Indices: 19293341--19293658 Score: 163
Period size: 23 Copynumber: 13.7 Consensus size: 23
19293331 ACTAAATTTT
19293341 GAATCACGTGACTAGTTAATATG
1 GAATCACGTGACTAGTTAATATG
* ** *
19293364 GAATCACGTGACTAATCGATTTG
1 GAATCACGTGACTAGTTAATATG
* * *
19293387 GAATCGCGTGACTTGTAAATATG
1 GAATCACGTGACTAGTTAATATG
* * * * *
19293410 GAGTCATGTGAAC-CGTTAAGATTTA
1 GAATCACGTG-ACTAGTT-A-ATATG
** * *
19293435 GAATCGTGTGAGTAGTTAATATT
1 GAATCACGTGACTAGTTAATATG
* * *
19293458 GAGTCACGTGAGTAGTAAATATG
1 GAATCACGTGACTAGTTAATATG
* * * *
19293481 GAGTGACGTTACTAGTTATTATG
1 GAATCACGTGACTAGTTAATATG
* * *
19293504 GAATCGCATGACTAGTTATTATG
1 GAATCACGTGACTAGTTAATATG
** * *
19293527 GAATCGTGTGACTAGTTGATATT
1 GAATCACGTGACTAGTTAATATG
* ** *
19293550 GAGTCGTGTGAGTAG-TATATATG
1 GAATCACGTGACTAGTTA-ATATG
* ** * *
19293573 GAGTGGCGTTACTAGTTATTATG
1 GAATCACGTGACTAGTTAATATG
* * *
19293596 GAATCACGTGAGTAGTAAATATA
1 GAATCACGTGACTAGTTAATATG
* ** * *
19293619 GAGTCGTGTGACTGGTTATTATG
1 GAATCACGTGACTAGTTAATATG
19293642 GAATCACGTGACTAGTT
1 GAATCACGTGACTAGTT
19293659 GTTGTTGAGT
Statistics
Matches: 217, Mismatches: 72, Indels: 12
0.72 0.24 0.04
Matches are distributed among these distances:
22 1 0.00
23 195 0.90
24 7 0.03
25 14 0.06
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.34
Consensus pattern (23 bp):
GAATCACGTGACTAGTTAATATG
Found at i:19293541 original size:46 final size:46
Alignment explanation
Indices: 19293438--19293750 Score: 204
Period size: 46 Copynumber: 6.8 Consensus size: 46
19293428 AGATTTAGAA
* * * * * * * *
19293438 TCGTGTGAGTAGTTAATATTGAGTCACGTGAGTAGTAAATATGGAG
1 TCGTGTGACTAGTTATTATGGAATCGCGTGACTAGTTATTATGGAG
* *
19293484 TGACGT-T-ACTAGTTATTATGGAATCGCATGACTAGTTATTATGGAA
1 T--CGTGTGACTAGTTATTATGGAATCGCGTGACTAGTTATTATGGAG
* * * *
19293530 TCGTGTGACTAGTTGA-TATTGAGTCGTGTGAGTAG-TATATATGGAG
1 TCGTGTGACTAGTT-ATTATGGAATCGCGTGACTAGTTAT-TATGGAG
* * * * * * * *
19293576 TGGCGTTACTAGTTATTATGGAATCACGTGAGTAGTAAATATAGAG
1 TCGTGTGACTAGTTATTATGGAATCGCGTGACTAGTTATTATGGAG
* * * * *
19293622 TCGTGTGACTGGTTATTATGGAATCACGTGACTAGTTGTTGTTGAG
1 TCGTGTGACTAGTTATTATGGAATCGCGTGACTAGTTATTATGGAG
* * * * * * * * *
19293668 TCGGGTGAGTAG-TATATATGGAGTGGCATTACCACTTATTATGGAA
1 TCGTGTGACTAGTTAT-TATGGAATCGCGTGACTAGTTATTATGGAG
* *
19293714 TCGTGTGACTAGTTGTTATGGAGTCGCGTGACTAGTT
1 TCGTGTGACTAGTTATTATGGAATCGCGTGACTAGTT
19293751 GATATGGGAT
Statistics
Matches: 199, Mismatches: 58, Indels: 20
0.72 0.21 0.07
Matches are distributed among these distances:
44 3 0.02
45 8 0.04
46 180 0.90
47 5 0.03
48 3 0.02
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.35
Consensus pattern (46 bp):
TCGTGTGACTAGTTATTATGGAATCGCGTGACTAGTTATTATGGAG
Found at i:19293623 original size:69 final size:69
Alignment explanation
Indices: 19293447--19293749 Score: 216
Period size: 69 Copynumber: 4.4 Consensus size: 69
19293437 ATCGTGTGAG
* * * *
19293447 TAGTTAATATTGAGTCACGTGAGTAGTAAATATGGAGTGACGT-T-ACTAGTTATTATGGAATCG
1 TAGTTATTATGGAATCACGTGAGTAGTAAATATAGAGT--CGTGTGACTAGTTATTATGGAATCG
19293510 CATGAC
64 CATGAC
** * ** * * * *
19293516 TAGTTATTATGGAATCGTGTGACTAGTTGATATTGAGTCGTGTGAGTAG-TATATATGGAGTGGC
1 TAGTTATTATGGAATCACGTGAGTAGTAAATATAGAGTCGTGTGACTAGTTAT-TATGGAATCGC
* *
19293580 GTTAC
65 ATGAC
* * *
19293585 TAGTTATTATGGAATCACGTGAGTAGTAAATATAGAGTCGTGTGACTGGTTATTATGGAATCACG
1 TAGTTATTATGGAATCACGTGAGTAGTAAATATAGAGTCGTGTGACTAGTTATTATGGAATCGCA
19293650 TGAC
66 TGAC
* * * * ** * * * ** * * * **
19293654 TAGTTGTTGTTGAGTCGGGTGAGTAGTATATATGGAGTGGCATTACCACTTATTATGGAATCGTG
1 TAGTTATTATGGAATCACGTGAGTAGTAAATATAGAGTCGTGTGACTAGTTATTATGGAATCGCA
19293719 TGAC
66 TGAC
* * * *
19293723 TAGTTGTTATGGAGTCGCGTGACTAGT
1 TAGTTATTATGGAATCACGTGAGTAGT
19293750 TGATATGGGA
Statistics
Matches: 183, Mismatches: 47, Indels: 8
0.77 0.20 0.03
Matches are distributed among these distances:
67 3 0.02
68 4 0.02
69 173 0.95
70 3 0.02
ACGTcount: A:0.27, C:0.10, G:0.28, T:0.35
Consensus pattern (69 bp):
TAGTTATTATGGAATCACGTGAGTAGTAAATATAGAGTCGTGTGACTAGTTATTATGGAATCGCA
TGAC
Found at i:19293626 original size:92 final size:92
Alignment explanation
Indices: 19293433--19293657 Score: 288
Period size: 92 Copynumber: 2.4 Consensus size: 92
19293423 CGTTAAGATT
*
19293433 TAGAATCGTGTGAGTAGTTAATATTGAGTCACGTGAGTAGTAAATATGGAGTGACGTTACTAGTT
1 TAGAATCGTGTGACTAGTTAATATTGAGTCACGTGAGTAGTAAATATGGAGTGACGTTACTAGTT
* * *
19293498 ATTATGGAATCGCATGACTAGTTATTA
66 ATTATGGAATCACATGACTAGTAAATA
* * ** * *
19293525 TGGAATCGTGTGACTAGTTGATATTGAGTCGTGTGAGTAGTATATATGGAGTGGCGTTACTAGTT
1 TAGAATCGTGTGACTAGTTAATATTGAGTCACGTGAGTAGTAAATATGGAGTGACGTTACTAGTT
* *
19293590 ATTATGGAATCACGTGAGTAGTAAATA
66 ATTATGGAATCACATGACTAGTAAATA
* * * * * *
19293617 TAGAGTCGTGTGACTGGTTATTATGGAATCACGTGACTAGT
1 TAGAATCGTGTGACTAGTTAATATTGAGTCACGTGAGTAGT
19293658 TGTTGTTGAG
Statistics
Matches: 111, Mismatches: 22, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
92 111 1.00
ACGTcount: A:0.29, C:0.09, G:0.28, T:0.35
Consensus pattern (92 bp):
TAGAATCGTGTGACTAGTTAATATTGAGTCACGTGAGTAGTAAATATGGAGTGACGTTACTAGTT
ATTATGGAATCACATGACTAGTAAATA
Found at i:19293691 original size:23 final size:22
Alignment explanation
Indices: 19293438--19293757 Score: 133
Period size: 23 Copynumber: 13.9 Consensus size: 22
19293428 AGATTTAGAA
* *
19293438 TCGTGTGAGTAGTTAATATTGAG
1 TCGTGTGACTAGTT-ATATGGAG
** * *
19293461 TCACGTGAGTAGTAAATATGGAG
1 TCGTGTGACTAGT-TATATGGAG
*
19293484 TGACGT-T-ACTAGTTATTATGGAA
1 T--CGTGTGACTAGTTA-TATGGAG
** *
19293507 TCGCATGACTAGTTATTATGGAA
1 TCGTGTGACTAGTTA-TATGGAG
*
19293530 TCGTGTGACTAGTTGATATTGAG
1 TCGTGTGACTAGTT-ATATGGAG
*
19293553 TCGTGTGAGTAGTATATATGGAG
1 TCGTGTGACTAGT-TATATGGAG
* * * *
19293576 TGGCGTTACTAGTTATTATGGAA
1 TCGTGTGACTAGTTA-TATGGAG
** * * *
19293599 TCACGTGAGTAGTAAATATAGAG
1 TCGTGTGACTAGT-TATATGGAG
* *
19293622 TCGTGTGACTGGTTATTATGGAA
1 TCGTGTGACTAGTTA-TATGGAG
** *
19293645 TCACGTGACTAGTTGT-TGTTGAG
1 TCGTGTGACTAGTTATATG--GAG
* *
19293668 TCGGGTGAGTAGTATATATGGAG
1 TCGTGTGACTAGT-TATATGGAG
* ** * * * *
19293691 TGGCATTACCACTTATTATGGAA
1 TCGTGTGACTAGTTA-TATGGAG
*
19293714 TCGTGTGACTAGTTGTTATGGAG
1 TCGTGTGACTAGTT-ATATGGAG
*
19293737 TCGCGTGACTAGTTGATATGG
1 TCGTGTGACTAGTT-ATATGG
19293758 GATTATGTGA
Statistics
Matches: 218, Mismatches: 62, Indels: 34
0.69 0.20 0.11
Matches are distributed among these distances:
21 4 0.02
22 8 0.04
23 197 0.90
24 6 0.03
25 3 0.01
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.35
Consensus pattern (22 bp):
TCGTGTGACTAGTTATATGGAG
Found at i:19298221 original size:62 final size:62
Alignment explanation
Indices: 19298111--19298231 Score: 172
Period size: 62 Copynumber: 2.0 Consensus size: 62
19298101 ATAGTATCTC
* ** * *
19298111 TTGATAGTTTTCCACTCGCAAGCAAGTCAGTCGTAGTAGCTATTGATAGATGACAACATATA
1 TTGATAGTTTTCCACTCGCAAGCAAGTCAGCCACAGTAGATATCGATAGATGACAACATATA
*
19298173 TTGATAGTTTTCCACTCGCAAGCAAGAT-AGCCACGGTAGATATCGATAGATGACAACAT
1 TTGATAGTTTTCCACTCGCAAGCAAG-TCAGCCACAGTAGATATCGATAGATGACAACAT
19298232 CTGTCGATAG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
62 51 0.98
63 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (62 bp):
TTGATAGTTTTCCACTCGCAAGCAAGTCAGCCACAGTAGATATCGATAGATGACAACATATA
Found at i:19298614 original size:12 final size:12
Alignment explanation
Indices: 19298584--19298617 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
19298574 CTAAACCATA
19298584 TACCCTAAACAC
1 TACCCTAAACAC
19298596 -A-CCTAAACAC
1 TACCCTAAACAC
19298606 TACCCTAAACAC
1 TACCCTAAACAC
19298618 CATATAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.45
11 2 0.10
12 9 0.45
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (12 bp):
TACCCTAAACAC
Found at i:19301463 original size:12 final size:12
Alignment explanation
Indices: 19301446--19301472 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
19301436 AAATCAGATG
19301446 CATCTTCAATAT
1 CATCTTCAATAT
19301458 CATCTTCAATAT
1 CATCTTCAATAT
19301470 CAT
1 CAT
19301473 TTACATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (12 bp):
CATCTTCAATAT
Found at i:19302249 original size:181 final size:183
Alignment explanation
Indices: 19301941--19302273 Score: 499
Period size: 181 Copynumber: 1.8 Consensus size: 183
19301931 GCAATGCCTA
19301941 AAAACTAGTGAACAAAAGCCTCAAAACAAGAGATAAATTGCACAAGTCAGTCACGCACCGCCAGT
1 AAAACTAGTGAACAAAAGCCTCAAAACAAGAGATAAATTGCACAA--CAGTCACGCACCGCCAGT
** * *
19302006 CTTGCAATACCTAAGAATAAGTCACTCAATGCCTTATACCCACTCACATTATGCCAACATAACCA
64 CTCACAATACCTAACAATAAGTCACTCAATGCCTAATACCCACTCACATTATGCCAACATAACCA
*
19302071 GTCACGTACTAGCCCAATGTCATATAATACATAAAAATCAATCACTCAAACCCTC
129 GTCACGTAATAGCCCAATGTCATATAATACATAAAAATCAATCACTCAAACCCTC
* * * *
19302126 AAAACTAGTGAACAAAAGTCTCAAAACAAGAGATGAATTTCAC-A-AGTCACGCACTGCCAGTCT
1 AAAACTAGTGAACAAAAGCCTCAAAACAAGAGATAAATTGCACAACAGTCACGCACCGCCAGTCT
* ** * *
19302189 CACAATACCTAACAATAAGTTACTCAATGTGTAATATCCACTCACATTATGCCAACATAACTAGT
66 CACAATACCTAACAATAAGTCACTCAATGCCTAATACCCACTCACATTATGCCAACATAACCAGT
*
19302254 CACGTAATGGCCCAATGTCA
131 CACGTAATAGCCCAATGTCA
19302274 CGCAATACAT
Statistics
Matches: 133, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
181 92 0.69
184 1 0.01
185 40 0.30
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.22
Consensus pattern (183 bp):
AAAACTAGTGAACAAAAGCCTCAAAACAAGAGATAAATTGCACAACAGTCACGCACCGCCAGTCT
CACAATACCTAACAATAAGTCACTCAATGCCTAATACCCACTCACATTATGCCAACATAACCAGT
CACGTAATAGCCCAATGTCATATAATACATAAAAATCAATCACTCAAACCCTC
Found at i:19302443 original size:201 final size:203
Alignment explanation
Indices: 19302126--19302528 Score: 519
Period size: 201 Copynumber: 2.0 Consensus size: 203
19302116 TCAAACCCTC
* * * * *
19302126 AAAACTAGTGAACAAAAGTCTCAAAACAAGAGATGAATTTCACAAGTCACGCACTGCCAGTCTCA
1 AAAAATAGTGAACAAAAGCCTCAAAACAAGAGATGAATTGCACAAGTCACACACTGCCAATCTCA
* ** *
19302191 CAATACCTAACAATAAGTTACTCAATGTGTAATATCCACTCACATTATGCCAACATAACTAGTCA
66 CAATACCTAACAATAAGTCACTCAATGCCTAATATCCACTCACATTATGCCAACATAACCAGTCA
* * * * * *
19302256 CGTAATGGCCCAATGTCACGCAATACATAACAATAGGTCATGCA-ATACATAAAAATTAA-TCAC
131 CGTAATGGCCCAACGTCACACAATACATAACAACAAGTCA-CCATATACATAAAAA-CAAGTCAC
19302319 GTAATGTCTA
194 GTAATGTCTA
* * * *
19302329 AAAAATAGTGAACAAAAGCCTCAAAA-TA-AGATGAATTGCGCAAGTCACACACCT-CTAATCTT
1 AAAAATAGTGAACAAAAGCCTCAAAACAAGAGATGAATTGCACAAGTCACACA-CTGCCAATCTC
* * *
19302391 ACAATACCTAATAGTAAGTCACTCGATGCCTAATATCCACTCACATTATGCCAACATAACCAGTC
65 ACAATACCTAACAATAAGTCACTCAATGCCTAATATCCACTCACATTATGCCAACATAACCAGTC
* * *
19302456 ACGTACTGGCTCAACGTCACACAATACATAACAACAAGTCACCATATACATACAAACAAGTCACG
130 ACGTAATGGCCCAACGTCACACAATACATAACAACAAGTCACCATATACATAAAAACAAGTCACG
19302521 TAATGTCT
195 TAATGTCT
19302529 CAACAGAATA
Statistics
Matches: 172, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
200 4 0.02
201 141 0.82
202 3 0.02
203 24 0.14
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.23
Consensus pattern (203 bp):
AAAAATAGTGAACAAAAGCCTCAAAACAAGAGATGAATTGCACAAGTCACACACTGCCAATCTCA
CAATACCTAACAATAAGTCACTCAATGCCTAATATCCACTCACATTATGCCAACATAACCAGTCA
CGTAATGGCCCAACGTCACACAATACATAACAACAAGTCACCATATACATAAAAACAAGTCACGT
AATGTCTA
Found at i:19302496 original size:22 final size:22
Alignment explanation
Indices: 19302471--19302519 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
19302461 CTGGCTCAAC
19302471 GTCACACA-ATACATA-ACAACAA
1 GTCAC-CATATACATACA-AACAA
19302493 GTCACCATATACATACAAACAA
1 GTCACCATATACATACAAACAA
19302515 GTCAC
1 GTCAC
19302520 GTAATGTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 2 0.08
22 22 0.88
23 1 0.04
ACGTcount: A:0.49, C:0.29, G:0.06, T:0.16
Consensus pattern (22 bp):
GTCACCATATACATACAAACAA
Found at i:19305337 original size:11 final size:11
Alignment explanation
Indices: 19305321--19305358 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
19305311 TTCTATCAAG
19305321 CCTCTCACAAA
1 CCTCTCACAAA
19305332 CCTCTCACAAA
1 CCTCTCACAAA
*
19305343 CCTCTCATAAA
1 CCTCTCACAAA
19305354 CCTCT
1 CCTCT
19305359 TAATCCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.32, C:0.45, G:0.00, T:0.24
Consensus pattern (11 bp):
CCTCTCACAAA
Found at i:19306172 original size:12 final size:12
Alignment explanation
Indices: 19306139--19306172 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
19306129 CTAAATGAAG
*
19306139 CAAAATCACATT
1 CAAAATCATATT
19306151 CAAAATTCATATT
1 CAAAA-TCATATT
19306164 CAAAATCAT
1 CAAAATCAT
19306173 GGGTAAGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (12 bp):
CAAAATCATATT
Found at i:19307491 original size:119 final size:119
Alignment explanation
Indices: 19307334--19307566 Score: 349
Period size: 119 Copynumber: 2.0 Consensus size: 119
19307324 CATATCATAG
* * ***
19307334 AGTGGTCTTCCATGGACATAGCATAGTCACCTGCGGTGGCCAACTGATGGACAACATACATCATC
1 AGTGGTCTTCCATAGACATAACATAGTCACCTGCGGTGGCCAACTGACAAACAACATACATCATC
*
19307399 ATGTCATGCCCCATTGTCGAAGAAAATGGCAGAGTCTATAATCATCATCCGTAA
66 ATGTCACGCCCCATTGTCGAAGAAAATGGCAGAGTCTATAATCATCATCCGTAA
* ** *
19307453 AGTGGTCTTCCCTAGACATAACATAGTCATGTGTGGTGGCCAACTGACAAACAACATACATCATC
1 AGTGGTCTTCCATAGACATAACATAGTCACCTGCGGTGGCCAACTGACAAACAACATACATCATC
* * *
19307518 ATGTCACGTCCCATTGTTGAAGCAAATGGCAGAGTCTATAATCATCATC
66 ATGTCACGCCCCATTGTCGAAGAAAATGGCAGAGTCTATAATCATCATC
19307567 TAGAGTATTC
Statistics
Matches: 101, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
119 101 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (119 bp):
AGTGGTCTTCCATAGACATAACATAGTCACCTGCGGTGGCCAACTGACAAACAACATACATCATC
ATGTCACGCCCCATTGTCGAAGAAAATGGCAGAGTCTATAATCATCATCCGTAA
Found at i:19308001 original size:21 final size:20
Alignment explanation
Indices: 19307957--19307998 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
19307947 TGTTGGGTAG
19307957 TTAATTTAAGTTATTTTAGT
1 TTAATTTAAGTTATTTTAGT
*
19307977 TTAATTTTATGTTATTTT-GT
1 TTAA-TTTAAGTTATTTTAGT
19307997 TT
1 TT
19307999 TAAATTACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.67
Consensus pattern (20 bp):
TTAATTTAAGTTATTTTAGT
Found at i:19311266 original size:29 final size:29
Alignment explanation
Indices: 19311234--19311299 Score: 69
Period size: 32 Copynumber: 2.2 Consensus size: 29
19311224 ATGCATTATG
19311234 TCATTCATGTGCCAAACATATGCACAACA
1 TCATTCATGTGCCAAACATATGCACAACA
* * * *
19311263 TCATTATTTATGTGCCAAACGTTTGCACAATA
1 TC---ATTCATGTGCCAAACATATGCACAACA
19311295 TCATT
1 TCATT
19311300 TAAACTTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
29 5 0.17
32 25 0.83
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (29 bp):
TCATTCATGTGCCAAACATATGCACAACA
Found at i:19318311 original size:2 final size:2
Alignment explanation
Indices: 19318304--19318357 Score: 76
Period size: 2 Copynumber: 28.0 Consensus size: 2
19318294 GAGAACAATA
*
19318304 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG -G TG TA TG TG T-
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
19318344 TG TG TA TG TG TG TG
1 TG TG TG TG TG TG TG
19318358 CCCTATTGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.04, C:0.00, G:0.46, T:0.50
Consensus pattern (2 bp):
TG
Found at i:19323245 original size:29 final size:29
Alignment explanation
Indices: 19323212--19323551 Score: 291
Period size: 29 Copynumber: 11.7 Consensus size: 29
19323202 CTTTTATATA
19323212 TTTGTCTTAATTTAGACAAGAAAACATGT
1 TTTGTCTTAATTTAGACAAGAAAACATGT
19323241 TTTGTCTTAATTTAGACAAGAAAACATGT
1 TTTGTCTTAATTTAGACAAGAAAACATGT
*
19323270 TATT-TCTTAATTTAGACAAGAAAACATAT
1 T-TTGTCTTAATTTAGACAAGAAAACATGT
* ****** * *
19323299 TTTGTTTTAATTTTTTTTTGAATAGTCATAT
1 TTTGTCTTAATTTAGACAAGAA-A-ACATGT
* * * * *
19323330 TTTGTTTTAATCTACATAAGAAAATATGT
1 TTTGTCTTAATTTAGACAAGAAAACATGT
19323359 TTTGTCTTAATTTAGGA-AAGAAAACATG-
1 TTTGTCTTAATTTA-GACAAGAAAACATGT
* * *
19323387 TTCGTCTTAATTTAGATAAG-AAACTATGC
1 TTTGTCTTAATTTAGACAAGAAAAC-ATGT
19323416 TTTGTCTTAATTTAGACAAGAAAACATG-
1 TTTGTCTTAATTTAGACAAGAAAACATGT
* * *
19323444 --TGTCTTAATTTAAGACAAAAAAAATATAT
1 TTTGTCTTAATTT-AGAC-AAGAAAACATGT
* * *
19323473 TTTGTTTTAATCTAGACAAGAAAACAT-A
1 TTTGTCTTAATTTAGACAAGAAAACATGT
* * * *
19323501 TTTGTCTCAATTTAGATAAGATAACATAT
1 TTTGTCTTAATTTAGACAAGAAAACATGT
*
19323530 TTTGTCTTAATTAAAGACAAGA
1 TTTGTCTTAATT-TAGACAAGA
19323552 GTTGTCTTAA
Statistics
Matches: 253, Mismatches: 42, Indels: 31
0.78 0.13 0.10
Matches are distributed among these distances:
26 11 0.04
27 10 0.04
28 51 0.20
29 131 0.52
30 20 0.08
31 30 0.12
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (29 bp):
TTTGTCTTAATTTAGACAAGAAAACATGT
Found at i:19323309 original size:58 final size:57
Alignment explanation
Indices: 19323212--19323551 Score: 303
Period size: 57 Copynumber: 5.9 Consensus size: 57
19323202 CTTTTATATA
*
19323212 TTTGTCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATTTAGACAAGAAAACATG
1 TTTGTCTTAATTTAGACAAGAAAACATATTTTGTCTTAATTTAGACAAGAAAACATG
* * ****** * *
19323269 TTATTTCTTAATTTAGACAAGAAAACATATTTTGTTTTAATTTTTTTTTGAATAGTCATAT
1 TT-TGTCTTAATTTAGACAAGAAAACATATTTTGTCTTAATTTAGACAAGAA-A-ACAT-G
* * * * * *
19323330 TTTGTTTTAATCTACATAAGAAAATATGTTTTGTCTTAATTTAGGA-AAGAAAACATG
1 TTTGTCTTAATTTAGACAAGAAAACATATTTTGTCTTAATTTA-GACAAGAAAACATG
* *
19323387 TTCGTCTTAATTTAGATAAG-AAAC-TATGCTTTGTCTTAATTTAGACAAGAAAACATG
1 TTTGTCTTAATTTAGACAAGAAAACATAT--TTTGTCTTAATTTAGACAAGAAAACATG
* * * * *
19323444 --TGTCTTAATTTAAGACAAAAAAAATATATTTTGTTTTAATCTAGACAAGAAAACATA
1 TTTGTCTTAATTT-AGAC-AAGAAAACATATTTTGTCTTAATTTAGACAAGAAAACATG
* * * *
19323501 TTTGTCTCAATTTAGATAAGATAACATATTTTGTCTTAATTAAAGACAAGA
1 TTTGTCTTAATTTAGACAAGAAAACATATTTTGTCTTAATT-TAGACAAGA
19323552 GTTGTCTTAA
Statistics
Matches: 221, Mismatches: 47, Indels: 29
0.74 0.16 0.10
Matches are distributed among these distances:
55 12 0.05
56 8 0.04
57 89 0.40
58 57 0.26
59 15 0.07
60 38 0.17
61 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (57 bp):
TTTGTCTTAATTTAGACAAGAAAACATATTTTGTCTTAATTTAGACAAGAAAACATG
Found at i:19329910 original size:26 final size:26
Alignment explanation
Indices: 19329881--19329934 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
19329871 GGGTTACGAC
* *
19329881 ATCCATTCACTTATGGTTGTAAAATT
1 ATCCATCCACTTATGGTGGTAAAATT
*
19329907 ATCCATCCACTTCTGGTGGTAAAATT
1 ATCCATCCACTTATGGTGGTAAAATT
19329933 AT
1 AT
19329935 TCTTAGATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (26 bp):
ATCCATCCACTTATGGTGGTAAAATT
Found at i:19329953 original size:25 final size:25
Alignment explanation
Indices: 19329925--19329992 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 25
19329915 ACTTCTGGTG
19329925 GTAAAATTATTCTTAGATTCTGATA
1 GTAAAATTATTCTTAGATTCTGATA
* * * *
19329950 GTAAAATTATCCACTTA-TTTCTGGTG
1 GTAAAATTAT--TCTTAGATTCTGATA
19329976 GTAAAATTATTCTTAGA
1 GTAAAATTATTCTTAGA
19329993 ATTAAAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
24 4 0.12
25 10 0.29
26 16 0.47
27 4 0.12
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (25 bp):
GTAAAATTATTCTTAGATTCTGATA
Found at i:19329979 original size:26 final size:26
Alignment explanation
Indices: 19329894--19329985 Score: 82
Period size: 26 Copynumber: 3.6 Consensus size: 26
19329884 CATTCACTTA
* * *
19329894 TGGTTGTAAAATTATCCA-TCCACTTC
1 TGGTGGTAAAATTATCCACT-TAATTC
*
19329920 TGGTGGTAAAATTAT--TCTTAGATTC
1 TGGTGGTAAAATTATCCACTTA-ATTC
* * *
19329945 TGATAGTAAAATTATCCACTTATTTC
1 TGGTGGTAAAATTATCCACTTAATTC
19329971 TGGTGGTAAAATTAT
1 TGGTGGTAAAATTAT
19329986 TCTTAGAATT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
24 1 0.02
25 17 0.33
26 30 0.58
27 4 0.08
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (26 bp):
TGGTGGTAAAATTATCCACTTAATTC
Found at i:19336426 original size:29 final size:28
Alignment explanation
Indices: 19336388--19336446 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
19336378 AAAAAATTTA
*
19336388 AACATGGCATGTAACAATAATATTTTTTC
1 AACATGGCATGTAACAACAAT-TTTTTTC
* * *
19336417 AACATTGCATGTACCAACAGTTTTTTTC
1 AACATGGCATGTAACAACAATTTTTTTC
19336445 AA
1 AA
19336447 TATAACGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (28 bp):
AACATGGCATGTAACAACAATTTTTTTC
Found at i:19336593 original size:27 final size:25
Alignment explanation
Indices: 19336563--19336618 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
19336553 ATAATCCGTA
*
19336563 ATAACAATATTTTTTTTAATATGATGT
1 ATAACAATA-TTTTTTT-ATATGACGT
19336590 ATAACAATATTTTTTTATATGACGT
1 ATAACAATATTTTTTTATATGACGT
19336615 ATAA
1 ATAA
19336619 TATAATTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 12 0.43
26 7 0.25
27 9 0.32
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.48
Consensus pattern (25 bp):
ATAACAATATTTTTTTATATGACGT
Found at i:19336602 original size:25 final size:25
Alignment explanation
Indices: 19336563--19336660 Score: 81
Period size: 25 Copynumber: 3.8 Consensus size: 25
19336553 ATAATCCGTA
19336563 ATAACAATATTTTTTTTAATATGATGT
1 ATAACAATA--TTTTTTAATATGATGT
* *
19336590 ATAACAATATTTTTTTATATGACGT
1 ATAACAATATTTTTTAATATGATGT
* * *
19336615 ATAA-TATAATTTTGAATATGAAATGT
1 ATAACAATATTTTTTAATATG--ATGT
* *
19336641 AACAATAATATTTTTTAATA
1 -ATAACAATATTTTTTAATA
19336661 AAACGTGTAA
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
24 12 0.21
25 18 0.32
26 3 0.05
27 12 0.21
28 11 0.20
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (25 bp):
ATAACAATATTTTTTAATATGATGT
Found at i:19339799 original size:3 final size:3
Alignment explanation
Indices: 19339791--19339824 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
19339781 AAGGGTGATA
19339791 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
19339825 TCAAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19340927 original size:2 final size:2
Alignment explanation
Indices: 19340920--19340961 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
19340910 AACGTGTATG
19340920 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19340962 AGATCAATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19341610 original size:15 final size:15
Alignment explanation
Indices: 19341590--19341635 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
19341580 AAACTCATCT
*
19341590 ACTCATCGTCCAACA
1 ACTCATAGTCCAACA
19341605 ACTCATAGTCCAACA
1 ACTCATAGTCCAACA
19341620 ACTCATAGTCCAACA
1 ACTCATAGTCCAACA
19341635 A
1 A
19341636 ACATCCTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.39, C:0.35, G:0.07, T:0.20
Consensus pattern (15 bp):
ACTCATAGTCCAACA
Found at i:19354792 original size:19 final size:19
Alignment explanation
Indices: 19354768--19354810 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
19354758 TTTTCTTCAC
*
19354768 TTTCATGCTCCCATGCCAT
1 TTTCATGCTCCCACGCCAT
*
19354787 TTTCATGCTTCCACGCCAT
1 TTTCATGCTCCCACGCCAT
19354806 TTTCA
1 TTTCA
19354811 CCTGGCCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.35, G:0.09, T:0.40
Consensus pattern (19 bp):
TTTCATGCTCCCACGCCAT
Found at i:19365480 original size:6 final size:6
Alignment explanation
Indices: 19365471--19365519 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
19365461 ACATTTGGTT
* * * *
19365471 TACATT TACATT TACATA TACATA TACATA TACATA TGCATA TATATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
19365519 T
1 T
19365520 GTATATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (6 bp):
TACATA
Found at i:19365520 original size:12 final size:12
Alignment explanation
Indices: 19365485--19365531 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
19365475 TTTACATTTA
*
19365485 CATATACATATA
1 CATATACATATG
19365497 CATATACATATG
1 CATATACATATG
*
19365509 CATATATATATG
1 CATATACATATG
* *
19365521 TATATATATAT
1 CATATACATAT
19365532 ATATGAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (12 bp):
CATATACATATG
Found at i:19366821 original size:69 final size:67
Alignment explanation
Indices: 19366630--19366832 Score: 235
Period size: 68 Copynumber: 3.0 Consensus size: 67
19366620 GCTTGCTCAT
* * * * * * *
19366630 CTCATAAGGTATATGGAAAATGCATCATATACATAATCTCATGGCATATATCATGCTTTCTCAAT
1 CTCATATGGTATATGGAATATACATCATATACATAATCTCAT-ACATATATCATGCATACTTAAT
*
19366695 CAT
65 CAC
* * *
19366698 CTCATGTAGTATATGGAATATACATCATATACATAATCTCATGACATTTATCATGCATACTTAAT
1 CTCATATGGTATATGGAATATACATCATATACATAATCTCAT-ACATATATCATGCATACTTAAT
19366763 CAC
65 CAC
* * * *
19366766 CTCATATGGTATATGGAATTTTACATCATATACATAATCTTATATTATACATCATGCATACTTAA
1 CTCATATGGTATATGGAA-TATACATCATATACATAATCTCATA-CATATATCATGCATACTTAA
19366831 TC
64 TC
19366833 GTGTGGCATT
Statistics
Matches: 115, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
68 74 0.64
69 41 0.36
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (67 bp):
CTCATATGGTATATGGAATATACATCATATACATAATCTCATACATATATCATGCATACTTAATC
AC
Found at i:19368093 original size:16 final size:16
Alignment explanation
Indices: 19368069--19368099 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19368059 AAAAATATAA
19368069 AAAAAAATCAAAATCC
1 AAAAAAATCAAAATCC
*
19368085 AAAACAATCAAAATC
1 AAAAAAATCAAAATC
19368100 TAAATTTTAG
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:0.68, C:0.19, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAAAATCAAAATCC
Found at i:19381191 original size:29 final size:29
Alignment explanation
Indices: 19381120--19381182 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
19381110 AGTCCTTAAT
*
19381120 TTTTAATTATAATTTA-TTTATTTTTTGTTA
1 TTTT-ATTATAA-TTAGTTTATTTTTTGTGA
19381150 TTTTATTATAATTAGTTTATTTTTTAGTGA
1 TTTTATTATAATTAGTTTATTTTTT-GTGA
19381180 TTT
1 TTT
19381183 ATTTCAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 3 0.10
29 17 0.57
30 10 0.33
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.68
Consensus pattern (29 bp):
TTTTATTATAATTAGTTTATTTTTTGTGA
Found at i:19398822 original size:568 final size:568
Alignment explanation
Indices: 19397739--19398878 Score: 2079
Period size: 568 Copynumber: 2.0 Consensus size: 568
19397729 TTTGTCGAGG
* *
19397739 GTTGCTTTTGAATTTGCATCCTTAGAAATCGAAGGTCTACAGTCTTGTATATTTTTGGTTATTTT
1 GTTGCTTTTGAATTTGCATCCTTAAAAATCGAAGGTCTACAGTCTTGTATATTTTCGGTTATTTT
19397804 TTGGGCCCACATGTCATTGTAGAATATTTTTGTATACCTGGTTTAGTGTGCTATTATATATATGA
66 TTGGGCCCACATGTCATTGTAGAATATTTTTGTATACCTGGTTTAGTGTGCTATTATATATATGA
*
19397869 ATTTATTTTACTCTTACGCTACAAAATTGTTTATGCAGAATTCTATAAATATTGTTTTATAAGAA
131 ATTTATTTTACTCTTACGCTACAAAATTATTTATGCAGAATTCTATAAATATTGTTTTATAAGAA
*
19397934 AATAGAATATTTTATTTAATATTTTTATTTAGTTTGATTAGTCATAATTTCACTTTAAATGGATG
196 AATAGAATATTTTATTTAATATTTTTATTTAGTTTGATTAGTAATAATTTCACTTTAAATGGATG
*
19397999 ATTTAGATTACTAAAATTATTTTTAGATAAGAAATGTATATTTTTCGATCGTATGCTGTATTTTC
261 ATTTAGATTACTAAAATTATTTTTAGATAAGAAATGTATATTTTTCGATCGTATGCTATATTTTC
*
19398064 ACTAGTTTCAAAATTTTTGAAAAAAAATAACCAAAATACCCCTGTGTGGCAGAAATTACTTTTTG
326 ACTAGTTTCAAAATTTTCGAAAAAAAATAACCAAAATACCCCTGTGTGGCAGAAATTACTTTTTG
19398129 TTTGTTTTTTATTTTAAAATAGTTTATATTCCCTTAAAACATGATATTTAGTAACTGTTGCTCAC
391 TTTGTTTTTTATTTTAAAATAGTTTATATTCCCTTAAAACATGATATTTAGTAACTGTTGCTCAC
* *
19398194 AAGGGAGACATAAAATTGATGCAAGAGCCTTGCGAGGTTTCGGTTGACATTCTGGGTAATGAATG
456 AAGGGAGACATAAAATTGATGCAAGAGCCTTACGAGGTTTCGGTTGACATTCTAGGTAATGAATG
*
19398259 TCTATCGAGACATCGCGACTGTTGTCACGGGCTCGAAGGGAGTATCGA
521 TCTATCGAGACATCGCGACTGTTGTCACGGGCTCAAAGGGAGTATCGA
19398307 GTTGCTTTTGAATTTGCATCCTTAAAAATCGAAGGTCTACAGTCTTGTATATTTTCGGTTA-TTT
1 GTTGCTTTTGAATTTGCATCCTTAAAAATCGAAGGTCTACAGTCTTGTATATTTTCGGTTATTTT
19398371 TTGGGCCCACATGTCATTGTAGAAT-TTTTTGTATACCTGGTTTAGTGTGCTATTATATATATGA
66 TTGGGCCCACATGTCATTGTAGAATATTTTTGTATACCTGGTTTAGTGTGCTATTATATATATGA
*
19398435 ATTTATTTTGCTCTTACGCTACAAAAATTATTTATGCAGAATTCTATAAATATTGTTTTATAAGA
131 ATTTATTTTACTCTTACGCTAC-AAAATTATTTATGCAGAATTCTATAAATATTGTTTTATAAGA
* * *
19398500 AAAT-GAAATATTTTATTTAATATTTTTATTTAGTTTGATTAGTAATAATTTCATTTTTATTGGA
195 AAATAG-AATATTTTATTTAATATTTTTATTTAGTTTGATTAGTAATAATTTCACTTTAAATGGA
19398564 TGATTTAGATTACTAAAATTATTTTTAGATAAGAAATGTATATTTTTCGATCGTATGCTATATTT
259 TGATTTAGATTACTAAAATTATTTTTAGATAAGAAATGTATATTTTTCGATCGTATGCTATATTT
19398629 TCACTAGTTTCAAAATTTTCGAAAAAAAAATAACCAAAATACCCCTGTGTGGCAGAAATTACTTT
324 TCACTAGTTTCAAAATTTTCG-AAAAAAAATAACCAAAATACCCCTGTGTGGCAGAAATTACTTT
**
19398694 TTGTTTGTTTTTTATTTTAAAATAGTTTATATTCCCTTAAAACATGATATTTAGTAGTTGTTGCT
388 TTGTTTGTTTTTTATTTTAAAATAGTTTATATTCCCTTAAAACATGATATTTAGTAACTGTTGCT
*
19398759 CACAGGGGAGACATAAAATTGATGCAAGAGCCTTACGAGGTTTCGGTTGACATTCTAGGTAATGA
453 CACAAGGGAGACATAAAATTGATGCAAGAGCCTTACGAGGTTTCGGTTGACATTCTAGGTAATGA
*
19398824 ATGTCTATCGAGACATCGCGACTGTTGTCACGGGCTCAAAGGGAGTATCGG
518 ATGTCTATCGAGACATCGCGACTGTTGTCACGGGCTCAAAGGGAGTATCGA
19398875 GTTG
1 GTTG
19398879 TGACAAGTTT
Statistics
Matches: 552, Mismatches: 17, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
566 61 0.11
567 211 0.38
568 280 0.51
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (568 bp):
GTTGCTTTTGAATTTGCATCCTTAAAAATCGAAGGTCTACAGTCTTGTATATTTTCGGTTATTTT
TTGGGCCCACATGTCATTGTAGAATATTTTTGTATACCTGGTTTAGTGTGCTATTATATATATGA
ATTTATTTTACTCTTACGCTACAAAATTATTTATGCAGAATTCTATAAATATTGTTTTATAAGAA
AATAGAATATTTTATTTAATATTTTTATTTAGTTTGATTAGTAATAATTTCACTTTAAATGGATG
ATTTAGATTACTAAAATTATTTTTAGATAAGAAATGTATATTTTTCGATCGTATGCTATATTTTC
ACTAGTTTCAAAATTTTCGAAAAAAAATAACCAAAATACCCCTGTGTGGCAGAAATTACTTTTTG
TTTGTTTTTTATTTTAAAATAGTTTATATTCCCTTAAAACATGATATTTAGTAACTGTTGCTCAC
AAGGGAGACATAAAATTGATGCAAGAGCCTTACGAGGTTTCGGTTGACATTCTAGGTAATGAATG
TCTATCGAGACATCGCGACTGTTGTCACGGGCTCAAAGGGAGTATCGA
Found at i:19399864 original size:19 final size:20
Alignment explanation
Indices: 19399833--19399919 Score: 69
Period size: 22 Copynumber: 4.5 Consensus size: 20
19399823 TTAAAAATGT
*
19399833 TTAATTAAGTTGT-GCCTAA
1 TTAATTAAATTGTGGCCTAA
*
19399852 TTATTTAAATTGTTGGGCCTAA
1 TTAATTAAATTG-T-GGCCTAA
*
19399874 TTAATTAAATTGT---TTAA
1 TTAATTAAATTGTGGCCTAA
* *
19399891 TTAAGT-CATTG-GGCCTAA
1 TTAATTAAATTGTGGCCTAA
19399909 TTAATTAAATT
1 TTAATTAAATT
19399920 AAACAATTAA
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
16 4 0.08
17 8 0.15
18 8 0.15
19 13 0.25
20 1 0.02
21 1 0.02
22 17 0.33
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TTAATTAAATTGTGGCCTAA
Found at i:19399871 original size:22 final size:22
Alignment explanation
Indices: 19399841--19399887 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
19399831 GTTTAATTAA
* *
19399841 GTTGTGCCTAATTATTTAAATT
1 GTTGGGCCTAATTAATTAAATT
19399863 GTTGGGCCTAATTAATTAAATT
1 GTTGGGCCTAATTAATTAAATT
19399885 GTT
1 GTT
19399888 TAATTAAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.47
Consensus pattern (22 bp):
GTTGGGCCTAATTAATTAAATT
Found at i:19399905 original size:35 final size:35
Alignment explanation
Indices: 19399864--19400061 Score: 225
Period size: 35 Copynumber: 5.6 Consensus size: 35
19399854 ATTTAAATTG
*
19399864 TTGGGCCTAATTAATTAAATTGTTTAATTAAGTCA
1 TTGGGCCTAATTAATTAAATTGTTTAATTAAGTTA
****
19399899 TTGGGCCTAATTAATTAAATTAAACAATTAAGTTA
1 TTGGGCCTAATTAATTAAATTGTTTAATTAAGTTA
* * *
19399934 TTGGACCTAATTGATTAAATTTGTTTAATTAAGTCA
1 TTGGGCCTAATTAATTAAA-TTGTTTAATTAAGTTA
* * * *
19399970 TTTGGCCTAATTCATTAAAATTGTTTAATTAAATTT
1 TTGGGCCTAATTAATT-AAATTGTTTAATTAAGTTA
* * *
19400006 TTAGGCTTAATTAATTAAATTATTTAATTAAGTTA
1 TTGGGCCTAATTAATTAAATTGTTTAATTAAGTTA
**
19400041 TTGGGCCTAATCGATTAAATT
1 TTGGGCCTAATTAATTAAATT
19400062 AAACAATTAA
Statistics
Matches: 133, Mismatches: 28, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
35 80 0.60
36 50 0.38
37 3 0.02
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (35 bp):
TTGGGCCTAATTAATTAAATTGTTTAATTAAGTTA
Found at i:19400017 original size:107 final size:106
Alignment explanation
Indices: 19399867--19400061 Score: 282
Period size: 107 Copynumber: 1.8 Consensus size: 106
19399857 TAAATTGTTG
* *
19399867 GGCCTAATTAATTAAATTGTTTAATTAAGTCATTGGGCCTAATTAATTAAATTAAACAATTAAGT
1 GGCCTAATTAATTAAATTGTTTAATTAAATCATTAGGCCTAATTAATTAAATTAAACAATTAAGT
*
19399932 TATTGGACCTAATTGATTAAATTTGTTTAATTAAGTCATTT
66 TATTGGACCTAATCGATTAAATTTGTTTAATTAAGTCATTT
* ** * ***
19399973 GGCCTAATTCATTAAAATTGTTTAATTAAATTTTTAGGCTTAATTAATTAAATTATTTAATTAAG
1 GGCCTAATTAATT-AAATTGTTTAATTAAATCATTAGGCCTAATTAATTAAATTAAACAATTAAG
*
19400038 TTATTGGGCCTAATCGATTAAATT
65 TTATTGGACCTAATCGATTAAATT
19400062 AAACAATTAA
Statistics
Matches: 77, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
106 12 0.16
107 65 0.84
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (106 bp):
GGCCTAATTAATTAAATTGTTTAATTAAATCATTAGGCCTAATTAATTAAATTAAACAATTAAGT
TATTGGACCTAATCGATTAAATTTGTTTAATTAAGTCATTT
Found at i:19403628 original size:35 final size:35
Alignment explanation
Indices: 19403589--19403696 Score: 189
Period size: 35 Copynumber: 3.1 Consensus size: 35
19403579 CTGTGGATAG
* *
19403589 TGATGTTGATGTGTGCGAATAGGGAGTGCACATGA
1 TGATGTTGATGTGTGCGAGTAGGGAGTGCACACGA
19403624 TGATGTTGATGTGTGCGAGTAGGGAGTGCACACGA
1 TGATGTTGATGTGTGCGAGTAGGGAGTGCACACGA
*
19403659 TGATGTTGAAGTGTGCGAGTAGGGAGTGCACACGA
1 TGATGTTGATGTGTGCGAGTAGGGAGTGCACACGA
19403694 TGA
1 TGA
19403697 CATTGCCTTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 70 1.00
ACGTcount: A:0.25, C:0.10, G:0.39, T:0.26
Consensus pattern (35 bp):
TGATGTTGATGTGTGCGAGTAGGGAGTGCACACGA
Found at i:19403709 original size:35 final size:34
Alignment explanation
Indices: 19403589--19403725 Score: 166
Period size: 35 Copynumber: 3.9 Consensus size: 34
19403579 CTGTGGATAG
* *
19403589 TGATGTTGATGTGTGCGAATAGGGAGTGCACATGA
1 TGATGTTGAT-TGTGCGAGTAGGGAGTGCACACGA
19403624 TGATGTTGATGTGTGCGAGTAGGGAGTGCACACGA
1 TGATGTTGAT-TGTGCGAGTAGGGAGTGCACACGA
*
19403659 TGATGTTGAAGTGTGCGAGTAGGGAGTGCACACGA
1 TGATGTTG-ATTGTGCGAGTAGGGAGTGCACACGA
** * * *
19403694 TGACATTGCCTTGTGCGTGTAGAGAGTGCACA
1 TGATGTTG-ATTGTGCGAGTAGGGAGTGCACA
19403726 TTGGCTGAGT
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
35 90 0.99
36 1 0.01
ACGTcount: A:0.24, C:0.12, G:0.37, T:0.26
Consensus pattern (34 bp):
TGATGTTGATTGTGCGAGTAGGGAGTGCACACGA
Found at i:19403709 original size:70 final size:70
Alignment explanation
Indices: 19403589--19403725 Score: 186
Period size: 70 Copynumber: 2.0 Consensus size: 70
19403579 CTGTGGATAG
* * ** *
19403589 TGATGTTGATGTGTGCGAATAGGGAGTGCACATGATGATGTTGATGTGTGCGAGTAGGGAGTGCA
1 TGATGTTGAAGTGTGCGAATAGGGAGTGCACACGATGACATTGATGTGTGCGAGTAGAGAGTGCA
19403654 CACGA
66 CACGA
* * *
19403659 TGATGTTGAAGTGTGCGAGTAGGGAGTGCACACGATGACATTGCCT-TGTGCGTGTAGAGAGTGC
1 TGATGTTGAAGTGTGCGAATAGGGAGTGCACACGATGACATTG-ATGTGTGCGAGTAGAGAGTGC
19403723 ACA
65 ACA
19403726 TTGGCTGAGT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
70 57 0.98
71 1 0.02
ACGTcount: A:0.24, C:0.12, G:0.37, T:0.26
Consensus pattern (70 bp):
TGATGTTGAAGTGTGCGAATAGGGAGTGCACACGATGACATTGATGTGTGCGAGTAGAGAGTGCA
CACGA
Found at i:19404582 original size:23 final size:23
Alignment explanation
Indices: 19404552--19404596 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
19404542 GGAAGGCTTG
19404552 CTTGGGCTTAGTGAGCTATGCCC
1 CTTGGGCTTAGTGAGCTATGCCC
*
19404575 CTTGGGCTTAGTGGGCTATGCC
1 CTTGGGCTTAGTGAGCTATGCC
19404597 TATTGAGCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.33, T:0.31
Consensus pattern (23 bp):
CTTGGGCTTAGTGAGCTATGCCC
Found at i:19405626 original size:66 final size:66
Alignment explanation
Indices: 19405538--19405718 Score: 283
Period size: 66 Copynumber: 2.7 Consensus size: 66
19405528 AATTGCAGAC
* *
19405538 AGAGAG-ATCTTATTCGATTGACTTGGTCGACTAAGTTGATTCTATTTCTGGTTTATAAATCTTG
1 AGAGAGCA-CTTAGTCGACTGACTTGGTCGACTAAGTTGATTCTATTTCTGGTTTATAAATCTTG
19405602 GT
65 GT
* *
19405604 AGAGAGCACTTAGTCGACTGACTTGGTCGACTAAGTTGATTTTATTTTTGGTTTATAAATCTTGG
1 AGAGAGCACTTAGTCGACTGACTTGGTCGACTAAGTTGATTCTATTTCTGGTTTATAAATCTTGG
19405669 T
66 T
* * *
19405670 AGAGAGCACTTAGTCGACTGACTTGGTCGACTAAATTGGTTCTGTTTCT
1 AGAGAGCACTTAGTCGACTGACTTGGTCGACTAAGTTGATTCTATTTCT
19405719 CAAACTTTTC
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
66 104 0.99
67 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.40
Consensus pattern (66 bp):
AGAGAGCACTTAGTCGACTGACTTGGTCGACTAAGTTGATTCTATTTCTGGTTTATAAATCTTGG
T
Found at i:19414811 original size:66 final size:66
Alignment explanation
Indices: 19414705--19414886 Score: 229
Period size: 66 Copynumber: 2.8 Consensus size: 66
19414695 AAATTGCAAA
** * *
19414705 CAGAGAGCTTTTAGTCGACTGACTTGGTCGACTAAGTTGATTATGTTTCTAGTTTGCAGATCTTG
1 CAGAGAGCACTTAGTCGACTGACTTGGTCGACTAAGTTGATTATGTTTCTAGTTTACAAATCTTG
19414770 G
66 G
* * * * *
19414771 CAGAGAGGACTTAGTCGACTGACTTGGTCGACTAAGTTGATTTTATTTCTGGTTTATAAATCTTG
1 CAGAGAGCACTTAGTCGACTGACTTGGTCGACTAAGTTGATTATGTTTCTAGTTTACAAATCTTG
19414836 G
66 G
* * * * * *
19414837 CAGAGAGCACTTAGGCTACTGACTTGGTCTACTAAATTGGTTCTGTTTCT
1 CAGAGAGCACTTAGTCGACTGACTTGGTCGACTAAGTTGATTATGTTTCT
19414887 CAAACTCTTC
Statistics
Matches: 99, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 99 1.00
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (66 bp):
CAGAGAGCACTTAGTCGACTGACTTGGTCGACTAAGTTGATTATGTTTCTAGTTTACAAATCTTG
G
Found at i:19434187 original size:22 final size:22
Alignment explanation
Indices: 19434162--19434237 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
19434152 CACGTAGTAC
*
19434162 TTAAAAATTAGTCACGCAATGT
1 TTAAAAACTAGTCACGCAATGT
19434184 TTAAAAACTAGTCACGCAATGT
1 TTAAAAACTAGTCACGCAATGT
** * *
19434206 CCAAAAACT-GATTACGCAATGC
1 TTAAAAACTAG-TCACGCAATGT
19434228 TTAAAAACTA
1 TTAAAAACTA
19434238 CCAAAACTAC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
21 1 0.02
22 44 0.98
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.26
Consensus pattern (22 bp):
TTAAAAACTAGTCACGCAATGT
Found at i:19434434 original size:60 final size:60
Alignment explanation
Indices: 19434341--19434453 Score: 181
Period size: 60 Copynumber: 1.9 Consensus size: 60
19434331 GCAAAGAATA
* *
19434341 CTCAAAATGCTCAAAGGTTTTTCTTCATATATTAAAAACCATACCAAAATGCTTAAAATG
1 CTCAAAACGCTCAAAGGTTTTTCTTCATATATTAAAAACCACACCAAAATGCTTAAAATG
* * *
19434401 CTCAAAACGCTCAAAGGTTTTTCTTCGTGTATTAAAAATCACACCAAAATGCT
1 CTCAAAACGCTCAAAGGTTTTTCTTCATATATTAAAAACCACACCAAAATGCT
19434454 CGAAATGTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (60 bp):
CTCAAAACGCTCAAAGGTTTTTCTTCATATATTAAAAACCACACCAAAATGCTTAAAATG
Found at i:19439836 original size:26 final size:26
Alignment explanation
Indices: 19439807--19439980 Score: 138
Period size: 26 Copynumber: 6.8 Consensus size: 26
19439797 ATGGGTTATT
19439807 CACTTCTGGTGGTAAAATTATCCATC
1 CACTTCTGGTGGTAAAATTATCCATC
* * **
19439833 CACTTTTAGTGAAAAAATTATCCATC
1 CACTTCTGGTGGTAAAATTATCCATC
* * *
19439859 CACTTCTGGTGGAAAAATTATCCTTA
1 CACTTCTGGTGGTAAAATTATCCATC
* ** *
19439885 GA-TTCTAATAGTAAAATTATCCATC
1 CACTTCTGGTGGTAAAATTATCCATC
* * * *
19439910 CACTTCTGATGGTAAAATTATTCTTA
1 CACTTCTGGTGGTAAAATTATCCATC
* * * *
19439936 GA-TTCTGATAGTAAAATTAT-TATC
1 CACTTCTGGTGGTAAAATTATCCATC
* *
19439960 CACTTCTAGTGATAAAATTAT
1 CACTTCTGGTGGTAAAATTAT
19439981 AATTACAATT
Statistics
Matches: 114, Mismatches: 32, Indels: 5
0.75 0.21 0.03
Matches are distributed among these distances:
24 2 0.02
25 49 0.43
26 63 0.55
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (26 bp):
CACTTCTGGTGGTAAAATTATCCATC
Found at i:19439890 original size:25 final size:25
Alignment explanation
Indices: 19439862--19439955 Score: 98
Period size: 25 Copynumber: 3.7 Consensus size: 25
19439852 ATCCATCCAC
* *
19439862 TTCTGGTGGAAAAATTATCCTTAGA
1 TTCTGATGGTAAAATTATCCTTAGA
* * * **
19439887 TTCTAATAGTAAAATTATCCATCCA
1 TTCTGATGGTAAAATTATCCTTAGA
*
19439912 CTTCTGATGGTAAAATTATTCTTAGA
1 -TTCTGATGGTAAAATTATCCTTAGA
*
19439938 TTCTGATAGTAAAATTAT
1 TTCTGATGGTAAAATTAT
19439956 TATCCACTTC
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
25 35 0.65
26 19 0.35
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (25 bp):
TTCTGATGGTAAAATTATCCTTAGA
Found at i:19439927 original size:51 final size:51
Alignment explanation
Indices: 19439846--19439980 Score: 193
Period size: 51 Copynumber: 2.7 Consensus size: 51
19439836 TTTTAGTGAA
* *
19439846 AAAATTATCCATCCACTTCTGGTGGAAAAATTATCCTTAGATTCTAATAGT
1 AAAATTATCCATCCACTTCTGATGGTAAAATTATCCTTAGATTCTAATAGT
* *
19439897 AAAATTATCCATCCACTTCTGATGGTAAAATTATTCTTAGATTCTGATAGT
1 AAAATTATCCATCCACTTCTGATGGTAAAATTATCCTTAGATTCTAATAGT
* *
19439948 AAAATTAT-TATCCACTTCT-AGTGATAAAATTAT
1 AAAATTATCCATCCACTTCTGA-TGGTAAAATTAT
19439981 AATTACAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
49 1 0.01
50 21 0.27
51 55 0.71
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (51 bp):
AAAATTATCCATCCACTTCTGATGGTAAAATTATCCTTAGATTCTAATAGT
Found at i:19439956 original size:25 final size:25
Alignment explanation
Indices: 19439872--19439955 Score: 105
Period size: 25 Copynumber: 3.3 Consensus size: 25
19439862 TTCTGGTGGA
*
19439872 AAAATTATCCTTAGATTCTAATAGT
1 AAAATTATCCTTAGATTCTGATAGT
* ** *
19439897 AAAATTATCCATCCACTTCTGATGGT
1 AAAATTATCCTTAGA-TTCTGATAGT
*
19439923 AAAATTATTCTTAGATTCTGATAGT
1 AAAATTATCCTTAGATTCTGATAGT
19439948 AAAATTAT
1 AAAATTAT
19439956 TATCCACTTC
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
25 29 0.60
26 19 0.40
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (25 bp):
AAAATTATCCTTAGATTCTGATAGT
Found at i:19439966 original size:25 final size:25
Alignment explanation
Indices: 19439887--19439966 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 25
19439877 TATCCTTAGA
* *
19439887 TTCTAATAGTAAAATTATCCATCCAC
1 TTCTGATAGTAAAATTAT-TATCCAC
* * * *
19439913 TTCTGATGGTAAAATTATTCT-TAGA
1 TTCTGATAGTAAAATTATTATCCA-C
19439938 TTCTGATAGTAAAATTATTATCCAC
1 TTCTGATAGTAAAATTATTATCCAC
19439963 TTCT
1 TTCT
19439967 AGTGATAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
24 1 0.02
25 24 0.57
26 17 0.40
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (25 bp):
TTCTGATAGTAAAATTATTATCCAC
Found at i:19439998 original size:51 final size:51
Alignment explanation
Indices: 19439846--19439998 Score: 132
Period size: 51 Copynumber: 3.0 Consensus size: 51
19439836 TTTTAGTGAA
* ** * **
19439846 AAAATTATCCATCCACTTCTGGTGGA-AAAATTATCCTTAGATTCTAATAGT
1 AAAATTATCCATCCACTTCTGAT-GATAAAATTATAATTAAATTAAAATAGT
* ** * ***
19439897 AAAATTATCCATCCACTTCTGATGGTAAAATTATTCTTAGATTCTGATAGT
1 AAAATTATCCATCCACTTCTGATGATAAAATTATAATTAAATTAAAATAGT
*
19439948 AAAATTAT-TATCCACTTCT-AGTGATAAAATTATAATTACAATTAAAATAGT
1 AAAATTATCCATCCACTTCTGA-TGATAAAATTATAATTA-AATTAAAATAGT
19439999 GATAGTGTAA
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
49 1 0.01
50 25 0.29
51 61 0.70
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (51 bp):
AAAATTATCCATCCACTTCTGATGATAAAATTATAATTAAATTAAAATAGT
Found at i:19441110 original size:27 final size:27
Alignment explanation
Indices: 19441072--19441135 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
19441062 AATGTCCTAG
19441072 TCAACATGTATACATTACATATGATTA
1 TCAACATGTATACATTACATATGATTA
*
19441099 TCAACATGTATACATTACATGTGATTA
1 TCAACATGTATACATTACATATGATTA
19441126 TCAACATGTA
1 TCAACATGTA
19441136 ACACATAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (27 bp):
TCAACATGTATACATTACATATGATTA
Found at i:19442304 original size:19 final size:20
Alignment explanation
Indices: 19442269--19442306 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
19442259 GGGATATATA
19442269 ATTATATATATAATTAATAG
1 ATTATATATATAATTAATAG
19442289 ATTA-ATATA-AACTTAATA
1 ATTATATATATAA-TTAATA
19442307 ATTTATGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.12
19 11 0.65
20 4 0.24
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTATATATATAATTAATAG
Found at i:19447016 original size:27 final size:27
Alignment explanation
Indices: 19446978--19447040 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
19446968 AGCTTTTTTG
* *
19446978 TCATCTACTTAGGTGCAGCCCCTTGGA
1 TCATCTGCTTAGGTGCAGCCCCGTGGA
19447005 TCATCTGCTTAGGTGCAGCCCCGTGGA
1 TCATCTGCTTAGGTGCAGCCCCGTGGA
19447032 TCATCTGCT
1 TCATCTGCT
19447041 AAGATGCAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.16, C:0.30, G:0.24, T:0.30
Consensus pattern (27 bp):
TCATCTGCTTAGGTGCAGCCCCGTGGA
Found at i:19447048 original size:27 final size:27
Alignment explanation
Indices: 19446991--19447048 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
19446981 TCTACTTAGG
* * *
19446991 TGCAGCCCCTTGGATCATCTGCTTAGG
1 TGCAGCCCCGTGGATCATCTGCTAAGA
19447018 TGCAGCCCCGTGGATCATCTGCTAAGA
1 TGCAGCCCCGTGGATCATCTGCTAAGA
19447045 TGCA
1 TGCA
19447049 AGCCATTGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (27 bp):
TGCAGCCCCGTGGATCATCTGCTAAGA
Found at i:19469458 original size:7 final size:7
Alignment explanation
Indices: 19469448--19469473 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
19469438 AGAAAATAGT
19469448 AAAATGC
1 AAAATGC
19469455 AAAATGC
1 AAAATGC
19469462 AAAATGC
1 AAAATGC
19469469 AAAAT
1 AAAAT
19469474 CATCATCATC
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:0.62, C:0.12, G:0.12, T:0.15
Consensus pattern (7 bp):
AAAATGC
Found at i:19470905 original size:30 final size:30
Alignment explanation
Indices: 19470869--19470934 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
19470859 CAATCAAATC
* *
19470869 CTTATATTTGAATTTTGAACCAAACAAGTT
1 CTTATATTTGAATTTTAAACCAAACAAGCT
** * *
19470899 CTTATATTTTTATTTTAAATCAAATAAGCT
1 CTTATATTTGAATTTTAAACCAAACAAGCT
19470929 CTTATA
1 CTTATA
19470935 ACTACTTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (30 bp):
CTTATATTTGAATTTTAAACCAAACAAGCT
Found at i:19471651 original size:44 final size:44
Alignment explanation
Indices: 19471555--19471653 Score: 119
Period size: 44 Copynumber: 2.3 Consensus size: 44
19471545 ATAAAAACAC
* * *
19471555 AATGACTT-GATTGAACGTAATAAAAAAATAATAACTTATTTGA
1 AATGACTTAAATTGAACATAATAAAAAAATAATAACTTATTTAA
* * *
19471598 AGTGACTTAAATTGAACATAATAAAAAATTAATAATTTATTTAA
1 AATGACTTAAATTGAACATAATAAAAAAATAATAACTTATTTAA
**
19471642 AATTTCTTAAAT
1 AATGACTTAAAT
19471654 AGTATTTGTA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 7 0.15
44 39 0.85
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.36
Consensus pattern (44 bp):
AATGACTTAAATTGAACATAATAAAAAAATAATAACTTATTTAA
Found at i:19483281 original size:43 final size:43
Alignment explanation
Indices: 19483227--19483333 Score: 117
Period size: 43 Copynumber: 2.5 Consensus size: 43
19483217 AAAGGTAAGA
* ** * * * *
19483227 AAAAATAGGTATATGTGAAAATTTATATGAGAACAAGGTCAAAG
1 AAAAAT-GGTATAAGTGAAAAAATAGACGAGAACAACGTAAAAG
19483271 AAAAATGGTATACA-TGAAAAAATAGACGAGAACAACGTAAAAG
1 AAAAATGGTATA-AGTGAAAAAATAGACGAGAACAACGTAAAAG
*
19483314 AAAAAAGGTATAAGTGAAAA
1 AAAAATGGTATAAGTGAAAA
19483334 CGTACAAGAG
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 1 0.02
43 46 0.87
44 6 0.11
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.19
Consensus pattern (43 bp):
AAAAATGGTATAAGTGAAAAAATAGACGAGAACAACGTAAAAG
Found at i:19483345 original size:43 final size:43
Alignment explanation
Indices: 19483227--19483348 Score: 111
Period size: 43 Copynumber: 2.8 Consensus size: 43
19483217 AAAGGTAAGA
* ** * * * *
19483227 AAAAATAGGTATATGTGAAAATTTATATGAGAACAAGGTCAAAG
1 AAAAA-AGGTATAAGTGAAAAAATACAAGAGAACAACGTAAAAG
* * *
19483271 AAAAATGGTATACA-TGAAAAAATAGACGAGAACAACGTAAAAG
1 AAAAAAGGTATA-AGTGAAAAAATACAAGAGAACAACGTAAAAG
**
19483314 AAAAAAGGTATAAGTGAAAACGTACAAGAGAACAA
1 AAAAAAGGTATAAGTGAAAAAATACAAGAGAACAA
19483349 GACAAGGGAA
Statistics
Matches: 63, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
42 1 0.02
43 57 0.90
44 5 0.08
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.17
Consensus pattern (43 bp):
AAAAAAGGTATAAGTGAAAAAATACAAGAGAACAACGTAAAAG
Found at i:19489679 original size:104 final size:104
Alignment explanation
Indices: 19489490--19489702 Score: 259
Period size: 104 Copynumber: 2.0 Consensus size: 104
19489480 ACAAGCCATA
** * * **
19489490 TGTGACACGACTGTGATGCGATAAGGTTTAGAATTTGTGACACGTCATGGTGGGAATGTGTGATG
1 TGTGACACGACTGTGACACGATAAGGTTTAAAATTTGTGACACGCCATGGTGGGAATGTGTGACA
* * ** *
19489555 CTGCATGTTGAAAATGTGTGACATGACATGGTAAGAATG
66 CTGCATGGTGAAAATCTGTGACACAACATGATAAGAATG
* * *
19489594 TGTGACATGGCTGTGACACGATAAGG-TTAAAAGTTTGTGACATGCCATGGTGGGAATGTGTGAC
1 TGTGACACGACTGTGACACGATAAGGTTTAAAA-TTTGTGACACGCCATGGTGGGAATGTGTGAC
*
19489658 AC-GACATGGTGAGAATCTGTGACACAACATGATAAGAATG
65 ACTG-CATGGTGAAAATCTGTGACACAACATGATAAGAATG
19489698 TGTGA
1 TGTGA
19489703 TACGGATGGT
Statistics
Matches: 92, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
103 6 0.07
104 86 0.93
ACGTcount: A:0.30, C:0.12, G:0.31, T:0.28
Consensus pattern (104 bp):
TGTGACACGACTGTGACACGATAAGGTTTAAAATTTGTGACACGCCATGGTGGGAATGTGTGACA
CTGCATGGTGAAAATCTGTGACACAACATGATAAGAATG
Found at i:19489895 original size:122 final size:124
Alignment explanation
Indices: 19489747--19489982 Score: 293
Period size: 122 Copynumber: 1.9 Consensus size: 124
19489737 ACGACAGGGT
* *
19489747 TGTGACATGGCATGGTGGGAATGTGTGA-GACGACATGGTGAGA-ATGTGTGACACGACCGTG-A
1 TGTGACATGACATGGTGAGAATGTGTGACG-CGACATGGTGA-ACATGTGTGACACGACCGTGAA
* *
19489809 -CAGGGTTTAGAGTTTGT-GACACGGCATGGTGGAAATGTGTGACACGGCATGATGAGAATG
64 GCAGGGTTTAGAGTTT-TCAACACGGCATGATGGAAATGTGTGACACGGCATGATGAGAATG
* * **
19489869 TGTGACATGATATGGTGAGAATGTGTGACGCGACATGGTGAACATGTGTGACTCGATTGTGACAT
1 TGTGACATGACATGGTGAGAATGTGTGACGCGACATGGTGAACATGTGTGACACGACCGTGA-A-
* *
19489934 GGCAGGGTTTAGAGTTTTCAACATGGCATGATGGGAATGTGTGACACGG
64 -GCAGGGTTTAGAGTTTTCAACACGGCATGATGGAAATGTGTGACACGG
19489983 TGTCACGAAC
Statistics
Matches: 96, Mismatches: 10, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
121 1 0.01
122 51 0.53
123 1 0.01
124 1 0.01
126 1 0.01
127 41 0.43
ACGTcount: A:0.26, C:0.12, G:0.36, T:0.26
Consensus pattern (124 bp):
TGTGACATGACATGGTGAGAATGTGTGACGCGACATGGTGAACATGTGTGACACGACCGTGAAGC
AGGGTTTAGAGTTTTCAACACGGCATGATGGAAATGTGTGACACGGCATGATGAGAATG
Found at i:19489915 original size:23 final size:23
Alignment explanation
Indices: 19489629--19489920 Score: 171
Period size: 23 Copynumber: 12.3 Consensus size: 23
19489619 GTTAAAAGTT
* * *
19489629 TGTGACATGCCATGGTGGGAATG
1 TGTGACACGACATGGTGAGAATG
*
19489652 TGTGACACGACATGGTGAGAATC
1 TGTGACACGACATGGTGAGAATG
* * *
19489675 TGTGACACAACATGATAAGAATG
1 TGTGACACGACATGGTGAGAATG
* * *
19489698 TGTGATACG-GATGGTGAGAATA
1 TGTGACACGACATGGTGAGAATG
* * *
19489720 CGTGACACG--ATTGTGACACGACAGGG
1 TGTGACACGACATGGTG--A-GA-A-TG
* * *
19489746 TTGTGACATGGCATGGTGGGAATG
1 -TGTGACACGACATGGTGAGAATG
*
19489770 TGTGAGACGACATGGTGAGAATG
1 TGTGACACGACATGGTGAGAATG
* * * *
19489793 TGTGACACGACCGTGACAGGGTTTAGAGTT
1 TGTG--AC-A-C--GACATGG-TGAGAATG
*
19489823 TGTGACACGGCATGGTG-GAAATG
1 TGTGACACGACATGGTGAG-AATG
* *
19489846 TGTGACACGGCATGATGAGAATG
1 TGTGACACGACATGGTGAGAATG
* *
19489869 TGTGACATGATATGGTGAGAATG
1 TGTGACACGACATGGTGAGAATG
*
19489892 TGTGACGCGACATGGTGA-ACATG
1 TGTGACACGACATGGTGAGA-ATG
19489915 TGTGAC
1 TGTGAC
19489921 TCGATTGTGA
Statistics
Matches: 205, Mismatches: 46, Indels: 36
0.71 0.16 0.13
Matches are distributed among these distances:
21 5 0.02
22 18 0.09
23 135 0.66
24 9 0.04
25 3 0.01
26 4 0.02
27 9 0.04
28 2 0.01
29 11 0.05
30 9 0.04
ACGTcount: A:0.28, C:0.13, G:0.35, T:0.24
Consensus pattern (23 bp):
TGTGACACGACATGGTGAGAATG
Found at i:19490961 original size:35 final size:35
Alignment explanation
Indices: 19490916--19491002 Score: 140
Period size: 35 Copynumber: 2.5 Consensus size: 35
19490906 TTTCACTAAG
19490916 CTTT-ACAATGGCTTTTACCAAGCTTAGCCAAAAC
1 CTTTCACAATGGCTTTTACCAAGCTTAGCCAAAAC
*
19490950 CTTTCACAATGGCTTTTACCAGGCTTAGCCAAAAC
1 CTTTCACAATGGCTTTTACCAAGCTTAGCCAAAAC
* *
19490985 CTTTCATAATGGTTTTTA
1 CTTTCACAATGGCTTTTA
19491003 TCGGGATCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 4 0.08
35 45 0.92
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (35 bp):
CTTTCACAATGGCTTTTACCAAGCTTAGCCAAAAC
Found at i:19491017 original size:35 final size:34
Alignment explanation
Indices: 19490943--19491122 Score: 145
Period size: 35 Copynumber: 5.2 Consensus size: 34
19490933 CCAAGCTTAG
* * * *
19490943 CCAAAACCTTTCACAATGGCTTTTACCAGGCTTAG
1 CCAAAACCTTTCACAATGGTTTTTA-CGGGCTCAA
* *
19490978 CCAAAACCTTTCATAATGGTTTTTATCGGGATCAA
1 CCAAAACCTTTCACAATGGTTTTTA-CGGGCTCAA
*
19491013 CCAAAACC---CA-AAGTGGTTTCT-CAGAGGCTCAA
1 CCAAAACCTTTCACAA-TGGTTTTTAC-G-GGCTCAA
*
19491045 CCACAACCTTTCACAATGGTTTTTCACGGGCTCAA
1 CCAAAACCTTTCACAATGGTTTTT-ACGGGCTCAA
* * * * *
19491080 CCACAACCTATAACAATGATTTTTCACGGGATCAA
1 CCAAAACCTTTCACAATGGTTTTT-ACGGGCTCAA
19491115 CCAAAACC
1 CCAAAACC
19491123 CAACAACTAA
Statistics
Matches: 120, Mismatches: 16, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
30 1 0.01
31 3 0.03
32 22 0.18
35 90 0.75
36 3 0.03
37 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (34 bp):
CCAAAACCTTTCACAATGGTTTTTACGGGCTCAA
Found at i:19496967 original size:23 final size:23
Alignment explanation
Indices: 19496937--19496992 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
19496927 CCCATGACAC
19496937 ACGACATGATGAAAATGTGTGAA
1 ACGACATGATGAAAATGTGTGAA
* * *
19496960 ACGACATGGTGAGAATGTGTGAC
1 ACGACATGATGAAAATGTGTGAA
19496983 ACGACTATGA
1 ACGAC-ATGA
19496993 CACGGCAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 25 0.89
24 3 0.11
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (23 bp):
ACGACATGATGAAAATGTGTGAA
Found at i:19497118 original size:23 final size:23
Alignment explanation
Indices: 19497088--19497152 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 23
19497078 TGTGAAATGG
19497088 CATGGTGAGAATATGTGACACAC
1 CATGGTGAGAATATGTGACACAC
**
19497111 CA-GTGTGAG-A-ATGTGACATGC
1 CATG-GTGAGAATATGTGACACAC
*
19497132 CATGGTGACAATATGTGACAC
1 CATGGTGAGAATATGTGACAC
19497153 GGTTGTGACA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 15 0.44
22 4 0.12
23 15 0.44
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (23 bp):
CATGGTGAGAATATGTGACACAC
Found at i:19497139 original size:21 final size:23
Alignment explanation
Indices: 19497073--19497151 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 23
19497063 CCCATTAAGG
* *
19497073 GAATATGTGAAATGGCATGGTGA
1 GAATATGTGACATGCCATGGTGA
**
19497096 GAATATGTGACACACCA-GTGTGA
1 GAATATGTGACATGCCATG-GTGA
19497119 G-A-ATGTGACATGCCATGGTGA
1 GAATATGTGACATGCCATGGTGA
*
19497140 CAATATGTGACA
1 GAATATGTGACA
19497152 CGGTTGTGAC
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
21 15 0.33
22 4 0.09
23 26 0.58
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.24
Consensus pattern (23 bp):
GAATATGTGACATGCCATGGTGA
Found at i:19497285 original size:23 final size:23
Alignment explanation
Indices: 19497259--19497309 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
19497249 TATATATAAA
19497259 TGACACGCCATGACTTGAATATG
1 TGACACGCCATGACTTGAATATG
*
19497282 TGACACGCCATGGCTTGAATATG
1 TGACACGCCATGACTTGAATATG
19497305 TGACA
1 TGACA
19497310 AACATAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (23 bp):
TGACACGCCATGACTTGAATATG
Found at i:19498213 original size:31 final size:31
Alignment explanation
Indices: 19498173--19498241 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
19498163 TTGGCGTGTT
*
19498173 ACAACATTTTACTTAGTCTGCATAGCATCTA
1 ACAACATTTTACTTAGTATGCATAGCATCTA
* * * *
19498204 ACAATATTTTACTTGGTATGCATAGCGTGTA
1 ACAACATTTTACTTAGTATGCATAGCATCTA
19498235 ACAACAT
1 ACAACAT
19498242 ATATTTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (31 bp):
ACAACATTTTACTTAGTATGCATAGCATCTA
Found at i:19499035 original size:30 final size:29
Alignment explanation
Indices: 19499001--19499056 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
19498991 TCAAATCCTT
*
19499001 AAAAAGACC-TTAAAAATACTTAGAAATAA
1 AAAAAAACCATTAAAAATACTTA-AAATAA
* *
19499030 AAAAAAACCATTACAAATGCTTAAAAT
1 AAAAAAACCATTAAAAATACTTAAAAT
19499057 GACTCTAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 12 0.52
30 11 0.48
ACGTcount: A:0.61, C:0.12, G:0.05, T:0.21
Consensus pattern (29 bp):
AAAAAAACCATTAAAAATACTTAAAATAA
Found at i:19499246 original size:31 final size:31
Alignment explanation
Indices: 19499204--19499270 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
19499194 GAAAAATATC
* *
19499204 TAAAAAAGCTTAAATAT-CATTAAAAAGACCT
1 TAAAAAAGCTTAAAAATCCA-TAAAAAAACCT
* *
19499235 TAAAAATGCTTAAAAATCCATAAAAAAACTT
1 TAAAAAAGCTTAAAAATCCATAAAAAAACCT
19499266 TAAAA
1 TAAAA
19499271 TGATTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.58, C:0.12, G:0.04, T:0.25
Consensus pattern (31 bp):
TAAAAAAGCTTAAAAATCCATAAAAAAACCT
Found at i:19499369 original size:21 final size:22
Alignment explanation
Indices: 19499340--19499396 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
19499330 AATTTCTTTG
*
19499340 AAAATCCTTGAAAAGATCA-T-A
1 AAAAACCTTGAAAA-ATCATTGA
*
19499361 AAAAACCTT-ACAAATCATTGGA
1 AAAAACCTTGAAAAATCATT-GA
19499383 AAAAACCTTGAAAA
1 AAAAACCTTGAAAA
19499397 TGCTTAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 4 0.14
20 4 0.14
21 8 0.28
22 10 0.34
23 3 0.10
ACGTcount: A:0.54, C:0.16, G:0.09, T:0.21
Consensus pattern (22 bp):
AAAAACCTTGAAAAATCATTGA
Found at i:19499612 original size:21 final size:21
Alignment explanation
Indices: 19499588--19499632 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
19499578 AAAGGAATTT
*
19499588 AAAAATGCTTAAAAAT-CTATA
1 AAAAAT-CATAAAAATACTATA
*
19499609 AAAAATCATAAAAATACTTTA
1 AAAAATCATAAAAATACTATA
19499630 AAA
1 AAA
19499633 GACTATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.62, C:0.09, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAAATCATAAAAATACTATA
Found at i:19499636 original size:352 final size:350
Alignment explanation
Indices: 19498993--19501624 Score: 2148
Period size: 353 Copynumber: 7.5 Consensus size: 350
19498983 AAAACCATTC
* * * * *
19498993 AAATCCTTAAAAAGACCTTAAAAATACTTAGAAAT-A--AAAAAAAACCATTACAAATGCTTAAA
1 AAATCCTTGAAAAGACCTTAAAAATCCTTACAAATCATTGAAAAAAACC-TTAAAAATGCTT-AA
* ** * * * *
19499055 ATGA-CTCTAAACATCTTTAAAAAGTTCTTCAAAATCCTTTCAAAAGCCATACAAAACTTAAAAA
64 ATGACCT-TAAACATCCTTAAAAAGACCCTAAAAAT-CTTTAAAAAACCATACAAAACTTAAAAA
* * * *
19499119 ATCCTTAAAAATCGTAAA-AGAA-AATTAAAAAAATTAGAATTCCCTTAAAAAA-ATAATAAATC
127 ATCCTTAAAAATCG-AAATA-AATAATTAAAAAAATTAAAAATCTCTTAAAAAATA-AAAAAATC
* * * **
19499181 CTTCAAATTCCTTGAAAAATA-TCTAAAAAAGCTTAAATATCATTAAAAAGACCTTAAAAATGCT
189 CTTCAAATTCCTTGAAAAAAACTCTAAAAAACCTTAAATATCATTAAAAGGAATTTAAAAATGCT
* * * *
19499245 TAAAAATCCAT-AAAAAAACTTTAAAATGATTTAAAAGACTTTAAAAATCTTGTTAAAATAACTT
254 TAAAAATCTATGAAAAAACCTTAAAAATGCTTTAAAAGACTTTAAAAATCTTGTTAAAATAACTT
19499309 ACAAAACCTTTAAAATCTAAAAATTTCTTTGA
319 ACAAAACCTTTAAAATCTAAAAATTTCTTTGA
* * * * *
19499341 AAATCCTTGAAAAGATCATAAAAAACCTTACAAATCATTGGAAAAAACCTTGAAAATGCTTAATA
1 AAATCCTTGAAAAGACCTTAAAAATCCTTACAAATCATTGAAAAAAACCTTAAAAATGCTTAA-A
* * * * *
19499406 TAACTTTAAACATCCTTAAAAAGACCCTTAAAATCTTGTACAAAATCATACAAAACTTAAAAAAA
65 TGACCTTAAACATCCTTAAAAAGACCCTAAAAATCTT-TAAAAAACCATACAAAACTT-AAAAAA
* *
19499471 TCTTTAAAAATCGAAATAAATAATTAAAAAAATTAAAAATCTCTTAAAAACATAAAAAAACCCTT
128 TCCTTAAAAATCGAAATAAATAATTAAAAAAATTAAAAATCTCTTAAAAA-ATAAAAAAATCCTT
* ** *
19499536 CAAATT-CTTGAAAAAAACTCTAAAAACCCTTAGGTATCCTTAAAAGGAATTTAAAAATGCTTAA
192 CAAATTCCTTGAAAAAAACTCTAAAAAACCTTAAATATCATTAAAAGGAATTTAAAAATGCTTAA
* * * *
19499600 AAATCTAT-AAAAAATCATAAAAATACTTTAAAAGACTATAAAAATCTT-TTAAAAATAACTTAC
257 AAATCTATGAAAAAACCTTAAAAATGCTTTAAAAGACTTTAAAAATCTTGTT-AAAATAACTTAC
*
19499663 AAAACC-TTAAAATCCATAAAATTTC-TTGA
321 AAAACCTTTAAAATCTA-AAAATTTCTTTGA
* * * * *
19499692 AAACCCTTGAAAACACCTTAAAAATCCTTAGAGATCCATTAAAAAAAAACCTTAAAAATGCTTAA
1 AAATCCTTGAAAAGACCTTAAAAATCCTTACAAAT-CATT-GAAAAAAACCTTAAAAATGCTT-A
** * * *
19499757 AATGACCTTAAACATCCTTAAAAAGATTCAAAAAATCCTTTAAAAAATCATACAAAACCTAAAGA
63 AATGACCTTAAACATCCTTAAAAAGACCCTAAAAAT-CTTTAAAAAACCATACAAAACTTAAA-A
** * *
19499822 AATCCTTAAAAATCGTAAA-AAATAATTAAAAAAATTTAAAAATC-CTTTCAAAACAGCAAAAAT
126 AATCCTTAAAAATCG-AAATAAATAATTAAAAAAA-TTAAAAATCTCTTAAAAAATA-AAAAAAT
** * * * * **
19499885 ATTTTAAATTCTTTG-AAAAATCTCTAAAAAACCTTAAATATCTTTAAAAGGACCTTAAAAATGC
188 CCTTCAAATTCCTTGAAAAAAACTCTAAAAAACCTTAAATATCATTAAAAGGAATTTAAAAATGC
* * *
19499949 TTAAAAATCTATGTAAAAAACCTTAAAAATGCTTTGAAAGACTTTTAAAATCTTGTAAAAATAAC
253 TTAAAAATCTATG-AAAAAACCTTAAAAATGCTTTAAAAGACTTTAAAAATCTTGTTAAAATAAC
*
19500014 TTACAAAACCTTTAAAATCTACGAAA-TTCTTTGAA
317 TTACAAAACCTTTAAAATCTA-AAAATTTCTTTG-A
* * * *
19500049 AAATCCTTGGAAAGATCTTAAAAATCCTTAAAAATCAAT-AAAAAAA-CTTAAAAATGCTTAGAA
1 AAATCCTTGAAAAGACCTTAAAAATCCTTACAAATCATTGAAAAAAACCTTAAAAATGCTTA-AA
* * * * ** *
19500112 TAACCTTAAACATCTTTCAAATGAGCCAAAAAAAAATCTTTTAAAAAACCATACAAAA-TCCAAA
65 TGACCTTAAACATCCTTAAAAAGA-CC--CTAAAAATC-TTTAAAAAACCATACAAAACT-TAAA
* * *
19500176 AAATCTTTAAAAATCGTAATAAATAATT-AAAAAATAAAAAATCTCTTAAAAAAT-AAAAAATCC
125 AAATCCTTAAAAATCGAAATAAATAATTAAAAAAATTAAAAATCTCTTAAAAAATAAAAAAATCC
* * * * * **
19500239 ATT-AAATTCCTT-TAAAAATCTATAAAAAAACCATAAATATCGTTAAAAGGACA-TTAACGATG
190 -TTCAAATTCCTTGAAAAAAACTCT-AAAAAACCTTAAATATCATTAAAAGGA-ATTTAAAAATG
* * * * *
19500301 CTTAAAAATTTATGAAAAAATCTTTAAAATGCTCTAGAACG-CTTTAAAAATCTT-TTAAAAATA
252 CTTAAAAATCTATGAAAAAACCTTAAAAATGCTTTA-AAAGACTTTAAAAATCTTGTT-AAAATA
** * **
19500364 ACTTACAAAACCTAAAAAATGCATAAAATTTTATAAAAACCTTTTC
315 ACTTACAAAACCTTTAAAAT-C-TAAAA-ATT-T------CTTTGA
* * * * ** * **
19500410 AAATCCTTCAAAAGACCGTAAAAATCTTTA-GAATCCATAAAAAAAAACCTTAAAGATAATTAGA
1 AAATCCTTGAAAAGACCTTAAAAATCCTTACAAAT-CATTGAAAAAAACCTTAAAAATGCTTA-A
* * * *
19500474 ATGACCTTAAACATCCTTAAAAAAATACTTAAAAA-CATTTTAAAAAGCCATACAAAACTTAAAA
64 ATGACCTTAAACATCCTTAAAAAGA-CCCTAAAAATC--TTTAAAAAACCATACAAAACTTAAAA
* * *
19500538 AATCTTTAAAAATC-ATAATAAATAATTAAAAATATTAAAAATC-CATCAAAAAA-ATAAAAAAT
126 AATCCTTAAAAATCGA-AATAAATAATTAAAAAAATTAAAAATCTC-TTAAAAAATA-AAAAAAT
* ** * * *
19500600 CCTTCAAATTCCTTGAAAAATA-TCTTTAAAACCGTAAGTATCATTAAAAGG-ATTTTAAAATGC
188 CCTTCAAATTCCTTGAAAAAAACTCTAAAAAACCTTAAATATCATTAAAAGGAATTTAAAAATGC
* * * ** *
19500663 TTAAAAATCCATAATAAAAACCATAAAAATGCTTGGAAAGACTTTAAAAATCTTATTAAAATAAC
253 TTAAAAATCTATGA-AAAAACCTTAAAAATGCTTTAAAAGACTTTAAAAATCTTGTTAAAATAAC
* * * *
19500728 TTAAAAAATCTTTAAAATCCATAAATTT-TCTTGA
317 TTACAAAACCTTTAAAATCTAAAAATTTCT-TTGA
* * * **
19500762 AAATCCTT-----G------AAAATCCATAGAAATCATTGAAAAAAACTTTAAAAATGCTTAGTT
1 AAATCCTTGAAAAGACCTTAAAAATCCTTACAAATCATTGAAAAAAACCTTAAAAATGCTTA-AA
* * * * *
19500816 TGACCTTAAACATCCTTAAAAAGACTCTAAAAATCTTTTAAAAAATCATGCAAAACTTAACAAGT
65 TGACCTTAAACATCCTTAAAAAGACCCTAAAAATC-TTTAAAAAACCATACAAAACTTAAAAAAT
* * **
19500881 CCTTAAAAATCGTAATAAATAATTAAAAAAAAATTAAAAATCCCTTAAAAAAT-AAAAAATTATT
129 CCTTAAAAATCGAAATAAATAATT--AAAAAAATTAAAAATCTCTTAAAAAATAAAAAAATCCTT
* * *
19500945 GAAATTCCTTGAAAAATA-TCTAAAAAACCTTAAATATCCTTAAAA--AATTTAAAAATGCTTAA
192 CAAATTCCTTGAAAAAAACTCTAAAAAACCTTAAATATCATTAAAAGGAATTTAAAAATGCTTAA
* * * *
19501007 AAATTTATGAAAAGAACCTTAAAAATGCTTGAAAAGACTTTAAAAATCTAGTTAAAATAACTTAT
257 AAATCTATGAAAA-AACCTTAAAAATGCTTTAAAAGACTTTAAAAATCTTGTTAAAATAACTTAC
*
19501072 AAAA-CTTTAAAAATC-AATAAATTTCGTTGA
321 AAAACCTTT-AAAATCTAA-AAATTTCTTTGA
* * * *
19501102 AAATCCTTGAAAAGAGCTTAAAAATCCTTACAAATAATTGAAAAAAACTTTAAAAATACTTAGAA
1 AAATCCTTGAAAAGACCTTAAAAATCCTTACAAATCATTGAAAAAAACCTTAAAAATGCTTA-AA
* * ** * * *
19501167 TGACCATGAACATCCTTAAAAAGACCCTAAAAATCCTTTTGAAAACCACAAAAAATCTAAAAAAA
65 TGACCTTAAACATCCTTAAAAAGACCCTAAAAAT-CTTTAAAAAACCATACAAAA-CTTAAAAAA
* * * * *
19501232 TCCTTAAAAATC-ATAATAAATAATTAAAAACATAAAAAATTTATTAAAAGAATAAAAAAAATCT
128 TCCTTAAAAATCGA-AATAAATAATTAAAAAAATTAAAAATCTCTTAAAA-AAT-AAAAAAATCC
* * * * * *
19501296 TTCAAATTCTTTG-AAAAATCTCT---AAA----AAA-AT-A-T-AAA-TACTCTAAAAATACTT
190 TTCAAATTCCTTGAAAAAAACTCTAAAAAACCTTAAATATCATTAAAAGGAATTTAAAAATGCTT
* * * * * *
19501348 AAAAAT-TCATAAAAAAACCTTAAAAATACTATAAAAGACTTTAAAAATCTTCTAAAAATAAATT
255 AAAAATCT-ATGAAAAAACCTTAAAAATGCTTTAAAAGACTTTAAAAATCTTGTTAAAATAACTT
* * *
19501412 ACAAAACCTGAAAAATGCATAAAATTCTATAAAAATCCTTT-C
319 ACAAAACCT------T---TAAAA-TCTA-AAAATTTCTTTGA
* * * * ***
19501454 AAATACTTCAAAAGACCTTAAAAATCTTTAGAAATCTACAAAAAAAAAAACCTTAAAAATGCTTA
1 AAATCCTTGAAAAGACCTTAAAAATCCTTACAAA--T-CATTGAAAAAAACCTTAAAAATGCTTA
* * * * * * * *
19501519 GAATGACTTTAAAGATCCTTAAAAAAACTCTAAAAATCCTTTACAACATCATACAAAACCT-AAA
63 -AATGACCTTAAACATCCTTAAAAAGACCCTAAAAAT-CTTTAAAAAACCATACAAAACTTAAAA
* *
19501583 AATCCTTAAAAAT-TATAATAAATATTTAAAAAAATTAAAAAT
126 AATCCTTAAAAATCGA-AATAAATAATTAAAAAAATTAAAAAT
19501625 ACCTCAAATT
Statistics
Matches: 1853, Mismatches: 311, Indels: 235
0.77 0.13 0.10
Matches are distributed among these distances:
339 8 0.00
340 148 0.08
341 102 0.06
342 76 0.04
343 28 0.02
345 3 0.00
346 3 0.00
347 1 0.00
348 29 0.02
349 7 0.00
350 79 0.04
351 199 0.11
352 284 0.15
353 335 0.18
354 47 0.03
355 147 0.08
356 48 0.03
357 30 0.02
358 1 0.00
359 2 0.00
360 8 0.00
361 103 0.06
362 105 0.06
363 56 0.03
364 4 0.00
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (350 bp):
AAATCCTTGAAAAGACCTTAAAAATCCTTACAAATCATTGAAAAAAACCTTAAAAATGCTTAAAT
GACCTTAAACATCCTTAAAAAGACCCTAAAAATCTTTAAAAAACCATACAAAACTTAAAAAATCC
TTAAAAATCGAAATAAATAATTAAAAAAATTAAAAATCTCTTAAAAAATAAAAAAATCCTTCAAA
TTCCTTGAAAAAAACTCTAAAAAACCTTAAATATCATTAAAAGGAATTTAAAAATGCTTAAAAAT
CTATGAAAAAACCTTAAAAATGCTTTAAAAGACTTTAAAAATCTTGTTAAAATAACTTACAAAAC
CTTTAAAATCTAAAAATTTCTTTGA
Found at i:19499721 original size:10 final size:10
Alignment explanation
Indices: 19499586--19500121 Score: 64
Period size: 10 Copynumber: 51.5 Consensus size: 10
19499576 TAAAAGGAAT
*
19499586 TTAAAAATGC
1 TTAAAAATCC
19499596 TTAAAAAT-C
1 TTAAAAATCC
19499605 TATAAAAAAT-C
1 T-T-AAAAATCC
* *
19499616 ATAAAAATAC
1 TTAAAAATCC
* **
19499626 TTTAAAAGAC
1 TTAAAAATCC
*
19499636 TATAAAAATCTT
1 T-TAAAAATC-C
*
19499648 TTAAAAATAAC
1 TTAAAAAT-CC
19499659 TTACAAAA-CC
1 TTA-AAAATCC
19499669 TT-AAAATCC
1 TTAAAAATCC
* * *
19499678 ATAAAATTTC
1 TTAAAAATCC
* *
19499688 TTGAAAACCC
1 TTAAAAATCC
19499698 TTGAAAACA-CC
1 TT-AAAA-ATCC
19499709 TTAAAAATCC
1 TTAAAAATCC
* *
19499719 TTAGAGATCC
1 TTAAAAATCC
*
19499729 ATTAAAAAAAAACC
1 -TT---AAAAATCC
*
19499743 TTAAAAATGC
1 TTAAAAATCC
19499753 TT-AAAATGACC
1 TTAAAAAT--CC
*
19499764 TTAAACATCC
1 TTAAAAATCC
*
19499774 TTAAAAAGATTC
1 TT-AAAA-ATCC
*
19499786 -AAAAAATCC
1 TTAAAAATCC
19499795 TTTAAAAAAT-C
1 -TT-AAAAATCC
*
19499806 ATACAAAA-CC
1 TTA-AAAATCC
*
19499816 TAAAGAAATCC
1 TTAA-AAATCC
*
19499827 TTAAAAATCG
1 TTAAAAATCC
* **
19499837 TAAAAAATAA
1 TTAAAAATCC
***
19499847 TTAAAAAAAT
1 TTAAAAATCC
19499857 TTAAAAATCC
1 TTAAAAATCC
* *
19499867 TTTCAAAA-CA
1 -TTAAAAATCC
** **
19499877 GCAAAAATAT
1 TTAAAAATCC
* * *
19499887 TTTAAATTCT
1 TTAAAAATCC
19499897 TTGAAAAAT-C
1 TT-AAAAATCC
*
19499907 TCTAAAAAACC
1 T-TAAAAATCC
* *
19499918 TTAAATATCT
1 TTAAAAATCC
19499928 TTAAAAGGA-CC
1 TTAAAA--ATCC
*
19499939 TTAAAAATGC
1 TTAAAAATCC
*
19499949 TTAAAAATCTA
1 TTAAAAATC-C
*
19499960 TGTAAAAAACC
1 T-TAAAAATCC
*
19499971 TTAAAAATGCT
1 TTAAAAAT-CC
* *
19499982 TTGAAAGA-CT
1 TT-AAAAATCC
* *
19499992 TTTAAAATCT
1 TTAAAAATCC
*
19500002 TGTAAAAATAAC
1 T-TAAAAAT-CC
19500014 TTACAAAA-CC
1 TTA-AAAATCC
*
19500024 TTTAAAAT-C
1 TTAAAAATCC
* *
19500033 -TACGAAATTCT
1 TTA--AAAATCC
19500044 TTGAAAAATCC
1 TT-AAAAATCC
*
19500055 TTGGAAAGAT-C
1 TT--AAAAATCC
19500066 TTAAAAATCC
1 TTAAAAATCC
*
19500076 TTAAAAATCA
1 TTAAAAATCC
* **
19500086 ATAAAAAAAC
1 TTAAAAATCC
*
19500096 TTAAAAATGC
1 TTAAAAATCC
19500106 TTAGAATAA-CC
1 TTA-AA-AATCC
19500117 TTAAA
1 TTAAA
19500122 CATCTTTCAA
Statistics
Matches: 372, Mismatches: 100, Indels: 108
0.64 0.17 0.19
Matches are distributed among these distances:
8 5 0.01
9 40 0.11
10 182 0.49
11 92 0.25
12 45 0.12
13 3 0.01
14 5 0.01
ACGTcount: A:0.52, C:0.15, G:0.05, T:0.29
Consensus pattern (10 bp):
TTAAAAATCC
Found at i:19499764 original size:21 final size:21
Alignment explanation
Indices: 19499740--19499779 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19499730 TTAAAAAAAA
*
19499740 ACCTTAAAAATGCTTAAAATG
1 ACCTTAAAAATCCTTAAAATG
*
19499761 ACCTTAAACATCCTTAAAA
1 ACCTTAAAAATCCTTAAAA
19499780 AGATTCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.28
Consensus pattern (21 bp):
ACCTTAAAAATCCTTAAAATG
Found at i:19500243 original size:19 final size:20
Alignment explanation
Indices: 19500201--19500244 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
19500191 GTAATAAATA
19500201 ATTAAAAAATAAAAAATCTC
1 ATTAAAAAATAAAAAATCTC
19500221 -TTAAAAAATAAAAAATC-C
1 ATTAAAAAATAAAAAATCTC
19500239 ATTAAA
1 ATTAAA
19500245 TTCCTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (20 bp):
ATTAAAAAATAAAAAATCTC
Found at i:19500597 original size:29 final size:30
Alignment explanation
Indices: 19500533--19500600 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
19500523 ATACAAAACT
*
19500533 TAAAAAATCTTTAAAAATCATAATAAATAA
1 TAAAAAATCATTAAAAATCATAATAAATAA
*
19500563 TTAAAAAT-ATTAAAAATCCATCAA-AAA-AA
1 TAAAAAATCATTAAAAAT-CAT-AATAAATAA
19500592 TAAAAAATC
1 TAAAAAATC
19500601 CTTCAAATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
29 17 0.53
30 13 0.41
31 2 0.06
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (30 bp):
TAAAAAATCATTAAAAATCATAATAAATAA
Found at i:19500996 original size:19 final size:18
Alignment explanation
Indices: 19500974--19501013 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
19500964 CTAAAAAACC
*
19500974 TTAAATATCCTTAAAAAAT
1 TTAAAAATCCTT-AAAAAT
*
19500993 TTAAAAATGCTTAAAAAT
1 TTAAAAATCCTTAAAAAT
19501011 TTA
1 TTA
19501014 TGAAAAGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.38
Consensus pattern (18 bp):
TTAAAAATCCTTAAAAAT
Found at i:19501005 original size:29 final size:29
Alignment explanation
Indices: 19500914--19501007 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
19500904 TAAAAAAAAA
* * **
19500914 TTAAAAATCCCTTAAAAAA-TAAAAAATTA
1 TTAAATAT-CCTTAAAAAATTTAAAAATCC
* *
19500943 TTGAAAT-TCCTTGAAAAATATCTAAAAAACC
1 TT-AAATATCCTT-AAAAA-ATTTAAAAATCC
*
19500974 TTAAATATCCTTAAAAAATTTAAAAATGC
1 TTAAATATCCTTAAAAAATTTAAAAATCC
19501003 TTAAA
1 TTAAA
19501008 AATTTATGAA
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
28 4 0.08
29 22 0.43
30 13 0.25
31 12 0.24
ACGTcount: A:0.54, C:0.12, G:0.03, T:0.31
Consensus pattern (29 bp):
TTAAATATCCTTAAAAAATTTAAAAATCC
Found at i:19501252 original size:20 final size:19
Alignment explanation
Indices: 19501235--19501290 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
19501225 AAAAAAATCC
*
19501235 TTAAAAATCATAATAAATAA
1 TTAAAAA-CATAAAAAATAA
*
19501255 TTAAAAACATAAAAAATTTA
1 TTAAAAACATAAAAAA-TAA
19501275 TTAAAAGA-ATAAAAAA
1 TTAAAA-ACATAAAAAA
19501291 AATCTTTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.25
20 23 0.72
21 1 0.03
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.27
Consensus pattern (19 bp):
TTAAAAACATAAAAAATAA
Found at i:19501351 original size:9 final size:11
Alignment explanation
Indices: 19501329--19501407 Score: 53
Period size: 11 Copynumber: 7.5 Consensus size: 11
19501319 AAAAAAATAT
19501329 AAATACTCTAA
1 AAATACTCTAA
19501340 AAATACT-TAA
1 AAATACTCTAA
19501350 AAAT--TCATAA
1 AAATACTC-TAA
*
19501360 AAAAAC-CTTAA
1 AAATACTC-TAA
*
19501371 AAATACTAT-A
1 AAATACTCTAA
* *
19501381 AAAGACTTTAA
1 AAATACTCTAA
19501392 AAAT-CTTCTAA
1 AAATAC-TCTAA
19501403 AAATA
1 AAATA
19501408 AATTACAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 15
0.69 0.11 0.20
Matches are distributed among these distances:
8 1 0.02
10 22 0.42
11 29 0.56
ACGTcount: A:0.58, C:0.13, G:0.01, T:0.28
Consensus pattern (11 bp):
AAATACTCTAA
Found at i:19501362 original size:21 final size:22
Alignment explanation
Indices: 19501329--19501383 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
19501319 AAAAAAATAT
* *
19501329 AAATACTCTAAAAATA-CTTAA
1 AAATACTATAAAAAAACCTTAA
*
19501350 AAATTC-ATAAAAAAACCTTAA
1 AAATACTATAAAAAAACCTTAA
19501371 AAATACTATAAAA
1 AAATACTATAAAA
19501384 GACTTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 7 0.25
21 15 0.54
22 6 0.21
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.25
Consensus pattern (22 bp):
AAATACTATAAAAAAACCTTAA
Found at i:19501872 original size:21 final size:21
Alignment explanation
Indices: 19501820--19501872 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
19501810 TGAAAAATCA
*
19501820 TTAAAAAAACCTTGAAAATGC
1 TTAAAAAGACCTTGAAAATGC
* * *
19501841 TTAGAATGACCTTGAACAT-C
1 TTAAAAAGACCTTGAAAATGC
19501861 GTTAAAAAGACC
1 -TTAAAAAGACC
19501873 CTAAAACTTC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.25
Consensus pattern (21 bp):
TTAAAAAGACCTTGAAAATGC
Found at i:19502211 original size:21 final size:21
Alignment explanation
Indices: 19502187--19502245 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
19502177 GAAAAAAACT
* * * *
19502187 TAAAAATGCTTAGAATGACCC
1 TAAAAATCCTTAAAAAGACAC
*
19502208 TAAACATCCTTAAAAAGACAC
1 TAAAAATCCTTAAAAAGACAC
*
19502229 TAAAAATCTTTTAAAAA
1 TAAAAATC-CTTAAAAA
19502246 ACCTTAAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 23 0.77
22 7 0.23
ACGTcount: A:0.51, C:0.17, G:0.07, T:0.25
Consensus pattern (21 bp):
TAAAAATCCTTAAAAAGACAC
Found at i:19502361 original size:21 final size:21
Alignment explanation
Indices: 19502335--19502375 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
19502325 TCTATAAAAA
*
19502335 ACCTTAAATATACTTAAAATG
1 ACCTTAAAAATACTTAAAATG
*
19502356 ACCTTAAAAATGCTTAAAAT
1 ACCTTAAAAATACTTAAAAT
19502376 CCTATGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.32
Consensus pattern (21 bp):
ACCTTAAAAATACTTAAAATG
Found at i:19502365 original size:41 final size:39
Alignment explanation
Indices: 19502277--19502374 Score: 97
Period size: 41 Copynumber: 2.4 Consensus size: 39
19502267 ATTTAAAAAA
* * *
19502277 TTAAAAATCTTATAAAAACATAAAAAATCCTTCAAATTAC
1 TTAAAAATCTTA-AAAAACATAAAAAATACTTAAAATGAC
* * *
19502317 TTGAAAAATCTATAAAAAACCTTAAATATACTTAAAATGACC
1 TT-AAAAATCT-TAAAAAACATAAAAAATACTTAAAATGA-C
19502359 TTAAAAATGCTTAAAA
1 TTAAAAAT-CTTAAAA
19502375 TCCTATGAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
40 2 0.04
41 39 0.81
42 7 0.15
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.30
Consensus pattern (39 bp):
TTAAAAATCTTAAAAAACATAAAAAATACTTAAAATGAC
Found at i:19502557 original size:21 final size:21
Alignment explanation
Indices: 19502507--19502606 Score: 71
Period size: 21 Copynumber: 4.9 Consensus size: 21
19502497 GAAATCAATG
* *
19502507 AAAAAAACCTTAAAAATGCTT
1 AAAAAGACCTTAAAAATCCTT
* *
19502528 AAAATGACCTTAAACATCCTT
1 AAAAAGACCTTAAAAATCCTT
* *
19502549 AAAAAGACC-CAAAAAGCCTGT
1 AAAAAGACCTTAAAAATCCT-T
* * **
19502570 AAAAAG-TCTTAAAATTTTTT
1 AAAAAGACCTTAAAAATCCTT
*
19502590 AAAAA-TCCTTAAAAATC
1 AAAAAGACCTTAAAAATC
19502607 ATAACAAATA
Statistics
Matches: 59, Mismatches: 17, Indels: 7
0.71 0.20 0.08
Matches are distributed among these distances:
20 22 0.37
21 37 0.63
ACGTcount: A:0.51, C:0.17, G:0.06, T:0.26
Consensus pattern (21 bp):
AAAAAGACCTTAAAAATCCTT
Found at i:19502601 original size:10 final size:10
Alignment explanation
Indices: 19502277--19502606 Score: 59
Period size: 10 Copynumber: 31.9 Consensus size: 10
19502267 ATTTAAAAAA
19502277 TTAAAAAT-C
1 TTAAAAATCC
* *
19502286 TTATAAAAACA
1 TTA-AAAATCC
*
19502297 TAAAAAATCC
1 TTAAAAATCC
* * *
19502307 TTCAAATTAC
1 TTAAAAATCC
19502317 TTGAAAAAT-C
1 TT-AAAAATCC
*
19502327 TATAAAAAACC
1 T-TAAAAATCC
* *
19502338 TTAAATATAC
1 TTAAAAATCC
19502348 TT-AAAATGACC
1 TTAAAAAT--CC
*
19502359 TTAAAAATGC
1 TTAAAAATCC
19502369 TT-AAAATCC
1 TTAAAAATCC
*
19502378 TATGAAAAAAGCC
1 T-T--AAAAATCC
* *
19502391 TTTAAAATAC
1 TTAAAAATCC
** *
19502401 TTCAAAAGGCT
1 TT-AAAAATCC
*
19502412 TTAAAAATCT
1 TTAAAAATCC
* *
19502422 TGTTAAAATAAC
1 T-TAAAAAT-CC
19502434 TTACAAAA-CC
1 TTA-AAAATCC
*
19502444 TTAAAAATCA
1 TTAAAAATCC
* **
19502454 ATAAATTTCC
1 TTAAAAATCC
* *
19502464 TTGACAATCC
1 TTAAAAATCC
19502474 TTGAAAACA-CC
1 TT-AAAA-ATCC
*
19502485 TTGAAAATCC
1 TTAAAAATCC
* *
19502495 -TAGAAATCAA
1 TTAAAAATC-C
* *
19502505 TGAAAAAAACC
1 T-TAAAAATCC
*
19502516 TTAAAAATGC
1 TTAAAAATCC
19502526 TT-AAAATGACC
1 TTAAAAAT--CC
*
19502537 TTAAACATCC
1 TTAAAAATCC
*
19502547 TTAAAAAGACC
1 TTAAAAA-TCC
* *
19502558 -CAAAAAGCC
1 TTAAAAATCC
19502567 TGTAAAAAGT-C
1 T-TAAAAA-TCC
* **
19502578 TTAAAATTTT
1 TTAAAAATCC
19502588 TTAAAAATCC
1 TTAAAAATCC
19502598 TTAAAAATC
1 TTAAAAATC
19502607 ATAACAAATA
Statistics
Matches: 219, Mismatches: 71, Indels: 61
0.62 0.20 0.17
Matches are distributed among these distances:
9 33 0.15
10 115 0.53
11 43 0.20
12 21 0.10
13 7 0.03
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (10 bp):
TTAAAAATCC
Found at i:19503153 original size:41 final size:41
Alignment explanation
Indices: 19503108--19503187 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
19503098 AAAGACTTTA
*
19503108 AAAATTTTTTAAAAATAACTT-ACAAA-ACCTTAAAAATCCAT
1 AAAATTTATTAAAAAT-ACTTGA-AAACACCTTAAAAATCCAT
* *
19503149 AAAATTTATTGAAAATCCTTGAAAACACCTTAAAAATCC
1 AAAATTTATTAAAAATACTTGAAAACACCTTAAAAATCC
19503188 TTTGAAATCT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 6 0.18
41 28 0.82
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (41 bp):
AAAATTTATTAAAAATACTTGAAAACACCTTAAAAATCCAT
Found at i:19503252 original size:21 final size:21
Alignment explanation
Indices: 19503202--19503252 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
19503192 AAATCTATGA
* *
19503202 AAAAAAACCTTAACAATGCTT
1 AAAAAGACCTTAACAATCCTT
* *
19503223 AGAATGACCTTAA-ACATCCTT
1 AAAAAGACCTTAACA-ATCCTT
19503244 AAAAAGACC
1 AAAAAGACC
19503253 CAAAAGATCC
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.49, C:0.22, G:0.08, T:0.22
Consensus pattern (21 bp):
AAAAAGACCTTAACAATCCTT
Found at i:19503368 original size:22 final size:22
Alignment explanation
Indices: 19503310--19503371 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
19503300 TTGAAAGGAC
* *
19503310 CTTAAAAATA-TTT-AAAAATT
1 CTTAAAAAAACTTTAAAAAATG
19503330 CATTAAAAAAAAC-TTAAAAAATG
1 C-TT-AAAAAAACTTTAAAAAATG
*
19503353 CTTAAAAAGACTTTAAAAA
1 CTTAAAAAAACTTTAAAAA
19503372 TCTTGTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
20 1 0.03
21 9 0.26
22 17 0.50
23 7 0.21
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.29
Consensus pattern (22 bp):
CTTAAAAAAACTTTAAAAAATG
Found at i:19503615 original size:20 final size:20
Alignment explanation
Indices: 19503578--19503628 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
19503568 ATTAAAAATA
*
19503578 CTTAAAAATCCATGAAAAAC
1 CTTAAAAATCCATCAAAAAC
* *
19503598 CTTAAAAATGCTTCAAAAGA-
1 CTTAAAAATCCATCAAAA-AC
19503618 CTTGAAAAATC
1 CTT-AAAAATC
19503629 TTTTTAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.51, C:0.18, G:0.08, T:0.24
Consensus pattern (20 bp):
CTTAAAAATCCATCAAAAAC
Found at i:19503894 original size:11 final size:11
Alignment explanation
Indices: 19503869--19504003 Score: 50
Period size: 11 Copynumber: 12.6 Consensus size: 11
19503859 TTCAAATTCC
*
19503869 TTAAAAAATATT
1 TTAAAAAA-ACT
19503881 TTAAAAAAACT
1 TTAAAAAAACT
* *
19503892 TTAAATATAC-
1 TTAAAAAAACT
**
19503902 TTAAAAGGACT
1 TTAAAAAAACT
* **
19503913 TTTAAAATTC-
1 TTAAAAAAACT
* *
19503923 TT-AAAAATCC
1 TTAAAAAAACT
*
19503933 ATAAAAAAACT
1 TTAAAAAAACT
*
19503944 TT-AAAAATCT
1 TTAAAAAAACT
* *
19503954 TTAAAAAGACG
1 TTAAAAAAACT
19503965 TTAAAAATAA-T
1 TTAAAAA-AACT
*
19503976 TTAAAAATGAC-
1 TTAAAAA-AACT
*
19503987 TT-AAAAAACC
1 TTAAAAAAACT
19503997 TTAAAAA
1 TTAAAAA
19504004 TTCATAAAAT
Statistics
Matches: 92, Mismatches: 23, Indels: 17
0.70 0.17 0.13
Matches are distributed among these distances:
9 8 0.09
10 25 0.27
11 50 0.54
12 9 0.10
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (11 bp):
TTAAAAAAACT
Found at i:19503907 original size:21 final size:21
Alignment explanation
Indices: 19503881--19503929 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
19503871 AAAAAATATT
19503881 TTAAAAAAAC-TTTAAATATAC
1 TTAAAAAAACTTTTAAA-ATAC
** *
19503902 TTAAAAGGACTTTTAAAATTC
1 TTAAAAAAACTTTTAAAATAC
19503923 TTAAAAA
1 TTAAAAA
19503930 TCCATAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (21 bp):
TTAAAAAAACTTTTAAAATAC
Found at i:19503990 original size:22 final size:21
Alignment explanation
Indices: 19503934--19503993 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
19503924 TAAAAATCCA
* * *
19503934 TAAAAAAACTTTAAAAATCTT
1 TAAAAAGACGTTAAAAATATT
19503955 TAAAAAGACGTTAAAAATAATT
1 TAAAAAGACGTTAAAAAT-ATT
19503977 TAAAAATGAC-TTAAAAA
1 TAAAAA-GACGTTAAAAA
19503994 ACCTTAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.47
22 15 0.44
23 3 0.09
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (21 bp):
TAAAAAGACGTTAAAAATATT
Found at i:19504004 original size:21 final size:21
Alignment explanation
Indices: 19503923--19504003 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 21
19503913 TTTAAAATTC
* * * *
19503923 TTAAAAATCCATAAAAAAACT
1 TTAAAAAACCTTAAAAAGACG
* *
19503944 TTAAAAATCTTTAAAAAGACG
1 TTAAAAAACCTTAAAAAGACG
**
19503965 TTAAAAATAATTTAAAAATGAC-
1 TTAAAAA-ACCTTAAAAA-GACG
19503987 TTAAAAAACCTTAAAAA
1 TTAAAAAACCTTAAAAA
19504004 TTCATAAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 32 0.64
22 15 0.30
23 3 0.06
ACGTcount: A:0.59, C:0.10, G:0.04, T:0.27
Consensus pattern (21 bp):
TTAAAAAACCTTAAAAAGACG
Found at i:19504122 original size:21 final size:21
Alignment explanation
Indices: 19504093--19504150 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
19504083 ACAAAAACCT
*
19504093 TAAACATCTTTAAAAAGATCC
1 TAAAAATCTTTAAAAAGATCC
* ** *
19504114 TAAAAATCTTTGAAAATTTCT
1 TAAAAATCTTTAAAAAGATCC
19504135 TAAAAAATCTTTAAAA
1 T-AAAAATCTTTAAAA
19504151 TTCTTAATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.34
Consensus pattern (21 bp):
TAAAAATCTTTAAAAAGATCC
Found at i:19504154 original size:20 final size:22
Alignment explanation
Indices: 19504115--19504162 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 22
19504105 AAAAGATCCT
19504115 AAAAATCTTTGAAAATTTCTTA
1 AAAAATCTTTGAAAATTTCTTA
19504137 AAAAATCTTT-AAAA-TTCTTA
1 AAAAATCTTTGAAAATTTCTTA
*
19504157 ATAAAT
1 AAAAAT
19504163 AATTTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 11 0.44
21 4 0.16
22 10 0.40
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (22 bp):
AAAAATCTTTGAAAATTTCTTA
Found at i:19504168 original size:21 final size:21
Alignment explanation
Indices: 19504115--19504171 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
19504105 AAAAGATCCT
*
19504115 AAAAATCTTTGAAAATTTCTTA
1 AAAAATATTT-AAAATTTCTTA
*
19504137 AAAAATCTTTAAAA-TTCTTA
1 AAAAATATTTAAAATTTCTTA
*
19504157 ATAAATAATTTAAAA
1 AAAAAT-ATTTAAAA
19504172 AATTAAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 11 0.34
21 11 0.34
22 10 0.31
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAAATATTTAAAATTTCTTA
Found at i:19504211 original size:59 final size:58
Alignment explanation
Indices: 19504135--19504250 Score: 137
Period size: 59 Copynumber: 2.0 Consensus size: 58
19504125 GAAAATTTCT
* *
19504135 TAAAAAATCTTTAAAATTC-TTAATAAATAATTTAAAAAA-TTAAACATCTCTTAAAAACA
1 TAAAAAATCCTTAAAATTCGTTAA-AAAT-ATATAAAAAACTTAAACATC-CTTAAAAACA
* * *
19504194 TAAAAAATCCTTCAAATTCGTTGAAAATATATAAAAAACCTTAAATATCCTTAAAAA
1 TAAAAAATCCTTAAAATTCGTTAAAAATATATAAAAAA-CTTAAACATCCTTAAAAA
19504251 GAATTTAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
58 9 0.18
59 29 0.59
60 11 0.22
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (58 bp):
TAAAAAATCCTTAAAATTCGTTAAAAATATATAAAAAACTTAAACATCCTTAAAAACA
Found at i:19504397 original size:21 final size:21
Alignment explanation
Indices: 19504355--19504400 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
19504345 AAATCCCATG
*
19504355 AAAATCTTTGAAAACACTTTA
1 AAAATCTTTGAAAACACATTA
*
19504376 AAAATCTTTTGAAATC-CATTA
1 AAAATC-TTTGAAAACACATTA
19504397 AAAA
1 AAAA
19504401 AAACTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (21 bp):
AAAATCTTTGAAAACACATTA
Found at i:19504420 original size:73 final size:73
Alignment explanation
Indices: 19504282--19504421 Score: 174
Period size: 73 Copynumber: 1.9 Consensus size: 73
19504272 ATCTAAGAAA
* * * *
19504282 AAAATCCTTAAAAAGACTTTAAAAATCTTTTAAAATTAACTTAAAAAACCTTAAATATCCATAAA
1 AAAATCCTTAAAAACACTTTAAAAATCTTTTAAAATCAACTTAAAAAAACTTAAAAATCCATAAA
19504347 ATCCCATG
66 ATCCCATG
* * * * * *
19504355 AAAATCTTTGAAAACACTTTAAAAATCTTTTGAAATCCA-TTAAAAAAAACTTAAAAATGCTTAA
1 AAAATCCTTAAAAACACTTTAAAAATCTTTTAAAATCAACTT-AAAAAAACTTAAAAATCCATAA
19504419 AAT
65 AAT
19504422 GATCGTAAAC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
72 2 0.04
73 54 0.96
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (73 bp):
AAAATCCTTAAAAACACTTTAAAAATCTTTTAAAATCAACTTAAAAAAACTTAAAAATCCATAAA
ATCCCATG
Found at i:19504571 original size:22 final size:21
Alignment explanation
Indices: 19504528--19504574 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
19504518 CTTTAAAACA
* **
19504528 TAAAAAATTCTTTAAATTCCT
1 TAAAAAATTCTTAAAAAACCT
19504549 TAAAAAATCTCTTAAAAAACCT
1 TAAAAAAT-TCTTAAAAAACCT
19504571 TAAA
1 TAAA
19504575 TATCTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAAAAATTCTTAAAAAACCT
Found at i:19504902 original size:21 final size:19
Alignment explanation
Indices: 19504766--19505168 Score: 90
Period size: 21 Copynumber: 19.4 Consensus size: 19
19504756 GACCCTAATC
*
19504766 ATCCTTAAAAAACCCTAAAA
1 ATCCTT-AAAAACCTTAAAA
* *
19504786 ATCCTTTAAAATGCCTGAAAAA
1 ATCC-TTAAAA-ACCT-TAAAA
* ** *
19504808 ATTCTTAAAATTCGTAATAA
1 ATCCTTAAAAACCTTAA-AA
** *
19504828 ATAATTAAAAA-ATTAAAA
1 ATCCTTAAAAACCTTAAAA
* * *
19504846 ATCCCTTAAAAGCATAAAAA
1 AT-CCTTAAAAACCTTAAAA
**
19504866 ATCCTTCAAATTCCTTGAAAA
1 ATCCTT-AAAAACCTT-AAAA
*
19504887 ATCTCTTAAAAACCTTAAAT
1 ATC-CTTAAAAACCTTAAAA
19504907 ATCCTTAAAAAGACCTTAAAA
1 ATCCTT-AAAA-ACCTTAAAA
* *
19504928 ATGCTTAAAAATCCATGAAAAAA
1 ATCCTTAAAAA-CC-T--TAAAA
* **
19504951 ATCTTTAAAATGCTTCAAAA
1 ATCCTTAAAAACCTT-AAAA
* * *
19504971 AGACTTTAAAAATCTTTTAAAA
1 A-TCCTTAAAAA-C-CTTAAAA
*
19504993 ATAACTTACAAAACCTTAAAA
1 AT-CCTTA-AAAACCTTAAAA
* *
19505014 ATCCATAAAATACTTTGAAAA
1 ATCCTTAAAA-ACCTT-AAAA
* **
19505035 CA-CCTTAAAAATCTTTTCAA
1 -ATCCTTAAAAA-CCTTAAAA
* *
19505055 ATCCATAAAAAAAACTTAAAA
1 ATCC-T-TAAAAACCTTAAAA
* *
19505076 ATGCTTAAAAATCCATGAAACA
1 ATCCTTAAAAA-CC-TTAAA-A
* * *
19505098 AACCTTAAAAATGCTTCAAA
1 ATCCTTAAAAA-CCTTAAAA
** *
19505118 AGACTTCAAAAATCTTTAAAAA
1 ATCCTT-AAAAA-CCTT-AAAA
*
19505140 ATGCTTTAAAAAACCTTAAAA
1 AT-CCTT-AAAAACCTTAAAA
*
19505161 AACCTTAA
1 ATCCTTAA
19505169 GAGTGGTGCA
Statistics
Matches: 277, Mismatches: 72, Indels: 69
0.66 0.17 0.17
Matches are distributed among these distances:
18 4 0.01
19 30 0.11
20 75 0.27
21 98 0.35
22 45 0.16
23 25 0.09
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.28
Consensus pattern (19 bp):
ATCCTTAAAAACCTTAAAA
Found at i:19504939 original size:10 final size:10
Alignment explanation
Indices: 19504766--19505168 Score: 131
Period size: 10 Copynumber: 38.8 Consensus size: 10
19504756 GACCCTAATC
19504766 ATCCTTAAAA
1 ATCCTTAAAA
* *
19504776 AACCCTAAAA
1 ATCCTTAAAA
*
19504786 ATCCTTTAAA
1 ATCCTTAAAA
*
19504796 ATGCCTGAAAAA
1 AT-CCT-TAAAA
*
19504808 ATTCTT-AAA
1 ATCCTTAAAA
* *
19504817 ATTCGTAATAA
1 ATCCTTAA-AA
**
19504828 ATAATTAAAA
1 ATCCTTAAAA
*
19504838 A--ATTAAAA
1 ATCCTTAAAA
19504846 ATCCCTT-AAA
1 AT-CCTTAAAA
* * *
19504856 AGCATAAAAA
1 ATCCTTAAAA
*
19504866 ATCCTTCAAA
1 ATCCTTAAAA
*
19504876 TTCCTTGAAAA
1 ATCCTT-AAAA
19504887 ATCTCTTAAAA
1 ATC-CTTAAAA
*
19504898 A-CCTTAAAT
1 ATCCTTAAAA
19504907 ATCCTTAAAA
1 ATCCTTAAAA
*
19504917 AGACCTTAAAA
1 A-TCCTTAAAA
*
19504928 ATGCTTAAAA
1 ATCCTTAAAA
*
19504938 ATCCATGAAAAAA
1 ATCC-T--TAAAA
*
19504951 AT-CTTTAAA
1 ATCCTTAAAA
*
19504960 ATGCTTCAAAA
1 ATCCTT-AAAA
* *
19504971 AGACTTTAAAA
1 A-TCCTTAAAA
*
19504982 ATCTTTTAAAA
1 ATC-CTTAAAA
*
19504993 ATAACTTACAAA
1 AT-CCTTA-AAA
19505005 A-CCTTAAAA
1 ATCCTTAAAA
*
19505014 ATCCAT-AAA
1 ATCCTTAAAA
*
19505023 ATACTTTGAAAA
1 AT-CCTT-AAAA
19505035 CA-CCTTAAAA
1 -ATCCTTAAAA
* **
19505045 ATCTTTTCAA
1 ATCCTTAAAA
*
19505055 ATCCATAAAAA
1 ATCC-TTAAAA
**
19505066 AAACTTAAAA
1 ATCCTTAAAA
*
19505076 ATGCTTAAAA
1 ATCCTTAAAA
*
19505086 ATCCATGAAACA
1 ATCC-TTAAA-A
*
19505098 AACCTTAAAA
1 ATCCTTAAAA
* *
19505108 ATGCTTCAAA
1 ATCCTTAAAA
**
19505118 AGACTTCAAAA
1 ATCCTT-AAAA
*
19505129 ATCTTTAAAAA
1 ATCCTT-AAAA
*
19505140 ATGCTTTAAAA
1 AT-CCTTAAAA
*
19505151 AACCTTAAAA
1 ATCCTTAAAA
*
19505161 AACCTTAA
1 ATCCTTAA
19505169 GAGTGGTGCA
Statistics
Matches: 288, Mismatches: 73, Indels: 64
0.68 0.17 0.15
Matches are distributed among these distances:
8 8 0.03
9 32 0.11
10 126 0.44
11 89 0.31
12 26 0.09
13 7 0.02
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.28
Consensus pattern (10 bp):
ATCCTTAAAA
Found at i:19505108 original size:32 final size:31
Alignment explanation
Indices: 19505031--19505168 Score: 100
Period size: 32 Copynumber: 4.4 Consensus size: 31
19505021 AAATACTTTG
* **
19505031 AAAACACCTTAAAAAT-CTTTTCAAATCCATA
1 AAAAAACCTTAAAAATGC-TTAAAAATCCATA
*
19505062 AAAAAAACTTAAAAATGCTTAAAAATCCATGA
1 AAAAAACCTTAAAAATGCTTAAAAATCCAT-A
* * ** * *
19505094 AACAAACCTTAAAAATGCTTCAAAAGACTTC
1 AAAAAACCTTAAAAATGCTTAAAAATCCATA
* * * *
19505125 AAAAATCTTTAAAAAATGCTTTAAAAAACC-TT
1 AAAAAACCTT-AAAAATGC-TTAAAAATCCATA
19505157 AAAAAACCTTAA
1 AAAAAACCTTAA
19505169 GAGTGGTGCA
Statistics
Matches: 83, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
31 33 0.40
32 43 0.52
33 7 0.08
ACGTcount: A:0.54, C:0.17, G:0.04, T:0.25
Consensus pattern (31 bp):
AAAAAACCTTAAAAATGCTTAAAAATCCATA
Found at i:19505140 original size:22 final size:22
Alignment explanation
Indices: 19505121--19505162 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
19505111 CTTCAAAAGA
* *
19505121 CTTCAAAAATCTTTAAAAAATG
1 CTTCAAAAAACCTTAAAAAATG
*
19505143 CTTTAAAAAACCTTAAAAAA
1 CTTCAAAAAACCTTAAAAAA
19505163 CCTTAAGAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.29
Consensus pattern (22 bp):
CTTCAAAAAACCTTAAAAAATG
Found at i:19505146 original size:12 final size:11
Alignment explanation
Indices: 19505125--19505162 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
19505115 AAAAGACTTC
19505125 AAAAATCTTTA
1 AAAAATCTTTA
19505136 AAAAATGCTTTA
1 AAAAAT-CTTTA
*
19505148 AAAAA-CCTTA
1 AAAAATCTTTA
19505158 AAAAA
1 AAAAA
19505163 CCTTAAGAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 9 0.36
11 6 0.24
12 10 0.40
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.26
Consensus pattern (11 bp):
AAAAATCTTTA
Found at i:19505311 original size:11 final size:10
Alignment explanation
Indices: 19505234--19505804 Score: 84
Period size: 10 Copynumber: 55.5 Consensus size: 10
19505224 ATTATAAAAA
*
19505234 AAAAAACCTT
1 AAAAATCCTT
19505244 AAAAATCCTTT
1 AAAAATCC-TT
* * * *
19505255 GAAATTCATGA
1 AAAAATCCT-T
*
19505266 AAAAAACCTT
1 AAAAATCCTT
* *
19505276 TAAAATGCTT
1 AAAAATCCTT
* *
19505286 AGAATTACCTT
1 AAAAAT-CCTT
19505297 AAAAATCCTT
1 AAAAATCCTT
*
19505307 GAAAACA-CTTT
1 -AAAA-ATCCTT
*
19505318 AAAAAATCTTT
1 -AAAAATCCTT
**
19505329 AAAAAAATTATT
1 --AAAAATCCTT
*
19505341 TAAAAAACCTT
1 -AAAAATCCTT
19505352 AAAAATCCTT
1 AAAAATCCTT
*
19505362 AAAATTCCTT
1 AAAAATCCTT
*
19505372 GGAAACAT-CTT
1 --AAAAATCCTT
* *
19505383 TAAAATCTTT
1 AAAAATCCTT
** *
19505393 TGAAATCCAAT
1 AAAAATCC-TT
*
19505404 AAAAAACCTT
1 AAAAATCCTT
* *
19505414 TAAAATGCTT
1 AAAAATCCTT
* **
19505424 CAAAAGACTT
1 AAAAATCCTT
*
19505434 CAAAAATCTTT
1 -AAAAATCCTT
*
19505445 AAAAAATGACTT
1 -AAAAAT-CCTT
19505457 -AAAA-CCTT
1 AAAAATCCTT
* *
19505465 AAAAATTCAT
1 AAAAATCCTT
*
19505475 -AAAATTCTT
1 AAAAATCCTT
*
19505484 GAAAACA-CTTT
1 -AAAA-ATCCTT
19505495 AAAAATCCTT
1 AAAAATCCTT
*
19505505 TAAAAT-CTAT
1 AAAAATCCT-T
*
19505515 GAAAAAAACCTT
1 --AAAAATCCTT
*
19505527 AAAAATACTT
1 AAAAATCCTT
19505537 -AAAATGACCTT
1 AAAAAT--CCTT
* **
19505548 AAACATTTTT
1 AAAAATCCTT
*
19505558 AAAAGAACC-T
1 AAAA-ATCCTT
19505568 AAAAATCCTT
1 AAAAATCCTT
19505578 GAAAAAAT-CTT
1 --AAAAATCCTT
19505589 AAGAAAT-CTT
1 AA-AAATCCTT
* * *
19505599 TAAAATTCGT
1 AAAAATCCTT
**
19505609 AATAAATAATT
1 AA-AAATCCTT
*
19505620 AAAAA--ATT
1 AAAAATCCTT
19505628 AAAAATCCCTT
1 AAAAAT-CCTT
* *
19505639 -AAAA-CATA
1 AAAAATCCTT
*
19505647 AAAAATCTTT
1 AAAAATCCTT
* *
19505657 CAAATTCCTT
1 AAAAATCCTT
19505667 GAAAAATCTCTT
1 -AAAAATC-CTT
*
19505679 AAAAA-CTTT
1 AAAAATCCTT
* *
19505688 AAATATGCTT
1 AAAAATCCTT
19505698 AAAAGGAT-CTT
1 AAAA--ATCCTT
*
19505709 AAAAATACTT
1 AAAAATCCTT
** *
19505719 AAAAATTATGA
1 AAAAATCCT-T
*
19505730 AAAAAACCTT
1 AAAAATCCTT
*
19505740 AAAAATGC--
1 AAAAATCCTT
19505748 AAAAATCCTT
1 AAAAATCCTT
*
19505758 AAAAAATGCTT
1 -AAAAATCCTT
*
19505769 GAAAAAACCTTT
1 -AAAAATCC-TT
*
19505781 AAAAGT-CTT
1 AAAAATCCTT
*
19505790 AAAATTCCTT
1 AAAAATCCTT
*
19505800 GAAAA
1 AAAAA
19505805 CATTATAAAA
Statistics
Matches: 396, Mismatches: 115, Indels: 100
0.65 0.19 0.16
Matches are distributed among these distances:
8 20 0.05
9 52 0.13
10 158 0.40
11 125 0.32
12 39 0.10
13 2 0.01
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (10 bp):
AAAAATCCTT
Found at i:19505365 original size:9 final size:10
Alignment explanation
Indices: 19505340--19505804 Score: 86
Period size: 10 Copynumber: 45.6 Consensus size: 10
19505330 AAAAAATTAT
*
19505340 TTAAAAAACC
1 TTAAAAATCC
19505350 TTAAAAATCC
1 TTAAAAATCC
*
19505360 TTAAAATTCC
1 TTAAAAATCC
*
19505370 TTGGAAACAT-C
1 TT--AAAAATCC
* *
19505381 TTTAAAATCT
1 TTAAAAATCC
**
19505391 TTTGAAATCC
1 TTAAAAATCC
* *
19505401 AATAAAAAACC
1 -TTAAAAATCC
* *
19505412 TTTAAAATGC
1 TTAAAAATCC
* **
19505422 TTCAAAAGAC
1 TTAAAAATCC
*
19505432 TTCAAAAATCT
1 TT-AAAAATCC
*
19505443 TTAAAAAATGAC
1 TT-AAAAAT-CC
19505455 TT-AAAA-CC
1 TTAAAAATCC
*
19505463 TTAAAAATTC
1 TTAAAAATCC
* *
19505473 AT-AAAATTC
1 TTAAAAATCC
*
19505482 TTGAAAACA-CT
1 TT-AAAA-ATCC
19505493 TTAAAAATCC
1 TTAAAAATCC
*
19505503 TTTAAAAT-C
1 TTAAAAATCC
*
19505512 TATGAAAAAAACC
1 T-T--AAAAATCC
*
19505525 TTAAAAATAC
1 TTAAAAATCC
19505535 TT-AAAATGACC
1 TTAAAAAT--CC
* **
19505546 TTAAACATTT
1 TTAAAAATCC
*
19505556 TTAAAAGAACC
1 TTAAAA-ATCC
19505567 -TAAAAATCC
1 TTAAAAATCC
19505576 TTGAAAAAAT-C
1 TT--AAAAATCC
19505587 TTAAGAAAT-C
1 TTAA-AAATCC
* *
19505597 TTTAAAATTC
1 TTAAAAATCC
* **
19505607 GTAATAAATAA
1 TTAA-AAATCC
*
19505618 TTAAAAA--A
1 TTAAAAATCC
19505626 TTAAAAATCCC
1 TTAAAAAT-CC
*
19505637 TT-AAAA-CA
1 TTAAAAATCC
* *
19505645 TAAAAAATCT
1 TTAAAAATCC
* *
19505655 TTCAAATTCC
1 TTAAAAATCC
19505665 TTGAAAAATCTC
1 TT-AAAAATC-C
*
19505677 TTAAAAA-CT
1 TTAAAAATCC
* *
19505686 TTAAATATGC
1 TTAAAAATCC
19505696 TTAAAAGGAT-C
1 TTAAAA--ATCC
*
19505707 TTAAAAATAC
1 TTAAAAATCC
**
19505717 TTAAAAATTA
1 TTAAAAATCC
* *
19505727 TGAAAAAAACC
1 T-TAAAAATCC
*
19505738 TTAAAAATGC
1 TTAAAAATCC
19505748 --AAAAATCC
1 TTAAAAATCC
*
19505756 TTAAAAAATGC
1 TT-AAAAATCC
*
19505767 TTGAAAAAACC
1 TT-AAAAATCC
*
19505778 TTTAAAAGT-C
1 -TTAAAAATCC
*
19505788 TTAAAATTCC
1 TTAAAAATCC
19505798 TTGAAAA
1 TT-AAAA
19505805 CATTATAAAA
Statistics
Matches: 325, Mismatches: 86, Indels: 87
0.65 0.17 0.17
Matches are distributed among these distances:
8 20 0.06
9 52 0.16
10 134 0.41
11 88 0.27
12 29 0.09
13 2 0.01
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (10 bp):
TTAAAAATCC
Found at i:19505540 original size:21 final size:20
Alignment explanation
Indices: 19505495--19505603 Score: 67
Period size: 21 Copynumber: 5.2 Consensus size: 20
19505485 AAAACACTTT
* *
19505495 AAAAATCCTTTAAAATCTATGA
1 AAAAAACCTTAAAAATCT-T-A
19505517 AAAAAACCTTAAAAATACTTA
1 AAAAAACCTTAAAAAT-CTTA
** * *
19505538 AAATGACCTTAAACATTTTTA
1 AAAAAACCTTAAA-AATCTTA
* *
19505559 AAAGAACC-TAAAAATCCTTG
1 AAAAAACCTTAAAAAT-CTTA
* *
19505579 AAAAAATCTTAAGAAATCTTT
1 AAAAAACCTTAA-AAATCTTA
19505600 AAAA
1 AAAA
19505604 TTCGTAATAA
Statistics
Matches: 68, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
19 2 0.03
20 12 0.18
21 31 0.46
22 21 0.31
23 2 0.03
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAAAACCTTAAAAATCTTA
Found at i:19506282 original size:116 final size:116
Alignment explanation
Indices: 19506154--19506409 Score: 291
Period size: 116 Copynumber: 2.2 Consensus size: 116
19506144 AAATGCTTAA
** * * *
19506154 AAATCCATGAAAAAAATGTTTAAAATGCTTCAAATGACTTCAAAAATCCTTAAAAAAAGATTTTA
1 AAATCCATGAAAAAAACCTTAAAAATGCTTCAAAAGACTTCAAAAAT-CTTAAAAAAAGACTTTA
* * *
19506219 AAAA-CCTTAAAAATTCTTAAAATTCCTTGAAAACATATAAAAAATCTTTTG
65 AAAAGCCTTAAAAATCCATAAAATTCCATGAAAACATATAAAAAATCTTTTG
* * ** *
19506270 AAATTCATGAAAAAAACCTTAAAAATGCTTCAAAAGATTTCAAAAATCTTTTAAAAATACTTTAA
1 AAATCCATGAAAAAAACCTTAAAAATGCTTCAAAAGACTTCAAAAATCTTAAAAAAAGACTTTAA
* ** ** *
19506335 AAAGCCTTAAAAATCCATAAAATTTCATGAAAACACCTTTAAAATCCTTTG
66 AAAGCCTTAAAAATCCATAAAATTCCATGAAAACATATAAAAAATCTTTTG
** *
19506386 AACGCTAT-AAAAAAACCTTAAAAA
1 AAATCCATGAAAAAAACCTTAAAAA
19506410 AACTTAAAAT
Statistics
Matches: 116, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
115 33 0.28
116 83 0.72
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.29
Consensus pattern (116 bp):
AAATCCATGAAAAAAACCTTAAAAATGCTTCAAAAGACTTCAAAAATCTTAAAAAAAGACTTTAA
AAAGCCTTAAAAATCCATAAAATTCCATGAAAACATATAAAAAATCTTTTG
Found at i:19506409 original size:11 final size:11
Alignment explanation
Indices: 19506393--19506473 Score: 51
Period size: 11 Copynumber: 7.6 Consensus size: 11
19506383 TTGAACGCTA
19506393 TAAAAAAACCT
1 TAAAAAAACCT
19506404 TAAAAAAA-CT
1 TAAAAAAACCT
**
19506414 TAAAATGACCT
1 TAAAAAAACCT
* * *
19506425 TAAACATA-TT
1 TAAAAAAACCT
* *
19506435 TAAAAAAAGCA
1 TAAAAAAACCT
*
19506446 T-AAAAATCCT
1 TAAAAAAACCT
* *
19506456 TCAAAAAACTT
1 TAAAAAAACCT
19506467 TAAAAAA
1 TAAAAAA
19506474 TCTTTAAAAT
Statistics
Matches: 51, Mismatches: 16, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
10 22 0.43
11 29 0.57
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.23
Consensus pattern (11 bp):
TAAAAAAACCT
Found at i:19506417 original size:21 final size:21
Alignment explanation
Indices: 19506393--19506482 Score: 63
Period size: 21 Copynumber: 4.3 Consensus size: 21
19506383 TTGAACGCTA
19506393 TAAAAAAACCTTAAAAAAACT
1 TAAAAAAACCTTAAAAAAACT
** * * *
19506414 TAAAATGACCTTAAACATATT
1 TAAAAAAACCTTAAAAAAACT
* * **
19506435 TAAAAAAAGCATAAAAATCCT
1 TAAAAAAACCTTAAAAAAACT
* * *
19506456 TCAAAAAACTTTAAAAAATCT
1 TAAAAAAACCTTAAAAAAACT
*
19506477 TTAAAA
1 TAAAAA
19506483 TTCGTAATGA
Statistics
Matches: 50, Mismatches: 19, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.59, C:0.13, G:0.02, T:0.26
Consensus pattern (21 bp):
TAAAAAAACCTTAAAAAAACT
Found at i:19506521 original size:19 final size:20
Alignment explanation
Indices: 19506497--19506534 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19506487 TAATGAATAA
*
19506497 TTAAAAA-ATTAAAAATCTC
1 TTAAAAACATAAAAAATCTC
19506516 TTAAAAACATAAAAAATCT
1 TTAAAAACATAAAAAATCT
19506535 TTCAAAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.29
Consensus pattern (20 bp):
TTAAAAACATAAAAAATCTC
Found at i:19506689 original size:41 final size:41
Alignment explanation
Indices: 19506644--19506751 Score: 98
Period size: 41 Copynumber: 2.6 Consensus size: 41
19506634 AAATACTTTA
19506644 AAAATCTTTTAAAAATGACTTAAAAAACC-TTAAAAATCCAT-
1 AAAAT-TTTTAAAAATGACTTAAAAAACCATT-AAAATCCATG
* * * *
19506685 AAAATTTCTTGAAAA-CACCTTAAAAATCCATTGAAATCCATG
1 AAAATTT-TTAAAAATGA-CTTAAAAAACCATTAAAATCCATG
19506727 AAAATTTTTTTAAAAATG-CTTAAAA
1 AAAA--TTTTTAAAAATGACTTAAAA
19506752 TGACCATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
40 3 0.06
41 29 0.54
42 13 0.24
43 6 0.11
44 3 0.06
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (41 bp):
AAAATTTTTAAAAATGACTTAAAAAACCATTAAAATCCATG
Done.