Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003676.1 Hibiscus syriacus cultivar Beakdansim tig00007856_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: 62930
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2289 original size:13 final size:13
Alignment explanation
Indices: 2271--2355 Score: 80
Period size: 13 Copynumber: 5.8 Consensus size: 13
2261 GTCAACGGGT
2271 CGGGTCGGGTTAA
1 CGGGTCGGGTTAA
2284 CGGGTCGTGTCGGGTTAA
1 C-GG--GT--CGGGTTAA
2302 CGGGTCGGGTTAA
1 CGGGTCGGGTTAA
2315 CGGGTCGTGTCGGGTTAA
1 C--G--G-GTCGGGTTAA
2333 CGGGTCGGGTTAA
1 CGGGTCGGGTTAA
2346 CGGGTCGGGT
1 CGGGTCGGGT
2356 CGTGACCGGT
Statistics
Matches: 62, Mismatches: 0, Indels: 20
0.76 0.00 0.24
Matches are distributed among these distances:
13 30 0.48
14 3 0.05
15 3 0.05
16 3 0.05
17 3 0.05
18 20 0.32
ACGTcount: A:0.12, C:0.16, G:0.47, T:0.25
Consensus pattern (13 bp):
CGGGTCGGGTTAA
Found at i:2306 original size:31 final size:31
Alignment explanation
Indices: 2271--2357 Score: 165
Period size: 31 Copynumber: 2.8 Consensus size: 31
2261 GTCAACGGGT
2271 CGGGTCGGGTTAACGGGTCGTGTCGGGTTAA
1 CGGGTCGGGTTAACGGGTCGTGTCGGGTTAA
2302 CGGGTCGGGTTAACGGGTCGTGTCGGGTTAA
1 CGGGTCGGGTTAACGGGTCGTGTCGGGTTAA
*
2333 CGGGTCGGGTTAACGGGTCGGGTCG
1 CGGGTCGGGTTAACGGGTCGTGTCG
2358 TGACCGGTTA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.11, C:0.17, G:0.47, T:0.24
Consensus pattern (31 bp):
CGGGTCGGGTTAACGGGTCGTGTCGGGTTAA
Found at i:2357 original size:18 final size:18
Alignment explanation
Indices: 2264--2342 Score: 105
Period size: 18 Copynumber: 4.7 Consensus size: 18
2254 GTCAACAGTC
2264 AACGGGTCGGGTCGGGTT
1 AACGGGTCGGGTCGGGTT
*
2282 AACGGGTCGTGTCGGGTT
1 AACGGGTCGGGTCGGGTT
2300 AA-----CGGGTCGGGTT
1 AACGGGTCGGGTCGGGTT
*
2313 AACGGGTCGTGTCGGGTT
1 AACGGGTCGGGTCGGGTT
2331 AACGGGTCGGGT
1 AACGGGTCGGGT
2343 TAACGGGTCG
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 12 0.23
18 40 0.77
ACGTcount: A:0.13, C:0.16, G:0.47, T:0.24
Consensus pattern (18 bp):
AACGGGTCGGGTCGGGTT
Found at i:3154 original size:20 final size:20
Alignment explanation
Indices: 3131--3191 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
3121 CACAAAATCT
3131 GAAGTTTTTAACCGAAATTG
1 GAAGTTTTTAACCGAAATTG
* *
3151 GAAG---AT-ACACAAAATCT-
1 GAAGTTTTTAAC-CGAAAT-TG
3168 GAAGTTTTTAACCGAAATTG
1 GAAGTTTTTAACCGAAATTG
3188 GAAG
1 GAAG
3192 ATGATAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 14
0.62 0.08 0.29
Matches are distributed among these distances:
16 2 0.07
17 10 0.33
18 1 0.03
19 1 0.03
20 14 0.47
21 2 0.07
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (20 bp):
GAAGTTTTTAACCGAAATTG
Found at i:3160 original size:37 final size:37
Alignment explanation
Indices: 3119--3193 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
3109 TTTGGGTTGT
3119 TACACAAAATCTGAAGTTTTTAACCGAAATTGGAAGA
1 TACACAAAATCTGAAGTTTTTAACCGAAATTGGAAGA
3156 TACACAAAATCTGAAGTTTTTAACCGAAATTGGAAGA
1 TACACAAAATCTGAAGTTTTTAACCGAAATTGGAAGA
3193 T
1 T
3194 GATAAAAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (37 bp):
TACACAAAATCTGAAGTTTTTAACCGAAATTGGAAGA
Found at i:10278 original size:31 final size:32
Alignment explanation
Indices: 10214--10320 Score: 101
Period size: 31 Copynumber: 3.2 Consensus size: 32
10204 AACTAAATTA
* * *
10214 AAATATTATTAAAAACATGCCATTA-TCCATT
1 AAATATTATTAAAAACAAGTCATTAGTCGATT
* *
10245 AAATATTATTAAAAATAAGTCATTAGTTGTTAAATT
1 AAATATTATTAAAAACAAGTCATTAGTCG----ATT
*
10281 AAAATATTATTAAAAGCAAGTCATTAGTCG-TT
1 -AAATATTATTAAAAACAAGTCATTAGTCGATT
10313 AAATATTA
1 AAATATTA
10321 GATATGAATA
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
31 30 0.48
32 3 0.05
36 3 0.05
37 26 0.42
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.37
Consensus pattern (32 bp):
AAATATTATTAAAAACAAGTCATTAGTCGATT
Found at i:10287 original size:37 final size:37
Alignment explanation
Indices: 10207--10316 Score: 124
Period size: 37 Copynumber: 3.1 Consensus size: 37
10197 AACATATAAC
* *
10207 TAAATTAAAATATTATTAAAAACATGCCATTA-TC--
1 TAAATTAAAATATTATTAAAAACAAGTCATTAGTCGT
* * *
10241 --CATT-AAATATTATTAAAAATAAGTCATTAGTTGT
1 TAAATTAAAATATTATTAAAAACAAGTCATTAGTCGT
*
10275 TAAATTAAAATATTATTAAAAGCAAGTCATTAGTCGT
1 TAAATTAAAATATTATTAAAAACAAGTCATTAGTCGT
10312 TAAAT
1 TAAAT
10317 ATTAGATATG
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
31 22 0.36
32 4 0.07
36 3 0.05
37 32 0.52
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.37
Consensus pattern (37 bp):
TAAATTAAAATATTATTAAAAACAAGTCATTAGTCGT
Found at i:11740 original size:20 final size:19
Alignment explanation
Indices: 11715--11767 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
11705 TGTTCATGTG
11715 AGTATCGATACTAACCTACC-
1 AGTATCGATACTAA-C-ACCA
*
11735 AGTATCGATACCAACACCA
1 AGTATCGATACTAACACCA
11754 TAGTATCGATACTA
1 -AGTATCGATACTA
11768 GAAAAACTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 3 0.10
19 1 0.03
20 25 0.86
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.25
Consensus pattern (19 bp):
AGTATCGATACTAACACCA
Found at i:13565 original size:30 final size:30
Alignment explanation
Indices: 13478--13594 Score: 107
Period size: 30 Copynumber: 3.9 Consensus size: 30
13468 AAAATTTTGG
* *
13478 TTAGTGACCAAAATGTA-AAATTT-AAAAGT
1 TTAGGGACCAAAA-GTACAATTTTAAAAAGT
* * *
13507 TTAGTG-CCATAA-TATAATGTTTAGAAAAGT
1 TTAGGGACCAAAAGTACAAT-TTTA-AAAAGT
* *
13537 TTTGGGACCAAAAGTGCAATTTTAAAAAGT
1 TTAGGGACCAAAAGTACAATTTTAAAAAGT
*
13567 TTAGGGACCAAATGTACAATTTTAAAAA
1 TTAGGGACCAAAAGTACAATTTTAAAAA
13595 ATTAAGTGTT
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
26 2 0.03
27 2 0.03
28 8 0.11
29 6 0.08
30 41 0.57
31 9 0.12
32 4 0.06
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.32
Consensus pattern (30 bp):
TTAGGGACCAAAAGTACAATTTTAAAAAGT
Found at i:16320 original size:61 final size:61
Alignment explanation
Indices: 16220--16340 Score: 188
Period size: 61 Copynumber: 2.0 Consensus size: 61
16210 TTACAGGTGA
* *
16220 TGGGCACAACCTTATGTGTCATATCCAGATCAACACTAGAGCGTAAAACTAGTGTAGGTTG
1 TGGGCACAACCTTATGTGTCATATCCAGATCAACACTAGAACGTAAAACTAGTGCAGGTTG
* * * *
16281 TGGGTACAACCTTATGTGTCATATCCGGATCAACACTAGAACGTAAGATTAGTGCAGGTT
1 TGGGCACAACCTTATGTGTCATATCCAGATCAACACTAGAACGTAAAACTAGTGCAGGTT
16341 TTGTACTACG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (61 bp):
TGGGCACAACCTTATGTGTCATATCCAGATCAACACTAGAACGTAAAACTAGTGCAGGTTG
Found at i:27261 original size:39 final size:39
Alignment explanation
Indices: 27214--27295 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
27204 ATCATTTGAT
27214 TTTTGCTGCACATATTCTGGAACTAATTAACACATTTCC
1 TTTTGCTGCACATATTCTGGAACTAATTAACACATTTCC
*
27253 TTTTGCTGCACATATTCTGGAAGTAATTAACACATTTCC
1 TTTTGCTGCACATATTCTGGAACTAATTAACACATTTCC
27292 TTTT
1 TTTT
27296 TCAGGTTGCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (39 bp):
TTTTGCTGCACATATTCTGGAACTAATTAACACATTTCC
Found at i:27390 original size:13 final size:13
Alignment explanation
Indices: 27374--27401 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
27364 CATATTGATG
27374 CTCAAAATTGCCA
1 CTCAAAATTGCCA
27387 CTCAAAATTGCCA
1 CTCAAAATTGCCA
27400 CT
1 CT
27402 TGAAGAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.32, G:0.07, T:0.25
Consensus pattern (13 bp):
CTCAAAATTGCCA
Found at i:28815 original size:3 final size:3
Alignment explanation
Indices: 28807--28856 Score: 82
Period size: 3 Copynumber: 16.3 Consensus size: 3
28797 TGTTCGGATT
*
28807 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA CTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
28853 TTA T
1 TTA T
28857 AAATAAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:29262 original size:6 final size:5
Alignment explanation
Indices: 29244--29328 Score: 61
Period size: 6 Copynumber: 16.2 Consensus size: 5
29234 GGGATTAAAA
*
29244 ATATAT ATATT ATACT -TATT ATTATT ATATT ATTATT ATTATT ATATT
1 ATAT-T ATATT ATATT ATATT A-TATT ATATT A-TATT A-TATT ATATT
29292 -TATT ATGATT ATGA-T -TATT ATTATT ATATT ATTATT A
1 ATATT AT-ATT AT-ATT ATATT A-TATT ATATT A-TATT A
29329 ATAATAATTA
Statistics
Matches: 68, Mismatches: 2, Indels: 18
0.77 0.02 0.20
Matches are distributed among these distances:
3 1 0.01
4 9 0.13
5 21 0.31
6 37 0.54
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:29263 original size:9 final size:8
Alignment explanation
Indices: 29245--29326 Score: 69
Period size: 9 Copynumber: 9.4 Consensus size: 8
29235 GGATTAAAAA
29245 TATATATAT
1 TATAT-TAT
29254 TATACTTA-
1 TATA-TTAT
29262 T-TATTAT
1 TATATTAT
29269 TATATTAT
1 TATATTAT
29277 TATTATTAT
1 TA-TATTAT
29286 TATATTTAT
1 TATA-TTAT
29295 TATGATTATGAT
1 TAT-A-T-T-AT
29307 TATTATTAT
1 TA-TATTAT
29316 TATATTAT
1 TATATTAT
29324 TAT
1 TAT
29327 TAATAATAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 19
0.77 0.00 0.23
Matches are distributed among these distances:
6 3 0.05
7 3 0.05
8 20 0.31
9 25 0.39
10 5 0.08
11 2 0.03
12 5 0.08
13 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.61
Consensus pattern (8 bp):
TATATTAT
Found at i:29341 original size:3 final size:3
Alignment explanation
Indices: 29259--29328 Score: 92
Period size: 3 Copynumber: 24.0 Consensus size: 3
29249 TATATTATAC
*
29259 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA -TA TTTA TTA TGA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
*
29303 TGA TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
29329 ATAATAATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
2 6 0.10
3 51 0.86
4 2 0.03
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:30521 original size:43 final size:43
Alignment explanation
Indices: 30460--30962 Score: 388
Period size: 43 Copynumber: 10.9 Consensus size: 43
30450 ATGAAGGACA
*
30460 ATCGTGATATGTAGGGGTTCTTTGATAACAAGCTTGAGAAACC
1 ATCGTGATATGTAGGGGTTCTTTGATGACAAGCTTGAGAAACC
* **
30503 ATCGTGATATGTAGGGGTT-TCTTGATGACAATCTTGAGGGACC
1 ATCGTGATATGTAGGGGTTCT-TTGATGACAAGCTTGAGAAACC
* *
30546 ATCGTGATATGTAGGGGTTCCTTGATGACAAACTTGATGATAAGCTTGAAGGACC
1 ATCGTGATATGTAGGGGTTCTTTGATGACAAGC-T--TG---A----GAA--ACC
*
30601 ATCGTGATATGTAGGGGTTCTTTGATAACAAGCTTGAGAAACC
1 ATCGTGATATGTAGGGGTTCTTTGATGACAAGCTTGAGAAACC
* *
30644 ATCGTGATATGTAGGGGTT-TCTTGATGACAATCTTGATG-GACC
1 ATCGTGATATGTAGGGGTTCT-TTGATGACAAGCTTGA-GAAACC
* *
30687 ATCGTGATATGTAGGGGTTCCTTGATGACAAACTTGATAATAAGCTTGAAGGACC
1 ATCGTGATATGTAGGGGTTCTTTGATGACAAGCTTG------A----GAA--ACC
* * *
30742 ATCGTGATATATAGGGGTTCTTTAATAACAAGCTTGAGAAACC
1 ATCGTGATATGTAGGGGTTCTTTGATGACAAGCTTGAGAAACC
* **
30785 ATCGTGATATGTAGGGGTT-TCTTGATGACAATCTTGAGGGACC
1 ATCGTGATATGTAGGGGTTCT-TTGATGACAAGCTTGAGAAACC
*
30828 ATCGTGATATGTAGGGGTT-TCTTGATGACAAACTTGATGATAAGCTTGAAGGACC
1 ATCGTGATATGTAGGGGTTCT-TTGATGACAAGC-T--TG---A----GAA--ACC
* * *
30883 ATCGTGATATGTAGGGGTTCTTTGATAACAATCTTGAGAGACC
1 ATCGTGATATGTAGGGGTTCTTTGATGACAAGCTTGAGAAACC
*
30926 ATCGTGATATGTAGGGGCTT-TTTGATGACAAACTTGA
1 ATCGTGATATGTAGGGG-TTCTTTGATGACAAGCTTGA
30963 TGAACACTTG
Statistics
Matches: 380, Mismatches: 36, Indels: 88
0.75 0.07 0.17
Matches are distributed among these distances:
42 3 0.01
43 244 0.64
44 5 0.01
45 8 0.02
46 4 0.01
49 6 0.02
52 6 0.02
53 2 0.01
54 2 0.01
55 99 0.26
56 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (43 bp):
ATCGTGATATGTAGGGGTTCTTTGATGACAAGCTTGAGAAACC
Found at i:30650 original size:98 final size:97
Alignment explanation
Indices: 30500--30998 Score: 480
Period size: 98 Copynumber: 5.2 Consensus size: 97
30490 AGCTTGAGAA
*
30500 ACCATCGTGATATGTAGGGGTT-TCTTGATGACAATCTTGAGGGACCATCGTGATATGTAGGGGT
1 ACCATCGTGATATGTAGGGGTTCT-TTGATGACAATCTTGAGAGACCATCGTGATATGTAGGGGT
30564 TCCTTGATGACAAACTTGATGATAAGCTTGAAGG
65 T-CTTGATGACAAACTTGATGATAAGCTTGAAGG
* * *
30598 ACCATCGTGATATGTAGGGGTTCTTTGATAACAAGCTTGAGAAACCATCGTGATATGTAGGGGTT
1 ACCATCGTGATATGTAGGGGTTCTTTGATGACAATCTTGAGAGACCATCGTGATATGTAGGGG-T
*
30663 TCTTGATG----AC---A--AT---CTTGATGG
65 TCTTGATGACAAACTTGATGATAAGCTTGAAGG
* *
30684 ACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTTGATAATAAGCTTGAAGGACCATCGTGA
1 ACCATCGTGATATGTAGGGGTTCTTTGATGACAATCTTG------A----G-A-GACCATCGTGA
* * *
30749 TATATAGGGGTTCTT--T----AA--T-A--ACAAGCTTG-AGAA
54 TATGTAGGGGTTCTTGATGACAAACTTGATGATAAGCTTGAAG-G
*
30782 ACCATCGTGATATGTAGGGGTT-TCTTGATGACAATCTTGAGGGACCATCGTGATATGTAGGGGT
1 ACCATCGTGATATGTAGGGGTTCT-TTGATGACAATCTTGAGAGACCATCGTGATATGTAGGGG-
30846 TTCTTGATGACAAACTTGATGATAAGCTTGAAGG
64 TTCTTGATGACAAACTTGATGATAAGCTTGAAGG
*
30880 ACCATCGTGATATGTAGGGGTTCTTTGATAACAATCTTGAGAGACCATCGTGATATGTAGGGGCT
1 ACCATCGTGATATGTAGGGGTTCTTTGATGACAATCTTGAGAGACCATCGTGATATGTAGGGG-T
*
30945 TTTTGATGACAAACTTGATGA-ACA-CTTG-AGG
65 TCTTGATGACAAACTTGATGATA-AGCTTGAAGG
*
30976 AGCCAACGTGATATGTAGGGGTT
1 A-CCATCGTGATATGTAGGGGTT
30999 AATTGGTGAT
Statistics
Matches: 340, Mismatches: 24, Indels: 75
0.77 0.05 0.17
Matches are distributed among these distances:
86 63 0.19
87 5 0.01
88 1 0.00
89 3 0.01
91 1 0.00
92 2 0.01
93 2 0.01
94 2 0.01
95 5 0.01
96 6 0.02
97 32 0.09
98 212 0.62
99 6 0.02
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (97 bp):
ACCATCGTGATATGTAGGGGTTCTTTGATGACAATCTTGAGAGACCATCGTGATATGTAGGGGTT
CTTGATGACAAACTTGATGATAAGCTTGAAGG
Found at i:30705 original size:141 final size:141
Alignment explanation
Indices: 30451--30962 Score: 927
Period size: 141 Copynumber: 3.6 Consensus size: 141
30441 CGAACGGTAA
*
30451 TGAAGGACAATCGTGATATGTAGGGGTTCTTTGATAACAAGCTTGAGAAACCATCGTGATATGTA
1 TGAAGGACCATCGTGATATGTAGGGGTTCTTTGATAACAAGCTTGAGAAACCATCGTGATATGTA
30516 GGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTT
66 GGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTT
30581 GATGATAAGCT
131 GATGATAAGCT
30592 TGAAGGACCATCGTGATATGTAGGGGTTCTTTGATAACAAGCTTGAGAAACCATCGTGATATGTA
1 TGAAGGACCATCGTGATATGTAGGGGTTCTTTGATAACAAGCTTGAGAAACCATCGTGATATGTA
*
30657 GGGGTTTCTTGATGACAATCTTGATGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTT
66 GGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTT
*
30722 GATAATAAGCT
131 GATGATAAGCT
* *
30733 TGAAGGACCATCGTGATATATAGGGGTTCTTTAATAACAAGCTTGAGAAACCATCGTGATATGTA
1 TGAAGGACCATCGTGATATGTAGGGGTTCTTTGATAACAAGCTTGAGAAACCATCGTGATATGTA
*
30798 GGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAGGGGTTTCTTGATGACAAACTT
66 GGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTT
30863 GATGATAAGCT
131 GATGATAAGCT
* *
30874 TGAAGGACCATCGTGATATGTAGGGGTTCTTTGATAACAATCTTGAGAGACCATCGTGATATGTA
1 TGAAGGACCATCGTGATATGTAGGGGTTCTTTGATAACAAGCTTGAGAAACCATCGTGATATGTA
*
30939 GGGGCTTT-TTGATGACAAACTTGA
66 GGGG-TTTCTTGATGACAATCTTGA
30963 TGAACACTTG
Statistics
Matches: 357, Mismatches: 13, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
141 354 0.99
142 3 0.01
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.31
Consensus pattern (141 bp):
TGAAGGACCATCGTGATATGTAGGGGTTCTTTGATAACAAGCTTGAGAAACCATCGTGATATGTA
GGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTT
GATGATAAGCT
Found at i:31177 original size:90 final size:90
Alignment explanation
Indices: 31012--31311 Score: 382
Period size: 90 Copynumber: 3.4 Consensus size: 90
31002 TGGTGATAAT
* *
31012 TAAGAAACCGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCA
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCATCA
* *
31077 GTGGATGATGTTTTCAAATGAGATA
66 GTGCAGGATGTTTTCAAATGAGATA
* * * * * *
31102 TAATAAACTGAGCCTTTGGAGGTTTCTTGATTTTTAAGTCTTTCGGGTCATACATAAGACCATCA
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCATCA
*
31167 GTGCAGGATGTTTTCAAATGAGATT
66 GTGCAGGATGTTTTCAAATGAGATA
* *
31192 TAAGAAACTGAGCCTTCGGGGGTTTCTTAATTTCTAAGTCCTTCGGGCCATCCATAAGACC-T--
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCATCA
*
31254 -T----GATGTTTTCAAATGAGATTT
66 GTGCAGGATGTTTTCAAATGAGA-TA
* * *
31275 TAAGAAACTAAGTCTTCGAGGGTTTCTTGATTTTTAA
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAA
31312 ATTATTCGGA
Statistics
Matches: 185, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
82 17 0.09
83 34 0.18
86 1 0.01
89 1 0.01
90 132 0.71
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (90 bp):
TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCATCA
GTGCAGGATGTTTTCAAATGAGATA
Found at i:31727 original size:132 final size:131
Alignment explanation
Indices: 31454--31755 Score: 430
Period size: 132 Copynumber: 2.3 Consensus size: 131
31444 ATAAACAGAT
* *
31454 CAACATTTCCAATAAAAAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATA
1 CAACATTTCCAAT-AAGAGTTCATAATGAGAAGAACTCATCCGACAGAAGGAG--AAAGTTCATA
* *
31519 AAGAGAAAAGCTTGTTCGACCTATCACGATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAG
63 AAGAGAAAAGCTTGTTCGACCTATCACGATTCACGACATTTCGAATCAATGACGCCTCGCTTAAG
*
31584 GGAT
128 GGAC
** * *
31588 TGACATTT-CAATAGAGAGTTCATGATGAGAAGAACTCATCCGACAGAAGGAG-AAGTTCATAAT
1 CAACATTTCCAATA-AGAGTTCATAATGAGAAGAACTCATCCGACAGAAGGAGAAAGTTCATAAA
*
31651 GAGAAAAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAATGACGCCTTGCTTAAG
65 GAGAAAAGCTTGTTCGACCTATCA--CGATTCACGACATTTCGAATCAATGACGCCTCGCTTAAG
31716 GGAC
128 GGAC
*
31720 CAACATTTCCAA-AAGAGTTCATAATGAAAAGAACTC
1 CAACATTTCCAATAAGAGTTCATAATGAGAAGAACTC
31756 GTTTTAAAAG
Statistics
Matches: 150, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
130 34 0.23
131 21 0.14
132 47 0.31
133 42 0.28
134 6 0.04
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (131 bp):
CAACATTTCCAATAAGAGTTCATAATGAGAAGAACTCATCCGACAGAAGGAGAAAGTTCATAAAG
AGAAAAGCTTGTTCGACCTATCACGATTCACGACATTTCGAATCAATGACGCCTCGCTTAAGGGA
C
Found at i:32017 original size:23 final size:22
Alignment explanation
Indices: 31992--32047 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 22
31982 GGGATTAAAT
31992 ATATATATATATATATATATATT
1 ATAT-TATATATATATATATATT
32015 ATACTTAT-TAT-TAT-TATATT
1 ATA-TTATATATATATATATATT
32035 ATTATTAT-TATAT
1 A-TATTATATATAT
32048 TTATTATGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 14 0.47
21 6 0.20
22 3 0.10
23 6 0.20
24 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATTATATATATATATATATT
Found at i:32022 original size:6 final size:5
Alignment explanation
Indices: 31991--32095 Score: 56
Period size: 6 Copynumber: 19.6 Consensus size: 5
31981 CGGGATTAAA
*
31991 TATAT ATATAT ATATAT ATATAT TATAC T-TAT TATTAT TATA- T-TAT
1 TATAT -TATAT -TATAT -TATAT TATAT TATAT TA-TAT TATAT TATAT
* *
32037 TATTAT TATAT T-TAT TATGGT TATTAT TATTAT TATTAA TATAT TATTAT
1 TA-TAT TATAT TATAT TAT-AT TA-TAT TA-TAT TA-TAT TATAT TA-TAT
32087 TATTAT TAT
1 TA-TAT TAT
32096 TAAGTATTAC
Statistics
Matches: 84, Mismatches: 6, Indels: 19
0.77 0.06 0.17
Matches are distributed among these distances:
3 2 0.02
4 9 0.11
5 17 0.20
6 55 0.65
7 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:32023 original size:9 final size:8
Alignment explanation
Indices: 31995--32095 Score: 70
Period size: 9 Copynumber: 12.4 Consensus size: 8
31985 ATTAAATATA
31995 TATATATAT
1 TATAT-TAT
32004 ATATATATAT
1 -TATAT-TAT
32014 TATACTTA-
1 TATA-TTAT
32022 T-TATTAT
1 TATATTAT
32029 TATATTA-
1 TATATTAT
32036 T-TATTAT
1 TATATTAT
32043 TATATTTAT
1 TATA-TTAT
*
32052 TATGGTTA-
1 TAT-ATTAT
32060 T-TATTAT
1 TATATTAT
*
32067 TATTATTAA
1 TA-TATTAT
32076 TATATTAT
1 TATATTAT
32084 TATTATTAT
1 TA-TATTAT
32093 TAT
1 TAT
32096 TAAGTATTAC
Statistics
Matches: 76, Mismatches: 4, Indels: 24
0.73 0.04 0.23
Matches are distributed among these distances:
6 11 0.14
7 7 0.09
8 17 0.22
9 31 0.41
10 10 0.13
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (8 bp):
TATATTAT
Found at i:32027 original size:3 final size:3
Alignment explanation
Indices: 32019--32097 Score: 101
Period size: 3 Copynumber: 27.0 Consensus size: 3
32009 TATATTATAC
**
32019 TTA TTA TTA TTA -TA TTA TTA TTA TTA -TA TTTA TTA TGG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
32063 TTA TTA TTA TTA ATA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
32098 AGTATTACAT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
2 6 0.09
3 59 0.88
4 2 0.03
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:32112 original size:23 final size:23
Alignment explanation
Indices: 32006--32098 Score: 84
Period size: 23 Copynumber: 4.0 Consensus size: 23
31996 ATATATATAT
32006 ATATAT-ATTA-TACTTATTATTA
1 ATATATCATTATTA-TTATTATTA
* *
32028 TTATATTATTATTATTA-TATTTA
1 ATATATCATTATTATTATTA-TTA
* * *
32051 TTATGGTTATTATTATTATTATTA
1 ATAT-ATCATTATTATTATTATTA
*
32075 ATATATTATTATTATTATTATTA
1 ATATATCATTATTATTATTATTA
32098 A
1 A
32099 GTATTACATT
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
22 7 0.11
23 33 0.53
24 20 0.32
25 2 0.03
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (23 bp):
ATATATCATTATTATTATTATTA
Found at i:38718 original size:64 final size:64
Alignment explanation
Indices: 38650--38817 Score: 169
Period size: 64 Copynumber: 2.6 Consensus size: 64
38640 CAAGGTGTAC
* **
38650 CGATGCACATGAAGTGCATCGATGCA-CTCTTTTAAAATAAAAACATCGAAT-GCAATTAATGCA
1 CGATGCACATGAAGTGCATCGATGCATCCCCATT-AAATAAAAACATCGAATAG-AATTAATGCA
38713 T
64 T
* * * * * *
38714 CGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTATGCAT
1 CGATGCACATGAAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATAGAATTAATGCAT
** *
38778 CGATGCATGGTGTAGTGCATCGATGCATACCTCCATTAAA
1 CGATGCA-CATGAAGTGCATCGATGCAT-CC-CCATTAAA
38818 AGATAAAAAT
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
64 55 0.64
65 21 0.24
66 2 0.02
67 8 0.09
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (64 bp):
CGATGCACATGAAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATAGAATTAATGCAT
Found at i:39099 original size:25 final size:25
Alignment explanation
Indices: 39044--39101 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
39034 ATAAGTCTAG
* *
39044 ATTCAATATTTTGATACATGATCGTA
1 ATTC-ATATTATGATACATGATCATA
*
39070 TTTCATATTATGATACATGA-CATGA
1 ATTCATATTATGATACATGATCAT-A
39095 ATTCATA
1 ATTCATA
39102 CCATATGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 2 0.07
25 22 0.81
26 3 0.11
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.41
Consensus pattern (25 bp):
ATTCATATTATGATACATGATCATA
Found at i:39448 original size:23 final size:23
Alignment explanation
Indices: 39397--39461 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
39387 CATTATTATA
*
39397 TGGCACTCCGGTGCAAATTCTACG
1 TGGCACTCCGGTGC-AATTCAACG
* *
39421 CGGCACTCCAGTGCAATTCAACG
1 TGGCACTCCGGTGCAATTCAACG
*
39444 TGGCACTTCGGTGCAATT
1 TGGCACTCCGGTGCAATT
39462 ATACGAGCTG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
23 23 0.66
24 12 0.34
ACGTcount: A:0.22, C:0.29, G:0.25, T:0.25
Consensus pattern (23 bp):
TGGCACTCCGGTGCAATTCAACG
Found at i:44613 original size:66 final size:67
Alignment explanation
Indices: 44543--44676 Score: 207
Period size: 67 Copynumber: 2.0 Consensus size: 67
44533 AACAAAATTG
* * * *
44543 ATAAACCTTTTAGATTGTTTCTCTTGAAAC-AAGTTTCGTATCTCTTGAGACAATTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCATATCGCTTGAGACAATTTCTCTTGAA
44607 AC
66 AC
* *
44609 ATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCATCTCGCTTGAGACAGTTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCATATCGCTTGAGACAATTTCTCTTGAA
44674 AC
66 AC
44676 A
1 A
44677 AAATTTTTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
66 28 0.46
67 33 0.54
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (67 bp):
ATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCATATCGCTTGAGACAATTTCTCTTGAA
AC
Found at i:44710 original size:37 final size:37
Alignment explanation
Indices: 44625--44711 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 37
44615 CTTTGAGATT
* * *
44625 GTTTCTCTCGAAACAAAGTTTCATCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAAATTTCATCTCGCTTAAGACA
** *
44662 GTTTCTCTTGAAACAAAATTTTTTCTCTCTTAAGACA
1 GTTTCTCTTGAAACAAAATTTCATCTCGCTTAAGACA
*
44699 GTTTCTATTGAAA
1 GTTTCTCTTGAAA
44712 TAAATTATCC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (37 bp):
GTTTCTCTTGAAACAAAATTTCATCTCGCTTAAGACA
Found at i:45072 original size:139 final size:138
Alignment explanation
Indices: 44720--45267 Score: 670
Period size: 138 Copynumber: 4.0 Consensus size: 138
44710 AATAAATTAT
* * * *
44720 CCCTAAAGATGGCCAGACGTCATCATCACGTAGGAACCATGTTATCCACTGAACCAGATCTCCTC
1 CCCTAAAGATGGCCAGACGTCCTCATCACGTAGGAACAATGTCATCCACCG-ACCAGATCTCCTC
** * * **
44785 ATCATATAGGGGTCGCGTAATCCTTAGATAGCCAGACTTCCTCATTGCGTAGGAATCGTGTTATC
65 ATCACGTAGGAGTCGCGTCATCCTTAGATAGCCAGACTTCCTCATCACGTAGGAATCGTGTTATC
44850 TCCA-TTAC
130 TCCATTTAC
* ** * *
44858 CTCTAAAGATAACCAGACGTCCTCATCACGTAGGAACAGTGTTATCCACCGACCAGATCTCCTCA
1 CCCTAAAGATGGCCAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCTCCTCA
* * **
44923 TTACGGAGGAGTCGCGTCATCCTTAGATAGCCAGACTTCCTCATCGTGTAGGAATCGTGTTATCT
66 TCACGTAGGAGTCGCGTCATCCTTAGATAGCCAGACTTCCTCATCACGTAGGAATCGTGTTATCT
44988 CCATTTACC
131 CCATTTA-C
* * * *
44997 CCCTAAAGATGGCCAGACGTCCTCATCACGTAGAAATAATGCCATCCACCGATCAGATCTCCTCA
1 CCCTAAAGATGGCCAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCTCCTCA
*** * * *
45062 TCACGTAGGAGAAACATTATCCTTAGATAGCCAGACTTCCTCGTCACGTAGGAATCGTGTTATCT
66 TCACGTAGGAGTCGCGTCATCCTTAGATAGCCAGACTTCCTCATCACGTAGGAATCGTGTTATCT
* *
45127 CAATTTAT
131 CCATTTAC
** * *
45135 CCCTAAAGATGGTTAGACGTCCTCATCACGTAGGAACAATGACATCCACCGACCAGATCTCTTCA
1 CCCTAAAGATGGCCAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCTCCTCA
* * * * * *
45200 TCACGTAGGAG-CAGCTTCA-CCTTTAGATAACCAGATTTTCTCATCAAGTAGGAACCGTGTTAT
66 TCACGTAGGAGTC-GCGTCATCC-TTAGATAGCCAGACTTCCTCATCACGTAGGAATCGTGTTAT
45263 CTCCA
129 CTCCA
45268 AATTTGCCTA
Statistics
Matches: 352, Mismatches: 54, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
137 76 0.22
138 158 0.45
139 118 0.34
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (138 bp):
CCCTAAAGATGGCCAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCTCCTCA
TCACGTAGGAGTCGCGTCATCCTTAGATAGCCAGACTTCCTCATCACGTAGGAATCGTGTTATCT
CCATTTAC
Found at i:45228 original size:277 final size:277
Alignment explanation
Indices: 44720--45267 Score: 699
Period size: 277 Copynumber: 2.0 Consensus size: 277
44710 AATAAATTAT
* * ** *
44720 CCCTAAAGATGGCCAGACGTCATCATCACGTAGGAACCATGTTATCCACTGAACCAGATCTCCTC
1 CCCTAAAGATGGCCAGACGTCATCATCACGTAGAAACAATGCCATCCACCGAACCAGATCTCCTC
* * *** * **
44785 ATCATATAGGGGTCGCGTAATCCTTAGATAGCCAGACTTCCTCATTGCGTAGGAATCGTGTTATC
66 ATCACATAGGAGAAACATAATCCTTAGATAGCCAGACTTCCTCATCACGTAGGAATCGTGTTATC
* * **
44850 TCCATTACCTCTAAAGATAACCAGACGTCCTCATCACGTAGGAACAGTGTTATCCACCGACCAGA
131 TCAATTACCTCTAAAGATAACCAGACGTCCTCATCACGTAGGAACAATGACATCCACCGACCAGA
* * ** *
44915 TCTCCTCATTACGGAGGAGTCGCGTCATCCTTAGATAGCCAGACTTCCTCATCGTGTAGGAATCG
196 TCTCCTCATCACGGAGGAGTCGCGTCATCCTTAGATAACCAGACTTCCTCATCAAGTAGGAACCG
44980 TGTTATCTCCATTTACC
261 TGTTATCTCCATTTACC
* * *
44997 CCCTAAAGATGGCCAGACGTCCTCATCACGTAGAAATAATGCCATCCACCG-ATCAGATCTCCTC
1 CCCTAAAGATGGCCAGACGTCATCATCACGTAGAAACAATGCCATCCACCGAACCAGATCTCCTC
* * *
45061 ATCACGTAGGAGAAACATTATCCTTAGATAGCCAGACTTCCTCGTCACGTAGGAATCGTGTTATC
66 ATCACATAGGAGAAACATAATCCTTAGATAGCCAGACTTCCTCATCACGTAGGAATCGTGTTATC
****
45126 TCAATTTATCC-CTAAAGATGGTTAGACGTCCTCATCACGTAGGAACAATGACATCCACCGACCA
131 TCAA-TTA-CCTCTAAAGATAACCAGACGTCCTCATCACGTAGGAACAATGACATCCACCGACCA
* * * * *
45190 GATCTCTTCATCACGTAGGAG-CAGCTTCA-CCTTTAGATAACCAGATTTTCTCATCAAGTAGGA
194 GATCTCCTCATCACGGAGGAGTC-GCGTCATCC-TTAGATAACCAGACTTCCTCATCAAGTAGGA
45253 ACCGTGTTATCTCCA
257 ACCGTGTTATCTCCA
45268 AATTTGCCTA
Statistics
Matches: 230, Mismatches: 37, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
276 72 0.31
277 156 0.68
278 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (277 bp):
CCCTAAAGATGGCCAGACGTCATCATCACGTAGAAACAATGCCATCCACCGAACCAGATCTCCTC
ATCACATAGGAGAAACATAATCCTTAGATAGCCAGACTTCCTCATCACGTAGGAATCGTGTTATC
TCAATTACCTCTAAAGATAACCAGACGTCCTCATCACGTAGGAACAATGACATCCACCGACCAGA
TCTCCTCATCACGGAGGAGTCGCGTCATCCTTAGATAACCAGACTTCCTCATCAAGTAGGAACCG
TGTTATCTCCATTTACC
Found at i:45758 original size:2 final size:2
Alignment explanation
Indices: 45751--45789 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
45741 CAGTTTCATG
*
45751 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45790 TGAATATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49841 original size:29 final size:29
Alignment explanation
Indices: 49797--50029 Score: 279
Period size: 29 Copynumber: 8.3 Consensus size: 29
49787 GACCCGACCC
* **
49797 GTGATATTTTGGGAATTATTTCGAAGACG
1 GTGATATTTTGGGAATTATTTCGAAAAAA
* *
49826 GTGATATTTTGAGAATTATTTCGAAAAAG
1 GTGATATTTTGGGAATTATTTCGAAAAAA
49855 GTGATATTTTGGGAATTATTTC-AAAAAA
1 GTGATATTTTGGGAATTATTTCGAAAAAA
*
49883 -TGATA-TTTGGGAATTATTAT-GAAAAAG
1 GTGATATTTTGGGAATTATT-TCGAAAAAA
49910 GTGATATTTT-GGAATTATTTCGAAAAAA
1 GTGATATTTTGGGAATTATTTCGAAAAAA
*
49938 GTGATATTTTGAGAATTATTTCG--AAAA
1 GTGATATTTTGGGAATTATTTCGAAAAAA
49965 GTGATATTTTGGGAATTATTTC-AAAAAA
1 GTGATATTTTGGGAATTATTTCGAAAAAA
* * * *
49993 -TGTTATTTTAGGAATTATTT-TAAAAAG
1 GTGATATTTTGGGAATTATTTCGAAAAAA
*
50020 GTGTTATTTT
1 GTGATATTTT
50030 CGTAATAGTT
Statistics
Matches: 182, Mismatches: 12, Indels: 21
0.85 0.06 0.10
Matches are distributed among these distances:
26 13 0.07
27 60 0.33
28 48 0.26
29 61 0.34
ACGTcount: A:0.36, C:0.03, G:0.20, T:0.41
Consensus pattern (29 bp):
GTGATATTTTGGGAATTATTTCGAAAAAA
Found at i:49888 original size:27 final size:27
Alignment explanation
Indices: 49797--50029 Score: 263
Period size: 27 Copynumber: 8.4 Consensus size: 27
49787 GACCCGACCC
**
49797 GTGATATTTTGGGAATTATTTCGAAGACG
1 GTGATATTTTGGGAATTATTTC-AA-AAA
*
49826 GTGATATTTTGAGAATTATTTCGAAAAA
1 GTGATATTTTGGGAATTATTTC-AAAAA
49854 GGTGATATTTTGGGAATTATTTCAAAAA
1 -GTGATATTTTGGGAATTATTTCAAAAA
* *
49882 ATGATA-TTTGGGAATTATTATGAAAAA
1 GTGATATTTTGGGAATTATT-TCAAAAA
49909 GGTGATATTTT-GGAATTATTTCGAAAAAA
1 -GTGATATTTTGGGAATTATTTC--AAAAA
* *
49938 GTGATATTTTGAGAATTATTTCGAAAA
1 GTGATATTTTGGGAATTATTTCAAAAA
49965 GTGATATTTTGGGAATTATTTCAAAAA
1 GTGATATTTTGGGAATTATTTCAAAAA
* * * *
49992 ATGTTATTTTAGGAATTATTTTAAAAA
1 GTGATATTTTGGGAATTATTTCAAAAA
*
50019 GGTGTTATTTT
1 -GTGATATTTT
50030 CGTAATAGTT
Statistics
Matches: 179, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
26 13 0.07
27 64 0.36
28 39 0.22
29 63 0.35
ACGTcount: A:0.36, C:0.03, G:0.20, T:0.41
Consensus pattern (27 bp):
GTGATATTTTGGGAATTATTTCAAAAA
Found at i:49954 original size:83 final size:83
Alignment explanation
Indices: 49798--50029 Score: 308
Period size: 83 Copynumber: 2.8 Consensus size: 83
49788 ACCCGACCCG
* *
49798 TGATATTTTGGGAATTATTTCGAAGACGGTGATATTTTGAGAATTATTTCGAAAAAGGTGATATT
1 TGATATTTTGGGAATTATTT-GAAAAAGGTGATATTTTG-GAATTATTTCGAAAAAGGTGATATT
*
49863 TTGGGAATTATTTCAAAAAA
64 TTGAGAATTATTTCAAAAAA
*
49883 TGATA-TTTGGGAATTATTATGAAAAAGGTGATATTTTGGAATTATTTCGAAAAAAGTGATATTT
1 TGATATTTTGGGAATTATT-TGAAAAAGGTGATATTTTGGAATTATTTCGAAAAAGGTGATATTT
* *
49947 TGAGAATTATTTCGAAAAG
65 TGAGAATTATTTCAAAAAA
* * * * *
49966 TGATATTTTGGGAATTATTTCAAAAA-ATGTTATTTTAGGAATTATTT-TAAAAAGGTGTTATTT
1 TGATATTTTGGGAATTATTTGAAAAAGGTGATATTTT-GGAATTATTTCGAAAAAGGTGATATTT
50029 T
65 T
50030 CGTAATAGTT
Statistics
Matches: 132, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
82 22 0.17
83 62 0.47
84 42 0.32
85 6 0.05
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.41
Consensus pattern (83 bp):
TGATATTTTGGGAATTATTTGAAAAAGGTGATATTTTGGAATTATTTCGAAAAAGGTGATATTTT
GAGAATTATTTCAAAAAA
Found at i:57545 original size:29 final size:28
Alignment explanation
Indices: 57500--57733 Score: 260
Period size: 27 Copynumber: 8.4 Consensus size: 28
57490 ACCCGATCCG
* *
57500 GTGATATTTTGGGAATTATTTCGAAGAC
1 GTGATATTTTGGGAATTATTTCGAAAAA
** *
57528 GATGATATTTTGAAAATTATTCCGAAAAA
1 G-TGATATTTTGGGAATTATTTCGAAAAA
*
57557 GGTGATATTTTGGGAATTATTTTGAAAAA
1 -GTGATATTTTGGGAATTATTTCGAAAAA
* * *
57586 -TGATATTCTGGGAATTATTAC-AAAAT
1 GTGATATTTTGGGAATTATTTCGAAAAA
57612 GTGATATTTTGGGAATTATTTCGAAAAA
1 GTGATATTTTGGGAATTATTTCGAAAAA
*
57640 GGTGATATTTTGGGAATTATTTTG-AAAA
1 -GTGATATTTTGGGAATTATTTCGAAAAA
57668 GTGATATTTTGGGAATTATTT-GAAAAA
1 GTGATATTTTGGGAATTATTTCGAAAAA
* * * **
57695 ATGTTATTTTAGGAATTATTTTAAAAAA
1 GTGATATTTTGGGAATTATTTCGAAAAA
*
57723 GGTGTTATTTT
1 -GTGATATTTT
57734 CGTAATAGTT
Statistics
Matches: 176, Mismatches: 22, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.03
27 80 0.45
28 14 0.08
29 76 0.43
30 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.41
Consensus pattern (28 bp):
GTGATATTTTGGGAATTATTTCGAAAAA
Found at i:57642 original size:83 final size:83
Alignment explanation
Indices: 57501--57733 Score: 299
Period size: 83 Copynumber: 2.8 Consensus size: 83
57491 CCCGATCCGG
* * * ** *
57501 TGATATTTTGGGAATTATTTCGAAGACGATGATATTTTGAAAATTATTCCGAAAAAGGTGATATT
1 TGATATTTTGGGAATTATTAC-AAAATG-TGATATTTTGGGAATTATTTCGAAAAAGGTGATATT
57566 TTGGGAATTATTTTGAAAAA
64 TTGGGAATTATTTTGAAAAA
*
57586 TGATATTCTGGGAATTATTACAAAATGTGATATTTTGGGAATTATTTCGAAAAAGGTGATATTTT
1 TGATATTTTGGGAATTATTACAAAATGTGATATTTTGGGAATTATTTCGAAAAAGGTGATATTTT
*
57651 GGGAATTATTTTGAAAAG
66 GGGAATTATTTTGAAAAA
* * ** *
57669 TGATATTTTGGGAATTATTTGAAAAAATGT--TATTTTAGGAATTATTTTAAAAAAGGTGTTATT
1 TGATATTTTGGGAATTA-TT-ACAAAATGTGATATTTTGGGAATTATTTCGAAAAAGGTGATATT
57732 TT
64 TT
57734 CGTAATAGTT
Statistics
Matches: 132, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
83 99 0.75
84 6 0.05
85 27 0.20
ACGTcount: A:0.36, C:0.03, G:0.20, T:0.42
Consensus pattern (83 bp):
TGATATTTTGGGAATTATTACAAAATGTGATATTTTGGGAATTATTTCGAAAAAGGTGATATTTT
GGGAATTATTTTGAAAAA
Found at i:58844 original size:23 final size:23
Alignment explanation
Indices: 58818--58863 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
58808 CACCACAGCT
*
58818 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
58841 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
58864 TATAATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:59080 original size:149 final size:149
Alignment explanation
Indices: 58841--59293 Score: 843
Period size: 149 Copynumber: 3.0 Consensus size: 149
58831 CGAAGTGCCA
58841 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
58906 CATATACATATACTAGGGATCAAGTATGTGTCTTACGAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
*
58971 TATATATTCCGAAGGACCG
131 TATATATCCCGAAGGACCG
* * *
58990 CGTAGAATTGCACCGTAATGCCTTATAATAATGTCAATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
59055 CATATACATATACTAGGGATCAAGTATGTTTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
59120 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
59139 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
59204 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACATAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
59269 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
59288 CGTAGA
1 CGTAGA
59294 CCCTCTACCC
Statistics
Matches: 293, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 293 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCG
Found at i:59855 original size:63 final size:63
Alignment explanation
Indices: 59749--59907 Score: 203
Period size: 63 Copynumber: 2.5 Consensus size: 63
59739 TAATAGAGGC
* * * * *
59749 ATGCATCGATGCACTCCTGATGCATCGATGCAATGAGGGCATTCGATGTTCAT-TTTATTAGAA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTA-AAGAA
** **
59812 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTTAAATTA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAAGAA
* *
59875 ATGCATCGATGCACTTCATATGCATCGATGCAC
1 ATGCATCGATGCACTCCTTATGCATCGATGCAC
59908 CTTCAACAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 80 0.95
64 4 0.05
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAAGAA
Found at i:59899 original size:19 final size:20
Alignment explanation
Indices: 59875--59912 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
59865 ATTTAAATTA
59875 ATGCATCGATGCA-CTTCAT
1 ATGCATCGATGCACCTTCAT
59894 ATGCATCGATGCACCTTCA
1 ATGCATCGATGCACCTTCA
59913 ACAAATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGCATCGATGCACCTTCAT
Done.