Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold13
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: 2744999
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.26
Warning! 506982 characters in sequence are not A, C, G, or T
File 13 of 15
Found at i:2430195 original size:23 final size:24
Alignment explanation
Indices: 2430160--2430204 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
2430150 CATATAAAGT
*
2430160 TAAATATATAG-AATATTATAATG
1 TAAATATATAGAAATATGATAATG
2430183 TAAATAT-TAAGAAATATGATAA
1 TAAATATAT-AGAAATATGATAA
2430205 CCATTTCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 1 0.05
23 9 0.47
24 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (24 bp):
TAAATATATAGAAATATGATAATG
Found at i:2431296 original size:11 final size:11
Alignment explanation
Indices: 2431282--2431359 Score: 53
Period size: 11 Copynumber: 7.5 Consensus size: 11
2431272 AATTAGAACT
2431282 AGAAAAGAAAG
1 AGAAAAGAAAG
2431293 AGAAAAG-AAG
1 AGAAAAGAAAG
* *
2431303 -GAAGGAGGAAG
1 AGAA-AAGAAAG
2431314 AGAAAAGAAAG
1 AGAAAAGAAAG
2431325 A-AAAA-AAA-
1 AGAAAAGAAAG
*
2431333 AG-AAGGAAAG
1 AGAAAAGAAAG
*
2431343 A-AGATAGAAAG
1 AGA-AAAGAAAG
2431354 AGAAAA
1 AGAAAA
2431360 AAAAAAAGGG
Statistics
Matches: 51, Mismatches: 7, Indels: 18
0.67 0.09 0.24
Matches are distributed among these distances:
8 3 0.06
9 9 0.18
10 10 0.20
11 25 0.49
12 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.01
Consensus pattern (11 bp):
AGAAAAGAAAG
Found at i:2431318 original size:32 final size:28
Alignment explanation
Indices: 2431282--2431368 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 28
2431272 AATTAGAACT
*
2431282 AGAAAAGAAAGAGAAAAGAAGGAAGGAGGAA
1 AGAAAAGAAAGAGAAAA-AA--AAGAAGGAA
2431313 GAGAAAAGAAAGA-AAAAAAAAGAAGGAA
1 -AGAAAAGAAAGAGAAAAAAAAGAAGGAA
*
2431341 AGAAGATAGAAAGAGAAAAAAAAAAAGG
1 AGAA-A-AGAAAGAGAAAAAAAAGAAGG
2431369 GAGAAAAAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
27 4 0.08
28 9 0.18
29 7 0.14
30 14 0.28
31 4 0.08
32 12 0.24
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (28 bp):
AGAAAAGAAAGAGAAAAAAAAGAAGGAA
Found at i:2431335 original size:21 final size:21
Alignment explanation
Indices: 2431284--2431366 Score: 68
Period size: 21 Copynumber: 4.1 Consensus size: 21
2431274 TTAGAACTAG
*
2431284 AAAAGAAAGAGAAAAGAAGGA
1 AAAAGAAAGAGAAAAGAAAGA
** *
2431305 AGGAGGAAGAGAAAAGAAAGA
1 AAAAGAAAGAGAAAAGAAAGA
*
2431326 AAAA-AAA-AG-AAGGAAAGA
1 AAAAGAAAGAGAAAAGAAAGA
*
2431344 AGATAGAAAGAGAAAA-AAA-A
1 A-AAAGAAAGAGAAAAGAAAGA
2431364 AAA
1 AAA
2431367 GGGAGAAAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
18 9 0.19
19 5 0.11
20 7 0.15
21 24 0.51
22 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (21 bp):
AAAAGAAAGAGAAAAGAAAGA
Found at i:2431358 original size:35 final size:35
Alignment explanation
Indices: 2431285--2431366 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 35
2431275 TAGAACTAGA
* * *
2431285 AAAGAAAGAGAAAAGAAGGAAGGAGGAAGAGAAAAG
1 AAAGAAA-AAAAAAGAAGGAAAGAAGAAGAGAAAAG
*
2431321 AAAGAAAAAAAAAGAAGGAAAGAAGATAGA-AAGAG
1 AAAGAAAAAAAAAGAAGGAAAGAAGA-AGAGAAAAG
2431356 AAA-AAAAAAAA
1 AAAGAAAAAAAA
2431367 GGGAGAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
34 8 0.20
35 23 0.56
36 10 0.24
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (35 bp):
AAAGAAAAAAAAAGAAGGAAAGAAGAAGAGAAAAG
Found at i:2432474 original size:239 final size:238
Alignment explanation
Indices: 2432049--2432525 Score: 830
Period size: 239 Copynumber: 2.0 Consensus size: 238
2432039 TAAATTATAG
*
2432049 CTCTAATTTTGCATTGGTAACAGCCTCACTTTCACTTGAAAATTTGTTTTCAAGCCTCAAATGAT
1 CTCTAATTTTGCATTGGTAACAGCCTCACTTTCACTTGAAAATTTATTTTCAAGCCTCAAATGAT
2432114 TTTTACAGTTTTTTTGGTATTTTTCTCTTGAAGAGCATCGAATTATCTTTTCAAAAACCTTTTAT
66 TTTTACAGTTTTTTTGGTATTTTTCTCTTGAAGAGCATCGAATTATCTTTTCAAAAACCTTTTAT
* * * * *
2432179 TTCCTTAAAAAGAGTTCGTATAGGGGAGTTATGATTTTTCAAATATGTGTTATTTGAAACCCATA
131 TTCCTTAAAAAGAGTTCATAAAGAGGAGTTATGATTTTTCAAACATGTGCTATTTGAAACCCATA
* *
2432244 AGACTAATGATCAGACTTCATTATAGGCCATTTTTGGCCTACT
196 AGACTAATGACCAGACTTCATTATAAGCCATTTTTGGCCTACT
2432287 CTCTAATTTTGCATTGGTAACAGCC-CGACTTTCACTTGAAAATTTATTTTCAAGCCTCAAATGA
1 CTCTAATTTTGCATTGGTAACAGCCTC-ACTTTCACTTGAAAATTTATTTTCAAGCCTCAAATGA
*
2432351 TTTTTATAGTTTTTTTTGGTATTTTTCTCTTGAAGAGCATCGAATTATCTTTTCAAAAACCTTTT
65 TTTTTACAG-TTTTTTTGGTATTTTTCTCTTGAAGAGCATCGAATTATCTTTTCAAAAACCTTTT
*
2432416 ATTTCCTTAAGAAGAGTTCATAAAGAGGAGTTATGATTTTTCAAACATGTGCTATTTGAAACCCA
129 ATTTCCTTAAAAAGAGTTCATAAAGAGGAGTTATGATTTTTCAAACATGTGCTATTTGAAACCCA
*
2432481 TAAGACTAGTGACCAGACTTCATTATAAGCCATTTTTGGCCTACT
194 TAAGACTAATGACCAGACTTCATTATAAGCCATTTTTGGCCTACT
2432526 AGAAAATTTT
Statistics
Matches: 226, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
237 1 0.00
238 69 0.31
239 156 0.69
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (238 bp):
CTCTAATTTTGCATTGGTAACAGCCTCACTTTCACTTGAAAATTTATTTTCAAGCCTCAAATGAT
TTTTACAGTTTTTTTGGTATTTTTCTCTTGAAGAGCATCGAATTATCTTTTCAAAAACCTTTTAT
TTCCTTAAAAAGAGTTCATAAAGAGGAGTTATGATTTTTCAAACATGTGCTATTTGAAACCCATA
AGACTAATGACCAGACTTCATTATAAGCCATTTTTGGCCTACT
Found at i:2433201 original size:51 final size:52
Alignment explanation
Indices: 2433112--2433216 Score: 169
Period size: 51 Copynumber: 2.0 Consensus size: 52
2433102 ATATATATCC
*
2433112 TAACTGTCCCTCTTTTTTTTTGTTTCGAGTGTCTATTTTACACAATA-TTAT
1 TAACTGTCCCTCTTTTTTTTTGTTTCGAGTGTCCATTTTACACAATATTTAT
*
2433163 TAACTGTCCCTC-TTTTTTTTGTTTCGGGTGTTCCATTTTACACAATATTTAT
1 TAACTGTCCCTCTTTTTTTTTGTTTCGAGTG-TCCATTTTACACAATATTTAT
2433215 TA
1 TA
2433217 CATTTTTACG
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
50 17 0.34
51 27 0.54
52 6 0.12
ACGTcount: A:0.19, C:0.18, G:0.10, T:0.52
Consensus pattern (52 bp):
TAACTGTCCCTCTTTTTTTTTGTTTCGAGTGTCCATTTTACACAATATTTAT
Found at i:2438762 original size:17 final size:17
Alignment explanation
Indices: 2438736--2438793 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
2438726 GAGATTAACA
2438736 ATTAAA-TTTGATTTTT
1 ATTAAATTTTGATTTTT
*
2438752 ATTAAATTTTG--TTAT
1 ATTAAATTTTGATTTTT
2438767 -TTAAATTTT-ATTTTT
1 ATTAAATTTTGATTTTT
2438782 AATTAAATTTTG
1 -ATTAAATTTTG
2438794 TCATGCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 9 0.26
15 6 0.18
16 6 0.18
17 13 0.38
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
ATTAAATTTTGATTTTT
Found at i:2438771 original size:30 final size:31
Alignment explanation
Indices: 2438737--2438794 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
2438727 AGATTAACAA
2438737 TTAAATTTGATTTTT-ATTAAATTTTGTTAT
1 TTAAATTTGATTTTTAATTAAATTTTGTTAT
*
2438767 TTAAATTTTATTTTTAATTAAATTTTGT
1 TTAAATTTGATTTTTAATTAAATTTTGT
2438795 CATGCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (31 bp):
TTAAATTTGATTTTTAATTAAATTTTGTTAT
Found at i:2439253 original size:13 final size:13
Alignment explanation
Indices: 2439216--2439259 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
2439206 TTTAATTATA
2439216 AAAATATAATGAT
1 AAAATATAATGAT
*
2439229 AAATATTAATAATAAT
1 AAA-A-T-ATAATGAT
2439245 AAAATATAATGAT
1 AAAATATAATGAT
2439258 AA
1 AA
2439260 GTTTTAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 12 0.46
14 2 0.08
15 2 0.08
16 10 0.38
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (13 bp):
AAAATATAATGAT
Found at i:2439266 original size:29 final size:29
Alignment explanation
Indices: 2439183--2439267 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
2439173 TAGTATCGAG
* * *
2439183 ATAAAATAAAATGATAAG-TTTACTTTAATT
1 ATAAAATATAATGATAAGTTTTA--ATAATA
* *
2439213 ATAAAAATATAATGATAAATATTAATAATA
1 AT-AAAATATAATGATAAGTTTTAATAATA
2439243 ATAAAATATAATGATAAGTTTTAAT
1 ATAAAATATAATGATAAGTTTTAAT
2439268 GTACAATTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
29 21 0.46
30 8 0.17
31 14 0.30
32 3 0.07
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (29 bp):
ATAAAATATAATGATAAGTTTTAATAATA
Found at i:2439504 original size:9 final size:9
Alignment explanation
Indices: 2439477--2439544 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
2439467 AAGTGGCAGC
2439477 TTTTTTTAA
1 TTTTTTTAA
*
2439486 TTTTACTTAA
1 TTTT-TTTAA
2439496 TTTTTTTAA
1 TTTTTTTAA
* *
2439505 TTTGTGTAA
1 TTTTTTTAA
2439514 TTTTTTGT-A
1 TTTTTT-TAA
*
2439523 -TTTTAT-A
1 TTTTTTTAA
2439530 TTTTTTTATA
1 TTTTTTTA-A
2439540 TTTTT
1 TTTTT
2439545 ATCGTATTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
7 2 0.04
8 9 0.20
9 20 0.43
10 15 0.33
ACGTcount: A:0.21, C:0.01, G:0.04, T:0.74
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:2439544 original size:18 final size:18
Alignment explanation
Indices: 2439495--2439546 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 18
2439485 ATTTTACTTA
* *
2439495 ATTTTTTTA-ATTTGTGT
1 ATTTTTTTATATTTTTAT
* *
2439512 AATTTTTTGTA-TTTTAT
1 ATTTTTTTATATTTTTAT
2439529 ATTTTTTTATATTTTTAT
1 ATTTTTTTATATTTTTAT
2439547 CGTATTTATA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 20 0.74
18 7 0.26
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (18 bp):
ATTTTTTTATATTTTTAT
Found at i:2439685 original size:26 final size:26
Alignment explanation
Indices: 2439655--2439708 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
2439645 CGATTGTGAA
* *
2439655 ATCATGTGATATTTATTTTTTATTTT
1 ATCATATGATAATTATTTTTTATTTT
**
2439681 ATCATATTTTAATTATTTTTTATTTT
1 ATCATATGATAATTATTTTTTATTTT
2439707 AT
1 AT
2439709 GTTTGTATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (26 bp):
ATCATATGATAATTATTTTTTATTTT
Found at i:2441663 original size:16 final size:18
Alignment explanation
Indices: 2441627--2441663 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
2441617 TGTTTTTATA
*
2441627 ATTTTATATATAATTATT
1 ATTTTATATATAATTAAT
2441645 ATTTTA-ATA-AATTAAT
1 ATTTTATATATAATTAAT
2441661 ATT
1 ATT
2441664 AAATTTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 3 0.17
18 6 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTATATATAATTAAT
Found at i:2442072 original size:29 final size:31
Alignment explanation
Indices: 2442049--2442111 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
2442039 TATATATGAT
2442049 TTATA-TAAATAAA-ATAAAAAATATAATAA
1 TTATATTAAATAAATATAAAAAATATAATAA
** *
2442078 TTATATTAAATAAATATAAATTATATAAAAA
1 TTATATTAAATAAATATAAAAAATATAATAA
2442109 TTA
1 TTA
2442112 AAAATATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 5 0.17
30 8 0.28
31 16 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (31 bp):
TTATATTAAATAAATATAAAAAATATAATAA
Found at i:2442095 original size:22 final size:19
Alignment explanation
Indices: 2442063--2442143 Score: 60
Period size: 20 Copynumber: 4.2 Consensus size: 19
2442053 ATAAATAAAA
2442063 TAAAAAATATAATAATTATAT
1 TAAAAAATAT-A-AATTATAT
2442084 TAAATAAATATAAATTATA-
1 TAAA-AAATATAAATTATAT
* *
2442103 TAAAAATTA-AAAATATAT
1 TAAAAAATATAAATTATAT
* *
2442121 AAAATTAAAT-TAATTTATAT
1 TAAA--AAATATAAATTATAT
2442141 TAA
1 TAA
2442144 TTTAAGTGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
17 7 0.15
18 7 0.15
19 4 0.08
20 19 0.40
21 5 0.10
22 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAAATATAAATTATAT
Found at i:2442109 original size:17 final size:18
Alignment explanation
Indices: 2442051--2442124 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 18
2442041 TATATGATTT
* *
2442051 ATATAAATAAAATAAAAA
1 ATATAAATTATATAAAAA
2442069 ATATAATAATTATATTAAATAA
1 ATAT-A-AATTATA-TAAA-AA
2442091 ATATAAATTATATAAAAA
1 ATATAAATTATATAAAAA
* *
2442109 TTA-AAAATATATAAAA
1 ATATAAATTATATAAAA
2442125 TTAAATTAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
17 12 0.25
18 8 0.17
19 5 0.10
20 12 0.25
21 5 0.10
22 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATATAAATTATATAAAAA
Found at i:2442133 original size:47 final size:49
Alignment explanation
Indices: 2442031--2442133 Score: 122
Period size: 47 Copynumber: 2.1 Consensus size: 49
2442021 AATTTATTTA
* * * *
2442031 AAATTTAATATATATGATTTATATAAATAAAATAAAAAATATAATAATT
1 AAATTAAATAAATATAAATTATATAAATAAAATAAAAAATATAATAATT
* *
2442080 ATATTAAATAAATATAAATTATAT-AA-AAATTAAAAATATATAA-AATT
1 AAATTAAATAAATATAAATTATATAAATAAAATAAAAA-ATATAATAATT
2442127 AAATTAA
1 AAATTAA
2442134 TTTATATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
47 19 0.41
48 8 0.17
49 19 0.41
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (49 bp):
AAATTAAATAAATATAAATTATATAAATAAAATAAAAAATATAATAATT
Found at i:2442139 original size:37 final size:39
Alignment explanation
Indices: 2442051--2442140 Score: 96
Period size: 37 Copynumber: 2.3 Consensus size: 39
2442041 TATATGATTT
* * * *
2442051 ATATAAATAAAATAAAAAATATAATAATTATATTAAATAA
1 ATATAAATTATAT-AAAAATATAATAAATATATAAAATAA
2442091 ATATAAATTATATAAAAAT-TAA-AAATATATAAAATTAA
1 ATATAAATTATATAAAAATATAATAAATATATAAAA-TAA
*
2442129 AT-TAATTTATAT
1 ATATAAATTATAT
2442141 TAATTTAAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
37 19 0.43
38 8 0.18
39 6 0.14
40 11 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (39 bp):
ATATAAATTATATAAAAATATAATAAATATATAAAATAA
Found at i:2451125 original size:14 final size:15
Alignment explanation
Indices: 2451094--2451127 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2451084 CATTATATTT
2451094 ATAAATATAATCGTA
1 ATAAATATAATCGTA
2451109 ATAAATATAAT-GTA
1 ATAAATATAATCGTA
2451123 ATAAA
1 ATAAA
2451128 AAATATGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (15 bp):
ATAAATATAATCGTA
Found at i:2458575 original size:9 final size:9
Alignment explanation
Indices: 2458545--2458585 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
2458535 TTATGTCATG
2458545 TTAT-TTTA
1 TTATATTTA
2458553 TTATATTT-
1 TTATATTTA
2458561 TTATATTTA
1 TTATATTTA
* *
2458570 TTATATATG
1 TTATATTTA
2458579 TTATATT
1 TTATATT
2458586 AGTATTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
8 12 0.43
9 16 0.57
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (9 bp):
TTATATTTA
Found at i:2458594 original size:20 final size:17
Alignment explanation
Indices: 2458543--2458585 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
2458533 AATTATGTCA
2458543 TGTTAT-TTTATTATAT
1 TGTTATATTTATTATAT
*
2458559 TTTTATATTTATTATAT
1 TGTTATATTTATTATAT
2458576 ATGTTATATT
1 -TGTTATATT
2458586 AGTATTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 5 0.22
17 10 0.43
18 8 0.35
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (17 bp):
TGTTATATTTATTATAT
Found at i:2458704 original size:17 final size:17
Alignment explanation
Indices: 2458668--2458715 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
2458658 TTATATTAAA
2458668 ATTTATATTAAATATAT
1 ATTTATATTAAATATAT
* * *
2458685 ATTTTTATTAATTATTT
1 ATTTATATTAAATATAT
*
2458702 A-TTATATTTAATAT
1 ATTTATATTAAATAT
2458716 TAAAATTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTATATTAAATATAT
Found at i:2459094 original size:15 final size:15
Alignment explanation
Indices: 2459011--2459100 Score: 51
Period size: 17 Copynumber: 5.6 Consensus size: 15
2459001 GTATTTTTAT
*
2459011 ATTTTTATTATATTAA
1 ATTTATATTATA-TAA
2459027 TATTTATATT-TA-AA
1 -ATTTATATTATATAA
2459041 ATATTATAAATTTATATAA
1 AT-TTAT--A-TTATATAA
*
2459060 ATTT-TAATATATTAATA
1 ATTTATATTATA-T-A-A
2459077 ATTTATATTATATAA
1 ATTTATATTATATAA
*
2459092 ATTTTTATT
1 ATTTATATT
2459101 TTTATTATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 22
0.69 0.05 0.26
Matches are distributed among these distances:
13 2 0.03
14 10 0.17
15 11 0.19
16 5 0.08
17 17 0.29
18 10 0.17
19 4 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTATATTATATAA
Found at i:2459119 original size:19 final size:19
Alignment explanation
Indices: 2459092--2459129 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2459082 TATTATATAA
* *
2459092 ATTTTTATTTTTATTATTT
1 ATTTATATTTTAATTATTT
2459111 ATTTATATTTTAATTATTT
1 ATTTATATTTTAATTATTT
2459130 TTTTGATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
ATTTATATTTTAATTATTT
Found at i:2459385 original size:24 final size:25
Alignment explanation
Indices: 2459335--2459419 Score: 79
Period size: 24 Copynumber: 3.4 Consensus size: 25
2459325 AATTTGATTA
* *
2459335 AATTTAAATTTAA-ATTTTTTAATTT
1 AATTTAAA-ATAATATTTTTTAAATT
2459360 AATTTAAAATAATA-TTTTTAAATT
1 AATTTAAAATAATATTTTTTAAATT
**
2459384 AAAAT-AAA-AATATTTTTTAAATTT
1 AATTTAAAATAATATTTTTTAAA-TT
2459408 AATTATAAAATA
1 AATT-TAAAATA
2459420 TATAAATTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
22 4 0.08
23 11 0.23
24 19 0.40
25 10 0.21
26 3 0.06
27 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AATTTAAAATAATATTTTTTAAATT
Found at i:2459420 original size:24 final size:24
Alignment explanation
Indices: 2459348--2459420 Score: 89
Period size: 23 Copynumber: 3.1 Consensus size: 24
2459338 TTAAATTTAA
2459348 ATTTTTT-AATTTAATT-TAAAAT
1 ATTTTTTAAATTTAATTATAAAAT
* *
2459370 AATATTTTTAAATTAAAATA-AAAAT
1 -AT-TTTTTAAATTTAATTATAAAAT
2459395 ATTTTTTAAATTTAATTATAAAAT
1 ATTTTTTAAATTTAATTATAAAAT
2459419 AT
1 AT
2459421 ATAAATTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
23 16 0.38
24 14 0.33
25 12 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTTTTTAAATTTAATTATAAAAT
Found at i:2459447 original size:48 final size:46
Alignment explanation
Indices: 2459332--2459448 Score: 116
Period size: 48 Copynumber: 2.5 Consensus size: 46
2459322 TTTAATTTGA
* * *
2459332 TTAAATTTAAAT-TTAAATTTTTTAATTTAATTTAAAATAATATTT
1 TTAAATTAAAATAATAAATTTTTTAATTTAATTTAAAATAATAATT
*
2459377 TTAAATTAAAATAAAAATATTTTTTAAATTTAATTATAAAATATATAAATT
1 TTAAATTAAAATAATAA-ATTTTTT-AATTTAATT-TAAAATA-AT-AATT
2459428 TT-AA-TATAAA-AATAAATTTTT
1 TTAAATTA-AAATAATAAATTTTT
2459449 AATATTTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
45 11 0.18
46 2 0.03
47 7 0.12
48 15 0.25
49 13 0.22
50 7 0.12
51 5 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (46 bp):
TTAAATTAAAATAATAAATTTTTTAATTTAATTTAAAATAATAATT
Found at i:2459450 original size:19 final size:21
Alignment explanation
Indices: 2459401--2459453 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 21
2459391 AAATATTTTT
2459401 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
2459422 TAAATTTTAATATAAAA-ATA
1 TAAATTTTAATATAAAATATA
*
2459442 -AATTTTTAATAT
1 TAAATTTTAATAT
2459454 TTTTTAATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 11 0.37
20 3 0.10
21 11 0.37
22 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:2459653 original size:22 final size:22
Alignment explanation
Indices: 2459628--2459669 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2459618 AAAATAAGAT
*
2459628 ATATAAAAATAATATTAATTTG
1 ATATAAAAATAATATAAATTTG
* *
2459650 ATATGAATATAATATAAATT
1 ATATAAAAATAATATAAATT
2459670 ATTAATTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
ATATAAAAATAATATAAATTTG
Found at i:2460981 original size:21 final size:21
Alignment explanation
Indices: 2460955--2460994 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2460945 TTTAAAAAAT
2460955 TATTTTAT-ATTAAAATTTATA
1 TATTTTATAATT-AAATTTATA
2460976 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
2460995 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:2461249 original size:19 final size:18
Alignment explanation
Indices: 2461225--2461278 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
2461215 TAATTTTATC
2461225 ATATAAATTTATTATATTT
1 ATAT-AATTTATTATATTT
2461244 ATATAATTATATTAT-TTT
1 ATATAATT-TATTATATTT
*
2461262 -TATATTTTATTATATTT
1 ATATAATTTATTATATTT
2461279 TTAATTAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 6 0.19
17 9 0.28
18 7 0.22
19 10 0.31
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATATAATTTATTATATTT
Found at i:2461297 original size:35 final size:35
Alignment explanation
Indices: 2461232--2461298 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
2461222 ATCATATAAA
*
2461232 TTTATTATATTTATATAATTATATTATTTTTATAT
1 TTTATTATATTTATATAATTAAATTATTTTTATAT
2461267 TTTATTATATTT-T-TAATTAAATTGAGTTTTTA
1 TTTATTATATTTATATAATTAAATT-A-TTTTTA
2461299 AACAAGAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 9 0.31
34 2 0.07
35 18 0.62
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (35 bp):
TTTATTATATTTATATAATTAAATTATTTTTATAT
Found at i:2461860 original size:19 final size:18
Alignment explanation
Indices: 2461821--2461872 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
2461811 ATATTTGAGA
*
2461821 TAAATTAAATAATAATAT
1 TAAATTAAAAAATAATAT
2461839 TAAATTTAAAAAATTAAT-T
1 TAAA-TTAAAAAA-TAATAT
* *
2461858 TAAGTAAAAAAATAA
1 TAAATTAAAAAATAA
2461873 AACCCTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 3 0.10
18 11 0.38
19 11 0.38
20 4 0.14
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
TAAATTAAAAAATAATAT
Found at i:2462040 original size:12 final size:13
Alignment explanation
Indices: 2462001--2462043 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
2461991 ATCATATAAA
2462001 AAATAAATATATT
1 AAATAAATATATT
2462014 ATAATATAA-ATATT
1 A-AATA-AATATATT
2462028 AAA-AAATATATT
1 AAATAAATATATT
2462040 AAAT
1 AAAT
2462044 TATTTATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 2 0.08
12 9 0.35
13 3 0.12
14 10 0.38
15 2 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAATAAATATATT
Found at i:2462912 original size:3 final size:3
Alignment explanation
Indices: 2462900--2462937 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2462890 CCCTTTTCTA
2462900 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2462938 AGATTTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2463703 original size:16 final size:16
Alignment explanation
Indices: 2463649--2463693 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
2463639 CTATTTCGTG
*
2463649 TTTAAATCATTTTTAA
1 TTTAAATCATTTTAAA
2463665 TTTAAATCATTTTAAA
1 TTTAAATCATTTTAAA
2463681 TTTAAATCATTTT
1 TTTAAATCATTTT
2463694 GGATTCAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAAATCATTTTAAA
Found at i:2463900 original size:13 final size:13
Alignment explanation
Indices: 2463882--2463916 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2463872 TTAATAAGTC
2463882 ATTTTTTATTTTT
1 ATTTTTTATTTTT
*
2463895 ATTTTTTACTTTT
1 ATTTTTTATTTTT
*
2463908 ATTTGTTAT
1 ATTTTTTAT
2463917 GATTTTTGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (13 bp):
ATTTTTTATTTTT
Found at i:2464354 original size:2 final size:2
Alignment explanation
Indices: 2464347--2464412 Score: 59
Period size: 2 Copynumber: 34.5 Consensus size: 2
2464337 ATTTATTTAT
* * * *
2464347 TA TA TA TA TA TA TA TA TA TA T- TA T- TT TGA CA CA T- TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
2464387 T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2464413 TGTTATTTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
1 4 0.07
2 50 0.93
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2464387 original size:49 final size:47
Alignment explanation
Indices: 2464319--2464412 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
2464309 CAACATATTC
*
2464319 TATTTTGACACATTATTTATTTATTTATTATATATATATATATATATAT
1 TATTTTGACACATTATTTA-TTATATA-TATATATATATATATATATAT
2464368 TATTTTGACACATTATTTATTATATATATATATATATATATATAT
1 TATTTTGACACATTATTTATTATATATATATATATATATATATAT
2464413 TGTTATTTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 19 0.43
48 6 0.14
49 19 0.43
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (47 bp):
TATTTTGACACATTATTTATTATATATATATATATATATATATATAT
Found at i:2464696 original size:2 final size:2
Alignment explanation
Indices: 2464691--2464727 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2464681 ATATATATAT
2464691 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2464728 AATGATATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2464765 original size:15 final size:16
Alignment explanation
Indices: 2464745--2464779 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
2464735 TGTAAATGTT
2464745 AAAGTAGGAAAG-AGG
1 AAAGTAGGAAAGTAGG
2464760 AAAGTAGGAAAGTAGG
1 AAAGTAGGAAAGTAGG
2464776 AAAG
1 AAAG
2464780 AAAAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.54, C:0.00, G:0.37, T:0.09
Consensus pattern (16 bp):
AAAGTAGGAAAGTAGG
Found at i:2464768 original size:8 final size:8
Alignment explanation
Indices: 2464745--2464779 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
2464735 TGTAAATGTT
2464745 AAAGTAGG
1 AAAGTAGG
2464753 AAAG-AGG
1 AAAGTAGG
2464760 AAAGTAGG
1 AAAGTAGG
2464768 AAAGTAGG
1 AAAGTAGG
2464776 AAAG
1 AAAG
2464780 AAAAGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.54, C:0.00, G:0.37, T:0.09
Consensus pattern (8 bp):
AAAGTAGG
Found at i:2466519 original size:23 final size:23
Alignment explanation
Indices: 2466471--2466536 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
2466461 TAATAAAATA
* *
2466471 TAAATTTAAACT-TAAACCCATT
1 TAAATTTAAACTAAAAACCCATC
* *
2466493 TAAATCTAAACTAAAAACCTATC
1 TAAATTTAAACTAAAAACCCATC
2466516 TAAATTTAAACTAAAAACCCA
1 TAAATTTAAACTAAAAACCCA
2466537 ATTAAAACAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 11 0.30
23 26 0.70
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAATTTAAACTAAAAACCCATC
Found at i:2470458 original size:17 final size:17
Alignment explanation
Indices: 2470433--2470465 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2470423 TCTTTTGTAG
2470433 CTTAATTTTTACAAGTT
1 CTTAATTTTTACAAGTT
*
2470450 CTTACTTTTTACAAGT
1 CTTAATTTTTACAAGT
2470466 ACCAATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (17 bp):
CTTAATTTTTACAAGTT
Found at i:2474263 original size:13 final size:13
Alignment explanation
Indices: 2474253--2474278 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2474243 TTTTTTTAGT
2474253 AGTTAGGTTTACA
1 AGTTAGGTTTACA
2474266 AGTTAGGTTTACA
1 AGTTAGGTTTACA
2474279 TGTTGTGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
AGTTAGGTTTACA
Found at i:2484015 original size:21 final size:21
Alignment explanation
Indices: 2483977--2484016 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2483967 AAATCCTAAG
*
2483977 TAGAGATAAAGATCTATTGCC
1 TAGAGATAAAGATATATTGCC
**
2483998 TAGAGATAGTGATATATTG
1 TAGAGATAAAGATATATTG
2484017 GAATGGACCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (21 bp):
TAGAGATAAAGATATATTGCC
Found at i:2484812 original size:18 final size:17
Alignment explanation
Indices: 2484781--2484832 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
2484771 AATAAATTTT
2484781 TATATTATTTATTTAAGA
1 TATA-TATTTATTTAAGA
2484799 TATATATTTAATTTAAG-
1 TATATATTT-ATTTAAGA
* *
2484816 TAAATAATTATTTAAGA
1 TATATATTTATTTAAGA
2484833 CTAGAATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 7 0.23
17 12 0.40
18 11 0.37
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
TATATATTTATTTAAGA
Found at i:2485729 original size:179 final size:179
Alignment explanation
Indices: 2485429--2485787 Score: 691
Period size: 179 Copynumber: 2.0 Consensus size: 179
2485419 ACTAAAGAGC
*
2485429 GAAACCTTTGAAAAAGTCAAAGAGAATCATGCGGAAATGGAAAGTAATCGGATAAATCCATGAAG
1 GAAACCTTTGAAAAAGTCAAAGAGAATCATGCGAAAATGGAAAGTAATCGGATAAATCCATGAAG
2485494 ACACTTTGATTTGATCGAGGTGATAAATACCTCTCCAATGATTTTCTAGGACACCTCATAGAGAA
66 ACACTTTGATTTGATCGAGGTGATAAATACCTCTCCAATGATTTTCTAGGACACCTCATAGAGAA
2485559 TAGGATTTTATCCCAATTGACTACGCTAGGTAGTCCACAACAAAATGGT
131 TAGGATTTTATCCCAATTGACTACGCTAGGTAGTCCACAACAAAATGGT
2485608 GAAACCTTTGAAAAAGTCAAAGAGAATCATGCGAAAATGGAAAGTAATCGGATAAATCCATGAAG
1 GAAACCTTTGAAAAAGTCAAAGAGAATCATGCGAAAATGGAAAGTAATCGGATAAATCCATGAAG
*
2485673 ACACTTTGATTTGATCGAGGTTATAAATACCTCTCCAATGATTTTCTAGGACACCTCATAGAGAA
66 ACACTTTGATTTGATCGAGGTGATAAATACCTCTCCAATGATTTTCTAGGACACCTCATAGAGAA
*
2485738 TAGGATTTTTTCCCAATTGACTACGCTAGGTAGTCCACAACAAAATGGT
131 TAGGATTTTATCCCAATTGACTACGCTAGGTAGTCCACAACAAAATGGT
2485787 G
1 G
2485788 CGGCCAAAAG
Statistics
Matches: 177, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
179 177 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.26
Consensus pattern (179 bp):
GAAACCTTTGAAAAAGTCAAAGAGAATCATGCGAAAATGGAAAGTAATCGGATAAATCCATGAAG
ACACTTTGATTTGATCGAGGTGATAAATACCTCTCCAATGATTTTCTAGGACACCTCATAGAGAA
TAGGATTTTATCCCAATTGACTACGCTAGGTAGTCCACAACAAAATGGT
Found at i:2492191 original size:2 final size:2
Alignment explanation
Indices: 2492184--2492220 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2492174 ACATGGAGGT
*
2492184 GA GA GA GA GA GA GA GA GT GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2492221 TGAGGAAAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.51, T:0.03
Consensus pattern (2 bp):
GA
Found at i:2493169 original size:33 final size:33
Alignment explanation
Indices: 2493121--2493183 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
2493111 TATCAGAGAG
**
2493121 AGCAGAAACTGCACAAAATAAC-GACTGTAAAGT
1 AGCAGAAACCACACAAAATAACAG-CTGTAAAGT
2493154 AGCAGAAACCACACAAAATAACAGCTGTAA
1 AGCAGAAACCACACAAAATAACAGCTGTAA
2493184 CGTCGCCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.51, C:0.21, G:0.16, T:0.13
Consensus pattern (33 bp):
AGCAGAAACCACACAAAATAACAGCTGTAAAGT
Found at i:2493544 original size:2 final size:2
Alignment explanation
Indices: 2493537--2493567 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2493527 CAATAAGCAA
2493537 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2493568 TAAATGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2494412 original size:18 final size:19
Alignment explanation
Indices: 2494375--2494413 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
2494365 ATTTATTTTA
2494375 TAAATTTGATAAAAAATTT
1 TAAATTTGATAAAAAATTT
2494394 TAAATTT-A-AAAATAATTT
1 TAAATTTGATAAAA-AATTT
2494412 TA
1 TA
2494414 TTTATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 8 0.42
19 7 0.37
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
TAAATTTGATAAAAAATTT
Found at i:2494500 original size:15 final size:16
Alignment explanation
Indices: 2494458--2494500 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
2494448 ATTTGATATA
*
2494458 AAATATATTTATTTTT
1 AAATATATTTAATTTT
2494474 AAAGTATTATTTAATTTT
1 AAA-TA-TATTTAATTTT
2494492 AAATA-ATTT
1 AAATATATTT
2494501 TTTATTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 4 0.17
16 3 0.12
17 4 0.17
18 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
AAATATATTTAATTTT
Found at i:2494542 original size:15 final size:17
Alignment explanation
Indices: 2494521--2494562 Score: 61
Period size: 15 Copynumber: 2.5 Consensus size: 17
2494511 ATTTTTATTT
2494521 TTATTTTTATT-TAAAA
1 TTATTTTTATTATAAAA
2494537 -TATTTTTAATTATAAAA
1 TTATTTTT-ATTATAAAA
2494554 TTATTTTTA
1 TTATTTTTA
2494563 ATTACTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 7 0.30
16 3 0.13
17 6 0.26
18 7 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTTTTATTATAAAA
Found at i:2494560 original size:18 final size:18
Alignment explanation
Indices: 2494521--2494566 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
2494511 ATTTTTATTT
2494521 TTATTTTT-ATT-TAAAA
1 TTATTTTTAATTATAAAA
2494537 -TATTTTTAATTATAAAA
1 TTATTTTTAATTATAAAA
2494554 TTATTTTTAATTA
1 TTATTTTTAATTA
2494567 CTATTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.26
16 3 0.11
17 5 0.19
18 12 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATTTTTAATTATAAAA
Found at i:2494761 original size:18 final size:19
Alignment explanation
Indices: 2494740--2494782 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
2494730 GTACCAAAAT
2494740 ATTTTAAATTTAT-CATTA
1 ATTTTAAATTTATGCATTA
* *
2494758 A-TTTAATTTTATGTATTA
1 ATTTTAAATTTATGCATTA
2494776 ATTTTAA
1 ATTTTAA
2494783 TATTAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 10 0.48
18 6 0.29
19 5 0.24
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTTAAATTTATGCATTA
Found at i:2494825 original size:25 final size:27
Alignment explanation
Indices: 2494787--2494840 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
2494777 TTTTAATATT
* **
2494787 AATATATTATATTATTTTTA-TTTAAA
1 AATAAATTATATTATCATTATTTTAAA
2494813 AATAAATTA-ATTATCATTATTTTAAA
1 AATAAATTATATTATCATTATTTTAAA
2494839 AA
1 AA
2494841 GTTTAAAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
AATAAATTATATTATCATTATTTTAAA
Found at i:2495071 original size:29 final size:29
Alignment explanation
Indices: 2495036--2495114 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 29
2495026 TCACTAAATT
2495036 TTTAAATAATAATAATTAATTAATTT-AAA
1 TTTAAATAAT-ATAATTAATTAATTTCAAA
* * *
2495065 TTTAAATACTATAATAAATTTATTTCAAA
1 TTTAAATAATATAATTAATTAATTTCAAA
*
2495094 GTT-AAT-ATATAATTGAATTAA
1 TTTAAATAATATAATT-AATTAA
2495115 AAATAAGCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
27 6 0.15
28 21 0.51
29 14 0.34
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (29 bp):
TTTAAATAATATAATTAATTAATTTCAAA
Found at i:2497024 original size:115 final size:115
Alignment explanation
Indices: 2496901--2497180 Score: 364
Period size: 115 Copynumber: 2.4 Consensus size: 115
2496891 TCTCACTTAT
* *
2496901 TTATTTAATTAATTTATTTGAGCCTATTTTATCTAATTATATTAGGTTATAAAGTATTTAATTTA
1 TTATTTAATTAATTTATTTGAGCTTATTTTATTTAATTATATTAGGTTATAAAGTATTTAATTTA
* * **
2496966 AGGTCAAGTCTTATAAAAAATATATATTAGATAAAATAAATCCCATGTAC
66 AGGTCAAGCCTTATAAAAAATATATATTAGATAAAATAAAGCCCACATAC
* ** *
2497016 TTATTTAATTAATTTATTTG-GATTTATTTTATTTAATTATATTAAATTATAAATTATTTAATTT
1 TTATTTAATTAATTTATTTGAG-CTTATTTTATTTAATTATATTAGGTTATAAAGTATTTAATTT
* * ** *
2497080 AAGGTCAAGCCTTATAAAAATTATATATTGGATAAAATAGGGCCCACATGC
65 AAGGTCAAGCCTTATAAAAAATATATATTAGATAAAATAAAGCCCACATAC
* * * *
2497131 ATATTTAATTTATTTATTTGAGGCTTATTTTATTTAATTATGTTGGGTTA
1 TTATTTAATTAATTTATTTGA-GCTTATTTTATTTAATTATATTAGGTTA
2497181 ATTTTTAAAT
Statistics
Matches: 140, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
114 1 0.01
115 116 0.83
116 22 0.16
117 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (115 bp):
TTATTTAATTAATTTATTTGAGCTTATTTTATTTAATTATATTAGGTTATAAAGTATTTAATTTA
AGGTCAAGCCTTATAAAAAATATATATTAGATAAAATAAAGCCCACATAC
Found at i:2497864 original size:2 final size:2
Alignment explanation
Indices: 2497857--2497906 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2497847 CTTAGTAAGC
2497857 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2497899 TA TA TA TA
1 TA TA TA TA
2497907 AAGCTATGAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2502537 original size:19 final size:18
Alignment explanation
Indices: 2502491--2502581 Score: 66
Period size: 19 Copynumber: 5.1 Consensus size: 18
2502481 TTTCAACAAT
2502491 TTGTATCGATACAAACTGTAA
1 TTGTATCGATACAAA--GT-A
*
2502512 CTGTATCGATACATAAGTA
1 TTGTATCGATACA-AAGTA
2502531 TTGTATCGATAC--A--A
1 TTGTATCGATACAAAGTA
* *
2502545 -TGTATCAATACATAAGTT
1 TTGTATCGATACA-AAGTA
*
2502563 TTGTATCGATACAATGTA
1 TTGTATCGATACAAAGTA
2502581 T
1 T
2502582 CGCTACGAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
13 10 0.18
14 1 0.02
16 2 0.04
18 4 0.07
19 23 0.41
20 2 0.04
21 12 0.21
22 2 0.04
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (18 bp):
TTGTATCGATACAAAGTA
Found at i:2502556 original size:32 final size:32
Alignment explanation
Indices: 2502513--2502582 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
2502503 AAACTGTAAC
*
2502513 TGTATCGATACATAAGTATTGTATCGATACAA
1 TGTATCAATACATAAGTATTGTATCGATACAA
*
2502545 TGTATCAATACATAAGTTTTGTATCGATACAA
1 TGTATCAATACATAAGTATTGTATCGATACAA
2502577 TGTATC
1 TGTATC
2502583 GCTACGAAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCAATACATAAGTATTGTATCGATACAA
Found at i:2502646 original size:13 final size:13
Alignment explanation
Indices: 2502628--2502655 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2502618 ATTACTCAAA
2502628 TGTATCGATACAT
1 TGTATCGATACAT
2502641 TGTATCGATACAT
1 TGTATCGATACAT
2502654 TG
1 TG
2502656 ACCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2507903 original size:27 final size:27
Alignment explanation
Indices: 2507867--2507925 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
2507857 CACCATATTT
*
2507867 TCCTACTCAACCTCCATACCCGTCATA
1 TCCTACTCAACCTCCATACCCATCATA
*
2507894 TCCTACTCAACCTCTATACCCATCATA
1 TCCTACTCAACCTCCATACCCATCATA
2507921 TCCTA
1 TCCTA
2507926 TCACGACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.27, C:0.42, G:0.02, T:0.29
Consensus pattern (27 bp):
TCCTACTCAACCTCCATACCCATCATA
Found at i:2512744 original size:22 final size:23
Alignment explanation
Indices: 2512719--2512772 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
2512709 CAAGCATAAC
*
2512719 TTGAAT-ATCCTTAAAAGCTGGT
1 TTGAATCATCCTTAAAAGCTAGT
*
2512741 TTG-ATCATCTTTAAAAGCTAGT
1 TTGAATCATCCTTAAAAGCTAGT
2512763 TTG-ATCATCC
1 TTGAATCATCC
2512773 AATGAACGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (23 bp):
TTGAATCATCCTTAAAAGCTAGT
Found at i:2517545 original size:13 final size:12
Alignment explanation
Indices: 2517491--2517548 Score: 50
Period size: 13 Copynumber: 4.9 Consensus size: 12
2517481 TCAATTAAGT
2517491 TTTTATTAA-TA
1 TTTTATTAATTA
2517502 TTTT-TT-ATTA
1 TTTTATTAATTA
*
2517512 TTTTTTTAATTAA
1 TTTTATTAATT-A
**
2517525 TTAAATTAATTCA
1 TTTTATTAATT-A
2517538 TTTTATTAATT
1 TTTTATTAATT
2517549 TCATTTAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 1 0.03
10 8 0.22
11 6 0.16
12 3 0.08
13 19 0.51
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTATTAATTA
Found at i:2522838 original size:6 final size:6
Alignment explanation
Indices: 2522807--2522837 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2522797 GCTAAGTCCC
*
2522807 TATAAA TATAAA TATAAA TATAAA TTTAAA T
1 TATAAA TATAAA TATAAA TATAAA TATAAA T
2522838 TATATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
TATAAA
Found at i:2523086 original size:16 final size:16
Alignment explanation
Indices: 2523065--2523096 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2523055 ATTAAGTGAC
*
2523065 CAATATATGTATATAT
1 CAATATATATATATAT
2523081 CAATATATATATATAT
1 CAATATATATATATAT
2523097 ATTACCTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (16 bp):
CAATATATATATATAT
Found at i:2523888 original size:23 final size:22
Alignment explanation
Indices: 2523859--2523901 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
2523849 AAAAAATATT
2523859 TCTTT-AATCATTTTTATATTTCA
1 TCTTTAAAT-ATTTTT-TATTTCA
2523882 TCTTTAAATATTTTTTATTT
1 TCTTTAAATATTTTTTATTT
2523902 TGAAATACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 11 0.58
24 3 0.16
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (22 bp):
TCTTTAAATATTTTTTATTTCA
Found at i:2525969 original size:2 final size:2
Alignment explanation
Indices: 2525962--2526010 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2525952 GAAATTTGCA
2525962 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2526004 AT AT AT A
1 AT AT AT A
2526011 AAACACTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2527212 original size:3 final size:3
Alignment explanation
Indices: 2527204--2527229 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2527194 TGTTTGGATA
2527204 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2527230 AGAAAGTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2527550 original size:2 final size:2
Alignment explanation
Indices: 2527543--2527578 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2527533 TAAGTTTCTC
2527543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2527579 GTTATGAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2528141 original size:19 final size:20
Alignment explanation
Indices: 2528119--2528156 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2528109 TTGTTTTCTT
*
2528119 TTATTTAAAC-AAAAAAAAC
1 TTATCTAAACTAAAAAAAAC
2528138 TTATCTAAACTAAAAAAAA
1 TTATCTAAACTAAAAAAAA
2528157 AAAAAATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (20 bp):
TTATCTAAACTAAAAAAAAC
Found at i:2528406 original size:22 final size:22
Alignment explanation
Indices: 2528363--2528420 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
2528353 GTTAAGTATG
* *
2528363 TTTTATTTTTCTTAAAATATTT
1 TTTTATTTTTTTTGAAATATTT
2528385 TTTTAATTTTTTTTGAAA-ATTT
1 TTTT-ATTTTTTTTGAAATATTT
*
2528407 TTATTTTTTTTTTT
1 TT-TTATTTTTTTT
2528421 TGCATCTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTTTTGAAATATTT
Found at i:2528408 original size:23 final size:23
Alignment explanation
Indices: 2528363--2528422 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
2528353 GTTAAGTATG
*
2528363 TTTTATTTTTCTT-AAAATATTT
1 TTTTATTTTTTTTGAAAATATTT
2528385 TTTTAATTTTTTTTGAAAAT-TTT
1 TTTT-ATTTTTTTTGAAAATATTT
*
2528408 TATTTTTTTTTTTTG
1 T-TTTATTTTTTTTG
2528423 CATCTTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 4 0.12
23 21 0.64
24 8 0.24
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.73
Consensus pattern (23 bp):
TTTTATTTTTTTTGAAAATATTT
Found at i:2530831 original size:16 final size:15
Alignment explanation
Indices: 2530807--2530849 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
2530797 ACATAATTTT
*
2530807 TATTAAATATTTATTA
1 TATTTAATATTTA-TA
*
2530823 TATTTAATATTTATG
1 TATTTAATATTTATA
2530838 TATTTAAT-TTTA
1 TATTTAATATTTA
2530850 AAATTACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 4 0.16
15 9 0.36
16 12 0.48
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TATTTAATATTTATA
Found at i:2531166 original size:14 final size:14
Alignment explanation
Indices: 2531147--2531173 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2531137 TAAATATATA
2531147 ATATTATTTTTATT
1 ATATTATTTTTATT
2531161 ATATTATTTTTAT
1 ATATTATTTTTAT
2531174 ATTTATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATATTATTTTTATT
Found at i:2531188 original size:20 final size:20
Alignment explanation
Indices: 2531150--2531188 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2531140 ATATATAATA
* * *
2531150 TTATTTTTATTATATTATTT
1 TTATATTTATTAAAGTATTT
2531170 TTATATTTATTAAAGTATT
1 TTATATTTATTAAAGTATT
2531189 ATATTTATAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
TTATATTTATTAAAGTATTT
Found at i:2534981 original size:22 final size:22
Alignment explanation
Indices: 2534951--2534993 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2534941 CCTCTAATGT
2534951 AGTTCAATTGGAATCATGGTTG
1 AGTTCAATTGGAATCATGGTTG
*
2534973 AGTTTAATTGGAATCATGGTT
1 AGTTCAATTGGAATCATGGTT
2534994 AGAAAAAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.07, G:0.26, T:0.40
Consensus pattern (22 bp):
AGTTCAATTGGAATCATGGTTG
Found at i:2536513 original size:14 final size:15
Alignment explanation
Indices: 2536489--2536517 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2536479 TATCTGCAAA
2536489 CAAAAAGTAAAAAAT
1 CAAAAAGTAAAAAAT
2536504 CAAAAA-TAAAAAAT
1 CAAAAAGTAAAAAAT
2536518 AATTAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.76, C:0.07, G:0.03, T:0.14
Consensus pattern (15 bp):
CAAAAAGTAAAAAAT
Found at i:2536535 original size:16 final size:17
Alignment explanation
Indices: 2536506--2536549 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2536496 TAAAAAATCA
*
2536506 AAAATAAAAAATAAT-T
1 AAAATATAAAATAATAT
*
2536522 AAAATATAATATAATAT
1 AAAATATAAAATAATAT
2536539 AAATATATAAA
1 AAA-ATATAAA
2536550 TGTCTCAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 13 0.57
17 4 0.17
18 6 0.26
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATATAAAATAATAT
Found at i:2537538 original size:27 final size:28
Alignment explanation
Indices: 2537474--2537539 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
2537464 AAAAAATTAA
* *
2537474 AATATAATAT-AAAAATAATATTAATAT
1 AATATAATATAAAAAATAATATAAAAAT
2537501 AATATAA-ATAAAGAAAT-ATATAAAAAT
1 AATATAATATAAA-AAATAATATAAAAAT
2537528 -ATATAATATAAA
1 AATATAATATAAA
2537540 TTATTAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 8 0.24
27 22 0.65
28 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (28 bp):
AATATAATATAAAAAATAATATAAAAAT
Found at i:2537563 original size:25 final size:27
Alignment explanation
Indices: 2537534--2537619 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
2537524 AAATATATAA
*
2537534 TATAAATTAT-TAA-TATATTAAATTT
1 TATAAAATATATAATTATATTAAATTT
* *
2537559 TATAAAATATATAATTATTTTAAATGT
1 TATAAAATATATAATTATATTAAATTT
* * * *
2537586 AATTATAATATATAAATATA-TAAA-TA
1 TA-TAAAATATATAATTATATTAAATTT
2537612 TATAAAAT
1 TATAAAAT
2537620 TATCAATATT
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
25 14 0.30
26 4 0.09
27 15 0.32
28 14 0.30
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (27 bp):
TATAAAATATATAATTATATTAAATTT
Found at i:2537563 original size:30 final size:32
Alignment explanation
Indices: 2537515--2537608 Score: 77
Period size: 30 Copynumber: 2.8 Consensus size: 32
2537505 TAAATAAAGA
2537515 AATATATAAAAATATAT-AATATA-AATTATT
1 AATATATAAAAATATATAAATATATAATTATT
* * *
2537545 AATATATTAAATTTTATAAAATATATAATTATTTT
1 AATATATAAAAATATAT-AAATATATAATTA--TT
*
2537580 AA-ATGTAATTATAATATATAAATATATAA
1 AATATATAA--A-AATATATAAATATATAA
2537609 ATATATAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
30 14 0.29
32 6 0.12
33 5 0.10
34 4 0.08
35 4 0.08
36 11 0.22
37 5 0.10
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (32 bp):
AATATATAAAAATATATAAATATATAATTATT
Found at i:2537605 original size:8 final size:8
Alignment explanation
Indices: 2537447--2537617 Score: 86
Period size: 8 Copynumber: 20.9 Consensus size: 8
2537437 TAATTATGTG
2537447 ATATAAAT
1 ATATAAAT
2537455 ATA-AAAT
1 ATATAAAT
* *
2537462 -TAAAAAA
1 ATATAAAT
2537469 AT-TAAA-
1 ATATAAAT
2537475 ATAT-AAT
1 ATATAAAT
*
2537482 ATAAAAAT
1 ATATAAAT
2537490 AATATTAATAT
1 -ATA-TAA-AT
2537501 AATATAAAT
1 -ATATAAAT
* *
2537510 AAAGAAAT
1 ATATAAAT
*
2537518 ATATAAAA
1 ATATAAAT
*
2537526 ATATATA-
1 ATATAAAT
2537533 ATATAAAT
1 ATATAAAT
*
2537541 -TATTAAT
1 ATATAAAT
2537548 ATATTAAATT
1 ATA-TAAA-T
*
2537558 TTATAAAAT
1 ATAT-AAAT
*
2537567 ATATAATT
1 ATATAAAT
*
2537575 ATTTTAAAT
1 A-TATAAAT
*
2537584 GTAATTATAAT
1 AT-A-TA-AAT
2537595 ATATAAAT
1 ATATAAAT
2537603 ATATAAAT
1 ATATAAAT
2537611 ATATAAA
1 ATATAAA
2537618 ATTATCAATA
Statistics
Matches: 125, Mismatches: 21, Indels: 34
0.69 0.12 0.19
Matches are distributed among these distances:
6 6 0.05
7 26 0.21
8 49 0.39
9 20 0.16
10 14 0.11
11 10 0.08
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (8 bp):
ATATAAAT
Found at i:2537990 original size:22 final size:21
Alignment explanation
Indices: 2537965--2538032 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 21
2537955 ATAATATCAT
2537965 ATATATAATATTATATATTTAA
1 ATATATAATATTAT-TATTTAA
* *
2537987 ATATAATTAATATAATTTTTTAA
1 ATAT-A-TAATATTATTATTTAA
* *
2538010 TATATATTATATTTTTATTTAA
1 -ATATATAATATTATTATTTAA
2538032 A
1 A
2538033 ATTTTAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
21 1 0.03
22 16 0.43
23 8 0.22
24 12 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATATAATATTATTATTTAA
Found at i:2537992 original size:20 final size:20
Alignment explanation
Indices: 2537967--2538026 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2537957 AATATCATAT
*
2537967 ATATAATATTATATATTTAA
1 ATATAATATTATATTTTTAA
* *
2537987 ATATAATTAATATAATTTTTTA
1 ATATAA-TATTAT-ATTTTTAA
2538009 ATAT-ATATTATATTTTTA
1 ATATAATATTATATTTTTA
2538027 TTTAAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
19 6 0.18
20 11 0.33
21 6 0.18
22 10 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATAATATTATATTTTTAA
Found at i:2538532 original size:3 final size:3
Alignment explanation
Indices: 2538517--2538560 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
2538507 TGCAATGCAT
*
2538517 TAA TAA GAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2538561 TATTATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2538773 original size:21 final size:20
Alignment explanation
Indices: 2538722--2538773 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
2538712 TTAATATATG
*
2538722 TATATTTA-ATTTTTAAAAT
1 TATATTTATATTTTAAAAAT
*
2538741 T-TTTTATATATTTTAAAAAAT
1 TATATT-TATATTTT-AAAAAT
2538762 TATATTTATATT
1 TATATTTATATT
2538774 AAATACGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 3 0.12
19 3 0.12
20 5 0.19
21 12 0.46
22 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATATTTATATTTTAAAAAT
Found at i:2539545 original size:3 final size:3
Alignment explanation
Indices: 2539537--2539571 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2539527 ATCAAGTTAA
2539537 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2539572 GTACAGTCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2540002 original size:24 final size:24
Alignment explanation
Indices: 2539930--2540010 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
2539920 GTAGGTATTA
*
2539930 TATTTAAAAATATATTATTAATAATT
1 TATTTAAAAATA-ATTATT-TTAATT
*
2539956 T-TTAAAAAAT-ATTATTTT-A-T
1 TATTTAAAAATAATTATTTTAATT
*
2539976 TATTTAAATATAATTATTTTAATT
1 TATTTAAAAATAATTATTTTAATT
*
2540000 TATTTATAAAT
1 TATTTAAAAAT
2540011 TTTTTTACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
20 2 0.04
21 8 0.18
22 9 0.20
23 7 0.16
24 10 0.22
25 8 0.18
26 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTTAAAAATAATTATTTTAATT
Found at i:2540342 original size:60 final size:61
Alignment explanation
Indices: 2540227--2540390 Score: 217
Period size: 61 Copynumber: 2.7 Consensus size: 61
2540217 CAAAAACCCA
* * * * *
2540227 AATTTT-CAACTTAATTTAAAATAAAATATATATATATAAGTTTATTCAATTATTAAAATATT
1 AATTTTCCAA-TTAAATTAAAATAAAA-ATAAATATATAAATTTACTAAATTATTAAAATATT
*
2540289 -ATTTTCCAATTAAATTAAAATAAAAATAAATATATAAATTTACTAAATTATTAAAATTTT
1 AATTTTCCAATTAAATTAAAATAAAAATAAATATATAAATTTACTAAATTATTAAAATATT
*
2540349 AATTTTCCAATTAAATTAAAATAAAAAATAAATA-AAAAATTT
1 AATTTTCCAATTAAATTAAAAT-AAAAATAAATATATAAATTT
2540391 TTAAATAGAG
Statistics
Matches: 92, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
60 30 0.33
61 48 0.52
62 14 0.15
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.41
Consensus pattern (61 bp):
AATTTTCCAATTAAATTAAAATAAAAATAAATATATAAATTTACTAAATTATTAAAATATT
Found at i:2540792 original size:2 final size:2
Alignment explanation
Indices: 2540785--2540814 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2540775 GACAATATTT
2540785 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2540815 ACAAATTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2542569 original size:16 final size:15
Alignment explanation
Indices: 2542543--2542573 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2542533 TAAAAAAAGA
2542543 ATTTTTTATTATTTT
1 ATTTTTTATTATTTT
2542558 ATTTTGTTATTATTTT
1 ATTTT-TTATTATTTT
2542574 TATGGAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Found at i:2544054 original size:10 final size:11
Alignment explanation
Indices: 2544016--2544057 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
2544006 TTATGGGCGG
2544016 GAAAGAAAGAA
1 GAAAGAAAGAA
*
2544027 GGAAGATGAAGAA
1 GAAAGA--AAGAA
2544040 GAAAGAAAGAA
1 GAAAGAAAGAA
2544051 -AAAGAAA
1 GAAAGAAA
2544058 AAATATGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 7 0.26
11 10 0.37
13 10 0.37
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (11 bp):
GAAAGAAAGAA
Found at i:2550555 original size:36 final size:35
Alignment explanation
Indices: 2550476--2550555 Score: 85
Period size: 36 Copynumber: 2.3 Consensus size: 35
2550466 TCAAAATGAC
*
2550476 AAAA-AAAAAGTCAAAAGCAAAAGCACAAAAAATG
1 AAAACAAAAAGTCAAAAGCAAAAGCACAAAAAAGG
* *
2550510 AAAAGAAAAAGTGCAAAAGCAAAA-TA-AAAAAAGGG
1 AAAACAAAAAGT-CAAAAGCAAAAGCACAAAAAA-GG
2550545 AACAACAAAAA
1 AA-AACAAAAA
2550556 TAAAAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
34 10 0.26
35 11 0.28
36 18 0.46
ACGTcount: A:0.71, C:0.10, G:0.14, T:0.05
Consensus pattern (35 bp):
AAAACAAAAAGTCAAAAGCAAAAGCACAAAAAAGG
Found at i:2551932 original size:27 final size:27
Alignment explanation
Indices: 2551889--2552355 Score: 709
Period size: 27 Copynumber: 17.0 Consensus size: 27
2551879 GTGGCATTTT
* *
2551889 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
2551917 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
2551944 CTTTTAAAGTCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
2551972 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
2551999 CTTTTAAAATCCATAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
2552027 CTTTTAAGTCCACAACTCTGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
2552055 CTGTTTAAGACCACAACTCCGTGGCACC
1 CT-TTTAAGTCCACAACTCCGTGGCACC
* * **
2552083 CTTTTAAGTCCATAACTTCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
2552110 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
2552137 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
2552164 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
2552191 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
2552218 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
2552246 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
2552274 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
2552301 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
2552328 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
2552355 C
1 C
2552356 ATTTCAAAGC
Statistics
Matches: 404, Mismatches: 30, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
27 267 0.66
28 116 0.29
29 21 0.05
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:2551957 original size:55 final size:54
Alignment explanation
Indices: 2551889--2552355 Score: 709
Period size: 55 Copynumber: 8.5 Consensus size: 54
2551879 GTGGCATTTT
* * *
2551889 CTTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
2551944 CTTTTAAAGTCCACAACTCCGTGGTACCCTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* * *
2551999 CTTTTAAAATCCATAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCATCC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
* * * **
2552055 CTGTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCATAACTTCGTGGCATT
1 CT-TTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
*
2552110 CTTTTAAGTCCACAACTCCGTGGCACCTTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
2552164 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
2552218 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCA-CC
* *
2552274 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
2552328 CTTTTAAATCCACAACTCTGTGGCACCC
1 CTTTTAAGTCCACAACTCCGTGGCACCC
2552356 ATTTCAAAGC
Statistics
Matches: 384, Mismatches: 24, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
54 152 0.40
55 158 0.41
56 71 0.18
57 3 0.01
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (54 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
Found at i:2552397 original size:32 final size:32
Alignment explanation
Indices: 2552338--2552811 Score: 745
Period size: 32 Copynumber: 14.8 Consensus size: 32
2552328 CTTTTAAATC
* *
2552338 CACAACTCTGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
2552369 CACAAGTCGGTGGCAACCTATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
2552401 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
2552433 CACAAGTCGGTGGCAACCTATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
2552465 CACAAGTTGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
2552497 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
2552529 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
2552561 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
2552593 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
2552625 CACAAGTCGGTGGCAACCCA-TTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTC-AAAGCCCA
*
2552657 CACAAGTAGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** *
2552689 CACAAGTCGGTGGCAACCTTTTTCAAAGCCCC
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
2552721 CAGAAGTTGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
2552753 CGCAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
2552785 CGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
2552812 TCACCATTTT
Statistics
Matches: 413, Mismatches: 27, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
31 15 0.04
32 395 0.96
33 3 0.01
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:2554070 original size:10 final size:11
Alignment explanation
Indices: 2554032--2554073 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
2554022 TTATGGGCGG
2554032 GAAAGAAAGAA
1 GAAAGAAAGAA
*
2554043 GGAAGATGAAGAA
1 GAAAGA--AAGAA
2554056 GAAAGAAAGAA
1 GAAAGAAAGAA
2554067 -AAAGAAA
1 GAAAGAAA
2554074 AAATATGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 7 0.26
11 10 0.37
13 10 0.37
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (11 bp):
GAAAGAAAGAA
Found at i:2557255 original size:16 final size:16
Alignment explanation
Indices: 2557234--2557267 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2557224 TTTTTTGAAT
*
2557234 ATTTTTTATTTCTTTA
1 ATTTTTAATTTCTTTA
*
2557250 ATTTTTAATTTTTTTA
1 ATTTTTAATTTCTTTA
2557266 AT
1 AT
2557268 ATATATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTTAATTTCTTTA
Found at i:2557256 original size:15 final size:15
Alignment explanation
Indices: 2557236--2557281 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
2557226 TTTTGAATAT
*
2557236 TTTTTATTTCTTTAA
1 TTTTTATTTTTTTAA
2557251 TTTTTAATTTTTTTAA
1 TTTTT-ATTTTTTTAA
* *
2557267 TATATATTTTTTTAA
1 TTTTTATTTTTTTAA
2557282 AAAAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTATTTTTTTAA
Found at i:2557864 original size:42 final size:42
Alignment explanation
Indices: 2557775--2559061 Score: 786
Period size: 42 Copynumber: 29.6 Consensus size: 42
2557765 TTCTCCCGAG
* * * * * *
2557775 TCAAAGCCAACGGGCAAACTTAGGGAAAGAAAAGCCTCTAAGG-
1 TCAAAGCCGACAGGCAGAC-TAAGGAAAGAAAAGTCTC-CAGGA
* * *
2557818 TCAAAGCCGACAGGCAGAATTAGGAAATAAAAGTCTCCAGGA
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGGA
* * *
2557860 TCAAAGCCGACAGGCAGACTAAGGGATGAAAAGTCTCTAGGGA
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCA-GGA
* * * * * *
2557903 T-GAAGCCGACAGGCATACTGAGCG-ATGAAAAGCCTCTAGGGA
1 TCAAAGCCGACAGGCAGACTAAG-GAAAGAAAAGTCTCCA-GGA
* * * * * *
2557945 -CGAAGCCGACAGGCATACTAAGGGAAGGAAAGTCTCTAGGG
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGGA
* * * *
2557986 GCAAAACCGATAGGCAGACTAAAGAAAGAAAAGTCTCCAGGA
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGGA
* ***
2558028 TCAAAGCCGACAGACAGACTAAGGGTTGAAAAGTCTCCAGGGA
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCA-GGA
* * * *
2558071 -CGAAGCCGTCAGGCAGACTAAGGGAAGGAAAGTCTCCAGGA
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGGA
* * * *
2558112 ACGAAGCCGACAGGCAGACTAAAGAAAGAAAAGTCTCCAGGG
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGGA
* * ***
2558154 TCAAAGCCGACAGACAGACTGAGGGTTGAAAAGTCTCCAGGGA
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCA-GGA
* * * *
2558197 -CAAAGCCGACAAGTAGACTAAGGGAAGGAAAGAAAAGTCTTCAGGG
1 TCAAAGCCGACAGGCAGACT-----AAGGAAAGAAAAGTCTCCAGGA
* * * ***
2558243 TCAAAGCCGACAGGCAAATTGAGGGTTGAAAAGTCTCCAGGGA
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCA-GGA
* * * * *
2558286 -CGAAGCCGATAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGA
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCA-GGA
* * * *
2558328 ACGAAGCCGACAAGCAGACTAAGGGAAGGAAAGAAAAGTCTCCAGGG
1 TCAAAGCCGACAGGCAGACT-----AAGGAAAGAAAAGTCTCCAGGA
* ***
2558375 TCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGA
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCA-GGA
* * * *
2558418 -CGAAGCCAACAGGTAGACTAAGGGAAGGAAAGAAAAGTCTCCAGGG
1 TCAAAGCCGACAGGCAGACT-----AAGGAAAGAAAAGTCTCCAGGA
* * ***
2558464 TCAAAGCCGACAAGCAGACTGAGGGTTGAAAAGTCTCCAGGGA
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCA-GGA
* * * * *
2558507 -CGAAGCTGACAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGA
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCA-GGA
* * * *
2558549 ACGAAGCCGACAAGCAGACTAAGGGAAGGAAAGAAAAGTCTCCAGGG
1 TCAAAGCCGACAGGCAGACT-----AAGGAAAGAAAAGTCTCCAGGA
* ***
2558596 TCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAAGGA
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCC-AGGA
* * *
2558639 -CGAAGCCGACAGGTAGACTAAGGGAAGGAAAGAAAAGTCTCCAGGG
1 TCAAAGCCGACAGGCAGACT-----AAGGAAAGAAAAGTCTCCAGGA
* * ***
2558685 TTAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGA
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCA-GGA
* * * *
2558728 -CAAAGCCGATAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGA
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCA-GGA
* * * *
2558770 ACGAAGCCGACAAGCAGACTAAAGGAAGGAAAGAAAAGTCTCCAGGG
1 TCAAAGCCGACAGGCAGACT-----AAGGAAAGAAAAGTCTCCAGGA
* * ***
2558817 TCAAAGCCGACAGGTAGACTGAGGGTTGAAAAGTCTCCAAGGA
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCC-AGGA
* * *
2558860 -CGAAGCCGACAGGTAGACTAAGGGAAGGAAAGAAAAGTCTCCAGGG
1 TCAAAGCCGACAGGCAGACT-----AAGGAAAGAAAAGTCTCCAGGA
* * ***
2558906 TCAAAGCCGACAAGCAGACTGAGGGTTGAAAAGTCTCCAGGGA
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCA-GGA
* * * * *
2558949 ACGAAGCCGACAAGTAGACTAAAGAAAGAAAAGTCTCCAGGGA
1 TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCA-GGA
* *
2558992 -CGAAGCCGACAGGTAGACTAAGGGAAGGAAAGAAAAGTCAT-C-GGA
1 TCAAAGCCGACAGGCAGACT-----AAGGAAAGAAAAGTC-TCCAGGA
*
2559037 GTCAAAGCCGACAGGTAGACTAAGG
1 -TCAAAGCCGACAGGCAGACTAAGG
2559062 GAAAACAAAA
Statistics
Matches: 973, Mismatches: 205, Indels: 133
0.74 0.16 0.10
Matches are distributed among these distances:
41 9 0.01
42 568 0.58
43 123 0.13
45 3 0.00
46 10 0.01
47 208 0.21
48 52 0.05
ACGTcount: A:0.39, C:0.19, G:0.31, T:0.11
Consensus pattern (42 bp):
TCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGGA
Found at i:2558266 original size:89 final size:89
Alignment explanation
Indices: 2557798--2559062 Score: 779
Period size: 89 Copynumber: 14.5 Consensus size: 89
2557788 GCAAACTTAG
* * * * * **
2557798 GGAAAGAAAAGCCTCTAAGGTCAAAGCCGACAGGCAGAATTAGGAAAT-AAAAGTCTCCA-GGAT
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGG-GTTGAAAAGTCTCCAGGGA-
2557861 CAAAGCCGACAGGCAGACTAA--G--
64 CAAAGCCGACAGGCAGACTAAGGGAA
* * * * * * * *
2557883 GG-ATGAAAAGTCTCTAGGGAT-GAAGCCGACAGGCATACTGAGCGATGAAAAGCCTCTAGGGAC
1 GGAAAGAAAAGTCTCCAGGG-TCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGAC
* *
2557946 GAAGCCGACAGGCATACTAAGGGAA
65 AAAGCCGACAGGCAGACTAAGGGAA
* * * * * * ***
2557971 -G---G-AAAGTCTCTAGGGGCAAAACCGATAGGCAGACTAAAGAAAGAAAAGTCTCCA-GGATC
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGA-C
*
2558030 AAAGCCGACAGACAGACTAA--G--
65 AAAGCCGACAGGCAGACTAAGGGAA
** * * * * ** * * *
2558051 GG-TTGAAAAGTCTCCAGGGACGAAGCCGTCAGGCAGACTAAGGGAAGGAAAGTCTCCAGGAACG
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGACA
2558115 AAGCCGACAGGCAGACT-A---AA
66 AAGCCGACAGGCAGACTAAGGGAA
*
2558135 -GAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGACAGACTGAGGGTTGAAAAGTCTCCAGGGACA
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGACA
* *
2558199 AAGCCGACAAGTAGACTAAGGGAA
66 AAGCCGACAGGCAGACTAAGGGAA
* * * *
2558223 GGAAAGAAAAGTCTTCAGGGTCAAAGCCGACAGGCAAATTGAGGGTTGAAAAGTCTCCAGGGACG
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGACA
* *
2558288 AAGCCGATAGGTAGACTAAGGGAA
66 AAGCCGACAGGCAGACTAAGGGAA
* * * ***
2558312 -G---G-AAAGTCTCCAGGGAACGAAGCCGACAAGCAGACTAAGGGAAGGAAAGAAAAGTCTCCA
1 GGAAAGAAAAGTCTCCAGGG-TCAAAGCCGACAGGCAGACT----G-AGGGTTGAAAAGTCTCCA
*
2558372 GGGTCAAAGCCGACAGGCAGACT----G-A
60 GGGACAAAGCCGACAGGCAGACTAAGGGAA
*** * * * * ***
2558397 GGGTTGAAAAGTCTCCAGGGACGAAGCCAACAGGTAGACTAAGGGAAGGAAAGAAAAGTCTCCAG
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACT----G-AGGGTTGAAAAGTCTCCAG
* *
2558462 GGTCAAAGCCGACAAGCAGACT----G-A
61 GGACAAAGCCGACAGGCAGACTAAGGGAA
*** * * * * * ** *
2558486 GGGTTGAAAAGTCTCCAGGGACGAAGCTGACAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGAAC
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGG-AC
* *
2558551 GAAGCCGACAAGCAGACTAAGGGAA
65 AAAGCCGACAGGCAGACTAAGGGAA
* *
2558576 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAAGGACG
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGACA
*
2558641 AAGCCGACAGGTAGACTAAGGGAA
66 AAGCCGACAGGCAGACTAAGGGAA
*
2558665 GGAAAGAAAAGTCTCCAGGGTTAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGACA
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGACA
* *
2558730 AAGCCGATAGGTAGACTAAGGGAA
66 AAGCCGACAGGCAGACTAAGGGAA
* * * ***
2558754 -G---G-AAAGTCTCCAGGGAACGAAGCCGACAAGCAGACTAAAGGAAGGAAAGAAAAGTCTCCA
1 GGAAAGAAAAGTCTCCAGGG-TCAAAGCCGACAGGCAGACT----G-AGGGTTGAAAAGTCTCCA
* *
2558814 GGGTCAAAGCCGACAGGTAGACT----G-A
60 GGGACAAAGCCGACAGGCAGACTAAGGGAA
*** * * * * ***
2558839 GGGTTGAAAAGTCTCCAAGGACGAAGCCGACAGGTAGACTAAGGGAAGGAAAGAAAAGTCTCCAG
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACT----G-AGGGTTGAAAAGTCTCCAG
* *
2558904 GGTCAAAGCCGACAAGCAGACT----G-A
61 GGACAAAGCCGACAGGCAGACTAAGGGAA
*** * * * * * * ***
2558928 GGGTTGAAAAGTCTCCAGGGAACGAAGCCGACAAGTAGACTAAAGAAAGAAAAGTCTCCAGGGAC
1 GGAAAGAAAAGTCTCCAGGG-TCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGAC
* *
2558993 GAAGCCGACAGGTAGACTAAGGGAA
65 AAAGCCGACAGGCAGACTAAGGGAA
* *
2559018 GGAAAGAAAAGTCAT-C-GGAGTCAAAGCCGACAGGTAGACTAAGGG
1 GGAAAGAAAAGTC-TCCAGG-GTCAAAGCCGACAGGCAGACTGAGGG
2559063 AAAACAAAAA
Statistics
Matches: 988, Mismatches: 134, Indels: 112
0.80 0.11 0.09
Matches are distributed among these distances:
81 1 0.00
82 1 0.00
83 8 0.01
84 285 0.29
85 99 0.10
86 5 0.01
87 1 0.00
88 4 0.00
89 405 0.41
90 178 0.18
91 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.31, T:0.11
Consensus pattern (89 bp):
GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGACA
AAGCCGACAGGCAGACTAAGGGAA
Found at i:2558386 original size:132 final size:131
Alignment explanation
Indices: 2557839--2559064 Score: 1059
Period size: 132 Copynumber: 9.4 Consensus size: 131
2557829 AGGCAGAATT
* * * * * *
2557839 AGGAAATAAAAGTCTCCAGGATCAAAGCCGACAGGCAGACTAAGGGATGAAAAGTCTCTAGGGAT
1 AGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGAAAAGTCTCCAGGGAC
* * * * * *
2557904 GAAGCCGACAGGCATACTGAGCGATGAAAAGCCTCTAGGGACGAAGCCGACAGGCATACTAAGGG
66 GAAGCCGACAGGCAGACTAAGGGATGAAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTAAGGG
2557969 A
131 A
* * * * * * *
2557970 A-G---G-AAAGTCTCTAGGGGCAAAACCGATAGGCAGACTAAAGAAAGAAAAGTCTCCA-GGAT
1 AGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGAAAAGTCTCCAGGGA-
* * * *
2558029 CAAAGCCGACAGACAGACTAAGGGTTGAAAAGTCTCCAGGGACGAAGCCGTCAGGCAGACTAAGG
65 CGAAGCCGACAGGCAGACTAAGGGATGAAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTAAGG
2558094 GA
130 GA
** * * * * *
2558096 A-G---G-AAAGTCTCCAGGAACGAAGCCGACAGGCAGACTAAAGAAAGAAAAGTCTCCAGGGTC
1 AGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGAAAAGTCTCCAGGGAC
* * * * * * *
2558156 AAAGCCGACAGACAGACTGAGGGTTGAAAAGTCTCCAGGGACAAAGCCGACAAGTAGACTAAGGG
66 GAAGCCGACAGGCAGACTAAGGGATGAAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTAAGGG
2558221 A
131 A
* * * **
2558222 AGGAAAGAAAAGTCTTCAGGGTCAAAGCCGACAGGCAAATTGAGGGTTGAAAAGTCTCCAGGGAC
1 AGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGAAAAGTCTCCAGGGAC
* * * * *
2558287 GAAGCCGATAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGAACGAAGCCGACAAGCAGACTAAGG
66 GAAGCCGACAGGCAGACTAAGGGATGAAAAGTCTCCAGGG-ACGAAGCCGACAGGCAGACTAAGG
2558352 GA
130 GA
**
2558354 AGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGAC
1 AGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGAAAAGTCTCCAGGGAC
* * * * * *
2558419 GAAGCCAACAGGTAGACTAAGGGAAGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAAGCAGACT
66 GAAGCCGACAGGCAGACTAA--G--GG-ATGAAAAGTCTCCAGGGACGAAGCCGACAGGCAGACT
2558484 ----G-
126 AAGGGA
*** * * * * * *
2558485 AGGGTTGAAAAGTCTCCAGGGACGAAGCTGACAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGAA
1 AGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGAAAAGTCTCCAGGG-A
* * * *
2558550 CGAAGCCGACAAGCAGACTAAGGGAAGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGAC
65 CGAAGCCGACAGGCAGACTAA--G--GG-ATGAAAAGTCTCCAGGGACGAAGCCGACAGGCAGAC
2558615 T----G-
125 TAAGGGA
*** * * * * *
2558617 AGGGTTGAAAAGTCTCCAAGGACGAAGCCGACAGGTAGACTAAGGGAAGGAAAGAAAAGTCTCCA
1 AGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACT----G-AGGGAAGAAAAGTCTCCA
*** * * * * *
2558682 GGGTTAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGACAAAGCCGATAGGTAGACT
61 GGGACGAAGCCGACAGGCAGACTAAGGGATGAAAAGTCTCCAGGGACGAAGCCGACAGGCAGACT
2558747 AAGGGA
126 AAGGGA
* * * *
2558753 A-G---G-AAAGTCTCCAGGGAACGAAGCCGACAAGCAGACTAAAGGAAGGAAAGAAAAGTCTCC
1 AGGAAAGAAAAGTCTCCAGGG-TCAAAGCCGACAGGCAGACT----G-AGGGAAGAAAAGTCTCC
* * * * * * *
2558813 AGGGTCAAAGCCGACAGGTAGACTGAGGGTTGAAAAGTCTCCAAGGACGAAGCCGACAGGTAGAC
60 AGGGACGAAGCCGACAGGCAGACTAAGGGATGAAAAGTCTCCAGGGACGAAGCCGACAGGCAGAC
2558878 TAAGGGA
125 TAAGGGA
* **
2558885 AGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGAGGGTTGAAAAGTCTCCAGGGAA
1 AGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGAAAAGTCTCCAGGG-A
* * * * * *
2558950 CGAAGCCGACAAGTAGACTAAAGAAAGAAAAGTCTCCAGGGACGAAGCCGACAGGTAGACTAAGG
65 CGAAGCCGACAGGCAGACTAAGGGATGAAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTAAGG
2559015 GA
130 GA
* *
2559017 AGGAAAGAAAAGTCAT-C-GGAGTCAAAGCCGACAGGTAGACTAAGGGAA
1 AGGAAAGAAAAGTC-TCCAGG-GTCAAAGCCGACAGGCAGACTGAGGGAA
2559065 AACAAAAAAG
Statistics
Matches: 941, Mismatches: 121, Indels: 65
0.83 0.11 0.06
Matches are distributed among these distances:
125 3 0.00
126 211 0.22
127 3 0.00
130 2 0.00
131 194 0.21
132 417 0.44
133 2 0.00
134 2 0.00
135 2 0.00
136 57 0.06
137 48 0.05
ACGTcount: A:0.38, C:0.19, G:0.31, T:0.11
Consensus pattern (131 bp):
AGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGAAAAGTCTCCAGGGAC
GAAGCCGACAGGCAGACTAAGGGATGAAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTAAGGG
A
Found at i:2558449 original size:221 final size:221
Alignment explanation
Indices: 2557798--2559062 Score: 1723
Period size: 221 Copynumber: 5.8 Consensus size: 221
2557788 GCAAACTTAG
* * * * * **
2557798 GGAAAGAAAAGCCTCTAAGGTCAAAGCCGACAGGCAGAATTAGGAAAT-AAAAGTCTCCA-GGAT
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGG-GTTGAAAAGTCTCCAGGGA-
* * * * * * * * *
2557861 CAAAGCCGACAGGCAGACTAAGGGATGAAAAGTCTCTAGGG-ATGAAGCCGACAGGCATACT---
64 CGAAGCCGATAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGAACGAAGCCGACAAGCAGACTAAG
* * * * * * * ** * * *
2557922 -G-AGCG-ATGAAAAGCCTCTAGGGACGAAGCCGACAGGCATACTAAGGGAAGGAAAGTCTCTAG
129 GGAAG-GAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAA
* * * * *
2557984 GGGCAAAACCGATAGGCAGACT-A---AA
193 GGACGAAGCCGACAGGTAGACTAAGGGAA
* * *
2558009 -GAAAGAAAAGTCTCCAGGATCAAAGCCGACAGACAGACTAAGGGTTGAAAAGTCTCCAGGGACG
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGACG
* *
2558073 AAGCCG-TCAGGCAGACTAAGGGAAGGAAAGTCTCCA-GGAACGAAGCCGACAGGCAGACT-A--
66 AAGCCGAT-AGGTAGACTAAGGGAAGGAAAGTCTCCAGGGAACGAAGCCGACAAGCAGACTAAGG
* *
2558133 -AA-GAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGACAGACTGAGGGTTGAAAAGTCTCCAGGG
130 GAAGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAAGG
* *
2558196 ACAAAGCCGACAAGTAGACTAAGGGAA
195 ACGAAGCCGACAGGTAGACTAAGGGAA
* * *
2558223 GGAAAGAAAAGTCTTCAGGGTCAAAGCCGACAGGCAAATTGAGGGTTGAAAAGTCTCCAGGGACG
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGACG
2558288 AAGCCGATAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGAACGAAGCCGACAAGCAGACTAAGGG
66 AAGCCGATAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGAACGAAGCCGACAAGCAGACTAAGGG
*
2558353 AAGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGA
131 AAGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAAGGA
*
2558418 CGAAGCCAACAGGTAGACTAAGGGAA
196 CGAAGCCGACAGGTAGACTAAGGGAA
*
2558444 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGAGGGTTGAAAAGTCTCCAGGGACG
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGACG
* *
2558509 AAGCTGACAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGAACGAAGCCGACAAGCAGACTAAGGG
66 AAGCCGATAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGAACGAAGCCGACAAGCAGACTAAGGG
2558574 AAGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAAGGA
131 AAGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAAGGA
2558639 CGAAGCCGACAGGTAGACTAAGGGAA
196 CGAAGCCGACAGGTAGACTAAGGGAA
* *
2558665 GGAAAGAAAAGTCTCCAGGGTTAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGACA
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGACG
*
2558730 AAGCCGATAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGAACGAAGCCGACAAGCAGACTAAAGG
66 AAGCCGATAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGAACGAAGCCGACAAGCAGACTAAGGG
*
2558795 AAGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGTAGACTGAGGGTTGAAAAGTCTCCAAGGA
131 AAGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAAGGA
2558860 CGAAGCCGACAGGTAGACTAAGGGAA
196 CGAAGCCGACAGGTAGACTAAGGGAA
*
2558886 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAAGCAGACTGAGGGTTGAAAAGTCTCCAGGGAAC
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGG-AC
* * * * * * *
2558951 GAAGCCGACAAGTAGACTAAAGAAAGAAAAGTCTCCAGGG-ACGAAGCCGACAGGTAGACTAAGG
65 GAAGCCGATAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGAACGAAGCCGACAAGCAGACTAAGG
* *
2559015 GAAGGAAAGAAAAGTCAT-C-GGAGTCAAAGCCGACAGGTAGACTAAGGG
130 GAAGGAAAGAAAAGTC-TCCAGG-GTCAAAGCCGACAGGCAGACTGAGGG
2559063 AAAACAAAAA
Statistics
Matches: 960, Mismatches: 72, Indels: 34
0.90 0.07 0.03
Matches are distributed among these distances:
209 4 0.00
210 159 0.17
211 5 0.01
214 2 0.00
215 91 0.09
216 23 0.02
217 1 0.00
220 4 0.00
221 634 0.66
222 37 0.04
ACGTcount: A:0.38, C:0.19, G:0.31, T:0.11
Consensus pattern (221 bp):
GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGACG
AAGCCGATAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGAACGAAGCCGACAAGCAGACTAAGGG
AAGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAAGGA
CGAAGCCGACAGGTAGACTAAGGGAA
Found at i:2571412 original size:16 final size:15
Alignment explanation
Indices: 2571386--2571416 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2571376 TAAAAAAAGA
2571386 ATTTTTTATTATTTT
1 ATTTTTTATTATTTT
2571401 ATTTTGTTATTATTTT
1 ATTTT-TTATTATTTT
2571417 TATGAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Found at i:2572561 original size:16 final size:16
Alignment explanation
Indices: 2572540--2572573 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2572530 TTTTTTGAAT
*
2572540 ATTTTTTATTTCTTTA
1 ATTTTTAATTTCTTTA
*
2572556 ATTTTTAATTTTTTTA
1 ATTTTTAATTTCTTTA
2572572 AT
1 AT
2572574 ATATATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTTAATTTCTTTA
Found at i:2572562 original size:15 final size:15
Alignment explanation
Indices: 2572542--2572587 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
2572532 TTTTGAATAT
*
2572542 TTTTTATTTCTTTAA
1 TTTTTATTTTTTTAA
2572557 TTTTTAATTTTTTTAA
1 TTTTT-ATTTTTTTAA
* *
2572573 TATATATTTTTTTAA
1 TTTTTATTTTTTTAA
2572588 AAAAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTATTTTTTTAA
Found at i:2573043 original size:9 final size:9
Alignment explanation
Indices: 2573029--2573065 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
2573019 TATGTATTTA
2573029 TATTATATT
1 TATTATATT
2573038 TATTATATT
1 TATTATATT
*
2573047 TAATATA-T
1 TATTATATT
2573055 TA-TATATT
1 TATTATATT
2573063 TAT
1 TAT
2573066 AAAAATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
7 4 0.16
8 6 0.24
9 15 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TATTATATT
Found at i:2573090 original size:16 final size:16
Alignment explanation
Indices: 2573027--2573097 Score: 56
Period size: 16 Copynumber: 4.3 Consensus size: 16
2573017 ATTATGTATT
*
2573027 TATATT-ATATTTATTA
1 TATATTAATAATT-TTA
*
2573043 TAT-TTAATATATTATA
1 TATATTAATA-ATTTTA
* *
2573059 TATTTATAAAAATTTTA
1 TATAT-TAATAATTTTA
2573076 TATATTAATAATTTTA
1 TATATTAATAATTTTA
2573092 TTATAT
1 -TATAT
2573098 AAATTTATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
15 2 0.05
16 21 0.48
17 17 0.39
18 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATATTAATAATTTTA
Found at i:2573111 original size:34 final size:33
Alignment explanation
Indices: 2573016--2573152 Score: 101
Period size: 32 Copynumber: 4.1 Consensus size: 33
2573006 ATATTTATAA
2573016 AATTATGTATTTATATTATATT-TATTATAT-TTAAT
1 AATTAT-TATTTATA--ATATTATATTATATATT-AT
* *
2573051 ATATTATATATTTATAA-A-AATTTTATATATTAAT
1 A-ATTAT-TATTTATAATATTATATTATATATT-AT
2573085 AATT-TTATTATATAA-ATTTATATTATAT-TTAT
1 AATTATTATT-TATAATA-TTATATTATATATTAT
*
2573117 -ATTAATTATTTATAATATTATATTTTATATTAT
1 AATT-ATTATTTATAATATTATATTATATATTAT
2573150 AAT
1 AAT
2573153 CGTATCATTA
Statistics
Matches: 85, Mismatches: 6, Indels: 23
0.75 0.05 0.20
Matches are distributed among these distances:
31 7 0.08
32 24 0.28
33 23 0.27
34 17 0.20
35 1 0.01
36 13 0.15
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.58
Consensus pattern (33 bp):
AATTATTATTTATAATATTATATTATATATTAT
Found at i:2573116 original size:40 final size:35
Alignment explanation
Indices: 2573017--2573150 Score: 101
Period size: 36 Copynumber: 3.5 Consensus size: 35
2573007 TATTTATAAA
*
2573017 ATTATGTATTTATATTATATTTATTATATTTAATAT
1 ATTATATATTTATATTATATTTA-TATATTTAATAT
* * *
2573053 ATTATATATTTATA-AAAATTTTATATATTAATAATTTT
1 ATTATATATTTATATTATA-TTTATATATT--TAA-TAT
*
2573091 ATTATATAAATTTATATTATATTTATATTAATTATTTATAAT
1 ATTATAT--ATTTATATTATATTTATA-T-A-T-TTAAT-AT
2573133 ATTATAT-TTTATATTATA
1 ATTATATATTTATATTATA
2573151 ATCGTATCAT
Statistics
Matches: 78, Mismatches: 8, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
35 8 0.10
36 17 0.22
37 3 0.04
38 9 0.12
39 11 0.14
40 13 0.17
41 4 0.05
42 11 0.14
43 1 0.01
44 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (35 bp):
ATTATATATTTATATTATATTTATATATTTAATAT
Found at i:2573800 original size:19 final size:18
Alignment explanation
Indices: 2573772--2573811 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
2573762 GTAATTAATT
2573772 TTATTATTTAAATAAATA
1 TTATTATTTAAATAAATA
*
2573790 TTATATATTTAAATATATA
1 TTAT-TATTTAAATAAATA
2573809 TTA
1 TTA
2573812 ATTAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATTATTTAAATAAATA
Found at i:2574204 original size:33 final size:34
Alignment explanation
Indices: 2574153--2574219 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
2574143 GTAACATATA
*
2574153 AATATATTAAAATCTATATAAAATA-A-ATTATT
1 AATATATCAAAATCTATATAAAATATATATTATT
*
2574185 AATATTATCAAAATTTATATAAAATATATATTATT
1 AATA-TATCAAAATCTATATAAAATATATATTATT
2574220 TTGAACTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 4 0.13
33 19 0.63
34 1 0.03
35 6 0.20
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (34 bp):
AATATATCAAAATCTATATAAAATATATATTATT
Found at i:2574214 original size:11 final size:11
Alignment explanation
Indices: 2574148--2574215 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
2574138 AATATGTAAC
2574148 ATAT-AAATAT
1 ATATAAAATAT
*
2574158 AT-TAAAATCT
1 ATATAAAATAT
*
2574168 ATATAAAATAA
1 ATATAAAATAT
*
2574179 AT-TATTAATAT
1 ATATA-AAATAT
*
2574190 -TATCAAAATTT
1 ATAT-AAAATAT
2574201 ATATAAAATAT
1 ATATAAAATAT
2574212 ATAT
1 ATAT
2574216 TATTTTGAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
9 1 0.02
10 12 0.27
11 27 0.61
12 4 0.09
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (11 bp):
ATATAAAATAT
Found at i:2575898 original size:28 final size:28
Alignment explanation
Indices: 2575857--2575925 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
2575847 AGAAATCCAA
* *
2575857 ATAAAAATCTCTTAATAAGACAATATAG
1 ATAAAATTATCTTAATAAGACAATATAG
* * * *
2575885 ATAAGATTGTCTTATTAAGGCAATATAG
1 ATAAAATTATCTTAATAAGACAATATAG
2575913 ATAAAATTATCTT
1 ATAAAATTATCTT
2575926 TTCAAAATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (28 bp):
ATAAAATTATCTTAATAAGACAATATAG
Found at i:2578133 original size:27 final size:24
Alignment explanation
Indices: 2578070--2578133 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 24
2578060 TTTAAAGCTA
*
2578070 ATTA-ATTTATTATTTATAATAAT
1 ATTATATTAATTATTTATAATAAT
2578093 ATTATATTAA--ATTTAGTAATTAAT
1 ATTATATTAATTATTTA-TAA-TAAT
*
2578117 AATTTTATTAATTATTT
1 -ATTATATTAATTATTT
2578134 TCAAAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
22 5 0.15
23 7 0.21
24 8 0.24
25 9 0.27
27 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTATATTAATTATTTATAATAAT
Done.