Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 84 of 126
Found at i:25647505 original size:17 final size:17
Alignment explanation
Indices: 25647483--25647558 Score: 70
Period size: 17 Copynumber: 4.6 Consensus size: 17
25647473 ATCTACAAGC
25647483 TAAATATTAAATTAAAT
1 TAAATATTAAATTAAAT
25647500 TAAATATTAAATT-AAT
1 TAAATATTAAATTAAAT
* * *
25647516 AAAATACT--GTTAAGA-
1 TAAATATTAAATTAA-AT
*
25647531 TAAATATTAAATTTAAT
1 TAAATATTAAATTAAAT
*
25647548 TTAATATTAAA
1 TAAATATTAAA
25647559 CTATTAAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
14 2 0.04
15 7 0.15
16 11 0.24
17 26 0.57
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (17 bp):
TAAATATTAAATTAAAT
Found at i:25648000 original size:19 final size:19
Alignment explanation
Indices: 25647976--25648015 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
25647966 AAAATATCAT
*
25647976 ATTAATTTTAA-TTTATTTG
1 ATTAA-TTTAACTTTACTTG
25647995 ATTAATTTAACTTTACTTG
1 ATTAATTTAACTTTACTTG
25648014 AT
1 AT
25648016 AAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (19 bp):
ATTAATTTAACTTTACTTG
Found at i:25653817 original size:17 final size:17
Alignment explanation
Indices: 25653797--25653858 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
25653787 CCCATGGGAG
25653797 ATACTGTCCACTAGGCA
1 ATACTGTCCACTAGGCA
* * *
25653814 ATACTATTCGCTAGGCGA
1 ATACTGTCCACTAGGC-A
**
25653832 A-ACTGTCTGCTAGGCA
1 ATACTGTCCACTAGGCA
*
25653848 AAACTGTCCAC
1 ATACTGTCCAC
25653859 CACATGATAC
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
16 2 0.06
17 31 0.89
18 2 0.06
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.24
Consensus pattern (17 bp):
ATACTGTCCACTAGGCA
Found at i:25654488 original size:6 final size:6
Alignment explanation
Indices: 25654477--25654501 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
25654467 AAATATGCAA
25654477 CCATTT CCATTT CCATTT CCATTT C
1 CCATTT CCATTT CCATTT CCATTT C
25654502 ATATATTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (6 bp):
CCATTT
Found at i:25656528 original size:22 final size:18
Alignment explanation
Indices: 25656483--25656520 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
25656473 TTAATGTTTA
25656483 TATAATTAAAATGAATAT
1 TATAATTAAAATGAATAT
25656501 TATAATTAAAATGAAT-T
1 TATAATTAAAATGAATAT
25656518 TAT
1 TAT
25656521 TTTATAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
TATAATTAAAATGAATAT
Found at i:25656959 original size:19 final size:19
Alignment explanation
Indices: 25656935--25656976 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
25656925 CAATTGAGGG
*
25656935 TAATTAGCGACTTAATTGA
1 TAATTAGCGACTTAATCGA
* *
25656954 TAATTAGTGATTTAATCGA
1 TAATTAGCGACTTAATCGA
25656973 TAAT
1 TAAT
25656977 AGGCCGAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.40
Consensus pattern (19 bp):
TAATTAGCGACTTAATCGA
Found at i:25657060 original size:28 final size:28
Alignment explanation
Indices: 25657027--25657080 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
25657017 TCCATTAAGT
*
25657027 TATTTT-AGATTAATTAATTTTATTAGGA
1 TATTTTGAGA-TAATTAATTTAATTAGGA
*
25657055 TATTTTGGGATAATTAATTTAATTAG
1 TATTTTGAGATAATTAATTTAATTAG
25657081 TTTAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (28 bp):
TATTTTGAGATAATTAATTTAATTAGGA
Found at i:25659950 original size:15 final size:14
Alignment explanation
Indices: 25659899--25659950 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
25659889 TTTAGTTTGG
25659899 ATTATTTTTA-TTT
1 ATTATTTTTACTTT
* *
25659912 TTTATTTTTTCTATT
1 ATTATTTTTACT-TT
*
25659927 ATTAATTTTAACTTT
1 ATT-ATTTTTACTTT
25659942 ATTATTTTT
1 ATTATTTTT
25659951 TTGATTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 8 0.27
14 6 0.20
15 9 0.30
16 7 0.23
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTATTTTTACTTT
Found at i:25660980 original size:15 final size:14
Alignment explanation
Indices: 25660929--25660980 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
25660919 TTTAGTTTGG
25660929 ATTATTTTTA-TTT
1 ATTATTTTTACTTT
* *
25660942 TTTATTTTTTCTATT
1 ATTATTTTTACT-TT
*
25660957 ATTAATTTTAACTTT
1 ATT-ATTTTTACTTT
25660972 ATTATTTTT
1 ATTATTTTT
25660981 TTGATTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 8 0.27
14 6 0.20
15 9 0.30
16 7 0.23
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTATTTTTACTTT
Found at i:25664694 original size:6 final size:6
Alignment explanation
Indices: 25664683--25664717 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
25664673 ATAAATAAGT
* *
25664683 TTTATG TTTATG TTTATG TTTATT TTTATT TTTAT
1 TTTATG TTTATG TTTATG TTTATG TTTATG TTTAT
25664718 TTTCATCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (6 bp):
TTTATG
Found at i:25664718 original size:6 final size:6
Alignment explanation
Indices: 25664682--25664720 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
25664672 AATAAATAAG
* * *
25664682 TTTTAT GTTTAT GTTTAT GTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
25664721 CATCTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:25664718 original size:12 final size:12
Alignment explanation
Indices: 25664682--25664720 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
25664672 AATAAATAAG
25664682 TTTTATGTTTAT
1 TTTTATGTTTAT
*
25664694 GTTTATGTTTAT
1 TTTTATGTTTAT
*
25664706 TTTTATTTTTAT
1 TTTTATGTTTAT
25664718 TTT
1 TTT
25664721 CATCTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTTATGTTTAT
Found at i:25664765 original size:17 final size:17
Alignment explanation
Indices: 25664738--25664779 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
25664728 TTTTCATTTA
25664738 TTTAATCTTAATCTTAAT
1 TTTAAT-TTAATCTTAAT
* *
25664756 TTTAATTTAATTTTATT
1 TTTAATTTAATCTTAAT
25664773 TTTAATT
1 TTTAATT
25664780 AGTTGTCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTAATTTAATCTTAAT
Found at i:25664767 original size:11 final size:11
Alignment explanation
Indices: 25664737--25664770 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
25664727 ATTTTCATTT
*
25664737 ATTTAATCTTA
1 ATTTAATTTTA
25664748 ATCTTAATTTTA
1 AT-TTAATTTTA
25664760 ATTTAATTTTA
1 ATTTAATTTTA
25664771 TTTTTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTAATTTTA
Found at i:25664770 original size:6 final size:6
Alignment explanation
Indices: 25664738--25664779 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
25664728 TTTTCATTTA
* * *
25664738 TTTAAT CTTAAT CTTAAT TTTAA- TTTAAT TTTATT TTTAAT T
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT T
25664780 AGTTGTCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (6 bp):
TTTAAT
Found at i:25667950 original size:35 final size:35
Alignment explanation
Indices: 25667904--25667975 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
25667894 GAACTTACTC
* * *
25667904 TACTCTTAAAACTA-TCTGTTCAGTTCATGATTTGT
1 TACTCTAAAAACTAGT-TGTTCAATTCATCATTTGT
25667939 TACTCTAAAAACTAGTTGTTCAATTCATCATTTGT
1 TACTCTAAAAACTAGTTGTTCAATTCATCATTTGT
25667974 TA
1 TA
25667976 GCATTTAGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 32 0.97
36 1 0.03
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.44
Consensus pattern (35 bp):
TACTCTAAAAACTAGTTGTTCAATTCATCATTTGT
Found at i:25674052 original size:42 final size:41
Alignment explanation
Indices: 25673988--25674143 Score: 141
Period size: 42 Copynumber: 3.7 Consensus size: 41
25673978 GCCCGAAGGC
*
25673988 TGAACAGAAGCTCATGAGAGCTAAACAGAAACCCATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTAAAC-GAAACCCATAAGGGT
* * * *
25674030 TGAATAGAAGCTCGTAAGAGCTAAACAAAAACCTATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTAAAC-GAAACCCATAAGGGT
* * * * * * ***
25674072 TAAACAAAAGCTCAAAAGAGTTGAACGAAAACTCATATCAGT
1 TGAACAGAAGCTCATAAGAGCTAAACG-AAACCCATAAGGGT
* *
25674114 TGAATAGAAGCTCGTAAGAGCTAAACGAAA
1 TGAACAGAAGCTCATAAGAGCTAAACGAAA
25674144 AGTAAACACG
Statistics
Matches: 88, Mismatches: 25, Indels: 3
0.76 0.22 0.03
Matches are distributed among these distances:
41 3 0.03
42 85 0.97
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.17
Consensus pattern (41 bp):
TGAACAGAAGCTCATAAGAGCTAAACGAAACCCATAAGGGT
Found at i:25679911 original size:4 final size:4
Alignment explanation
Indices: 25679902--25679934 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
25679892 TATTTTTATT
25679902 TTTA TTTA TTTA TTTA TTTA TTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA
25679935 AATTTTTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:25681523 original size:42 final size:42
Alignment explanation
Indices: 25681471--25681615 Score: 150
Period size: 42 Copynumber: 3.5 Consensus size: 42
25681461 TCAGAAGCCC
* *
25681471 AAAGGCTGAACAGAAGCTCATGAGAGCTAAAC-AGAAACCCAT
1 AAAGGTTGAACAGAAGCTCATAAGAGCTAAACGA-AAACCCAT
*
25681513 AAAGGTTGAACAGAAGCTCGTAAGAGCTAAACGAAAACCCAT
1 AAAGGTTGAACAGAAGCTCATAAGAGCTAAACGAAAACCCAT
* * * * * * * *
25681555 AAGGGTTAAACAGAAGTTCAAAAGAGTTGAATGAAAACTCAT
1 AAAGGTTGAACAGAAGCTCATAAGAGCTAAACGAAAACCCAT
*
25681597 -ATGAGTTGAACAGAAGCTC
1 AAAG-GTTGAACAGAAGCTC
25681616 GTGAAAGCTA
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
41 2 0.02
42 83 0.97
43 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.17
Consensus pattern (42 bp):
AAAGGTTGAACAGAAGCTCATAAGAGCTAAACGAAAACCCAT
Found at i:25686669 original size:13 final size:13
Alignment explanation
Indices: 25686651--25686675 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25686641 AAATTCAATG
25686651 TCAATTTCATATA
1 TCAATTTCATATA
25686664 TCAATTTCATAT
1 TCAATTTCATAT
25686676 CCAAACATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (13 bp):
TCAATTTCATATA
Found at i:25687748 original size:23 final size:24
Alignment explanation
Indices: 25687704--25687749 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
25687694 AAATTCCTCC
*
25687704 TGAGCTGATAAATAGTAGGCTCTGT
1 TGAGCTGA-AAATAGTAAGCTCTGT
*
25687729 TGAGCTG-AAATGGTAAGCTCT
1 TGAGCTGAAAATAGTAAGCTCT
25687750 AACGAGCTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
25 7 0.37
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.30
Consensus pattern (24 bp):
TGAGCTGAAAATAGTAAGCTCTGT
Found at i:25688063 original size:49 final size:49
Alignment explanation
Indices: 25688009--25688102 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
25687999 ATCTATTCAT
*
25688009 TTAAATACATACATGTAAATACTCAATTCGCATGCCTTCTCAAATTTAA
1 TTAAATACATACATGTAAATACTCAATTCGCATACCTTCTCAAATTTAA
* *
25688058 TTAAATACATACATTTAAATACTCAATTCGCATACTTTCTCAAAT
1 TTAAATACATACATGTAAATACTCAATTCGCATACCTTCTCAAAT
25688103 CATATATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.36
Consensus pattern (49 bp):
TTAAATACATACATGTAAATACTCAATTCGCATACCTTCTCAAATTTAA
Found at i:25688127 original size:65 final size:66
Alignment explanation
Indices: 25688051--25688337 Score: 461
Period size: 65 Copynumber: 4.3 Consensus size: 66
25688041 TGCCTTCTCA
*
25688051 AATTTAATTAAATACATACATTTAAATACTCAATTCGCATACTTTCTCAAAT-CATATATATAAT
1 AATTTAATTAAATACATACATTTAAATACTCAATTCACATACTTTCTCAAATACATATATATAAT
*
25688115 T
66 C
* *
25688116 GATTTAATTAAATACATACATTTAAATACTCAATTCGCATACTTTCTCAAAT-CATATATATAAT
1 AATTTAATTAAATACATACATTTAAATACTCAATTCACATACTTTCTCAAATACATATATATAAT
*
25688180 T
66 C
* *
25688181 GATTTAATTAAATACATACATTTAAATACTCAATTCACATACTTTCTCAAATCACATATATTTAA
1 AATTTAATTAAATACATACATTTAAATACTCAATTCACATACTTTCTCAAAT-ACATATATATAA
25688246 TC
65 TC
* *
25688248 AATTTAATTAACTACATACATTTAAATACTCAATTCACATACTTTCTCAAATAACGTATATATAA
1 AATTTAATTAAATACATACATTTAAATACTCAATTCACATACTTTCTCAAAT-ACATATATATAA
25688313 TC
65 TC
25688315 AATTTAATTAAATACATACATTT
1 AATTTAATTAAATACATACATTT
25688338 TATTACTAAT
Statistics
Matches: 210, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
65 115 0.55
67 95 0.45
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.39
Consensus pattern (66 bp):
AATTTAATTAAATACATACATTTAAATACTCAATTCACATACTTTCTCAAATACATATATATAAT
C
Found at i:25694253 original size:6 final size:6
Alignment explanation
Indices: 25694242--25694270 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
25694232 ATATAGGAAA
25694242 TTTATT TTTATT TTTATT TTTATT TTTAT
1 TTTATT TTTATT TTTATT TTTATT TTTAT
25694271 GCTTTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTATT
Found at i:25694947 original size:8 final size:8
Alignment explanation
Indices: 25694929--25694964 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
25694919 TGAACAATGA
25694929 AAAACTTAG
1 AAAA-TTAG
*
25694938 AAATTTAG
1 AAAATTAG
25694946 AAAATTAG
1 AAAATTAG
25694954 AAAATTAG
1 AAAATTAG
25694962 AAA
1 AAA
25694965 TGTTGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 22 0.88
9 3 0.12
ACGTcount: A:0.61, C:0.03, G:0.11, T:0.25
Consensus pattern (8 bp):
AAAATTAG
Found at i:25697353 original size:13 final size:12
Alignment explanation
Indices: 25697319--25697365 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
25697309 TTAAATAATA
*
25697319 ATTTCACATAT-
1 ATTTCATATATC
25697330 ATTTCCATATAATC
1 ATTT-CATAT-ATC
25697344 ATTTCATATATCC
1 ATTTCATATAT-C
25697357 ATTTCATAT
1 ATTTCATAT
25697366 CACCATTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 4 0.13
12 6 0.19
13 17 0.55
14 4 0.13
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTTCATATATC
Found at i:25700437 original size:27 final size:27
Alignment explanation
Indices: 25700392--25700450 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
25700382 GTCAAAAAAT
**
25700392 GGAAGCCTTTGTGGCAATCTAAGAAAC
1 GGAAGCCTTTGCAGCAATCTAAGAAAC
* *
25700419 GGAAGCCTTTGCAGTAATCTAAGAAAT
1 GGAAGCCTTTGCAGCAATCTAAGAAAC
25700446 GGAAG
1 GGAAG
25700451 TATTTTTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.22
Consensus pattern (27 bp):
GGAAGCCTTTGCAGCAATCTAAGAAAC
Found at i:25709039 original size:10 final size:9
Alignment explanation
Indices: 25709021--25709049 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
25709011 TTTCAACTGG
25709021 AAGAAAAAA
1 AAGAAAAAA
25709030 AAGAAAAAA
1 AAGAAAAAA
25709039 AAGAAAAAA
1 AAGAAAAAA
25709048 AA
1 AA
25709050 CAATTTTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:25712329 original size:28 final size:29
Alignment explanation
Indices: 25712295--25712360 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
25712285 TATTTAATCA
*
25712295 TTTTTTAAAT-CTATATGTATAT-ATTTAT
1 TTTTTTAAATGCT-CATGTATATAATTTAT
* *
25712323 TTTTTTATATGGTCATGTATATACATTTAT
1 TTTTTTAAATGCTCATGTATATA-ATTTAT
25712353 TTTTTTAA
1 TTTTTTAA
25712361 TGAATGTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 17 0.55
29 1 0.03
30 13 0.42
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.61
Consensus pattern (29 bp):
TTTTTTAAATGCTCATGTATATAATTTAT
Found at i:25718722 original size:88 final size:88
Alignment explanation
Indices: 25718612--25719274 Score: 950
Period size: 88 Copynumber: 7.5 Consensus size: 88
25718602 AGCAGATCGG
*
25718612 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCAACAGCGAAGCAGATCGAAGACACCAACCTTGCCT
*
25718677 CCCTGGGTTGTAGTGGAGCAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
* ** * *
25718700 TAAAAATAGAAGATCTTGCCTTCCTGCACTGACAGCGAAACAGATCAAAGACACCAACCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCAACAGCGAAGCAGATCGAAGACACCAACCTTGCCT
*
25718765 TCCTGGGTTGCAGTGGAGCAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
* * *
25718788 TAAAAATAGCAGATCTTGCCTTCCTACACCAACAGCGAAGCAGATCGAAGACATCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCAACAGCGAAGCAGATCGAAGACACCAACCTTGCCT
*
25718853 CCCTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
* *
25718876 TAAAAATAGCAGATCTTGCCTTCCTACACCAACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCAACAGCGAAGCAGATCGAAGACACCAACCTTGCCT
*
25718941 CCCTGGGTTGCAGTGGAGTAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
* * * * * *
25718964 TAAAAATAGCAGATCTTGCCTTCCTACGCCAATAGCGAAGCAGATCGAAGACATCAACCTTTCTT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCAACAGCGAAGCAGATCGAAGACACCAACCTTGCCT
* * *
25719029 CCCTAGGTTGCAGCGGAGCAAGT
66 CCCTGGGTTGCAGTGGAGCAGGT
* * * * *
25719052 TAAAAATAGTAGATCTTGCCTTCCTGCACCGATAGGGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCAACAGCGAAGCAGATCGAAGACACCAACCTTGCCT
** *
25719117 CCCTGGGTTGCAGCAGAGCAGGC
66 CCCTGGGTTGCAGTGGAGCAGGT
* * *
25719140 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCGACCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCAACAGCGAAGCAGATCGAAGACACCAACCTTGCCT
** * *
25719205 CTTTGGGTTGTAGTGGAGCAGGC
66 CCCTGGGTTGCAGTGGAGCAGGT
* *
25719228 T-AAAATAGTAGATCTTGCCTTCCTGCACCAACAGTGAAGCAGATCGA
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCAACAGCGAAGCAGATCGA
25719275 TGACCCCAGC
Statistics
Matches: 518, Mismatches: 57, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
87 42 0.08
88 476 0.92
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (88 bp):
TAAAAATAGCAGATCTTGCCTTCCTGCACCAACAGCGAAGCAGATCGAAGACACCAACCTTGCCT
CCCTGGGTTGCAGTGGAGCAGGT
Found at i:25718806 original size:44 final size:44
Alignment explanation
Indices: 25718670--25718988 Score: 158
Period size: 44 Copynumber: 7.2 Consensus size: 44
25718660 AGACACCAAC
* * * *
25718670 CTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTAAAAATAGAAGAT
1 CTTGCCTTCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
*** * * * * * * * *
25718714 CTTGCCTTCCTGCACTGACAGCGAAACAGATCAAAGACACCA-AC
1 CTTGCCTTCCTGGGTTG-CAGCGGAGCAGGTTAAAAATAGCAGAT
*
25718758 CTTGCCTTCCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTTCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
****** * * ** * * * *
25718802 CTTGCCTTCCTACACCAACAGCGAAGCAGATCGAAGACATCAG-C
1 CTTGCCTTCCT-GGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
*
25718846 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTTCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
****** * * ** * * * *
25718890 CTTGCCTTCCTACACCAACAGCGAAGCAGATCGAAGACACCAG-C
1 CTTGCCTTCCT-GGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
* * *
25718934 CTTGCCTCCCTGGGTTGCAGTGGAGTAGGTTAAAAATAGCAGAT
1 CTTGCCTTCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
25718978 CTTGCCTTCCT
1 CTTGCCTTCCT
25718989 ACGCCAATAG
Statistics
Matches: 179, Mismatches: 90, Indels: 12
0.64 0.32 0.04
Matches are distributed among these distances:
43 50 0.28
44 80 0.45
45 49 0.27
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (44 bp):
CTTGCCTTCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
Found at i:25718918 original size:45 final size:45
Alignment explanation
Indices: 25718781--25718918 Score: 127
Period size: 45 Copynumber: 3.1 Consensus size: 45
25718771 GTTGCAGTGG
25718781 AGCAGGTTAAAAATAGCAGATCTTGCCTTCCTACACCAACAGCGA
1 AGCAGGTTAAAAATAGCAGATCTTGCCTTCCTACACCAACAGCGA
* ** * * * * * ****** *
25718826 AGCAGATCGAAGACATCAG-CCTTGCCTCCCT-GGGTTGCAGCGG
1 AGCAGGTTAAAAATAGCAGATCTTGCCTTCCTACACCAACAGCGA
25718869 AGCAGGTTAAAAATAGCAGATCTTGCCTTCCTACACCAACAGCGA
1 AGCAGGTTAAAAATAGCAGATCTTGCCTTCCTACACCAACAGCGA
25718914 AGCAG
1 AGCAG
25718919 ATCGAAGACA
Statistics
Matches: 61, Mismatches: 30, Indels: 4
0.64 0.32 0.04
Matches are distributed among these distances:
43 18 0.30
44 20 0.33
45 23 0.38
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (45 bp):
AGCAGGTTAAAAATAGCAGATCTTGCCTTCCTACACCAACAGCGA
Found at i:25719351 original size:44 final size:44
Alignment explanation
Indices: 25719285--25719620 Score: 332
Period size: 44 Copynumber: 7.8 Consensus size: 44
25719275 TGACCCCAGC
* * * *
25719285 CCTATCTCCCTAGTCAGTAGTGGAATAGGTTAAAGATTTTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
25719329 CCTATCTCCCTGGTCAGCAGTGGAATTGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
25719373 TCTATCTCCCTAGG-CAGCAGTGGAATAGATT-AA-A----GAAT
1 CCTATCTCCCT-GGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * * *
25719411 CCTATTTCCCTCGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * *
25719455 CCTATCTCCTTGATCAGCAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * * *
25719499 TCTATCTCCCTAGG-CAGCAGTGAAATAGATTGAAGATTGT-AGGT
1 CCTATCTCCCT-GGTCAGCAGTGGAATAGGTTGAAGATTGTGA-AT
* * * * *
25719543 CTTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGCTCGTGAAC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
25719587 CCTATCTCCCTAAG-CAGCAGTGGAGTAGGTTGAA
1 CCTATCTCCCT-GGTCAGCAGTGGAATAGGTTGAA
25719621 AATAGTAGAT
Statistics
Matches: 239, Mismatches: 40, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
37 1 0.00
38 29 0.12
39 2 0.01
40 1 0.00
42 1 0.00
43 5 0.02
44 195 0.82
45 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:25719421 original size:38 final size:38
Alignment explanation
Indices: 25719368--25719446 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
25719358 TTGAAGATTG
* *
25719368 AGAATTCTATCTCCCTAGGCAGCAGTGGAATAGATTAA
1 AGAATCCTATCTCCCTAGACAGCAGTGGAATAGATTAA
* * *
25719406 AGAATCCTATTTCCCTCGACAGCAGTGGAATAGGTTAA
1 AGAATCCTATCTCCCTAGACAGCAGTGGAATAGATTAA
25719444 AGA
1 AGA
25719447 TTGTGAATCC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (38 bp):
AGAATCCTATCTCCCTAGACAGCAGTGGAATAGATTAA
Found at i:25719447 original size:82 final size:82
Alignment explanation
Indices: 25719325--25719482 Score: 219
Period size: 82 Copynumber: 1.9 Consensus size: 82
25719315 TAAAGATTTT
* * * * *
25719325 GAATCCTATCTCCCTGGTCAGCAGTGGAATTGGTTGAAGATTGAGAATTCTATCTCCCTAG-GCA
1 GAATCCTATCTCCCTCGACAGCAGTGGAATAGGTTAAAGATTGAGAATCCTATCT-CCTAGAGCA
25719389 GCAGTGGAATAGATTAAA
65 GCAGTGGAATAGATTAAA
* * * *
25719407 GAATCCTATTTCCCTCGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCTTGATCAG
1 GAATCCTATCTCCCTCGACAGCAGTGGAATAGGTTAAAGATTGAGAATCCTATCTCCTAGAGCAG
25719472 CAGTGGAATAG
66 CAGTGGAATAG
25719483 GTTGAAGATT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
81 4 0.06
82 62 0.94
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (82 bp):
GAATCCTATCTCCCTCGACAGCAGTGGAATAGGTTAAAGATTGAGAATCCTATCTCCTAGAGCAG
CAGTGGAATAGATTAAA
Found at i:25719510 original size:126 final size:131
Alignment explanation
Indices: 25719285--25719620 Score: 457
Period size: 126 Copynumber: 2.6 Consensus size: 131
25719275 TGACCCCAGC
* *
25719285 CCTATCTCCCTAGTCAGTAGTGGAATAGGTTAAAGATTTTGAATCCTATCTCCCTGGTCAGCAGT
1 CCTATCTCCCTAGTCAGTAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGATCAGCAGT
* *
25719350 GGAATTGGTTGAAGATTGAGAATTCTATCTCCCTAGGCAGCAGTGGAATAGATT-AA-A-G-A-A
66 GGAATAGGTTGAAGATTGAGAATTCTATCTCCCTAGGCAGCAGTGAAATAGATTGAAGATGTAGA
25719410 T
131 T
* * * * *
25719411 CCTATTTCCCTCGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCTTGATCAGCAGT
1 CCTATCTCCCTAGTCAGTAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGATCAGCAGT
25719476 GGAATAGGTTGAAGATTGAGAATTCTATCTCCCTAGGCAGCAGTGAAATAGATTGAAGATTGTAG
66 GGAATAGGTTGAAGATTGAGAATTCTATCTCCCTAGGCAGCAGTGAAATAGATTGAAGA-TGTAG
*
25719541 GT
130 AT
* * * * * * * *
25719543 CTTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGCTCGTGAACCCTATCTCCCTAAGCAGCAGT
1 CCTATCTCCCTAGTCAGTAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGATCAGCAGT
*
25719608 GGAGTAGGTTGAA
66 GGAATAGGTTGAA
25719621 AATAGTAGAT
Statistics
Matches: 181, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
126 110 0.61
127 2 0.01
128 1 0.01
130 1 0.01
131 1 0.01
132 66 0.36
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (131 bp):
CCTATCTCCCTAGTCAGTAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGATCAGCAGT
GGAATAGGTTGAAGATTGAGAATTCTATCTCCCTAGGCAGCAGTGAAATAGATTGAAGATGTAGA
T
Found at i:25721518 original size:27 final size:27
Alignment explanation
Indices: 25721443--25721512 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
25721433 TATTATTTAA
* *
25721443 TTATTATTTTTAATCTATATGTATATAT
1 TTATT-TTTTTAATCGACATGTATATAT
*
25721471 TTA-TTTTTTATATGGACATGTATATACAT
1 TTATTTTTTTA-ATCGACATGTATAT--AT
25721500 TTATTTTTTTAAT
1 TTATTTTTTTAAT
25721513 GAATGTTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
26 6 0.17
27 12 0.34
28 3 0.09
29 7 0.20
30 7 0.20
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (27 bp):
TTATTTTTTTAATCGACATGTATATAT
Found at i:25732821 original size:30 final size:30
Alignment explanation
Indices: 25732784--25732859 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
25732774 TAATCGAATT
*
25732784 ATTCGAGTCAACTCGAAATTT-CTTTTCGA
1 ATTCGAGTCAACTCGAAATTTGATTTTCGA
* *
25732813 ATTTCGAGTTCAAATC-AATTTTGATTTTCGA
1 A-TTCGAG-TCAACTCGAAATTTGATTTTCGA
*
25732844 ATTCGAAT-AACTCGAA
1 ATTCGAGTCAACTCGAA
25732860 TAAAACGAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
28 4 0.11
29 4 0.11
30 16 0.42
31 14 0.37
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (30 bp):
ATTCGAGTCAACTCGAAATTTGATTTTCGA
Found at i:25733343 original size:18 final size:18
Alignment explanation
Indices: 25733304--25733343 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
25733294 TAAAAAATTC
*
25733304 ATATTTTTTACATTTAAT
1 ATATTTTTTACATTTAAA
25733322 ATATTTTTTA-ATTTCAAA
1 ATATTTTTTACATTT-AAA
25733340 ATAT
1 ATAT
25733344 AGAGTGACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTTTTTACATTTAAA
Found at i:25734434 original size:21 final size:21
Alignment explanation
Indices: 25734410--25734449 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
25734400 TTAGATTTAA
25734410 ATTTTTAAAAATTAAAAAATT
1 ATTTTTAAAAATTAAAAAATT
*
25734431 ATTTTTAGAAATTAAAAAA
1 ATTTTTAAAAATTAAAAAA
25734450 GCCTCTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
ATTTTTAAAAATTAAAAAATT
Found at i:25738179 original size:20 final size:21
Alignment explanation
Indices: 25738156--25738198 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
25738146 TACAATATAT
25738156 ATTA-GAATT-TAACAAAGAAA
1 ATTATGAATTGTAACAAA-AAA
*
25738176 ATTATGAGTTGTAACAAAAAA
1 ATTATGAATTGTAACAAAAAA
25738197 AT
1 AT
25738199 AAAAAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 9 0.45
22 7 0.35
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.28
Consensus pattern (21 bp):
ATTATGAATTGTAACAAAAAA
Found at i:25740033 original size:17 final size:17
Alignment explanation
Indices: 25740011--25740044 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25740001 CAAAGGTCCT
25740011 CCTTACCAGGAATGACC
1 CCTTACCAGGAATGACC
**
25740028 CCTTACTGGGAATGACC
1 CCTTACCAGGAATGACC
25740045 ACCATTTCCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.21
Consensus pattern (17 bp):
CCTTACCAGGAATGACC
Found at i:25759205 original size:18 final size:18
Alignment explanation
Indices: 25759179--25759230 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
25759169 GTTCCCCCTA
* * *
25759179 AGAAAAAAGATGCCGGTG
1 AGAAGAAAGACGCCGGAG
*
25759197 AGAAGAAAGACGGCGGAG
1 AGAAGAAAGACGCCGGAG
*
25759215 AGAAGAATGACGCCGG
1 AGAAGAAAGACGCCGG
25759231 CGGTGATAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.42, C:0.13, G:0.38, T:0.06
Consensus pattern (18 bp):
AGAAGAAAGACGCCGGAG
Found at i:25759327 original size:39 final size:41
Alignment explanation
Indices: 25759274--25759398 Score: 154
Period size: 39 Copynumber: 3.1 Consensus size: 41
25759264 TGCTGCAGGC
* *
25759274 GGCGGCGGGAAGAAGGGAGGAGGA-G-GTGGAG-AGAAGGAA
1 GGCGGC-GGAAGAAGGAAGGAGGAGGCGGGGAGAAGAAGGAA
25759313 GGCGGCGAGAAGAAGGAAGGAGGAGGCGGGGAGAAGAAGGAA
1 GGCGGCG-GAAGAAGGAAGGAGGAGGCGGGGAGAAGAAGGAA
*
25759355 GGCGGCGGAGAGAA-GAAGGA--AGGCGGGGAGAAGAAAGAA
1 GGCGGCGGA-AGAAGGAAGGAGGAGGCGGGGAGAAGAAGGAA
25759394 GGCGG
1 GGCGG
25759399 TGGTGAAGCC
Statistics
Matches: 78, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
38 1 0.01
39 44 0.56
40 1 0.01
41 13 0.17
42 19 0.24
ACGTcount: A:0.36, C:0.07, G:0.56, T:0.01
Consensus pattern (41 bp):
GGCGGCGGAAGAAGGAAGGAGGAGGCGGGGAGAAGAAGGAA
Found at i:25759328 original size:18 final size:19
Alignment explanation
Indices: 25759274--25759398 Score: 105
Period size: 21 Copynumber: 6.3 Consensus size: 19
25759264 TGCTGCAGGC
25759274 GGCGGCGG-GAAGAAGGGAGGA
1 GGCGGCGGAGAAGAA-GGA--A
* *
25759295 GGAGGTGGAG-AGAAGGAA
1 GGCGGCGGAGAAGAAGGAA
25759313 GGCGGCGAGAAGAAGGAAGGAGGA
1 GGCGGCG-G-AGAA-GAAGGA--A
25759337 GGCGG-GGAGAAGAAGGAA
1 GGCGGCGGAGAAGAAGGAA
25759355 GGCGGCGGAGAGAAGAAGGAA
1 GGCGGC-G-GAGAAGAAGGAA
*
25759376 GGCGG-GGAGAAGAAAGAA
1 GGCGGCGGAGAAGAAGGAA
25759394 GGCGG
1 GGCGG
25759399 TGGTGAAGCC
Statistics
Matches: 89, Mismatches: 5, Indels: 23
0.76 0.04 0.20
Matches are distributed among these distances:
18 28 0.31
19 2 0.02
20 12 0.13
21 32 0.36
22 8 0.09
23 1 0.01
24 6 0.07
ACGTcount: A:0.36, C:0.07, G:0.56, T:0.01
Consensus pattern (19 bp):
GGCGGCGGAGAAGAAGGAA
Found at i:25760708 original size:15 final size:15
Alignment explanation
Indices: 25760682--25760722 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
25760672 TATAAATAAA
25760682 TTAAAA-ATTAAGTG
1 TTAAAATATTAAGTG
*
25760696 TTAAAATATTAAGTT
1 TTAAAATATTAAGTG
25760711 TTGAAAAT-TTAA
1 TT-AAAATATTAA
25760723 TTACTATATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 13 0.54
16 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (15 bp):
TTAAAATATTAAGTG
Found at i:25763898 original size:23 final size:23
Alignment explanation
Indices: 25763852--25763937 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 23
25763842 AAATATAAAA
* *
25763852 ATAATATATTTGAAACAATTTAAT
1 ATAAAATATTT-AAAAAATTTAAT
25763876 ATAAAATA-TTAAATAAATTTAAT
1 ATAAAATATTTAAA-AAATTTAAT
*
25763899 ATAAAATATTTAAAAAATTTATT
1 ATAAAATATTTAAAAAATTTAAT
* *
25763922 TTAAATTATATTAAAA
1 ATAAAATAT-TTAAAA
25763938 TATATATTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
22 3 0.06
23 33 0.61
24 18 0.33
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (23 bp):
ATAAAATATTTAAAAAATTTAAT
Found at i:25763909 original size:14 final size:14
Alignment explanation
Indices: 25763869--25763911 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
25763859 ATTTGAAACA
25763869 ATTTAATATAAAAT
1 ATTTAATATAAAAT
25763883 A-TTAA-AT--AA-
1 ATTTAATATAAAAT
25763892 ATTTAATATAAAAT
1 ATTTAATATAAAAT
25763906 ATTTAA
1 ATTTAA
25763912 AAAATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
9 1 0.04
10 6 0.25
11 2 0.08
12 2 0.08
13 6 0.25
14 7 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATTTAATATAAAAT
Found at i:25764139 original size:16 final size:16
Alignment explanation
Indices: 25764114--25764148 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
25764104 TTACTGATTG
*
25764114 CAACTCTATTCCATTA
1 CAACTCTATTCAATTA
*
25764130 CAACTTTATTCAATTA
1 CAACTCTATTCAATTA
25764146 CAA
1 CAA
25764149 TCCTATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (16 bp):
CAACTCTATTCAATTA
Found at i:25769133 original size:18 final size:19
Alignment explanation
Indices: 25769106--25769142 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
25769096 CTCGAAAAGT
*
25769106 ATATTGTGTGA-TGTGATG
1 ATATTATGTGATTGTGATG
25769124 ATATTATGTGATTGTGATG
1 ATATTATGTGATTGTGATG
25769143 TTTGTGCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (19 bp):
ATATTATGTGATTGTGATG
Found at i:25769414 original size:22 final size:22
Alignment explanation
Indices: 25769389--25769431 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
25769379 ATATATGGCA
25769389 GTTTATCTA-CAATTATGTGGTT
1 GTTTATC-AGCAATTATGTGGTT
25769411 GTTTATCAGCAATTATGTGGT
1 GTTTATCAGCAATTATGTGGT
25769432 GGCTTGTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.47
Consensus pattern (22 bp):
GTTTATCAGCAATTATGTGGTT
Found at i:25770286 original size:17 final size:17
Alignment explanation
Indices: 25770264--25770300 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
25770254 CTATTTGGCC
25770264 CGTGTGGGCCATACGGG
1 CGTGTGGGCCATACGGG
*
25770281 CGTGTGGGTCATACGGG
1 CGTGTGGGCCATACGGG
25770298 CGT
1 CGT
25770301 ATGTTACACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.22, G:0.46, T:0.22
Consensus pattern (17 bp):
CGTGTGGGCCATACGGG
Found at i:25771649 original size:26 final size:25
Alignment explanation
Indices: 25771620--25771676 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 25
25771610 TTATTATTAG
* *
25771620 TATAAATATGTACAAATTATATAAAA
1 TATAAATATATAAAAATTATA-AAAA
* *
25771646 TATAAAAATATAAAAATTCTAAAAA
1 TATAAATATATAAAAATTATAAAAA
25771671 -ATAAAT
1 TATAAAT
25771677 TTTTTTGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 5 0.19
25 4 0.15
26 17 0.65
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (25 bp):
TATAAATATATAAAAATTATAAAAA
Found at i:25780228 original size:23 final size:23
Alignment explanation
Indices: 25780195--25780247 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
25780185 AATGTTATTG
*
25780195 ATCAGTAGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
25780218 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
25780241 ATCAGTG
1 ATCAGTG
25780248 TGGCACTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:25780506 original size:15 final size:16
Alignment explanation
Indices: 25780476--25780508 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
25780466 TAGTTATATG
25780476 TTAAAAGAGTTAATTA
1 TTAAAAGAGTTAATTA
*
25780492 TTAAATGAG-TAATTA
1 TTAAAAGAGTTAATTA
25780507 TT
1 TT
25780509 GTTTACATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (16 bp):
TTAAAAGAGTTAATTA
Found at i:25781519 original size:63 final size:63
Alignment explanation
Indices: 25781420--25781545 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
25781410 AAGTTAGATA
*
25781420 ACATCTCGTACTCGATTCCGACGATGGTCTCGGGTAAGGGGTGTTACATAATTAGATTCTAAC
1 ACATCTCGTACTCGATTCCGACGATGGTCTCAGGTAAGGGGTGTTACATAATTAGATTCTAAC
*
25781483 ACATCTCGTACTCGATTCCGGCGATGGTCTCAGGTAAGGGGTGTTACATAATTAGATTCTAAC
1 ACATCTCGTACTCGATTCCGACGATGGTCTCAGGTAAGGGGTGTTACATAATTAGATTCTAAC
25781546 TTAGTTCTTA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (63 bp):
ACATCTCGTACTCGATTCCGACGATGGTCTCAGGTAAGGGGTGTTACATAATTAGATTCTAAC
Found at i:25793517 original size:138 final size:138
Alignment explanation
Indices: 25793265--25793545 Score: 492
Period size: 138 Copynumber: 2.0 Consensus size: 138
25793255 TAGAAAAATG
*
25793265 AATTACATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTACATTCGTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
25793330 TATAATTGTTTATATTAATAAATTAGGGAAAATATATACAATTAATATTTTGTATGAAT-AAAGT
66 TATAATTGTTTATATTAATAAATTAGGGAAAATATATACAATTAATATTTTGTATGAATCAAA-T
25793394 TCATATATT
130 TCATATATT
* *
25793403 AATTATATTCGTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
1 AATTACATTCGTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * *
25793468 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAGTATTTTGTATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTAGGGAAAATATATACAATTAATATTTTGTATGAATCAAATT
25793533 CATATATT
131 CATATATT
25793541 AATTA
1 AATTA
25793546 ATTATATCTA
Statistics
Matches: 136, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
138 133 0.98
139 3 0.02
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (138 bp):
AATTACATTCGTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAATTGTTTATATTAATAAATTAGGGAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:25797165 original size:51 final size:50
Alignment explanation
Indices: 25797015--25797165 Score: 148
Period size: 51 Copynumber: 3.0 Consensus size: 50
25797005 AGTGATGGTT
* *
25797015 ACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCGGAACGATAGGTTG--C
1 ACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACC-GAAC-ATA--TTGATC
* * * * *
25797067 A--TGTGTAGTACTATGTGTAGGCTACTATGCGTACCGGATAGTTTTGATC
1 ACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAACA-TATTGATC
*
25797116 ACGTGTGTAGTACTATGTGCAGGCTACTATGTGAACCGAACATCATTGAT
1 ACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAACAT-ATTGAT
25797166 TAGAAAGGTG
Statistics
Matches: 80, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
47 3 0.04
48 1 0.01
49 5 0.06
50 31 0.39
51 39 0.49
52 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (50 bp):
ACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAACATATTGATC
Found at i:25797223 original size:45 final size:45
Alignment explanation
Indices: 25797150--25797241 Score: 132
Period size: 45 Copynumber: 2.0 Consensus size: 45
25797140 TACTATGTGA
* * *
25797150 ACCGAACATCATTGATTAGAAAGGTGGTTGCTATGTGTTGATTCC
1 ACCGAACATCATTGATTAGAAAGCTGGTTGCTATGTGCTGAATCC
*
25797195 ACCGGACATCATTGATTA-ATAAGCTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAGA-AAGCTGGTTGCTATGTGCTGAATCC
25797240 AC
1 AC
25797242 TGAGTATCTG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 1 0.02
45 41 0.98
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (45 bp):
ACCGAACATCATTGATTAGAAAGCTGGTTGCTATGTGCTGAATCC
Found at i:25807543 original size:20 final size:19
Alignment explanation
Indices: 25807505--25807541 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
25807495 AAAAAAATTT
25807505 AAAATTCAAAATATTTATA
1 AAAATTCAAAATATTTATA
*
25807524 AAAATTCCAAA-ATTTATA
1 AAAATTCAAAATATTTATA
25807542 TATTTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATTCAAAATATTTATA
Found at i:25814770 original size:17 final size:19
Alignment explanation
Indices: 25814736--25814772 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
25814726 GAGGAAATGA
25814736 TCAACTATAATGATTTTTT
1 TCAACTATAATGATTTTTT
25814755 TCAACTAT-AT-ATTTTTT
1 TCAACTATAATGATTTTTT
25814772 T
1 T
25814773 ATCAGTAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 2 0.11
19 8 0.44
ACGTcount: A:0.30, C:0.11, G:0.03, T:0.57
Consensus pattern (19 bp):
TCAACTATAATGATTTTTT
Found at i:25822202 original size:21 final size:21
Alignment explanation
Indices: 25822176--25822232 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
25822166 TGAATGGCCG
25822176 ATTAAAACATGCATATATCGA
1 ATTAAAACATGCATATATCGA
*
25822197 ATTAAAACATGCATATATTGA
1 ATTAAAACATGCATATATCGA
25822218 ATTAAAACATGCATA
1 ATTAAAACATGCATA
25822233 GTATAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (21 bp):
ATTAAAACATGCATATATCGA
Found at i:25823063 original size:15 final size:14
Alignment explanation
Indices: 25823040--25823092 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
25823030 GTTTTTATAT
*
25823040 TAATTATAAAGGTTA
1 TAATAATAAA-GTTA
25823055 TAATAATAAA-TTA
1 TAATAATAAAGTTA
*
25823068 TATATTATAAAGTTA
1 TA-ATAATAAAGTTA
*
25823083 TTATAATAAA
1 TAATAATAAA
25823093 AACAAAACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 5 0.16
14 14 0.44
15 13 0.41
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (14 bp):
TAATAATAAAGTTA
Found at i:25823615 original size:43 final size:44
Alignment explanation
Indices: 25823510--25823624 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 44
25823500 TGTGTTATCG
* * * **
25823510 TGTAAGACCACATCTGGGACGTTGACATCGATTTATGATTTATG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATATGATTTACA
*
25823554 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATGTGA-TTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATATGATTTACA
*
25823597 TGTAAGACCACGTTTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
25823625 TGTACGATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
42 1 0.02
43 27 0.45
44 31 0.52
45 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATATGATTTACA
Found at i:25825652 original size:18 final size:18
Alignment explanation
Indices: 25825626--25825661 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
25825616 CTTTTGAATA
*
25825626 AAAATTGTAGATAAACCT
1 AAAACTGTAGATAAACCT
*
25825644 AAAACTGTAGATAGACCT
1 AAAACTGTAGATAAACCT
25825662 TGTAGGGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (18 bp):
AAAACTGTAGATAAACCT
Found at i:25826521 original size:15 final size:15
Alignment explanation
Indices: 25826501--25826541 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
25826491 ATAAGGGCCT
25826501 GTGGTGAACCCAAGA
1 GTGGTGAACCCAAGA
25826516 GTGGTGAACCCAAGA
1 GTGGTGAACCCAAGA
* *
25826531 ATGGTAAACCC
1 GTGGTGAACCC
25826542 GCTTGTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.34, C:0.22, G:0.29, T:0.15
Consensus pattern (15 bp):
GTGGTGAACCCAAGA
Found at i:25836387 original size:29 final size:29
Alignment explanation
Indices: 25836345--25836402 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
25836335 CACGGCCTCA
*
25836345 CACATGCCCTATCACATGCCAGTGTGTCG
1 CACATGCCCTATCACATGACAGTGTGTCG
*
25836374 CACATGGCCTATCACATGACAGTGTGTCG
1 CACATGCCCTATCACATGACAGTGTGTCG
25836403 TACACAGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.24
Consensus pattern (29 bp):
CACATGCCCTATCACATGACAGTGTGTCG
Found at i:25851654 original size:27 final size:27
Alignment explanation
Indices: 25851624--25851676 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
25851614 CGGTGTTGTT
25851624 CCAGAACAAGATCTATAGAAAATTCAC
1 CCAGAACAAGATCTATAGAAAATTCAC
25851651 CCAGAACAAGATCTATAGAAAATTCA
1 CCAGAACAAGATCTATAGAAAATTCA
25851677 AGTTCTCTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.49, C:0.21, G:0.11, T:0.19
Consensus pattern (27 bp):
CCAGAACAAGATCTATAGAAAATTCAC
Found at i:25855308 original size:25 final size:24
Alignment explanation
Indices: 25855167--25855308 Score: 81
Period size: 25 Copynumber: 5.7 Consensus size: 24
25855157 GGTAGCACCG
* *
25855167 AAGAGCCATTAGTCAGGAAGCTCCT
1 AAGAGCCATTA-TCGGGAAGCTCCA
* * *
25855192 AATAGCTATATATCGGGAAG-TTCA
1 AAGAGCCAT-TATCGGGAAGCTCCA
* * * *
25855216 ATCGAGCCA-TATCAGGAAGCTTCG
1 A-AGAGCCATTATCGGGAAGCTCCA
* * *
25855240 GAGAGCCATTAGTCCGGAAGCTCATA
1 AAGAGCCATTA-TCGGGAAGCTC-CA
* *
25855266 AAGAGCCCTTAATAGGGAAGCTCCA
1 AAGAGCCATT-ATCGGGAAGCTCCA
25855291 AAGAGCCATATATCGGGA
1 AAGAGCCAT-TATCGGGA
25855309 TGCTTTAAGA
Statistics
Matches: 86, Mismatches: 23, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
23 15 0.17
24 8 0.09
25 42 0.49
26 20 0.23
27 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (24 bp):
AAGAGCCATTATCGGGAAGCTCCA
Found at i:25860089 original size:18 final size:20
Alignment explanation
Indices: 25860052--25860093 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
25860042 GTAGGACCTG
25860052 TATACTGTATAATCTGTTAC
1 TATACTGTATAATCTGTTAC
*
25860072 TATACT-TATTAT-TGTTAC
1 TATACTGTATAATCTGTTAC
25860090 TATA
1 TATA
25860094 ATAGGCCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 5 0.24
20 6 0.29
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (20 bp):
TATACTGTATAATCTGTTAC
Found at i:25881686 original size:9 final size:9
Alignment explanation
Indices: 25881672--25881700 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
25881662 TAAACAATTC
25881672 AATAATATA
1 AATAATATA
25881681 AATAATATA
1 AATAATATA
25881690 AATAATATA
1 AATAATATA
25881699 AA
1 AA
25881701 ATGTGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AATAATATA
Found at i:25882248 original size:9 final size:9
Alignment explanation
Indices: 25882234--25882270 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
25882224 TATAGTTTGA
25882234 TATTCGAAT
1 TATTCGAAT
25882243 TATTCGAAT
1 TATTCGAAT
*
25882252 TATTCGAGT
1 TATTCGAAT
25882261 TATTCGAAT
1 TATTCGAAT
25882270 T
1 T
25882271 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:25883066 original size:22 final size:22
Alignment explanation
Indices: 25883040--25883095 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
25883030 GCTATCTACA
*
25883040 AAATCAAATC-ACTAATATTAC
1 AAATCAAATCTACTAAGATTAC
* *
25883061 AGAATCATATCTTCTAAGATTAC
1 A-AATCAAATCTACTAAGATTAC
*
25883084 AAATCATATCTA
1 AAATCAAATCTA
25883096 AGATTACATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 1 0.03
22 18 0.62
23 10 0.34
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.32
Consensus pattern (22 bp):
AAATCAAATCTACTAAGATTAC
Found at i:25883082 original size:23 final size:22
Alignment explanation
Indices: 25883051--25883094 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
25883041 AATCAAATCA
*
25883051 CTAATATTACAGAATCATATCTT
1 CTAAGATTACA-AATCATATCTT
25883074 CTAAGATTACAAATCATATCT
1 CTAAGATTACAAATCATATCT
25883095 AAGATTACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (22 bp):
CTAAGATTACAAATCATATCTT
Found at i:25888620 original size:37 final size:37
Alignment explanation
Indices: 25888529--25888641 Score: 92
Period size: 37 Copynumber: 3.1 Consensus size: 37
25888519 ATCTACAAGA
* *
25888529 TAAACATTAAATTTAAT-TT-AA-TATTAAGATAATTACT
1 TAAATATTAAA-TTAATATTAAACTATGAAGATAA-TA-T
*
25888566 TTAATATTAAATTAATA-TAAGACTATGAAGATAAGTAT
1 TAAATATTAAATTAATATTAA-ACTATGAAGATAA-TAT
* * *
25888604 TAAAT-TTAATTTAATATTAAACTATTAAAATAATAT
1 TAAATATTAAATTAATATTAAACTATGAAGATAATAT
25888640 TA
1 TA
25888642 TTTTTGGAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
36 11 0.17
37 31 0.49
38 9 0.14
39 12 0.19
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (37 bp):
TAAATATTAAATTAATATTAAACTATGAAGATAATAT
Found at i:25890279 original size:15 final size:15
Alignment explanation
Indices: 25890255--25890286 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
25890245 AATGCATGTA
*
25890255 AAATATAAAAGACAT
1 AAATACAAAAGACAT
25890270 AAATACAAAAGACAT
1 AAATACAAAAGACAT
25890285 AA
1 AA
25890287 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:25895341 original size:13 final size:13
Alignment explanation
Indices: 25895323--25895347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25895313 AAAAATATTT
25895323 AAAATATTAATAC
1 AAAATATTAATAC
25895336 AAAATATTAATA
1 AAAATATTAATA
25895348 TTTTTAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATATTAATAC
Found at i:25895415 original size:16 final size:16
Alignment explanation
Indices: 25895394--25895444 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
25895384 ATATTTAGTC
25895394 ATATAATAAATTATTA
1 ATATAATAAATTATTA
**
25895410 ATATAATCTATTATT-
1 ATATAATAAATTATTA
*
25895425 -TCTAATAAATTATTTA
1 ATATAATAAATTA-TTA
25895441 ATAT
1 ATAT
25895445 TTAAATTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
14 9 0.35
15 2 0.08
16 13 0.50
17 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:25897082 original size:17 final size:17
Alignment explanation
Indices: 25897050--25897083 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25897040 TACCAAATAT
**
25897050 TAAAATAAATTTAAAAA
1 TAAAATAAATCCAAAAA
25897067 TAAAATAAATCCAAAAA
1 TAAAATAAATCCAAAAA
25897084 AGTTATTAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAAATAAATCCAAAAA
Found at i:25904938 original size:35 final size:35
Alignment explanation
Indices: 25904892--25904960 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
25904882 GATCTCTTAT
* *
25904892 AAGTTGCATTTCTCTTTTTAG-TTGACTTGGTTTGC
1 AAGTTGCATTTCTCTGTTGAGTTTGACTT-GTTTGC
25904927 AAGTTGCATTTCTCTGTTGAGTTTGACTTGTTTG
1 AAGTTGCATTTCTCTGTTGAGTTTGACTTGTTTG
25904961 GCTGAATGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 24 0.77
36 7 0.23
ACGTcount: A:0.14, C:0.13, G:0.22, T:0.51
Consensus pattern (35 bp):
AAGTTGCATTTCTCTGTTGAGTTTGACTTGTTTGC
Found at i:25910787 original size:31 final size:30
Alignment explanation
Indices: 25910751--25910830 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 30
25910741 TATGACAGGT
* *
25910751 AAATATAAATGATTTCAGA-GTATGAATATGC
1 AAATATGAAT-ATTTCA-ATGTATGAAAATGC
*
25910782 AAATATGAATTATTACAATGTATGAAAATGC
1 AAATATGAA-TATTTCAATGTATGAAAATGC
*
25910813 ATATATGAATATTT-AATG
1 AAATATGAATATTTCAATG
25910831 CCCATGTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
29 4 0.10
30 5 0.12
31 32 0.76
32 1 0.02
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (30 bp):
AAATATGAATATTTCAATGTATGAAAATGC
Found at i:25912337 original size:50 final size:50
Alignment explanation
Indices: 25912269--25912414 Score: 184
Period size: 50 Copynumber: 2.9 Consensus size: 50
25912259 TTTCTTGTAC
* * **
25912269 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATAGG
* ** * * *
25912319 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATAGG
* *
25912369 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATA
25912415 ATCTCAATGA
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 81 1.00
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATAGG
Found at i:25912430 original size:56 final size:50
Alignment explanation
Indices: 25912219--25912466 Score: 178
Period size: 50 Copynumber: 4.9 Consensus size: 50
25912209 TGGATATAAC
* * * * * *
25912219 ATGCCAAAGCTATGTCCCAGACATAGCCTTACATGGGA--TGT-TTCTTG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
* * * * ** * *
25912266 TACTGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAG
1 -A-TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
* * * **
25912318 GTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
*
25912368 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCT---TG
*** * *
25912424 ATGCCAATATCATGTCCCAAACATGGTCTTACATGGGATCTCT
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
25912467 TTACCCAAAT
Statistics
Matches: 158, Mismatches: 32, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
48 1 0.01
49 30 0.19
50 79 0.50
51 2 0.01
52 3 0.02
53 4 0.03
56 39 0.25
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (50 bp):
ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
Found at i:25923365 original size:50 final size:50
Alignment explanation
Indices: 25923297--25923491 Score: 264
Period size: 50 Copynumber: 3.9 Consensus size: 50
25923287 TTTCTTGTAC
* * * ** *
25923297 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGG
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* * * ** *
25923347 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* *
25923397 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
25923447 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCAT
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCAT
25923492 AATCTCAATG
Statistics
Matches: 129, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 129 1.00
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
Found at i:25927545 original size:21 final size:22
Alignment explanation
Indices: 25927521--25927583 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
25927511 TCTTGGCAAA
25927521 TATCCTAGTCCA-TCTAAGGAT
1 TATCCTAGTCCAGTCTAAGGAT
* *
25927542 TATCCTAGTCTATTCCT--GGAT
1 TATCCTAGTCCAGT-CTAAGGAT
25927563 TATCCTAGT-CAGTCTAAGGAT
1 TATCCTAGTCCAGTCTAAGGAT
25927584 ATTCTATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
19 2 0.06
20 2 0.06
21 28 0.80
22 1 0.03
23 2 0.06
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (22 bp):
TATCCTAGTCCAGTCTAAGGAT
Found at i:25929563 original size:18 final size:19
Alignment explanation
Indices: 25929536--25929578 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
25929526 GTACTCTTGA
* *
25929536 ATAAACAATCAATT-TCAG
1 ATAAATAATCAATTAACAG
*
25929554 ATAAATAATCACTTAACAG
1 ATAAATAATCAATTAACAG
25929573 ATAAAT
1 ATAAAT
25929579 TAGTTAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (19 bp):
ATAAATAATCAATTAACAG
Found at i:25930555 original size:27 final size:27
Alignment explanation
Indices: 25930524--25930579 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
25930514 TATCAATATA
25930524 AAATGGTGCTAATTCAATAATATTGTC
1 AAATGGTGCTAATTCAATAATATTGTC
* *
25930551 AAATGGTGTTAATTCAATAATGTTGTC
1 AAATGGTGCTAATTCAATAATATTGTC
25930578 AA
1 AA
25930580 TGATTTGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (27 bp):
AAATGGTGCTAATTCAATAATATTGTC
Found at i:25932183 original size:27 final size:29
Alignment explanation
Indices: 25932153--25932209 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 29
25932143 CAATTTATAG
* *
25932153 AATTATGCTTTGTTAAT-T-TTTAAATAT
1 AATTATGCATTATTAATATATTTAAATAT
25932180 AATTATGCATTATTAATATATTTAAATAT
1 AATTATGCATTATTAATATATTTAAATAT
25932209 A
1 A
25932210 TCAAGTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 15 0.58
28 1 0.04
29 10 0.38
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (29 bp):
AATTATGCATTATTAATATATTTAAATAT
Found at i:25932430 original size:9 final size:9
Alignment explanation
Indices: 25932409--25932461 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 9
25932399 AATTCATGAA
25932409 AAAATATTTT
1 AAAATA-TTT
25932419 AAAATATTT
1 AAAATATTT
25932428 AAAATTATTT
1 AAAA-TATTT
25932438 AAAA-ATTAT
1 AAAATATT-T
25932447 AAAAATTATTT
1 -AAAA-TATTT
25932458 AAAA
1 AAAA
25932462 ATATAATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
8 3 0.08
9 8 0.21
10 23 0.61
11 1 0.03
12 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AAAATATTT
Found at i:25932473 original size:20 final size:20
Alignment explanation
Indices: 25932391--25932467 Score: 88
Period size: 20 Copynumber: 3.8 Consensus size: 20
25932381 TTATTTAATA
*
25932391 TATTTAAAAATTCATGAAAAAA
1 TATTTAAAAATT-AT-AAAAAT
25932413 TATTTTAAAATATT-T-AAAAT
1 TA-TTTAAAA-ATTATAAAAAT
25932433 TATTTAAAAATTATAAAAAT
1 TATTTAAAAATTATAAAAAT
25932453 TATTTAAAAA-TATAA
1 TATTTAAAAATTATAA
25932468 TTAATTGCTA
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
18 3 0.06
19 13 0.26
20 21 0.42
22 3 0.06
23 7 0.14
24 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (20 bp):
TATTTAAAAATTATAAAAAT
Found at i:25936216 original size:112 final size:108
Alignment explanation
Indices: 25936048--25936260 Score: 345
Period size: 112 Copynumber: 1.9 Consensus size: 108
25936038 GGCACCAGAA
* * *
25936048 TCATTTAAAAAAAATTGGGTGCTGGCCAGTAGATGACCGGCACCAAGTACATTTTTCGGGTCCCA
1 TCATTTAAAAAAAATTGGATGCTGGCCAGTAGATGACCGACACAAAGTACATTTTTCGGGTCCCA
25936113 ATGCACTTTTTTTTTTACTTTGGGACACTGATCGCCGGTACAGTG
66 ATGCAC--TTTTTTTTACTTTGGGACACTGATCGCCGGTACAGTG
*
25936158 TCATTTAAAAAAAGATTTGGATGCTGGCCAGTAGATGGCCGACACAAAGTACATTTTTCGGGTCC
1 TCATTTAAAAAAA-A-TTGGATGCTGGCCAGTAGATGACCGACACAAAGTACATTTTTCGGGTCC
*
25936223 CAATGCACTTTTTTTTACTTTGGGACACTGATGGCCGG
64 CAATGCACTTTTTTTTACTTTGGGACACTGATCGCCGG
25936261 CACCAACTTT
Statistics
Matches: 96, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
110 42 0.44
111 1 0.01
112 53 0.55
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (108 bp):
TCATTTAAAAAAAATTGGATGCTGGCCAGTAGATGACCGACACAAAGTACATTTTTCGGGTCCCA
ATGCACTTTTTTTTACTTTGGGACACTGATCGCCGGTACAGTG
Found at i:25936971 original size:90 final size:88
Alignment explanation
Indices: 25936877--25937358 Score: 528
Period size: 90 Copynumber: 5.4 Consensus size: 88
25936867 TAATTTTTAT
* * ** *
25936877 ATTTTCGTGTATTAATTTCTTA-GAATGTTTGTA-TTTTTTTTGTATCTGTAAATTTAATTTAGT
1 ATTTTCGTGTATTAA-TT-TTACCAATGTTTGTAGTTTGTTGGGTGT-T-TAAATTTAATTTAGT
*
25936940 CTGTATTATATGTAGTTTGAATTTAAA
62 CTGTATTATATATAGTTTGAATTTAAA
* *
25936967 ATTTTCATGTATTAATTTTACCCATTTGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTCT
1 ATTTTCGTGTATTAATTTTA-CCA-ATGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTCT
*
25937032 GTGTTATATATAGTTTGAATTTAAA
64 GTATTATATATAGTTTGAATTTAAA
* *
25937057 ATTTTCGTGCT-CTAATTTTACCCATCTGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTC
1 ATTTTCGTG-TATTAATTTTA-CCA-ATGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTC
* *
25937121 TGTGTTATATATAGTTTAAATTTAAA
63 TGTATTATATATAGTTTGAATTTAAA
* * *
25937147 ATTTTCGTGCT-CTAATTTTACCCATCCGTTTGTAGTTTGTTGGGGGTTTAAATTTAATTTAGTC
1 ATTTTCGTG-TATTAATTTTACCAAT--GTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTC
* *
25937211 CGTATTATATGTAGTTTGAATTTAAA
63 TGTATTATATATAGTTTGAATTTAAA
*
25937237 ATTTTCGTGTATTAATTTTACCCATCTGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTGC
1 ATTTTCGTGTATTAATTTTA-CCA-ATGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGT-C
* * * * *
25937302 -GTATTAT-TTTTGTTTTAATTTTAT
63 TGTATTATATATAGTTTGAATTTAAA
* *
25937326 ATTTTTGTGTATTAATATT-CCAGAATGTTTGTA
1 ATTTTCGTGTATTAATTTTACC--AATGTTTGTA
25937359 TTTTATTGTA
Statistics
Matches: 347, Mismatches: 32, Indels: 28
0.85 0.08 0.07
Matches are distributed among these distances:
87 2 0.01
88 12 0.03
89 35 0.10
90 276 0.80
91 13 0.04
92 9 0.03
ACGTcount: A:0.24, C:0.07, G:0.16, T:0.53
Consensus pattern (88 bp):
ATTTTCGTGTATTAATTTTACCAATGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTCTGT
ATTATATATAGTTTGAATTTAAA
Found at i:25937114 original size:180 final size:180
Alignment explanation
Indices: 25936925--25937308 Score: 612
Period size: 180 Copynumber: 2.1 Consensus size: 180
25936915 TTTGTATCTG
* * *
25936925 TAAATTTAATTTAGTCTGTATTATATGTAGTTTGAATTTAAAATTTTCATG-TATTAATTTTACC
1 TAAATTTAATTTAGTCTGTATTATATATAGTTTAAATTTAAAATTTTCATGCT-CTAATTTTACC
** * * *
25936989 CATTTGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTCTGTGTTATATATAGTTTGAATTT
65 CATCCGTTTGTAGTTTGTTGGGGGTTTAAATTTAATTTAGTCCGTATTATATATAGTTTGAATTT
25937054 AAAATTTTCGTGCT-CTAATTTTACCCATCTGTTTGTAGTTTGTTGGGTGTT
130 AAAATTTTCGTG-TACTAATTTTACCCATCTGTTTGTAGTTTGTTGGGTGTT
* *
25937105 TAAATTTAATTTAGTCTGTGTTATATATAGTTTAAATTTAAAATTTTCGTGCTCTAATTTTACCC
1 TAAATTTAATTTAGTCTGTATTATATATAGTTTAAATTTAAAATTTTCATGCTCTAATTTTACCC
*
25937170 ATCCGTTTGTAGTTTGTTGGGGGTTTAAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTA
66 ATCCGTTTGTAGTTTGTTGGGGGTTTAAATTTAATTTAGTCCGTATTATATATAGTTTGAATTTA
*
25937235 AAATTTTCGTGTATTAATTTTACCCATCTGTTTGTAGTTTGTTGGGTGTT
131 AAATTTTCGTGTACTAATTTTACCCATCTGTTTGTAGTTTGTTGGGTGTT
25937285 TAAATTTAATTTAGTGC-GTATTAT
1 TAAATTTAATTTAGT-CTGTATTAT
25937309 TTTTGTTTTA
Statistics
Matches: 188, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
179 1 0.01
180 185 0.98
181 2 0.01
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.51
Consensus pattern (180 bp):
TAAATTTAATTTAGTCTGTATTATATATAGTTTAAATTTAAAATTTTCATGCTCTAATTTTACCC
ATCCGTTTGTAGTTTGTTGGGGGTTTAAATTTAATTTAGTCCGTATTATATATAGTTTGAATTTA
AAATTTTCGTGTACTAATTTTACCCATCTGTTTGTAGTTTGTTGGGTGTT
Found at i:25939899 original size:6 final size:6
Alignment explanation
Indices: 25939888--25939921 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
25939878 ACTTTTTTTT
25939888 CATTTC CATTTC CATTTC CATTTC CATTT- CATTT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTT
25939922 AAATGATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.18, C:0.29, G:0.00, T:0.53
Consensus pattern (6 bp):
CATTTC
Found at i:25940091 original size:23 final size:23
Alignment explanation
Indices: 25940065--25940149 Score: 82
Period size: 23 Copynumber: 3.5 Consensus size: 23
25940055 TTAAGCTTTC
*
25940065 ATTCCATTTCATAATCATTACAA
1 ATTCCATTTCATATTCATTACAA
*
25940088 ATTCATTTCATTTCATATTCATTTA-AC
1 ATTC----CATTTCATATTCA-TTACAA
*
25940115 ATTTCATTTCATATTCATTACAA
1 ATTCCATTTCATATTCATTACAA
*
25940138 ATTACATTTCAT
1 ATTCCATTTCAT
25940150 TAATTGTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
22 3 0.06
23 29 0.57
27 16 0.31
28 3 0.06
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTCCATTTCATATTCATTACAA
Found at i:25940122 original size:12 final size:10
Alignment explanation
Indices: 25940061--25940133 Score: 56
Period size: 11 Copynumber: 6.7 Consensus size: 10
25940051 TCATTTAAGC
*
25940061 TTTCATTCCA
1 TTTCATTTCA
*
25940071 TTTCATAATCA
1 TTTCAT-TTCA
* *
25940082 TTACAAATTCA
1 TTTC-ATTTCA
25940093 TTTCATTTCA
1 TTTCATTTCA
25940103 TATTCATTTAACA
1 T-TTCATTT--CA
25940116 TTTCATTTCA
1 TTTCATTTCA
25940126 TATTCATT
1 T-TTCATT
25940134 ACAAATTACA
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
10 15 0.30
11 24 0.48
12 8 0.16
13 3 0.06
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (10 bp):
TTTCATTTCA
Found at i:25940245 original size:20 final size:20
Alignment explanation
Indices: 25940220--25940275 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 20
25940210 GTAGTCTCAT
25940220 TTCAATTTATTTTTTTTCAA
1 TTCAATTTATTTTTTTTCAA
25940240 TTCAA--T-TTTTTTTTCAA
1 TTCAATTTATTTTTTTTCAA
*
25940257 TTC-ATTTCATATTTTTTCA
1 TTCAATTT-ATTTTTTTTCA
25940276 TATTAATTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
16 1 0.03
17 14 0.45
18 2 0.06
20 14 0.45
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.64
Consensus pattern (20 bp):
TTCAATTTATTTTTTTTCAA
Found at i:25940328 original size:21 final size:21
Alignment explanation
Indices: 25940302--25940341 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25940292 TCTCAATTAC
*
25940302 ATTTTATTTACAGTTTTTCAT
1 ATTTTATTTAAAGTTTTTCAT
*
25940323 ATTTTATTTAAATTTTTTC
1 ATTTTATTTAAAGTTTTTC
25940342 TCAATTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.65
Consensus pattern (21 bp):
ATTTTATTTAAAGTTTTTCAT
Found at i:25940603 original size:27 final size:27
Alignment explanation
Indices: 25940572--25940648 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
25940562 TTTCATTTCA
25940572 TTTCCATTTCATTTAAATTATCTTTTT
1 TTTCCATTTCATTTAAATTATCTTTTT
**
25940599 TTT-C----CATTTAAATT-TAATTTT
1 TTTCCATTTCATTTAAATTATCTTTTT
25940620 TTTCTCATTTCATTTAAATTATCTTTTT
1 TTTC-CATTTCATTTAAATTATCTTTTT
25940648 T
1 T
25940649 CCATTTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
21 8 0.21
22 10 0.26
23 1 0.03
26 1 0.03
27 13 0.33
28 6 0.15
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTCCATTTCATTTAAATTATCTTTTT
Found at i:25940636 original size:21 final size:21
Alignment explanation
Indices: 25940581--25940629 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
25940571 ATTTCCATTT
**
25940581 CATTTAAATTATCTTTTTTTTC
1 CATTTAAATT-TAATTTTTTTC
25940603 CATTTAAATTTAATTTTTTTC
1 CATTTAAATTTAATTTTTTTC
25940624 TCATTT
1 -CATTT
25940630 CATTTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.63
Consensus pattern (21 bp):
CATTTAAATTTAATTTTTTTC
Found at i:25940892 original size:35 final size:36
Alignment explanation
Indices: 25940844--25940911 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
25940834 GGTGCTGACT
* *
25940844 AATGTAAGGCCATCTGTGGCAGG-CTTAGTGCCAGC
1 AATGTAAGACCATCTCTGGCAGGCCTTAGTGCCAGC
*
25940879 AATGTAAGACCATCTCTGGCAGGCCTTGGTGCC
1 AATGTAAGACCATCTCTGGCAGGCCTTAGTGCC
25940912 GGCATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 21 0.72
36 8 0.28
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (36 bp):
AATGTAAGACCATCTCTGGCAGGCCTTAGTGCCAGC
Found at i:25940924 original size:36 final size:35
Alignment explanation
Indices: 25940853--25940925 Score: 83
Period size: 36 Copynumber: 2.1 Consensus size: 35
25940843 TAATGTAAGG
* **
25940853 CCATCTGTGGCAGGCTTAGTGCCAGCAATGTAAGA
1 CCATCTCTGGCAGGCTTAGTGCCAGCAATAAAAGA
* * *
25940888 CCATCTCTGGCAGGCCTTGGTGCCGGCATTAAAAGA
1 CCATCTCTGGCAGG-CTTAGTGCCAGCAATAAAAGA
25940924 CC
1 CC
25940926 TTTTTGGCAG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
35 13 0.42
36 18 0.58
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.22
Consensus pattern (35 bp):
CCATCTCTGGCAGGCTTAGTGCCAGCAATAAAAGA
Found at i:25941120 original size:44 final size:44
Alignment explanation
Indices: 25941070--25941306 Score: 386
Period size: 44 Copynumber: 5.4 Consensus size: 44
25941060 TTAATATATA
*
25941070 TAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATAATT
1 TAATGTGTTTTAAATTAAATATGTATGTATATTGTATTATAATT
* *
25941114 TAATGTGTTTTAAAATAAACATGTATGTATATTGTATTATAATT
1 TAATGTGTTTTAAATTAAATATGTATGTATATTGTATTATAATT
*
25941158 TAATGTGCTTT-AATTCAAATATGTATGTATATTGTATTATAATT
1 TAATGTGTTTTAAATT-AAATATGTATGTATATTGTATTATAATT
**
25941202 TAATGTGTTTTAAATTAAATATACATGTATATTGTATTATAATT
1 TAATGTGTTTTAAATTAAATATGTATGTATATTGTATTATAATT
*
25941246 TAATGTGTTTTAAATTAAATATGCATGTATATTGTATTATAATT
1 TAATGTGTTTTAAATTAAATATGTATGTATATTGTATTATAATT
*
25941290 TAACGTGTTTTAAATTA
1 TAATGTGTTTTAAATTA
25941307 GGAATAAGAA
Statistics
Matches: 182, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
43 3 0.02
44 175 0.96
45 4 0.02
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (44 bp):
TAATGTGTTTTAAATTAAATATGTATGTATATTGTATTATAATT
Found at i:25957171 original size:49 final size:49
Alignment explanation
Indices: 25957116--25957214 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
25957106 ATCTCATTCA
25957116 CAACATATTCAATCTGTTGAAATACAAGTAGGGTTAGTACGAAACTTAC
1 CAACATATTCAATCTGTTGAAATACAAGTAGGGTTAGTACGAAACTTAC
* *
25957165 CAACATATTCAATCTGTTGAAATACAAGTAGGGTTAGTATGGAACTTAC
1 CAACATATTCAATCTGTTGAAATACAAGTAGGGTTAGTACGAAACTTAC
25957214 C
1 C
25957215 TCTTTTGTCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (49 bp):
CAACATATTCAATCTGTTGAAATACAAGTAGGGTTAGTACGAAACTTAC
Found at i:25971675 original size:27 final size:27
Alignment explanation
Indices: 25971607--25971676 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
25971597 CGCCAATGGG
*
25971607 ATTGGCGGCACCAAAGGTCCCAAAGCC
1 ATTGGCGGCACCAATGGTCCCAAAGCC
* * *
25971634 ATTAGCGGCAACAATGGTGCCAATA-CC
1 ATTGGCGGCACCAATGGTCCCAA-AGCC
25971661 ATTGGCGGCACCAATG
1 ATTGGCGGCACCAATG
25971677 TATATTAGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
27 35 0.97
28 1 0.03
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTCCCAAAGCC
Found at i:25971728 original size:4 final size:4
Alignment explanation
Indices: 25971719--25971859 Score: 64
Period size: 4 Copynumber: 36.0 Consensus size: 4
25971709 GAAGGAGAGG
* * * *
25971719 GAAA GAAA GAAA GAAA GGAAT GAAT GAGAG GAAA GAAA G-AA -AAA GAAG
1 GAAA GAAA GAAA GAAA -GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA
** *
25971767 GAAA GAAA -AGG GAAG GAGAA GAGAA -AAA -AAA GAAA GAAA G-AA G-AA
1 GAAA GAAA GAAA GAAA GA-AA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
** * * * *
25971812 GAAA -AGG GAAG GAGAA GAAA AAAA GAAA GAAA GAAG GAAG GAAA GAAA
1 GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
25971860 AGGAAAGGAG
Statistics
Matches: 110, Mismatches: 17, Indels: 20
0.75 0.12 0.14
Matches are distributed among these distances:
3 17 0.15
4 78 0.71
5 15 0.14
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:25971794 original size:19 final size:20
Alignment explanation
Indices: 25971772--25971836 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
25971762 AGAAGGAAAG
25971772 AAAAGGGAAGGAGAAGAGAA
1 AAAAGGGAAGGAGAAGAGAA
** *
25971792 AAAAAAGAAAGA-AAGAAGAA
1 AAAAGGGAAGGAGAAG-AGAA
25971812 GAAAAGGGAAGGAGAAGA-AA
1 -AAAAGGGAAGGAGAAGAGAA
25971832 AAAAG
1 AAAAG
25971837 AAAGAAAGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 8 0.22
20 15 0.42
21 10 0.28
22 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (20 bp):
AAAAGGGAAGGAGAAGAGAA
Found at i:25971799 original size:41 final size:41
Alignment explanation
Indices: 25971745--25971890 Score: 181
Period size: 41 Copynumber: 3.5 Consensus size: 41
25971735 GGAATGAATG
* *
25971745 AGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGGAAGGAGA
1 AGAGAAAAAAAAGAAAAAGAAGGAAAGAAAAGGGAAGGAGA
25971786 AGAGAAAAAAAAGAAAGAAAGAA-G-AAGAAAAGGGAAGGAGA
1 AGAGAAAAAAAAG-AA-AAAGAAGGAAAGAAAAGGGAAGGAGA
* *
25971827 AGAAAAAAAGAAAGAAAGAAGGAAGGAAAGAAAAGGAAAGGAGA
1 AGAGAAAAA-AAAGAAA-AA-GAAGGAAAGAAAAGGGAAGGAGA
*
25971871 AGAGAAAAAAAA-AAGAAGAA
1 AGAGAAAAAAAAGAAAAAGAA
25971891 AAGGGAAGGA
Statistics
Matches: 92, Mismatches: 6, Indels: 15
0.81 0.05 0.13
Matches are distributed among these distances:
40 4 0.04
41 42 0.46
42 12 0.13
43 10 0.11
44 24 0.26
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (41 bp):
AGAGAAAAAAAAGAAAAAGAAGGAAAGAAAAGGGAAGGAGA
Found at i:25971829 original size:16 final size:16
Alignment explanation
Indices: 25971808--25971900 Score: 63
Period size: 16 Copynumber: 6.1 Consensus size: 16
25971798 GAAAGAAAGA
25971808 AGAAGAAAAGGGAAGG
1 AGAAGAAAAGGGAAGG
*
25971824 AGAAGAAAA---AAAG
1 AGAAGAAAAGGGAAGG
*
25971837 A-AAGAAAGAAGGAAGG
1 AGAAGAAA-AGGGAAGG
*
25971853 A-AAGAAAAGGAAAGG
1 AGAAGAAAAGGGAAGG
** **
25971868 AGAAGAGAAA-AAAAAA
1 AGAAGA-AAAGGGAAGG
25971884 AGAAGAAAAGGGAAGG
1 AGAAGAAAAGGGAAGG
25971900 A
1 A
25971901 AGGAAAAGAA
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
12 6 0.10
13 5 0.08
15 10 0.17
16 35 0.59
17 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
AGAAGAAAAGGGAAGG
Found at i:25971904 original size:41 final size:42
Alignment explanation
Indices: 25971754--25971906 Score: 152
Period size: 41 Copynumber: 3.6 Consensus size: 42
25971744 GAGAGGAAAG
* * *
25971754 AAAGAAAAAGAAGGAAAGAAAAGGGAAGGAGAAGAGAAAAAAA
1 AAAGAAGAA-AAGGGAAGAAAAGGAAAGGAGAAGAGAAAAAAA
* * * *
25971797 AGA-AAG-AAAGAAGAAGAAAAGGGAAGGAGAAGA-AAAAAAG
1 AAAGAAGAAAAG-GGAAGAAAAGGAAAGGAGAAGAGAAAAAAA
*
25971837 AAAGAAAGAAGGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAA
1 AAAG-AAGAA--AAGGGAAGAAAAGGAAAGGAGAAGAGAAAAAAA
*
25971882 AAAGAAGAAAAGGGAAG-GAAGGAAA
1 AAAGAAGAAAAGGGAAGAAAAGGAAA
25971907 AGAAAAGAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 16
0.76 0.10 0.13
Matches are distributed among these distances:
40 11 0.12
41 28 0.31
42 12 0.13
43 3 0.03
44 24 0.26
45 13 0.14
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (42 bp):
AAAGAAGAAAAGGGAAGAAAAGGAAAGGAGAAGAGAAAAAAA
Found at i:25971911 original size:5 final size:5
Alignment explanation
Indices: 25971783--25971920 Score: 51
Period size: 5 Copynumber: 27.8 Consensus size: 5
25971773 AAAGGGAAGG
* * * *
25971783 AGAAG AGAAA A-AAA AG-AA AG-AA AGAAGA AGAAA AGGGAA GGAGA AG-AA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAA-A AGAAA A-GAAA AGAAA AGAAA
* *
25971831 A-AAA AG-AA AG-AA AGAAGGA AGGAA AGAAA AGGAAA GGAGAAG AGAAA
1 AGAAA AGAAA AGAAA AGAA--A AGAAA AGAAA A-GAAA --AGAAA AGAAA
** * *
25971878 A-AAA A-AAGA AGAAA AGGGA AGGAA GGAAA AGAAA AGAAA AGAA
1 AGAAA AGAA-A AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAA
25971921 GAGGTAATTT
Statistics
Matches: 102, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
4 31 0.30
5 49 0.48
6 14 0.14
7 7 0.07
8 1 0.01
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:25971915 original size:85 final size:83
Alignment explanation
Indices: 25971750--25971922 Score: 224
Period size: 85 Copynumber: 2.1 Consensus size: 83
25971740 GAATGAGAGG
* *
25971750 AAAGAAAGAAAAAGAAGGAAAGAAAAGGGAAGGAGAAGAGAAAAAAAAGAAAGAAAGAAGAAGAA
1 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAAAGAAAGAAGAAGAA
* * *
25971815 AAGGGAAGGAGAAGAAAA
66 AAGGAAAAGAAAAGAAAA
*
25971833 AAAGAAAGAAAGAAGGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAGAAGAAA-AGGGA
1 AAAGAAAGAAA-AA-GAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAA-AAGAAAGA-AGA
*
25971897 AG-GAAGGAAAAGAAAAGAAAA
62 AGAAAAGGAAAAGAAAAGAAAA
*
25971918 GAAGA
1 AAAGA
25971923 GGTAATTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
83 11 0.14
84 2 0.03
85 55 0.71
86 10 0.13
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (83 bp):
AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAAAGAAAGAAGAAGAA
AAGGAAAAGAAAAGAAAA
Found at i:25973055 original size:394 final size:394
Alignment explanation
Indices: 25972327--25973114 Score: 1549
Period size: 394 Copynumber: 2.0 Consensus size: 394
25972317 ACGATATTTT
25972327 TAAAAATAATAAAATGCGGATAAAAAAATACGAACAAATGGTCGAAGTAAGAGTGTATTAGTAAA
1 TAAAAATAATAAAATGCGGATAAAAAAATACGAACAAATGGTCGAAGTAAGAGTGTATTAGTAAA
25972392 TTTTTAAAAAAAATTCAGAAATAAGTTATACAACTAATTGAAACAAAAATGTACTGAAATAATGT
66 TTTTTAAAAAAAATTCAGAAATAAGTTATACAACTAATTGAAACAAAAATGTACTGAAATAATGT
*
25972457 AAAATGATAAAATGCGAGAAGAATATATTGTTATTTAAAGTAATAAAAATCGAGAAAATAATACG
131 AAAATGATAAAATACGAGAAGAATATATTGTTATTTAAAGTAATAAAAATCGAGAAAATAATACG
25972522 AGCAAAGGGTAGGGGCAAGGGCTATTTTTTACAAAAATTAATTTAAATAACACACTAGATTAATA
196 AGCAAAGGGTAGGGGCAAGGGCTATTTTTTACAAAAATTAATTTAAATAACACACTAGATTAATA
25972587 AAATTCAAACATTATGCACTGAAATAATGTAAAATTATAAATTTAGAAATTATGATAATTTTTAA
261 AAATTCAAACATTATGCACTGAAATAATGTAAAATTATAAATTTAGAAATTATGATAATTTTTAA
25972652 AGGAATAAAATGCAGAGAAAAATACGAAGCGATATTAGACACATATCTGATGCGGCTAATAAATT
326 AGGAATAAAATGCAGAGAAAAATACGAAGCGATATTAGACACATATCTGATGCGGCTAATAAATT
25972717 TAGA
391 TAGA
25972721 TAAAAATAATAAAATGCGGATAAAAAAATACGAACAAATGGTCGAAGTAAGAGTGTATTAGTAAA
1 TAAAAATAATAAAATGCGGATAAAAAAATACGAACAAATGGTCGAAGTAAGAGTGTATTAGTAAA
25972786 TTTTTAAAAAAAATTCAGAAATAAGTTATACAACTAATTGAAACAAAAATGTACTGAAATAATGT
66 TTTTTAAAAAAAATTCAGAAATAAGTTATACAACTAATTGAAACAAAAATGTACTGAAATAATGT
* *
25972851 AAAATGATAAAATACGAGAATAATATATTTTTATTTAAAGTAATAAAAATCGAGAAAATAATACG
131 AAAATGATAAAATACGAGAAGAATATATTGTTATTTAAAGTAATAAAAATCGAGAAAATAATACG
25972916 AGCAAAGGGTAGGGGCAAGGGCTATTTTTTACAAAAATTAATTTAAATAACACACTAGATTAATA
196 AGCAAAGGGTAGGGGCAAGGGCTATTTTTTACAAAAATTAATTTAAATAACACACTAGATTAATA
25972981 AAATTCAAACATTATGCACTGAAATAATGTAAAATTATAAATTTAGAAATTATGATAATTTTTAA
261 AAATTCAAACATTATGCACTGAAATAATGTAAAATTATAAATTTAGAAATTATGATAATTTTTAA
25973046 AGGAATAAAATGCAGAGAAAAATACGAAGCGATATTAGACACATATCTGATGCGGCTAATAAATT
326 AGGAATAAAATGCAGAGAAAAATACGAAGCGATATTAGACACATATCTGATGCGGCTAATAAATT
25973111 TAGA
391 TAGA
25973115 AATTATAAAT
Statistics
Matches: 391, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
394 391 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.28
Consensus pattern (394 bp):
TAAAAATAATAAAATGCGGATAAAAAAATACGAACAAATGGTCGAAGTAAGAGTGTATTAGTAAA
TTTTTAAAAAAAATTCAGAAATAAGTTATACAACTAATTGAAACAAAAATGTACTGAAATAATGT
AAAATGATAAAATACGAGAAGAATATATTGTTATTTAAAGTAATAAAAATCGAGAAAATAATACG
AGCAAAGGGTAGGGGCAAGGGCTATTTTTTACAAAAATTAATTTAAATAACACACTAGATTAATA
AAATTCAAACATTATGCACTGAAATAATGTAAAATTATAAATTTAGAAATTATGATAATTTTTAA
AGGAATAAAATGCAGAGAAAAATACGAAGCGATATTAGACACATATCTGATGCGGCTAATAAATT
TAGA
Found at i:25973124 original size:15 final size:15
Alignment explanation
Indices: 25973104--25973135 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
25973094 GATGCGGCTA
25973104 ATAAATTTAGAAATT
1 ATAAATTTAGAAATT
25973119 ATAAATTTAGAAATT
1 ATAAATTTAGAAATT
25973134 AT
1 AT
25973136 GATATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (15 bp):
ATAAATTTAGAAATT
Found at i:25977611 original size:18 final size:18
Alignment explanation
Indices: 25977590--25977628 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
25977580 ATGATCGCTG
*
25977590 CCACCTTCTTCTTCGCCA
1 CCACCTTCTTCTTCACCA
25977608 CCACCTTCTTCTTCACCA
1 CCACCTTCTTCTTCACCA
25977626 CCA
1 CCA
25977629 ACCATGTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.51, G:0.03, T:0.31
Consensus pattern (18 bp):
CCACCTTCTTCTTCACCA
Found at i:25978310 original size:36 final size:35
Alignment explanation
Indices: 25978250--25978330 Score: 103
Period size: 34 Copynumber: 2.3 Consensus size: 35
25978240 TCCTTATAAC
* *
25978250 TAATACACTAATAATATTAATAATTTTATACTCAAAA
1 TAATACACTAATAAAATTAATAA-TTT-TACTAAAAA
*
25978287 TAATACAC-AATAAAATTATTAATTTTACTAAAAA
1 TAATACACTAATAAAATTAATAATTTTACTAAAAA
25978321 TAATA-ACTAA
1 TAATACACTAA
25978331 CTAACTAACT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
33 2 0.05
34 15 0.38
35 3 0.08
36 12 0.30
37 8 0.20
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (35 bp):
TAATACACTAATAAAATTAATAATTTTACTAAAAA
Found at i:25978326 original size:37 final size:38
Alignment explanation
Indices: 25978245--25978334 Score: 89
Period size: 36 Copynumber: 2.4 Consensus size: 38
25978235 ACTAATCCTT
* **
25978245 ATAACTAATACACTAATAATATTAATAATTTTATACTCA
1 ATAA-TAATACACTAATAAAATTAATAATTTTATACAAA
*
25978284 A-AATAATACAC-AATAAAATTATTAATTTTACTA-AAA
1 ATAATAATACACTAATAAAATTAATAATTTTA-TACAAA
25978320 ATAATAACTA-ACTAA
1 ATAATAA-TACACTAA
25978335 CTAACTATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
36 19 0.44
37 17 0.40
38 6 0.14
39 1 0.02
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (38 bp):
ATAATAATACACTAATAAAATTAATAATTTTATACAAA
Found at i:25978644 original size:10 final size:11
Alignment explanation
Indices: 25978627--25978655 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
25978617 AAAAAAATAC
25978627 CTTCTTTTTCT
1 CTTCTTTTTCT
25978638 C-TCTTTTTCT
1 CTTCTTTTTCT
25978648 CTTCTTTT
1 CTTCTTTT
25978656 CCGCAGCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:25978882 original size:28 final size:29
Alignment explanation
Indices: 25978845--25978913 Score: 115
Period size: 28 Copynumber: 2.4 Consensus size: 29
25978835 GTTTTTTGTT
25978845 TATATATTTTGGTAAATAAAAAAAA-TTA
1 TATATATTTTGGTAAATAAAAAAAAGTTA
25978873 TATATATTTTGGTAAATAAAAAAAAGTTA
1 TATATATTTTGGTAAATAAAAAAAAGTTA
*
25978902 TA-ACATTTTGGT
1 TATATATTTTGGT
25978914 TATTTTTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 34 0.87
29 5 0.13
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.41
Consensus pattern (29 bp):
TATATATTTTGGTAAATAAAAAAAAGTTA
Found at i:25980089 original size:24 final size:24
Alignment explanation
Indices: 25980057--25980108 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
25980047 TTTTTAAAAG
* *
25980057 ATTTTGTATTTATTAGTATAATAT
1 ATTTAGTATTTATTAGCATAATAT
*
25980081 ATTTAGTATTTATTAGCATAATTT
1 ATTTAGTATTTATTAGCATAATAT
25980105 ATTT
1 ATTT
25980109 GAGCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.58
Consensus pattern (24 bp):
ATTTAGTATTTATTAGCATAATAT
Done.