Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 183 of 208
Found at i:57377440 original size:5 final size:5
Alignment explanation
Indices: 57377406--57377431 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
57377396 TTATTTTTTA
57377406 TAATT TAATT TAATT TAATT TAATT T
1 TAATT TAATT TAATT TAATT TAATT T
57377432 TTTTATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TAATT
Found at i:57379557 original size:23 final size:25
Alignment explanation
Indices: 57379530--57379580 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
57379520 TTATAGATTG
*
57379530 TAATATA-CTTTTT-ATTAAAATAT
1 TAATATAGCTTTTTCAATAAAATAT
*
57379553 TAATATAGCTTTTTCAATAAATTAT
1 TAATATAGCTTTTTCAATAAAATAT
57379578 TAA
1 TAA
57379581 GAAAATTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.29
24 6 0.25
25 11 0.46
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (25 bp):
TAATATAGCTTTTTCAATAAAATAT
Found at i:57379574 original size:24 final size:24
Alignment explanation
Indices: 57379530--57379580 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
57379520 TTATAGATTG
*
57379530 TAATATACTTTTTATTAAAA-TAT
1 TAATATACTTTTTAATAAAATTAT
57379553 TAATATAGCTTTTTCAAT-AAATTAT
1 TAATATA-CTTTTT-AATAAAATTAT
57379578 TAA
1 TAA
57379581 GAAAATTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 7 0.29
24 9 0.38
25 8 0.33
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (24 bp):
TAATATACTTTTTAATAAAATTAT
Found at i:57383703 original size:2 final size:2
Alignment explanation
Indices: 57383696--57383724 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57383686 AACAACTCAT
57383696 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
57383725 GTAAGATGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:57387179 original size:40 final size:40
Alignment explanation
Indices: 57387120--57387306 Score: 277
Period size: 40 Copynumber: 4.6 Consensus size: 40
57387110 GGCCTATTTT
*
57387120 TATTTTAAAAATTTTAAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTTAAAAAAATTAAAAAAGTATTTTAAAAA
57387161 TATTTTAAAATTTAAAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTT-AAAAAAATT-AAAAAAGTATTTTAAAAA
* *
57387203 TATTTTAAAA-TTAAAAAATTTAAAAAAGTATTTTAAAAG
1 TATTTTAAAATTTAAAAAAATTAAAAAAGTATTTTAAAAA
* *
57387242 TATTTTAAAATTTAAAAAAATTAAAAAAGTATGTAAAAAA
1 TATTTTAAAATTTAAAAAAATTAAAAAAGTATTTTAAAAA
* *
57387282 TATTTTAAAATTTTAAAAAAGTAAA
1 TATTTTAAAATTTAAAAAAATTAAA
57387307 TATATTGCCC
Statistics
Matches: 134, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
39 27 0.20
40 63 0.47
41 16 0.12
42 28 0.21
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (40 bp):
TATTTTAAAATTTAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:57387222 original size:8 final size:9
Alignment explanation
Indices: 57387123--57387301 Score: 51
Period size: 9 Copynumber: 18.0 Consensus size: 9
57387113 CTATTTTTAT
*
57387123 TTTAAAAAT
1 TTTAAAAAA
57387132 TTTAAAAAA
1 TTTAAAAAA
*
57387141 TTAAAAAAGTA
1 TTTAAAAA--A
57387152 TTTTAAAAATA
1 -TTTAAAAA-A
*
57387163 TTT-TAAAA
1 TTTAAAAAA
57387171 TTTAAAAAAAA
1 TTT--AAAAAA
*
57387182 TTAAAAAAAGTA
1 TT-TAAAAA--A
57387194 TTTTAAAAATA
1 -TTTAAAAA-A
*
57387205 TTT-TAAAA
1 TTTAAAAAA
57387213 -TTAAAAAA
1 TTTAAAAAA
57387221 TTTAAAAAAGTA
1 TTT-AAAAA--A
*
57387233 TTTTAAAAGTA
1 -TTTAAAA-AA
*
57387244 TTT-TAAAA
1 TTTAAAAAA
57387252 TTTAAAAAA
1 TTTAAAAAA
*
57387261 ATTAAAAAA
1 TTTAAAAAA
57387270 GTATGTAAAAAATA
1 -T-T-T-AAAAA-A
* *
57387284 TTTTAAAAT
1 TTTAAAAAA
57387293 TTTAAAAAA
1 TTTAAAAAA
57387302 GTAAATATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 46
0.66 0.10 0.24
Matches are distributed among these distances:
7 2 0.02
8 13 0.10
9 44 0.34
10 23 0.18
11 14 0.11
12 20 0.16
13 11 0.09
14 1 0.01
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:57387229 original size:17 final size:17
Alignment explanation
Indices: 57387196--57387228 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
57387186 AAAAAGTATT
*
57387196 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
57387213 TTAAAAA-ATTTAAAAA
1 TTAAAAATATTTAAAAA
57387229 AGTATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:57387291 original size:11 final size:11
Alignment explanation
Indices: 57387120--57387251 Score: 83
Period size: 11 Copynumber: 12.9 Consensus size: 11
57387110 GGCCTATTTT
57387120 TATTTT-AAAA
1 TATTTTAAAAA
57387130 -ATTTTAAAAA
1 TATTTTAAAAA
*
57387140 -A-TTAAAAAA
1 TATTTTAAAAA
57387149 GTATTTTAAAAA
1 -TATTTTAAAAA
57387161 TATTTT--AAA
1 TATTTTAAAAA
*
57387170 -ATTTAAAAAA
1 TATTTTAAAAA
* **
57387180 AATTAAAAAAA
1 TATTTTAAAAA
57387191 GTATTTTAAAAA
1 -TATTTTAAAAA
57387203 TATTTT--AAA
1 TATTTTAAAAA
57387212 -A--TTAAAAA
1 TATTTTAAAAA
*
57387220 -ATTTAAAAAA
1 TATTTTAAAAA
*
57387230 GTATTTTAAAAG
1 -TATTTTAAAAA
57387242 TATTTTAAAA
1 TATTTTAAAA
57387252 TTTAAAAAAA
Statistics
Matches: 98, Mismatches: 10, Indels: 27
0.73 0.07 0.20
Matches are distributed among these distances:
6 2 0.02
8 9 0.09
9 18 0.18
10 14 0.14
11 32 0.33
12 23 0.23
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:57388059 original size:17 final size:19
Alignment explanation
Indices: 57388039--57388081 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
57388029 TATTTTTTAT
57388039 ATTTTTA-TATTTT-AATA
1 ATTTTTAGTATTTTAAATA
*
57388056 ATTTTTAGTTTTTTAAAATA
1 ATTTTTAGTATTTT-AAATA
57388076 ATTTTT
1 ATTTTT
57388082 TTGAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 5 0.23
20 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTTTTAGTATTTTAAATA
Found at i:57388608 original size:20 final size:19
Alignment explanation
Indices: 57388583--57388629 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
57388573 ACTAGTAGGA
57388583 TTTTTATTAACATCTAGAAT
1 TTTTTATTAACATCTA-AAT
* **
57388603 TTTTTAATAATTTCTAAAT
1 TTTTTATTAACATCTAAAT
57388622 TTTTTATT
1 TTTTTATT
57388630 TTTTATTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTTATTAACATCTAAAT
Found at i:57393011 original size:71 final size:71
Alignment explanation
Indices: 57392895--57393036 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
57392885 TAAAATACAA
57392895 TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
1 TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
57392960 AAAAGG
66 AAAAGG
57392966 TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
1 TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
57393031 AAAAGG
66 AAAAGG
57393037 AGGAAATTGT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (71 bp):
TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
AAAAGG
Found at i:57400519 original size:7 final size:7
Alignment explanation
Indices: 57400507--57400545 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
57400497 AAAGTATTTT
57400507 AAAATTA
1 AAAATTA
57400514 AAAATTA
1 AAAATTA
*
57400521 AAAAATA
1 AAAATTA
*
57400528 AAAAATA
1 AAAATTA
57400535 AAAA-TA
1 AAAATTA
57400541 AAAAT
1 AAAAT
57400546 ATATATTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (7 bp):
AAAATTA
Found at i:57400529 original size:14 final size:13
Alignment explanation
Indices: 57400505--57400545 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
57400495 TTAAAGTATT
*
57400505 TTAAAATTAAAAA
1 TTAAAAATAAAAA
57400518 TTAAAAAATAAAAA
1 TT-AAAAATAAAAA
*
57400532 ATAAAAATAAAAA
1 TTAAAAATAAAAA
57400545 T
1 T
57400546 ATATATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TTAAAAATAAAAA
Found at i:57407587 original size:27 final size:27
Alignment explanation
Indices: 57407545--57407616 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
57407535 TTTATTTTTA
*
57407545 AATATTTTTA-ATTTTTTGT-AAGTTT
1 AATATTTTTATATTTTTTGTGAACTTT
* *
57407570 AATTATTTTTATATTTTTTTTGCACTTT
1 AA-TATTTTTATATTTTTTGTGAACTTT
57407598 AATATTTTTATATATTTTT
1 AATATTTTTATAT-TTTTT
57407617 AAAACTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
25 2 0.05
26 8 0.20
27 19 0.47
28 11 0.28
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.67
Consensus pattern (27 bp):
AATATTTTTATATTTTTTGTGAACTTT
Found at i:57407626 original size:28 final size:27
Alignment explanation
Indices: 57407545--57407640 Score: 79
Period size: 28 Copynumber: 3.6 Consensus size: 27
57407535 TTTATTTTTA
** *
57407545 AATATTTTTA-AT-TTTTTGTAAGTTT
1 AATATTTTTATATATTTTTAAAACTTT
* ***
57407570 AATTATTTTTATATTTTTTTTGCACTTT
1 AA-TATTTTTATATATTTTTAAAACTTT
57407598 AATATTTTTATATATTTTTAAAACTTTT
1 AATATTTTTATATATTTTTAAAAC-TTT
* *
57407626 AATAATTTTAAATAT
1 AATATTTTTATATAT
57407641 ATAATACCAA
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
25 2 0.04
26 8 0.14
27 20 0.35
28 27 0.47
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (27 bp):
AATATTTTTATATATTTTTAAAACTTT
Found at i:57407986 original size:8 final size:8
Alignment explanation
Indices: 57407975--57407999 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
57407965 CCACCTACCC
57407975 CCCACTTG
1 CCCACTTG
57407983 CCCACTTG
1 CCCACTTG
57407991 CCCACTTG
1 CCCACTTG
57407999 C
1 C
57408000 GCCGAACACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.52, G:0.12, T:0.24
Consensus pattern (8 bp):
CCCACTTG
Found at i:57409013 original size:3 final size:3
Alignment explanation
Indices: 57408989--57409059 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
57408979 AATATCCTTG
* * * *
57408989 TTA TTT TTA -TA TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
57409036 TGTA TTA GTA TATA TTT TTA TTA T
1 T-TA TTA TTA T-TA TTA TTA TTA T
57409060 GTACGTGTAT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:57409056 original size:23 final size:22
Alignment explanation
Indices: 57409001--57409062 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
57408991 ATTTTTATAT
*
57409001 TATTAGTATTATTA-GTATTAC
1 TATTATTATTATTATGTATTAC
*
57409022 TATTATTATTATTATGTATTAG
1 TATTATTATTATTATGTATTAC
*
57409044 TATATATTTTTATTATGTA
1 TAT-TATTATTATTATGTA
57409063 CGTGTATACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 13 0.36
22 9 0.25
23 14 0.39
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (22 bp):
TATTATTATTATTATGTATTAC
Found at i:57409069 original size:23 final size:23
Alignment explanation
Indices: 57408996--57409070 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
57408986 TTGTTATTTT
* *
57408996 TATATTATTAGTATTAT-TAGTAT
1 TATA-TATTATTATTATGTAGTAG
*
57409019 TACTATTATTATTATTATGTATTAG
1 TA-TA-TATTATTATTATGTAGTAG
*
57409044 TATATATTTTTATTATGTACGT-G
1 TATATATTATTATTATGTA-GTAG
57409067 TATA
1 TATA
57409071 CATATATATA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
23 21 0.48
24 17 0.39
25 6 0.14
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (23 bp):
TATATATTATTATTATGTAGTAG
Found at i:57409134 original size:25 final size:24
Alignment explanation
Indices: 57409087--57409134 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
57409077 TATATATTCA
*
57409087 TATTTAATATTTTTATTTCATTTT
1 TATTTAATATTTTTATTTAATTTT
57409111 TATTCTAATA-TTTTATTATAATTT
1 TATT-TAATATTTTTATT-TAATTT
57409135 ATATATATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (24 bp):
TATTTAATATTTTTATTTAATTTT
Found at i:57411163 original size:3 final size:3
Alignment explanation
Indices: 57411153--57411190 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
57411143 AATAATAATA
*
57411153 ATT A-T ATT ATT ATT ATT ATT ATG ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
57411191 GATTTTGGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:57412956 original size:33 final size:33
Alignment explanation
Indices: 57412915--57412980 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
57412905 CCTTTTAGCC
*
57412915 CTATCTATATTTATATATATAATTTGGTGATTT
1 CTATCTATATTTATATATACAATTTGGTGATTT
57412948 CTATCTATATTTATATATACAATTTGGTGATTT
1 CTATCTATATTTATATATACAATTTGGTGATTT
57412981 TTACAGTTCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (33 bp):
CTATCTATATTTATATATACAATTTGGTGATTT
Found at i:57415247 original size:25 final size:24
Alignment explanation
Indices: 57415211--57415257 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
57415201 CTCATGTTTT
57415211 AAAAAATAAATCAT-AAAATTAATA
1 AAAAAATAAATC-TCAAAATTAATA
*
57415235 AAAAAATTTAATCTCAAAATTAA
1 AAAAAA-TAAATCTCAAAATTAA
57415258 AAATAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAAAATAAATCTCAAAATTAATA
Found at i:57417990 original size:21 final size:21
Alignment explanation
Indices: 57417964--57418003 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
57417954 ATCGGTTGGA
57417964 TAAGCTCTTACGAGCTTCTGT
1 TAAGCTCTTACGAGCTTCTGT
57417985 TAAGCTCTTACGAGCTTCT
1 TAAGCTCTTACGAGCTTCT
57418004 ACTGGAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TAAGCTCTTACGAGCTTCTGT
Found at i:57427014 original size:2 final size:2
Alignment explanation
Indices: 57427007--57427059 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
57426997 ATGATAAATT
*
57427007 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
57427049 AG AG AG AG AG A
1 AG AG AG AG AG A
57427060 TGCATGGGTG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:57428582 original size:34 final size:35
Alignment explanation
Indices: 57428542--57428615 Score: 98
Period size: 34 Copynumber: 2.1 Consensus size: 35
57428532 AGCATATATT
* *
57428542 TATACTTATCAAT-TACATGTGCCGAATGC-ACATA
1 TATACTTAT-AATCCACATATGCCGAATGCAACATA
57428576 TATACTTATAATCCACATATGCCGAATGCATACATA
1 TATACTTATAATCCACATATGCCGAATGCA-ACATA
57428612 TATA
1 TATA
57428616 TATATATCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 3 0.09
34 23 0.66
36 9 0.26
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.32
Consensus pattern (35 bp):
TATACTTATAATCCACATATGCCGAATGCAACATA
Found at i:57428841 original size:41 final size:40
Alignment explanation
Indices: 57428786--57428922 Score: 168
Period size: 41 Copynumber: 3.3 Consensus size: 40
57428776 TTAATTTAAA
*
57428786 CAGATTCACTGGCACTTAGCCTGTTAGGCTTAAAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGTTAGGCTTAAA-CCTGATT
* *
57428828 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTAATT
1 CAGATCACCGGCACTTAGCCTGTTAGGCTTA-AACCTGATT
* *
57428869 CAGATCACCGACACTTAGCCTGTTAGGTTTTAAAACCTGATT
1 CAGATCACCGGCACTTAGCCTGTTAGG-CTT-AAACCTGATT
57428911 CAG-TACACCGGC
1 CAGAT-CACCGGC
57428923 TTTTTGCCTA
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
41 57 0.69
42 25 0.30
43 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (40 bp):
CAGATCACCGGCACTTAGCCTGTTAGGCTTAAACCTGATT
Found at i:57429556 original size:19 final size:18
Alignment explanation
Indices: 57429514--57429556 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
57429504 ATTCAATCCA
57429514 AACATATACAAATATATT
1 AACATATACAAATATATT
* *
57429532 ATACATATATATATATATGT
1 A-ACATATACAAATATAT-T
57429552 AACAT
1 AACAT
57429557 CCATACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 18 0.86
20 2 0.10
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.37
Consensus pattern (18 bp):
AACATATACAAATATATT
Found at i:57429672 original size:75 final size:78
Alignment explanation
Indices: 57429551--57429919 Score: 325
Period size: 78 Copynumber: 4.8 Consensus size: 78
57429541 TATATATATG
* * * * * * *
57429551 TAACATCCATACTTTTAA-TAAAATCCAAGAATTTATAC-TCGTATATACATACCTATTCAAACC
1 TAACATACATACTATTAACT-AAATTCAAGAACTTATTCAT-GTATATACATACATATCCAAACC
* * *
57429614 TCTTGTAAACATATA
64 TCATATAAACAAATA
* * * * *
57429629 TAACATTCA-AC-ATTAACTAAATTCAA-AACTTATTCATGTATATACACATATATCCGAACTTC
1 TAACATACATACTATTAACTAAATTCAAGAACTTATTCATGTATATACATACATATCCAAACCTC
* *
57429691 ATATATATAAATA
66 ATATAAACAAATA
* * * * * *
57429704 TAACATACATACTTTTAACTAAATTCAAGAACTTATTCATGTATATACATATATATTCGAACTTT
1 TAACATACATACTATTAACTAAATTCAAGAACTTATTCATGTATATACATACATATCCAAACCTC
* *
57429769 ATATATATAAATA
66 ATATAAACAAATA
* * * * * * * *
57429782 TAACATACATGCTTTTAAATAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTT
1 TAACATACATACTATTAACTAAATTCAAGAACTTATTCATGTATATACATACATATCCAAACCTC
* *
57429847 ATATATATAAATA
66 ATATAAACAAATA
* * * *
57429860 TAACATACATACTTTTAACTAAGTTCAAGAACTTATACATGTATATACATATATTATCCA
1 TAACATACATACTATTAACTAAATTCAAGAACTTATTCATGTATATACATACA-TATCCA
57429920 CTAGTAGTTC
Statistics
Matches: 254, Mismatches: 31, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
75 42 0.17
76 14 0.06
77 17 0.07
78 176 0.69
79 5 0.02
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.37
Consensus pattern (78 bp):
TAACATACATACTATTAACTAAATTCAAGAACTTATTCATGTATATACATACATATCCAAACCTC
ATATAAACAAATA
Found at i:57429758 original size:78 final size:78
Alignment explanation
Indices: 57429641--57429918 Score: 468
Period size: 78 Copynumber: 3.6 Consensus size: 78
57429631 ACATTCAACA
* *
57429641 TTAACTAAATTCAA-AACTTATTCATGTATATACACATATATCCGAACTTCATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
57429705 AACATACATACTT
66 AACATACATACTT
*
57429718 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATTCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
*
57429783 AACATACATGCTT
66 AACATACATACTT
* *
57429796 TTAAATAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
57429861 AACATACATACTT
66 AACATACATACTT
* *
57429874 TTAACTAAGTTCAAGAACTTATACATGTATATACATATATTATCC
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATA-TATCC
57429919 ACTAGTAGTT
Statistics
Matches: 187, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
77 14 0.07
78 168 0.90
79 5 0.03
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.38
Consensus pattern (78 bp):
TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
AACATACATACTT
Found at i:57436744 original size:2 final size:2
Alignment explanation
Indices: 57436739--57436782 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
57436729 ATGCAGAGGC
57436739 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
57436781 AG
1 AG
57436783 CAAAACTGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:57437306 original size:25 final size:25
Alignment explanation
Indices: 57437278--57437352 Score: 141
Period size: 25 Copynumber: 3.0 Consensus size: 25
57437268 ATATCATTAG
*
57437278 TTAGTTGAAAATTTGAAATAATTGA
1 TTAGTTGAAATTTTGAAATAATTGA
57437303 TTAGTTGAAATTTTGAAATAATTGA
1 TTAGTTGAAATTTTGAAATAATTGA
57437328 TTAGTTGAAATTTTGAAATAATTGA
1 TTAGTTGAAATTTTGAAATAATTGA
57437353 CACCTTTAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (25 bp):
TTAGTTGAAATTTTGAAATAATTGA
Found at i:57438875 original size:2 final size:2
Alignment explanation
Indices: 57438868--57438912 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
57438858 ATGATAAATT
57438868 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
57438910 AG A
1 AG A
57438913 AATGCATGGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:57439244 original size:2 final size:2
Alignment explanation
Indices: 57439237--57439265 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57439227 CCAACAAAAT
57439237 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
57439266 AGTTTAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:57439775 original size:32 final size:34
Alignment explanation
Indices: 57439708--57439776 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 34
57439698 GTAGTTATCG
* *
57439708 CGATACCAGGCTCTAGGTATCGTGATATCAGTAT
1 CGATACCAGGCTCTAGGTATCGCGATATCACTAT
*
57439742 CGATACCAGGCTCT-GG-GTCGCGATATCACTAT
1 CGATACCAGGCTCTAGGTATCGCGATATCACTAT
57439774 CGA
1 CGA
57439777 AGTGAGACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 16 0.50
33 2 0.06
34 14 0.44
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (34 bp):
CGATACCAGGCTCTAGGTATCGCGATATCACTAT
Found at i:57443440 original size:21 final size:21
Alignment explanation
Indices: 57443416--57443457 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
57443406 CTGTTGAAAA
57443416 AAATTCAGTTTGAAAATGGTT
1 AAATTCAGTTTGAAAATGGTT
57443437 AAATTCAGTTTGAAAATGGTT
1 AAATTCAGTTTGAAAATGGTT
57443458 TTCTTGCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (21 bp):
AAATTCAGTTTGAAAATGGTT
Found at i:57443513 original size:36 final size:36
Alignment explanation
Indices: 57443473--57443544 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 36
57443463 GCACAGCAAA
57443473 AATT-AAAATTTTAAAAACTGAAC-CGGTTTGTGATAT
1 AATTAAAAATTTT-AAAACTG-ACTCGGTTTGTGATAT
57443509 AATTAAAAATTTTAAAACTGACTCGGTTTGTGATAT
1 AATTAAAAATTTTAAAACTGACTCGGTTTGTGATAT
57443545 TTATAGTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 2 0.06
36 24 0.71
37 8 0.24
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (36 bp):
AATTAAAAATTTTAAAACTGACTCGGTTTGTGATAT
Found at i:57444443 original size:9 final size:10
Alignment explanation
Indices: 57444426--57444454 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
57444416 TATTTATCTT
57444426 TTTCTATTCA
1 TTTCTATTCA
57444436 TTTC-ATTCA
1 TTTCTATTCA
57444445 TTTCTATTCA
1 TTTCTATTCA
57444455 AACACGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:57447205 original size:59 final size:59
Alignment explanation
Indices: 57447045--57447683 Score: 893
Period size: 59 Copynumber: 10.8 Consensus size: 59
57447035 TGTTTATGTA
* * *
57447045 AATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATAATTGTTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
57447104 AATTAAT-AAAAA-TAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
*
57447161 AATGAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
*
57447220 AATTATTCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATATGGTTATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATG--A---TTATTTATTT
*
57447284 AATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATATGTTTATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATG--A---TTATTTATTT
*
57447348 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGGTTATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
**
57447407 AATTGGTCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
* * * * * * *
57447466 AATTAATC--GAA--CACTAATTATTCGTACAATTATTATGAAATAAGATTATTTAATT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
*** **
57447521 AATTAATTGGAAATTAATTAATTATTTGTAAAATTATTATGAAATATGATTATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
* *
57447580 AACTAATC--AAA--AATTAATTATTCATAAAATTATTATGAAATATGATGATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
* *
57447635 AATTAATAAAAAATTAATTAATTATTCGTAAAATTATTATGAAATATGA
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGA
57447684 CCCAGCATTT
Statistics
Matches: 526, Mismatches: 39, Indels: 30
0.88 0.07 0.05
Matches are distributed among these distances:
55 92 0.17
57 59 0.11
58 9 0.02
59 247 0.47
61 1 0.00
64 118 0.22
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (59 bp):
AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
Found at i:57447370 original size:19 final size:20
Alignment explanation
Indices: 57447346--57447383 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
57447336 GTTTATTTAT
57447346 TTAATTAATCA-AAAATTAA
1 TTAATTAATCATAAAATTAA
*
57447365 TTAATTATTCATAAAATTA
1 TTAATTAATCATAAAATTA
57447384 TTATGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAATTAATCATAAAATTAA
Found at i:57447500 original size:114 final size:115
Alignment explanation
Indices: 57447045--57447683 Score: 877
Period size: 114 Copynumber: 5.4 Consensus size: 115
57447035 TGTTTATGTA
* * *
57447045 AATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATAATTGTTTATTTAATTAA
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAA
*
57447110 TAAAAATAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
66 T-CAAATAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
* *
57447161 AATGAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAA
57447226 TCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATATGGTTATTTATTT
66 TC--AAA-TAATTAATTATTCATAAAATTATTATGAAATATG--A---TTATTTATTT
*
57447284 AATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATATGTTTATTTATTTA
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATG--A---TTATTTATTTA
*
57447349 ATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGGTTATTTATTT
61 ATTAATC--AAA-TAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
**
57447407 AATTGGTCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAA
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAA
* * * * * * *
57447472 TCGAA-CACTAATTATTCGTACAATTATTATGAAATAAGATTATTTAATT
66 TCAAATAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
*** ** *
57447521 AATTAATTGGAAATTAATTAATTATTTGTAAAATTATTATGAAATATGATTATTTATTTAACTAA
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAA
*
57447586 TCAAA-AATTAATTATTCATAAAATTATTATGAAATATGATGATTTATTT
66 TCAAATAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
* *
57447635 AATTAATAAAAAATTAATTAATTATTCGTAAAATTATTATGAAATATGA
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGA
57447684 CCCAGCATTT
Statistics
Matches: 469, Mismatches: 41, Indels: 28
0.87 0.08 0.05
Matches are distributed among these distances:
114 180 0.38
116 63 0.13
117 3 0.01
118 52 0.11
120 1 0.00
121 1 0.00
123 111 0.24
125 1 0.00
128 57 0.12
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (115 bp):
AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAA
TCAAATAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
Found at i:57447536 original size:51 final size:53
Alignment explanation
Indices: 57447426--57447641 Score: 182
Period size: 55 Copynumber: 3.9 Consensus size: 53
57447416 AAAATTAATT
* *
57447426 AATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAATCGAACAC
1 AATTATTCATAAAATTATTATGAAATAAGATTATTTAATTAATTAATCG-ACAC
* * * * *
57447480 TAATTATTCGTACAATTATTATGAAATAAGATTATTTAATTAATTAATTGGAAATT
1 -AATTATTCATAAAATTATTATGAAATAAGATTATTTAATTAATTAA-TCGACA-C
* * * * * *
57447536 AATTAATT-ATTTGTAAAATTATTATGAAATATGATTATTTATTTAACTAATCAAAAATT
1 AATT-ATTCA----TAAAATTATTATGAAATAAGATTATTTAATTAATTAATC-GACA-C
* * *
57447595 AATTATTCATAAAATTATTATGAAATATGATGATTTATTTAATTAAT
1 AATTATTCATAAAATTATTATGAAATAAGATTATTTAATTAATTAAT
57447642 AAAAAATTAA
Statistics
Matches: 136, Mismatches: 16, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
55 84 0.62
56 5 0.04
58 4 0.03
59 43 0.32
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (53 bp):
AATTATTCATAAAATTATTATGAAATAAGATTATTTAATTAATTAATCGACAC
Found at i:57447559 original size:19 final size:19
Alignment explanation
Indices: 57447515--57447556 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
57447505 ATAAGATTAT
*
57447515 TTAATTAATTAATTGGAAA
1 TTAATTAATTAATTGAAAA
*
57447534 TTAATTAATTATTTGTAAAA
1 TTAATTAATTAATTG-AAAA
57447554 TTA
1 TTA
57447557 TTATGAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (19 bp):
TTAATTAATTAATTGAAAA
Found at i:57461348 original size:17 final size:17
Alignment explanation
Indices: 57461326--57461364 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
57461316 TCTTTTTTAA
57461326 AAAATTT-TCATGTCTTC
1 AAAATTTCTCATGT-TTC
*
57461343 AAAATTTCTCGTGTTTC
1 AAAATTTCTCATGTTTC
57461360 AAAAT
1 AAAAT
57461365 AATAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (17 bp):
AAAATTTCTCATGTTTC
Found at i:57461606 original size:18 final size:18
Alignment explanation
Indices: 57461579--57462006 Score: 169
Period size: 17 Copynumber: 25.0 Consensus size: 18
57461569 AAATTTTGTG
*
57461579 TTTTCATGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
57461597 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
57461615 -TCT-GTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
57461631 TTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
57461648 TTTTCGTGTTTTAAAAAAAA
1 TTTTCGTGTTTT--CAAAAA
* * *
57461668 ATTACGTGTTTTCACAAA
1 TTTTCGTGTTTTCAAAAA
* *
57461686 TTTTCGT-CTTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
57461703 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
57461721 -CTCCG-GTGTTTC-AAAG
1 TTTTCGTGT-TTTCAAAAA
* *
57461737 TTTCCATGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * * *
57461755 TTCTGGCG-TTTAAAAAA
1 TTTTCGTGTTTTCAAAAA
**
57461772 AATTCGTG-TTTCAAAATA
1 TTTTCGTGTTTTCAAAA-A
* **
57461790 TTCTCG-CATTTC---AA
1 TTTTCGTGTTTTCAAAAA
**
57461804 TTTT--TGTTTT-TTAAA
1 TTTTCGTGTTTTCAAAAA
57461819 ---TCGTG-TTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* *
57461834 ATGTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
57461851 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
* *
57461868 TTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
** *
57461885 TTCCCGT-ATTTCAAAAAAA
1 TTTTCGTGTTTTC--AAAAA
* * *
57461904 ATGTCGTGTTTTAAAAAA
1 TTTTCGTGTTTTCAAAAA
*
57461922 ATTTCGT-TTTTCTAAAAA
1 TTTTCGTGTTTTC-AAAAA
**
57461940 TTTT-GTG-TTTCTGAAA
1 TTTTCGTGTTTTCAAAAA
*
57461956 TTTTCGTG-TTT-ACAAA
1 TTTTCGTGTTTTCAAAAA
*
57461972 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
57461990 TTCTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
57462007 AAAACTTTCG
Statistics
Matches: 307, Mismatches: 68, Indels: 71
0.69 0.15 0.16
Matches are distributed among these distances:
12 1 0.00
13 6 0.02
14 6 0.02
15 6 0.02
16 41 0.13
17 119 0.39
18 98 0.32
19 12 0.04
20 18 0.06
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:57461747 original size:89 final size:89
Alignment explanation
Indices: 57461585--57461754 Score: 218
Period size: 89 Copynumber: 1.9 Consensus size: 89
57461575 TGTGTTTTCA
* * *
57461585 TGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAATTCTGGCGTTTCAAAAATT
1 TGTTTTCAAAAATTTTCGTGCTTTCAAAAATCTGTGTTTTCAAAAACTCCGGCGTTTCAAAAATT
* *
57461650 TTCGTGTTTTAAAAAAAAATTACG
66 TCCATGTTTTAAAAAAAAATTACG
* * * *
57461674 TGTTTTCACAAATTTTCGT-CTTTCACAAATTCTCGTGTTTTCAAAAACTCCGGTGTTTC-AAAG
1 TGTTTTCAAAAATTTTCGTGCTTTCA-AAAATCT-GTGTTTTCAAAAACTCCGGCGTTTCAAAAA
*
57461737 TTTCCATGTTTTCAAAAA
64 TTTCCATGTTTTAAAAAA
57461755 TTCTGGCGTT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
88 5 0.07
89 42 0.61
90 22 0.32
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (89 bp):
TGTTTTCAAAAATTTTCGTGCTTTCAAAAATCTGTGTTTTCAAAAACTCCGGCGTTTCAAAAATT
TCCATGTTTTAAAAAAAAATTACG
Found at i:57461937 original size:19 final size:19
Alignment explanation
Indices: 57461819--57461939 Score: 71
Period size: 18 Copynumber: 6.8 Consensus size: 19
57461809 GTTTTTTAAA
57461819 TCGTGTTTC-AAAAAAATG
1 TCGTGTTTCTAAAAAAATG
* *
57461837 TCGTGTTT-T-AAAAATTT
1 TCGTGTTTCTAAAAAAATG
*
57461854 TCGTGTTTCT---AAAATT
1 TCGTGTTTCTAAAAAAATG
* * *
57461870 TCCCTGTTT-T-AAAAATTC
1 T-CGTGTTTCTAAAAAAATG
* * *
57461888 CCGTATTTCAAAAAAAATG
1 TCGTGTTTCTAAAAAAATG
*
57461907 TCGTGTTT-TAAAAAAATT
1 TCGTGTTTCTAAAAAAATG
*
57461925 TCGTTTTTCTAAAAA
1 TCGTGTTTCTAAAAA
57461940 TTTTGTGTTT
Statistics
Matches: 78, Mismatches: 17, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
16 7 0.09
17 25 0.32
18 28 0.36
19 18 0.23
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (19 bp):
TCGTGTTTCTAAAAAAATG
Found at i:57473865 original size:66 final size:66
Alignment explanation
Indices: 57473722--57473889 Score: 223
Period size: 66 Copynumber: 2.5 Consensus size: 66
57473712 CTTTCCAAGG
* **
57473722 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTAATTTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTAATTTTTT
57473787 T
66 T
* * *
57473788 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGCACGCCGAGGTATTTTAGTTTATG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTAATTT-T-
57473852 TTT
64 TTT
** *
57473855 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
57473890 TTTAATTTTT
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
65 19 0.21
66 69 0.76
67 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (66 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTAATTTTTT
T
Found at i:57474019 original size:74 final size:74
Alignment explanation
Indices: 57473907--57474669 Score: 464
Period size: 73 Copynumber: 10.5 Consensus size: 74
57473897 TTTGTTTTTC
* **
57473907 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCATTTCTG
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCATTTCTG
57473972 TTGTTAAAAA
66 TT-TTAAAAA
*
57473982 AAAATCAACTCATATTGCGA-AAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC-ATTTCT
*
57474046 GTTTT---CA
65 GTTTTAAAAA
* * *
57474053 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTT-T
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC-ATTTCT
*
57474117 -TTTT---CA
65 GTTTTAAAAA
* * * * *
57474123 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCATTTCTG
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCATTTCTG
57474188 TTTTCAAAAA
66 TTTT-AAAAA
* ** * * * *
57474198 AAAATCAACTTATATTGC-AGAGGTGAGTTGAGCCTC-GTTCACATGCTGAGGTATTTTAATTTC
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAG--GACACGCTGAGGTAATTTCATTTC
57474261 TG-TTTAAAAA
64 TGTTTTAAAAA
* ** * * * * *
57474271 AAAATCAACGCATATTGCGAGAGGTGAGTTGAGCTTCAGATTACACACTGTGGT-ATTT-TTTTC
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAG--GACACGCTGAGGTAATTTCATTTC
** * * **
57474334 -AATTCATATT
64 TGTTTTAAAAA
*** * ** * * ** * * ** ** **
57474344 GCGA-GAGGTGA-GTT--GAG-CCTCAAG-TCA-CAC-CGAGGTATTTC-C--ATTTCTGTTTCA
1 AAAATCAACTCATATTGCGAGAAAT-GAGTTGAGC-CTC-AGG-A-CACGCTGAGGT-AATTTCA
* *
57474398 TTATATGTTTT--GAA
60 TT-TCTGTTTTAAAAA
* * * **
57474412 AGAATCAACTCACATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC-ATTTCT
*
57474477 GTTTT---CA
65 GTTTTAAAAA
* * * * *
57474484 AAATTCAACTCATATTGCGAGAAATGAGTTGAGACTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC-ATTTCT
*
57474549 GCTTTT---CA
65 G-TTTTAAAAA
*
57474557 AAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC-ATTTCT
* *
57474622 GTTGT-CAAA
65 GTTTTAAAAA
57474631 AAAATCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCAG
1 AAAATCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCAG
57474670 TTCATATGTT
Statistics
Matches: 550, Mismatches: 99, Indels: 79
0.76 0.14 0.11
Matches are distributed among these distances:
65 1 0.00
67 7 0.01
68 9 0.02
69 13 0.02
70 65 0.12
71 27 0.05
72 114 0.21
73 118 0.21
74 117 0.21
75 79 0.14
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (74 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCATTTCTG
TTTTAAAAA
Found at i:57474158 original size:70 final size:71
Alignment explanation
Indices: 57473902--57474669 Score: 493
Period size: 72 Copynumber: 10.6 Consensus size: 71
57473892 TAATTTTTGT
* * ** *
57473902 TTTTC-AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA
1 TTTTCAAAAATCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCA
57473966 TTTCTG
66 TTTCTG
* *
57473972 TTGTTAAAAAAAAATCAACTCATATTGCGA-AAATGAGTTGAGCCTCAGGACACACTGAGGTAAT
1 TT-TT---CAAAAATCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAAT
57474036 TTCAATTTCTG
62 TTC-ATTTCTG
*
57474047 TTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCA
1 TTTTCAAAAATCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTC-
57474112 ATTT-T-
65 ATTTCTG
* * ** *
57474117 TTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
1 TTTTCAAAAATCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCA
57474182 TTTCTG
66 TTTCTG
** **
57474188 TTTTCAAAAAAAAATCAACTTATATTGC-AGAGGTGAGTTGAGCCTC-GTTCACATGCTGAGGTA
1 TTTTC----AAAAATCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACA--CTGAGGTA
* *
57474251 TTTTAATTTCTG
60 ATTTCATTTCTG
** ** ** * * *
57474263 TTTAAAAAAAAATCAACGCATATTGCGAGAGGTGAGTTGAGCTTCAGATTACACACTGTGGT-AT
1 TTT--TCAAAAATCAACTTATATTGCGAGAAATGAGTTGAGCCTCAG--GACACACTGAGGTAAT
*
57474327 TT--TTT-TC
62 TTCATTTCTG
** * * * * * ** * *
57474334 AATTC-ATATTGCGAGAGGTGA-GTT--GAG-CCTCAAG-TCA-CAC-CGAGGTATTTC-CA-T-
1 TTTTCAAAAAT-C-A-A-CTTATATTGCGAGAAAT-GAGTTGAGC-CTC-AGG-A---CACACTG
*** * *
57474388 TTCT-GTTTCATTATATG
55 AGGTAATTTCATT-TCTG
* * * * *
57474405 TTTTGAAAGAATCAACTCACATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTC
1 TTTTCAAA-AATCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTC
57474470 AATTTCTG
65 -ATTTCTG
* * * * ** *
57474478 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGACTCAAGACACGTTGAGGTATTTTCA
1 TTTTCAAAAATCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTC-
57474543 ATTTCTG
65 ATTTCTG
* * *
57474550 CTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
1 -TTTTCAAAAATCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTC
57474615 AATTTCTG
65 -ATTTCTG
* *
57474623 TTGTCAAAAAAATCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCAG
1 TTTTC--AAAAATCAACTTATATTGCGAGAAA-TGAGTTGAGCCTCAG
57474670 TTCATATGTT
Statistics
Matches: 564, Mismatches: 80, Indels: 104
0.75 0.11 0.14
Matches are distributed among these distances:
67 8 0.01
68 9 0.02
69 17 0.03
70 71 0.13
71 37 0.07
72 118 0.21
73 113 0.20
74 112 0.20
75 74 0.13
77 5 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (71 bp):
TTTTCAAAAATCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCA
TTTCTG
Found at i:57474326 original size:75 final size:73
Alignment explanation
Indices: 57473907--57474329 Score: 414
Period size: 75 Copynumber: 5.8 Consensus size: 73
57473897 TTTGTTTTTC
* ** * * *
57473907 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCATTTCTG
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTATTTTAATTTCTG
57473972 TTGTTAAAAA
66 -T-TTAAAAA
*
57473982 AAAATCAACTCATATTGCGA-AAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGT-ATTTTAATTTCT
**
57474046 GTTT--TCA
65 GTTTAAAAA
* * *
57474053 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTT-T
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGT-ATTTTAATTTCT
**
57474117 -TTT--TCA
65 GTTTAAAAA
* * * ** *
57474123 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCATTTCTG
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTATTTTAATTTCTG
57474188 TTTTCAAAAA
66 -TTT-AAAAA
* ** **
57474198 AAAATCAACTTATATTGC-AGAGGTGAGTTGAGCCTC-GTTCACATGCTGAGGTATTTTAATTTC
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACA--CTGAGGTATTTTAATTTC
57474261 TGTTTAAAAA
64 TGTTTAAAAA
* ** * * *
57474271 AAAATCAACGCATATTGCGAGAGGTGAGTTGAGCTTCAGATTACACACTGTGGTATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAG--GACACACTGAGGTATTTT
57474330 TTTCAATTCA
Statistics
Matches: 302, Mismatches: 32, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
69 8 0.03
70 56 0.19
71 20 0.07
72 45 0.15
73 26 0.09
74 65 0.22
75 77 0.25
77 5 0.02
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (73 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTATTTTAATTTCTG
TTTAAAAA
Found at i:57476816 original size:17 final size:17
Alignment explanation
Indices: 57476764--57476819 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
57476754 TTCGTGTTTC
*
57476764 TTTCTAAAAAAAATCGTG
1 TTTC-AAAAAAATTCGTG
57476782 TTTTC--AAAAATTCCCGTG
1 -TTTCAAAAAAATT--CGTG
57476800 TTTCAAAAAAATTCGTG
1 TTTCAAAAAAATTCGTG
57476817 TTT
1 TTT
57476820 TCGTGTTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 6 0.19
17 11 0.34
18 4 0.12
19 11 0.34
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (17 bp):
TTTCAAAAAAATTCGTG
Found at i:57476821 original size:18 final size:18
Alignment explanation
Indices: 57476764--57476821 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
57476754 TTCGTGTTTC
*
57476764 TTTCTAAAAAAAATCGTGT
1 TTTC-AAAAAAATTCGTGT
57476783 TTTC--AAAAATTCCCGTG-
1 TTTCAAAAAAATT--CGTGT
57476800 TTTCAAAAAAATTCGTGT
1 TTTCAAAAAAATTCGTGT
57476818 TTTC
1 TTTC
57476822 GTGTTTTCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
16 6 0.18
17 8 0.24
18 8 0.24
19 11 0.33
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (18 bp):
TTTCAAAAAAATTCGTGT
Found at i:57476842 original size:27 final size:25
Alignment explanation
Indices: 57476796--57476846 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
57476786 CAAAAATTCC
57476796 CGTGTTTCAAAAAAATTCGTGTTTT
1 CGTGTTTCAAAAAAATTCGTGTTTT
* *
57476821 CGTGTTTTCGAAAACATCTCGTGTTT
1 CGTG-TTTCAAAAAAAT-TCGTGTTT
57476847 CAAAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 10 0.45
27 8 0.36
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.43
Consensus pattern (25 bp):
CGTGTTTCAAAAAAATTCGTGTTTT
Found at i:57476981 original size:17 final size:18
Alignment explanation
Indices: 57476933--57477342 Score: 182
Period size: 17 Copynumber: 24.8 Consensus size: 18
57476923 TTTTGTGTTT
*
57476933 TCGTGTTTTCAAAAATTT
1 TCGTGTTTTCAAAAATTC
57476951 TCGTGTTTTCAAAAA-TC
1 TCGTGTTTTCAAAAATTC
57476968 T-GTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
* * *
57476985 TGGCG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTC
*
57477002 TCGTGTTTTAAAAAAAATT-
1 TCGTGTTTT--CAAAAATTC
* * *
57477021 ACGTG-TTTCACAAATTT
1 TCGTGTTTTCAAAAATTC
*
57477038 TCGTG-TTTCACAAATTC
1 TCGTGTTTTCAAAAATTC
*
57477055 TCGTGTTTTCAAAAACTC
1 TCGTGTTTTCAAAAATTC
*
57477073 -CG-GTATTTC-AAAGTT-
1 TCGTGT-TTTCAAAAATTC
*
57477088 TCCTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
* ** *
57477106 TCGCGTTTAAAAAAAAT-
1 TCGTGTTTTCAAAAATTC
57477123 TCGTG-TTTCAAAATATTC
1 TCGTGTTTTCAAAA-ATTC
**
57477141 TCG-CATTTC---AATT-
1 TCGTGTTTTCAAAAATTC
* **
57477154 T-TTGTTTT-TTAAA---
1 TCGTGTTTTCAAAAATTC
* *
57477167 TCGTG-TTTCAAAAAATG
1 TCGTGTTTTCAAAAATTC
*
57477184 TCGTGTTTT--AAAATTT
1 TCGTGTTTTCAAAAATTC
* *
57477200 TCGTG-TTTCTAAATTTC
1 TCGTGTTTTCAAAAATTC
*
57477217 -CCTG-TTT--AAAATTC
1 TCGTGTTTTCAAAAATTC
*
57477231 T-GTG-TTTCAAAAA-TG
1 TCGTGTTTTCAAAAATTC
* *
57477246 TCGTGTTTTAAAAAAAT-
1 TCGTGTTTTCAAAAATTC
* *
57477263 T-GT-TTTTCTAAAATTT
1 TCGTGTTTTCAAAAATTC
* *
57477279 TCGTG-TTTCTAAAATTT
1 TCGTGTTTTCAAAAATTC
*
57477296 TCGTG-TTT-ACAAATTC
1 TCGTGTTTTCAAAAATTC
57477312 TCGTGTTTTC-AAAATTC
1 TCGTGTTTTCAAAAATTC
57477329 TCGTGTTTT-AAAAA
1 TCGTGTTTTCAAAAA
57477343 AACTTTCGTT
Statistics
Matches: 304, Mismatches: 49, Indels: 79
0.70 0.11 0.18
Matches are distributed among these distances:
13 8 0.03
14 19 0.06
15 17 0.06
16 72 0.24
17 121 0.40
18 56 0.18
19 4 0.01
20 7 0.02
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTC
Found at i:57477206 original size:33 final size:33
Alignment explanation
Indices: 57477167--57477343 Score: 134
Period size: 33 Copynumber: 5.5 Consensus size: 33
57477157 GTTTTTTAAA
57477167 TCGTGTTTCAAAAAATGTCGTGTTTTAAAATTT
1 TCGTGTTTCAAAAAATGTCGTGTTTTAAAATTT
* * * *
57477200 TCGTGTTTC--TAAATTTCCCTG-TTTAAAATTC
1 TCGTGTTTCAAAAAATGT-CGTGTTTTAAAATTT
**
57477231 T-GTGTTTC-AAAAATGTCGTGTTTTAAAAAAAT
1 TCGTGTTTCAAAAAATGTCGTGTTTT-AAAATTT
* * * *
57477263 T-GTTTTTCTAAAATTTTCGTGTTTCTAAAATTT
1 TCGTGTTTCAAAAAATGTCGTGTTT-TAAAATTT
* * * *
57477296 TCGTGTTT-ACAAATTCTCGTGTTTTCAAAATTC
1 TCGTGTTTCAAAAAATGTCGTGTTTT-AAAATTT
*
57477329 TCGTGTTTTAAAAAA
1 TCGTGTTTCAAAAAA
57477344 ACTTTCGTTT
Statistics
Matches: 113, Mismatches: 22, Indels: 17
0.74 0.14 0.11
Matches are distributed among these distances:
30 10 0.09
31 23 0.20
32 15 0.13
33 55 0.49
34 10 0.09
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (33 bp):
TCGTGTTTCAAAAAATGTCGTGTTTTAAAATTT
Found at i:57477215 original size:61 final size:63
Alignment explanation
Indices: 57477116--57477258 Score: 154
Period size: 61 Copynumber: 2.3 Consensus size: 63
57477106 TCGCGTTTAA
* *** * *
57477116 AAAAAAT-TCGTGTTTCAAAATATTCTCGCATTTCAATTTTTGTTTTTTAAA-TC-GTGTTTC
1 AAAAAATGTCGTGTTTTAAAATATTCTCGCATTTCAATTTCCCTGTTTAAAATTCTGTGTTTC
**
57477176 AAAAAATGTCGTGTTTTAAAAT-TT-TCGTGTTTCTAAATTTCCCTGTTTAAAATTCTGTGTTTC
1 AAAAAATGTCGTGTTTTAAAATATTCTCGCATTTC--AATTTCCCTGTTTAAAATTCTGTGTTTC
57477239 -AAAAATGTCGTGTTTTAAAA
1 AAAAAATGTCGTGTTTTAAAA
57477259 AAATTGTTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
59 7 0.10
60 9 0.13
61 25 0.36
62 22 0.31
63 7 0.10
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (63 bp):
AAAAAATGTCGTGTTTTAAAATATTCTCGCATTTCAATTTCCCTGTTTAAAATTCTGTGTTTC
Found at i:57497362 original size:69 final size:70
Alignment explanation
Indices: 57497242--57497415 Score: 228
Period size: 69 Copynumber: 2.5 Consensus size: 70
57497232 CTTTCCAAGG
* **
57497242 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTT-T
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
57497306 -TTTT
66 GTTTT
** * *
57497310 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTA
57497375 TGTTTT
65 TGTTTT
** *
57497381 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
57497416 TTTAATTTTT
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
69 88 0.95
70 1 0.01
71 4 0.04
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
GTTTT
Found at i:57497629 original size:72 final size:72
Alignment explanation
Indices: 57497429--57498212 Score: 546
Period size: 72 Copynumber: 10.6 Consensus size: 72
57497419 AATTTTTTGT
* ** *
57497429 TTTTC-AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCA
*
57497493 TTTTCTG
66 ATTTCTG
* *
57497500 TTGTTAAAAAAAAATCAACTCATATTGCGAAAAATGAGTTGAGCCTCAGGACACACTGAGGTAAT
1 TT-TT---CAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAAT
57497565 TTCAATTTCTG
62 TTCAATTTCTG
* *
57497576 TTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCA
*
57497641 ATTTCTT
66 ATTTCTG
* * * ** *
57497648 TTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCA
57497713 ATTTCTG
66 ATTTCTG
* * ** *
57497720 TTTTCAAAAAAAAAAATCAACTTATATTGCAAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAG
1 TTTTC------AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG-ACACA--CTGAG
* *
57497784 GTATTTTTAATTTCTG
57 GTAATTTCAATTTCTG
** * ** * * *
57497800 TTTAAAAAAAAAATCAACGCATATTGCGAGAGGTGAGTTGAGCTTCAGATTACACACTGTGG---
1 TTT---TCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAG--GACACACTGAGGTAA
57497862 --T--ATTT-T-
61 TTTCAATTTCTG
* * * * ** ** *
57497868 TTTTC--AATTCATATTGCGAGA--G-GTGAGTTGAGCCTCAAGTCACACCGAGGTATTTTC-CA
1 TTTTCAAAAATCA-ACT-C-ATATTGCGAGAAATGAG--TTGAG-C-C-TC-AGG-A----CACA
* *** * *
57497927 TTTCTGT--TTTCATTATTATG
52 CTGAGGTAATTTCAAT-TTCTG
* * * *
57497947 TTTTTGAAAGAATCAACTCACATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTT
1 -TTTTCAAA-AATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTT
57498012 CAATTTCTG
64 CAATTTCTG
* * * ** *
57498021 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGACTCAAGACACGTTGAGGTATTTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCA
57498086 ATTTCTG
66 ATTTCTG
* *
57498093 CTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
1 -TTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTC
57498158 AATTTCTG
65 AATTTCTG
*
57498166 TTGTCAAAAAAATCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCAG
1 TTTTC--AAAAATCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCAG
57498213 TTCATATGTT
Statistics
Matches: 576, Mismatches: 81, Indels: 109
0.75 0.11 0.14
Matches are distributed among these distances:
63 13 0.02
64 2 0.00
65 4 0.01
66 3 0.01
68 5 0.01
69 3 0.01
70 4 0.01
71 6 0.01
72 203 0.35
73 84 0.15
74 40 0.07
75 8 0.01
76 64 0.11
77 44 0.08
78 40 0.07
79 5 0.01
80 29 0.05
81 4 0.01
82 4 0.01
83 11 0.02
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (72 bp):
TTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCA
ATTTCTG
Found at i:57497721 original size:144 final size:146
Alignment explanation
Indices: 57497429--57498212 Score: 619
Period size: 144 Copynumber: 5.3 Consensus size: 146
57497419 AATTTTTTGT
* ** * *
57497429 TTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAT
1 TTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAA
*
57497494 TTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAAAAATGAGTTGAGCCTCAGGACACACTGA
66 TTTCTGTTGTT-AAAAAAAATCAACTCATATTGCGAAAAATGAGTTGAGCCTCAAGACACACTGA
57497559 GGTAATTTCAATTTCTG
130 GGTAATTTCAATTTCTG
*
57497576 TTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCA
1 TTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCA
** * * * **
57497641 ATTTCT-TT-TT-TCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGA
65 ATTTCTGTTGTTAAAAAAAATCAACTCATATTGCGAAAAATGAGTTGAGCCTCAAGACACACTGA
*
57497703 GGTATTTTCAATTTCTG
130 GGTAATTTCAATTTCTG
* * ** *
57497720 TTTTCAAAAAAAAAAATCAACTTATATTGCAAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAG
1 TTTTC-------AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG-ACACA--CTGAG
* * * * * ** *
57497784 GTATTTTTAATTTCTGTT-TAAAAAAAAAATCAACGCATATTGCGAGAGGTGAGTTGAGCTTCAG
56 GTAATTTCAATTTCTGTTGT-TAAAAAAAATCAACTCATATTGCGAAAAATGAGTTGAGCCTCA-
* *
57497848 ATTACACACTGTGG-----T--ATTT-T-
119 A-GACACACTGAGGTAATTTCAATTTCTG
** * * * * *
57497868 TTTTC--AAT----TCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCACACCGAGGTATTTTCCA
1 TTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAA
* *
57497927 TTTCTGTT-TTCATTATTATGTTTTTGAAAGAATCAACTCACATTGCGAGAAATGAGTTGAGCCT
66 TTTCTGTTGTT-A--A--A--------AAA-AATCAACTCATATTGCGAAAAATGAGTTGAGCCT
*
57497991 CAAGACACATTGAGGTAATTTCAATTTCTG
117 CAAGACACACTGAGGTAATTTCAATTTCTG
* * ** *
57498021 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGACTCAAGACACGTTGAGGTATTTTCA
1 TTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCA
* * * * *
57498086 ATTTCTGCTT-TT--CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTG
65 ATTTCTG-TTGTTAAAAAAAATCAACTCATATTGCGAAAAATGAGTTGAGCCTCAAGACACACTG
57498148 AGGTAATTTCAATTTCTG
129 AGGTAATTTCAATTTCTG
*
57498166 TTGTCAAAAAAATCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCAG
1 TTTTC---AAAATCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCAG
57498213 TTCATATGTT
Statistics
Matches: 519, Mismatches: 66, Indels: 104
0.75 0.10 0.15
Matches are distributed among these distances:
133 22 0.04
135 32 0.06
136 1 0.00
137 1 0.00
139 3 0.01
144 74 0.14
145 67 0.13
146 39 0.08
147 40 0.08
148 64 0.12
149 4 0.01
150 38 0.07
151 8 0.02
152 20 0.04
153 8 0.02
155 35 0.07
156 2 0.00
157 8 0.02
160 49 0.09
161 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (146 bp):
TTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAA
TTTCTGTTGTTAAAAAAAATCAACTCATATTGCGAAAAATGAGTTGAGCCTCAAGACACACTGAG
GTAATTTCAATTTCTG
Found at i:57497872 original size:220 final size:208
Alignment explanation
Indices: 57497428--57498210 Score: 525
Period size: 220 Copynumber: 3.6 Consensus size: 208
57497418 TAATTTTTTG
* * * *
57497428 TTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA
1 TTTTTCAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCA
* **
57497493 TTTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAA-AAATGAGTTGAGCCTCAGGACACA-C
66 ATTTCTGTT-TTAAAAAAAAATCAACTCATATTGC-AAGAGGTGAGTTGAGCCTC-GGACACAGC
* * * * ** *
57497556 TGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAG
128 TGAGGTATTTTTAATTTCTG-TTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
* *
57497621 -GACACACTGAGGTAATTTCAATTTCT
191 TTACACACTGTGG-----T--A-TT-T
* * *
57497647 TTTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTC
1 TTTTTCAAAA-TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTC
* *
57497712 AATTTCTGTTTTCAAAAAAAAAAATCAACTTATATTGCAAGAGGTGAGTTGAGCCTCGGTTCACA
65 AATTTCTGTTTT---AAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGG-ACACA
*
57497777 TGCTGAGGTATTTTTAATTTCTGTTTAAAAAAAAAATCAACGCATATTGCGAGAGGTGAGTTGAG
126 -GCTGAGGTATTTTTAATTTCTGTTT-----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
57497842 CTTCAGATTACACACTGTGGTATTT
185 CTTCAG-TTACACACTGTGGTATTT
* * * * *
57497867 TTTTTC--AAT----TCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCACACCGAGGTATTTTCC
1 TTTTTCAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCA
* * * **
57497926 ATTTCTGTTTTCATTATTATGTTTTTGAAAGAATCAACTCACATTGCGAGAAATGAGTTGAGCCT
66 ATTTCTGTTTT-A--A--A--------AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT
* * * * * **
57497991 CAAGACACA-TTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAG
118 C-GGACACAGCTGAGGTATTTTTAATTTCTG-TTT-AAAAATCAACTCATATTGCGAGAGGTGAG
** *
57498055 TTGAGAC-TCAAG--ACACGTTGAGGTATTTTCAATTT
180 TTGAG-CTTC-AGTTACACACTGTGG-----T--ATTT
* * *
57498090 CTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAAT
1 -T--TTTTCAAAA-TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTATT
* * *
57498155 TTCAATTTCTGTTGT-CAAAAAAATCAACTCATATTGCGAA-AAGTGAGTTGAGCCTC
62 TTCAATTTCTGTTTTAAAAAAAAATCAACTCATATTGC-AAGAGGTGAGTTGAGCCTC
57498211 AGTTCATATG
Statistics
Matches: 451, Mismatches: 65, Indels: 96
0.74 0.11 0.16
Matches are distributed among these distances:
211 1 0.00
213 54 0.12
215 1 0.00
216 8 0.02
217 1 0.00
218 34 0.08
219 48 0.11
220 64 0.14
221 25 0.06
222 44 0.10
223 44 0.10
224 22 0.05
226 5 0.01
227 35 0.08
228 2 0.00
229 11 0.02
233 52 0.12
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (208 bp):
TTTTTCAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCA
ATTTCTGTTTTAAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGACACAGCTGA
GGTATTTTTAATTTCTGTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGTTACA
CACTGTGGTATTT
Found at i:57498143 original size:73 final size:72
Alignment explanation
Indices: 57497959--57498211 Score: 391
Period size: 73 Copynumber: 3.5 Consensus size: 72
57497949 TTTGAAAGAA
* *
57497959 TCAACTCACATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
57498024 TCAAAAT
66 TCAAAAT
* *
57498031 TCAACTCATATTGCGAGAAATGAGTTGAGACTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTG-TT
57498096 TTCAAAAT
65 TTCAAAAT
* * *
57498104 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTG
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
*
57498169 TCAAAAAAA
66 TC--AAAAT
57498178 TCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCA
1 TCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCA
57498212 GTTCATATGT
Statistics
Matches: 167, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
72 62 0.37
73 71 0.43
74 34 0.20
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (72 bp):
TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
TCAAAAT
Found at i:57500254 original size:17 final size:17
Alignment explanation
Indices: 57500232--57500270 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
57500222 TCGTTTTTAA
57500232 AAAATTT-TCATGTCTTC
1 AAAATTTCTCATGT-TTC
*
57500249 AAAATTTCTCGTGTTTC
1 AAAATTTCTCATGTTTC
57500266 AAAAT
1 AAAAT
57500271 AATAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (17 bp):
AAAATTTCTCATGTTTC
Found at i:57500344 original size:18 final size:18
Alignment explanation
Indices: 57500318--57500374 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
57500308 TTCGTGTTTC
*
57500318 TTTCTAAAAAAATCGTGT
1 TTTCAAAAAAAATCGTGT
****
57500336 TTTCAAAAATTCCCGTG-
1 TTTCAAAAAAAATCGTGT
*
57500353 TTTCAAAAAAATTCGTGT
1 TTTCAAAAAAAATCGTGT
57500371 TTTC
1 TTTC
57500375 GTGTTTTCGA
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
17 13 0.45
18 16 0.55
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (18 bp):
TTTCAAAAAAAATCGTGT
Found at i:57500369 original size:17 final size:17
Alignment explanation
Indices: 57500318--57500372 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
57500308 TTCGTGTTTC
57500318 TTTCTAAAAAAA-TCGTG
1 TTTC-AAAAAAATTCGTG
57500335 TTTTC--AAAAATTCCCGTG
1 -TTTCAAAAAAATT--CGTG
57500353 TTTCAAAAAAATTCGTG
1 TTTCAAAAAAATTCGTG
57500370 TTT
1 TTT
57500373 TCGTGTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
15 5 0.16
16 1 0.03
17 11 0.34
18 8 0.25
19 7 0.22
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (17 bp):
TTTCAAAAAAATTCGTG
Found at i:57500395 original size:27 final size:25
Alignment explanation
Indices: 57500349--57500399 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
57500339 CAAAAATTCC
57500349 CGTGTTTCAAAAAAATTCGTGTTTT
1 CGTGTTTCAAAAAAATTCGTGTTTT
* *
57500374 CGTGTTTTCGAAAACATCTCGTGTTT
1 CGTG-TTTCAAAAAAAT-TCGTGTTT
57500400 CAAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 10 0.45
27 8 0.36
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.43
Consensus pattern (25 bp):
CGTGTTTCAAAAAAATTCGTGTTTT
Found at i:57500505 original size:18 final size:18
Alignment explanation
Indices: 57500484--57500912 Score: 207
Period size: 17 Copynumber: 25.0 Consensus size: 18
57500474 AAATTTTGTG
57500484 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
57500502 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
57500520 -TCT-GTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
57500536 TTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
57500553 TTTTCGTGTTTTAAAAAAA
1 TTTTCGTGTTTT-CAAAAA
* * *
57500572 ATTACGTGTTTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
57500590 TTTTCGTG-TTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
57500607 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
57500625 -CTCCG-GTATTTC-AAAG
1 TTTTCGTGT-TTTCAAAAA
* *
57500641 TTTCCATGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * **
57500659 TTCTCGCGTTTAAAAAAAA
1 TTTTCGTGTTT-TCAAAAA
**
57500678 AATTCGTG-TTTCAAAATA
1 TTTTCGTGTTTTCAAAA-A
* **
57500696 TTCTCG-CATTTC---AA
1 TTTTCGTGTTTTCAAAAA
**
57500710 TTTT--TGTTTT-TTAAA
1 TTTTCGTGTTTTCAAAAA
57500725 ---TCGTG-TTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* *
57500740 ATGTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
57500757 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
* *
57500774 TTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
57500791 --TTCCTGTGTTTCAAAAAA
1 TTTTCGTGT-TTTC-AAAAA
* * *
57500809 ATGTCGTGTTTTAAAAAAA
1 TTTTCGTGTTTT-CAAAAA
*
57500828 ATTT-GT-TTTTCTAAAAA
1 TTTTCGTGTTTTC-AAAAA
*
57500845 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
*
57500862 TTTTCGTG-TTT-ACAAA
1 TTTTCGTGTTTTCAAAAA
*
57500878 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
57500896 TTCTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
57500913 AAACTTTCGT
Statistics
Matches: 314, Mismatches: 60, Indels: 75
0.70 0.13 0.17
Matches are distributed among these distances:
12 1 0.00
13 6 0.02
14 6 0.02
15 12 0.04
16 34 0.11
17 112 0.36
18 100 0.32
19 38 0.12
20 5 0.02
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:57500651 original size:88 final size:88
Alignment explanation
Indices: 57500488--57500658 Score: 220
Period size: 88 Copynumber: 1.9 Consensus size: 88
57500478 TTTGTGTTTT
* * *
57500488 CGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAATTCTGGCGTTTCAAAAA
1 CGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAACTCCGGCATTTCAAAAA
* *
57500553 TTTTCGTGTTTTAAAAAAAATTA
66 TTTCCATGTTTTAAAAAAAATTA
* * *
57500576 CGTGTTTTCACAAATTTTCGTG-TTTCACAAATTCTCGTGTTTTCAAAAACTCCGGTATTTC-AA
1 CGTGTTTTCAAAAATTTTCGTGTTTTCA-AAAATCT-GTGTTTTCAAAAACTCCGGCATTTCAAA
* *
57500639 AGTTTCCATGTTTTCAAAAA
64 AATTTCCATGTTTTAAAAAA
57500659 TTCTCGCGTT
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
87 5 0.07
88 45 0.63
89 21 0.30
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (88 bp):
CGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAACTCCGGCATTTCAAAAA
TTTCCATGTTTTAAAAAAAATTA
Found at i:57500810 original size:19 final size:18
Alignment explanation
Indices: 57500786--57500830 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
57500776 TCCCTGTTTT
*
57500786 AAAAATTCCTGTGTTTCAA
1 AAAAATTCCTGT-TTTAAA
*
57500805 AAAAATGTCGTGTTTTAAA
1 AAAAAT-TCCTGTTTTAAA
57500824 AAAAATT
1 AAAAATT
57500831 TGTTTTTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 17 0.74
20 5 0.22
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (18 bp):
AAAAATTCCTGTTTTAAA
Found at i:57500846 original size:88 final size:86
Alignment explanation
Indices: 57500725--57500925 Score: 246
Period size: 88 Copynumber: 2.3 Consensus size: 86
57500715 GTTTTTTAAA
* * *
57500725 TCGTG-TTTCAAAAAAATGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAA
1 TCGTGTTTTAAAAAAAAT-TTGTTTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTG-TTTAAA
*
57500789 AATTC-C-TGTGTTTCAAAAAAATG
64 AATTCTCGTGT-TTTC-AAAAAATC
* * *
57500812 TCGTGTTTTAAAAAAAATTTGTTTTTCTAAAAATTTTCGTGTTTCTAAAATTTTCGTGTTTACAA
1 TCGTGTTTTAAAAAAAATTTGTTTTT-TAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTAAAA
*
57500877 ATTCTCGTGTTTTCAAAAATTC
65 ATTCTCGTGTTTTCAAAAAATC
57500899 TCGTGTTTTAAAAAAAACTTTCGTTTT
1 TCGTGTTTTAAAAAAAA-TTT-GTTTT
57500926 AAAAAGAAAT
Statistics
Matches: 100, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
87 44 0.44
88 48 0.48
89 8 0.08
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (86 bp):
TCGTGTTTTAAAAAAAATTTGTTTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTAAAAA
TTCTCGTGTTTTCAAAAAATC
Found at i:57500925 original size:105 final size:104
Alignment explanation
Indices: 57500743--57500935 Score: 236
Period size: 105 Copynumber: 1.8 Consensus size: 104
57500733 CAAAAAAATG
*
57500743 TCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCTGTGTTTCAAAAA
1 TCGTGTTTTAAAAATTTTCGTGTTTC-AAAATTTCCCTGTTTTAAAAATTCCTGTGTTTAAAAAA
57500808 AATGTCGTGTTTTAAAAA-AAATTTGTTTTTCTAAAAATTT
65 AATGTCG-GTTTTAAAAAGAAATTTGTTTTTCTAAAAATTT
*
57500848 TCGTGTTTCT-AAAATTTTCGTGTTT-ACAAA-TTCTCGTGTTTTCAAAAATT-CTCGTGTTTTA
1 TCGTGTTT-TAAAAATTTTCGTGTTTCA-AAATTTC-CCTGTTTT-AAAAATTCCT-GTG-TTTA
*
57500909 AAAAAAACTTTC-GTTTTAAAAAGAAAT
60 AAAAAAA-TGTCGGTTTTAAAAAGAAAT
57500936 ACTGCGCTTC
Statistics
Matches: 77, Mismatches: 3, Indels: 15
0.81 0.03 0.16
Matches are distributed among these distances:
103 4 0.05
104 12 0.16
105 43 0.56
106 15 0.19
107 3 0.04
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (104 bp):
TCGTGTTTTAAAAATTTTCGTGTTTCAAAATTTCCCTGTTTTAAAAATTCCTGTGTTTAAAAAAA
ATGTCGGTTTTAAAAAGAAATTTGTTTTTCTAAAAATTT
Found at i:57516076 original size:18 final size:17
Alignment explanation
Indices: 57516053--57516094 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
57516043 AATCCAAGTC
57516053 AAATAAAAAAATTAAAAT
1 AAATAAAAAAA-TAAAAT
*
57516071 AAATAACTAAAATAAAAT
1 AAATAA-AAAAATAAAAT
57516089 -AATAAA
1 AAATAAA
57516095 TCAAAGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 5 0.24
18 12 0.57
19 4 0.19
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (17 bp):
AAATAAAAAAATAAAAT
Found at i:57516094 original size:13 final size:14
Alignment explanation
Indices: 57516053--57516094 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
57516043 AATCCAAGTC
* *
57516053 AAATAAAAAAATTA
1 AAATAAAATAACTA
57516067 AAAT-AAATAACTA
1 AAATAAAATAACTA
57516080 AAATAAAATAA-TA
1 AAATAAAATAACTA
57516093 AA
1 AA
57516095 TCAAAGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAATAACTA
Found at i:57517627 original size:17 final size:17
Alignment explanation
Indices: 57517605--57517657 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
57517595 AATGTAAGGT
57517605 AAAATAAATTAATTACA
1 AAAATAAATTAATTACA
**
57517622 AAAAT-AA-T-A-T-GG
1 AAAATAAATTAATTACA
57517634 AAAATAAATTAATTACA
1 AAAATAAATTAATTACA
57517651 AAAATAA
1 AAAATAA
57517658 GACATTTGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 10
0.66 0.10 0.24
Matches are distributed among these distances:
12 5 0.19
13 3 0.11
14 2 0.07
15 2 0.07
16 3 0.11
17 12 0.44
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (17 bp):
AAAATAAATTAATTACA
Found at i:57528892 original size:15 final size:14
Alignment explanation
Indices: 57528872--57528901 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
57528862 ATAACCTTCT
57528872 AAATATTTATTATTA
1 AAATATTTA-TATTA
57528887 AAATATTTATATTA
1 AAATATTTATATTA
57528901 A
1 A
57528902 TCAAAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATATTTATATTA
Found at i:57530357 original size:29 final size:27
Alignment explanation
Indices: 57530283--57530357 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
57530273 CTTTGGGTGG
*
57530283 TTTAATTTGGGGATTTTGGGTAAGGGT
1 TTTAATTTTGGGATTTTGGGTAAGGGT
* ** *
57530310 TTTGATTTTGGGAATTTTTGTTTAGGGGTT
1 TTTAATTTTGGG-A-TTTTGGGTAAGGG-T
57530340 TTTAATTTTGGAGATTTT
1 TTTAATTTTGG-GATTTT
57530358 AGGGATATCT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 10 0.26
28 1 0.03
29 14 0.37
30 12 0.32
31 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.53
Consensus pattern (27 bp):
TTTAATTTTGGGATTTTGGGTAAGGGT
Found at i:57534542 original size:22 final size:22
Alignment explanation
Indices: 57534514--57534557 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
57534504 GCAACTCGAG
57534514 ATAACTTAATTTGTGGTTTAAC
1 ATAACTTAATTTGTGGTTTAAC
57534536 ATAACTTAATTTGTGGTTTAAC
1 ATAACTTAATTTGTGGTTTAAC
57534558 CTCATATCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (22 bp):
ATAACTTAATTTGTGGTTTAAC
Found at i:57535255 original size:17 final size:17
Alignment explanation
Indices: 57535203--57535255 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 17
57535193 TATGGAAACA
* *
57535203 TAATCTTCGAGGATATG
1 TAATCTTAGAAGATATG
*
57535220 CAATCTTAGATATGATATG
1 TAATCTTAGA-A-GATATG
57535239 TAATCTTAGAAGATATG
1 TAATCTTAGAAGATATG
57535256 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 14 0.47
18 1 0.03
19 15 0.50
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (17 bp):
TAATCTTAGAAGATATG
Found at i:57535255 original size:22 final size:23
Alignment explanation
Indices: 57535227--57535271 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
57535217 ATGCAATCTT
57535227 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
57535249 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
57535272 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:57535281 original size:22 final size:23
Alignment explanation
Indices: 57535237--57535281 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
57535227 AGATATGATA
*
57535237 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
57535260 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
57535282 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:57535720 original size:3 final size:3
Alignment explanation
Indices: 57535712--57535751 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
57535702 ATTAATTTTG
*
57535712 TTA TTA TTA TTT TTA TTA TTA -TA TTA TCTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
57535752 ACCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:57535720 original size:15 final size:15
Alignment explanation
Indices: 57535696--57535750 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
57535686 GTTTTTAGTC
57535696 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
57535710 TGTTATTATTATTTT
1 TATTATTATTAATTT
57535725 TATTATTA-T-ATTAT
1 TATTATTATTAATT-T
57535739 CTATTATTATTA
1 -TATTATTATTA
57535751 TACCTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
14 5 0.16
15 24 0.75
16 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:57535727 original size:12 final size:12
Alignment explanation
Indices: 57535698--57535749 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
57535688 TTTTAGTCTA
57535698 TTTTATTAATT-T
1 TTTTATT-ATTAT
*
57535710 TGTTATTATTAT
1 TTTTATTATTAT
57535722 TTTTATTATTAT
1 TTTTATTATTAT
57535734 ATTATCTATTATTAT
1 -TT-T-TATTATTAT
57535749 T
1 T
57535750 ATACCTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.53
13 2 0.06
14 2 0.06
15 9 0.26
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:57554215 original size:3 final size:3
Alignment explanation
Indices: 57554207--57554239 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
57554197 CATTCCCATT
57554207 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
57554240 TTACAATTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:57554652 original size:26 final size:28
Alignment explanation
Indices: 57554614--57554666 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 28
57554604 GGTAATTTTC
*
57554614 TTTCATTTGCTTAATCCATGAC-ATGCT
1 TTTCATTTCCTTAATCCATGACTATGCT
* *
57554641 TTTCA-TTCCTTAGTTCATGACTATGC
1 TTTCATTTCCTTAATCCATGACTATGC
57554667 AATGATTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (28 bp):
TTTCATTTCCTTAATCCATGACTATGCT
Found at i:57559224 original size:19 final size:18
Alignment explanation
Indices: 57559200--57559253 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
57559190 TTACAACTTG
57559200 AATTTAATTTAAATAATAA
1 AATTTAATTTAAA-AATAA
* * *
57559219 AATTTATTTTTAAAATTCA
1 AATTTA-ATTTAAAAATAA
57559238 AATTTAA-TTAAAAATA
1 AATTTAATTTAAAAATA
57559254 TAAAAATGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
17 7 0.25
19 15 0.54
20 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTAATTTAAAAATAA
Found at i:57570233 original size:19 final size:19
Alignment explanation
Indices: 57570205--57570247 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
57570195 TCACAACTTT
*
57570205 TTCACCTTT-CATTTATCAA
1 TTCACCTTTCCATTT-CCAA
*
57570224 TTCACTTTTCCATTTCCAA
1 TTCACCTTTCCATTTCCAA
57570243 TTCAC
1 TTCAC
57570248 ATATTTTGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (19 bp):
TTCACCTTTCCATTTCCAA
Found at i:57577021 original size:20 final size:20
Alignment explanation
Indices: 57576997--57577053 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
57576987 CATAGAACAC
**
57576997 AATAATAATAATGACGTAAT
1 AATAATAATAATGACCAAAT
* * *
57577017 TATAATATTAATCACCAAAT
1 AATAATAATAATGACCAAAT
*
57577037 AATAATAACAATGACCA
1 AATAATAATAATGACCA
57577054 TATTAATTAC
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.28
Consensus pattern (20 bp):
AATAATAATAATGACCAAAT
Found at i:57582721 original size:19 final size:19
Alignment explanation
Indices: 57582684--57582723 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
57582674 ACTTTAAAAT
*
57582684 AATTAAATTCCCTATTTTC
1 AATTAAATTCCCTAATTTC
57582703 AATTAAA-TCCCTAAATTTC
1 AATTAAATTCCCT-AATTTC
57582722 AA
1 AA
57582724 AATTTTCACA
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:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTAAATTCCCTAATTTC
Found at i:57588934 original size:25 final size:25
Alignment explanation
Indices: 57588900--57588949 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
57588890 TTCACTGCTT
*
57588900 CATTTTCAGTTCTAATCTCTCAACA
1 CATTTTCAGTTCTAATCTATCAACA
57588925 CATTTTCAGTTCTAATCTATCAACA
1 CATTTTCAGTTCTAATCTATCAACA
57588950 GTTTTAGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.40
Consensus pattern (25 bp):
CATTTTCAGTTCTAATCTATCAACA
Found at i:57595264 original size:22 final size:22
Alignment explanation
Indices: 57595213--57595267 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
57595203 ATATGAAAAT
*
57595213 CGATATGATATAAGATGTGCTC
1 CGATATGCTATAAGATGTGCTC
57595235 CGATATGCTATAAGATGTGCTC
1 CGATATGCTATAAGATGTGCTC
57595257 CGATATGCTAT
1 CGATATGCTAT
57595268 GATACATTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (22 bp):
CGATATGCTATAAGATGTGCTC
Found at i:57595612 original size:38 final size:38
Alignment explanation
Indices: 57595565--57595660 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 38
57595555 AATAAACCAT
* * *
57595565 AGTTATAAGGTAAATTTGCTATAATGCTTTCTGCTGCA
1 AGTTTTAAGGTAAATTTGCTATAATGCTGTCCGCTGCA
*
57595603 AGTTTTAAGGTCAATTTGCTATAATGCTGTCCGCTGCA
1 AGTTTTAAGGTAAATTTGCTATAATGCTGTCCGCTGCA
**
57595641 AGTTTTATTG-AAATTTGCTA
1 AGTTTTAAGGTAAATTTGCTA
57595661 AGATGTTTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 9 0.18
38 42 0.82
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.41
Consensus pattern (38 bp):
AGTTTTAAGGTAAATTTGCTATAATGCTGTCCGCTGCA
Found at i:57596649 original size:25 final size:25
Alignment explanation
Indices: 57596615--57596665 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
57596605 ATTTTTAAAT
* *
57596615 TTTTATAAATTTGC-AAAAATTTATA
1 TTTTAAAAATTT-CTAAAAATATATA
57596640 TTTTAAAAATTTCTAAAAATATATA
1 TTTTAAAAATTTCTAAAAATATATA
57596665 T
1 T
57596666 AAATAAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (25 bp):
TTTTAAAAATTTCTAAAAATATATA
Found at i:57601261 original size:26 final size:27
Alignment explanation
Indices: 57601233--57601285 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
57601223 GGTAATTTTC
57601233 TTTCATTTGCGTCATTCATGAC-ATGCT
1 TTTC-TTTGCGTCATTCATGACTATGCT
*
57601260 TTTCTTTGCTTCATTCATGACTATGC
1 TTTCTTTGCGTCATTCATGACTATGC
57601286 AATGATTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.17, C:0.23, G:0.13, T:0.47
Consensus pattern (27 bp):
TTTCTTTGCGTCATTCATGACTATGCT
Found at i:57605711 original size:16 final size:16
Alignment explanation
Indices: 57605678--57605726 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
57605668 TTTTTACAAA
*
57605678 TTTTTTATTGTTCA-TT
1 TTTTTTAAT-TTCAGTT
57605694 TTTTTTAATTTCAGTT
1 TTTTTTAATTTCAGTT
* *
57605710 TTATTTAATTTTAGTT
1 TTTTTTAATTTCAGTT
57605726 T
1 T
57605727 GTTTAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 4 0.14
16 25 0.86
ACGTcount: A:0.18, C:0.04, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTTTTAATTTCAGTT
Found at i:57606114 original size:22 final size:22
Alignment explanation
Indices: 57606086--57606133 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
57606076 TGCCACCAAT
57606086 CCATAGCTCCATCTAATAAACG
1 CCATAGCTCCATCTAATAAACG
57606108 CCATAGCTCCATCTAATAAACG
1 CCATAGCTCCATCTAATAAACG
57606130 CCAT
1 CCAT
57606134 TGCTTGAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.33, G:0.08, T:0.23
Consensus pattern (22 bp):
CCATAGCTCCATCTAATAAACG
Found at i:57613466 original size:76 final size:76
Alignment explanation
Indices: 57613205--57613805 Score: 661
Period size: 76 Copynumber: 7.9 Consensus size: 76
57613195 AGTGAAATTT
** * * * * * *
57613205 AAAATACCTCGGCGTGCAACCCGGGGCTCAACTCACCTCTCGGATTATAAGTTGATCTTTAAAAA
1 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
*
57613270 ACA-ACAATTG-
66 ATAGA-AATTGA
* * ** * **
57613280 AAAATACGTTAGTGTGCGACCCTAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTCAAAAA
1 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
57613345 ATAGAAATT-A
66 ATAGAAATTGA
* * *
57613355 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACCTATCAGATTATGAGTTGATTTTTGAAAA
1 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
*
57613420 ATAGAAACTGA
66 ATAGAAATTGA
* * * * * *
57613431 AAAATACCTCAGCGTGCGACCCAAGGCTTAGCTCACCTCTCAGATTATGAGTTGATTTTTGAAAA
1 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
57613496 ATAGAAATTGA
66 ATAGAAATTGA
** **
57613507 AAAATACCTCAACGTATGACCTAAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
1 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
57613572 ATAGAAATTG-
66 ATAGAAATTGA
* ** ** * * ** *
57613582 AAAATACATCAGTGTATGACCCGAGGCTCAACTAACTTATCAAATTATGAGTTAATTTTTGAAAA
1 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
* *
57613647 ACAGAACTTGA
66 ATAGAAATTGA
* * * * * *
57613658 AAAATACCTCAACATGCGACCTGAGGCTCGACTCACTTCTTGGATTATGAGTTTATTTTTAAAAA
1 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
*
57613723 AGAGAAATTGA
66 ATAGAAATTGA
* * * * * *
57613734 TAAATACCTCAACGTGCGACCCAAGGCTCAACTCTCTTCTTGGATTATGAATTGATTTTTGACAA
1 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
*
57613799 ACAGAAA
66 ATAGAAA
57613806 GGAAATTATT
Statistics
Matches: 445, Mismatches: 77, Indels: 7
0.84 0.15 0.01
Matches are distributed among these distances:
75 186 0.42
76 259 0.58
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (76 bp):
AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
ATAGAAATTGA
Found at i:57613605 original size:227 final size:227
Alignment explanation
Indices: 57613205--57613805 Score: 726
Period size: 227 Copynumber: 2.7 Consensus size: 227
57613195 AGTGAAATTT
* * * * * * *
57613205 AAAATACCTCGGCGTGCAACCCGGGGCTCAACTCACCTCTCGGATTATAAGTTGATCTTTAAAAA
1 AAAATACCTCAGCGTGCGACCCGAGGCTTAGCTCACCTCTCGGATTATGAGTTGATTTTTAAAAA
* * **
57613270 ACA-ACAATTG-AAAATACGTTAGTGTGCGACCCT-AGGCTCAACTCACTTCTCGGATTATGAGT
66 ACAGA-AATTGAAAAATACCTCAACGTGCGA-CCTAAGGCTCAACTCACTTCTCGGATTATGAGT
** * * *
57613332 TGATTTTCAAAAAATAGAAATTAAAAATACCTCAACGTGCGACCCGAGGCTCAACTCACCTATCA
129 TGATTTTTGAAAAATAGAAATTAAAAATACATCAACGTACGACCCGAGGCTCAACTAACCTATCA
* * *
57613397 GATTATGAGTTGATTTTTGAAAAATAGAAAC-TGA
194 AATTATGAGTTAATTTTTGAAAAACAG-AACTTGA
* * *
57613431 AAAATACCTCAGCGTGCGACCCAAGGCTTAGCTCACCTCTCAGATTATGAGTTGATTTTTGAAAA
1 AAAATACCTCAGCGTGCGACCCGAGGCTTAGCTCACCTCTCGGATTATGAGTTGATTTTTAAAAA
* **
57613496 ATAGAAATTGAAAAATACCTCAACGTATGACCTAAGGCTCAACTCACTTCTCGGATTATGAGTTG
66 ACAGAAATTGAAAAATACCTCAACGTGCGACCTAAGGCTCAACTCACTTCTCGGATTATGAGTTG
* ** * *
57613561 ATTTTTGAAAAATAGAAATTGAAAATACATCAGTGTATGACCCGAGGCTCAACTAACTTATCAAA
131 ATTTTTGAAAAATAGAAATTAAAAATACATCAACGTACGACCCGAGGCTCAACTAACCTATCAAA
57613626 TTATGAGTTAATTTTTGAAAAACAGAACTTGA
196 TTATGAGTTAATTTTTGAAAAACAGAACTTGA
* * * * * * *
57613658 AAAATACCTCAACATGCGACCTGAGGC-TCGACTCACTTCTTGGATTATGAGTTTATTTTTAAAA
1 AAAATACCTCAGCGTGCGACCCGAGGCTTAG-CTCACCTCTCGGATTATGAGTTGATTTTTAAAA
* * * * * *
57613722 AAGAGAAATTGATAAATACCTCAACGTGCGACCCAAGGCTCAACTCTCTTCTTGGATTATGAATT
65 AACAGAAATTGAAAAATACCTCAACGTGCGACCTAAGGCTCAACTCACTTCTCGGATTATGAGTT
* *
57613787 GATTTTTGACAAACAGAAA
130 GATTTTTGAAAAATAGAAA
57613806 GGAAATTATT
Statistics
Matches: 320, Mismatches: 50, Indels: 9
0.84 0.13 0.02
Matches are distributed among these distances:
226 70 0.22
227 250 0.78
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (227 bp):
AAAATACCTCAGCGTGCGACCCGAGGCTTAGCTCACCTCTCGGATTATGAGTTGATTTTTAAAAA
ACAGAAATTGAAAAATACCTCAACGTGCGACCTAAGGCTCAACTCACTTCTCGGATTATGAGTTG
ATTTTTGAAAAATAGAAATTAAAAATACATCAACGTACGACCCGAGGCTCAACTAACCTATCAAA
TTATGAGTTAATTTTTGAAAAACAGAACTTGA
Found at i:57614706 original size:15 final size:15
Alignment explanation
Indices: 57614683--57614727 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
57614673 AATTTACTTC
*
57614683 TGTTGACTTCTGTTT
1 TGTTTACTTCTGTTT
*
57614698 TGTTTACTTTTGTTT
1 TGTTTACTTCTGTTT
57614713 T-TTTACTTCTGTTT
1 TGTTTACTTCTGTTT
57614727 T
1 T
57614728 TTCGGTACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.07, C:0.11, G:0.13, T:0.69
Consensus pattern (15 bp):
TGTTTACTTCTGTTT
Found at i:57614719 original size:14 final size:14
Alignment explanation
Indices: 57614688--57614729 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
57614678 ACTTCTGTTG
57614688 ACTTCTGTTTTGTTT
1 ACTTCTGTTTT-TTT
*
57614703 ACTTTTGTTTTTTT
1 ACTTCTGTTTTTTT
57614717 ACTTCTGTTTTTT
1 ACTTCTGTTTTTT
57614730 CGGTACTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.07, C:0.12, G:0.10, T:0.71
Consensus pattern (14 bp):
ACTTCTGTTTTTTT
Found at i:57619889 original size:14 final size:15
Alignment explanation
Indices: 57619862--57619891 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
57619852 ATAACCTTCT
57619862 AAATATTTATTATTA
1 AAATATTTATTATTA
57619877 AAATATTTA-TATTA
1 AAATATTTATTATTA
57619891 A
1 A
57619892 TCAAAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATATTTATTATTA
Found at i:57622735 original size:14 final size:15
Alignment explanation
Indices: 57622716--57622755 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
57622706 ACGTTGTGTA
57622716 TTTAATTTTTA-TAT
1 TTTAATTTTTAGTAT
*
57622730 TTTAATTTTTAGTTT
1 TTTAATTTTTAGTAT
*
57622745 TTTAAATTTTA
1 TTTAATTTTTA
57622756 AAATTTTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTAATTTTTAGTAT
Found at i:57626055 original size:40 final size:40
Alignment explanation
Indices: 57626010--57626103 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
57626000 TTTAGCAACA
*
57626010 TTTTTGAAAAAGCGCCGCT-AATTCTCTATTTTTAGCGGCG
1 TTTTTGAAAAAGCGCCG-TGAATGCTCTATTTTTAGCGGCG
* *
57626050 TTTTTGAAGAAGCGCTGTGAATGCTCTATTTTTAGCGGCG
1 TTTTTGAAAAAGCGCCGTGAATGCTCTATTTTTAGCGGCG
*
57626090 TTTTTAAAAAAGCG
1 TTTTTGAAAAAGCG
57626104 TCGCAATAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.02
40 47 0.98
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.37
Consensus pattern (40 bp):
TTTTTGAAAAAGCGCCGTGAATGCTCTATTTTTAGCGGCG
Found at i:57626940 original size:28 final size:28
Alignment explanation
Indices: 57626871--57626933 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
57626861 GATAAGCTTT
*
57626871 AATTGAAAAAGGAATACTCGGTTACTTA
1 AATTCAAAAAGGAATACTCGGTTACTTA
57626899 AATTCAAAAAGGAATACTCGGTTACTTA
1 AATTCAAAAAGGAATACTCGGTTACTTA
57626927 AATTCAA
1 AATTCAA
57626934 CGAGGAAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (28 bp):
AATTCAAAAAGGAATACTCGGTTACTTA
Found at i:57627287 original size:19 final size:18
Alignment explanation
Indices: 57627260--57627296 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
57627250 TAATATATAT
57627260 ATTAAAATATTAAAATAA
1 ATTAAAATATTAAAATAA
*
57627278 ATTAACAATATTGAAATAA
1 ATTAA-AATATTAAAATAA
57627297 GTTGAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
ATTAAAATATTAAAATAA
Found at i:57627676 original size:9 final size:9
Alignment explanation
Indices: 57627647--57627680 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
57627637 TAATATTATC
*
57627647 AATAATAGC
1 AATAATAGT
57627656 AATAATAGT
1 AATAATAGT
*
57627665 AATAATATT
1 AATAATAGT
57627674 AATAATA
1 AATAATA
57627681 ATGAAAGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (9 bp):
AATAATAGT
Found at i:57628408 original size:20 final size:18
Alignment explanation
Indices: 57628383--57628419 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
57628373 CAATAATAAT
57628383 AAAAAGAAACAGAGAAATCG
1 AAAAAGAAA-AG-GAAATCG
57628403 AAAAAGAAAAGGAAATC
1 AAAAAGAAAAGGAAATC
57628420 ACCTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.68, C:0.08, G:0.19, T:0.05
Consensus pattern (18 bp):
AAAAAGAAAAGGAAATCG
Found at i:57629012 original size:7 final size:7
Alignment explanation
Indices: 57629002--57629055 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
57628992 GAGTTATTAT
*
57629002 TTTAAGG
1 TTTATGG
57629009 TTTATGG
1 TTTATGG
*
57629016 ATTATGGG
1 TTTAT-GG
*
57629024 TTTAAGG
1 TTTATGG
*
57629031 GTTATGG
1 TTTATGG
57629038 TTTATGG
1 TTTATGG
*
57629045 TATATGG
1 TTTATGG
57629052 TTTA
1 TTTA
57629056 AAGGCTGGGG
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (7 bp):
TTTATGG
Found at i:57629027 original size:22 final size:22
Alignment explanation
Indices: 57629002--57629044 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
57628992 GAGTTATTAT
*
57629002 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGGTTATGGATTATGGG
*
57629024 TTTAAGGGTTATGGTTTATGG
1 TTTAAGGGTTATGGATTATGG
57629045 TATATGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.47
Consensus pattern (22 bp):
TTTAAGGGTTATGGATTATGGG
Found at i:57629137 original size:16 final size:16
Alignment explanation
Indices: 57629116--57629148 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
57629106 TAGTGTTTTC
57629116 TAATTTA-TATATTAAT
1 TAATTTATTATA-TAAT
57629132 TAATTTATTATATAAT
1 TAATTTATTATATAAT
57629148 T
1 T
57629149 GTAAAATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATTTATTATATAAT
Found at i:57630052 original size:21 final size:23
Alignment explanation
Indices: 57630028--57630074 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
57630018 TGAAATTTAT
*
57630028 TTTTTTATTTTTAT-TTT-AAAA
1 TTTTTAATTTTTATATTTCAAAA
57630049 TTTTTAATTTTTATATTTCAAAA
1 TTTTTAATTTTTATATTTCAAAA
57630072 TTT
1 TTT
57630075 AAAATTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.57
22 3 0.13
23 7 0.30
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTTAATTTTTATATTTCAAAA
Found at i:57630080 original size:23 final size:21
Alignment explanation
Indices: 57630034--57630089 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
57630024 TTATTTTTTT
**
57630034 ATTTTTATTTTAAAATTTTTA
1 ATTTTTATTTTAAAATTTAAA
57630055 ATTTTTATATTTCAAAATTTAAA
1 ATTTTTAT-TTT-AAAATTTAAA
*
57630078 A-TTTAATTTTAA
1 ATTTTTATTTTAA
57630090 TTATTAGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 2 0.07
21 11 0.37
22 8 0.27
23 9 0.30
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTTATTTTAAAATTTAAA
Found at i:57635002 original size:20 final size:20
Alignment explanation
Indices: 57634977--57635023 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
57634967 GATATTTGTT
57634977 TTTATATTGATATT-ACTA-TA
1 TTTATATT-ATATTGA-TATTA
57634997 TTTATATTATATTGATATTA
1 TTTATATTATATTGATATTA
57635017 TTTATAT
1 TTTATAT
57635024 CTTTCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTATATTATATTGATATTA
Found at i:57639369 original size:17 final size:17
Alignment explanation
Indices: 57639341--57639390 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
57639331 GTATAAAATT
57639341 ATTTTAAAAAAAATTAAA
1 ATTTT-AAAAAAATTAAA
**
57639359 ATTTTAAAAAAAGAAAA
1 ATTTTAAAAAAATTAAA
*
57639376 ATGTTTATAAAAATT
1 AT-TTTAAAAAAATT
57639391 CTAGAAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (17 bp):
ATTTTAAAAAAATTAAA
Found at i:57646430 original size:44 final size:43
Alignment explanation
Indices: 57646380--57646501 Score: 145
Period size: 43 Copynumber: 2.8 Consensus size: 43
57646370 ACGTCGCTAA
* *
57646380 CTTTAGCGGCGTTTTTAGAAAAAAACGCCGCTAAAGACCACGAC
1 CTTTAGCGGCGCTTTT-GCAAAAAACGCCGCTAAAGACCACGAC
* * * * * *
57646424 CTTTAGCAGTGCTTTTGCCACAAACGCCGCTAAAGATCATGAC
1 CTTTAGCGGCGCTTTTGCAAAAAACGCCGCTAAAGACCACGAC
*
57646467 CTTTAGCGGCGCTTCTCGCAAAAAACGCCGCTAAA
1 CTTTAGCGGCGCTT-TTGCAAAAAACGCCGCTAAA
57646502 AACATAACCT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 34 0.53
44 30 0.47
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTGCAAAAAACGCCGCTAAAGACCACGAC
Found at i:57651225 original size:7 final size:7
Alignment explanation
Indices: 57651215--57651244 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
57651205 ATAAACCTTA
57651215 AACCCCT
1 AACCCCT
57651222 AACCCCT
1 AACCCCT
57651229 AACCCCT
1 AACCCCT
57651236 AACCCCT
1 AACCCCT
57651243 AA
1 AA
57651245 ACATTAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.33, C:0.53, G:0.00, T:0.13
Consensus pattern (7 bp):
AACCCCT
Found at i:57651793 original size:7 final size:7
Alignment explanation
Indices: 57651763--57651834 Score: 56
Period size: 7 Copynumber: 10.3 Consensus size: 7
57651753 CGTATCACCC
57651763 AACCCTT
1 AACCCTT
* *
57651770 AAACCAT
1 AACCCTT
* *
57651777 AAACCAT
1 AACCCTT
57651784 AACCCTT
1 AACCCTT
*
57651791 AACTCTT
1 AACCCTT
*
57651798 AACCCTC
1 AACCCTT
57651805 AACTCC-T
1 AAC-CCTT
57651812 AACCCTT
1 AACCCTT
*
57651819 AACCCCT
1 AACCCTT
*
57651826 AAACCTT
1 AACCCTT
57651833 AA
1 AA
57651835 TCTATAAATC
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
6 2 0.04
7 48 0.92
8 2 0.04
ACGTcount: A:0.38, C:0.39, G:0.00, T:0.24
Consensus pattern (7 bp):
AACCCTT
Found at i:57651802 original size:14 final size:14
Alignment explanation
Indices: 57651783--57651834 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
57651773 CCATAAACCA
*
57651783 TAACCCTTAACTCT
1 TAACCCTTAACTCC
*
57651797 TAACCCTCAACTCC
1 TAACCCTTAACTCC
*
57651811 TAACCCTTAACCCC
1 TAACCCTTAACTCC
*
57651825 TAAACCTTAA
1 TAACCCTTAA
57651835 TCTATAAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.27
Consensus pattern (14 bp):
TAACCCTTAACTCC
Found at i:57651842 original size:14 final size:14
Alignment explanation
Indices: 57651815--57651898 Score: 62
Period size: 14 Copynumber: 5.9 Consensus size: 14
57651805 AACTCCTAAC
* *
57651815 CCTTAACCCCTAAA
1 CCTTAAACCATAAA
* *
57651829 CCTTAATCTATAAA
1 CCTTAAACCATAAA
*
57651843 TCTTAAACCATAAA
1 CCTTAAACCATAAA
* * * *
57651857 CCGTAACCCTTAAG
1 CCTTAAACCATAAA
57651871 CCTTAAACGCATAAA
1 CCTTAAAC-CATAAA
57651886 -CTATAAACCATAA
1 CCT-TAAACCATAA
57651899 TCTATAAACC
Statistics
Matches: 53, Mismatches: 15, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
14 44 0.83
15 9 0.17
ACGTcount: A:0.43, C:0.29, G:0.04, T:0.25
Consensus pattern (14 bp):
CCTTAAACCATAAA
Found at i:57651851 original size:21 final size:21
Alignment explanation
Indices: 57651838--57651913 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
57651828 ACCTTAATCT
*
57651838 ATAAATCTTAAACCATAAACC
1 ATAAACCTTAAACCATAAACC
* * * *
57651859 GTAACCCTTAAGCCTTAAACGC
1 ATAAACCTTAAACCATAAAC-C
* *
57651881 ATAAA-CTATAAACCATAATCT
1 ATAAACCT-TAAACCATAAACC
57651902 ATAAACCTTAAA
1 ATAAACCTTAAA
57651914 ATAGTAACTC
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
21 26 0.63
22 15 0.37
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.25
Consensus pattern (21 bp):
ATAAACCTTAAACCATAAACC
Done.