Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 58 of 206
Found at i:16468029 original size:49 final size:49
Alignment explanation
Indices: 16467955--16468080 Score: 143
Period size: 51 Copynumber: 2.6 Consensus size: 49
16467945 AATTTATATT
** *
16467955 TATA-TTTAATTTT-TTATTATTTATTTGTA-AAAATAATTGTTTTAAAA
1 TATATTTTAATTTTATTATTATTTATTTGTACAAAA-AATCATTATAAAA
*
16468002 TCTATTTTAATTTTATTATTATTTATTTGTACCAAAAAATCATTATAAAA
1 TATATTTTAATTTTATTATTATTTATTTGTA-CAAAAAATCATTATAAAA
*
16468052 TATATTTTAAATTTAAATT-TTATTTATTT
1 TATATTTT-AATTT-TATTATTATTTATTT
16468081 ATTTTAAATT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
47 3 0.04
48 9 0.13
49 16 0.24
50 17 0.25
51 19 0.28
52 3 0.04
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.56
Consensus pattern (49 bp):
TATATTTTAATTTTATTATTATTTATTTGTACAAAAAATCATTATAAAA
Found at i:16485651 original size:95 final size:97
Alignment explanation
Indices: 16485465--16485658 Score: 311
Period size: 95 Copynumber: 2.0 Consensus size: 97
16485455 TTCAGATGAC
* * * * *
16485465 TTTAATTACTGGATTGCCCCCATTGCACTGTTTAAAAAAAATGAAAAGTAGAAAAAAAAAAGGTT
1 TTTAATTACCGGATTACCCCAATTGCACTGTTTAAAAAAAATGAAAAGGAGAAAAAAAAAAGCTT
* *
16485530 TTTAATGAATGCTGAGGCCTCGCTATTTTCAT
66 CTTAATGAATGCTGAGCCCTCGCTATTTTCAT
16485562 TTTAATTACCGGATTACCCCAATTGCACTGTTT-AAAAAAATGAAAAGGAG-AAAAAAAAAGCTT
1 TTTAATTACCGGATTACCCCAATTGCACTGTTTAAAAAAAATGAAAAGGAGAAAAAAAAAAGCTT
16485625 CTTAATGAATGCTGAGCCCTCGCTATTTTCAT
66 CTTAATGAATGCTGAGCCCTCGCTATTTTCAT
16485657 TT
1 TT
16485659 CGTCACTTCC
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
95 44 0.49
96 16 0.18
97 30 0.33
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.31
Consensus pattern (97 bp):
TTTAATTACCGGATTACCCCAATTGCACTGTTTAAAAAAAATGAAAAGGAGAAAAAAAAAAGCTT
CTTAATGAATGCTGAGCCCTCGCTATTTTCAT
Found at i:16486785 original size:14 final size:14
Alignment explanation
Indices: 16486765--16486799 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
16486755 AATCAACCTT
16486765 CACCTCCACCAATC
1 CACCTCCACCAATC
* *
16486779 TACCTCCACCGATC
1 CACCTCCACCAATC
16486793 CACCTCC
1 CACCTCC
16486800 GGTCCTCCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.23, C:0.57, G:0.03, T:0.17
Consensus pattern (14 bp):
CACCTCCACCAATC
Found at i:16488543 original size:24 final size:24
Alignment explanation
Indices: 16488516--16488563 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
16488506 GAATTTTTAA
16488516 GTTTTAAATTGTTTAAACTCAATT
1 GTTTTAAATTGTTTAAACTCAATT
*
16488540 GTTTTAAATTGTTTAAATTCAATT
1 GTTTTAAATTGTTTAAACTCAATT
16488564 TTTAAGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52
Consensus pattern (24 bp):
GTTTTAAATTGTTTAAACTCAATT
Found at i:16493864 original size:3 final size:3
Alignment explanation
Indices: 16493856--16493881 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16493846 CCCAAAGTGT
16493856 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
16493882 GTCAAGAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16496497 original size:13 final size:14
Alignment explanation
Indices: 16496472--16496524 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 14
16496462 AAAAAAGAAC
16496472 AATATATATATATA
1 AATATATATATATA
16496486 AATATA-ATATATA
1 AATATATATATATA
* *
16496499 AATAAACTATGA-AAA
1 AATATA-TAT-ATATA
16496514 AATATATATAT
1 AATATATATAT
16496525 GTGTGTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 13 0.41
14 9 0.28
15 9 0.28
16 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (14 bp):
AATATATATATATA
Found at i:16496659 original size:19 final size:20
Alignment explanation
Indices: 16496632--16496670 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
16496622 AAGCTTAAAA
*
16496632 ATTATATAT-ATATATATAT
1 ATTAAATATCATATATATAT
16496651 ATTAAATATGCATATATATA
1 ATTAAATAT-CATATATATA
16496671 AAATATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (20 bp):
ATTAAATATCATATATATAT
Found at i:16496665 original size:17 final size:17
Alignment explanation
Indices: 16496645--16496678 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16496635 ATATATATAT
*
16496645 ATATATATTAAATATGC
1 ATATATATAAAATATGC
16496662 ATATATATAAAATATGC
1 ATATATATAAAATATGC
16496679 GAATGTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (17 bp):
ATATATATAAAATATGC
Found at i:16506340 original size:26 final size:27
Alignment explanation
Indices: 16506284--16506344 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 27
16506274 TATTTAAAAG
16506284 GAAAAATAAATTTGGAAAATTCCATTT
1 GAAAAATAAATTTGGAAAATTCCATTT
* *
16506311 -AAAAAGTAAATTT-GAATA-TGCATTT
1 GAAAAA-TAAATTTGGAAAATTCCATTT
16506336 G-AAAATAAA
1 GAAAAATAAA
16506345 AAAAAATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
24 4 0.13
25 10 0.33
26 9 0.30
27 7 0.23
ACGTcount: A:0.52, C:0.05, G:0.11, T:0.31
Consensus pattern (27 bp):
GAAAAATAAATTTGGAAAATTCCATTT
Found at i:16507488 original size:21 final size:21
Alignment explanation
Indices: 16507462--16507514 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
16507452 AGCGGTGGCG
*
16507462 GTGAGATTAGTTACTATAGCA
1 GTGAGATTAGATACTATAGCA
* * *
16507483 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTATAGCA
16507504 GTGAGATTAGA
1 GTGAGATTAGA
16507515 AACAGTGGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.08, G:0.32, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACTATAGCA
Found at i:16507643 original size:17 final size:18
Alignment explanation
Indices: 16507617--16507656 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
16507607 TATATAATAG
* *
16507617 AAATTTTTTAAATTATTT
1 AAATTTTTAAAATTATTA
16507635 AAATTTTTAAAATTATTA
1 AAATTTTTAAAATTATTA
16507653 AAAT
1 AAAT
16507657 ATGTGAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AAATTTTTAAAATTATTA
Found at i:16514323 original size:2 final size:2
Alignment explanation
Indices: 16514316--16514340 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16514306 CGTATCTAGT
16514316 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16514341 GTGGCAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16516354 original size:12 final size:12
Alignment explanation
Indices: 16516337--16516362 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16516327 TGACTCTTTA
16516337 TAGTATTCAAGT
1 TAGTATTCAAGT
16516349 TAGTATTCAAGT
1 TAGTATTCAAGT
16516361 TA
1 TA
16516363 TGATCCCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
TAGTATTCAAGT
Found at i:16522174 original size:43 final size:43
Alignment explanation
Indices: 16522012--16522182 Score: 120
Period size: 43 Copynumber: 4.0 Consensus size: 43
16522002 CATAGGATTC
* * * **
16522012 CGATATGTGATTACATGTAAGGCCACGTCTATGACGTTGGCAT
1 CGATATTTGATTTCATGTAAGACCACGTCTGGGACGTTGGCAT
* * * * * *
16522055 CGAT-TTGCGATTTACGTGTAAGACCATGTCTGGG-CATCGACAT
1 CGATATT-TGATTT-CATGTAAGACCACGTCTGGGACGTTGGCAT
** * *
16522098 CG-TATAGGAGTTT-GTGTAAGACC-CTGTCGGGGACAG-TGGCAT
1 CGATATTTGA-TTTCATGTAAGACCAC-GTCTGGGAC-GTTGGCAT
16522140 CGATATTTGATTTCATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATTTGATTTCATGTAAGACCACGTCTGGGACGTTGGCAT
16522183 TGAATGAGCT
Statistics
Matches: 95, Mismatches: 22, Indels: 22
0.68 0.16 0.16
Matches are distributed among these distances:
41 16 0.17
42 15 0.16
43 48 0.51
44 16 0.17
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (43 bp):
CGATATTTGATTTCATGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:16524403 original size:54 final size:54
Alignment explanation
Indices: 16524316--16524431 Score: 187
Period size: 54 Copynumber: 2.1 Consensus size: 54
16524306 GTTGAGACTA
* *
16524316 ATTCAGAATAGGTTACAAAATCGATGACAACTCTATAGAGAGGTAGAACACCGAT
1 ATTC-GAATAGGTTACAAAATCGATGACAACTCTACAGAGAGGTAAAACACCGAT
* *
16524371 ATTCGAATAGGTTACAAAATTGATGACAACTCTACAGAGAGGTAAAAGACCGAT
1 ATTCGAATAGGTTACAAAATCGATGACAACTCTACAGAGAGGTAAAACACCGAT
16524425 ATTCGAA
1 ATTCGAA
16524432 AATAATGTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
54 53 0.93
55 4 0.07
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (54 bp):
ATTCGAATAGGTTACAAAATCGATGACAACTCTACAGAGAGGTAAAACACCGAT
Found at i:16530042 original size:23 final size:22
Alignment explanation
Indices: 16529999--16530056 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
16529989 AAAGGATATC
* *
16529999 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
16530020 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
16530043 TGCATATCATATCT
1 TACAAATCATATCT
16530057 AAGATTGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:16534964 original size:3 final size:3
Alignment explanation
Indices: 16534956--16535515 Score: 1120
Period size: 3 Copynumber: 186.7 Consensus size: 3
16534946 NNNNNNNNNN
16534956 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16535004 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16535052 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16535100 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16535148 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16535196 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16535244 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16535292 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16535340 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16535388 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16535436 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16535484 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16535516 ATCAATCATG
Statistics
Matches: 557, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 557 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16535734 original size:29 final size:28
Alignment explanation
Indices: 16535662--16535739 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 28
16535652 AATAGATAAA
*
16535662 AATTATAAAATATAA-ATATATATATGT
1 AATTATAAAAAATAATATATATATATGT
* * *
16535689 -ATATATAAGAAA-AATATATATGTGTGT
1 AAT-TATAAAAAATAATATATATATATGT
16535716 GAATTATAAAAAATAATATATATA
1 -AATTATAAAAAATAATATATATA
16535740 AATATACATA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
26 4 0.10
27 17 0.43
28 8 0.20
29 11 0.28
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (28 bp):
AATTATAAAAAATAATATATATATATGT
Found at i:16535840 original size:36 final size:36
Alignment explanation
Indices: 16535800--16535875 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
16535790 TGAAACATAG
*
16535800 AAAATATATAAAAGTATGT-GTATATATATAT-TTATA
1 AAAAT-TA-AAAAATATGTAGTATATATATATATTATA
* *
16535836 AAAATTAAAAAATGTGTACGTATATGTATATATTATA
1 AAAATTAAAAAATATGTA-GTATATATATATATTATA
16535873 AAA
1 AAA
16535876 CGTATGTATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 8 0.24
35 2 0.06
36 16 0.47
37 8 0.24
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (36 bp):
AAAATTAAAAAATATGTAGTATATATATATATTATA
Found at i:16536432 original size:23 final size:22
Alignment explanation
Indices: 16536389--16536446 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
16536379 AAAGGATATC
* *
16536389 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
16536410 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
16536433 TGCATATCATATCT
1 TACAAATCATATCT
16536447 AAGATTGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:16537367 original size:100 final size:100
Alignment explanation
Indices: 16537274--16538239 Score: 582
Period size: 100 Copynumber: 9.3 Consensus size: 100
16537264 GCCAAAGAGA
* * * * * *
16537274 TAAGATTTGCCGTTGTGGCTTTAATCTATTTAATTGCAATGTCGGGGGAACCAGATTCGCCGTCG
1 TAAGATTCGCCGTTGTGGCTTCAATCTATTTAACTGCAATGTTGGGGAAACAAGATTCGCCGTCG
*
16537339 TAGCTTCAATCTATTCCACTACACCGCCAGGGAAG
66 TAGCTTCAATCTGTTCCACTACACCGCCAGGGAAG
*
16537374 TAAGATTCGCCGTTGTGGCTTCAATCCATTTAACTGCAATGTTGGGGAAACAAGATTCGCCGTCG
1 TAAGATTCGCCGTTGTGGCTTCAATCTATTTAACTGCAATGTTGGGGAAACAAGATTCGCCGTCG
16537439 TAGCTTCAATCTGTTCCACTACACCGCCAGGGAAG
66 TAGCTTCAATCTGTTCCACTACACCGCCAGGGAAG
*
16537474 TAAGATTTC-CCGTTGTGGCTTCAATCTATTTAACTGCAATGTTGGAGAAACAAGATTCGCCGTC
1 TAAGA-TTCGCCGTTGTGGCTTCAATCTATTTAACTGCAATGTTGGGGAAACAAGATTCGCCGTC
16537538 GTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAG
65 GTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAG
** * **** * * * *
16537574 TAAGATTCGCCGTTGTGGCTTCAATCTATTCCACTGTAATGTCAAAGAGATAAGATTCGCTGCCC
1 TAAGATTCGCCGTTGTGGCTTCAATCTATTTAACTGCAATGTTGGGGAAACAAGATTCGCCG-TC
** * * * * * * **
16537639 ACAGCTTTAATCCGCTCCACTTCATCTAATCTAAGTCTTAATGCCAG
65 GTAGCTTCAATCTGTTCCAC-T-A-C--A-C--CG-C--CAGGGAAG
** ** * * * * * * * * **
16537686 GGAGATAAG--ATTCGCTGCCCTCAGCTTTAATCT-ACTCCACTATAACGTTAGGGAAGTAAGAT
1 TAAGATTCGCCGTT-G-TGGCTTCA-ATCT-ATTTAACTGCA--AT---GTTGGGGAAACAAGAT
** * * ** * ** **
16537748 TCGCCGTTTTGGCTTCAATCTATTTGACTGCAATGCCA-ATAAG
57 TCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAG
** **** * * ** * ** ** *
16537791 -ATAGTATTCGTTGCCCACGGCTTCAATCCGCTCCACTTCAGCTATTTTAATTCTTAACGCTAAG
1 TA-AG-ATTCGCCG-TTGTGGCTTCAAT---CT--A-TTTA---ACTGCAA-TGTT-GGGGAAAC
* ** ** * * * * ** * *
16537855 GAGATAAG-ATTCGCT-GCCCTC-AGCTTTAATCTGCTCCGCTATAACGTCAGGGAAG
52 AAGATTCGCCGTCG-TAG-CTTCAATCTGT--TC--CACTAC---ACCGCCAGGGAAG
* * * * * *
16537910 TAAGATTCGCCATTTTGGCTTCAATCTATTTGACTGCAATGTCGGGGAACCAAGATTCACCGTCG
1 TAAGATTCGCCGTTGTGGCTTCAATCTATTTAACTGCAATGTTGGGGAAACAAGATTCGCCGTCG
* *
16537975 TAGCTTCAATTTGTTCCACTACACCGCCAAGGAAG
66 TAGCTTCAATCTGTTCCACTACACCGCCAGGGAAG
** *
16538010 TAAGATTCGCCGTTGTGGCTTCAATCTATTTAACTGCAATGTTGGGGAAACAAGATTTACCGTCA
1 TAAGATTCGCCGTTGTGGCTTCAATCTATTTAACTGCAATGTTGGGGAAACAAGATTCGCCGTCG
16538075 TAGCTTCAATCTGTTCCACTACACCGCCAGGGAAG
66 TAGCTTCAATCTGTTCCACTACACCGCCAGGGAAG
* * *
16538110 TAAGATTCGCCGTTGTGGCTTCAATCTTTTTAACTACAATGTTGGAGAAACAAGATTCGCCGTCG
1 TAAGATTCGCCGTTGTGGCTTCAATCTATTTAACTGCAATGTTGGGGAAACAAGATTCGCCGTCG
16538175 TAGCTTCAATCTGTTCCACTACACCGCCAGGGAAG
66 TAGCTTCAATCTGTTCCACTACACCGCCAGGGAAG
16538210 TAAGATTCGCCGTTGTGGCTTCAATCTATT
1 TAAGATTCGCCGTTGTGGCTTCAATCTATT
16538240 CCATTGTAAT
Statistics
Matches: 652, Mismatches: 161, Indels: 106
0.71 0.18 0.12
Matches are distributed among these distances:
99 3 0.00
100 459 0.70
101 19 0.03
102 1 0.00
103 4 0.01
104 1 0.00
105 6 0.01
106 16 0.02
107 15 0.02
108 5 0.01
109 3 0.00
110 4 0.01
111 12 0.02
112 29 0.04
113 8 0.01
114 6 0.01
115 8 0.01
116 1 0.00
117 20 0.03
118 26 0.04
119 5 0.01
120 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (100 bp):
TAAGATTCGCCGTTGTGGCTTCAATCTATTTAACTGCAATGTTGGGGAAACAAGATTCGCCGTCG
TAGCTTCAATCTGTTCCACTACACCGCCAGGGAAG
Found at i:16537380 original size:50 final size:50
Alignment explanation
Indices: 16537326--16537608 Score: 282
Period size: 50 Copynumber: 5.7 Consensus size: 50
16537316 CGGGGGAACC
16537326 AGATTCGCCGTCGTAGCTTCAATCTATTCCACTACACCGCCAGGGAAGTA
1 AGATTCGCCGTCGTAGCTTCAATCTATTCCACTACACCGCCAGGGAAGTA
* * * ** * ** *** **
16537376 AGATTCGCCGTTGTGGCTTCAATCCATTTAACTGCAATGTTGGGGAAACA
1 AGATTCGCCGTCGTAGCTTCAATCTATTCCACTACACCGCCAGGGAAGTA
*
16537426 AGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTA
1 AGATTCGCCGTCGTAGCTTCAATCTATTCCACTACACCGCCAGGGAAGTA
* * ** * ** ** **
16537476 AGATTTC-CCGTTGTGGCTTCAATCTATTTAACTGCAATG-TTGGAGAAACA
1 AGA-TTCGCCGTCGTAGCTTCAATCTATTCCACTACACCGCCAGG-GAAGTA
*
16537526 AGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTA
1 AGATTCGCCGTCGTAGCTTCAATCTATTCCACTACACCGCCAGGGAAGTA
* *
16537576 AGATTCGCCGTTGTGGCTTCAATCTATTCCACT
1 AGATTCGCCGTCGTAGCTTCAATCTATTCCACT
16537609 GTAATGTCAA
Statistics
Matches: 175, Mismatches: 54, Indels: 8
0.74 0.23 0.03
Matches are distributed among these distances:
49 5 0.03
50 165 0.94
51 5 0.03
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (50 bp):
AGATTCGCCGTCGTAGCTTCAATCTATTCCACTACACCGCCAGGGAAGTA
Found at i:16537633 original size:50 final size:49
Alignment explanation
Indices: 16537241--16537609 Score: 247
Period size: 50 Copynumber: 7.4 Consensus size: 49
16537231 ACTACCTTTA
* * * * ** *
16537241 GCTTTAATCTGTTCTACTGTAACGCCAAAGAGATAAGATTTGCCGTTGTG
1 GCTTCAATCTATTCCACTGCAACGCCAGGGA-ATAAGATTCGCCGTTGTG
* ** * * ** ** * *
16537291 GCTTTAATCTATTTAATTGCAATGTCGGGGGAACCAGATTCGCCGTCGTA
1 GCTTCAATCTATTCCACTGCAACG-CCAGGGAATAAGATTCGCCGTTGTG
* *
16537341 GCTTCAATCTATTCCACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTG
1 GCTTCAATCTATTCCACTGCAACGCCAGGGAA-TAAGATTCGCCGTTGTG
* ** * *** * * *
16537391 GCTTCAATCCATTTAACTGCAATGTTGGGGAAACAAGATTCGCCGTCGTA
1 GCTTCAATCTATTCCACTGCAACGCCAGGG-AATAAGATTCGCCGTTGTG
* * *
16537441 GCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTTC-CCGTTGTG
1 GCTTCAATCTATTCCACTGCAACGCCAGGGAA-TAAGA-TTCGCCGTTGTG
** * ** * * *
16537491 GCTTCAATCTATTTAACTGCAATG-TTGGAGAAACAAGATTCGCCGTCGTA
1 GCTTCAATCTATTCCACTGCAACGCCAGG-G-AATAAGATTCGCCGTTGTG
* * *
16537541 GCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTG
1 GCTTCAATCTATTCCACTGCAACGCCAGGGAA-TAAGATTCGCCGTTGTG
16537591 GCTTCAATCTATTCCACTG
1 GCTTCAATCTATTCCACTG
16537610 TAATGTCAAA
Statistics
Matches: 232, Mismatches: 77, Indels: 20
0.71 0.23 0.06
Matches are distributed among these distances:
49 15 0.06
50 205 0.88
51 12 0.05
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.30
Consensus pattern (49 bp):
GCTTCAATCTATTCCACTGCAACGCCAGGGAATAAGATTCGCCGTTGTG
Found at i:16537860 original size:168 final size:168
Alignment explanation
Indices: 16537566--16537950 Score: 567
Period size: 168 Copynumber: 2.3 Consensus size: 168
16537556 ACTACACCGC
* ** * *
16537566 CAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTATTCCACTGTAATGTCAAAGAGATAAGATT
1 CAGGGAAGTAAGATTCGCCGTTTTGGCTTCAATCTATTTGACTGCAATGCCAAAGAGATAAGATT
* * * *
16537631 CGCTGCCCACAGCTTTAATCCGCTCCACTTCATCTAATCTAAGTCTTAATGCCAGGGAGATAAGA
66 CGCTGCCCACAGCTTCAATCCGCTCCACTTCAGCTAATCTAAGTCTTAACGCCAAGGAGATAAGA
16537696 TTCGCTGCCCTCAGCTTTAATCTACTCCACTATAACGT
131 TTCGCTGCCCTCAGCTTTAATCTACTCCACTATAACGT
*
16537734 TAGGGAAGTAAGATTCGCCGTTTTGGCTTCAATCTATTTGACTGCAATGCCAATA-AGAT-AGTA
1 CAGGGAAGTAAGATTCGCCGTTTTGGCTTCAATCTATTTGACTGCAATGCCAA-AGAGATAAG-A
* * * * * *
16537797 TTCGTTGCCCACGGCTTCAATCCGCTCCACTTCAGCTATTTTAATTCTTAACGCTAAGGAGATAA
64 TTCGCTGCCCACAGCTTCAATCCGCTCCACTTCAGCTAATCTAAGTCTTAACGCCAAGGAGATAA
* *
16537862 GATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTATAACGT
129 GATTCGCTGCCCTCAGCTTTAATCTACTCCACTATAACGT
*
16537902 CAGGGAAGTAAGATTCGCCATTTTGGCTTCAATCTATTTGACTGCAATG
1 CAGGGAAGTAAGATTCGCCGTTTTGGCTTCAATCTATTTGACTGCAATG
16537951 TCGGGGAACC
Statistics
Matches: 195, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
167 2 0.01
168 192 0.98
169 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (168 bp):
CAGGGAAGTAAGATTCGCCGTTTTGGCTTCAATCTATTTGACTGCAATGCCAAAGAGATAAGATT
CGCTGCCCACAGCTTCAATCCGCTCCACTTCAGCTAATCTAAGTCTTAACGCCAAGGAGATAAGA
TTCGCTGCCCTCAGCTTTAATCTACTCCACTATAACGT
Found at i:16537958 original size:50 final size:50
Alignment explanation
Indices: 16537897--16538242 Score: 262
Period size: 50 Copynumber: 6.9 Consensus size: 50
16537887 GCTCCGCTAT
* * * ** *
16537897 AACGTCAGGGAAGTAAGATTCGCCATTTTGGCTTCAATCTATTTGACTGC
1 AACGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTATTCCACTAC
* * * ** * * * * *
16537947 AATGTCGGGGAACCAAGATTCACCGTCGTAGCTTCAATTTGTTCCACTAC
1 AACGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTATTCCACTAC
* * ** *
16537997 ACCGCCAAGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTATTTAACTGC
1 AACGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTATTCCACTAC
* *** ** ** ** * *
16538047 AATGTTGGGGAAACAAGATTTACCGTCATAGCTTCAATCTGTTCCACTAC
1 AACGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTATTCCACTAC
* * **
16538097 ACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAACTAC
1 AACGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTATTCCACTAC
* ** ** * * *
16538147 AATG-TTGGAGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTAC
1 AACGCCAGG-GAAGTAAGATTCGCCGTTGTGGCTTCAATCTATTCCACTAC
*
16538197 ACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTATTCCA
1 AACGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTATTCCA
16538243 TTGTAATGCC
Statistics
Matches: 213, Mismatches: 81, Indels: 4
0.71 0.27 0.01
Matches are distributed among these distances:
49 2 0.01
50 209 0.98
51 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (50 bp):
AACGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTATTCCACTAC
Found at i:16543264 original size:16 final size:15
Alignment explanation
Indices: 16543232--16543274 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
16543222 TTTGTAAAGT
*
16543232 TTTA-TTTTTATTTA
1 TTTATTTTTTATTAA
16543246 TTTATTTTTTACTTAA
1 TTTATTTTTTA-TTAA
16543262 TTTAATTTTTTAT
1 TTT-ATTTTTTAT
16543275 GTAAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 4 0.16
15 6 0.24
16 7 0.28
17 8 0.32
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATTTTTTATTAA
Found at i:16546244 original size:18 final size:18
Alignment explanation
Indices: 16546221--16546255 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
16546211 TTATGGGGCA
16546221 TTTATTCTATTT-GTTTTT
1 TTTATT-TATTTAGTTTTT
16546239 TTTATTTATTTAGTTTT
1 TTTATTTATTTAGTTTT
16546256 ATATAAGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (18 bp):
TTTATTTATTTAGTTTTT
Found at i:16546494 original size:45 final size:44
Alignment explanation
Indices: 16546430--16546541 Score: 136
Period size: 45 Copynumber: 2.5 Consensus size: 44
16546420 GTTCCCTTCC
* * * *
16546430 TTCAACCTACTCCACTGCAACTTCAGGGAGATAAGATTTGT-CAT
1 TTCAATCTACTCCATTGCAACTTCAGAGAGATAAGACTTGTAC-T
* *
16546474 CTTCAGTCTACTTCATTGCAACTTCAGAGAGATAAGACTTGTACT
1 -TTCAATCTACTCCATTGCAACTTCAGAGAGATAAGACTTGTACT
*
16546519 TTCAATCTGCTCCATTGCAACTT
1 TTCAATCTACTCCATTGCAACTT
16546542 AAGATTCGTA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
44 20 0.35
45 36 0.63
46 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (44 bp):
TTCAATCTACTCCATTGCAACTTCAGAGAGATAAGACTTGTACT
Found at i:16546711 original size:44 final size:44
Alignment explanation
Indices: 16546658--16546990 Score: 135
Period size: 44 Copynumber: 7.6 Consensus size: 44
16546648 CGATATGCTG
*
16546658 CACTACTGCTTAGGGAGACAGGA-TCTACAATCTTCAACCTACTC
1 CACTACTGCTTAGGGAGATAGGATTC-ACAATCTTCAACCTACTC
* * ** * * * *
16546702 CACTGCTGCTCAGGGAGATAGGATTGGC-AGCTTAAATCTGCTTC
1 CACTACTGCTTAGGGAGATAGGATTCACAATCTTCAACCTAC-TC
* * ** * * *
16546746 C-CTACTACATT-GGGAGGATAAGATTCACCGTCTTCGATCTGCTC
1 CACTACTGC-TTAGGGA-GATAGGATTCACAATCTTCAACCTACTC
* * * *
16546790 CACTACTGCTTGGGGAGACAGGA-TCTACAATCCTCAACTTACTC
1 CACTACTGCTTAGGGAGATAGGATTC-ACAATCTTCAACCTACTC
* * ***** * * *
16546834 CACTGCTGCTCAGGGAGATAGGATT-GGTGGCTTAAATCTGCTTC
1 CACTACTGCTTAGGGAGATAGGATTCACAATCTTCAACCTAC-TC
* * * ** * * *
16546878 C-CTACTACATT-GGGAGGATAAGATTCGCCGTCTTCGATCTGCTC
1 CACTACTGC-TTAGGGA-GATAGGATTCACAATCTTCAACCTACTC
* *
16546922 CACTACTGCTTGGGGAGACAGGA-TCTACAATCTTCAACCTACTC
1 CACTACTGCTTAGGGAGATAGGATTC-ACAATCTTCAACCTACTC
* * *
16546966 CGCTGCTGCTCAGGGAGATAGGATT
1 CACTACTGCTTAGGGAGATAGGATT
16546991 GGTAATTTGT
Statistics
Matches: 206, Mismatches: 66, Indels: 33
0.68 0.22 0.11
Matches are distributed among these distances:
43 37 0.18
44 126 0.61
45 43 0.21
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (44 bp):
CACTACTGCTTAGGGAGATAGGATTCACAATCTTCAACCTACTC
Found at i:16546993 original size:132 final size:132
Alignment explanation
Indices: 16546645--16546994 Score: 619
Period size: 132 Copynumber: 2.7 Consensus size: 132
16546635 GATTTGCTGC
* * *
16546645 CTTCGATATGCTGCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTG
1 CTTCGATCTGCTCCACTACTGCTTGGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTG
*
16546710 CTCAGGGAGATAGGATTGGCAGCTTAAATCTGCTTCCCTACTACATTGGGAGGATAAGATTCACC
66 CTCAGGGAGATAGGATTGGTAGCTTAAATCTGCTTCCCTACTACATTGGGAGGATAAGATTCACC
16546775 GT
131 GT
* *
16546777 CTTCGATCTGCTCCACTACTGCTTGGGGAGACAGGATCTACAATCCTCAACTTACTCCACTGCTG
1 CTTCGATCTGCTCCACTACTGCTTGGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTG
* *
16546842 CTCAGGGAGATAGGATTGGTGGCTTAAATCTGCTTCCCTACTACATTGGGAGGATAAGATTCGCC
66 CTCAGGGAGATAGGATTGGTAGCTTAAATCTGCTTCCCTACTACATTGGGAGGATAAGATTCACC
16546907 GT
131 GT
*
16546909 CTTCGATCTGCTCCACTACTGCTTGGGGAGACAGGATCTACAATCTTCAACCTACTCCGCTGCTG
1 CTTCGATCTGCTCCACTACTGCTTGGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTG
16546974 CTCAGGGAGATAGGATTGGTA
66 CTCAGGGAGATAGGATTGGTA
16546995 ATTTGTAACT
Statistics
Matches: 206, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 206 1.00
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (132 bp):
CTTCGATCTGCTCCACTACTGCTTGGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTG
CTCAGGGAGATAGGATTGGTAGCTTAAATCTGCTTCCCTACTACATTGGGAGGATAAGATTCACC
GT
Found at i:16547090 original size:50 final size:50
Alignment explanation
Indices: 16547036--16547211 Score: 181
Period size: 50 Copynumber: 3.5 Consensus size: 50
16547026 TCGAGGAAAC
* * * * * *
16547036 AAGATTTGTTGTTGTAGCTTCAATTTGTTCCACTATACCGCCAGGAAAGT
1 AAGATTTGCTATTGTAGCTTCAATCTGTTCCACTACACCGTCAGGGAAGT
* * ** * ** * **
16547086 AAGATTCGCTATTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAACC
1 AAGATTTGCTATTGTAGCTTCAATCTGTTCCACTACACCGTCAGGGAAGT
* * *
16547136 AAGATTTACTGTCGTAGCTTCAATCTGTTCCACTACACCGTCAGGGAAGT
1 AAGATTTGCTATTGTAGCTTCAATCTGTTCCACTACACCGTCAGGGAAGT
16547186 AAGATTTGCTATTGTAGCTTCAATCT
1 AAGATTTGCTATTGTAGCTTCAATCT
16547212 ATTTAACTGC
Statistics
Matches: 94, Mismatches: 32, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
50 94 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (50 bp):
AAGATTTGCTATTGTAGCTTCAATCTGTTCCACTACACCGTCAGGGAAGT
Found at i:16547141 original size:100 final size:100
Alignment explanation
Indices: 16546997--16547225 Score: 341
Period size: 100 Copynumber: 2.3 Consensus size: 100
16546987 GATTGGTAAT
* * * ** * *
16546997 TTGTAACTTTAATCTGTTTAACTGCAATGTCGAGGAAACAAGATTTGTTGTTGTAGCTTCAATTT
1 TTGTAGCTTCAATCTATTTAACTGCAATGTCGAGGAAACAAGATTTACTGTCGTAGCTTCAATCT
*
16547062 GTTCCACTATACCGCCAGGAAAGTAAGATTCGCTA
66 GTTCCACTACACCGCCAGGAAAGTAAGATTCGCTA
* *
16547097 TTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAACCAAGATTTACTGTCGTAGCTTCAATCT
1 TTGTAGCTTCAATCTATTTAACTGCAATGTCGAGGAAACAAGATTTACTGTCGTAGCTTCAATCT
* * *
16547162 GTTCCACTACACCGTCAGGGAAGTAAGATTTGCTA
66 GTTCCACTACACCGCCAGGAAAGTAAGATTCGCTA
16547197 TTGTAGCTTCAATCTATTTAACTGCAATG
1 TTGTAGCTTCAATCTATTTAACTGCAATG
16547226 CCAAAGAGAT
Statistics
Matches: 116, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 116 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (100 bp):
TTGTAGCTTCAATCTATTTAACTGCAATGTCGAGGAAACAAGATTTACTGTCGTAGCTTCAATCT
GTTCCACTACACCGCCAGGAAAGTAAGATTCGCTA
Found at i:16547511 original size:50 final size:50
Alignment explanation
Indices: 16547448--16547555 Score: 144
Period size: 50 Copynumber: 2.2 Consensus size: 50
16547438 AGAGAAGTAA
* * *
16547448 GATTCGCTATTGTAGCTTCAATCTATTTAACTGCAATGCCAAATAGATAG
1 GATTCGCTATTGTAGCTTCAACCTATTCAACTGCAATGCCAAAGAGATAG
* * * * *
16547498 GATTCGTTGTTGTAGCTTCAACCTATTCCATTGTAATGCCAAAGAGATAG
1 GATTCGCTATTGTAGCTTCAACCTATTCAACTGCAATGCCAAAGAGATAG
16547548 GATTCGCT
1 GATTCGCT
16547556 GCCCACAGCT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (50 bp):
GATTCGCTATTGTAGCTTCAACCTATTCAACTGCAATGCCAAAGAGATAG
Found at i:16547652 original size:310 final size:313
Alignment explanation
Indices: 16547197--16547821 Score: 891
Period size: 310 Copynumber: 2.0 Consensus size: 313
16547187 AGATTTGCTA
* *
16547197 TTGTAGCTTCAATCTATTTAACTGCAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTCAATC
1 TTGTAGCTTCAACCTATTCAACTGCAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTCAATC
*
16547262 TGCTCCACTTCAGCTATTTCAAGTCTTAACATCAGGGAGATAAGATTCACTGCCCTCAGCTTTAA
66 TGCTCCACTTCAGCTATTTCAAGTCTTAACACCAGGGAGATAAGATTCACTGCCCTCAGCTTTAA
** * *
16547327 TCTGCTCTGCTATAACGTCAGGGAAGTAAGATTCGCCGTTTTGGCTTTAA-TTT-T-CAATGTCG
131 TCTGCTCCACTATAACGTCAGGGAAGTAAGATTCACCGTTTTGGCTTCAACTTTATGCAATGTCG
* * * * * *
16547389 GGAAACCAAGATTCACTGTCGTAGTTTCAATCTGTTCCATTACACCGCCAGAGAAG-TAAGATTC
196 GGAAACCAAGATTCAATATCATAGCTTCAATCTGTTCCACTACACCACCAG-GAAGCTAAGATTC
* *
16547453 GCTATTGTAGCTTCAATCTATTTAACTGCAATGCCAAA-TAGATAGGATTCGTTG
260 GCCATTGTAGCTTCAATCTATTCAACTGCAATGCCAAAGT-GATAGGATTCGTTG
* * * *
16547507 TTGTAGCTTCAACCTATTCCATTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATC
1 TTGTAGCTTCAACCTATTCAACTGCAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTCAATC
* * * *
16547572 TGCTTCACTTCAGCTATTTCAAGTCTTAACGCCATGGAGATAAGATTCGCTGCCCTCAGCTTTAA
66 TGCTCCACTTCAGCTATTTCAAGTCTTAACACCAGGGAGATAAGATTCACTGCCCTCAGCTTTAA
16547637 TCTGCTCCACTATAACGTCAGGGAAGTAAGATTCACCGTTTTGGCTTCAATCTCTTTAACTGCAA
131 TCTGCTCCACTATAACGTCAGGGAAGTAAGATTCACCGTTTTGGCTTCAA---CTTT-A-TGCAA
* * *
16547702 TGTTGGGGAACCAAGATTCAATATCATAGCTTCAATCTGTTCCACTACACCACCAGGGAGCTAAG
191 TGTCGGGAAACCAAGATTCAATATCATAGCTTCAATCTGTTCCACTACACCACCAGGAAGCTAAG
* * *
16547767 ATTCGCCGTTGTAGCTTCAATCTATTCCACTGTAATGCCAAAGTGATAGGATTCG
256 ATTCGCCATTGTAGCTTCAATCTATTCAACTGCAATGCCAAAGTGATAGGATTCG
16547822 CTGCCCACAG
Statistics
Matches: 276, Mismatches: 29, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
310 165 0.60
314 3 0.01
317 4 0.01
318 103 0.37
319 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (313 bp):
TTGTAGCTTCAACCTATTCAACTGCAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTCAATC
TGCTCCACTTCAGCTATTTCAAGTCTTAACACCAGGGAGATAAGATTCACTGCCCTCAGCTTTAA
TCTGCTCCACTATAACGTCAGGGAAGTAAGATTCACCGTTTTGGCTTCAACTTTATGCAATGTCG
GGAAACCAAGATTCAATATCATAGCTTCAATCTGTTCCACTACACCACCAGGAAGCTAAGATTCG
CCATTGTAGCTTCAATCTATTCAACTGCAATGCCAAAGTGATAGGATTCGTTG
Found at i:16548070 original size:44 final size:44
Alignment explanation
Indices: 16547990--16548075 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 44
16547980 AGACAGGATC
* * * * *
16547990 TACAATCTTTCACTTATTCCATTGTTATTTAAGGAGCTAGGACT
1 TACAATCTTCCACCTATTCCACTGCTATTCAAGGAGCTAGGACT
* *
16548034 TACAATCTTCCACCTATTCCACTGCTGTTCAGGGAGCTAGGA
1 TACAATCTTCCACCTATTCCACTGCTATTCAAGGAGCTAGGA
16548076 TTTGTGGTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (44 bp):
TACAATCTTCCACCTATTCCACTGCTATTCAAGGAGCTAGGACT
Found at i:16550146 original size:10 final size:10
Alignment explanation
Indices: 16550133--16550157 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
16550123 CTTTTCTTTT
16550133 TTTTCCATCA
1 TTTTCCATCA
16550143 TTTTCCATCA
1 TTTTCCATCA
16550153 TTTTC
1 TTTTC
16550158 ATTTTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.28, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTTCCATCA
Found at i:16550920 original size:8 final size:8
Alignment explanation
Indices: 16550907--16550934 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
16550897 ATATACAAAA
16550907 GAATTTAT
1 GAATTTAT
16550915 GAATTTAT
1 GAATTTAT
16550923 GAATTTAT
1 GAATTTAT
16550931 GAAT
1 GAAT
16550935 AATTATTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.46
Consensus pattern (8 bp):
GAATTTAT
Found at i:16552273 original size:19 final size:20
Alignment explanation
Indices: 16552235--16552275 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
16552225 AATAGTCTTT
16552235 AATGCATATAATGTAATGCA
1 AATGCATATAATGTAATGCA
16552255 AATGCATGA-AATG-AATGCA
1 AATGCAT-ATAATGTAATGCA
16552274 AA
1 AA
16552276 AAGAGACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 11 0.55
21 1 0.05
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24
Consensus pattern (20 bp):
AATGCATATAATGTAATGCA
Found at i:16554131 original size:3 final size:3
Alignment explanation
Indices: 16554123--16554173 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
16554113 GATCAAGAAC
16554123 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16554171 AAT
1 AAT
16554174 GAAAAGATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16554530 original size:36 final size:36
Alignment explanation
Indices: 16554490--16554565 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
16554480 TGAAACATAG
*
16554490 AAAATATATAAAATTATGT-GTATATATATAT-TTATA
1 AAAAT-TA-AAAAATATGTAGTATATATATATATTATA
* *
16554526 AAAATTAAAAAATGTGTACGTATATGTATATATTATA
1 AAAATTAAAAAATATGTA-GTATATATATATATTATA
16554563 AAA
1 AAA
16554566 CGTATGTATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 8 0.24
35 2 0.06
36 16 0.47
37 8 0.24
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.39
Consensus pattern (36 bp):
AAAATTAAAAAATATGTAGTATATATATATATTATA
Found at i:16555124 original size:23 final size:22
Alignment explanation
Indices: 16555094--16555138 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
16555084 AAATTAAATC
16555094 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-AAATCATATCT
*
16555117 TCTAAGATTACATATCATATCT
1 TCTAAGATTACAAATCATATCT
16555139 AAGATTGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (22 bp):
TCTAAGATTACAAATCATATCT
Found at i:16555141 original size:19 final size:19
Alignment explanation
Indices: 16555094--16555170 Score: 91
Period size: 19 Copynumber: 3.8 Consensus size: 19
16555084 AAATTAAATC
*
16555094 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
16555114 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
16555136 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
16555155 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
16555171 CTTGAAGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 34 0.65
22 7 0.13
23 11 0.21
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:16558794 original size:27 final size:26
Alignment explanation
Indices: 16558764--16558832 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
16558754 TGTTCTGACC
16558764 CACAGCTCGTGTGAGCAAGCCCAT-ATT
1 CACAGCTCGTGTGAGCAA-CCC-TGATT
* **
16558791 CACAGCTTGTGTGAGC-ATTCTGATT
1 CACAGCTCGTGTGAGCAACCCTGATT
16558816 CACAGCTCGTGTGAGCA
1 CACAGCTCGTGTGAGCA
16558833 TACATGTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.03
25 19 0.53
26 1 0.03
27 15 0.42
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCAACCCTGATT
Found at i:16565596 original size:20 final size:23
Alignment explanation
Indices: 16565571--16565611 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
16565561 GTACTTAAGT
16565571 ACATTTT-GTT-GCA-TTTTATG
1 ACATTTTAGTTAGCACTTTTATG
16565591 ACATTTTAGTTAGCACTTTTA
1 ACATTTTAGTTAGCACTTTTA
16565612 ACATTGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 3 0.17
23 5 0.28
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.51
Consensus pattern (23 bp):
ACATTTTAGTTAGCACTTTTATG
Found at i:16568887 original size:43 final size:43
Alignment explanation
Indices: 16568840--16568922 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
16568830 TTATGTGATT
16568840 GATATTGAAATGGAAAAGATGAGAAATAAATATGAGATGAGAA
1 GATATTGAAATGGAAAAGATGAGAAATAAATATGAGATGAGAA
* * *
16568883 GATATTGAAATGGAAATGATGAGAAATGATTATGAGATGA
1 GATATTGAAATGGAAAAGATGAGAAATAAATATGAGATGA
16568923 AAAATGAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (43 bp):
GATATTGAAATGGAAAAGATGAGAAATAAATATGAGATGAGAA
Found at i:16569394 original size:11 final size:14
Alignment explanation
Indices: 16569365--16569399 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
16569355 TATGTTGATA
16569365 TTGTTATTAAGGTG
1 TTGTTATTAAGGTG
16569379 TTGTTATTAAGGTG
1 TTGTTATTAAGGTG
16569393 TTGTTAT
1 TTGTTAT
16569400 CTTTGACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.26, T:0.54
Consensus pattern (14 bp):
TTGTTATTAAGGTG
Found at i:16575301 original size:20 final size:20
Alignment explanation
Indices: 16575276--16575317 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
16575266 AAATAGATAC
16575276 AAAGAAACAAACAAAGAAAT
1 AAAGAAACAAACAAAGAAAT
16575296 AAAGAAACAAACAAAGAAAT
1 AAAGAAACAAACAAAGAAAT
16575316 AA
1 AA
16575318 TCCTTAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.76, C:0.10, G:0.10, T:0.05
Consensus pattern (20 bp):
AAAGAAACAAACAAAGAAAT
Found at i:16578314 original size:16 final size:16
Alignment explanation
Indices: 16578290--16578332 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
16578280 GGAATTATTT
16578290 TTTTAAAATTATAAAA
1 TTTTAAAATTATAAAA
* *
16578306 TTTTCAAATTATATAA
1 TTTTAAAATTATAAAA
*
16578322 TTTAAAAATTA
1 TTTTAAAATTA
16578333 AAAGAAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTTAAAATTATAAAA
Found at i:16605405 original size:20 final size:20
Alignment explanation
Indices: 16605376--16605413 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16605366 GTCGTACACC
*
16605376 AATAATAATTTATTTTTATA
1 AATAACAATTTATTTTTATA
16605396 AATAACAATTTATTTTTA
1 AATAACAATTTATTTTTA
16605414 ACATGATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
AATAACAATTTATTTTTATA
Found at i:16609363 original size:14 final size:15
Alignment explanation
Indices: 16609339--16609369 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
16609329 TACTATTCAG
16609339 TAATATTATTATTAT
1 TAATATTATTATTAT
16609354 TAAT-TTATTATTAT
1 TAATATTATTATTAT
16609368 TA
1 TA
16609370 TCACCATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TAATATTATTATTAT
Found at i:16609463 original size:23 final size:24
Alignment explanation
Indices: 16609437--16609488 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
16609427 TTAATTGCCA
*
16609437 TTATTTACGTAA-ATTATTTTATG
1 TTATTTACGTAATATTATTTTAGG
*
16609460 TTA-TTATGTAATATTATTTTAGG
1 TTATTTACGTAATATTATTTTAGG
16609483 TT-TTTA
1 TTATTTA
16609489 ATATTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (24 bp):
TTATTTACGTAATATTATTTTAGG
Found at i:16612087 original size:23 final size:23
Alignment explanation
Indices: 16612061--16612108 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
16612051 TTGGGTGTTG
**
16612061 TTGGTGATGTTTTTTGTGTTATT
1 TTGGTGATACTTTTTGTGTTATT
* *
16612084 TTGGTGCTACTTTTTGTGTTGTT
1 TTGGTGATACTTTTTGTGTTATT
16612107 TT
1 TT
16612109 ATTGTTGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.06, C:0.04, G:0.25, T:0.65
Consensus pattern (23 bp):
TTGGTGATACTTTTTGTGTTATT
Found at i:16616060 original size:22 final size:21
Alignment explanation
Indices: 16616032--16616092 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
16616022 CTTCGTAATT
16616032 TCATTTATTATAT-TTATATTG
1 TCATTTATTATATATTATA-TG
16616053 CTCATTTATTTGATATATTATATG
1 -TCATTTA-TT-ATATATTATATG
* *
16616077 TCATTCATTATTTATT
1 TCATTTATTATATATT
16616093 TGTTCATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 6 0.18
22 9 0.26
23 8 0.24
24 6 0.18
25 5 0.15
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (21 bp):
TCATTTATTATATATTATATG
Found at i:16616445 original size:98 final size:98
Alignment explanation
Indices: 16616322--16616518 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
16616312 TTTTAAATAA
* * * *
16616322 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
16616387 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTCGATAAGTGGATGTTCTTTTAAAG
16616420 TAAAGGAAATATTCCAAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
16616485 TTAAATCTTCGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTCGATAAGTGGATGTTCTTTTAAAG
16616518 T
1 T
16616519 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCAAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTCGATAAGTGGATGTTCTTTTAAAG
Found at i:16622007 original size:44 final size:41
Alignment explanation
Indices: 16621913--16622160 Score: 169
Period size: 44 Copynumber: 5.8 Consensus size: 41
16621903 AGATTGTAAA
** * * *
16621913 TCTTATCTCCCT-AAGCAGTAGTGGAGCAGATTAAAGCTGATAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAAAC--CTAG
*
16621956 TCCTATCTCCCTGAAGTTGCAGTGGAGC-GAATTAAAACCTCAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAG-A-TAAAACCT-AG
* * *** *
16621999 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCGCATCTAG
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAAACCTAG
* *
16622040 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAA--AACCTAG
* * * ** *
16622084 TCTTATCTTCCTGAATTTGCAGTGGGGCAGACTGAAGATGGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-AA-A-ACCTAG
16622129 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
16622161 TGTAATGGCC
Statistics
Matches: 166, Mismatches: 28, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
40 21 0.13
41 9 0.05
42 6 0.04
43 19 0.11
44 76 0.46
45 35 0.21
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (41 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAAACCTAG
Found at i:16622088 original size:84 final size:87
Alignment explanation
Indices: 16621953--16622159 Score: 214
Period size: 84 Copynumber: 2.4 Consensus size: 87
16621943 TTAAAGCTGA
* * *
16621953 TAGTCCTATCTCCCTGAAGTTGCAGTGGAGC-GAATTAAAACCTCAGATCTTATC-TCTCTGAAG
1 TAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG-ACTAAAACCTAAGATCTTATCTTC-CTGAAG
16622016 TTGCAG-AGAGCAGA-TCG-CAT-C
64 TTGCAGTAGAGCAGACT-GACATGC
* *
16622037 TAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-AAG-TCTTATCTTCCTGAAT
1 TAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA--AACCTAAGATCTTATCTTCCTGAAG
* * *
16622100 TTGCAGTGGGGCAGACTGAAGATGGC
64 TTGCAGTAGAGCAGACTG-ACAT-GC
*
16622126 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 TAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
16622160 TTGTAATGGC
Statistics
Matches: 104, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
84 52 0.50
85 12 0.12
86 4 0.04
87 2 0.02
89 34 0.33
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.28
Consensus pattern (87 bp):
TAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAACCTAAGATCTTATCTTCCTGAAGTT
GCAGTAGAGCAGACTGACATGC
Found at i:16622143 original size:45 final size:44
Alignment explanation
Indices: 16621954--16622159 Score: 185
Period size: 44 Copynumber: 4.8 Consensus size: 44
16621944 TAAAGCTGAT
* * * *
16621954 AGTCCTATCTCCCTGAAGTTGCAGTGGAGC-GAATTAA--AACCTC
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG-ACTAAGTAAGC-A
* * * * * *
16621997 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CG-CATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
16622038 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* * * *
16622082 AGTCTTATCTTCCTGAATTTGCAGTGGGGCAGACTGAAG-ATGGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTA-AGCA
16622127 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
16622160 TTGTAATGGC
Statistics
Matches: 134, Mismatches: 20, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
40 21 0.16
41 9 0.07
42 4 0.03
43 8 0.06
44 56 0.42
45 36 0.27
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
Found at i:16623016 original size:30 final size:29
Alignment explanation
Indices: 16622972--16623028 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
16622962 TCCGAGCCTT
16622972 GGGGCAAAAATGTAATTATGCAAAAGTTTA
1 GGGGCAAAAATGTAATTATG-AAAAGTTTA
* * *
16623002 GGGGTAAAATTGTAATTTTGAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAGTT
16623029 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.32
Consensus pattern (29 bp):
GGGGCAAAAATGTAATTATGAAAAGTTTA
Found at i:16623258 original size:13 final size:13
Alignment explanation
Indices: 16623240--16623271 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16623230 TTTCCAGCAA
16623240 TTATGAATTTATT
1 TTATGAATTTATT
16623253 TTATGAATTTATT
1 TTATGAATTTATT
*
16623266 TGATGA
1 TTATGA
16623272 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:16623477 original size:50 final size:50
Alignment explanation
Indices: 16623366--16623614 Score: 336
Period size: 50 Copynumber: 4.8 Consensus size: 50
16623356 ATTTGGGTAA
*
16623366 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
*
16623422 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
16623472 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
16623522 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
16623572 AGAACATCCTATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16623615 TGTTATGATC
Statistics
Matches: 178, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
50 99 0.56
51 34 0.19
53 3 0.02
55 2 0.01
56 40 0.22
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:16625050 original size:44 final size:44
Alignment explanation
Indices: 16624999--16625107 Score: 132
Period size: 44 Copynumber: 2.4 Consensus size: 44
16624989 GATCGCATCT
*
16624999 AGTCTTATCTCCTTGAAGTTACAGTGGAGCAGA-TTAAGTAAGA-A
1 AGTCTTATCTCC-TGAAGTTACAGTGGAGCAGACTGAAG-AAGACA
* * *
16625043 AGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGACA
1 AGTCTTAT-CTCCTGAAGTTACAGTGGAGCAGACTGAAGAAGACA
16625088 AGTCTTATCTCCCTGAAGTT
1 AGTCTTATCT-CCTGAAGTT
16625108 GCAGATTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
44 31 0.54
45 26 0.46
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (44 bp):
AGTCTTATCTCCTGAAGTTACAGTGGAGCAGACTGAAGAAGACA
Found at i:16626878 original size:22 final size:21
Alignment explanation
Indices: 16626850--16626910 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
16626840 CTTCGTAATT
16626850 TCATTTATTATAT-TTATATTG
1 TCATTTATTATATATTATA-TG
16626871 CTCATTTATTTGATATATTATATG
1 -TCATTTA-TT-ATATATTATATG
* *
16626895 TCATTCATTATTTATT
1 TCATTTATTATATATT
16626911 TGTTCATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 6 0.18
22 9 0.26
23 8 0.24
24 6 0.18
25 5 0.15
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (21 bp):
TCATTTATTATATATTATATG
Found at i:16627274 original size:98 final size:98
Alignment explanation
Indices: 16627143--16627339 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
16627133 TTTAAAATAA
* * * *
16627143 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
16627208 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTCGATAAGTGGATGTTCTTTTAAAG
16627241 TAAAGGAAATATTCCAAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
16627306 TTAAATCTTCGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTCGATAAGTGGATGTTCTTTTAAAG
16627339 T
1 T
16627340 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCAAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTCGATAAGTGGATGTTCTTTTAAAG
Found at i:16637526 original size:16 final size:16
Alignment explanation
Indices: 16637505--16637553 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
16637495 TTCGCTGTAT
16637505 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
16637521 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
16637537 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
16637553 T
1 T
16637554 AGCAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.37, C:0.06, G:0.37, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:16637806 original size:18 final size:17
Alignment explanation
Indices: 16637785--16637819 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
16637775 TTATTATTAA
*
16637785 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
16637803 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
16637820 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:16637927 original size:75 final size:75
Alignment explanation
Indices: 16637699--16637928 Score: 230
Period size: 75 Copynumber: 3.1 Consensus size: 75
16637689 TAGATAAATG
* *
16637699 ATTATTGTTATTGTTATTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATA
1 ATTATTATTATTGTTATTAAATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATA
16637764 TTTTAACATA
66 TTTTAACATA
* * * * **
16637774 ATTATTATTA-----AATATATTTTAATTAA-AATATATAAT-TTAAT-A-AAATTCTTAATAAT
1 ATTATTATTATTGTTATTAAATTTTAA-TAAGATTAT-TAATATAAATAATAAATAATT--TAAT
* *
16637830 CAATATTGGT-ATATA
62 C-ATATT-TTAACATA
*
16637845 AAT-TTATTATTGTTATTAAATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATA
1 ATTATTATTATTGTTATTAAATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATA
16637909 TTTTAACATA
66 TTTTAACATA
16637919 ATTATTATTA
1 ATTATTATTA
16637929 AATATAATTT
Statistics
Matches: 119, Mismatches: 19, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
68 6 0.05
69 1 0.01
70 29 0.24
71 18 0.15
72 1 0.01
73 1 0.01
74 18 0.15
75 38 0.32
76 1 0.01
77 6 0.05
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (75 bp):
ATTATTATTATTGTTATTAAATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATA
TTTTAACATA
Found at i:16637953 original size:18 final size:18
Alignment explanation
Indices: 16637930--16637981 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
16637920 TTATTATTAA
16637930 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
16637948 ATATAATTTAAT-AAAAT
1 ATATAATTTAATAAAAAT
*
16637965 ATATGAATTTACTAAAA
1 ATAT-AATTTAATAAAA
16637982 TCATAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
17 9 0.29
18 19 0.61
19 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:16637982 original size:18 final size:17
Alignment explanation
Indices: 16637930--16638063 Score: 93
Period size: 17 Copynumber: 8.0 Consensus size: 17
16637920 TTATTATTAA
16637930 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
16637948 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
16637965 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
* * *
16637983 -CATAATAT-ATAATACT
1 ATATAATTTAATAA-AAT
* *
16637999 ATAAAATATAATTTAAAAT
1 ATATAATTTAA--TAAAAT
* *
16638018 A-ATTA-TT-AT-TAA-
1 ATATAATTTAATAAAAT
16638030 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
16638047 ATATAATTTGATAAAAT
1 ATATAATTTAATAAAAT
16638064 TCTTAGTATT
Statistics
Matches: 90, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
12 1 0.01
13 5 0.06
14 3 0.03
15 5 0.06
16 9 0.10
17 34 0.38
18 27 0.30
19 3 0.03
20 3 0.03
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:16643866 original size:85 final size:85
Alignment explanation
Indices: 16643765--16644058 Score: 360
Period size: 84 Copynumber: 3.4 Consensus size: 85
16643755 TTTTTGCACC
* ** * *
16643765 CAATTGAGTACTTGAACTTTCAAAATATATCAAAAAGACCTTTAAACTTTTTCAAAAAAAGCAAT
1 CAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACTTTTTCAAAAAAAGCAAT
*
16643830 TAAGCCCCTGTTTTCCCATT
66 TAAGCCCCTGTTTTCCCACT
*
16643850 CAATTGGGTACTTGAACTTTCAAAATGCATCAAAAA-ACCCTCAAACTTTTCCAAGAAAAA-CAA
1 CAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACTTTTTCAA-AAAAAGCAA
* * **
16643913 TTAATCCCCTTTTTTTTCACT
65 TTAAGCCCCTGTTTTCCCACT
* * *
16643934 CAATTGGGTGCTTGAACTTTCAAAATGCACCAAAAAGCCCCTCAAACTTTTTCAAAAAAAGCAAT
1 CAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACTTTTTCAAAAAAAGCAAT
*
16643999 TAAGCCCCAGTTTTCCCCCCCACT
66 TAAGCCCCTGTTTT----CCCACT
* *
16644023 AAATTGGGTACTTGAA-TTGCCAAAATGCATCAAAAA
1 CAATTGGGTACTTGAACTT-TCAAAATGCATCAAAAA
16644059 AGCCCTTTGA
Statistics
Matches: 177, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
84 73 0.41
85 69 0.39
88 2 0.01
89 33 0.19
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.29
Consensus pattern (85 bp):
CAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACTTTTTCAAAAAAAGCAAT
TAAGCCCCTGTTTTCCCACT
Found at i:16643999 original size:169 final size:172
Alignment explanation
Indices: 16643752--16644064 Score: 445
Period size: 169 Copynumber: 1.8 Consensus size: 172
16643742 AAGCTCATGT
* * * *
16643752 TTTTTTTTGCACCCAATTGAGTACTTGAACTTTCAAAATATATCAAAAAGACCTTTAAACTTTTT
1 TTTTTTTTGCACCCAATTGAGTACTTGAACTTTCAAAATACACCAAAAAGACCCTCAAACTTTTT
* * * *
16643817 CAAAAAAAGCAATTAAGCCCCTGTTTT-CCCATTCAATTGGGTACTTGAACTT-TCAAAATGCAT
66 CAAAAAAAGCAATTAAGCCCCAGTTTTCCCCACTAAATTGGGTACTTGAA-TTGCCAAAATGCAT
16643880 CAAAAAA-CCCTCAAACTTTTCCAAGAAAAACAATTAATCCCC
130 CAAAAAAGCCCTCAAACTTTTCCAAGAAAAACAATTAATCCCC
* * * * *
16643922 TTTTTTTT-CACTCAATTGGGTGCTTGAACTTTCAAAATGCACCAAAAAGCCCCTCAAACTTTTT
1 TTTTTTTTGCACCCAATTGAGTACTTGAACTTTCAAAATACACCAAAAAGACCCTCAAACTTTTT
16643986 CAAAAAAAGCAATTAAGCCCCAGTTTTCCCCCCCACTAAATTGGGTACTTGAATTGCCAAAATGC
66 CAAAAAAAGCAATTAAGCCCCAGTTTT---CCCCACTAAATTGGGTACTTGAATTGCCAAAATGC
16644051 ATCAAAAAAGCCCT
128 ATCAAAAAAGCCCT
16644065 TTGATCATTA
Statistics
Matches: 124, Mismatches: 13, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
169 73 0.59
170 8 0.06
172 2 0.02
173 37 0.30
174 4 0.03
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (172 bp):
TTTTTTTTGCACCCAATTGAGTACTTGAACTTTCAAAATACACCAAAAAGACCCTCAAACTTTTT
CAAAAAAAGCAATTAAGCCCCAGTTTTCCCCACTAAATTGGGTACTTGAATTGCCAAAATGCATC
AAAAAAGCCCTCAAACTTTTCCAAGAAAAACAATTAATCCCC
Found at i:16644184 original size:15 final size:14
Alignment explanation
Indices: 16644160--16644189 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
16644150 ATGACATGTG
16644160 AAAAAAAAAATAAA
1 AAAAAAAAAATAAA
16644174 AAAATAAAAAATAAA
1 AAAA-AAAAAATAAA
16644189 A
1 A
16644190 GTTATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAAAAAAAATAAA
Found at i:16644199 original size:10 final size:9
Alignment explanation
Indices: 16644184--16644315 Score: 59
Period size: 9 Copynumber: 13.7 Consensus size: 9
16644174 AAAATAAAAA
*
16644184 ATAAAAGTT
1 ATAAAAATT
16644193 ATAAAAATT
1 ATAAAAATT
* * *
16644202 ATTATATTT
1 ATAAAAATT
16644211 CAATAAAAATAT
1 --ATAAAAAT-T
* **
16644223 TTAAATTTT
1 ATAAAAATT
16644232 ATTAAAAATT
1 A-TAAAAATT
*
16644242 AGAAAAAAATTT
1 A-TAA-AAA-TT
16644254 ATAAAAATT
1 ATAAAAATT
* *
16644263 GTAAAAAAT
1 ATAAAAATT
16644272 ATAAAAA-T
1 ATAAAAATT
*
16644280 ATAAAATTTT
1 ATAAAA-ATT
16644290 ATAAAAATCAT
1 ATAAAAAT--T
*
16644301 AAAAAAATT
1 ATAAAAATT
16644310 ATAAAA
1 ATAAAA
16644316 TATATAGAAA
Statistics
Matches: 90, Mismatches: 23, Indels: 20
0.68 0.17 0.15
Matches are distributed among these distances:
8 7 0.08
9 37 0.41
10 24 0.27
11 18 0.20
12 4 0.04
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (9 bp):
ATAAAAATT
Found at i:16644218 original size:20 final size:21
Alignment explanation
Indices: 16644193--16644242 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
16644183 AATAAAAGTT
*
16644193 ATAAAAATTA-TTATATTTCA
1 ATAAAAATTATTTAAATTTCA
*
16644213 ATAAAAA-TATTTAAATTTTA
1 ATAAAAATTATTTAAATTTCA
*
16644233 TTAAAAATTA
1 ATAAAAATTA
16644243 GAAAAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.84
21 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAAAAATTATTTAAATTTCA
Found at i:16644337 original size:59 final size:56
Alignment explanation
Indices: 16644215--16644382 Score: 160
Period size: 59 Copynumber: 2.9 Consensus size: 56
16644205 ATATTTCAAT
* * * * *
16644215 AAAAATATTTAAATTTTATTAAAAATTAGAAAAAAATTTATAAAAATTGTAAAAAATAT
1 AAAAATA-TAAAATTTTA-TAAAAATCATAAAAAAA-TTATAAAAATTGTAAAAAAGAA
*
16644274 AAAAATATAAAATTTTATAAAAATCATAAAAAAATTATAAAATATATAG-AAATATAGAA
1 AAAAATATAAAATTTTATAAAAATCATAAAAAAATTATAAAA-AT-T-GTAAA-AAAGAA
* * * *
16644333 AAAAATTATCAAATTTTAT-AAAGTCATAAGAAAATTATAAAAAATGTAAA
1 AAAAA-TATAAAATTTTATAAAAATCATAAAAAAATTATAAAAATTGTAAA
16644383 GAAAATATAA
Statistics
Matches: 93, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
56 9 0.10
57 21 0.23
58 14 0.15
59 37 0.40
60 12 0.13
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (56 bp):
AAAAATATAAAATTTTATAAAAATCATAAAAAAATTATAAAAATTGTAAAAAAGAA
Found at i:16644401 original size:20 final size:19
Alignment explanation
Indices: 16644360--16644415 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
16644350 ATAAAGTCAT
16644360 AAGAAAATTATAAAAAATGTA
1 AAGAAAA-TAT-AAAAATGTA
*
16644381 AAGAAAATATAAAATTCGTA
1 AAGAAAATATAAAAAT-GTA
*
16644401 AA-AAAGTATAAAAAT
1 AAGAAAATATAAAAAT
16644416 TATCGTACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 16 0.52
20 8 0.26
21 7 0.23
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AAGAAAATATAAAAATGTA
Found at i:16644416 original size:20 final size:19
Alignment explanation
Indices: 16644363--16644416 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
16644353 AAGTCATAAG
* *
16644363 AAAATTATAAAAAATGTAA
1 AAAAATATAAAAATTGTAA
16644382 AGAAAATAT-AAAATTCGTAA
1 A-AAAATATAAAAATT-GTAA
*
16644402 AAAAGTATAAAAATT
1 AAAAATATAAAAATT
16644417 ATCGTACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (19 bp):
AAAAATATAAAAATTGTAA
Found at i:16644478 original size:20 final size:19
Alignment explanation
Indices: 16644433--16644478 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
16644423 CTAAAAGGAA
16644433 CATTTTATAATTTTTCTAT
1 CATTTTATAATTTTTCTAT
* *
16644452 AACTTTTATAGATTTTTTTAT
1 CA-TTTTATA-ATTTTTCTAT
16644473 CATTTT
1 CATTTT
16644479 TGTCACATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 11 0.50
21 10 0.45
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (19 bp):
CATTTTATAATTTTTCTAT
Found at i:16648995 original size:43 final size:42
Alignment explanation
Indices: 16648947--16649061 Score: 126
Period size: 43 Copynumber: 2.7 Consensus size: 42
16648937 TATCATACTA
* **
16648947 ATGCCAT-GTCCCAGAC-ATGGTCTTACATGGAAATCTCGTATCG
1 ATGCCATAG-CCCAG-CTATGGTCTTACA-CGAAATCTCAAATCG
*
16648990 ATGCCAATAGCCTAGCTATGGTCTTACACGAAATCTCAAATCG
1 ATGCC-ATAGCCCAGCTATGGTCTTACACGAAATCTCAAATCG
*
16649033 ATGCCAATAGCCCATCTATGGTCTTACAC
1 ATGCC-ATAGCCCAGCTATGGTCTTACAC
16649062 ATAAACACTG
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
43 45 0.71
44 17 0.27
45 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (42 bp):
ATGCCATAGCCCAGCTATGGTCTTACACGAAATCTCAAATCG
Found at i:16651866 original size:7 final size:7
Alignment explanation
Indices: 16651854--16651882 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
16651844 AGCTTTTGGT
16651854 TGATAGA
1 TGATAGA
16651861 TGATAGA
1 TGATAGA
16651868 TGATAGA
1 TGATAGA
16651875 TGATAGA
1 TGATAGA
16651882 T
1 T
16651883 TTGTGAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (7 bp):
TGATAGA
Found at i:16652474 original size:26 final size:26
Alignment explanation
Indices: 16652455--16652659 Score: 187
Period size: 26 Copynumber: 7.9 Consensus size: 26
16652445 TTTACTTAAT
16652455 AGGCTTTGAGCCGGTGTTTATTTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* * *
16652481 AGGTTTTGAGCCAGTTTTTA-TTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* *
16652506 AGGCTTTGAGCCGATGTTTATTTAGT
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* ** *
16652532 TGGCTTTGAGCCAATGATTATTTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* ** *
16652558 AGGCCTTGAGCTAGTGTGTATTTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* *
16652584 AGGCCTTGAGCCGGTGTGTATTTAGC
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* ** * * *
16652610 AGGCCTTGAGTTGATGTTTATCTAGT
1 AGGCTTTGAGCCGGTGTTTATTTAGC
* * *
16652636 AGGCTTTGAGTCAGTGATTATTTA
1 AGGCTTTGAGCCGGTGTTTATTTA
16652660 ACATGTACTA
Statistics
Matches: 146, Mismatches: 32, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
25 21 0.14
26 125 0.86
ACGTcount: A:0.20, C:0.14, G:0.28, T:0.39
Consensus pattern (26 bp):
AGGCTTTGAGCCGGTGTTTATTTAGC
Found at i:16662314 original size:19 final size:20
Alignment explanation
Indices: 16662275--16662312 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
16662265 AATATATTTT
16662275 TTTTCAAAAAATATTATAAA
1 TTTTCAAAAAATATTATAAA
16662295 TTTT-AAAAAATA-TATAAA
1 TTTTCAAAAAATATTATAAA
16662313 ATAAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
TTTTCAAAAAATATTATAAA
Found at i:16662360 original size:18 final size:19
Alignment explanation
Indices: 16662332--16662367 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
16662322 TTTTTGACAA
16662332 TAAATAATATAAAAAAATT
1 TAAATAATATAAAAAAATT
*
16662351 TAAA-AATATATAAAAAT
1 TAAATAATATAAAAAAAT
16662368 ATGTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAATAATATAAAAAAATT
Found at i:16662426 original size:6 final size:6
Alignment explanation
Indices: 16662417--16662466 Score: 57
Period size: 6 Copynumber: 8.0 Consensus size: 6
16662407 TTAATGTTAA
*
16662417 ATAAAT ATAAAT ATAAAT ATAAAT ATATTAAT ATTAAAT A-AAAT AAAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATA--AAT A-TAAAT ATAAAT ATAAAT
16662467 CCCTCACTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.12
6 25 0.62
7 4 0.10
8 4 0.10
9 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATAAAT
Found at i:16662976 original size:29 final size:28
Alignment explanation
Indices: 16662936--16662990 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
16662926 CTATATAATG
* *
16662936 TAAGTGCTTAAATTGCAAACTTTTTATTT
1 TAAGTGCTTAAAATG-AAAATTTTTATTT
16662965 TAAGTG-TCTAAAATGAAAATTTTTAT
1 TAAGTGCT-TAAAATGAAAATTTTTAT
16662991 AGTTAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (28 bp):
TAAGTGCTTAAAATGAAAATTTTTATTT
Found at i:16669221 original size:6 final size:6
Alignment explanation
Indices: 16669210--16669244 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
16669200 TATTTTTGCG
16669210 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
16669245 CAAATACCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:16670894 original size:32 final size:31
Alignment explanation
Indices: 16670832--16670898 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 31
16670822 ACCTAAAATT
* *
16670832 ATTAATTCTAATTATTCTAATATTTTATTTA
1 ATTAATTCTAATTATTCTAATATATAATTTA
16670863 ATTAATTCTTAATTATT-TAATTATATAATTTA
1 ATTAATTC-TAATTATTCTAA-TATATAATTTA
16670895 ATTA
1 ATTA
16670899 CGATTTCCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 11 0.34
32 21 0.66
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTAATTCTAATTATTCTAATATATAATTTA
Found at i:16682800 original size:44 final size:44
Alignment explanation
Indices: 16682712--16683659 Score: 825
Period size: 44 Copynumber: 21.5 Consensus size: 44
16682702 GCAGATCAGT
* * * * *
16682712 GAAGATAGCAGGTCCTGTATTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * *
16682756 GAAGATGCAGATTTTGTCTTCCCATATTGGTGGCGGAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * * *
16682800 GAAGAAAGCAAATCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * *
16682844 GAAAATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * *
16682888 GAAGATGCAGATATTCTCTTCCCATATTGGTGGCGGAGTACATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * * *
16682932 GAAGAAAGCAAATCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * *
16682976 GAAGATAGCAGGTCCTATCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * *
16683020 GAAGATACAGATCTTGTCTTCCCATATTGGTGGCGGAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * * *
16683064 GAAGAAGCAGATTTTGTCTTTCATGTATTGG-CGTGAAGTAGATC
1 GAAGATGCAGATCTTGTC-TTCCTATATTGGTGGCGAAGTAGATC
* * *
16683108 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* *
16683153 GAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * *
16683197 GAAGAAAT-CAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAG--ATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* *
16683241 GAAGATAGCAGGT-TCTGTCTTCCTATATTGGTAG-GAAGT-GAATC
1 GAAGAT-GCAGATCT-TGTCTTCCTATATTGGTGGCGAAGTAG-ATC
*
16683285 GAAGATGCAGATCTTGTCTTCCCATATTGGTGGC-AGAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGA-AGTAGATC
* * *
16683329 GAAGAAAGCAGATCTTGTC-TCCATGTATTGGT-GTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCC-TATATTGGTGGCGAAGTAGATC
* *
16683373 GAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* ** *
16683418 GAAGATGCAGATCTTGTCTTCCCATACCGGTGGTGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * * *
16683462 GAAGAAAGCAGATATTGTCTTCATGTATTGGT-GTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
* * * ** *
16683506 GAAGATAGTAGGTCCTGTCTTCCTATATTGGT-AAGAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
*
16683550 GAAGATGCAGATCTTGTCTT-CTCATACTGGTGGCGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCT-ATATTGGTGGCGAAGTAGATC
* * * * * *
16683594 GAAGAAAGCATATCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
*
16683638 GAAGATAGCAGATCTTGCCTTC
1 GAAGAT-GCAGATCTTGTCTTC
16683660 TTGCACCGAC
Statistics
Matches: 721, Mismatches: 147, Indels: 72
0.77 0.16 0.08
Matches are distributed among these distances:
42 4 0.01
43 111 0.15
44 427 0.59
45 176 0.24
46 3 0.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (44 bp):
GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATC
Found at i:16682953 original size:132 final size:132
Alignment explanation
Indices: 16682712--16683648 Score: 1534
Period size: 132 Copynumber: 7.1 Consensus size: 132
16682702 GCAGATCAGT
* *
16682712 GAAGATAGCAGGTCCTGTATTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATTTTGTCTTC
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
*
16682777 CCATATTGGTGGCGGAGTAGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGA
66 CCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
16682842 TC
131 TC
* * *
16682844 GAAAATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATATTCTCTTC
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
* *
16682909 CCATATTGGTGGCGGAGTACATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGA
66 CCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
16682974 TC
131 TC
* *
16682976 GAAGATAGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGATCTTGTCTTC
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
*
16683041 CCATATTGGTGGCGGAGTAGATCGAAG-AAGCAGATTTTGTCTTTCATGTATTGGCGTGAAGTAG
66 CCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTC-TTCATGTATTGGCGTGAAGTAG
16683105 ATC
130 ATC
*
16683108 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTT
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTT
* * *
16683173 CCCATACTGGTGGCGAAGTAGATCGAAGAAATCAGATCTTGTCTTCATGTATTGGCGTGAAGTAG
65 CCCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAG
16683238 ATC
130 ATC
* *
16683241 GAAGATAGCAGGTTCTGTCTTCCTATATTGGTAGGAAGTGAATCGAAGATGCAGATCTTGTCTTC
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
* * *
16683306 CCATATTGGTGGCAGAGTAGATCGAAGAAAGCAGATCTTGTCTCCATGTATTGGTGTGAAGTAGA
66 CCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
16683371 TC
131 TC
* *
16683373 GAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTT
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTT
** * * * *
16683438 CCCATACCGGTGGTGAAGTAGATCGAAGAAAGCAGATATTGTCTTCATGTATTGGTGTGAAGTAG
65 CCCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAG
16683503 ATC
130 ATC
* *
16683506 GAAGATAGTAGGTCCTGTCTTCCTATATTGGTAAGAAGTGGATCGAAGATGCAGATCTTGTCTTC
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
* * * *
16683571 TCATACTGGTGGCGAAGTAGATCGAAGAAAGCATATCTTGTCTTCATGTATTGGCGTGAAGTAGA
66 CCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
16683636 TC
131 TC
16683638 GAAGATAGCAG
1 GAAGATAGCAG
16683649 ATCTTGCCTT
Statistics
Matches: 750, Mismatches: 51, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
131 12 0.02
132 494 0.66
133 232 0.31
134 12 0.02
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (132 bp):
GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
CCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
TC
Found at i:16683288 original size:265 final size:265
Alignment explanation
Indices: 16682712--16683651 Score: 1578
Period size: 265 Copynumber: 3.6 Consensus size: 265
16682702 GCAGATCAGT
* *
16682712 GAAGATAGCAGGTCCTGTATTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATTTTGTCTTC
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
*
16682777 CCATATTGGTGGCGGAGTAGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGA
66 CCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
* * * *
16682842 TCGAAAATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATATTCTC
131 TCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTC
* * * *
16682906 TTCCCATATTGGTGGCGGAGTACATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGT
196 TTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
16682971 AGATC
261 AGATC
* *
16682976 GAAGATAGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGATCTTGTCTTC
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
*
16683041 CCATATTGGTGGCGGAGTAGATCGAAG-AAGCAGATTTTGTCTTTCATGTATTGGCGTGAAGTAG
66 CCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTC-TTCATGTATTGGCGTGAAGTAG
16683105 ATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGT
130 ATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGT
*
16683170 CTTCCCATACTGGTGGCGAAGTAGATCGAAGAAATCAGATCTTGTCTTCATGTATTGGCGTGAAG
195 CTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
16683235 TAGATC
260 TAGATC
* *
16683241 GAAGATAGCAGGTTCTGTCTTCCTATATTGGTAGGAAGTGAATCGAAGATGCAGATCTTGTCTTC
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
* * *
16683306 CCATATTGGTGGCAGAGTAGATCGAAGAAAGCAGATCTTGTCTCCATGTATTGGTGTGAAGTAGA
66 CCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
*
16683371 TCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTC
131 TCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTC
* * * *
16683436 TTCCCATACCGGTGGTGAAGTAGATCGAAGAAAGCAGATATTGTCTTCATGTATTGGTGTGAAGT
196 TTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
16683501 AGATC
261 AGATC
* *
16683506 GAAGATAGTAGGTCCTGTCTTCCTATATTGGTAAGAAGTGGATCGAAGATGCAGATCTTGTCTTC
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
* * * *
16683571 TCATACTGGTGGCGAAGTAGATCGAAGAAAGCATATCTTGTCTTCATGTATTGGCGTGAAGTAGA
66 CCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
16683636 TCGAAGATAGCAGATC
131 TCGAAGATAGCAGATC
16683652 TTGCCTTCTT
Statistics
Matches: 633, Mismatches: 40, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
263 12 0.02
264 145 0.23
265 463 0.73
266 13 0.02
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (265 bp):
GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
CCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
TCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTC
TTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGT
AGATC
Found at i:16683546 original size:397 final size:396
Alignment explanation
Indices: 16682712--16683648 Score: 1552
Period size: 397 Copynumber: 2.4 Consensus size: 396
16682702 GCAGATCAGT
* * *
16682712 GAAGATAGCAGGTCCTGTATTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATTTTGTCTTC
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAAGAAGTGGATCGAAGATGCAGATCTTGTCTTC
* *
16682777 CCATATTGGTGGCGGAGTAGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGA
66 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGA
* *
16682842 TCGAAAATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATATTCTCT
131 TCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGAATCGAAGATGCAGATATTCTCT
* *
16682907 TCCCATATTGGTGGCGGAGTACATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTA
196 TCCCATATTGGTGGCAGAGTACATCGAAGAAAGCAAATCTTGTCTCCATGTATTGGCGTGAAGTA
*
16682972 GATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGATCTTGT
261 GATCGAAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGATCTTGT
** * *
16683037 CTTCCCATATTGGTGGCGGAGTAGATCGAAGAAGCAGATTTTGTCTTTCATGTATTGGCGTGAAG
326 CTTCCCATACCGGTGGCGAAGTAGATCGAAGAAGCAGATATTGTCTTTCATGTATTGGCGTGAAG
16683102 TAGATC
391 TAGATC
* *
16683108 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTT
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTA-AGAAGTGGATCGAAGATGCAGATCTTGTCTT
* *
16683173 CCCATACTGGTGGCGAAGTAGATCGAAGAAATCAGATCTTGTCTTCATGTATTGGCGTGAAGTAG
65 CCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAG
* * *
16683238 ATCGAAGATAGCAGGTTCTGTCTTCCTATATTGGTAGGAAGTGAATCGAAGATGCAGATCTTGTC
130 ATCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGAATCGAAGATGCAGATATTCTC
* * *
16683303 TTCCCATATTGGTGGCAGAGTAGATCGAAGAAAGCAGATCTTGTCTCCATGTATTGGTGTGAAGT
195 TTCCCATATTGGTGGCAGAGTACATCGAAGAAAGCAAATCTTGTCTCCATGTATTGGCGTGAAGT
* * *
16683368 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTT
260 AGATCGAAGATAGCAGATCCTATCTTCCTATATTGGTAG-GAAGTGGATCGAAGATACAGATCTT
* *
16683433 GTCTTCCCATACCGGTGGTGAAGTAGATCGAAGAAAGCAGATATTGTC-TTCATGTATTGGTGTG
324 GTCTTCCCATACCGGTGGCGAAGTAGATCGAAG-AAGCAGATATTGTCTTTCATGTATTGGCGTG
16683497 AAGTAGATC
388 AAGTAGATC
*
16683506 GAAGATAGTAGGTCCTGTCTTCCTATATTGGTAAGAAGTGGATCGAAGATGCAGATCTTGTCTTC
1 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAAGAAGTGGATCGAAGATGCAGATCTTGTCTTC
* *
16683571 TCATACTGGTGGCGAAGTAGATCGAAGAAAGCATATCTTGTCTTCATGTATTGGCGTGAAGTAGA
66 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGA
16683636 TCGAAGATAGCAG
131 TCGAAGATAGCAG
16683649 ATCTTGCCTT
Statistics
Matches: 504, Mismatches: 34, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
396 31 0.06
397 352 0.70
398 108 0.21
399 13 0.03
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (396 bp):
GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAAGAAGTGGATCGAAGATGCAGATCTTGTCTTC
CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGA
TCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGAATCGAAGATGCAGATATTCTCT
TCCCATATTGGTGGCAGAGTACATCGAAGAAAGCAAATCTTGTCTCCATGTATTGGCGTGAAGTA
GATCGAAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGATCTTGT
CTTCCCATACCGGTGGCGAAGTAGATCGAAGAAGCAGATATTGTCTTTCATGTATTGGCGTGAAG
TAGATC
Found at i:16683808 original size:43 final size:43
Alignment explanation
Indices: 16683755--16683889 Score: 126
Period size: 43 Copynumber: 3.1 Consensus size: 43
16683745 CTTGCACCGA
*
16683755 CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
1 CAGCGAAGCAGATCGAAAACACCAGCCTTGCCTCCCTGGGTTG
* * ** * * * ****
16683798 CAGCGGAGCAGGTTAAAAACAGCAGATCTTGCCTTCCTGCACCG
1 CAGCGAAGCAGATCGAAAACACCAG-CCTTGCCTCCCTGGGTTG
* *
16683842 ACAGCGAAGCAGATCGAATACACCAGCCTTGCCTCCCTAGGTTG
1 -CAGCGAAGCAGATCGAAAACACCAGCCTTGCCTCCCTGGGTTG
16683886 CAGC
1 CAGC
16683890 AGAGCAGGTT
Statistics
Matches: 65, Mismatches: 25, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
43 23 0.35
44 23 0.35
45 19 0.29
ACGTcount: A:0.26, C:0.32, G:0.25, T:0.17
Consensus pattern (43 bp):
CAGCGAAGCAGATCGAAAACACCAGCCTTGCCTCCCTGGGTTG
Found at i:16683855 original size:88 final size:87
Alignment explanation
Indices: 16683642--16683957 Score: 508
Period size: 88 Copynumber: 3.6 Consensus size: 87
16683632 TAGATCGAAG
*
16683642 ATAGCAGATCTTGCCTTCTTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCT-
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
* *
16683706 GTTGCAGTGGAGCAGGCTAAAA
66 GTTGCAGCGGAGCAGGTTAAAA
*
16683728 ATAGCAGATCTTGCCTTCTTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCT-
16683793 GGTTGCAGCGGAGCAGGTTAAAA
65 GGTTGCAGCGGAGCAGGTTAAAA
* *
16683816 ACAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAATACACCAGCCTTGCCTCCCTA
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCT-
*
16683881 GGTTGCAGCAGAGCAGGTTAAAA
65 GGTTGCAGCGGAGCAGGTTAAAA
** * *
16683904 ATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGATGACCCCAGCC
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
16683958 CTATCTCCTT
Statistics
Matches: 215, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
86 64 0.30
88 151 0.70
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.19
Consensus pattern (87 bp):
ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
GTTGCAGCGGAGCAGGTTAAAA
Found at i:16683917 original size:44 final size:42
Alignment explanation
Indices: 16683781--16683924 Score: 110
Period size: 44 Copynumber: 3.3 Consensus size: 42
16683771 AGACACCAGC
16683781 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAACAGCAGAT
1 CTTGCCTCCCT-GGTTGCAGC-GAGCAGGTTAAAAACAGCAGAT
* *** * ** * * *
16683825 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAATACACCAG-C
1 CTTGCCTCCCTG-GTTG-CAGCG-AGCAGGTTAAAAACAGCAGAT
*
16683869 CTTGCCTCCCTAGGTTGCAGCAGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCT-GGTTGCAGC-GAGCAGGTTAAAAACAGCAGAT
*
16683913 CTTGCCTTCCTG
1 CTTGCCTCCCTG
16683925 CATTGACAGC
Statistics
Matches: 72, Mismatches: 22, Indels: 13
0.67 0.21 0.12
Matches are distributed among these distances:
43 19 0.26
44 34 0.47
45 19 0.26
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (42 bp):
CTTGCCTCCCTGGTTGCAGCGAGCAGGTTAAAAACAGCAGAT
Found at i:16684074 original size:68 final size:68
Alignment explanation
Indices: 16683958--16684088 Score: 174
Period size: 68 Copynumber: 1.9 Consensus size: 68
16683948 GACCCCAGCC
* * * *
16683958 CTATCTCCTTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGGA
1 CTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGATTGTGAATACTATCTCCCTGGTCAGCAGGA
16684023 ATT
66 ATT
* ** *
16684026 CTATCTCCCTGGGCAGTAGTGGAATAGATTGGAGATTGT-AGGTACTATCTCCCTGGTCAGCAG
1 CTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGATTGTGA-ATACTATCTCCCTGGTCAGCAG
16684089 TGGAATAGGT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
67 1 0.02
68 53 0.98
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (68 bp):
CTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGATTGTGAATACTATCTCCCTGGTCAGCAGGA
ATT
Found at i:16684118 original size:44 final size:43
Alignment explanation
Indices: 16684021--16684146 Score: 128
Period size: 44 Copynumber: 2.9 Consensus size: 43
16684011 TGGTCAGCAG
* * * *
16684021 GAATTCTATCTCCCTGGGCAGTAGTGGAATAGATTGGAGATTGT
1 GAATACTATCTCCCT-GGCAGCAGTGGAATAGGTTGAAGATTGT
*
16684065 -AGGTACTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT
1 GA-ATACTATCTCCCTGG-CAGCAGTGGAATAGGTTGAAGATTGT
* * * *
16684109 GAATCCTATCTTCCTGAGCAGCAGCGGAGTAGGTTGAA
1 GAATACTATCTCCCTG-GCAGCAGTGGAATAGGTTGAA
16684147 AATAGCAGAT
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
43 3 0.04
44 63 0.93
45 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (43 bp):
GAATACTATCTCCCTGGCAGCAGTGGAATAGGTTGAAGATTGT
Found at i:16684876 original size:24 final size:21
Alignment explanation
Indices: 16684812--16684865 Score: 85
Period size: 19 Copynumber: 2.7 Consensus size: 21
16684802 TCTTCAAGGA
*
16684812 TATGTAATCTTAGATATGA--
1 TATGCAATCTTAGATATGATT
16684831 TATGCAATCTTAGATATGATT
1 TATGCAATCTTAGATATGATT
16684852 TATGCAATCTTAGA
1 TATGCAATCTTAGA
16684866 AGATATGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.56
21 14 0.44
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (21 bp):
TATGCAATCTTAGATATGATT
Found at i:16685378 original size:17 final size:17
Alignment explanation
Indices: 16685356--16685390 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
16685346 TATATACATA
16685356 TATATACATT-TACATTT
1 TATATAC-TTATACATTT
16685373 TATATACTTATACATTT
1 TATATACTTATACATTT
16685390 T
1 T
16685391 TTATTTCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATACTTATACATTT
Found at i:16685576 original size:32 final size:32
Alignment explanation
Indices: 16685539--16685620 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 32
16685529 ATGTAATTAT
16685539 TATTATTTGTTTATATATATATATATATATGTA
1 TATTATTT-TTTATATATATATATATATATGTA
* *
16685572 -ATTATCTTTTT-CATA-ATCTATATATATGTA
1 TATTAT-TTTTTATATATATATATATATATGTA
*
16685602 TATAAATTTTTT-TATATAT
1 TAT-TATTTTTTATATATAT
16685621 GTACATGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
30 14 0.34
31 13 0.32
32 12 0.29
33 2 0.05
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (32 bp):
TATTATTTTTTATATATATATATATATATGTA
Found at i:16686111 original size:2 final size:2
Alignment explanation
Indices: 16686106--16686130 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16686096 AGATTTTTTA
16686106 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
16686131 AAGGAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16688086 original size:17 final size:17
Alignment explanation
Indices: 16688066--16688109 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
16688056 GGAAATAAAA
16688066 AAAATGTATATGTATAT
1 AAAATGTATATGTATAT
*
16688083 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
16688100 -ATATGTATAT
1 AAAATGTATAT
16688110 AAAAGTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:16688107 original size:10 final size:10
Alignment explanation
Indices: 16688092--16688174 Score: 53
Period size: 10 Copynumber: 8.2 Consensus size: 10
16688082 TAAAATGTAA
16688092 ATGTATATAT
1 ATGTATATAT
*
16688102 ATGTATATAA
1 ATGTATATAT
* *
16688112 AAGT-TATGCAA
1 ATGTATAT--AT
*
16688123 ATAGAATA-AT
1 AT-GTATATAT
*
16688133 ATCTATATAT
1 ATGTATATAT
*
16688143 ATATATATAT
1 ATGTATATAT
*
16688153 ATATATATAT
1 ATGTATATAT
*
16688163 ATATATATAT
1 ATGTATATAT
16688173 AT
1 AT
16688175 AATATGTGCA
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
9 6 0.10
10 48 0.80
11 3 0.05
12 1 0.02
13 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.43
Consensus pattern (10 bp):
ATGTATATAT
Found at i:16688143 original size:2 final size:2
Alignment explanation
Indices: 16688131--16688179 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
16688121 AAATAGAATA
*
16688131 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16688173 AT A- AT AT
1 AT AT AT AT
16688180 GTGCATGTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16688268 original size:3 final size:3
Alignment explanation
Indices: 16688260--16688307 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
16688250 GTATATATAG
* * *
16688260 TAA TAA TAA TAA TAA GAA TAA TAA TGA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16688308 CTTAATAACA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:16688673 original size:21 final size:21
Alignment explanation
Indices: 16688624--16688716 Score: 120
Period size: 21 Copynumber: 4.4 Consensus size: 21
16688614 AAATTAAATC
*
16688624 TCTAAGATTACA-AAATCATA
1 TCTAAGATTGCATAAATCATA
16688644 TCTTCTAAGATTGCATAAATCATA
1 ---TCTAAGATTGCATAAATCATA
*
16688668 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATAAATCATA
16688689 TCTAAGATTGCAT--ATCATA
1 TCTAAGATTGCATAAATCATA
16688708 TCTAAGATT
1 TCTAAGATT
16688717 ATTTATCCTT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
19 15 0.22
21 33 0.49
23 11 0.16
24 8 0.12
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.37
Consensus pattern (21 bp):
TCTAAGATTGCATAAATCATA
Found at i:16689501 original size:20 final size:20
Alignment explanation
Indices: 16689478--16689523 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
16689468 TCGGTATCCT
*
16689478 TGTTTGCACATACATGCCTC
1 TGTTTGCACATACATGCCCC
*
16689498 TGTTTGCACATACGTGCCCC
1 TGTTTGCACATACATGCCCC
16689518 TGTTTG
1 TGTTTG
16689524 TACTTCGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.28, G:0.20, T:0.37
Consensus pattern (20 bp):
TGTTTGCACATACATGCCCC
Found at i:16692484 original size:41 final size:41
Alignment explanation
Indices: 16692426--16692532 Score: 153
Period size: 41 Copynumber: 2.6 Consensus size: 41
16692416 GATGTGTGAA
* *
16692426 ATCAGG-CTTTGAGCCTAGTAGGTTTTGCGCCAGTGTAATGT
1 ATCAGGTC-TTGAACCTAGTAGGCTTTGCGCCAGTGTAATGT
* *
16692467 ATCAGGTCTTGAACCTAGCAGGCTTTGTGCCAGTGTAATGT
1 ATCAGGTCTTGAACCTAGTAGGCTTTGCGCCAGTGTAATGT
*
16692508 ATCAAGTCTTGAACCTAGTAGGCTT
1 ATCAGGTCTTGAACCTAGTAGGCTT
16692533 CATGCTGGTG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 58 0.98
42 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (41 bp):
ATCAGGTCTTGAACCTAGTAGGCTTTGCGCCAGTGTAATGT
Found at i:16692544 original size:41 final size:41
Alignment explanation
Indices: 16692458--16692593 Score: 164
Period size: 41 Copynumber: 3.3 Consensus size: 41
16692448 TTTTGCGCCA
* ** *
16692458 GTGTAATGTATCAGGTCTTGAACCTAGCAGGCTTTGTGCCA
1 GTGTAATGTATCAAGTCTTGAACCTAGCAGGCTTCATGCCG
* *
16692499 GTGTAATGTATCAAGTCTTGAACCTAGTAGGCTTCATGCTG
1 GTGTAATGTATCAAGTCTTGAACCTAGCAGGCTTCATGCCG
* * * *
16692540 GTGTAATATATCAAGCCTTGAGCCTAGCAAGCTTCATGCCG
1 GTGTAATGTATCAAGTCTTGAACCTAGCAGGCTTCATGCCG
**
16692581 GTGTGTTGTATCA
1 GTGTAATGTATCA
16692594 TGTAACTTGT
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 80 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (41 bp):
GTGTAATGTATCAAGTCTTGAACCTAGCAGGCTTCATGCCG
Found at i:16692670 original size:2 final size:2
Alignment explanation
Indices: 16692663--16692687 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16692653 TATACGATCT
16692663 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16692688 GGAGTTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16696002 original size:5 final size:5
Alignment explanation
Indices: 16695992--16696048 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
16695982 TATCATATGA
* * *
16695992 GATAT GATAT GATAC GATAC GATAT G-TAAT CCAATAT GATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT GAT-AT --GATAT GATAT GATAT
16696039 GATAT GATAT
1 GATAT GATAT
16696049 AAGATATACT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 1 0.02
5 40 0.91
7 2 0.05
8 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (5 bp):
GATAT
Found at i:16696055 original size:27 final size:27
Alignment explanation
Indices: 16695971--16696055 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
16695961 TGGGGGTAAT
* * * * *
16695971 ATATGATCTGTTATCATATGAGATATG
1 ATATGATATGATATGATATGATATAAG
* * *
16695998 ATATGATACGATACGATATG-TAATCCA-
1 ATATGATATGATATGATATGAT-AT-AAG
16696025 ATATGATATGATATGATATGATATAAG
1 ATATGATATGATATGATATGATATAAG
16696052 ATAT
1 ATAT
16696056 ACTTCGATAA
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
26 1 0.02
27 41 0.95
28 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.36
Consensus pattern (27 bp):
ATATGATATGATATGATATGATATAAG
Found at i:16698653 original size:21 final size:21
Alignment explanation
Indices: 16698629--16698669 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16698619 AATTTAACTA
*
16698629 AATTTAATACAATTCATATTC
1 AATTCAATACAATTCATATTC
* *
16698650 AATTCAGTCCAATTCATATT
1 AATTCAATACAATTCATATT
16698670 TTAGGCAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.41
Consensus pattern (21 bp):
AATTCAATACAATTCATATTC
Found at i:16701968 original size:28 final size:28
Alignment explanation
Indices: 16701928--16701983 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
16701918 ACTTTAGCAG
16701928 AGCTCGCACAATATAGCATAATTCACAA
1 AGCTCGCACAATATAGCATAATTCACAA
16701956 AGCTCGCACAATATAGCATAATTCACAA
1 AGCTCGCACAATATAGCATAATTCACAA
16701984 TTCATAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.25, G:0.11, T:0.21
Consensus pattern (28 bp):
AGCTCGCACAATATAGCATAATTCACAA
Found at i:16702190 original size:17 final size:18
Alignment explanation
Indices: 16702157--16702191 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16702147 AGCATAGCAG
*
16702157 GGTTCGCATATACAACAT
1 GGTTCGCATACACAACAT
16702175 GGTTCGCAT-CACAACAT
1 GGTTCGCATACACAACAT
16702192 AGCAGGGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (18 bp):
GGTTCGCATACACAACAT
Found at i:16702292 original size:35 final size:35
Alignment explanation
Indices: 16702195--16702499 Score: 217
Period size: 35 Copynumber: 8.7 Consensus size: 35
16702185 ACAACATAGC
* * * * *
16702195 AGGGTTCACACATAAGGTAGGCTTCACACTTTTGGTT
1 AGGGTTCACACATTAGGTAGGGTTCGCAC-ATTAG-T
* *
16702232 A-GGTTCACACATTGGGTAGGGTTCGCACGTTAGT
1 AGGGTTCACACATTAGGTAGGGTTCGCACATTAGT
* * * *
16702266 AGAGTTCACACTTTAGGTTGGATTCGCACATTAGGT
1 AGGGTTCACACATTAGGTAGGGTTCGCACATTA-GT
*
16702302 AGGGTTCTCACATT-GGTAGGGTTCGCACATTAGT
1 AGGGTTCACACATTAGGTAGGGTTCGCACATTAGT
** * *
16702336 AGGGTTTTCACTTTAGGAAGGGTTCGCACATTAGGT
1 AGGGTTCACACATTAGGTAGGGTTCGCACATTA-GT
** * * *
16702372 AGGGTTTGCACATTA-GTAGGGTTTGCACTTTAGGA
1 AGGGTTCACACATTAGGTAGGGTTCGCACATTA-GT
* * * * * *
16702407 AGGCTTCACACAGTA-GTAAGGTTTGCACTTTAGGA
1 AGGGTTCACACATTAGGTAGGGTTCGCACATTA-GT
** *
16702442 AGGGTTCACACATTA-GTAGGGTTCAAACTTTAGGT
1 AGGGTTCACACATTAGGTAGGGTTCGCACATTA-GT
* *
16702477 AGGGCTCGCACATT-GGTAGGGTT
1 AGGGTTCACACATTAGGTAGGGTT
16702500 TGCATGTAAG
Statistics
Matches: 223, Mismatches: 40, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
34 16 0.07
35 155 0.70
36 51 0.23
37 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (35 bp):
AGGGTTCACACATTAGGTAGGGTTCGCACATTAGT
Found at i:16702500 original size:70 final size:70
Alignment explanation
Indices: 16702233--16702535 Score: 225
Period size: 70 Copynumber: 4.3 Consensus size: 70
16702223 CTTTTGGTTA
* * * * * * * *
16702233 GGTTCACACATTGGGTAGGGTTCGCACGTTA-GTAGAGTTCACACTTTAGGTTGGATTCGCACAT
1 GGTTCACACATT-AGTAGGGTTCGCACTTTAGGTAGGGCTCACACATT-GGTAGGGTTTGCACAT
16702297 TAGGTAG
64 TAGGTAG
* * * * ** * * *
16702304 GGTTCTCACATTGGTAGGGTTCGCACATTA-GTAGGGTTTTCACTTTAGGAAGGGTTCGCACATT
1 GGTTCACACATTAGTAGGGTTCGCACTTTAGGTAGGGCTCACACATT-GGTAGGGTTTGCACATT
16702368 AGGTAG
65 AGGTAG
** * * * * * *
16702374 GGTTTGCACATTAGTAGGGTTTGCACTTTAGG-AAGGCTTCACACAGTAGTAAGGTTTGCACTTT
1 GGTTCACACATTAGTAGGGTTCGCACTTTAGGTAGGGC-TCACACATTGGTAGGGTTTGCACATT
*
16702438 AGGAAG
65 AGGTAG
** * ** *
16702444 GGTTCACACATTAGTAGGGTTCAAACTTTAGGTAGGGCTCGCACATTGGTAGGGTTTGCATGTAA
1 GGTTCACACATTAGTAGGGTTCGCACTTTAGGTAGGGCTCACACATTGGTAGGGTTTGCACATTA
16702509 GGTAG
66 GGTAG
** * *
16702514 GGTTTGCATATTAGTAGAGTTC
1 GGTTCACACATTAGTAGGGTTC
16702536 TTACAATGAC
Statistics
Matches: 186, Mismatches: 43, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
70 165 0.89
71 21 0.11
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (70 bp):
GGTTCACACATTAGTAGGGTTCGCACTTTAGGTAGGGCTCACACATTGGTAGGGTTTGCACATTA
GGTAG
Found at i:16702597 original size:33 final size:33
Alignment explanation
Indices: 16702560--16702664 Score: 131
Period size: 33 Copynumber: 3.2 Consensus size: 33
16702550 TAAGGTTCGT
* * * *
16702560 ACATCACATAGAAGTCATATAGCATAGGTTCAC
1 ACATCACATAGTAGTCACACAACATAGGTTCAC
*
16702593 ACATCACGTAGTAGTCACACAACATAGGTTCGA-
1 ACATCACATAGTAGTCACACAACATAGGTTC-AC
* *
16702626 AAATCACATAGTAGTCACACAACATAGGTTCGC
1 ACATCACATAGTAGTCACACAACATAGGTTCAC
16702659 ACATCA
1 ACATCA
16702665 TAATAGGGTT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
33 60 0.98
34 1 0.02
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (33 bp):
ACATCACATAGTAGTCACACAACATAGGTTCAC
Found at i:16702696 original size:22 final size:22
Alignment explanation
Indices: 16702671--16702730 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
16702661 ATCATAATAG
16702671 GGTTCACATGAAATTATAACAA
1 GGTTCACATGAAATTATAACAA
* * * * *
16702693 GGTTTACATGATATTTTAGCAG
1 GGTTCACATGAAATTATAACAA
* *
16702715 GGTTCGCATGACATTA
1 GGTTCACATGAAATTA
16702731 CCTAGGCTTT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (22 bp):
GGTTCACATGAAATTATAACAA
Found at i:16704577 original size:28 final size:29
Alignment explanation
Indices: 16704545--16704607 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
16704535 ACTTTGTGTA
16704545 TTTCTCAACCTCC-C-TTATTCATCTTATG
1 TTTCTCAA-CTCCTCATTATTCATCTTATG
*
16704573 TTTCTCAACTCCTCATTTTTTCATCTTATG
1 TTTCTCAACTCCTCA-TTATTCATCTTATG
16704603 TTTCT
1 TTTCT
16704608 AGAGATTTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 4 0.13
28 9 0.29
30 18 0.58
ACGTcount: A:0.16, C:0.29, G:0.03, T:0.52
Consensus pattern (29 bp):
TTTCTCAACTCCTCATTATTCATCTTATG
Found at i:16707640 original size:2 final size:2
Alignment explanation
Indices: 16707633--16707679 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
16707623 ATGTTATGAA
16707633 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16707675 AT AT A
1 AT AT A
16707680 AGAGGTTCGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16708016 original size:41 final size:41
Alignment explanation
Indices: 16707953--16708048 Score: 151
Period size: 41 Copynumber: 2.4 Consensus size: 41
16707943 AGCTCTGTGC
*
16707953 CTAGCA-GCTTAATACCAGTGAAATATTTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCAGTGAAATATTTCAGACTTTACGT
*
16707993 CTAGCAGGCTTAATGCC-GATGAAATATTTCAGACTTTATGT
1 CTAGCAGGCTTAATGCCAG-TGAAATATTTCAGACTTTACGT
16708034 CTAGCAGGCTTAATG
1 CTAGCAGGCTTAATG
16708049 TTGGTGTTCT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
40 7 0.13
41 45 0.87
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCAGTGAAATATTTCAGACTTTACGT
Done.