Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002341.1 Hibiscus syriacus cultivar Beakdansim tig00004779_pilon, whole genome shotgun sequence
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: 1266629
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:6087 original size:13 final size:13
Alignment explanation
Indices: 6034--6084 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
6024 AATTCAGTAG
*
6034 TTGATTTGATCAA
1 TTGATTTGATTAA
*
6047 TTAATTTGATTAA
1 TTGATTTGATTAA
*
6060 TTGATTTGA-AAA
1 TTGATTTGATTAA
6072 TTTGATTTGATTA
1 -TTGATTTGATTA
6085 TTTATATAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 2 0.06
13 28 0.90
14 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (13 bp):
TTGATTTGATTAA
Found at i:6096 original size:26 final size:27
Alignment explanation
Indices: 6050--6101 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
6040 TGATCAATTA
*
6050 ATTTGATTAATTGATTTGAAA-ATTTG
1 ATTTGATTAATTGATTAGAAATATTTG
*
6076 ATTTGATT-ATTTATATAGAAATATTT
1 ATTTGATTAATTGAT-TAGAAATATTT
6102 AGTAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 5 0.23
26 13 0.59
27 4 0.18
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.52
Consensus pattern (27 bp):
ATTTGATTAATTGATTAGAAATATTTG
Found at i:6209 original size:14 final size:14
Alignment explanation
Indices: 6190--6219 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6180 CATATATGTT
6190 GGGTGAAATTATTC
1 GGGTGAAATTATTC
6204 GGGTGAAATTATTC
1 GGGTGAAATTATTC
6218 GG
1 GG
6220 ATAAAATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.33, T:0.33
Consensus pattern (14 bp):
GGGTGAAATTATTC
Found at i:6307 original size:18 final size:20
Alignment explanation
Indices: 6262--6300 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6252 AGAAAATTAG
6262 TAAATA-TTTTTAAAAATTT
1 TAAATATTTTTTAAAAATTT
*
6281 TAAATATTTTTTTAAAATTT
1 TAAATATTTTTTAAAAATTT
6301 AATATTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAAATATTTTTTAAAAATTT
Found at i:8677 original size:16 final size:16
Alignment explanation
Indices: 8648--8680 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
8638 TTAAAATATC
*
8648 AAATATAGAAAAAATT
1 AAATATAAAAAAAATT
8664 AAATATAAAAAAAATT
1 AAATATAAAAAAAATT
8680 A
1 A
8681 CTCAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
AAATATAAAAAAAATT
Found at i:8711 original size:22 final size:24
Alignment explanation
Indices: 8686--8733 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
8676 AATTACTCAA
* *
8686 AAAATTTAAATAAA-TAAATT-TT
1 AAAATTAAAAAAAATTAAATTATT
8708 AAAATTAAAAAAAATTAAATTATT
1 AAAATTAAAAAAAATTAAATTATT
8732 AA
1 AA
8734 GGAAATACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 12 0.55
23 6 0.27
24 4 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAATTAAAAAAAATTAAATTATT
Found at i:10351 original size:6 final size:6
Alignment explanation
Indices: 10331--10363 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
10321 TTGAGGTAAC
*
10331 TAAAAA T-AGAA TAAAAA TAAAAA TAAAAA TAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAA
10364 TATTAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:11037 original size:3 final size:3
Alignment explanation
Indices: 11031--11084 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
11021 AATAATATAG
11031 TAT TAT TAT TAT TAT 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 TAT TAT TAT
11079 TAT TAT
1 TAT TAT
11085 ATATAATCCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:11602 original size:26 final size:25
Alignment explanation
Indices: 11555--11609 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
11545 CATTTAAATT
* *
11555 TTATTTGAATTCTGTTCGAATTAAA
1 TTATTTGAATTCAGTTCAAATTAAA
* *
11580 TTATTTGAGTTTCAGTTCAAATTTAA
1 TTATTTGA-ATTCAGTTCAAATTAAA
11606 TTAT
1 TTAT
11610 AAATATTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.51
Consensus pattern (25 bp):
TTATTTGAATTCAGTTCAAATTAAA
Found at i:12381 original size:23 final size:21
Alignment explanation
Indices: 12327--12383 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
12317 AATATGTAGA
12327 GTCAATTTCTTTTTAAAAAGG
1 GTCAATTTCTTTTTAAAAAGG
**
12348 GTCAAAATCTTTTTAAAAATGG
1 GTCAATTTCTTTTTAAAAA-GG
*
12370 TGTCATTTTCTTTT
1 -GTCAATTTCTTTT
12384 CTTTTAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 17 0.59
22 2 0.07
23 10 0.34
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (21 bp):
GTCAATTTCTTTTTAAAAAGG
Found at i:21306 original size:18 final size:17
Alignment explanation
Indices: 21279--21312 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
21269 TCATCTTCCT
21279 TTCTGCACTTATCAACTG
1 TTCTGCACTTAT-AACTG
*
21297 TTCTGTACTTATAACT
1 TTCTGCACTTATAACT
21313 ACTACAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.44
Consensus pattern (17 bp):
TTCTGCACTTATAACTG
Found at i:29836 original size:14 final size:14
Alignment explanation
Indices: 29817--29857 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
29807 CGTTCGTGAG
29817 TTAAATTAAAATTA
1 TTAAATTAAAATTA
29831 TTAAATT-AAATTA
1 TTAAATTAAAATTA
* *
29844 TGAAAATAAAATTA
1 TTAAATTAAAATTA
29858 CGTTTATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (14 bp):
TTAAATTAAAATTA
Found at i:32491 original size:2 final size:2
Alignment explanation
Indices: 32484--32517 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
32474 ACATACATAC
32484 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
32518 TAACGATGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42252 original size:2 final size:2
Alignment explanation
Indices: 42239--42302 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
42229 CTTTGCTCAC
*
42239 AT AT AC 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
42281 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
42303 GTAATAAACC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51524 original size:24 final size:24
Alignment explanation
Indices: 51460--51515 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
51450 TGAACGGTTC
51460 AACGGTTCTAGCCGTTTCACTAAT
1 AACGGTTCTAGCCGTTTCACTAAT
*
51484 AACGGTTCTGGCCGTTTCACTAAT
1 AACGGTTCTAGCCGTTTCACTAAT
51508 AACGGTTC
1 AACGGTTC
51516 AACCGGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (24 bp):
AACGGTTCTAGCCGTTTCACTAAT
Found at i:56421 original size:16 final size:15
Alignment explanation
Indices: 56400--56429 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
56390 TTAAAAAAAA
56400 TTAATAAACTATTATT
1 TTAATAAAC-ATTATT
56416 TTAATAAACATTAT
1 TTAATAAACATTAT
56430 AAAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAATAAACATTATT
Found at i:57282 original size:13 final size:13
Alignment explanation
Indices: 57264--57290 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
57254 TCACGTATAC
57264 AGAAAATTTAAAG
1 AGAAAATTTAAAG
57277 AGAAAATTTAAAG
1 AGAAAATTTAAAG
57290 A
1 A
57291 TTAAAGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (13 bp):
AGAAAATTTAAAG
Found at i:58629 original size:24 final size:25
Alignment explanation
Indices: 58575--58636 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 25
58565 ATTTATATGA
* *
58575 TAAACAAACACAAATGAACGAATAAATG
1 TAAACGAACACAAATGAAC--A-AAACG
58603 TAAACGAACACAAATGAAC-AAACG
1 TAAACGAACACAAATGAACAAAACG
58627 TAAACGAACA
1 TAAACGAACA
58637 TAATAAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 14 0.44
28 18 0.56
ACGTcount: A:0.60, C:0.18, G:0.11, T:0.11
Consensus pattern (25 bp):
TAAACGAACACAAATGAACAAAACG
Found at i:58872 original size:14 final size:14
Alignment explanation
Indices: 58855--58888 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
58845 CACATAAACA
*
58855 AACATAAACGAACT
1 AACATAAACGAACG
*
58869 AACATAAATGAACG
1 AACATAAACGAACG
58883 AACATA
1 AACATA
58889 TTACCAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.18, G:0.09, T:0.15
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:70076 original size:5 final size:5
Alignment explanation
Indices: 70066--70196 Score: 262
Period size: 5 Copynumber: 26.2 Consensus size: 5
70056 TGTAAGTGTG
70066 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
70116 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
70166 TATAA TATAA TATAA TATAA TATAA TATAA T
1 TATAA TATAA TATAA TATAA TATAA TATAA T
70197 TCTCGAGAGG
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 126 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:73341 original size:37 final size:38
Alignment explanation
Indices: 73291--73367 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 38
73281 TAATGTTACT
* *
73291 TTTTTTCCCTCTTATTTTACTCATCTATTATTAAAAAC
1 TTTTTTCCCTCTTATTTTACTCATCGATCATTAAAAAC
* *
73329 TTTTTT-CTTCTTATTTTACTCATCGATCGTTAAAAAC
1 TTTTTTCCCTCTTATTTTACTCATCGATCATTAAAAAC
73366 TT
1 TT
73368 AATGAAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
37 29 0.83
38 6 0.17
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (38 bp):
TTTTTTCCCTCTTATTTTACTCATCGATCATTAAAAAC
Found at i:79312 original size:2 final size:2
Alignment explanation
Indices: 79305--79335 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
79295 TCACTTTAAT
79305 TA TA TA 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 TA TA T
79336 TTGGATAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:85054 original size:130 final size:131
Alignment explanation
Indices: 84817--85065 Score: 317
Period size: 130 Copynumber: 1.9 Consensus size: 131
84807 TTTTGCGAAG
* *
84817 ATTTTTTGAATTATAATTGCTTAGGGAAAAGGGGCACTTAGAAATTGAAGAAATGGAATTAGCTG
1 ATTTTATGAATTATAATTGCTTAGGGAAAAGGAGCACTTAGAAATTGAAGAAATGGAATTAGCTG
* * * * * *
84882 GTGTGTTTTTGTAGTAATTTCTTGCTGAGTTTGTATTGCTTCAGGTAAAGCACTCGTTCTGATTT
66 GTGTGTTTTTGAAGTAATTTCTTGCTCAGGTTGAATTGCTTCAGGCAAACCACTCGTTCTGATTT
84947 C
131 C
* * *
84948 ATTTTATGGATTATAA-TGCTTAGGGGAAAA-GAGCACTTAGAAATTGAAGAAATGTAATTAGTT
1 ATTTTATGAATTATAATTGCTTA-GGGAAAAGGAGCACTTAGAAATTGAAGAAATGGAATTAGCT
** *
85011 TTTGTGTTTTTGAAGTTATTTCCTT-CTCAGGTTGCAATT-CTTCAGGCAAACCACT
65 GGTGTGTTTTTGAAGTAATTT-CTTGCTCAGGTTG-AATTGCTTCAGGCAAACCACT
85066 AATTATGGTA
Statistics
Matches: 101, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
130 74 0.73
131 27 0.27
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.39
Consensus pattern (131 bp):
ATTTTATGAATTATAATTGCTTAGGGAAAAGGAGCACTTAGAAATTGAAGAAATGGAATTAGCTG
GTGTGTTTTTGAAGTAATTTCTTGCTCAGGTTGAATTGCTTCAGGCAAACCACTCGTTCTGATTT
C
Found at i:99788 original size:271 final size:272
Alignment explanation
Indices: 99249--100328 Score: 1485
Period size: 271 Copynumber: 4.0 Consensus size: 272
99239 CCAGATCCTG
* * * * * *
99249 CAATGGGATTGTACCAAAAAATATTTCAAGAAACATAAAGGAAGAAT-ACAAAGTTTAAAAATGA
1 CAATGGCATTGTGCCAAACAAGATTTCAAGAAACATAAAGGAAGAATAACCAAGTTTAAAAATAA
* * * *
99313 CATCAGGAAAGCCTTTAGTCAAACCTAAGATCTTATTTGAAGCAACAAATGTTTAACAATACCTT
66 CATCAAGAAAGCCTTTAATCAAACCTAAGATCTTATTTGAAGCAACAAATGTATAAAAATACCTT
* * *
99378 CAGCTT-CTCATTTTCAGCAGTAA-TTTCTTTCATCAATTCACTGTCAATAACGGGGATCTCCTT
131 CAG-TTGCTCATTTTCAGCAGTAAGTTT-ATTCATCAATTCATTGTCAATAACGGGGATCTCCTG
* * * **
99441 AATC-ATAGGAACTAGTTCATCAATGCTT-TTTGTGGCTTCATGTTCCTCAACTAGTAACTCTTT
194 AATCGCTAGGAACTTGTTCAGCAATG-TTCTTTGCAGCTTCATGTTCCTCAACTAGTAACTCTTT
*
99504 TGTTTCTTGAACCTA
258 TGTTTCCTGAACCTA
*
99519 CAATGGCATTGTCCCAAACAAGATTTCAAGAAACATAAAGGAAGAATAACCAAGTTTAAAAATAA
1 CAATGGCATTGTGCCAAACAAGATTTCAAGAAACATAAAGGAAGAATAACCAAGTTTAAAAATAA
* * *
99584 CTTCAAGAAAGCCTTTAATCAAACCTAAGATCTTATTTGAAACAACAGATGTATAAAAATACCTT
66 CATCAAGAAAGCCTTTAATCAAACCTAAGATCTTATTTGAAGCAACAAATGTATAAAAATACCTT
** * * *
99649 CAGTTGCTCATTTTCAGCAGTTGGTTTATTCATCAATTCGTTGCCAATAACGGGGTTCTCCTGAA
131 CAGTTGCTCATTTTCAGCAGTAAGTTTATTCATCAATTCATTGTCAATAACGGGGATCTCCTGAA
* *
99714 TTGCT-GGAACTTGTTCAGCAATGTTCTTTGAAGCTTCATGTTCCTCAACTAGTAACTCTTTTGT
196 TCGCTAGGAACTTGTTCAGCAATGTTCTTTGCAGCTTCATGTTCCTCAACTAGTAACTCTTTTGT
99778 TTCCTGAACCTA
261 TTCCTGAACCTA
99790 CAATGGCATTGTGCCAAACAAGATTTCAAGAAACATAAAGGAAGAATAACCAAGTTTAAAAATAA
1 CAATGGCATTGTGCCAAACAAGATTTCAAGAAACATAAAGGAAGAATAACCAAGTTTAAAAATAA
* *
99855 CTTCAAGAAAGCCTTTAATCAAACCTAAGATCTTATTTGAAGCAACAGATGTATAAAAATACCTT
66 CATCAAGAAAGCCTTTAATCAAACCTAAGATCTTATTTGAAGCAACAAATGTATAAAAATACCTT
* * * * *
99920 CAGTTGCTCATTTTCAGCAGTAGGTTTACTCATCAATTCGTTGACAATAATGGGG-TCCTCCTGA
131 CAGTTGCTCATTTTCAGCAGTAAGTTTATTCATCAATTCATTGTCAATAACGGGGAT-CTCCTGA
* * * * * * *
99984 ACCG-TAGGAACTTGTTCAGCAATGTTCTTTTCAGCTTCAGGTTCCTCACCTCGTGACTCCTTTG
195 ATCGCTAGGAACTTGTTCAGCAATGTTCTTTGCAGCTTCATGTTCCTCAACTAGTAACTCTTTTG
100048 TTTCCTGAACCTA
260 TTTCCTGAACCTA
* * * *
100061 CAATGACATTGTGCCAAGCAAGATTTCAAGAAACATAAAGGAAGAACAACCAAGTTTAAAAATGA
1 CAATGGCATTGTGCCAAACAAGATTTCAAGAAACATAAAGGAAGAATAACCAAGTTTAAAAATAA
* * *
100126 CATCAAGAAAGCCTTTAGTCAAACCTAATATCTTATTTGAAGCAACAAATGTCTAAAAAATACCT
66 CATCAAGAAAGCCTTTAATCAAACCTAAGATCTTATTTGAAGCAACAAATGTAT-AAAAATACCT
* * * * * *
100191 TCAGCTGCTCATTTTCAGCAGTAAGTTTATTCATCAATTCATTGTCGACAGCTGGGATCTCCTTA
130 TCAGTTGCTCATTTTCAGCAGTAAGTTTATTCATCAATTCATTGTCAATAACGGGGATCTCCTGA
* * * * * *
100256 ATCGC-GGGAACTTGTTCAGCAATGTTCTTTGCAGCTTCACGTTCCTTAACTAGCAAGTCTTGTG
195 ATCGCTAGGAACTTGTTCAGCAATGTTCTTTGCAGCTTCATGTTCCTCAACTAGTAACTCTTTTG
100320 TTTCCTGAA
260 TTTCCTGAA
100329 GCTGAAGTTG
Statistics
Matches: 725, Mismatches: 75, Indels: 18
0.89 0.09 0.02
Matches are distributed among these distances:
270 49 0.07
271 549 0.76
272 126 0.17
273 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (272 bp):
CAATGGCATTGTGCCAAACAAGATTTCAAGAAACATAAAGGAAGAATAACCAAGTTTAAAAATAA
CATCAAGAAAGCCTTTAATCAAACCTAAGATCTTATTTGAAGCAACAAATGTATAAAAATACCTT
CAGTTGCTCATTTTCAGCAGTAAGTTTATTCATCAATTCATTGTCAATAACGGGGATCTCCTGAA
TCGCTAGGAACTTGTTCAGCAATGTTCTTTGCAGCTTCATGTTCCTCAACTAGTAACTCTTTTGT
TTCCTGAACCTA
Found at i:100346 original size:21 final size:21
Alignment explanation
Indices: 100321--100360 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
100311 AGTCTTGTGT
* *
100321 TTCCTGAAGCTGAAGTTGCAG
1 TTCCTGAAACTCAAGTTGCAG
100342 TTCCTGAAACTCAAGTTGC
1 TTCCTGAAACTCAAGTTGC
100361 TTTTCATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (21 bp):
TTCCTGAAACTCAAGTTGCAG
Found at i:100470 original size:96 final size:96
Alignment explanation
Indices: 100313--100625 Score: 466
Period size: 96 Copynumber: 3.3 Consensus size: 96
100303 AACTAGCAAG
* * * **
100313 TCTTGTGTTTCCTGAAGCTGAAGTTGCAGTTCCTGAAACTCAAGTTGCTT-TTCATTTATAGTAG
1 TCTTTTGTTTGCTGAAGCTCAAGTTGCAGTTCCTGAAACTCAAGTTGCTTCTTC-TGCATAGTAG
* *
100377 ATTCAAACCTTGCACTTTCCTGTTCTTGTAAC
65 ATTCAAACCTTGCACTTTCCTTTTCTAGTAAC
* *
100409 TCTTTTGTTTGCTGAAGTTCAAGTTGCAGTTCCTGAAACTCAAGTTCCTTCTTCTGCATAGTAGA
1 TCTTTTGTTTGCTGAAGCTCAAGTTGCAGTTCCTGAAACTCAAGTTGCTTCTTCTGCATAGTAGA
*
100474 TTCAAACCTTGAACTTTCCTTTTCTAGTAAC
66 TTCAAACCTTGCACTTTCCTTTTCTAGTAAC
* * * *
100505 TCTTTTGATTGCTGAAGCTCAAGTTGTAGTTCATGAAACTCAAGTTGCTTCTTATGCATAGTAGA
1 TCTTTTGTTTGCTGAAGCTCAAGTTGCAGTTCCTGAAACTCAAGTTGCTTCTTCTGCATAGTAGA
*
100570 TTCAAACCTTGCACTTTCCTTTTCTAGCAAC
66 TTCAAACCTTGCACTTTCCTTTTCTAGTAAC
*
100601 TCTTTTGTTTGCAGAAGCTCAAGTT
1 TCTTTTGTTTGCTGAAGCTCAAGTT
100626 CCAAATTCTG
Statistics
Matches: 196, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
96 193 0.98
97 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (96 bp):
TCTTTTGTTTGCTGAAGCTCAAGTTGCAGTTCCTGAAACTCAAGTTGCTTCTTCTGCATAGTAGA
TTCAAACCTTGCACTTTCCTTTTCTAGTAAC
Found at i:100924 original size:66 final size:66
Alignment explanation
Indices: 100846--101117 Score: 436
Period size: 66 Copynumber: 4.1 Consensus size: 66
100836 CAACTTGCAG
* * * * * *
100846 TTCCTCAAACTCAAGTTGCTTATTGTGCATAGTAGATTCAAACCTTTCACTTTCCTGTTTTTTAG
1 TTCCTCAAACTCAAGTTGCATCTTCTGCAAAGTAGATTCAAACCTTGCACTTTCCTGTTTTTTGG
100911 A
66 A
* *
100912 TTCCTCGAACTCAAGTTGCATCTTCTGCAAAGTAGATTCATACCTTGCACTTTCCTGTTTTTTGG
1 TTCCTCAAACTCAAGTTGCATCTTCTGCAAAGTAGATTCAAACCTTGCACTTTCCTGTTTTTTGG
100977 A
66 A
* *
100978 TTCCTCAAACTCAAGTTGCATCTTCTGCAAAGTAGATTCAAATCTTGCATTTTCCTGTTTTTTGG
1 TTCCTCAAACTCAAGTTGCATCTTCTGCAAAGTAGATTCAAACCTTGCACTTTCCTGTTTTTTGG
101043 A
66 A
* *
101044 TTCCTCAAACTCAAGTTGCATCTTCTTCAAAGTAGATTCAAACCTGGCACTTTCCTGTTTTTTGG
1 TTCCTCAAACTCAAGTTGCATCTTCTGCAAAGTAGATTCAAACCTTGCACTTTCCTGTTTTTTGG
101109 A
66 A
101110 TTCCTCAA
1 TTCCTCAA
101118 GGTCAACCTG
Statistics
Matches: 190, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 190 1.00
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (66 bp):
TTCCTCAAACTCAAGTTGCATCTTCTGCAAAGTAGATTCAAACCTTGCACTTTCCTGTTTTTTGG
A
Found at i:116524 original size:22 final size:22
Alignment explanation
Indices: 116499--116543 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
116489 AGGTTAAAGC
*
116499 ATAGAAAAGCAACTATTCATTG
1 ATAGAAAAGCAACCATTCATTG
*
116521 ATAGAAAAGTAACCATTCATTG
1 ATAGAAAAGCAACCATTCATTG
116543 A
1 A
116544 AATATAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (22 bp):
ATAGAAAAGCAACCATTCATTG
Found at i:121881 original size:2 final size:2
Alignment explanation
Indices: 121874--121907 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
121864 TTCTAGTCCA
121874 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
121908 CAATTTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:121994 original size:14 final size:13
Alignment explanation
Indices: 121969--122001 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
121959 TCAATATTAT
121969 TATAAAAATTAAA
1 TATAAAAATTAAA
121982 TATAAACAATTAAA
1 TATAAA-AATTAAA
121996 TATAAA
1 TATAAA
122002 TAATAAAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (13 bp):
TATAAAAATTAAA
Found at i:122893 original size:24 final size:24
Alignment explanation
Indices: 122861--122915 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
122851 AATTTATGTC
*
122861 ATTCACACACTTAGTTTTCTCTTG
1 ATTCACACACTTAGTTTTCTCTTA
*
122885 ATTCACACACTTAGTTTTTTCTTA
1 ATTCACACACTTAGTTTTCTCTTA
122909 ATTCACA
1 ATTCACA
122916 ATCCCCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.25, C:0.24, G:0.05, T:0.45
Consensus pattern (24 bp):
ATTCACACACTTAGTTTTCTCTTA
Found at i:123517 original size:2 final size:2
Alignment explanation
Indices: 123510--123547 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
123500 TTTGAGTTTA
123510 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
123548 TAAATATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123548 original size:12 final size:11
Alignment explanation
Indices: 123510--123554 Score: 58
Period size: 10 Copynumber: 4.2 Consensus size: 11
123500 TTTGAGTTTA
123510 ATATA-TATAT
1 ATATATTATAT
123520 ATATA-TATAT
1 ATATATTATAT
123530 ATATATTATAT
1 ATATATTATAT
*
123541 ACTATATTAAAT
1 A-TATATTATAT
123553 AT
1 AT
123555 TAAATATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
10 15 0.47
11 7 0.22
12 10 0.31
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (11 bp):
ATATATTATAT
Found at i:124535 original size:27 final size:27
Alignment explanation
Indices: 124500--124555 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
124490 AACCGAATAC
124500 AAGCACGACAACATTTTAGAACAAACA
1 AAGCACGACAACATTTTAGAACAAACA
124527 AAGCACGACAACATTTTAGAACAAACA
1 AAGCACGACAACATTTTAGAACAAACA
124554 AA
1 AA
124556 TGAACCGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.54, C:0.21, G:0.11, T:0.14
Consensus pattern (27 bp):
AAGCACGACAACATTTTAGAACAAACA
Found at i:134397 original size:20 final size:21
Alignment explanation
Indices: 134352--134400 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
134342 ATGACATGTT
*
134352 TTTTTTTTGTCTTTATGACATA
1 TTTTTTTTG-CTTTATGACACA
*
134374 TTTTTTTTG-TTTATGACACG
1 TTTTTTTTGCTTTATGACACA
134394 TTTTTTT
1 TTTTTTT
134401 ACCGTTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 16 0.64
22 9 0.36
ACGTcount: A:0.14, C:0.08, G:0.10, T:0.67
Consensus pattern (21 bp):
TTTTTTTTGCTTTATGACACA
Found at i:134726 original size:167 final size:167
Alignment explanation
Indices: 134447--134773 Score: 530
Period size: 167 Copynumber: 2.0 Consensus size: 167
134437 AGACATGGTC
* * *
134447 ACGACTGATCAAGATGTCGTTTATCTGTTATATTGTCGATCTTTCTTGCTTTGGACCATCGAATT
1 ACGACTGATCAAGATGTCGTTTATATATTATATTATCGATCTTTCTTGCTTTGGACCATCGAATT
* *
134512 AGATTTAGATATCTGTTATGCGTTCGTGGATAGTTTTTCATGTCGCTTGAGTATGATTTACGATT
66 AGATTTAGATATCCGTTATGCGTTCGTGGATAGTTTTTCACGTCGCTTGAGTATGATTTACGATT
*
134577 TGTCGTGGTCTTTCAGTAGT-TTGATCTCATCATCGCA
131 TGTCGTGGTATTTCAGTA-TCTTGATCTCATCATCGCA
* *
134614 ACGACTGATCAATATGTCGTTTATATATTATATTATTGATCTTTCTTGCTTTGGACCATCGAATT
1 ACGACTGATCAAGATGTCGTTTATATATTATATTATCGATCTTTCTTGCTTTGGACCATCGAATT
* * * *
134679 GGATTTAGATATCCGTTATGCGTTCGTGGATAGTTTTTCACGTCGCTTGAGTCTGATTTGCGGTT
66 AGATTTAGATATCCGTTATGCGTTCGTGGATAGTTTTTCACGTCGCTTGAGTATGATTTACGATT
134744 TGTCGTGGTATTTCAGTATCTTGATCTCAT
131 TGTCGTGGTATTTCAGTATCTTGATCTCAT
134774 TTTGTAGTTC
Statistics
Matches: 147, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
166 1 0.01
167 146 0.99
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (167 bp):
ACGACTGATCAAGATGTCGTTTATATATTATATTATCGATCTTTCTTGCTTTGGACCATCGAATT
AGATTTAGATATCCGTTATGCGTTCGTGGATAGTTTTTCACGTCGCTTGAGTATGATTTACGATT
TGTCGTGGTATTTCAGTATCTTGATCTCATCATCGCA
Found at i:154652 original size:20 final size:21
Alignment explanation
Indices: 154614--154653 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
154604 GTTGCCTTTT
154614 AAAATAAAAAAACAAATATATG
1 AAAATAAAAAAAC-AATATATG
*
154636 AAAATAAAAATAC-ATATA
1 AAAATAAAAAAACAATATA
154654 AATATTAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
22 12 0.71
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (21 bp):
AAAATAAAAAAACAATATATG
Found at i:163075 original size:250 final size:248
Alignment explanation
Indices: 162594--163192 Score: 881
Period size: 251 Copynumber: 2.4 Consensus size: 248
162584 CTTATTCATA
* * * *
162594 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGATCGAGTTTCTAATTAATATAGTCGGGT
1 TATTGAATAAAAATAATTTTTTATTATTTCGGGTCGG-TCGGGTTTCTAATTCATATATTCGGGT
162659 CGGGTGAAACTTTATTTTGGTCGGGTCGGG-TCGTTTTTTTAAGTGTGATATTCGGGTCGGTTGA
65 CGGGTGAAACTTTATTTTGGTCGGGTCGGGTTCGTTTTTTTAAGTGTGATATTCGGGTC-G--GA
* *
162723 GTTCGGGTTCAGGGTGAAAATACCCGACCCGAATATATATATAATTTTACCATATATACTTAGGA
127 GTTCGGGTTCAGGGTGAAAATACCCGACCCGAAAAAATATATAATTTTACCATATATACTTAGGA
* *
162788 ATAATTATAATAATACCCTTCTATATATAATTTTTTTT-CAATTAAGTTATTGTTTT
192 ATAATTACAATAATACCCCTCTATATATAATTTTTTTTCCAATTAAGTTATTGTTTT
162844 TATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATAATTTTTTATTATTTCGGGTC-GGTCGGGTTTCTAATTCATATATTCGGGT
*
162909 CGGGTGAAACTTTATTTTGGTCGGGTCGGGTTGGTTTTTTTAAGTGTGATATTCGGGTC-GAG-T
65 CGGGTGAAACTTTATTTTGGTCGGGTCGGGTTCGTTTTTTTAAGTGTGATATTCGGGTCGGAGTT
* *
162972 CGGGTTCAGGGTGAAAAATACCCGACCCGACCCAAAAAATATATAATTTTACCTTATATATTTAG
130 CGGGTTCAGGGTG-AAAATACCCGACCCG----AAAAAATATATAATTTTACCATATATACTTAG
*
163037 GAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCCAATTAAGTTATTTTTTT
190 GAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCCAATTAAGTTATTGTTTT
*
163096 TATTGAATAAAAATAATTTTTTTATTATTTCGGGT---T-GGGTTTCTAATTCATATATTTGGGT
1 TATTGAATAAAAATAA-TTTTTTATTATTTCGGGTCGGTCGGGTTTCTAATTCATATATTCGGGT
163157 CAAGTTGGGTGAAACTTTATTTTGGTCGGGTCGGGT
65 C-----GGGTGAAACTTTATTTTGGTCGGGTCGGGT
163193 CTCAGATGGA
Statistics
Matches: 322, Mismatches: 13, Indels: 25
0.89 0.04 0.07
Matches are distributed among these distances:
246 14 0.04
247 18 0.06
248 25 0.08
249 1 0.00
250 88 0.27
251 95 0.30
252 33 0.10
253 48 0.15
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (248 bp):
TATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGTCGGGTTTCTAATTCATATATTCGGGTC
GGGTGAAACTTTATTTTGGTCGGGTCGGGTTCGTTTTTTTAAGTGTGATATTCGGGTCGGAGTTC
GGGTTCAGGGTGAAAATACCCGACCCGAAAAAATATATAATTTTACCATATATACTTAGGAATAA
TTACAATAATACCCCTCTATATATAATTTTTTTTCCAATTAAGTTATTGTTTT
Found at i:163576 original size:17 final size:18
Alignment explanation
Indices: 163551--163597 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
163541 TATGGAATTG
* *
163551 GATTCCAATTCC-TGACA
1 GATTTCAATTCCTTCACA
163568 GATTTCAATTCCTTCACA
1 GATTTCAATTCCTTCACA
163586 GATTTCAATTCC
1 GATTTCAATTCC
163598 CTCAGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (18 bp):
GATTTCAATTCCTTCACA
Found at i:163779 original size:19 final size:19
Alignment explanation
Indices: 163737--163779 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
163727 CAACCTTCCC
*
163737 TTGTCATTCATAACTTCTT
1 TTGTTATTCATAACTTCTT
163756 TTGTTATTCATAACTTCTT
1 TTGTTATTCATAACTTCTT
163775 TTGTT
1 TTGTT
163780 TTGTTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.19, C:0.16, G:0.07, T:0.58
Consensus pattern (19 bp):
TTGTTATTCATAACTTCTT
Found at i:170527 original size:15 final size:16
Alignment explanation
Indices: 170502--170531 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
170492 ATATAAATAA
170502 AAAAAACATATTATTC
1 AAAAAACATATTATTC
170518 AAAAAA-ATATTATT
1 AAAAAACATATTATT
170532 ATACATACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAAACATATTATTC
Found at i:182498 original size:30 final size:30
Alignment explanation
Indices: 182434--183478 Score: 707
Period size: 30 Copynumber: 35.6 Consensus size: 30
182424 TTGTGGTGGA
** * * * *
182434 GGTGACTTGTAAGTATATGGAGGAGGTGGA
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* *
182464 GGTGATTTGTACTTGTATAGAGGTGGAGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
** * * *
182494 GGTGACTCATACTTGTATGAAGGAGGTGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* *
182524 GGTTATTTGTACTTGTATGGAGGTGGAGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
** * *
182554 GGTGACTCATACTTGTACGGAGGTGGTGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* *
182584 GGTGAC-T-TAC--G-GTGG-CG-GG-GGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* * * * *
182606 GGAGACTCGTACTTGTAAGGAGGAGGTGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
182636 GGTGACTTGTAC--G-ATGGA-G-GG-GGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* * * * * *
182660 GGAGACTCGTACTTGTAAGGAGGAGGTGGG
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
*
182690 GGTGACTTGTATTTGTATGGAGGTGGAGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* * *
182720 -G-GACTCGTACTTGTACGGAGGTGG-TGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* *
182747 GGGTGACTTGTACTTGTATGGAAGTGGATGT
1 -GGTGACTTGTACTTGTATGGAGGTGGAGGT
* * * *
182778 GGAGATTTATACTTGTACGGAGGT-GATGG-
1 GGTGACTTGTACTTGTATGGAGGTGGA-GGT
* *
182807 GGTGACTTGTAATTGTATGGAGGTGGAGAT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
** * * *
182837 GGTGACTCATACTTGTAAGGAGGTGGTGGG
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* *
182867 GGTGACTTGTACTTATATAGAGGTGGAGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* * * * *
182897 GGTGACTTATACTTGTAAGGAGGAGGTGGC
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* * * * *
182927 AGTGACTTGTACGTGTACGGAGATGGTGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
*
182957 GGTGATTTGTACTTG--T--A--TGGAGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
** * *
182981 GGTGACTCATACTTGTACGGAGGTGGTGG-
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* *
183010 GGTGACTTGTA-ATG-A--GATGGTGGTGGT
1 GGTGACTTGTACTTGTATGGA-GGTGGAGGT
*
183037 GGTGAGTTGTACTTGTATGGAGGTGGAGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
** * * * *
183067 GGTGACTCATACTTGTAAGGAGGAGGTGGC
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* *
183097 AGTGACTTGTACTTGTATGGAGGTGGAAGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* * * * *
183127 TGTGA-TTCATACTTGTAAGGATGTGGTGGT
1 GGTGACTT-GTACTTGTATGGAGGTGGAGGT
* *
183157 GGTGACTTGTATTTGTATAGAGGTGGAGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* ** * * *
183187 GGCGACTCATACTTGTAAGGAGGAGGTGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
*
183217 TGTGACTTGTACTTGTATGGAGGTGGAGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
** * *
183247 GGTGACTCATACTTGTACGGAGGTGGTGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
** * * *
183277 GGTGACTCATACTTGTAAGGAGGAGGTGACAGT
1 GGTGACTTGTACTTGTATGGAGG-TG-GA-GGT
* **
183310 GGTGACTTGTATTTGTATGGAGGTAAAGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* * * **
183340 GGTGA-TTCATACTTGTAAGGAGG-AGATGAC
1 GGTGACTT-GTACTTGTATGGAGGTGGA-GGT
183370 GGTGACTTGTACTTGTATGGAGGTGGAGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* ** * * *
183400 GATGACTCATACTTGTAAGGAGGAGGTGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* *
183430 GGTGACATGTACTTGTATGGAGGTGAAGGT
1 GGTGACTTGTACTTGTATGGAGGTGGAGGT
* **
183460 GATGACTCATACTTGTATG
1 GGTGACTTGTACTTGTATG
183479 AGTAATTTGT
Statistics
Matches: 770, Mismatches: 203, Indels: 84
0.73 0.19 0.08
Matches are distributed among these distances:
22 8 0.01
23 2 0.00
24 35 0.05
25 6 0.01
26 13 0.02
27 23 0.03
28 31 0.04
29 44 0.06
30 573 0.74
31 13 0.02
32 1 0.00
33 21 0.03
ACGTcount: A:0.21, C:0.08, G:0.40, T:0.31
Consensus pattern (30 bp):
GGTGACTTGTACTTGTATGGAGGTGGAGGT
Found at i:182518 original size:60 final size:60
Alignment explanation
Indices: 182452--183299 Score: 845
Period size: 60 Copynumber: 14.6 Consensus size: 60
182442 GTAAGTATAT
* * * *
182452 GGAGGAGGTGGAGGTGATTTGTACTTGTATAGAGGTGGAGGTGGTGACTCATACTTGTAT
1 GGAGGAGGTGGTGGTGACTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAA
* * * *
182512 GAAGGAGGTGGTGGTTATTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAC
1 GGAGGAGGTGGTGGTGACTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAA
* * * * *
182572 GGAGGTGGTGGTGGTGAC-T-TAC--G-GTGG-CG-GG-GGTGGAGACTCGTACTTGTAA
1 GGAGGAGGTGGTGGTGACTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAA
* *
182624 GGAGGAGGTGGTGGTGACTTGTAC--G-ATGGA-G-GG-GGTGGAGACTCGTACTTGTAA
1 GGAGGAGGTGGTGGTGACTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAA
* * * *
182678 GGAGGAGGTGGGGGTGACTTGTATTTGTATGGAGGTGGAGGT-G-GACTCGTACTTGTAC
1 GGAGGAGGTGGTGGTGACTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAA
* * * * * * *
182736 GGAGGTGGT-GTGGGTGACTTGTACTTGTATGGAAGTGGATGTGGAGATTTATACTTGTAC
1 GGAGGAGGTGGT-GGTGACTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAA
* * * *
182796 GGAGGTGATGG-GGTGACTTGTAATTGTATGGAGGTGGAGATGGTGACTCATACTTGTAA
1 GGAGGAGGTGGTGGTGACTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAA
* * * * *
182855 GGAGGTGGTGGGGGTGACTTGTACTTATATAGAGGTGGAGGTGGTGACTTATACTTGTAA
1 GGAGGAGGTGGTGGTGACTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAA
** * * * * * **
182915 GGAGGAGGTGGCAGTGACTTGTACGTGTACGGAGATGGTGGTGGTGATTTGTACTTGT-A
1 GGAGGAGGTGGTGGTGACTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAA
* ** * * ** *
182974 --TGGA---GGTGGTGACTCATACTTGTACGGAGGTGGTGG-GGTGACTTGTA-ATG--A
1 GGAGGAGGTGGTGGTGACTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAA
* *
183025 -GATGGTGGTGGTGGTGAGTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAA
1 GGA-GGAGGTGGTGGTGACTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAA
** * * *
183085 GGAGGAGGTGGCAGTGACTTGTACTTGTATGGAGGTGGAAGTTGTGATTCATACTTGTAA
1 GGAGGAGGTGGTGGTGACTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAA
* * * * *
183145 GGATGTGGTGGTGGTGACTTGTATTTGTATAGAGGTGGAGGTGGCGACTCATACTTGTAA
1 GGAGGAGGTGGTGGTGACTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAA
* *
183205 GGAGGAGGTGGTTGTGACTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAC
1 GGAGGAGGTGGTGGTGACTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAA
* ** *
183265 GGAGGTGGTGGTGGTGACTCATACTTGTAAGGAGG
1 GGAGGAGGTGGTGGTGACTTGTACTTGTATGGAGG
183300 AGGTGACAGT
Statistics
Matches: 663, Mismatches: 101, Indels: 48
0.82 0.12 0.06
Matches are distributed among these distances:
51 1 0.00
52 37 0.06
53 15 0.02
54 80 0.12
55 3 0.00
56 29 0.04
57 18 0.03
58 55 0.08
59 56 0.08
60 366 0.55
61 3 0.00
ACGTcount: A:0.20, C:0.08, G:0.41, T:0.31
Consensus pattern (60 bp):
GGAGGAGGTGGTGGTGACTTGTACTTGTATGGAGGTGGAGGTGGTGACTCATACTTGTAA
Found at i:183633 original size:25 final size:25
Alignment explanation
Indices: 183605--183694 Score: 180
Period size: 25 Copynumber: 3.6 Consensus size: 25
183595 CTCATCTTAC
183605 TATAATCTAATCCTTTAAATTTATT
1 TATAATCTAATCCTTTAAATTTATT
183630 TATAATCTAATCCTTTAAATTTATT
1 TATAATCTAATCCTTTAAATTTATT
183655 TATAATCTAATCCTTTAAATTTATT
1 TATAATCTAATCCTTTAAATTTATT
183680 TATAATCTAATCCTT
1 TATAATCTAATCCTT
183695 AGGAGCATAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 65 1.00
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (25 bp):
TATAATCTAATCCTTTAAATTTATT
Found at i:187239 original size:9 final size:9
Alignment explanation
Indices: 187223--187272 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
187213 AGTGCCCAAC
187223 AATAATAAA
1 AATAATAAA
*
187232 ATTAATAAA
1 AATAATAAA
187241 AA-AATAAA
1 AATAATAAA
187249 AATAATTAATA
1 AATAA-TAA-A
*
187260 AA-AATAAT
1 AATAATAAA
187268 AATAA
1 AATAA
187273 AATCGATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
8 10 0.29
9 16 0.47
10 5 0.15
11 3 0.09
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AATAATAAA
Found at i:187244 original size:12 final size:11
Alignment explanation
Indices: 187223--187274 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 11
187213 AGTGCCCAAC
*
187223 AATAATAAAATT
1 AATAA-AAAAAT
187235 AATAAAAAAAT
1 AATAAAAAAAT
* *
187246 AA-AAATAATT
1 AATAAAAAAAT
187256 AATAAAAATAAT
1 AATAAAAA-AAT
187268 AATAAAA
1 AATAAAA
187275 TCGATAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
10 8 0.24
11 11 0.33
12 14 0.42
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
AATAAAAAAAT
Found at i:187250 original size:18 final size:19
Alignment explanation
Indices: 187226--187272 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
187216 GCCCAACAAT
*
187226 AATAAAATTAA-TAA-AAA
1 AATAAAAATAATTAATAAA
187243 AATAAAAATAATTAATAAA
1 AATAAAAATAATTAATAAA
*
187262 AATAATAATAA
1 AATAAAAATAA
187273 AATCGATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 10 0.38
18 3 0.12
19 13 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
AATAAAAATAATTAATAAA
Found at i:187261 original size:13 final size:12
Alignment explanation
Indices: 187243--187274 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
187233 TTAATAAAAA
187243 AATAAAAATAATT
1 AATAAAAATAA-T
187256 AATAAAAATAAT
1 AATAAAAATAAT
187268 AATAAAA
1 AATAAAA
187275 TCGATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
AATAAAAATAAT
Found at i:187597 original size:3 final size:3
Alignment explanation
Indices: 187591--187650 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
187581 ATTAATAAAA
* * *
187591 TAT TAT TAT AAA TAT TAT TAT TTT TAT TAAT T-T TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
187635 TAT TGAT T-T TAT TAT T
1 TAT T-AT TAT TAT TAT T
187651 GTTGGTTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
2 6 0.13
3 34 0.74
4 6 0.13
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:187664 original size:15 final size:15
Alignment explanation
Indices: 187603--187666 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 15
187593 TTATTATAAA
187603 TATT-ATTATTTTTAT
1 TATTGATTA-TTTTAT
*
187618 TAATTTTATTATTTTAT
1 T-A-TTGATTATTTTAT
187635 TATTGATT-TTATTAT
1 TATTGATTATT-TTAT
* *
187650 TGTTGGTTATTTTAT
1 TATTGATTATTTTAT
187665 TA
1 TA
187667 GAAATATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
14 2 0.05
15 21 0.52
16 4 0.10
17 9 0.22
18 4 0.10
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (15 bp):
TATTGATTATTTTAT
Found at i:191900 original size:296 final size:296
Alignment explanation
Indices: 191366--191960 Score: 1181
Period size: 296 Copynumber: 2.0 Consensus size: 296
191356 TCGTCTCTTG
191366 AAATTACTATTTACTTTAGAATTCATGCCTTTGATGTACATATGAGTCGTGATTGAGCACCAAAT
1 AAATTACTATTTACTTTAGAATTCATGCCTTTGATGTACATATGAGTCGTGATTGAGCACCAAAT
191431 TATCGATTTTTGTCAATCTTTCTTTGCATTTAACCTCTTTTCAATTGTTTTCCTTTCTGCCATGT
66 TATCGATTTTTGTCAATCTTTCTTTGCATTTAACCTCTTTTCAATTGTTTTCCTTTCTGCCATGT
191496 ATGTATTATATGCGGTTCTTGGCGGAGGCCCTGAAGATTCTCGTGTTAACTGATAGATGTTGAGA
131 ATGTATTATATGCGGTTCTTGGCGGAGGCCCTGAAGATTCTCGTGTTAACTGATAGATGTTGAGA
191561 TAGTATTGTGTTCTTAGTTGATTGATAACTTGATGTTTTATTGTGTTTCAGTTTCTTGTGTTGGA
196 TAGTATTGTGTTCTTAGTTGATTGATAACTTGATGTTTTATTGTGTTTCAGTTTCTTGTGTTGGA
*
191626 GAAAGTCAGGACACCAGTTCGTCTGCAACATCGTGA
261 GAAAGTCAGGACACCAGTTCGTCTGCAACATCGTCA
191662 AAATTACTATTTACTTTAGAATTCATGCCTTTGATGTACATATGAGTCGTGATTGAGCACCAAAT
1 AAATTACTATTTACTTTAGAATTCATGCCTTTGATGTACATATGAGTCGTGATTGAGCACCAAAT
191727 TATCGATTTTTGTCAATCTTTCTTTGCATTTAACCTCTTTTCAATTGTTTTCCTTTCTGCCATGT
66 TATCGATTTTTGTCAATCTTTCTTTGCATTTAACCTCTTTTCAATTGTTTTCCTTTCTGCCATGT
191792 ATGTATTATATGCGGTTCTTGGCGGAGGCCCTGAAGATTCTCGTGTTAACTGATAGATGTTGAGA
131 ATGTATTATATGCGGTTCTTGGCGGAGGCCCTGAAGATTCTCGTGTTAACTGATAGATGTTGAGA
191857 TAGTATTGTGTTCTTAGTTGATTGATAACTTGATGTTTTATTGTGTTTCAGTTTCTTGTGTTGGA
196 TAGTATTGTGTTCTTAGTTGATTGATAACTTGATGTTTTATTGTGTTTCAGTTTCTTGTGTTGGA
191922 GAAAGTCAGGACACCAGTTCGTCTGCAACATCGTCA
261 GAAAGTCAGGACACCAGTTCGTCTGCAACATCGTCA
191958 AAA
1 AAA
191961 ATGATAGCTC
Statistics
Matches: 298, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
296 298 1.00
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (296 bp):
AAATTACTATTTACTTTAGAATTCATGCCTTTGATGTACATATGAGTCGTGATTGAGCACCAAAT
TATCGATTTTTGTCAATCTTTCTTTGCATTTAACCTCTTTTCAATTGTTTTCCTTTCTGCCATGT
ATGTATTATATGCGGTTCTTGGCGGAGGCCCTGAAGATTCTCGTGTTAACTGATAGATGTTGAGA
TAGTATTGTGTTCTTAGTTGATTGATAACTTGATGTTTTATTGTGTTTCAGTTTCTTGTGTTGGA
GAAAGTCAGGACACCAGTTCGTCTGCAACATCGTCA
Found at i:199158 original size:108 final size:107
Alignment explanation
Indices: 199038--199232 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 107
199028 TATATATAAA
* * * * *
199038 TAAGATATTTATTTATTTAGAAATATCAGAAAAGAGCTTCTAGGTGCTTTAAGACAGCTCTTTTC
1 TAAGATATTTATTTATTCAAAAATATCAGAAAAGAGCTTCTAGGTACCTTAAGACAACTCTTTTC
*
199103 TTTGATATAAATAAATAACTAAAAAAAAATTATTTTAATATAG
66 TTTGATATAAA-AAATAAATAAAAAAAAATTATTTTAATATAG
*
199146 TAAGATATTTATTTATTCAAAAATATCAGAAAAGAGCTTCTAGGTACCTTAAGACAACTTTTTTC
1 TAAGATATTTATTTATTCAAAAATATCAGAAAAGAGCTTCTAGGTACCTTAAGACAACTCTTTTC
*
199211 TTTGATATTAAAAATAAATAAA
66 TTTGATATAAAAAATAAATAAA
199233 TATCAAAATA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
107 10 0.13
108 69 0.87
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.37
Consensus pattern (107 bp):
TAAGATATTTATTTATTCAAAAATATCAGAAAAGAGCTTCTAGGTACCTTAAGACAACTCTTTTC
TTTGATATAAAAAATAAATAAAAAAAAATTATTTTAATATAG
Found at i:199278 original size:13 final size:13
Alignment explanation
Indices: 199256--199285 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
199246 TTATTTTTCT
199256 TAAAAGTAATTTA
1 TAAAAGTAATTTA
*
199269 TAAAATTAATTTA
1 TAAAAGTAATTTA
199282 TAAA
1 TAAA
199286 TAGGAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (13 bp):
TAAAAGTAATTTA
Found at i:200060 original size:13 final size:13
Alignment explanation
Indices: 200042--200070 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
200032 CCACCGTACT
200042 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
200055 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
200068 CCG
1 CCG
200071 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:200817 original size:2 final size:2
Alignment explanation
Indices: 200810--200834 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
200800 AGTTCTTGTA
200810 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
200835 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:201753 original size:76 final size:76
Alignment explanation
Indices: 201008--201728 Score: 1370
Period size: 76 Copynumber: 9.5 Consensus size: 76
200998 GATGGAAATG
*
201008 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
201073 CCCGAAGGCTT
66 CCCGAAGGCTT
*
201084 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
201149 CCCGAATGCTT
66 CCCGAAGGCTT
201160 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
201225 CCCGAAGGCTT
66 CCCGAAGGCTT
*
201236 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAATGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
201301 CCCGAAGGCTT
66 CCCGAAGGCTT
201312 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
201377 CCCGAAGGCTT
66 CCCGAAGGCTT
201388 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
201453 CCCGAAGGCTT
66 CCCGAAGGCTT
201464 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
201529 CCCGAAGGCTT
66 CCCGAAGGCTT
*
201540 TTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
201605 CCCGAAGGCTT
66 CCCGAAGGCTT
201616 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
201681 CCCGAAGGCTTTT
66 CCCGAAGGC--TT
*
201694 TTTGGAAACATCATGCACTGAAGGAATTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
201729 TGAGAAATAG
Statistics
Matches: 633, Mismatches: 10, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
76 597 0.94
78 36 0.06
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:205151 original size:83 final size:83
Alignment explanation
Indices: 205012--205193 Score: 328
Period size: 83 Copynumber: 2.2 Consensus size: 83
205002 TCTACTATGA
* * * *
205012 GCAAATTCATCTTCCAAATTTAATGATTGGTTTTGTCAAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
205077 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
205095 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
205160 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
205178 GCAAATTCATCTTCTA
1 GCAAATTCATCTTCTA
205194 GTTAATGTTT
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 95 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.30
Consensus pattern (83 bp):
GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATTG
Found at i:212827 original size:108 final size:107
Alignment explanation
Indices: 212707--212901 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 107
212697 TATATATAAA
* * * * *
212707 TAAGATATTTATTTATTTAGAAATATCAGAAAAGAGCTTCTAGGTGCTTTAAGACAGCTCTTTTC
1 TAAGATATTTATTTATTCAAAAATATCAGAAAAGAGCTTCTAGGTACCTTAAGACAACTCTTTTC
*
212772 TTTGATATAAATAAATAACTAAAAAAAAATTATTTTAATATAG
66 TTTGATATAAA-AAATAAATAAAAAAAAATTATTTTAATATAG
*
212815 TAAGATATTTATTTATTCAAAAATATCAGAAAAGAGCTTCTAGGTACCTTAAGACAACTTTTTTC
1 TAAGATATTTATTTATTCAAAAATATCAGAAAAGAGCTTCTAGGTACCTTAAGACAACTCTTTTC
*
212880 TTTGATATTAAAAATAAATAAA
66 TTTGATATAAAAAATAAATAAA
212902 TATCAAAATA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
107 10 0.13
108 69 0.87
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.37
Consensus pattern (107 bp):
TAAGATATTTATTTATTCAAAAATATCAGAAAAGAGCTTCTAGGTACCTTAAGACAACTCTTTTC
TTTGATATAAAAAATAAATAAAAAAAAATTATTTTAATATAG
Found at i:214489 original size:2 final size:2
Alignment explanation
Indices: 214482--214514 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
214472 AGTTCTTGTA
214482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
214515 ATAATAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:214520 original size:3 final size:3
Alignment explanation
Indices: 214512--214564 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
214502 ATATATATAT
* * *
214512 ATA ATA ATA ATA ATA ATA ATA TTTA GTA ATA ATA A-A TTTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA -ATA ATA ATA
214558 ATA ATA A
1 ATA ATA A
214565 AATTTAAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
2 1 0.02
3 38 0.90
4 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:214533 original size:22 final size:23
Alignment explanation
Indices: 214480--214564 Score: 79
Period size: 22 Copynumber: 3.7 Consensus size: 23
214470 TGAGTTCTTG
214480 TAATATAT-ATATATATATATATATA
1 TAATATATAATA-ATA-ATA-ATATA
214505 TATATATATAATAATAATAATA-A
1 TA-ATATATAATAATAATAATATA
* * *
214528 TAATATTTAGTAATAATAA-ATT
1 TAATATATAATAATAATAATATA
214550 TAATA-ATAATAATAA
1 TAATATATAATAATAA
214565 AATTTAAATG
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
21 9 0.17
22 20 0.38
23 3 0.06
24 3 0.06
25 5 0.10
26 9 0.17
27 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (23 bp):
TAATATATAATAATAATAATATA
Found at i:214533 original size:28 final size:30
Alignment explanation
Indices: 214502--214563 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
214492 ATATATATAT
214502 ATATATA-TATATAAT-AA-TAATAATAATA
1 ATATATAGTA-ATAATAAATTAATAATAATA
*
214530 ATATTTAGTAATAATAAATTTAATAATAATA
1 ATATATAGTAATAATAAA-TTAATAATAATA
214561 ATA
1 ATA
214564 AAATTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 11 0.38
29 4 0.14
31 14 0.48
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (30 bp):
ATATATAGTAATAATAAATTAATAATAATA
Found at i:222532 original size:2 final size:2
Alignment explanation
Indices: 222525--222556 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
222515 GGTAACTTAC
222525 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
222557 GAGAGAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:222561 original size:2 final size:2
Alignment explanation
Indices: 222556--222590 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
222546 ATATATATAT
222556 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 A
222591 TGGGGGGCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:228065 original size:21 final size:21
Alignment explanation
Indices: 228049--228092 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
228039 TTGCCACTTT
228049 CATCACCTCCACCGCCACCTC
1 CATCACCTCCACCGCCACCTC
* * *
228070 CATCATCTCCATCACCACCTC
1 CATCACCTCCACCGCCACCTC
228091 CA
1 CA
228093 CCTCCTCTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.57, G:0.02, T:0.18
Consensus pattern (21 bp):
CATCACCTCCACCGCCACCTC
Found at i:232774 original size:20 final size:20
Alignment explanation
Indices: 232726--232775 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
232716 ATGACCAACA
232726 AATTCGCAACGCGAATATGT
1 AATTCGCAACGCGAATATGT
* *
232746 AAATCGCAACGCGAATTTGT
1 AATTCGCAACGCGAATATGT
*
232766 AATTTGCAAC
1 AATTCGCAAC
232776 ACAGAAGTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (20 bp):
AATTCGCAACGCGAATATGT
Found at i:233443 original size:30 final size:30
Alignment explanation
Indices: 233407--233470 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
233397 TGGAATATTT
*
233407 TTTTAAAAAATAATTCAACGTGGTCCTCTA
1 TTTTAAAAAATAATTCAACGTGGTCCTCCA
*
233437 TTTT-AAAAATAATTCAATGTGGTCCTCCA
1 TTTTAAAAAATAATTCAACGTGGTCCTCCA
233466 TTTTA
1 TTTTA
233471 TGTGAATCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (30 bp):
TTTTAAAAAATAATTCAACGTGGTCCTCCA
Found at i:234976 original size:10 final size:10
Alignment explanation
Indices: 234963--235078 Score: 52
Period size: 10 Copynumber: 10.2 Consensus size: 10
234953 AACACAAATG
234963 AACGAACATA
1 AACGAACATA
234973 AACGAACTGATGTA
1 AACGAAC--A--TA
*
234987 AATGAACATA
1 AACGAACATA
234997 AACGAACACAATA
1 AACG-A-AC-ATA
*
235010 AACGAACACAAACA
1 AACG-A-AC--ATA
*
235024 AACGAACGTA
1 AACGAACATA
235034 AACGAACACAATA
1 AACG-A-AC-ATA
*
235047 AATGAACATA
1 AACGAACATA
*
235057 AACGAACGTA
1 AACGAACATA
*
235067 AACGAAAATA
1 AACGAACATA
235077 AA
1 AA
235079 TGAAAATAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
10 38 0.45
11 4 0.05
12 9 0.11
13 18 0.21
14 15 0.18
ACGTcount: A:0.59, C:0.18, G:0.12, T:0.11
Consensus pattern (10 bp):
AACGAACATA
Found at i:234978 original size:24 final size:24
Alignment explanation
Indices: 234946--235022 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
234936 CATTTAAATG
* *
234946 ATAAGCGAACACAAATGAACGAAC
1 ATAAACGAACACAAATAAACGAAC
** ** *
234970 ATAAACGAACTGATGTAAATGAAC
1 ATAAACGAACACAAATAAACGAAC
234994 ATAAACGAACAC-AATAAACGAAC
1 ATAAACGAACACAAATAAACGAAC
*
235017 ACAAAC
1 ATAAAC
235023 AAACGAACGT
Statistics
Matches: 40, Mismatches: 13, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
23 13 0.32
24 27 0.68
ACGTcount: A:0.56, C:0.19, G:0.13, T:0.12
Consensus pattern (24 bp):
ATAAACGAACACAAATAAACGAAC
Found at i:235012 original size:13 final size:13
Alignment explanation
Indices: 234994--235054 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
234984 GTAAATGAAC
234994 ATAAACGAACACA
1 ATAAACGAACACA
235007 ATAAACGAACACAA
1 ATAAACGAACAC-A
*
235021 ACAAACG-A-AC-
1 ATAAACGAACACA
*
235031 GTAAACGAACACA
1 ATAAACGAACACA
*
235044 ATAAATGAACA
1 ATAAACGAACA
235055 TAAACGAACG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
10 5 0.13
11 1 0.03
12 4 0.10
13 22 0.56
14 7 0.18
ACGTcount: A:0.61, C:0.21, G:0.10, T:0.08
Consensus pattern (13 bp):
ATAAACGAACACA
Found at i:235014 original size:37 final size:37
Alignment explanation
Indices: 234990--235064 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
234980 TGATGTAAAT
234990 GAACATAAACGAACACAATAAACGAACACAAACAAAC
1 GAACATAAACGAACACAATAAACGAACACAAACAAAC
* * * *
235027 GAACGTAAACGAACACAATAAATGAACATAAACGAAC
1 GAACATAAACGAACACAATAAACGAACACAAACAAAC
235064 G
1 G
235065 TAAACGAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.59, C:0.21, G:0.12, T:0.08
Consensus pattern (37 bp):
GAACATAAACGAACACAATAAACGAACACAAACAAAC
Found at i:235058 original size:23 final size:24
Alignment explanation
Indices: 235007--235063 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
234997 AACGAACACA
235007 ATAAACGAACACAAACAAACGAAC
1 ATAAACGAACACAAACAAACGAAC
* * *
235031 GTAAACGAACAC-AATAAATGAAC
1 ATAAACGAACACAAACAAACGAAC
235054 ATAAACGAAC
1 ATAAACGAAC
235064 GTAAACGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.60, C:0.21, G:0.11, T:0.09
Consensus pattern (24 bp):
ATAAACGAACACAAACAAACGAAC
Found at i:235280 original size:14 final size:14
Alignment explanation
Indices: 235247--235289 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
235237 AGATTGGGCT
*
235247 AAACATAAATGAAC
1 AAACATAAACGAAC
**
235261 GCACATAAACGAAC
1 AAACATAAACGAAC
*
235275 AAACATAGACGAAC
1 AAACATAAACGAAC
235289 A
1 A
235290 TAAATAAATA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (14 bp):
AAACATAAACGAAC
Found at i:235690 original size:55 final size:55
Alignment explanation
Indices: 235596--235707 Score: 208
Period size: 55 Copynumber: 2.0 Consensus size: 55
235586 AATGAGACAG
235596 AAGAAGAGGAGGCTTCCATTTCAGACAGACCTTTCGCCATTATCAGATGAAAAGA
1 AAGAAGAGGAGGCTTCCATTTCAGACAGACCTTTCGCCATTATCAGATGAAAAGA
235651 AAGAAGAGGGAGGCTTCCATTTCAGACAGACC-TTCGCCATTATCAGATGAAAAGA
1 AAGAAGA-GGAGGCTTCCATTTCAGACAGACCTTTCGCCATTATCAGATGAAAAGA
235706 AA
1 AA
235708 ATGATCAGCC
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
55 32 0.57
56 24 0.43
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.21
Consensus pattern (55 bp):
AAGAAGAGGAGGCTTCCATTTCAGACAGACCTTTCGCCATTATCAGATGAAAAGA
Found at i:242571 original size:3 final size:3
Alignment explanation
Indices: 242563--242588 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
242553 AAGTTTCCAA
242563 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
242589 AATCATTAAT
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:244141 original size:31 final size:31
Alignment explanation
Indices: 244106--244166 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
244096 CAACATGTTA
244106 AGACTATGGCATATGTACACCGATTCAGATT
1 AGACTATGGCATATGTACACCGATTCAGATT
*
244137 AGACTATGGCATTTGTACACCGATTCAGAT
1 AGACTATGGCATATGTACACCGATTCAGAT
244167 ATGGACATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (31 bp):
AGACTATGGCATATGTACACCGATTCAGATT
Found at i:249980 original size:31 final size:31
Alignment explanation
Indices: 249942--250037 Score: 113
Period size: 31 Copynumber: 3.1 Consensus size: 31
249932 GAACCTCGGC
* *
249942 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
249973 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
250004 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
250035 AAC
1 AAC
250038 CCTCGACTCT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 50 0.94
32 3 0.06
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:250811 original size:64 final size:64
Alignment explanation
Indices: 250698--250862 Score: 201
Period size: 64 Copynumber: 2.6 Consensus size: 64
250688 TCTTTCAATG
* * *
250698 AATGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTT-TATTT-
1 AATGCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTA
* * *
250760 AATGGGGATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATT
1 AAT--GCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCC-ATTCGATGTTTTCTATT
250824 TA
63 TA
* * *
250826 AATTCATGCATCGATGCACTGCATGTGCATCGATGCA
1 AATGCATGCATCGATGCACTACTTGTGCATCGATGCA
250863 CCTTAAACAA
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
62 3 0.03
63 5 0.06
64 72 0.82
65 5 0.06
66 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (64 bp):
AATGCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTA
Found at i:252972 original size:20 final size:20
Alignment explanation
Indices: 252949--253010 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
252939 TGCTTTTCTT
252949 TTGTATTATGTTCTTTTGCG
1 TTGTATTATGTTCTTTTGCG
* * * * * *
252969 TTGTCTTTTATCCTATTGCTT
1 TTGTATTATGTTCTTTTGC-G
252990 TTGTATTATGTTCTTTTGCG
1 TTGTATTATGTTCTTTTGCG
253010 T
1 T
253011 CGTCTTTTAT
Statistics
Matches: 29, Mismatches: 12, Indels: 2
0.67 0.28 0.05
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.10, C:0.13, G:0.16, T:0.61
Consensus pattern (20 bp):
TTGTATTATGTTCTTTTGCG
Found at i:252993 original size:21 final size:21
Alignment explanation
Indices: 252964--253030 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 21
252954 TTATGTTCTT
252964 TTGC-GTTGTCTTTTATCCTA
1 TTGCTGTTGTCTTTTATCCTA
* * * * * *
252984 TTGCTTTTGTATTATGTTCTT
1 TTGCTGTTGTCTTTTATCCTA
*
253005 TTGC-GTCGTCTTTTATCCTA
1 TTGCTGTTGTCTTTTATCCTA
253025 TTGCTG
1 TTGCTG
253031 GAGGTGTAAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.09, C:0.18, G:0.16, T:0.57
Consensus pattern (21 bp):
TTGCTGTTGTCTTTTATCCTA
Found at i:253003 original size:41 final size:41
Alignment explanation
Indices: 252946--253029 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
252936 TGTTGCTTTT
*
252946 CTTTTGTATTATGTTCTTTTGCGTTGTCTTTTATCCTATTG
1 CTTTTGTATTATGTTCTTTTGCGTCGTCTTTTATCCTATTG
252987 CTTTTGTATTATGTTCTTTTGCGTCGTCTTTTATCCTATTG
1 CTTTTGTATTATGTTCTTTTGCGTCGTCTTTTATCCTATTG
253028 CT
1 CT
253030 GGAGGTGTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.10, C:0.17, G:0.14, T:0.60
Consensus pattern (41 bp):
CTTTTGTATTATGTTCTTTTGCGTCGTCTTTTATCCTATTG
Found at i:254822 original size:2 final size:2
Alignment explanation
Indices: 254815--254851 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
254805 AGTATGACAA
254815 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
254852 AAAGAAAAAC
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:260776 original size:19 final size:19
Alignment explanation
Indices: 260752--260800 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
260742 ATGACCAACA
260752 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
*
260771 AAATCGCAACGCGATCTCT
1 AAATCGCAATGCGATCTCT
*
260790 ATTATCGCAAT
1 A-AATCGCAAT
260801 TCAGTTCCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.27
Consensus pattern (19 bp):
AAATCGCAATGCGATCTCT
Found at i:260903 original size:20 final size:20
Alignment explanation
Indices: 260880--260918 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
260870 AGATAATCAC
260880 AATGCGAATATGTAAATCGT
1 AATGCGAATATGTAAATCGT
260900 AATGCGAATATGTAAATCG
1 AATGCGAATATGTAAATCG
260919 CAACGCGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (20 bp):
AATGCGAATATGTAAATCGT
Found at i:260926 original size:20 final size:20
Alignment explanation
Indices: 260883--260926 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
260873 TAATCACAAT
* *
260883 GCGAATATGTAAATCGTAAT
1 GCGAATATGTAAATCGCAAC
260903 GCGAATATGTAAATCGCAAC
1 GCGAATATGTAAATCGCAAC
260923 GCGA
1 GCGA
260927 TAACACTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (20 bp):
GCGAATATGTAAATCGCAAC
Found at i:260964 original size:20 final size:20
Alignment explanation
Indices: 260936--261037 Score: 125
Period size: 20 Copynumber: 5.0 Consensus size: 20
260926 ATAACACTTG
260936 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
260956 ATTGCAACGCGATTCGGACT
1 ATCGCAACGCGATTCTGACT
**
260976 ATCGCAACGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
*
260996 GATCGCAACGCGATTCTAACT
1 -ATCGCAACGCGATTCTGACT
*
261017 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
261037 A
1 A
261038 ACGTATCATT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.03
20 50 0.72
21 15 0.22
22 2 0.03
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:261002 original size:21 final size:19
Alignment explanation
Indices: 260915--261029 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 19
260905 GAATATGTAA
*
260915 ATCGCAACGCGATAACACTT
1 ATCGCAACGCGATAATAC-T
**
260935 GATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATAAT-ACT
* ***
260956 ATTGCAACGCGATTCGGACT
1 ATCGCAACGCGA-TAATACT
260976 ATCGCAACGCGATAATACGT
1 ATCGCAACGCGATAATAC-T
**
260996 GATCGCAACGCGATTCTAACT
1 -ATCGCAACGCGATAAT-ACT
*
261017 ATCGCAATGCGAT
1 ATCGCAACGCGAT
261030 TCTGACTAAC
Statistics
Matches: 75, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.04
20 38 0.51
21 30 0.40
22 4 0.05
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.23
Consensus pattern (19 bp):
ATCGCAACGCGATAATACT
Found at i:261010 original size:61 final size:61
Alignment explanation
Indices: 260915--261037 Score: 192
Period size: 61 Copynumber: 2.0 Consensus size: 61
260905 GAATATGTAA
* * *
260915 ATCGCAACGCGATAACACTTGATCGCAACGCGATTCTGACTATTGCAACGCGATTCGGACT
1 ATCGCAACGCGATAACACGTGATCGCAACGCGATTCTAACTATCGCAACGCGATTCGGACT
* * *
260976 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTAACTATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATAACACGTGATCGCAACGCGATTCTAACTATCGCAACGCGATTCGGACT
261037 A
1 A
261038 ACGTATCATT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (61 bp):
ATCGCAACGCGATAACACGTGATCGCAACGCGATTCTAACTATCGCAACGCGATTCGGACT
Found at i:261915 original size:24 final size:24
Alignment explanation
Indices: 261858--261917 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
261848 TAGTCGGTAT
261858 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* * *
261882 CCGTACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
*
261906 TCGAATTTTGAT
1 TCGAAATTTGAT
261918 GATGTTTCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:264443 original size:34 final size:33
Alignment explanation
Indices: 264390--264485 Score: 129
Period size: 34 Copynumber: 2.8 Consensus size: 33
264380 GAATATGACT
** *
264390 ATCGCAACGCGAATTTGACTATCGCAACGGGATA
1 ATCGCAACGC-AAAATGACTATCGCAACGAGATA
*
264424 ATCGCAATGCAAAAATGACTATCGCAACGAGATA
1 ATCGCAACGC-AAAATGACTATCGCAACGAGATA
*
264458 ATCGCAACGCGAAATGACTATCGCAACG
1 ATCGCAACGCAAAATGACTATCGCAACG
264486 CGAATTTGAC
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 17 0.31
34 38 0.69
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.18
Consensus pattern (33 bp):
ATCGCAACGCAAAATGACTATCGCAACGAGATA
Found at i:264589 original size:20 final size:20
Alignment explanation
Indices: 264362--264585 Score: 240
Period size: 20 Copynumber: 11.8 Consensus size: 20
264352 ATACACATTC
*
264362 ATTTGACTATCGTAACGCGA
1 ATTTGACTATCGCAACGCGA
*
264382 ATATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
264402 ATTTGACTATCGCAACG-GG
1 ATTTGACTATCGCAACGCGA
* *
264421 A--T-A--ATCGCAATGCAA
1 ATTTGACTATCGCAACGCGA
** *
264436 AAATGACTATCGCAACGAG-
1 ATTTGACTATCGCAACGCGA
264455 A--T-A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
264470 A-ATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
264489 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
264509 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
264529 ATTTGATTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
264549 ATTTGATTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
264569 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
264586 AGAAAATCGC
Statistics
Matches: 177, Mismatches: 15, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
14 18 0.10
15 2 0.01
16 3 0.02
17 4 0.02
18 1 0.01
19 16 0.09
20 133 0.75
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:264769 original size:30 final size:30
Alignment explanation
Indices: 264735--264800 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
264725 TTAAGCAAGC
264735 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
264765 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
264795 ACAAAT
1 ACAAAT
264801 CAACTCTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.29
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:266216 original size:21 final size:21
Alignment explanation
Indices: 266192--266256 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
266182 GGACATTTTC
266192 AACGATGACAGGGGCCTCTTG
1 AACGATGACAGGGGCCTCTTG
* ** *
266213 AACGGTGGGAGGGGACTCTTG
1 AACGATGACAGGGGCCTCTTG
** *
266234 AGGGATGATAGGGGCCTCTTG
1 AACGATGACAGGGGCCTCTTG
266255 AA
1 AA
266257 TGATAGGAGA
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (21 bp):
AACGATGACAGGGGCCTCTTG
Found at i:266275 original size:42 final size:42
Alignment explanation
Indices: 266195--266276 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
266185 CATTTTCAAC
* * *
266195 GATGACAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATAGGAGAGGACTCTTGAGG
* *
266237 GATGATAGGGGCCTCTTGAATGATAGGAGAGG-CTTCTTGA
1 GATGACAGGGGCCTCTTGAACGATAGGAGAGGAC-TCTTGA
266277 ATGATGAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.03
42 33 0.97
ACGTcount: A:0.22, C:0.15, G:0.40, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATAGGAGAGGACTCTTGAGG
Found at i:266789 original size:20 final size:20
Alignment explanation
Indices: 266764--266807 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
266754 AATAGTTTCT
266764 GAAACTTAAAATCGCAAAAC
1 GAAACTTAAAATCGCAAAAC
* *
266784 GAAACTTAAAATTGCAACAC
1 GAAACTTAAAATCGCAAAAC
266804 GAAA
1 GAAA
266808 ATGATTATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.18, G:0.11, T:0.16
Consensus pattern (20 bp):
GAAACTTAAAATCGCAAAAC
Found at i:266820 original size:20 final size:20
Alignment explanation
Indices: 266797--266866 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
266787 ACTTAAAATT
* *
266797 GCAACACGAAAATGATTATC
1 GCAACGCGAAAATGACTATC
**
266817 GCAACGCGAATTTGACTATC
1 GCAACGCGAAAATGACTATC
266837 GCAACGCG-AAATGACTATC
1 GCAACGCGAAAATGACTATC
266856 GCAACGCGAAA
1 GCAACGCGAAA
266867 CTAAATTCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.40
20 26 0.60
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:266853 original size:19 final size:19
Alignment explanation
Indices: 266806--266866 Score: 95
Period size: 19 Copynumber: 3.2 Consensus size: 19
266796 TGCAACACGA
*
266806 AAATGATTATCGCAACGCG
1 AAATGACTATCGCAACGCG
*
266825 AATTTGACTATCGCAACGCG
1 AA-ATGACTATCGCAACGCG
266845 AAATGACTATCGCAACGCG
1 AAATGACTATCGCAACGCG
266864 AAA
1 AAA
266867 CTAAATTCGC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 21 0.55
20 17 0.45
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (19 bp):
AAATGACTATCGCAACGCG
Found at i:266876 original size:19 final size:19
Alignment explanation
Indices: 266813--266876 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
266803 CGAAAATGAT
* * *
266813 TATCGCAACGCGAATTTGAC
1 TATCGCAACGCGAA-ATAAA
* *
266833 TATCGCAACGCGAAATGAC
1 TATCGCAACGCGAAATAAA
266852 TATCGCAACGCGAAACTAAA
1 TATCGCAACGCGAAA-TAAA
266872 T-TCGC
1 TATCGC
266877 GTTGCGATAG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (19 bp):
TATCGCAACGCGAAATAAA
Found at i:266920 original size:20 final size:20
Alignment explanation
Indices: 266869--266909 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
266859 ACGCGAAACT
*
266869 AAATTCGCGTTGCGATAGTC
1 AAATTCGCGTTGCGATAATC
266889 AAATTCGCGTTGCGATAATC
1 AAATTCGCGTTGCGATAATC
266909 A
1 A
266910 TTTTCGTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (20 bp):
AAATTCGCGTTGCGATAATC
Found at i:267095 original size:32 final size:31
Alignment explanation
Indices: 267036--267097 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
267026 CTACTACCGA
267036 ATGAATTTACTAAGCAATCCAAAAGACAAAT
1 ATGAATTTACTAAGCAATCCAAAAGACAAAT
*
267067 ATGAATTTACTAACTTCAA-CCAAAAGACAAA
1 ATGAATTTACTAA--GCAATCCAAAAGACAAA
267098 ACAAAGACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.46
32 12 0.43
33 3 0.11
ACGTcount: A:0.52, C:0.18, G:0.08, T:0.23
Consensus pattern (31 bp):
ATGAATTTACTAAGCAATCCAAAAGACAAAT
Found at i:268997 original size:19 final size:19
Alignment explanation
Indices: 268915--269006 Score: 85
Period size: 20 Copynumber: 4.7 Consensus size: 19
268905 GAAACTTAAA
* **
268915 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCG-AAATGACT
* *
268935 ATCGCAACACGAAAATGATT
1 ATCGCAACGCG-AAATGACT
* *
268955 ATCGCAACGTGAATTTGACT
1 ATCGCAACGCGAA-ATGACT
*
268975 ATCGCAACGCGAAATGGCT
1 ATCGCAACGCGAAATGACT
268994 ATCGCAACGCGAA
1 ATCGCAACGCGAA
269007 TTTTGTCGTT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
19 19 0.31
20 43 0.69
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:269366 original size:20 final size:21
Alignment explanation
Indices: 269341--269383 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
269331 TCTGAGAGAT
269341 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
*
269361 GGAGATGGGGACGGATTTCGCC
1 GGAGAT-GAGACGGATTTCGCC
269383 G
1 G
269384 TAGAGAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.21, C:0.19, G:0.42, T:0.19
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:269571 original size:20 final size:20
Alignment explanation
Indices: 269546--269672 Score: 141
Period size: 20 Copynumber: 6.2 Consensus size: 20
269536 TTATCGCAAC
*
269546 GCGATAGTCAGAATCTCGTT
1 GCGATAGTCAGAATCGCGTT
269566 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
**
269586 GCGATCACGT-ATTATCGCGTT
1 GCGAT-A-GTCAGAATCGCGTT
**
269607 GCGATCACGT-ATTATCGCGTT
1 GCGAT-A-GTCAGAATCGCGTT
* *
269628 GCGATAGTCCGAATGGCGTT
1 GCGATAGTCAGAATCGCGTT
269648 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
269668 GCGAT
1 GCGAT
269673 CAAGTGTTAT
Statistics
Matches: 95, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
19 2 0.02
20 55 0.58
21 36 0.38
22 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:269604 original size:21 final size:20
Alignment explanation
Indices: 269578--269693 Score: 110
Period size: 21 Copynumber: 5.7 Consensus size: 20
269568 GATAGTCAGA
269578 ATCGCGTTGCGATCACGTATT
1 ATCGCGTTGCGATCA-GTATT
269599 ATCGCGTTGCGATCACGTATT
1 ATCGCGTTGCGATCA-GTATT
***
269620 ATCGCGTTGCGAT-AGTCCGA
1 ATCGCGTTGCGATCAGT-ATT
* **
269640 ATGGCGTTGCGAT-AGTCAGA
1 ATCGCGTTGCGATCAGT-ATT
*
269660 ATCGCGTTGCGATCAAGTGTT
1 ATCGCGTTGCGATC-AGTATT
269681 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
269694 TTATATATTC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 31 0.37
21 47 0.57
22 3 0.04
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (20 bp):
ATCGCGTTGCGATCAGTATT
Found at i:269710 original size:20 final size:20
Alignment explanation
Indices: 269682--269734 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
269672 TCAAGTGTTA
* *
269682 TCGCGTTGCGATTTATATAT
1 TCGCATTGCGATTTACATAT
269702 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
269722 TTGCATTGCGATT
1 TCGCATTGCGATT
269735 ATCTAAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:276151 original size:2 final size:2
Alignment explanation
Indices: 276144--276172 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
276134 AAGAAAATGA
276144 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
276173 TTTCAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:278780 original size:353 final size:348
Alignment explanation
Indices: 278139--278839 Score: 1339
Period size: 353 Copynumber: 2.0 Consensus size: 348
278129 GAATACCTAC
278139 TACATGCGTACAAGAATGTCAAATTGACAATATATATTATATGCATTGGTGGAACATCGTGGGGG
1 TACATGCGTACAAGAATGTCAAATTGACAATATATATTATATGCATTGGTGGAACATCGTGGGGG
*
278204 GGGGGGGCAAGGGAGCCTTGGTCTCCGCCAATATTTTTTTTAAATATTAATTAATATTAAATATA
66 GGGGGGGCAAGGGAGCCTTGGTCTCCGCCAATAATTTTTTTAAATATTAATTAATATTAAATATA
278269 TATATATATATATTAAAAAAATAAATAAAGAACAAAAATTTATCAGTTTCTCTAAATTTTAAAAA
131 TATATATATATATTAAAAAAATAAATAAAGAACAAAAATTTATCAGTTTCTCTAAATTTTAAAAA
278334 ATATTTTATTTATAAAAAATAAAAAATACTTTAACCTTATCTACTATAATAAATTTCTAGTTCCG
196 ATATTTTATTTATAAAAAATAAAAAATACTTTAACCTTATCTACTATAATAAATTTCTAGTTCCG
278399 CCTATCATATGACCCACTATAATTGAGTAGTCGACTATGTTAGCTTAGATGCCCCTACAATAAGG
261 CCTATCATATGACCCACTATAATTGAGTAGTCGACTATGTTAGCTTAGATGCCCCTACAATAAGG
278464 GTTGGTAAACATTAGAAATCGTA
326 GTTGGTAAACATTAGAAATCGTA
278487 TACATGCGTACAAGAATGTCAAATTGACAATATATATTATATGCATTGGTGGAACATCGTGGGGG
1 TACATGCGTACAAGAATGTCAAATTGACAATATATATTATATGCATTGGTGGAACATCGT-GGGG
278552 GGGGGGGGCAAGGGAGCCTTGGTCTCCGCCAATAATTTTTTTAAATATTAATTAATATTAAATAT
65 GGGGGGGGCAAGGGAGCCTTGGTCTCCGCCAATAATTTTTTTAAATATTAATTAATATT--A-A-
278617 ATATATATATATATATATTAAAAAAATAAATAAAGAACAAAAATTTATCAGTTTCTCTAAATTTT
126 ATATATATATATATATATTAAAAAAATAAATAAAGAACAAAAATTTATCAGTTTCTCTAAATTTT
278682 AAAAAATATTTTATTTATAAAAAATAAAAAATACTTTAACCTTATCTACTATAATAAATTTCTAG
191 AAAAAATATTTTATTTATAAAAAATAAAAAATACTTTAACCTTATCTACTATAATAAATTTCTAG
*
278747 TTCCGCCTATCATATGACCCACTATAATTGAGTAGTCGACTATGTTAGCTTAGATGTCCCTACAA
256 TTCCGCCTATCATATGACCCACTATAATTGAGTAGTCGACTATGTTAGCTTAGATGCCCCTACAA
278812 TAAGGGTTGGTAAACATTAGAAATCGTA
321 TAAGGGTTGGTAAACATTAGAAATCGTA
278840 AGCCGAAAAA
Statistics
Matches: 346, Mismatches: 2, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
348 60 0.17
349 62 0.18
351 1 0.00
352 1 0.00
353 222 0.64
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (348 bp):
TACATGCGTACAAGAATGTCAAATTGACAATATATATTATATGCATTGGTGGAACATCGTGGGGG
GGGGGGGCAAGGGAGCCTTGGTCTCCGCCAATAATTTTTTTAAATATTAATTAATATTAAATATA
TATATATATATATTAAAAAAATAAATAAAGAACAAAAATTTATCAGTTTCTCTAAATTTTAAAAA
ATATTTTATTTATAAAAAATAAAAAATACTTTAACCTTATCTACTATAATAAATTTCTAGTTCCG
CCTATCATATGACCCACTATAATTGAGTAGTCGACTATGTTAGCTTAGATGCCCCTACAATAAGG
GTTGGTAAACATTAGAAATCGTA
Found at i:285416 original size:2 final size:2
Alignment explanation
Indices: 285411--285465 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
285401 CCATATATGC
285411 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
285453 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
285466 AAAAATAAAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:285565 original size:17 final size:17
Alignment explanation
Indices: 285516--285565 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
285506 TTGTTCATGT
285516 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
*
285533 TTTGAG----TATCAATG
1 TTTG-GTTTCTATGAATG
285547 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
285564 TT
1 TT
285566 AGAAGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
17 13 0.50
18 1 0.04
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.52
Consensus pattern (17 bp):
TTTGGTTTCTATGAATG
Found at i:286537 original size:4 final size:4
Alignment explanation
Indices: 286528--286554 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
286518 ATGTAATTGT
286528 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
286555 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:286795 original size:35 final size:37
Alignment explanation
Indices: 286748--286818 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 37
286738 TTAAAACAAA
*
286748 AATAATATATTCAATTCA-ATTAAAAATATA-AATTAC
1 AATAATATATTCAA-ACATATTAAAAATATATAATTAC
*
286784 AATAAT-TATTCAAACATATTAAAATTATATAATTA
1 AATAATATATTCAAACATATTAAAAATATATAATTA
286819 TAATTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 2 0.06
35 18 0.58
36 11 0.35
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (37 bp):
AATAATATATTCAAACATATTAAAAATATATAATTAC
Found at i:292023 original size:184 final size:181
Alignment explanation
Indices: 291705--292089 Score: 619
Period size: 184 Copynumber: 2.1 Consensus size: 181
291695 ATTAAATTTT
* * * *
291705 AAATTTTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAATCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATAGGCTAAACCCAAACCATTTAAAACCCAATTAATAA
*
291770 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
*
291835 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTTAATTAAA
131 TTATTTTATAA-T-TATA-TATTTAAATTAATTATAAACTATTTTTTAATTAAA
*
291889 AAATATTATATATATTATATATAACATATAGGCTAAACCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATAGGCTAAACCCAAACCATTTAAAACCCAATTAATAA
* *
291954 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATCTGAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
*
292019 TTATTTTATAATTATATATTTAAATTAATTATAAACTTTTTTTTAATTAAA
131 TTATTTTATAATTATATATTTAAATTAATTATAAACTATTTTTTAATTAAA
* * *
292070 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
292090 AATTAGAAAA
Statistics
Matches: 187, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
180 8 0.04
181 41 0.22
182 4 0.02
183 1 0.01
184 133 0.71
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (181 bp):
AAATATTAAATATATTATATATAACATATAGGCTAAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
TTATTTTATAATTATATATTTAAATTAATTATAAACTATTTTTTAATTAAA
Found at i:294184 original size:24 final size:23
Alignment explanation
Indices: 294130--294216 Score: 72
Period size: 23 Copynumber: 3.7 Consensus size: 23
294120 GTTAGTTTAC
* *
294130 GTTCGTTTATGTTCATT-TATTGT
1 GTTCGTTTACGTTCGTTAT-TTGT
*
294153 G-TCTGTTTACGTTCGTTCGTTTGT
1 GTTC-GTTTACGTTCGTT-ATTTGT
*
294177 GTTCGTTTACATTCGTATATTT-T
1 GTTCGTTTACGTTCGT-TATTTGT
*
294200 GTTCGTTTATGTTCGTT
1 GTTCGTTTACGTTCGTT
294217 TACATCCGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
22 3 0.06
23 27 0.51
24 19 0.36
25 4 0.08
ACGTcount: A:0.10, C:0.13, G:0.20, T:0.57
Consensus pattern (23 bp):
GTTCGTTTACGTTCGTTATTTGT
Found at i:294213 original size:33 final size:34
Alignment explanation
Indices: 294167--294243 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 34
294157 GTTTACGTTC
* *
294167 GTTCGTTTGTGTTCGTTTACATTCGTAT-ATTT-T
1 GTTCGTTTATGTTCGTTTACATCCGT-TCATTTAT
*
294200 GTTCGTTTATGTTCGTTTACATCCGTTCGTTTAT
1 GTTCGTTTATGTTCGTTTACATCCGTTCATTTAT
294234 GTTCGTTTAT
1 GTTCGTTTAT
294244 TATTTAATTG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 27 0.69
34 11 0.28
ACGTcount: A:0.12, C:0.14, G:0.18, T:0.56
Consensus pattern (34 bp):
GTTCGTTTATGTTCGTTTACATCCGTTCATTTAT
Found at i:294214 original size:10 final size:10
Alignment explanation
Indices: 294115--294243 Score: 69
Period size: 10 Copynumber: 11.5 Consensus size: 10
294105 TATTTTTTCA
*
294115 TTTATGTTAG
1 TTTATGTTCG
*
294125 TTTACGTTCG
1 TTTATGTTCG
*
294135 TTTATGTTCA
1 TTTATGTTCG
294145 TTTATTGTGTCTG
1 TTTA-TGT-TC-G
294158 TTTACGTTCGTTCG
1 TTTA---T-GTTCG
*
294172 TTTGTGTTCG
1 TTTATGTTCG
**
294182 TTTACATTCG
1 TTTATGTTCG
*
294192 TATATTTTGTTCG
1 --T-TTATGTTCG
294205 TTTATGTTCG
1 TTTATGTTCG
294215 TTTACATCCGTTCG
1 TTT--AT--GTTCG
294229 TTTATGTTCG
1 TTTATGTTCG
294239 TTTAT
1 TTTAT
294244 TATTTAATTG
Statistics
Matches: 93, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
10 53 0.57
11 5 0.05
12 7 0.08
13 10 0.11
14 12 0.13
15 4 0.04
16 2 0.02
ACGTcount: A:0.12, C:0.13, G:0.18, T:0.57
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:294267 original size:15 final size:15
Alignment explanation
Indices: 294247--294277 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
294237 CGTTTATTAT
294247 TTAATTGAACGAACA
1 TTAATTGAACGAACA
294262 TTAATTGAACGAACA
1 TTAATTGAACGAACA
294277 T
1 T
294278 GAACGAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (15 bp):
TTAATTGAACGAACA
Found at i:294282 original size:10 final size:10
Alignment explanation
Indices: 294267--294291 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
294257 GAACATTAAT
294267 TGAACGAACA
1 TGAACGAACA
294277 TGAACGAACA
1 TGAACGAACA
294287 TGAAC
1 TGAAC
294292 AAGCTACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.12
Consensus pattern (10 bp):
TGAACGAACA
Found at i:314109 original size:15 final size:15
Alignment explanation
Indices: 314089--314119 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
314079 CATGTATCTT
314089 ACCTGTAATCTTATC
1 ACCTGTAATCTTATC
314104 ACCTGTAATCTTATC
1 ACCTGTAATCTTATC
314119 A
1 A
314120 AATTAATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39
Consensus pattern (15 bp):
ACCTGTAATCTTATC
Found at i:328671 original size:83 final size:80
Alignment explanation
Indices: 328535--328694 Score: 257
Period size: 83 Copynumber: 2.0 Consensus size: 80
328525 ATCGATTCTC
* * *
328535 CACATCTGCATTAGTTAAATACAACTTATAGTATTTATTTTTTATTTCCATGTACTTATAATACA
1 CACATCTGCATTAATTAAATACAACTTATAGTATTAATATTTTATTTCCATGTACTTATAATACA
*
328600 TGTAACATATTTGGT
66 CGTAACATATTTGGT
328615 CACATCTGCATTAATTAAATAATGCAACTTATAGTATTAATATTTTATTTCCATGTACTTATAAT
1 CACATCTGCATTAATTAAAT-A--CAACTTATAGTATTAATATTTTATTTCCATGTACTTATAAT
328680 ACACGTAACATATTT
63 ACACGTAACATATTT
328695 ACGTAGGTCA
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
80 19 0.26
81 1 0.01
83 53 0.73
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.43
Consensus pattern (80 bp):
CACATCTGCATTAATTAAATACAACTTATAGTATTAATATTTTATTTCCATGTACTTATAATACA
CGTAACATATTTGGT
Found at i:332559 original size:21 final size:21
Alignment explanation
Indices: 332533--332577 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
332523 GATTTCTGGG
* *
332533 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
332554 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
332575 CAA
1 CAA
332578 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Done.