Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005006.1 Hibiscus syriacus cultivar Beakdansim tig00011233_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: 144286
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:11322 original size:15 final size:15
Alignment explanation
Indices: 11302--11334 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
11292 TAGTGTGACT
11302 AAAATATAAATA-TTA
1 AAAATA-AAATACTTA
11317 AAAATAAAATACTTA
1 AAAATAAAATACTTA
11332 AAA
1 AAA
11335 CAAAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAAAATACTTA
Found at i:12682 original size:3 final size:3
Alignment explanation
Indices: 12667--12712 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
12657 TAAACACACT
* *
12667 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
12713 TTTTTTAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 1 0.03
3 37 0.97
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:21239 original size:11 final size:12
Alignment explanation
Indices: 21220--21318 Score: 64
Period size: 11 Copynumber: 8.1 Consensus size: 12
21210 TATTACGCCT
21220 AAGAAAAGAGAA
1 AAGAAAAGAGAA
*
21232 GA-AAAAGA-AA
1 AAGAAAAGAGAA
21242 AAGAAAAGAGAAA
1 AAGAAAAGAG-AA
* *
21255 ATAAAAAAGATAA
1 A-AGAAAAGAGAA
21268 AAGAAAAAGAGAAAA
1 AAG-AAAAGAG--AA
*
21283 TAATGAAAA-ATAA
1 -AA-GAAAAGAGAA
21296 AAGAAAAGAG-A
1 AAGAAAAGAGAA
21307 AAGAAAAG-GAA
1 AAGAAAAGAGAA
21318 A
1 A
21319 TTAATGAAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 23
0.69 0.08 0.23
Matches are distributed among these distances:
10 4 0.06
11 28 0.41
12 5 0.07
13 14 0.21
14 7 0.10
15 3 0.04
16 6 0.09
17 1 0.01
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (12 bp):
AAGAAAAGAGAA
Found at i:21241 original size:6 final size:6
Alignment explanation
Indices: 21230--21318 Score: 69
Period size: 6 Copynumber: 15.0 Consensus size: 6
21220 AAGAAAAGAG
*
21230 AAGAAA AAGAAA AAGAAA AGAGAAA ATA-AAA AAGATAA AAGAAA AAGAGA
1 AAGAAA AAGAAA AAGAAA A-AGAAA A-AGAAA AAGA-AA AAGAAA AAGAAA
* * * * *
21280 AA-ATA ATGAAA AA-TAA AAG-AA AAGAGA AAGAAA AGGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
21319 TTAATGAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 12
0.75 0.11 0.13
Matches are distributed among these distances:
5 13 0.19
6 41 0.61
7 13 0.19
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (6 bp):
AAGAAA
Found at i:21245 original size:22 final size:22
Alignment explanation
Indices: 21220--21318 Score: 83
Period size: 22 Copynumber: 4.3 Consensus size: 22
21210 TATTACGCCT
21220 AAGAAAAGAGAAGAAAAAGAAA
1 AAGAAAAGAGAAGAAAAAGAAA
*
21242 AAGAAAAGAGAAAATAAAAAAGATAA
1 AAGAAAAGAG--AA-GAAAAAGA-AA
*
21268 AAGAAAAAGAGAA-AATAATGAAA
1 AAG-AAAAGAGAAGAA-AAAGAAA
* * *
21291 AATAAAAGAAAAGAGAAAGAAA
1 AAGAAAAGAGAAGAAAAAGAAA
*
21313 AGGAAA
1 AAGAAA
21319 TTAATGAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
22 28 0.45
23 7 0.11
24 6 0.10
25 9 0.15
26 5 0.08
27 7 0.11
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (22 bp):
AAGAAAAGAGAAGAAAAAGAAA
Found at i:21269 original size:27 final size:26
Alignment explanation
Indices: 21230--21308 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 26
21220 AAGAAAAGAG
*
21230 AAGAAAAAGAAAAAGAAAAGAGAAAAT
1 AAGAAAAA-TAAAAGAAAAGAGAAAAT
21257 AA-AAAAGATAAAAGAAAAAGAGAAAAT
1 AAGAAAA-ATAAAAG-AAAAGAGAAAAT
21284 AATGAAAAATAAAAGAAAAGAGAAA
1 AA-GAAAAATAAAAGAAAAGAGAAA
21309 GAAAAGGAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
26 9 0.19
27 27 0.57
28 7 0.15
29 4 0.09
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.06
Consensus pattern (26 bp):
AAGAAAAATAAAAGAAAAGAGAAAAT
Found at i:22511 original size:13 final size:13
Alignment explanation
Indices: 22490--22526 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
22480 ACCTTAGCTC
22490 CATTCCATCACTT
1 CATTCCATCACTT
*
22503 CATTACATCACTT
1 CATTCCATCACTT
22516 CATTCCATCAC
1 CATTCCATCAC
22527 AAAAGAAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.27, C:0.38, G:0.00, T:0.35
Consensus pattern (13 bp):
CATTCCATCACTT
Found at i:22896 original size:159 final size:159
Alignment explanation
Indices: 22665--22979 Score: 395
Period size: 160 Copynumber: 2.0 Consensus size: 159
22655 TCAGCACTTT
* * * * *
22665 GCTCATCCTTCGCATATGGAGTTGGGTAGCATGATCACTTTGTTTGACTCCATCACAGAAAGAGA
1 GCTCATCCATCGCATATGGAATTGGATAGCATCATCACTTTGTTTGAATCCATCACAGAAAGAGA
* * * *
22730 TGAATCAATATTT-CTA-GGAGAGAGTTCATAATAAGAAGAACTT-ATCCGATGAGAAAGAAGAA
66 TGAATCAAAATTTCCAATGGAAAG-GTTCATAATAAGAAGAA-TTCATCCAATGAGAAAGAAGAA
*
22792 GTTCATAATGAGAAGAACTTGTTCAACCTTA
129 GTTAATAATGAGAAGAACTTGTTCAACCTTA
22823 GCTCATCCATCGCATATGGAATTGGATCAGCATCATCACTTTGTTTGAATCCATCACAG-AAGCA
1 GCTCATCCATCGCATATGGAATTGGAT-AGCATCATCACTTTGTTTGAATCCATCACAGAAAG-A
* * * * **
22887 GGTGGATCAAAATTTCCAATGGAAAGGTTCGTAATGAGAAGAATTCATCCAATGAGGGAGAAGAA
64 GATGAATCAAAATTTCCAATGGAAAGGTTCATAATAAGAAGAATTCATCCAATGAGAAAGAAGAA
* * *
22952 GTTAATAATGAGAATAATTTTTTCAACC
129 GTTAATAATGAGAAGAACTTGTTCAACC
22980 AGATTTAATC
Statistics
Matches: 133, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
158 27 0.20
159 44 0.33
160 57 0.43
161 5 0.04
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.28
Consensus pattern (159 bp):
GCTCATCCATCGCATATGGAATTGGATAGCATCATCACTTTGTTTGAATCCATCACAGAAAGAGA
TGAATCAAAATTTCCAATGGAAAGGTTCATAATAAGAAGAATTCATCCAATGAGAAAGAAGAAGT
TAATAATGAGAAGAACTTGTTCAACCTTA
Found at i:23179 original size:14 final size:14
Alignment explanation
Indices: 23157--23225 Score: 56
Period size: 14 Copynumber: 5.1 Consensus size: 14
23147 TATTTTTTCG
*
23157 TTTTGTATTTATTA
1 TTTTATATTTATTA
*
23171 TTTTATATTCATTA
1 TTTTATATTTATTA
*
23185 TTATTATATATATT-
1 TT-TTATATTTATTA
*
23199 TATT-TATTTA-T-
1 TTTTATATTTATTA
*
23210 TTTTATTTTTATTA
1 TTTTATATTTATTA
23224 TT
1 TT
23226 GAAAATATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
11 4 0.09
12 10 0.23
13 3 0.07
14 17 0.40
15 9 0.21
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (14 bp):
TTTTATATTTATTA
Found at i:23202 original size:33 final size:33
Alignment explanation
Indices: 23162--23224 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
23152 TTTCGTTTTG
23162 TATTTA-TTATTTTATATTCATTATTATTATATA
1 TATTTATTTA-TTTATATTCATTATTATTATATA
* * *
23195 TATTTATTTATTTATTTTTATTTTTATTAT
1 TATTTATTTATTTATATTCATTATTATTAT
23225 TGAAAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 23 0.88
34 3 0.12
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (33 bp):
TATTTATTTATTTATATTCATTATTATTATATA
Found at i:23673 original size:3 final size:3
Alignment explanation
Indices: 23665--23703 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
23655 TTATTTTAAA
23665 TAT TAT TAT TAT TAT TAT GT-T TAT TAAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT -TAT TAT T-AT TAT TAT TAT TA
23704 ATACAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 28 0.85
4 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:30630 original size:31 final size:31
Alignment explanation
Indices: 30543--30633 Score: 98
Period size: 30 Copynumber: 3.0 Consensus size: 31
30533 TTGAGACATT
* * *
30543 ATCTTTGAGTTTGTTTATCTTGAAAC-AAAA
1 ATCTTTGAGTCTGTTTCTATTGAAACAAAAA
* *
30573 GTCTTTGAGTCTGTTTCTATTAAAACAAAACA
1 ATCTTTGAGTCTGTTTCTATTGAAACAAAA-A
30605 ATCTTTGAGTC-GTTTCCT-TTGAAACAAAA
1 ATCTTTGAGTCTGTTT-CTATTGAAACAAAA
30634 TTTTGTCTCT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
30 21 0.41
31 17 0.33
32 13 0.25
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (31 bp):
ATCTTTGAGTCTGTTTCTATTGAAACAAAAA
Found at i:30715 original size:29 final size:30
Alignment explanation
Indices: 30674--30732 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
30664 CAAAATCATA
* * *
30674 TTTGGGTCTGTTTCTTTTGAAA-CATTATC
1 TTTGAGTCAGTTTCTCTTGAAACCATTATC
30703 TTTGAGTCAGTTTCTCTTGAAACCATTATC
1 TTTGAGTCAGTTTCTCTTGAAACCATTATC
30733 CCTAAAGATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (30 bp):
TTTGAGTCAGTTTCTCTTGAAACCATTATC
Found at i:30855 original size:43 final size:40
Alignment explanation
Indices: 30751--30856 Score: 99
Period size: 43 Copynumber: 2.6 Consensus size: 40
30741 TGGCCTTTCA
*
30751 TCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATC
* * * * *
30791 TTCTCATCACATAAGAGCCGTGTCA-CCTCTAGATAACCAG-TC
1 TCCTCATCACGTAGGAACCGTGTCATCC-CCAG---ACCAGATC
30833 GTCCTCATCACGTAGGAACCGTGT
1 -TCCTCATCACGTAGGAACCGTGT
30857 TATCGTCCTT
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
39 2 0.04
40 23 0.45
42 2 0.04
43 24 0.47
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.24
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATC
Found at i:31166 original size:3 final size:3
Alignment explanation
Indices: 31160--31220 Score: 81
Period size: 3 Copynumber: 20.0 Consensus size: 3
31150 ATTTTTTTAT
31160 TTA TTA TTA TTA TTA TTA TTA TTA TTA TGT- TTA TTA TTA TGT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA
31205 TTAA TTA TTA TTA TTA
1 TT-A TTA TTA TTA TTA
31221 ATACAAAGGC
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.04
3 46 0.87
4 5 0.09
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:33012 original size:15 final size:15
Alignment explanation
Indices: 32994--33037 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
32984 ACTTAAAATG
32994 CTGAAAATTAAAGGA
1 CTGAAAATTAAAGGA
*
33009 CTGAAATTTAAAGGA
1 CTGAAAATTAAAGGA
*
33024 TTGAAAATTAAAGG
1 CTGAAAATTAAAGG
33038 GTATAAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (15 bp):
CTGAAAATTAAAGGA
Found at i:37374 original size:46 final size:45
Alignment explanation
Indices: 37258--37528 Score: 382
Period size: 46 Copynumber: 5.9 Consensus size: 45
37248 CATTTCTTAT
* * * *
37258 CAATATATTTACCATTTATCCCATAATCTCGTAAGCTTATTTTAT
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* * * *
37303 CAACATACTTACCATATGTTTCATAAGCTCGTAAGCTTATTTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTA-TTTTAC
*
37349 CAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
*
37394 CAATATACCATAAACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATA-C-T-TACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
*
37442 CAATATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTT-ATTCCATAAGCTCGTAAGCTTATTTTAC
*
37488 CAATATACTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
37529 GCATGGTTAC
Statistics
Matches: 204, Mismatches: 17, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
44 24 0.12
45 54 0.26
46 83 0.41
47 2 0.01
48 41 0.20
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (45 bp):
CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:37435 original size:139 final size:138
Alignment explanation
Indices: 37268--37528 Score: 407
Period size: 139 Copynumber: 1.9 Consensus size: 138
37258 CAATATATTT
* * * **
37268 ACCATTTATCCCATAATCTCGTAAGCTTATTTTATCAACATACTTACCATAT-GTTTCATAAGCT
1 ACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATATAATACCATAAGCT
*
37332 CGTAAGCTTATTTTTACCAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAA
66 CGTAAGCTTA-TTTTACCAATATACTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAA
37397 TATACCATAA
129 TATACCATAA
* * *
37407 ACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATACCATAAGCT
1 ACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATATAATACCATAAGCT
*
37472 CGTAAGCTTATTTTACCAATATACTTGCCATTATTCCATAAGCTCGTAAGCTTATTT
66 CGTAAGCTTATTTTACCAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTT
37529 GCATGGTTAC
Statistics
Matches: 111, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
138 26 0.23
139 66 0.59
140 19 0.17
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (138 bp):
ACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATATAATACCATAAGCT
CGTAAGCTTATTTTACCAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAATA
TACCATAA
Found at i:37467 original size:94 final size:90
Alignment explanation
Indices: 37258--37528 Score: 382
Period size: 94 Copynumber: 3.0 Consensus size: 90
37248 CATTTCTTAT
* * * * * * *
37258 CAATATATTTACCATTTATCCCATAATCTCGTAAGCTTATTTTATCAACATACTTACCATATGTT
1 CAATATACTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATT
*
37323 TCATAAGCTCGTAAGCTTATTTTTAC
66 CCATAAGCTCGTAAGCTTA-TTTTAC
* * *
37349 CAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAATATACCATAAACCATTT
1 CAATATACTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATA-C-T-TACCATTT
37414 ATTCCATAAGCTCGTAAGCTTATTTTAC
63 ATTCCATAAGCTCGTAAGCTTATTTTAC
*
37442 CAATATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA-TTAT
1 CAATATACTTACCATTT-ATACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAT
37506 TCCATAAGCTCGTAAGCTTATTT
65 TCCATAAGCTCGTAAGCTTATTT
37529 GCATGGTTAC
Statistics
Matches: 162, Mismatches: 14, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
90 27 0.17
91 49 0.30
92 2 0.01
93 25 0.15
94 59 0.36
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (90 bp):
CAATATACTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATT
CCATAAGCTCGTAAGCTTATTTTAC
Found at i:43933 original size:80 final size:80
Alignment explanation
Indices: 43795--44085 Score: 388
Period size: 80 Copynumber: 3.6 Consensus size: 80
43785 TGTAAGTCCT
* * *
43795 TACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTAGTTCCCTTTGTTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTACCTTTGTTGTG
* *
43860 TGCATAATGTAACCG
66 TGCATAAGGTAACCC
* * *
43875 TACGGACCTAGGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGTTTGGTTTCCTTTGTTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTACCTTTGTTGTG
*
43940 TGCATAAGGTAGCCC
66 TGCATAAGGTAACCC
* * * *
43955 TACGGACCTAAGGATATCTTGGAATAGG-CCCAAGGTACATCCTTAGGTTGGTTACCTTAGCTGT
1 TACGGACCTAAGGATATCTTGG-GTAGGTCCCAAGGTATATCCTTAGGTTGGTTACCTTTGTTGT
* *
44019 GTACTTAAGGTAACCC
65 GTGCATAAGGTAACCC
* * *
44035 TACGGATCTAAGGATGTCCTTGGGTAGAT-CCAAGGTATATCCTTAGGTTGG
1 TACGGACCTAAGGATAT-CTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGG
44086 CTCCCCATTT
Statistics
Matches: 185, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
80 176 0.95
81 9 0.05
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (80 bp):
TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTACCTTTGTTGTG
TGCATAAGGTAACCC
Found at i:50012 original size:18 final size:18
Alignment explanation
Indices: 49989--50033 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
49979 TCATGCATTT
* *
49989 TTTCATTTTTCATTTTCA
1 TTTCATTTTTAATATTCA
*
50007 TTTCATTATTAATATTCA
1 TTTCATTTTTAATATTCA
50025 TTTACATTT
1 TTT-CATTT
50034 ATATTTATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTCATTTTTAATATTCA
Found at i:50043 original size:22 final size:24
Alignment explanation
Indices: 49997--50050 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
49987 TTTTTCATTT
*
49997 TTCATTTTCATTTCATTATTAATA
1 TTCATTTACATTTCATTATTAATA
*
50021 TTCATTTACATTT-A-TATTTATA
1 TTCATTTACATTTCATTATTAATA
*
50043 TTAATTTA
1 TTCATTTA
50051 TTAAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 14 0.52
23 1 0.04
24 12 0.44
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (24 bp):
TTCATTTACATTTCATTATTAATA
Found at i:64397 original size:24 final size:24
Alignment explanation
Indices: 64370--64419 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
64360 ATAAAGAACC
64370 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
64394 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
64418 AA
1 AA
64420 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:69779 original size:69 final size:69
Alignment explanation
Indices: 69668--69801 Score: 243
Period size: 69 Copynumber: 1.9 Consensus size: 69
69658 AATTGCAATG
*
69668 TCATTATGTAGTCGTGTATTCATATTGGGTGGATTGTATCGAAGTAAGAAGCTTTTATATAAACC
1 TCATTATGTAGTCGTGTATTCATATTGGGTGGATTGTATCGAAGTAAGAAGCTTTTACATAAACC
69733 CGCA
66 CGCA
69737 TCATTATGTAG-CTGTGTATTCATATTGGGTGGATTGTATCGAAGTAAGAAGCTTTTACATAAAC
1 TCATTATGTAGTC-GTGTATTCATATTGGGTGGATTGTATCGAAGTAAGAAGCTTTTACATAAAC
69801 C
65 C
69802 TGCCCAAGAT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
68 1 0.02
69 62 0.98
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.37
Consensus pattern (69 bp):
TCATTATGTAGTCGTGTATTCATATTGGGTGGATTGTATCGAAGTAAGAAGCTTTTACATAAACC
CGCA
Found at i:81317 original size:10 final size:9
Alignment explanation
Indices: 81289--81380 Score: 61
Period size: 8 Copynumber: 10.2 Consensus size: 9
81279 ATACTTGAAG
*
81289 AAGAAAAGG
1 AAGAAAAGA
81298 AA-AAAAGA
1 AAGAAAAGA
81306 AAGAAGAAGAA
1 AAGAA-AAG-A
*
81317 AAGAAAAAAA
1 AAG-AAAAGA
81327 AAGAAAAGGAA
1 AAGAAAA-G-A
81338 AAGAAAAGA
1 AAGAAAAGA
81347 AA-AATAA-A
1 AAGAA-AAGA
*
81355 AGGAAAAGA
1 AAGAAAAGA
81364 AA-AAAA-A
1 AAGAAAAGA
81371 AAG-AAAGA
1 AAGAAAAGA
81379 AA
1 AA
81381 AAAGGAAAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
7 6 0.09
8 20 0.30
9 17 0.25
10 8 0.12
11 14 0.21
12 2 0.03
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (9 bp):
AAGAAAAGA
Found at i:81322 original size:5 final size:5
Alignment explanation
Indices: 81289--81381 Score: 80
Period size: 5 Copynumber: 17.4 Consensus size: 5
81279 ATACTTGAAG
* *
81289 AAGAA AAGGAA AAAAGA AAGAA GAAGAA AAGAA AAAAA AAGAA AAGGAA
1 AAGAA AA-GAA AAGA-A AAGAA -AAGAA AAGAA AAGAA AAGAA AA-GAA
* *
81338 AAGAA AAGAAA AATAA AAGGAA AAGAA AA-AA AAAAGA AAGAA AA
1 AAGAA AAG-AA AAGAA AA-GAA AAGAA AAGAA AAGA-A AAGAA AA
81382 AAGGAAAATA
Statistics
Matches: 73, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
4 4 0.05
5 38 0.52
6 31 0.42
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (5 bp):
AAGAA
Found at i:81325 original size:22 final size:21
Alignment explanation
Indices: 81285--81395 Score: 111
Period size: 22 Copynumber: 5.0 Consensus size: 21
81275 TAATATACTT
81285 GAAGAAGAAAAGGAAAAAAGAAA
1 GAAGAAGAAAA-GAAAAAA-AAA
81308 GAAGAAGAAAAGAAAAAAAAA
1 GAAGAAGAAAAGAAAAAAAAA
81329 GAA-AAGGAAAAGAAAAGAAAAA
1 GAAGAA-GAAAAGAAAA-AAAAA
*
81351 TAA-AAGGAAAAGAAAAAAAAAA
1 GAAGAA-GAAAAG-AAAAAAAAA
81373 GAAAGAA-AAAAGGAAAATAAAAA
1 G-AAGAAGAAAA-GAAAA-AAAAA
81396 AGGGGTTAAA
Statistics
Matches: 79, Mismatches: 2, Indels: 14
0.83 0.02 0.15
Matches are distributed among these distances:
20 2 0.03
21 16 0.20
22 36 0.46
23 23 0.29
24 2 0.03
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (21 bp):
GAAGAAGAAAAGAAAAAAAAA
Found at i:81396 original size:28 final size:27
Alignment explanation
Indices: 81314--81395 Score: 62
Period size: 28 Copynumber: 3.0 Consensus size: 27
81304 GAAAGAAGAA
*
81314 GAAAAG-AAAAAAAAAGAAAAGGAAAA-
1 GAAAAGAAAAAAAAAAGAAAA-AAAAAG
*
81340 GAAAAGAAAAATAAAAGGAAAAGAAAAA-
1 GAAAAGAAAAA-AAAAAGAAAA-AAAAAG
* *
81368 AAAAAGAAAGAAAAAAGGAAAATAAAAA
1 GAAAAGAAA-AAAAAAAGAAAA-AAAAA
81396 AGGGGTTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.12
27 4 0.08
28 37 0.76
29 2 0.04
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (27 bp):
GAAAAGAAAAAAAAAAGAAAAAAAAAG
Found at i:81398 original size:13 final size:11
Alignment explanation
Indices: 81292--81397 Score: 88
Period size: 11 Copynumber: 9.5 Consensus size: 11
81282 CTTGAAGAAG
*
81292 AAAAGGAAAAA
1 AAAAAGAAAAA
* *
81303 AGAAAGAAGAA
1 AAAAAGAAAAA
*
81314 GAAAAG-AAAA
1 AAAAAGAAAAA
*
81324 AAAAAGAAAAG
1 AAAAAGAAAAA
* *
81335 GAAAAGAAAAG
1 AAAAAGAAAAA
* *
81346 AAAAATAAAAG
1 AAAAAGAAAAA
*
81357 GAAAAGAAAAA
1 AAAAAGAAAAA
81368 AAAAAGAAAGAA
1 AAAAAGAAA-AA
*
81380 AAAAGGAAAATA
1 AAAAAGAAAA-A
81392 AAAAAG
1 AAAAAG
81398 GGGTTAAAGA
Statistics
Matches: 75, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
10 8 0.11
11 51 0.68
12 16 0.21
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:87430 original size:39 final size:39
Alignment explanation
Indices: 87387--87529 Score: 171
Period size: 39 Copynumber: 3.7 Consensus size: 39
87377 AAGGGCTTAC
*
87387 CCTGTGCACAAAGCATAGGAGCCTGC-GATAAGGTCATAT
1 CCTGTGCACAAAGCAGAGGAGCCTGCAG-TAAGGTCATAT
*
87426 CCTGTGCACAAAGCAGAGGAGCCTGCAGTAAGGTCTTAT
1 CCTGTGCACAAAGCAGAGGAGCCTGCAGTAAGGTCATAT
* * * * *
87465 CTTGTGCACAAAACAGAGGAGCCTACAGTAAGGACATAC
1 CCTGTGCACAAAGCAGAGGAGCCTGCAGTAAGGTCATAT
* * * *
87504 CCCGAGCACAAAGCCGAAGAGCCTGC
1 CCTGTGCACAAAGCAGAGGAGCCTGC
87530 GGTTAGAACT
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 87 0.99
40 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.16
Consensus pattern (39 bp):
CCTGTGCACAAAGCAGAGGAGCCTGCAGTAAGGTCATAT
Found at i:88573 original size:18 final size:18
Alignment explanation
Indices: 88550--88598 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
88540 TTTGGTCAAA
*
88550 GTCAATGGTCAACGGTCG
1 GTCAATGGTCAACGATCG
88568 GTCAATGGTCAACGATCG
1 GTCAATGGTCAACGATCG
88586 GTCAATGGTCAAC
1 GTCAATGGTCAAC
88599 AGTCAATGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (18 bp):
GTCAATGGTCAACGATCG
Found at i:93611 original size:39 final size:39
Alignment explanation
Indices: 93555--93710 Score: 186
Period size: 39 Copynumber: 4.0 Consensus size: 39
93545 ATGTACACCT
* * *
93555 AGTAAGGGCTTACCTTGTGCACAAAGCAGAGGAGCCTGC
1 AGTAAGGTCTTATCTTGTGCACAAAGCAGAGGAGCATGC
*
93594 AGTAAGGTCTTATCTTGTGCACAAAGCAGAGGAGTATGC
1 AGTAAGGTCTTATCTTGTGCACAAAGCAGAGGAGCATGC
* * *
93633 AGTAAGGTCTTATCATATGTACAAAGCAGAGGAGCATGC
1 AGTAAGGTCTTATCTTGTGCACAAAGCAGAGGAGCATGC
* * * * * **
93672 AGTAAGGACATACCCTGAGCACAAAGTTGAGGAGCATGC
1 AGTAAGGTCTTATCTTGTGCACAAAGCAGAGGAGCATGC
93711 GGTAGTTAGT
Statistics
Matches: 100, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 100 1.00
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.21
Consensus pattern (39 bp):
AGTAAGGTCTTATCTTGTGCACAAAGCAGAGGAGCATGC
Found at i:119132 original size:14 final size:14
Alignment explanation
Indices: 119113--119149 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
119103 TTGACATTTT
119113 GGTCAAAGTCAACG
1 GGTCAAAGTCAACG
119127 GGTCAAAGTCAACG
1 GGTCAAAGTCAACG
*
119141 AGTCAAAGT
1 GGTCAAAGT
119150 TAATGGGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.16
Consensus pattern (14 bp):
GGTCAAAGTCAACG
Found at i:124039 original size:36 final size:36
Alignment explanation
Indices: 123999--124265 Score: 186
Period size: 36 Copynumber: 7.3 Consensus size: 36
123989 TCTAAACAAA
* * *
123999 GTCTCACTTGAGATAGTTTCTCTTCAAACAAAATTC
1 GTCTCACTCGAGATAGTTTCTCTTAAAACAAAATTT
* * *
124035 GTCTCACTCGAGATAGTTTCCCTCGAAACAAAAAATTT
1 GTCTCACTCGAGATAGTTTCTCT-TAAA-ACAAAATTT
* * *
124073 ATCTCACTTGAGATAGTTAT-TCTTAAAACAAATTTT
1 GTCTCACTCGAGATAGTT-TCTCTTAAAACAAAATTT
* * * * *
124109 GTCTCACTCGATATAGTTTCCCTAAAAATATAAAATT
1 GTCTCACTCGAGATAGTTTCTCTTAAAACA-AAATTT
* * * *
124146 GATCTCACTTGAGATAGTTT-TCCTTAAGATAAATTTT
1 G-TCTCACTCGAGATAGTTTCT-CTTAAAACAAAATTT
* * *
124183 GTCTCACTCGATATAGTTTCTCTTGAAATAAAAGTTTT
1 GTCTCACTCGAGATAGTTTCTCTTAAAACAAAA--TTT
* **
124221 ATCTCA--CGAGATAGTTT-TCTGTAAAA-AATGTTTT
1 GTCTCACTCGAGATAGTTTCTCT-TAAAACAA-AATTT
124255 GTCTCACTCGA
1 GTCTCACTCGA
124266 AACAAAAATT
Statistics
Matches: 179, Mismatches: 38, Indels: 28
0.73 0.16 0.11
Matches are distributed among these distances:
34 8 0.04
35 6 0.03
36 92 0.51
37 16 0.09
38 56 0.31
39 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (36 bp):
GTCTCACTCGAGATAGTTTCTCTTAAAACAAAATTT
Found at i:124102 original size:74 final size:73
Alignment explanation
Indices: 124000--124265 Score: 322
Period size: 74 Copynumber: 3.6 Consensus size: 73
123990 CTAAACAAAG
* * * * * *
124000 TCTCACTTGAGATAGTTTCTCTTCAAACAAAATTCGTCTCACTCGAGATAGTTTCCCTCGAAACA
1 TCTCACTTGAGATAGTTT-TCTTAAAACAAATTTTGTCTCACTCGATATAGTTTCCCTAGAAATA
124065 AAAAATTTA
65 AAAAATTTA
*
124074 TCTCACTTGAGATAGTTATTCTTAAAACAAATTTTGTCTCACTCGATATAGTTTCCCTAAAAATA
1 TCTCACTTGAGATAGTT-TTCTTAAAACAAATTTTGTCTCACTCGATATAGTTTCCCTAGAAATA
* *
124139 TAAAATTGA
65 AAAAATTTA
* * * *
124148 TCTCACTTGAGATAGTTTTCCTTAAGATAAATTTTGTCTCACTCGATATAGTTTCTCTTGAAATA
1 TCTCACTTGAGATAGTTTT-CTTAAAACAAATTTTGTCTCACTCGATATAGTTTCCCTAGAAATA
**
124213 AAAGTTTTA
65 AAAAATTTA
*
124222 TCTCAC--GAGATAGTTTTCTGTAAAA-AATGTTTTGTCTCACTCGA
1 TCTCACTTGAGATAGTTTTCT-TAAAACAA-ATTTTGTCTCACTCGA
124266 AACAAAAATT
Statistics
Matches: 168, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
71 4 0.02
72 30 0.18
73 2 0.01
74 131 0.78
75 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (73 bp):
TCTCACTTGAGATAGTTTTCTTAAAACAAATTTTGTCTCACTCGATATAGTTTCCCTAGAAATAA
AAAATTTA
Found at i:124394 original size:36 final size:35
Alignment explanation
Indices: 124353--124475 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 35
124343 AATTTATCTA
*
124353 ACTTGAGATAATATCCCTTGCAACAAATTTTGTCTC
1 ACTTGAGATAATTTCCCTTG-AACAAATTTTGTCTC
* * ** *
124389 ACTTGAGACAGTTTCCCTTGAAACAAAAATTGCATCTT
1 ACTTGAGATAATTTCCCTTG-AACAAATTTTG--TCTC
* * * *
124427 ACTTGAGATATTTTCTCTTGAAAAAATTTTGTCCC
1 ACTTGAGATAATTTCCCTTGAACAAATTTTGTCTC
*
124462 ACTCGAGATAATTT
1 ACTTGAGATAATTT
124476 TTTGACATGG
Statistics
Matches: 68, Mismatches: 17, Indels: 5
0.76 0.19 0.06
Matches are distributed among these distances:
35 14 0.21
36 26 0.38
37 8 0.12
38 20 0.29
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (35 bp):
ACTTGAGATAATTTCCCTTGAACAAATTTTGTCTC
Found at i:126776 original size:8 final size:8
Alignment explanation
Indices: 126763--126795 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
126753 AGTGTTGATA
126763 ATATGTAT
1 ATATGTAT
126771 ATATGTAT
1 ATATGTAT
126779 ATATGT-T
1 ATATGTAT
*
126786 ACATGTAT
1 ATATGTAT
126794 AT
1 AT
126796 GTTATGTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.48
Consensus pattern (8 bp):
ATATGTAT
Found at i:126866 original size:15 final size:15
Alignment explanation
Indices: 126846--126875 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
126836 TTTTTAGTAA
126846 TTTATAAGTAATTAT
1 TTTATAAGTAATTAT
*
126861 TTTATAAGTTATTAT
1 TTTATAAGTAATTAT
126876 ACATATTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
TTTATAAGTAATTAT
Found at i:135743 original size:337 final size:333
Alignment explanation
Indices: 135117--136077 Score: 895
Period size: 337 Copynumber: 2.9 Consensus size: 333
135107 CGAGCTTCGC
* * * * * * * *
135117 AAAAAG-TGAAAACGCTTCTTATGAAAATAACCTTCCATTTTT-CAGAGCATTTTTGCATTTTTG
1 AAAAAGATGAAAACGCATCTTGTGAAAATTACCTTCCCTTTTTCCAGAGAATCTATGCA-TTTTC
* * * * * * *
135180 TAGTTAATTTTATCATT-AGATTATGTTCCCCTTTAGGAACTATTAATCACAACAACTCCCTCGA
65 CAGTCAATTTTATC-TTCAGATAATGTTCACCTTTGGGAACTATTCATCACAACAACTCCC-CGT
* * * *
135244 CTGATAGGATGCAACACTATGGCATGGCAAAGATTCCCTACAAAAGGTGAAAGCGCATCTTGTGA
128 CTGAT-GGATGCAACACTATGACATGACAGAGATT-CCTACAAAAGGTGAAAGCG-GTCTTGTGA
* * * ** *
135309 AAATAGCCTTCCCCTTTTTTCCAGAGAATCTC--TA-CAT-CAGTCAATT-TTATCTTCAAATAA
190 AAAAAACCTT-CCATTTTTT--AGAGAATCTCTGTATTTTCCAGTCAATTGTTATCTTCATATAA
*** * * *
135369 TGTTCCCCTTCAAAAAAATATTCTTCACAAGAACTCCCCTATCTGATGAGATGCGAA-ACTATGA
252 TGTTCCCCTTCAGGGAACTATTCTTCACAACAACTCCCCTATCTGATGAGAT-AGAACACTATGA
* *
135433 TATGGTAGAGATTCCCTA
316 CATAGTAGAGATTCCCTA
** * *
135451 CGAAAGATGAAAACGCATCTTGTGAAAA-TAGCCTTCTTCTTCTTTCCATAGAATCTATGCATTT
1 AAAAAGATGAAAACGCATCTTGTGAAAATTA-CCTTC-CCTT-TTTCCAGAGAATCTATGCATTT
* *
135515 TCCAGTCAATTTTATCTTCAGATAATGTTCACTTTTGGGGAACTATTCATCACATCAACTCCCCG
63 TCCAGTCAATTTTATCTTCAGATAATGTTCACCTTT-GGGAACTATTCATCACAACAACTCCCCG
* * *
135580 TCTGATGCGATGCAATACTATGACATGACAGAGATTCCTACAAAAAGTGAAAACGGTTCTTGTGA
127 TCTGATG-GATGCAACACTATGACATGACAGAGATTCCTACAAAAGGTGAAAGCGG-TCTTGTGA
* *
135645 AAAAAACCTTCCATTTTTTAGAGAATCTCTGTATTTTCCAGTTAATTGTT-TCTTCATATGATGT
190 AAAAAACCTTCCATTTTTTAGAGAATCTCTGTATTTTCCAGTCAATTGTTATCTTCATATAATGT
* * * * *
135709 TCCCCTTCAGGGAACTATTCATT-ATAACAACTCCCCTATCTGATGGGATATAACTCTATGGCAT
255 TCCCCTTCAGGGAACTATTC-TTCACAACAACTCCCCTATCTGATGAGATAGAACACTATGACAT
135773 AGTAGAGATTCCCTA
319 AGTAGAGATTCCCTA
* ** * * * * *
135788 AAAAAGGTGAAAGTGCTTCTTGTGAAAATTATCTTCCCTTTTTTCAGAGAATTTTTGCATTTTCC
1 AAAAAGATGAAAACGCATCTTGTGAAAATTACCTTCCCTTTTTCCAGAGAATCTATGCATTTTCC
* *
135853 AGTCAATTTTATCTTCAGATAATATT-ATCCTTCAGGGAACTATTCATCACAACAACTCCCCTGT
66 AGTCAATTTTATCTTCAGATAATGTTCA-CCTT-TGGGAACTATTCATCACAACAACTCCCC-GT
* * *
135917 TTAATGGGATGCAGCACTATGACATGGA-AGAGATT-CTATGCAAAAGGTGAAAGC-G-CTTGTG
128 CTGAT-GGATGCAACACTATGACAT-GACAGAGATTCCTA--CAAAAGGTGAAAGCGGTCTTGTG
* * **
135978 AAAATTGAA--TT-CATTTTTTTAGAGAATCTATGCCTTTTCCAGTCAA-TGTTATCTTCATATA
189 AAAA--AAACCTTCCA-TTTTTTAGAGAATCTCTGTATTTTCCAGTCAATTGTTATCTTCATATA
* * *
136039 ATGTTTCCCTTCGGGGAACTATT-TATCACCACAACTCCC
251 ATGTTCCCCTTCAGGGAACTATTCT-TCACAACAACTCCC
136078 ATTTTTATAT
Statistics
Matches: 516, Mismatches: 81, Indels: 60
0.79 0.12 0.09
Matches are distributed among these distances:
332 1 0.00
333 17 0.03
334 86 0.17
335 112 0.22
336 75 0.15
337 185 0.36
338 40 0.08
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.34
Consensus pattern (333 bp):
AAAAAGATGAAAACGCATCTTGTGAAAATTACCTTCCCTTTTTCCAGAGAATCTATGCATTTTCC
AGTCAATTTTATCTTCAGATAATGTTCACCTTTGGGAACTATTCATCACAACAACTCCCCGTCTG
ATGGATGCAACACTATGACATGACAGAGATTCCTACAAAAGGTGAAAGCGGTCTTGTGAAAAAAA
CCTTCCATTTTTTAGAGAATCTCTGTATTTTCCAGTCAATTGTTATCTTCATATAATGTTCCCCT
TCAGGGAACTATTCTTCACAACAACTCCCCTATCTGATGAGATAGAACACTATGACATAGTAGAG
ATTCCCTA
Found at i:135887 original size:169 final size:169
Alignment explanation
Indices: 135117--136077 Score: 823
Period size: 167 Copynumber: 5.7 Consensus size: 169
135107 CGAGCTTCGC
* * * * * * *
135117 AAAAA-GTGAAAACGCTTCTTATGAAAATAACCTT-CCATTTTTCAGAGCATTTTTGCATTTTTG
1 AAAAAGGTGAAAACGCTTCTTGTGAAAATTACCTTCCCTTTTTTCAGAGAATCTATGCA-TTTTC
* * * * * *
135180 TAGTTAATTTTATCATT-AGATTATGTTCCCCTTTA-GGAACTATTAATCACAACAACTCCCTCG
65 CAGTCAATTTTATC-TTCAGATAATGTTCCCCTTCAGGGAACTATTCATCACAACAACTCCC-CT
* * *
135243 A-CTGATAGGATGCAACACTATGGCATGGCAAAGATTCCCTA
128 ATCTGATGGGATGCAACACTATGACATGGCAGAGATTCCCTA
* * * * *
135284 CAAAAGGTGAAAGCGCATCTTGTGAAAA-TAGCCTTCCCCTTTTTTCCAGAGAATCTCTACA---
1 AAAAAGGTGAAAACGCTTCTTGTGAAAATTA-CCTT-CCCTTTTTT-CAGAGAATCTATGCATTT
* *** * * *
135345 T-CAGTCAATTTTATCTTCAAATAATGTTCCCCTTCAAAAAAATATTCTTCACAAGAACTCCCCT
63 TCCAGTCAATTTTATCTTCAGATAATGTTCCCCTTCAGGGAACTATTCATCACAACAACTCCCCT
* * *
135409 ATCTGATGAGATGCGAA-ACTATGATATGGTAGAGATTCCCTA
128 ATCTGATGGGATGC-AACACTATGACATGGCAGAGATTCCCTA
** * * * * *
135451 CGAAAGATGAAAACGCATCTTGTGAAAA-TAGCCTTCTTCTTCTTTCCATAGAATCTATGCATTT
1 AAAAAGGTGAAAACGCTTCTTGTGAAAATTA-CCTTC-CCTT-TTTTCAGAGAATCTATGCATTT
* * ** *
135515 TCCAGTCAATTTTATCTTCAGATAATGTTCACTTTTGGGGAACTATTCATCACATCAACTCCCC-
63 TCCAGTCAATTTTATCTTCAGATAATGTTCCCCTTCAGGGAACTATTCATCACAACAACTCCCCT
* * * *
135579 GTCTGATGCGATGCAATACTATGACATGACAGAGATT-CCTA
128 ATCTGATGGGATGCAACACTATGACATGGCAGAGATTCCCTA
* ** * * *
135620 CAAAAA-GTGAAAACGGTTCTTGTGAAAAAAACCTTCCATTTTTT-AGAGAATCTCTGTATTTTC
1 -AAAAAGGTGAAAACGCTTCTTGTGAAAATTACCTTCCCTTTTTTCAGAGAATCTATGCATTTTC
* * * * *
135683 CAGTTAATTGTT-TCTTCATATGATGTTCCCCTTCAGGGAACTATTCATTATAACAACTCCCCTA
65 CAGTCAATT-TTATCTTCAGATAATGTTCCCCTTCAGGGAACTATTCATCACAACAACTCCCCTA
** * * * *
135747 TCTGATGGGATATAACTCTATGGCATAGTAGAGATTCCCTA
129 TCTGATGGGATGCAACACTATGACATGGCAGAGATTCCCTA
** * * *
135788 AAAAAGGTGAAAGTGCTTCTTGTGAAAATTATCTTCCCTTTTTTCAGAGAATTTTTGCATTTTCC
1 AAAAAGGTGAAAACGCTTCTTGTGAAAATTACCTTCCCTTTTTTCAGAGAATCTATGCATTTTCC
* ** * *
135853 AGTCAATTTTATCTTCAGATAATATTATCCTTCAGGGAACTATTCATCACAACAACTCCCCTGTT
66 AGTCAATTTTATCTTCAGATAATGTTCCCCTTCAGGGAACTATTCATCACAACAACTCCCCTATC
* * * ** *
135918 TAATGGGATGCAGCACTATGACATGGAAGAGATTCTATG
131 TGATGGGATGCAACACTATGACATGGCAGAGATTCCCTA
* * * * * *
135957 CAAAAGGTG-AAA-GC-GCTTGTGAAAATTGA-ATT-CATTTTTTTAGAGAATCTATGCCTTTTC
1 AAAAAGGTGAAAACGCTTCTTGTGAAAATT-ACCTTCCCTTTTTTCAGAGAATCTATGCATTTTC
* * * * * *
136017 CAGTCAATGTTATCTTCATATAATGTTTCCCTTCGGGGAACTATTTATCACCACAACTCCC
65 CAGTCAATTTTATCTTCAGATAATGTTCCCCTTCAGGGAACTATTCATCACAACAACTCCC
136078 ATTTTTATAT
Statistics
Matches: 636, Mismatches: 133, Indels: 52
0.77 0.16 0.06
Matches are distributed among these distances:
165 78 0.12
166 109 0.17
167 143 0.22
168 69 0.11
169 135 0.21
170 41 0.06
171 61 0.10
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.34
Consensus pattern (169 bp):
AAAAAGGTGAAAACGCTTCTTGTGAAAATTACCTTCCCTTTTTTCAGAGAATCTATGCATTTTCC
AGTCAATTTTATCTTCAGATAATGTTCCCCTTCAGGGAACTATTCATCACAACAACTCCCCTATC
TGATGGGATGCAACACTATGACATGGCAGAGATTCCCTA
Found at i:137119 original size:21 final size:21
Alignment explanation
Indices: 137087--137133 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
137077 TATGCTTTAG
*
137087 GTTT-TCCATCATCTATCTCT
1 GTTTCTCCATCATCTACCTCT
* * *
137107 GTTTCTCCCTCATTTACCTTT
1 GTTTCTCCATCATCTACCTCT
137128 GTTTCT
1 GTTTCT
137134 ATATTATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.11, C:0.30, G:0.06, T:0.53
Consensus pattern (21 bp):
GTTTCTCCATCATCTACCTCT
Found at i:138973 original size:166 final size:165
Alignment explanation
Indices: 138588--139317 Score: 563
Period size: 166 Copynumber: 4.4 Consensus size: 165
138578 TATAGACATG
* * * * * *
138588 GGAGTTGTAGTCATGAATACTTCCCTGAAGGAGAAAATTATCTCAAGATAAAATTGACTGGAAAA
1 GGAGTTGTTGTGATGAATAGTTCCC-GAAGGGGAACATTATCTGAAGATAAAATTGACTGGAAAA
* * * * ** * * * * *
138653 TGAAGAGATTCTCTAAAAAAAAAGGAAGGATATTGACACAAGAA-AAGTTTTAACCTTTTGCAAG
65 TGAAAAGATTCTCT--ATAAAAGGGAA-GCTATTTTCACAAGAATCA-CTTTCACCTTTTGTAGG
* * * * *
138717 AAATCTC-GCCATGTCATTGTGTT-ATTTCCTATCAGAAAGG
126 AAATCTCTTCCATGTCATAGTGTTGA-ATCC-ATCAGATAGA
* * * * * *
138757 GGAATTGTTGTGATGAATAATTCCCTAAAGGGGGACATTATCTTAAGATAAAATTGACTGGTAAA
1 GGAGTTGTTGTGATGAATAGTTCCC-GAAGGGGAACATTATCTGAAGATAAAATTGACTGGAAAA
* * * * *
138822 TGAAAAGATTCTCTAAAAAAAGGAAGTTATTTTCACATGAATCACTTTCACCTTTTGTAGAAAAT
65 TGAAAAGATTCTCTATAAAAGGGAAGCTATTTTCACAAGAATCACTTTCACCTTTTGTAGGAAAT
** * *
138887 CTCTTCCATGTCATAGCATTGGATCCATCAGATAAA
130 CTCTTCCATGTCATAGTGTTGAATCCATCAGATAGA
* * * * *
138923 GAAGTTTTTGTGATGAATAGTTCACCGAAGGGGAACATTATCTGAAGATAAATTTGAATTGAAAA
1 GGAGTTGTTGTGATGAATAGTTC-CCGAAGGGGAACATTATCTGAAGATAAAATTGACTGGAAAA
* * * * * * * * *** * *
138988 TGCATACATTCTCT-TTAAAGGGAAGGCCATTATCAGAAAAATTGTTTTCACCTTTTGCAGGGAA
65 TGAAAAGATTCTCTATAAAAGGGAA-GCTATTTTCACAAGAATCACTTTCACCTTTTGTAGGAAA
* * *
139052 TCTCTGCCATGTCATAGTGTTGAATCCTATTAGATAGG
129 TCTCTTCCATGTCATAGTGTTGAATCC-ATCAGATAGA
* * * ** * * **
139090 GGAGTTGTTGGGATGAATAGTTACCTAATAGGAATATTATCTGAAGATAAAATTAACTAAAAAAT
1 GGAGTTGTTGTGATGAATAGTTCCCGAAGGGGAACATTATCTGAAGATAAAATTGACTGGAAAAT
* ** * *
139155 GTAGGGATTCTCTATAAAAGGGAAGACTATTTTTCACAAGAAACACTTTCACCATTTGTAGGAAA
66 GAAAAGATTCTCTATAAAAGGGAAG-CTA-TTTTCACAAGAATCACTTTCACCTTTTGTAGGAAA
* ** *
139220 TCTCCAT-CATGTCATAGTGTTGCACCCCA-CCGATAGA
129 TCT-CTTCCATGTCATAGTGTTG-AATCCATCAGATAGA
** *
139257 GGAGTTGTTGTGATGAATAGTTTCCCGAAGGATAACATTATCTGAATATAAAATTGACTGG
1 GGAGTTGTTGTGATGAATAG-TTCCCGAAGGGGAACATTATCTGAAGATAAAATTGACTGG
139318 CGAAGAGATT
Statistics
Matches: 435, Mismatches: 114, Indels: 25
0.76 0.20 0.04
Matches are distributed among these distances:
165 7 0.02
166 193 0.44
167 90 0.21
168 73 0.17
169 72 0.17
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (165 bp):
GGAGTTGTTGTGATGAATAGTTCCCGAAGGGGAACATTATCTGAAGATAAAATTGACTGGAAAAT
GAAAAGATTCTCTATAAAAGGGAAGCTATTTTCACAAGAATCACTTTCACCTTTTGTAGGAAATC
TCTTCCATGTCATAGTGTTGAATCCATCAGATAGA
Found at i:139233 original size:334 final size:331
Alignment explanation
Indices: 138699--139313 Score: 745
Period size: 334 Copynumber: 1.8 Consensus size: 331
138689 CACAAGAAAA
* *
138699 GTTTTAACCTTTTGCAAGAAATCTCGCCATGTCATTGTGTTATTTCCTATCAGAAAGGGGAATTG
1 GTTTTAACCTTTTGCAAGAAATCTCGCCATGTCATAGTGTTATATCCTATCAGAAAGGGGAATTG
* * * * * ***
138764 TTGTGATGAATAATTCCCTAAAGGGGGACATTATCTTAAGATAAAATTGACTGGTAAATGAAAAG
66 TTGGGATGAATAATTACCTAAA-GGGAACATTATCTGAAGATAAAATTAACTAAAAAATGAAAAG
* * * * *
138829 ATTCTCTAAAAAAAGGAAGTTATTTTCACATGAATCACTTTCACCTTTTGTAGAAAATCTCTTCC
130 ATTCTCTAAAAAAAGGAAGCTATTTTCACAAGAAACACTTTCACCATTTGTAGAAAATCTCATCC
* * * *
138894 ATGTCATAGCATTGGA-TCCATCAGATAAAGAAGTTTTTGTGATGAATAG-TTCACCGAAGGGGA
195 ATGTCATAGCATTGCACCCCA-CAGATAAAGAAGTTGTTGTGATGAATAGTTTC-CCGAAGGAGA
*
138957 ACATTATCTGAAGATAAATTTGAATTGAAAATGCATACATTCTCTTTAAAGGGAAGGCCATTATC
258 ACATTATCTGAAGATAAAATTGAATTGAAAATGCATACATTCTCTTTAAAGGGAAGGCCATTATC
139022 AGAAAAATT
323 AGAAAAATT
* * * * * *
139031 GTTTTCACCTTTTGCAGGGAATCTCTGCCATGTCATAGTGTTGA-ATCCTATTAGATAGGGGAGT
1 GTTTTAACCTTTTGCAAGAAATCTC-GCCATGTCATAGTGTT-ATATCCTATCAGAAAGGGGAAT
* * * *
139095 TGTTGGGATGAATAGTTACCTAATA-GGAATATTATCTGAAGATAAAATTAACTAAAAAATGTAG
64 TGTTGGGATGAATAATTACCTAA-AGGGAACATTATCTGAAGATAAAATTAACTAAAAAATGAAA
* * * *
139159 GGATTCTCTATAAAAGGGAAGACTATTTTTCACAAGAAACACTTTCACCATTTGTAGGAAATCTC
128 AGATTCTCTAAAAAAAGGAAG-CTA-TTTTCACAAGAAACACTTTCACCATTTGTAGAAAATCT-
** * * *
139224 CAT-CATGTCATAGTGTTGCACCCCACCGATAGAGGAGTTGTTGTGATGAATAGTTTCCCGAAGG
190 CATCCATGTCATAGCATTGCACCCCACAGATAAAGAAGTTGTTGTGATGAATAGTTTCCCGAAGG
* *
139288 ATAACATTATCTGAATATAAAATTGA
255 AGAACATTATCTGAAGATAAAATTGA
139314 CTGGCGAAGA
Statistics
Matches: 234, Mismatches: 41, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
332 70 0.30
333 53 0.23
334 103 0.44
335 8 0.03
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (331 bp):
GTTTTAACCTTTTGCAAGAAATCTCGCCATGTCATAGTGTTATATCCTATCAGAAAGGGGAATTG
TTGGGATGAATAATTACCTAAAGGGAACATTATCTGAAGATAAAATTAACTAAAAAATGAAAAGA
TTCTCTAAAAAAAGGAAGCTATTTTCACAAGAAACACTTTCACCATTTGTAGAAAATCTCATCCA
TGTCATAGCATTGCACCCCACAGATAAAGAAGTTGTTGTGATGAATAGTTTCCCGAAGGAGAACA
TTATCTGAAGATAAAATTGAATTGAAAATGCATACATTCTCTTTAAAGGGAAGGCCATTATCAGA
AAAATT
Found at i:139665 original size:2 final size:2
Alignment explanation
Indices: 139653--139690 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
139643 GGTTTAATAA
*
139653 AT AT A- AT AT AT AT AT AT AT AT AT AT AG 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 AT A
139691 GTTATACTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:140318 original size:26 final size:26
Alignment explanation
Indices: 140287--140393 Score: 111
Period size: 26 Copynumber: 4.3 Consensus size: 26
140277 ACACATAGTG
*
140287 TCATTTATCACTTGCACTCAAAGGTT
1 TCATTTATCAATTGCACTCAAAGGTT
*
140313 TCATTTAT---TTACACTCGAAAGTGTT
1 TCATTTATCAATTGCACTC-AAAG-GTT
140338 T-A--T-TCAATTGCACTCAAAGGTT
1 TCATTTATCAATTGCACTCAAAGGTT
* *
140360 CCATTTATCAATTGCACTCGAAGGTT
1 TCATTTATCAATTGCACTCAAAGGTT
140386 TCATTTAT
1 TCATTTAT
140394 ACCAAGATCT
Statistics
Matches: 67, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
21 1 0.01
22 4 0.06
23 12 0.18
24 12 0.18
25 5 0.07
26 33 0.49
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (26 bp):
TCATTTATCAATTGCACTCAAAGGTT
Done.