Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006483.1 Hibiscus syriacus cultivar Beakdansim tig00015742_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: 67522
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:468 original size:43 final size:43
Alignment explanation
Indices: 367--520 Score: 150
Period size: 42 Copynumber: 3.6 Consensus size: 43
357 GAACATGCAA
**
367 AAACGGTAAGGTCTTACCCTTGCACTTAGCAAAAGAGCCT-GGG
1 AAACGGTAAGG-CTTACCCTTGCACACAGCAAAAGAGCCTGGGG
** * * *
410 AAACTATAAAGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
1 AAACGGTAAGGCTTACCCTTGCACACAGCAAAAGAGCCTGGGG
* * * *
453 AAACTGTAAGGCTTA-CCTTGCACACAGTAAATGAGCCTGTGG
1 AAACGGTAAGGCTTACCCTTGCACACAGCAAAAGAGCCTGGGG
* * *
495 TAACGGTAAAGACTTAACCTTGCACA
1 AAACGGT-AAGGCTTACCCTTGCACA
521 TAACAGAGGA
Statistics
Matches: 92, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
42 52 0.57
43 31 0.34
44 9 0.10
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (43 bp):
AAACGGTAAGGCTTACCCTTGCACACAGCAAAAGAGCCTGGGG
Found at i:11992 original size:13 final size:13
Alignment explanation
Indices: 11974--11998 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11964 ATCAGTTTAT
11974 ATATATATATATA
1 ATATATATATATA
11987 ATATATATATAT
1 ATATATATATAT
11999 GTAAGTCGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATATATATA
Found at i:15216 original size:14 final size:15
Alignment explanation
Indices: 15194--15235 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
15184 ATTTTTATTT
*
15194 TAATGTAAAATAT-A
1 TAATTTAAAATATCA
*
15208 TAATTTAAAATATCT
1 TAATTTAAAATATCA
*
15223 TAAATTAAAATAT
1 TAATTTAAAATAT
15236 TATTATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
TAATTTAAAATATCA
Found at i:15258 original size:25 final size:25
Alignment explanation
Indices: 15229--15300 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 25
15219 ATCTTAAATT
15229 AAAATATTATTATTATTATAATATA
1 AAAATATTATTATTATTATAATATA
15254 AAAATATATATT-TTATTATTTAATATA
1 AAAATAT-TATTATTATTA--TAATATA
*
15281 AAATATATTTTTATTATTAT
1 AAA-ATATTATTATTATTAT
15301 CTTCACTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
25 13 0.32
26 5 0.12
27 13 0.32
28 10 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
AAAATATTATTATTATTATAATATA
Found at i:15289 original size:53 final size:54
Alignment explanation
Indices: 15172--15300 Score: 131
Period size: 53 Copynumber: 2.4 Consensus size: 54
15162 CTTACCTTAT
* * * *
15172 TAAATATATTTTATTTTTATTTTAATGTAAAATATATAATTTAAAATATCTTAAA
1 TAAA-ATATATTATTATTATTATAATATAAAATATATAATTTAAAATATCTTAAA
* * *
15227 TTAAA-ATATTATTATTATTATAATATAAAA-ATATATATTT-TATTAT-TTAATA
1 TAAAATATATTATTATTATTATAATATAAAATATATA-ATTTAAAATATCTTAA-A
*
15279 TAAAATATATTTTTATTATTAT
1 TAAAATATATTATTATTATTAT
15301 CTTCACTTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
51 4 0.06
52 14 0.23
53 40 0.65
54 1 0.02
55 3 0.05
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.53
Consensus pattern (54 bp):
TAAAATATATTATTATTATTATAATATAAAATATATAATTTAAAATATCTTAAA
Found at i:15302 original size:80 final size:82
Alignment explanation
Indices: 15173--15323 Score: 184
Period size: 80 Copynumber: 1.9 Consensus size: 82
15163 TTACCTTATT
* * *
15173 AAATATATTTTATTTTTATTTTAATGTAAAATATATAATTTAAAATATCTTAAATT-AAAATATT
1 AAATATATATTATTATTATTTTAATATAAAATATATAATTTAAAATATCTTAAATTAAAAATATT
15237 ATTATTATTATAATATAA
66 -TTATTATTATAATATAA
* * * * *
15255 AAATATATATT-TTATTA-TTTAATATAAAATATAT-TTTTATTATTATCTTCACTTAAAAATAT
1 AAATATATATTATTATTATTTTAATATAAAATATATAATTTA-AAATATCTTAAATTAAAAATAT
15317 TTTATTA
65 TTTATTA
15324 CTACTTAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
79 4 0.07
80 32 0.54
81 13 0.22
82 10 0.17
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.52
Consensus pattern (82 bp):
AAATATATATTATTATTATTTTAATATAAAATATATAATTTAAAATATCTTAAATTAAAAATATT
TTATTATTATAATATAA
Found at i:15553 original size:26 final size:26
Alignment explanation
Indices: 15524--15584 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
15514 ATATTATAAT
15524 AATAAAAAAAATATTTAATAAGTTAA-
1 AATAAAAAAAATATTTAA-AAGTTAAG
* * *
15550 AATAAAATATATTTTTAAAAGTTAAG
1 AATAAAAAAAATATTTAAAAGTTAAG
*
15576 AATATAAAA
1 AATAAAAAA
15585 TATTGTTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 7 0.24
26 22 0.76
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (26 bp):
AATAAAAAAAATATTTAAAAGTTAAG
Found at i:15556 original size:22 final size:20
Alignment explanation
Indices: 15514--15559 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
15504 AATATTTTTT
15514 ATATTATAATAATAAAAAAA
1 ATATTATAATAATAAAAAAA
15534 ATATT-TAATAAGTTAAAATAAA
1 ATATTATAATAA--TAAAA-AAA
15556 ATAT
1 ATAT
15560 ATTTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.26
20 5 0.22
21 5 0.22
22 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
ATATTATAATAATAAAAAAA
Found at i:15587 original size:26 final size:26
Alignment explanation
Indices: 15537--15594 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
15527 AAAAAAAATA
15537 TTTAATAAGTTAAAATAAAATATATT
1 TTTAATAAGTTAAAATAAAATATATT
15563 TTTAA-AAGTTAAGAATATAAA-ATATT
1 TTTAATAAGTTAA-AATA-AAATATATT
*
15589 GTTAAT
1 TTTAAT
15595 TTAAGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 7 0.25
26 18 0.64
27 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (26 bp):
TTTAATAAGTTAAAATAAAATATATT
Found at i:15930 original size:28 final size:28
Alignment explanation
Indices: 15898--15954 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
15888 CGATTAAATC
15898 AAAACATCAATGGTAAAAATGAAATCTG
1 AAAACATCAATGGTAAAAATGAAATCTG
15926 AAAACATCAATGGTAAAAATGAAATCTG
1 AAAACATCAATGGTAAAAATGAAATCTG
15954 A
1 A
15955 TAATTGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.54, C:0.11, G:0.14, T:0.21
Consensus pattern (28 bp):
AAAACATCAATGGTAAAAATGAAATCTG
Found at i:16375 original size:186 final size:186
Alignment explanation
Indices: 16060--16434 Score: 567
Period size: 186 Copynumber: 2.0 Consensus size: 186
16050 CCTCTTCTAT
* * *
16060 TTTGATCACTAAACTTTAAAAATTTTAATTTAATCATTGAATTTCAGAATTGCTCTTATTTTGGT
1 TTTGATCACTAAACTTTAAAAATTTTAATTTAATCATTGAACTTCAGAATTGCTCCTATTTTAGT
* * * * **
16125 CACTTCGCCGTTAAATAGTTAACGGCGTTATGTCATGACACACGAAATCAAAATGATGTCATTTT
66 CACTTCGCCATTAAATAGTTAACGACGTTATGACATGACACAAGAAATCAAAATGACATCATTTT
*
16190 GAAAAAAA-AA-ATTACATCAAAACGACATAGTTTTGAATCCCGTATAAAATCATA
131 GAAAAAAATAAGATTACATCAAAACGACATAGTTTTGAATCCCATATAAAATCATA
** *
16244 TTTGATCACTGCACTTTAAAAGTTTTTCAATTTAATCATTGAACTTCAGAATTGCTCCTATTTTA
1 TTTGATCACTAAACTTTAAAA-ATTTT-AATTTAATCATTGAACTTCAGAATTGCTCCTATTTTA
*
16309 GTCAC-TCTGCCATTAAATAGTTAACGACGTTATGACATGTCACAAGAAATCAAAATGACATCAT
64 GTCACTTC-GCCATTAAATAGTTAACGACGTTATGACATGACACAAGAAATCAAAATGACATCAT
*
16373 TTTGAAAAAAATAAGTTTACATCAAAACGACATAGTTTTGAATCCCATATAAAATCATA
128 TTTGAAAAAAATAAGATTACATCAAAACGACATAGTTTTGAATCCCATATAAAATCATA
16432 TTT
1 TTT
16435 TCTCCGTATA
Statistics
Matches: 171, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
184 19 0.11
185 6 0.04
186 99 0.58
187 2 0.01
188 45 0.26
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (186 bp):
TTTGATCACTAAACTTTAAAAATTTTAATTTAATCATTGAACTTCAGAATTGCTCCTATTTTAGT
CACTTCGCCATTAAATAGTTAACGACGTTATGACATGACACAAGAAATCAAAATGACATCATTTT
GAAAAAAATAAGATTACATCAAAACGACATAGTTTTGAATCCCATATAAAATCATA
Found at i:17275 original size:11 final size:11
Alignment explanation
Indices: 17259--17283 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17249 CATTGAAAAT
17259 AATATTAATAA
1 AATATTAATAA
17270 AATATTAATAA
1 AATATTAATAA
17281 AAT
1 AAT
17284 TCTACGTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATATTAATAA
Found at i:18824 original size:17 final size:18
Alignment explanation
Indices: 18787--18825 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
18777 TAAAATATAT
18787 AAATTATTAAATTAAATA
1 AAATTATTAAATTAAATA
*
18805 AAATT-TTAAATTAGATA
1 AAATTATTAAATTAAATA
18822 AAAT
1 AAAT
18826 ATAAACTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
AAATTATTAAATTAAATA
Found at i:18947 original size:49 final size:50
Alignment explanation
Indices: 18856--18957 Score: 197
Period size: 49 Copynumber: 2.1 Consensus size: 50
18846 AAAATATTTA
18856 TATCTATATTTTGCATTTATAAATATTTGGTGTTCTTATACATTCAAAAT
1 TATCTATATTTTGCATTTATAAATATTTGGTGTTCTTATACATTCAAAAT
18906 TATCTATATTTTGCATTTAT-AATATTTGGTGTTCTTATACATTCAAAAT
1 TATCTATATTTTGCATTTATAAATATTTGGTGTTCTTATACATTCAAAAT
18955 TAT
1 TAT
18958 ATTTCCTCTT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 32 0.62
50 20 0.38
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (50 bp):
TATCTATATTTTGCATTTATAAATATTTGGTGTTCTTATACATTCAAAAT
Found at i:18974 original size:45 final size:48
Alignment explanation
Indices: 18859--18975 Score: 161
Period size: 49 Copynumber: 2.5 Consensus size: 48
18849 ATATTTATAT
*
18859 CTATATTTTGCATTTATAAATATTTGGTGTTCTTATACATTCAAAATTA
1 CTATATTCTGCATTTAT-AATATTTGGTGTTCTTATACATTCAAAATTA
*
18908 TCTATATTTTGCATTTATAATATTTGGTGTTCTTATACATTCAAAATTA
1 -CTATATTCTGCATTTATAATATTTGGTGTTCTTATACATTCAAAATTA
18957 -TAT-TTCCT-C-TTTATAATAT
1 CTATATT-CTGCATTTATAATAT
18976 ATACGTTAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
45 10 0.15
46 3 0.05
47 4 0.06
49 31 0.48
50 17 0.26
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (48 bp):
CTATATTCTGCATTTATAATATTTGGTGTTCTTATACATTCAAAATTA
Found at i:19389 original size:26 final size:25
Alignment explanation
Indices: 19336--19389 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
19326 ACTATATCTC
*
19336 TTTTTTCATTTAGGTATCTAAACTT
1 TTTTTTCATTTAGGTATCTAAACGT
*
19361 TTTTTGTCAATTTAGGTGTCT-AACGT
1 TTTTT-TC-ATTTAGGTATCTAAACGT
19387 TTT
1 TTT
19390 CAACATTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.20
26 9 0.36
27 11 0.44
ACGTcount: A:0.20, C:0.11, G:0.13, T:0.56
Consensus pattern (25 bp):
TTTTTTCATTTAGGTATCTAAACGT
Found at i:19913 original size:24 final size:24
Alignment explanation
Indices: 19868--19918 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
19858 GTTTTTTTGA
** *
19868 AAAATAATAATTTTAAGTATTTTT
1 AAAATAATAATTTTAAAAATTTAT
19892 AAAATAA-AATTTTAAAAAATTTAT
1 AAAATAATAATTTT-AAAAATTTAT
19916 AAA
1 AAA
19919 CATGCCACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
AAAATAATAATTTTAAAAATTTAT
Found at i:20191 original size:26 final size:28
Alignment explanation
Indices: 20162--20227 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 28
20152 CTCAAAATTT
*
20162 AAAATTATATAATTA-ATTTAAAAA-TA
1 AAAATTATATAATTACATTAAAAAACTA
20188 AAAATTATAT--TTACATTAAAAAACTA
1 AAAATTATATAATTACATTAAAAAACTA
*
20214 AAACAATATATAAT
1 AAA-ATTATATAAT
20228 CTTAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
24 3 0.09
25 8 0.24
26 15 0.45
27 6 0.18
29 1 0.03
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.35
Consensus pattern (28 bp):
AAAATTATATAATTACATTAAAAAACTA
Found at i:20199 original size:19 final size:19
Alignment explanation
Indices: 20157--20200 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
20147 ATCGCCTCAA
* *
20157 AATTTAAAATTATATAATT
1 AATTTAAAAATATAAAATT
20176 AATTTAAAAATA-AAAATT
1 AATTTAAAAATATAAAATT
20194 ATATTTA
1 A-ATTTA
20201 CATTAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTTAAAAATATAAAATT
Found at i:21380 original size:41 final size:42
Alignment explanation
Indices: 21303--21381 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 42
21293 GAAAATGTAT
*
21303 GTTAAATTTGTATGAGTATTTACATGAAAAATGTATGTACAG
1 GTTAAATTTGTATGAGTATGTACATGAAAAATGTATGTACAG
* *
21345 GTTAAATTTGTAT-ATTATGTACATGGAAAATGTATGT
1 GTTAAATTTGTATGAGTATGTACATGAAAAATGTATGT
21382 TTGTATGTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 21 0.62
42 13 0.38
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.41
Consensus pattern (42 bp):
GTTAAATTTGTATGAGTATGTACATGAAAAATGTATGTACAG
Found at i:21462 original size:62 final size:62
Alignment explanation
Indices: 21345--21465 Score: 156
Period size: 62 Copynumber: 2.0 Consensus size: 62
21335 GTATGTACAG
* ** ***
21345 GTTAAATTTGTATATTATGTACATGGAAAATGTATGTTTGTATGTGTTTTGCTTACGAAAAC
1 GTTAAATTTGTATATTATGTACATGAAAAATGTATGTAGGTATAAATTTTGCTTACGAAAAC
21407 GTTAAATTTGTATATTATGTACATGAAAAATGTATGTACAGGT-TAAATTTT-CTTACGAA
1 GTTAAATTTGTATATTATGTACATGAAAAATGTATGT--AGGTATAAATTTTGCTTACGAA
21466 CATTGACTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
62 44 0.86
63 5 0.10
64 2 0.04
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (62 bp):
GTTAAATTTGTATATTATGTACATGAAAAATGTATGTAGGTATAAATTTTGCTTACGAAAAC
Found at i:25510 original size:18 final size:18
Alignment explanation
Indices: 25484--25518 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25474 TCGAAAGAAC
*
25484 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
25502 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
25519 CCGGATGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:28243 original size:25 final size:25
Alignment explanation
Indices: 28209--28260 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
28199 CCTAATCAAA
*
28209 TTATGAAATTTAAACCGAGCTATGC
1 TTATAAAATTTAAACCGAGCTATGC
28234 TTATAAAATTTAAACCGAGCTATGC
1 TTATAAAATTTAAACCGAGCTATGC
28259 TT
1 TT
28261 GTGAGATATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (25 bp):
TTATAAAATTTAAACCGAGCTATGC
Found at i:28712 original size:2 final size:2
Alignment explanation
Indices: 28707--28733 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28697 TAATGACAAT
28707 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 T
28734 TAAATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29381 original size:26 final size:26
Alignment explanation
Indices: 29349--29415 Score: 98
Period size: 26 Copynumber: 2.6 Consensus size: 26
29339 TAAAAAATAT
*
29349 ATTTATAAAATTTTAGGAGATGATAA
1 ATTTATAAAATTTTAGGAGACGATAA
* * *
29375 ATTTATAAAATTTTAGGAGGCGGTGA
1 ATTTATAAAATTTTAGGAGACGATAA
29401 ATTTATAAAATTTTA
1 ATTTATAAAATTTTA
29416 AGAGTGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.42, C:0.01, G:0.16, T:0.40
Consensus pattern (26 bp):
ATTTATAAAATTTTAGGAGACGATAA
Found at i:31643 original size:3 final size:3
Alignment explanation
Indices: 31635--31682 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
31625 CCGAGTCTTT
31635 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31681 TT
1 TT
31683 TATTTACAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:31930 original size:12 final size:12
Alignment explanation
Indices: 31913--31937 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31903 CTAACCCTAG
31913 GGATATCATTTT
1 GGATATCATTTT
31925 GGATATCATTTT
1 GGATATCATTTT
31937 G
1 G
31938 TTACCGCCGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (12 bp):
GGATATCATTTT
Found at i:34761 original size:154 final size:154
Alignment explanation
Indices: 34550--34858 Score: 618
Period size: 154 Copynumber: 2.0 Consensus size: 154
34540 ATAACATGAG
34550 CTCTAGACACGAGCTTCGATTCAAATTAGTCAGGGTGATTGCTTTACTCTTGTAAGAATTTATTC
1 CTCTAGACACGAGCTTCGATTCAAATTAGTCAGGGTGATTGCTTTACTCTTGTAAGAATTTATTC
34615 TTCGTATGAGTTTTAGCAAATAACCCATGGGATACATACTTTATACCTTCGTAGGGATTTATTCC
66 TTCGTATGAGTTTTAGCAAATAACCCATGGGATACATACTTTATACCTTCGTAGGGATTTATTCC
34680 TCGTATGGGTATAAGGCAATGAAT
131 TCGTATGGGTATAAGGCAATGAAT
34704 CTCTAGACACGAGCTTCGATTCAAATTAGTCAGGGTGATTGCTTTACTCTTGTAAGAATTTATTC
1 CTCTAGACACGAGCTTCGATTCAAATTAGTCAGGGTGATTGCTTTACTCTTGTAAGAATTTATTC
34769 TTCGTATGAGTTTTAGCAAATAACCCATGGGATACATACTTTATACCTTCGTAGGGATTTATTCC
66 TTCGTATGAGTTTTAGCAAATAACCCATGGGATACATACTTTATACCTTCGTAGGGATTTATTCC
34834 TCGTATGGGTATAAGGCAATGAAT
131 TCGTATGGGTATAAGGCAATGAAT
34858 C
1 C
34859 CCCTCGAATT
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
154 155 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (154 bp):
CTCTAGACACGAGCTTCGATTCAAATTAGTCAGGGTGATTGCTTTACTCTTGTAAGAATTTATTC
TTCGTATGAGTTTTAGCAAATAACCCATGGGATACATACTTTATACCTTCGTAGGGATTTATTCC
TCGTATGGGTATAAGGCAATGAAT
Found at i:37214 original size:25 final size:24
Alignment explanation
Indices: 37178--37224 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
37168 CAAATCAAAG
37178 AGAACAAAGAAAAAAACAAAGAGA
1 AGAACAAAGAAAAAAACAAAGAGA
* *
37202 AGAAGCAAAGAAAAGAGCAAAGA
1 AGAA-CAAAGAAAAAAACAAAGA
37225 AAAAGATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.70, C:0.09, G:0.21, T:0.00
Consensus pattern (24 bp):
AGAACAAAGAAAAAAACAAAGAGA
Found at i:37230 original size:13 final size:12
Alignment explanation
Indices: 37182--37227 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
37172 TCAAAGAGAA
* *
37182 CAAAGAAAAAAA
1 CAAAGAAAAGAG
*
37194 CAAAGAGAAGAAG
1 CAAAGAAAAG-AG
37207 CAAAGAAAAGAG
1 CAAAGAAAAGAG
37219 CAAAGAAAA
1 CAAAGAAAA
37228 AGATAACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.72, C:0.09, G:0.20, T:0.00
Consensus pattern (12 bp):
CAAAGAAAAGAG
Found at i:38329 original size:33 final size:32
Alignment explanation
Indices: 38269--38331 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
38259 AAGAAATATT
* *
38269 GAATGTTGGGGCATCTTTGGAGATTCAACATC
1 GAATATTGGGGCATATTTGGAGATTCAACATC
38301 GAATATTGGAGGCATATCTTGGAG-TTCAACA
1 GAATATTGG-GGCATAT-TTGGAGATTCAACA
38332 AATATCTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 8 0.30
33 13 0.48
34 6 0.22
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (32 bp):
GAATATTGGGGCATATTTGGAGATTCAACATC
Found at i:38546 original size:16 final size:16
Alignment explanation
Indices: 38525--38564 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
38515 AATTGAGAAA
**
38525 ACATACATCAATGCAT
1 ACATACATCAACACAT
38541 ACATACATCAACACAT
1 ACATACATCAACACAT
38557 ACATACAT
1 ACATACAT
38565 GATACATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.28, G:0.03, T:0.23
Consensus pattern (16 bp):
ACATACATCAACACAT
Found at i:39094 original size:105 final size:104
Alignment explanation
Indices: 38942--39176 Score: 293
Period size: 105 Copynumber: 2.3 Consensus size: 104
38932 AATTTCTCTT
* * *
38942 AAAAC-AACTTCGTCTTGCTTGAGACATTTTTTTCCTTTGATATACAAATTTCGAATTTGATTCA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTTTCCTTTGAAATACAAATTTCGAATTTGATTCA
*
39006 C-TTGAAAAAAAATTAATCTCACTTGAGATTGTTATTCTTTC-
66 CATT-AAAAAAAATTAATCTCACTTGAGATCGTT-TTC--TCA
* *
39047 AAAACAAATTTCGTCTCGTTTGAGACA-TTTTTT-CTTTGAGAATACAAATTTCGAATTTGTTTC
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTTTCCTTTGA-AATACAAATTTCGAATTTGATTC
* * *
39110 ACATTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
65 ACATTAAAAAAAATTAATCTCACTTGAGATCGTTTTCTCA
39150 AAAACAAACTTT-GTCTCGCTTGAGACA
1 AAAACAAA-TTTCGTCTCGCTTGAGACA
39177 ATTTCTCTAA
Statistics
Matches: 115, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
102 2 0.02
103 22 0.19
104 12 0.10
105 59 0.51
106 20 0.17
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (104 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTTTTCCTTTGAAATACAAATTTCGAATTTGATTCA
CATTAAAAAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:39172 original size:36 final size:36
Alignment explanation
Indices: 39143--39252 Score: 127
Period size: 36 Copynumber: 3.1 Consensus size: 36
39133 TTGAGATCGT
39143 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAACTTTGTCTCGCTTGAGACAA
** * *
39178 TTTCTCTAAAAACAATTTTTGTCTTGTTTGAGACAAA
1 TTTCTCTAAAAACAAACTTTGTCTCGCTTGAGAC-AA
* *
39215 TTT-TTTAAAAACAAA-TGTTGTCTCACTTGAGACAA
1 TTTCTCTAAAAACAAACT-TTGTCTCGCTTGAGACAA
39250 TTT
1 TTT
39253 TCCAAATTAT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
35 12 0.19
36 46 0.73
37 5 0.08
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (36 bp):
TTTCTCTAAAAACAAACTTTGTCTCGCTTGAGACAA
Found at i:39303 original size:32 final size:31
Alignment explanation
Indices: 39267--39348 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
39257 AATTATGAAT
* *
39267 TTGTTTCACTGGAAACAAACATCATCTTTGAG
1 TTGTTTCACTTGAAACAAA-AGCATCTTTGAG
** *
39299 TTGTTTCTTTTGAAAC-AAAGGATCTTTGAG
1 TTGTTTCACTTGAAACAAAAGCATCTTTGAG
39329 TCTGTTTCACTTGAAACAAA
1 T-TGTTTCACTTGAAACAAA
39349 TGAAAAAATC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
30 11 0.27
31 15 0.37
32 15 0.37
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (31 bp):
TTGTTTCACTTGAAACAAAAGCATCTTTGAG
Found at i:39582 original size:29 final size:30
Alignment explanation
Indices: 39550--39607 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
39540 TCGTGAAAAA
* *
39550 ATCTTTGAG-TCCTTTCTTTTGAAACACCT
1 ATCTTTGAGTTACTTTCTCTTGAAACACCT
*
39579 ATCTTTGAGTTAGTTTCTCTTGAAACACC
1 ATCTTTGAGTTACTTTCTCTTGAAACACC
39608 CACCTTTGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.43
Consensus pattern (30 bp):
ATCTTTGAGTTACTTTCTCTTGAAACACCT
Found at i:39966 original size:60 final size:60
Alignment explanation
Indices: 39893--40037 Score: 170
Period size: 61 Copynumber: 2.4 Consensus size: 60
39883 ATTTTCGGAA
*
39893 AAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTT-GAAAATCA-TTGAATAT-TTTCTTTGG
1 AAACAAA-ATTTGTCTCT-TTGAGACAATTTCTTTTAGAAAAT-ATTTGAATATGTTTC-TTGG
* * *
39954 AAACAAAATTTGTCTCTTTGAGATAGTTTCTTTTAAGAAAATATTTGAGTATGTTTCTTGG
1 AAACAAAATTTGTCTCTTTGAGACAATTTCTTTT-AGAAAATATTTGAATATGTTTCTTGG
*
40015 AAACAAAATTTATCATCTTTGAG
1 AAACAAAATTTGTC-TCTTTGAG
40038 TTTGTTTACC
Statistics
Matches: 74, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
59 15 0.20
60 10 0.14
61 37 0.50
62 12 0.16
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (60 bp):
AAACAAAATTTGTCTCTTTGAGACAATTTCTTTTAGAAAATATTTGAATATGTTTCTTGG
Found at i:40444 original size:28 final size:28
Alignment explanation
Indices: 40413--40506 Score: 127
Period size: 28 Copynumber: 3.4 Consensus size: 28
40403 AAAACACATC
40413 ATCTTTGAGTTTGTTTTTCTTGAAACAA
1 ATCTTTGAGTTTGTTTTTCTTGAAACAA
*
40441 ATCTTTGAGTTTGTTTTTCTTGGAACAA
1 ATCTTTGAGTTTGTTTTTCTTGAAACAA
* * **
40469 ATCTTTGAGTATATTTCTT-TTGAAACTT
1 ATCTTTGAGTTTGTTT-TTCTTGAAACAA
40497 ATCTTTGAGT
1 ATCTTTGAGT
40507 CAATTTCTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
28 57 0.97
29 2 0.03
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.51
Consensus pattern (28 bp):
ATCTTTGAGTTTGTTTTTCTTGAAACAA
Found at i:40512 original size:28 final size:28
Alignment explanation
Indices: 40469--40522 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
40459 CTTGGAACAA
40469 ATCTTTGAGTATATTTCTTTTGAAACTT
1 ATCTTTGAGTATATTTCTTTTGAAACTT
40497 ATCTTTGAGTCA-ATTTCTTTTGAAAC
1 ATCTTTGAGT-ATATTTCTTTTGAAAC
40523 CAGTATCCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.50
Consensus pattern (28 bp):
ATCTTTGAGTATATTTCTTTTGAAACTT
Found at i:41819 original size:22 final size:21
Alignment explanation
Indices: 41781--41824 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
41771 CGGGGATTTG
41781 AAAAAAATCAAACAGAAGAAA
1 AAAAAAATCAAACAGAAGAAA
41802 AAAACAAATCGAAA-AGAAGAAA
1 AAAA-AAATC-AAACAGAAGAAA
41824 A
1 A
41825 TAACCAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 14 0.67
23 3 0.14
ACGTcount: A:0.75, C:0.09, G:0.11, T:0.05
Consensus pattern (21 bp):
AAAAAAATCAAACAGAAGAAA
Found at i:46613 original size:12 final size:12
Alignment explanation
Indices: 46596--46647 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
46586 AATCAAAGAG
46596 AACAAAGAAAAA
1 AACAAAGAAAAA
*
46608 AACAAAGAGAAGA
1 AACAAAGA-AAAA
* *
46621 AGCAAAGAAAAG
1 AACAAAGAAAAA
*
46633 AGCAAAGAACAAA
1 AACAAAGAA-AAA
46646 AA
1 AA
46648 GATAACAAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
12 19 0.59
13 13 0.41
ACGTcount: A:0.73, C:0.10, G:0.17, T:0.00
Consensus pattern (12 bp):
AACAAAGAAAAA
Found at i:46628 original size:13 final size:12
Alignment explanation
Indices: 46598--46641 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
46588 TCAAAGAGAA
* *
46598 CAAAGAAAAAAA
1 CAAAGAAAAGAG
*
46610 CAAAGAGAAGAAG
1 CAAAGAAAAG-AG
46623 CAAAGAAAAGAG
1 CAAAGAAAAGAG
46635 CAAAGAA
1 CAAAGAA
46642 CAAAAAGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.70, C:0.09, G:0.20, T:0.00
Consensus pattern (12 bp):
CAAAGAAAAGAG
Found at i:46630 original size:25 final size:24
Alignment explanation
Indices: 46594--46640 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
46584 CAAATCAAAG
46594 AGAACAAAGAAAAAAACAAAGAGA
1 AGAACAAAGAAAAAAACAAAGAGA
* *
46618 AGAAGCAAAGAAAAGAGCAAAGA
1 AGAA-CAAAGAAAAAAACAAAGA
46641 ACAAAAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.70, C:0.09, G:0.21, T:0.00
Consensus pattern (24 bp):
AGAACAAAGAAAAAAACAAAGAGA
Found at i:47748 original size:33 final size:32
Alignment explanation
Indices: 47688--47749 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
47678 AAGAAATATT
* *
47688 GAATGTTGGGGCATCTTTGGAGATTCAACATC
1 GAATATTGGGGCATATTTGGAGATTCAACATC
47720 GAATATTGGAGGCATATCTTGGAG-TTCAAC
1 GAATATTGG-GGCATAT-TTGGAGATTCAAC
47750 GAATATCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 8 0.31
33 12 0.46
34 6 0.23
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (32 bp):
GAATATTGGGGCATATTTGGAGATTCAACATC
Found at i:47965 original size:16 final size:16
Alignment explanation
Indices: 47944--47983 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
47934 AATTGAGAAA
**
47944 ACATACATCAATGCAT
1 ACATACATCAACACAT
47960 ACATACATCAACACAT
1 ACATACATCAACACAT
47976 ACATACAT
1 ACATACAT
47984 GATACATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.28, G:0.03, T:0.23
Consensus pattern (16 bp):
ACATACATCAACACAT
Found at i:48531 original size:105 final size:104
Alignment explanation
Indices: 48361--48596 Score: 302
Period size: 105 Copynumber: 2.3 Consensus size: 104
48351 AATTTCTCTT
* * *
48361 AAAACAAACTTCGTCTTGCTTGAGACATTTTTTTCCTTTGATATACAAATTTCGAATTTGATTCA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTTTCCTTTGAAATACAAATTTCGAATTTGATTCA
*
48426 C-TTGAAAAAAAATTAATCTCACTTGAGATTGTTATTCTTTC-
66 CATT-AAAAAAAATTAATCTCACTTGAGATCGTT-TTC--TCA
* *
48467 AAAACAAATTTCGTCTCGTTTGAGACA-TTTTTT-CTTTGAGAATACAAATTTCGAATTTGTTTC
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTTTCCTTTGA-AATACAAATTTCGAATTTGATTC
* * *
48530 ACATTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
65 ACATTAAAAAAAATTAATCTCACTTGAGATCGTTTTCTCA
48570 AAAACAAACTTT-GTCTCGCTTGAGACA
1 AAAACAAA-TTTCGTCTCGCTTGAGACA
48597 ATTTCTCTAA
Statistics
Matches: 116, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
102 2 0.02
103 22 0.19
104 12 0.10
105 54 0.47
106 26 0.22
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (104 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTTTTCCTTTGAAATACAAATTTCGAATTTGATTCA
CATTAAAAAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:48592 original size:36 final size:36
Alignment explanation
Indices: 48563--48672 Score: 134
Period size: 36 Copynumber: 3.1 Consensus size: 36
48553 TTGAGATCGT
48563 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAACTTTGTCTCGCTTGAGACAA
** * *
48598 TTTCTCTAAAAACAATTTTTGTCTTGTTTGAGACAA
1 TTTCTCTAAAAACAAACTTTGTCTCGCTTGAGACAA
* * *
48634 ATTCTTTAAAAACAAA-TGTTGTCTCACTTGAGACAA
1 TTTCTCTAAAAACAAACT-TTGTCTCGCTTGAGACAA
48670 TTT
1 TTT
48673 TCCAAATTAT
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
35 7 0.11
36 55 0.89
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (36 bp):
TTTCTCTAAAAACAAACTTTGTCTCGCTTGAGACAA
Found at i:48723 original size:32 final size:31
Alignment explanation
Indices: 48687--48769 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 31
48677 AATTATGAAT
* *
48687 TTGTTTCACTGGAAACAAACATCATCTTTGAG
1 TTGTTTCACTTGAAACAAA-AGCATCTTTGAG
** *
48719 TTGTTTCTTTTGAAAC-AAAGGATCTTTGAG
1 TTGTTTCACTTGAAACAAAAGCATCTTTGAG
48749 TCTGTTTCACTTGAAACAAAA
1 T-TGTTTCACTTGAAACAAAA
48770 TGAAAAAATC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
30 11 0.26
31 15 0.36
32 16 0.38
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (31 bp):
TTGTTTCACTTGAAACAAAAGCATCTTTGAG
Found at i:48746 original size:30 final size:31
Alignment explanation
Indices: 48710--48768 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
48700 AACAAACATC
**
48710 ATCTTTGAGT-TGTTTCTTTTGAAACAAAGG
1 ATCTTTGAGTCTGTTTCACTTGAAACAAAGG
48740 ATCTTTGAGTCTGTTTCACTTGAAACAAA
1 ATCTTTGAGTCTGTTTCACTTGAAACAAA
48769 ATGAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.41
Consensus pattern (31 bp):
ATCTTTGAGTCTGTTTCACTTGAAACAAAGG
Found at i:48763 original size:31 final size:30
Alignment explanation
Indices: 48687--48768 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 30
48677 AATTATGAAT
* **
48687 TTGTTTCACTGGAAACAAACATCATCTTTGAG
1 TTGTTTCACTTGAAAC-AA-AGGATCTTTGAG
**
48719 TTGTTTCTTTTGAAACAAAGGATCTTTGAG
1 TTGTTTCACTTGAAACAAAGGATCTTTGAG
48749 TCTGTTTCACTTGAAACAAA
1 T-TGTTTCACTTGAAACAAA
48769 ATGAAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 11 0.26
31 18 0.43
32 13 0.31
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (30 bp):
TTGTTTCACTTGAAACAAAGGATCTTTGAG
Found at i:49003 original size:29 final size:30
Alignment explanation
Indices: 48971--49028 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
48961 TCGTGAAAAA
* *
48971 ATCTTTGAG-TCCTTTCTTTTGAAACACCT
1 ATCTTTGAGTTACTTTCTCTTGAAACACCT
*
49000 ATCTTTGAGTTAGTTTCTCTTGAAACACC
1 ATCTTTGAGTTACTTTCTCTTGAAACACC
49029 CACCTTTGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.43
Consensus pattern (30 bp):
ATCTTTGAGTTACTTTCTCTTGAAACACCT
Found at i:49393 original size:63 final size:64
Alignment explanation
Indices: 49318--49456 Score: 201
Period size: 65 Copynumber: 2.2 Consensus size: 64
49308 ATTTTCGGAA
*
49318 AAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTT-GAAAAATCA-TTGAATATGTTTCTTTGG
1 AAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTAGAAAAAT-ATTTGAATATGTTTCTTTGG
* * * *
49381 AAACAAAATTTTGTCTCTTTTGAGATAGTTTCTTTTAAGAAAAATATTTGAGTATGTTTCTTTGG
1 AAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTT-AGAAAAATATTTGAATATGTTTCTTTGG
49446 AAACAAAATTT
1 AAACAAAATTT
49457 ATCATCTTTG
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
63 32 0.47
64 1 0.01
65 35 0.51
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (64 bp):
AAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTAGAAAAATATTTGAATATGTTTCTTTGG
Found at i:49475 original size:36 final size:34
Alignment explanation
Indices: 49427--49520 Score: 98
Period size: 35 Copynumber: 2.6 Consensus size: 34
49417 AAGAAAAATA
* * ** *
49427 TTTGAGTATGTTTCTTTGGAAACAAAATTTATCATC
1 TTTGAGTTTGTTTCCTT-GAAACAAAA-CAAACATC
49463 TTTGAGTTTGTTTACCTTGAAACAAAACAAACATC
1 TTTGAGTTTGTTT-CCTTGAAACAAAACAAACATC
*
49498 TTTGAGATTGTTTCCCTTGAAAC
1 TTTGAGTTTGTTT-CCTTGAAAC
49521 GAATTATATC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
35 26 0.52
36 21 0.42
37 3 0.06
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (34 bp):
TTTGAGTTTGTTTCCTTGAAACAAAACAAACATC
Found at i:49892 original size:28 final size:28
Alignment explanation
Indices: 49861--49954 Score: 127
Period size: 28 Copynumber: 3.4 Consensus size: 28
49851 AAAACACATC
49861 ATCTTTGAGTTTGTTTTTCTTGAAACAA
1 ATCTTTGAGTTTGTTTTTCTTGAAACAA
*
49889 ATCTTTGAGTTTGTTTTTCTTGGAACAA
1 ATCTTTGAGTTTGTTTTTCTTGAAACAA
* * **
49917 ATCTTTGAGTATATTTCTT-TTGAAACTT
1 ATCTTTGAGTTTGTTT-TTCTTGAAACAA
49945 ATCTTTGAGT
1 ATCTTTGAGT
49955 CAATTTCTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
28 57 0.97
29 2 0.03
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.51
Consensus pattern (28 bp):
ATCTTTGAGTTTGTTTTTCTTGAAACAA
Found at i:49960 original size:28 final size:28
Alignment explanation
Indices: 49917--49970 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
49907 CTTGGAACAA
49917 ATCTTTGAGTATATTTCTTTTGAAACTT
1 ATCTTTGAGTATATTTCTTTTGAAACTT
49945 ATCTTTGAGTCA-ATTTCTTTTGAAAC
1 ATCTTTGAGT-ATATTTCTTTTGAAAC
49971 CAGTATCCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.50
Consensus pattern (28 bp):
ATCTTTGAGTATATTTCTTTTGAAACTT
Found at i:50219 original size:134 final size:132
Alignment explanation
Indices: 49990--50470 Score: 534
Period size: 134 Copynumber: 3.6 Consensus size: 132
49980 TAAATATGGA
* * * *
49990 CAGAACTCTTCATCATGTATGAGTCGTGTCATCCCCTGACTAGATCTCCTCATCGCGTAGGAGCC
1 CAGAACTCTTCATCACGTATGAGCCGTGTCATCCCC-GACCAGATCTCCTCATCACGTAGGAGCC
* * *
50055 GTGTCACCCTTAGATAACCAGTCGTCCTCATCACGTAAGAACCGAGTTATCATCCTTTCTAAAAA
65 GTGTCACCCATAGATAACCAGCCGTCCTCATCACGTAAGAACCGAGTTATCA-CCTTCCTAAAAA
50120 TAGC
129 TAGC
* *
50124 CAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGACCTCCTCATCATGTAGGAGCC
1 CAGAACTCTTCATCACGTATGAGCCGTGTCA-TCCCCGACCAGATCTCCTCATCACGTAGGAGCC
* * * * *
50189 GTGTCAACCATAGATAACCAGCCGTCCTCATCACGT-AGAAATCGTGTTATCGCCCTTCCTAAAG
65 GTGTCACCCATAGATAACCAGCCGTCCTCATCACGTAAG-AACCGAGTTATC-ACCTTCCTAAAA
*
50253 ATAAC
128 ATAGC
* * * * * * *
50258 CAAAACTGTTCATCACGTATGAGCCGTGTCATCCACCAACCAGATCTCTTAATTATGTAGGAGCC
1 CAGAACTCTTCATCACGTATGAGCCGTGTCATCC-CCGACCAGATCTCCTCATCACGTAGGAGCC
* * * * * *
50323 GTGTCACCCCTAGATAACCAGCCATCCTCATCGCGTAGGAACTGAGTTATCACACTTCCTAAATA
65 GTGTCACCCATAGATAACCAGCCGTCCTCATCACGTAAGAACCGAGTTATCAC-CTTCCTAAAAA
50388 T-GAC
129 TAG-C
* * ** * * **
50392 CATAAATCTTCATCACGTATGAGCAATATCATCCCTCGACCAGATTTCCTCATCACGTAGGAGTT
1 CAGAACTCTTCATCACGTATGAGCCGTGTCATCCC-CGACCAGATCTCCTCATCACGTAGGAGCC
*
50457 GTGTCACCCTTAGA
65 GTGTCACCCATAGA
50471 CGACCCGAAC
Statistics
Matches: 291, Mismatches: 48, Indels: 16
0.82 0.14 0.05
Matches are distributed among these distances:
133 7 0.02
134 278 0.96
135 6 0.02
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (132 bp):
CAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCGACCAGATCTCCTCATCACGTAGGAGCCG
TGTCACCCATAGATAACCAGCCGTCCTCATCACGTAAGAACCGAGTTATCACCTTCCTAAAAATA
GC
Found at i:50674 original size:13 final size:13
Alignment explanation
Indices: 50656--50693 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
50646 GGTATTCTTT
50656 TTATTATTTATTA
1 TTATTATTTATTA
50669 TTATTATTT-TTA
1 TTATTATTTATTA
*
50681 TATTTTATTTATT
1 T-TATTATTTATT
50694 TACAATTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 4 0.18
13 16 0.73
14 2 0.09
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTATTTATTA
Found at i:51305 original size:21 final size:20
Alignment explanation
Indices: 51276--51319 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
51266 CGGGGATTTG
51276 AAAAAAAATC-AAACAGAAAA
1 AAAAAAAATCGAAA-AGAAAA
51296 AAAAACAAATCGAAAAGAAGAA
1 AAAAA-AAATCGAAAAGAA-AA
51318 AA
1 AA
51320 TAACCAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.77, C:0.09, G:0.09, T:0.05
Consensus pattern (20 bp):
AAAAAAAATCGAAAAGAAAA
Found at i:53139 original size:17 final size:19
Alignment explanation
Indices: 53106--53141 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
53096 GGAGACGCAG
53106 ACTGAATTTTGTCTTAAAA
1 ACTGAATTTTGTCTTAAAA
53125 ACTG-ATTTT-TCTTAAAA
1 ACTGAATTTTGTCTTAAAA
53142 TTATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 5 0.29
19 4 0.24
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (19 bp):
ACTGAATTTTGTCTTAAAA
Found at i:55763 original size:18 final size:18
Alignment explanation
Indices: 55740--55781 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
55730 GCCTTCATCT
55740 GAAAACCAATCATCAGCA
1 GAAAACCAATCATCAGCA
55758 GAAAACCAATCATCAGCA
1 GAAAACCAATCATCAGCA
55776 GAAAAC
1 GAAAAC
55782 ATTAAATGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.52, C:0.26, G:0.12, T:0.10
Consensus pattern (18 bp):
GAAAACCAATCATCAGCA
Found at i:61682 original size:61 final size:61
Alignment explanation
Indices: 61617--61735 Score: 229
Period size: 61 Copynumber: 2.0 Consensus size: 61
61607 TCATAGTCGT
61617 TTTAAAAAAAAGTTATCTGACACATGTTGAGTTTATATTTTGTTTGAAATTTTTATTTTCG
1 TTTAAAAAAAAGTTATCTGACACATGTTGAGTTTATATTTTGTTTGAAATTTTTATTTTCG
*
61678 TTTAAAAAAAAGTTATCTTACACATGTTGAGTTTATATTTTGTTTGAAATTTTTATTT
1 TTTAAAAAAAAGTTATCTGACACATGTTGAGTTTATATTTTGTTTGAAATTTTTATTT
61736 AAAAAACATT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (61 bp):
TTTAAAAAAAAGTTATCTGACACATGTTGAGTTTATATTTTGTTTGAAATTTTTATTTTCG
Found at i:61866 original size:16 final size:16
Alignment explanation
Indices: 61845--61875 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61835 CTTATCGTCA
61845 TCTCAAACCCTTAAAT
1 TCTCAAACCCTTAAAT
*
61861 TCTCAAATCCTTAAA
1 TCTCAAACCCTTAAA
61876 CTTAAATCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (16 bp):
TCTCAAACCCTTAAAT
Found at i:62934 original size:6 final size:6
Alignment explanation
Indices: 62918--62949 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
62908 TGTCGGTTCG
62918 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
62950 AATACGTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:64419 original size:2 final size:2
Alignment explanation
Indices: 64414--64453 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
64404 TTAAAAAATA
64414 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
64454 TATTTAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64857 original size:2 final size:2
Alignment explanation
Indices: 64852--64881 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
64842 ACTTTTTTTA
64852 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
64882 TTTTAAGTTT
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):
AT
Found at i:66938 original size:119 final size:120
Alignment explanation
Indices: 66811--67172 Score: 543
Period size: 119 Copynumber: 3.0 Consensus size: 120
66801 ACAACTTTCA
* * * * *
66811 TTGGTTTCAGTCCAGATTCCTTCGTC-GCTTTAATGTCTCCTCATAGAACATCTCCTTACTTGGC
1 TTGGTTTCAGTTCTGCTTCCTTCATCGGCTTTAATGTCTCCTCATAGAACATATCCTTACTTGGC
* *
66875 TTCAGCTCTGCTTCCTTCTGCAGCTTTAATTCCTCCTCATAGATCATATCCTTAC
66 TTCAGCTCTGCTTCCTTCTTCGGCTTTAATTCCTCCTCATAGATCATATCCTTAC
66930 TTGGTTTCAGTTTCTGCTTCCTTCATCGGCTTTAATGTCT-C-CATAGAACATATCCTTACTTGG
1 TTGGTTTCAG-TTCTGCTTCCTTCATCGGCTTTAATGTCTCCTCATAGAACATATCCTTACTTGG
*
66993 CTTCAGCTCTGCTTCCTTCTTCGGCTTTAATTCCTCCTCACAGATCATATCCTTAC
65 CTTCAGCTCTGCTTCCTTCTTCGGCTTTAATTCCTCCTCATAGATCATATCCTTAC
* * * * *
67049 TCGGTTTCAGTTCTGCTTCCTTTATCGGCTTTAAAGCCTCCTCGTAGAACATATCCTTACTTGGC
1 TTGGTTTCAGTTCTGCTTCCTTCATCGGCTTTAATGTCTCCTCATAGAACATATCCTTACTTGGC
* *
67114 TTCAGCTCTGCATCCTTCTTCGGCTTTAATTCCTCCTCATAG-TACATATCCTTCC
66 TTCAGCTCTGCTTCCTTCTTCGGCTTTAATTCCTCCTCATAGAT-CATATCCTTAC
67169 TTGG
1 TTGG
67173 CCTCCAATCT
Statistics
Matches: 221, Mismatches: 17, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
118 26 0.12
119 95 0.43
120 88 0.40
121 12 0.05
ACGTcount: A:0.17, C:0.30, G:0.13, T:0.40
Consensus pattern (120 bp):
TTGGTTTCAGTTCTGCTTCCTTCATCGGCTTTAATGTCTCCTCATAGAACATATCCTTACTTGGC
TTCAGCTCTGCTTCCTTCTTCGGCTTTAATTCCTCCTCATAGATCATATCCTTAC
Found at i:67190 original size:60 final size:60
Alignment explanation
Indices: 66827--67173 Score: 445
Period size: 60 Copynumber: 5.8 Consensus size: 60
66817 TCAGTCCAGA
* *
66827 TTCCTTCGTC-GCTTTAATGT-CTCCTCATAGAACATCTCCTTACTTGGCTTCAGCTCTGC
1 TTCCTTCTTCGGCTTTAAT-TCCTCCTCATAGAACATATCCTTACTTGGCTTCAGCTCTGC
* * * * *
66886 TTCCTTCTGCAGCTTTAATTCCTCCTCATAGATCATATCCTTACTTGGTTTCAGTTTCTGC
1 TTCCTTCTTCGGCTTTAATTCCTCCTCATAGAACATATCCTTACTTGGCTTCAG-CTCTGC
*
66947 TTCCTTCATCGGCTTTAATGT-CT-C-CATAGAACATATCCTTACTTGGCTTCAGCTCTGC
1 TTCCTTCTTCGGCTTTAAT-TCCTCCTCATAGAACATATCCTTACTTGGCTTCAGCTCTGC
* * * * *
67005 TTCCTTCTTCGGCTTTAATTCCTCCTCACAGATCATATCCTTACTCGGTTTCAGTTCTGC
1 TTCCTTCTTCGGCTTTAATTCCTCCTCATAGAACATATCCTTACTTGGCTTCAGCTCTGC
** *
67065 TTCCTT-TATCGGCTTTAAAGCCTCCTCGTAGAACATATCCTTACTTGGCTTCAGCTCTGC
1 TTCCTTCT-TCGGCTTTAATTCCTCCTCATAGAACATATCCTTACTTGGCTTCAGCTCTGC
* * *
67125 ATCCTTCTTCGGCTTTAATTCCTCCTCATAGTACATATCCTTCCTTGGC
1 TTCCTTCTTCGGCTTTAATTCCTCCTCATAGAACATATCCTTACTTGGC
67174 CTCCAATCTA
Statistics
Matches: 247, Mismatches: 32, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
57 1 0.00
58 25 0.10
59 37 0.15
60 159 0.64
61 24 0.10
62 1 0.00
ACGTcount: A:0.17, C:0.31, G:0.13, T:0.40
Consensus pattern (60 bp):
TTCCTTCTTCGGCTTTAATTCCTCCTCATAGAACATATCCTTACTTGGCTTCAGCTCTGC
Done.