Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000377.1 Hibiscus syriacus cultivar Beakdansim tig00000693_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: 79895
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1532 original size:18 final size:18
Alignment explanation
Indices: 1511--1558 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1501 TCCACTTCGG
1511 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
* *
1529 GAGCTATCACCTCACTCA
1 GAGCCATCACCTCACCCA
1547 GAGCCATCACCT
1 GAGCCATCACCT
1559 GATCGACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.44, G:0.12, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2149 original size:19 final size:20
Alignment explanation
Indices: 2095--2161 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
2085 TAGTTTACTT
* *
2095 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2115 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
2135 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
2154 TCGCAACG
1 TCGCAACG
2162 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2188 original size:19 final size:19
Alignment explanation
Indices: 2095--2197 Score: 72
Period size: 19 Copynumber: 5.6 Consensus size: 19
2085 TAGTTTACTT
* **
2095 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
2115 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
2135 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2154 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
2168 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2187 TCGCAATGCGA
1 TCGCAACGCGA
2198 TTTGTGTTTC
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.15
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 27 0.40
20 24 0.35
21 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2228 original size:14 final size:14
Alignment explanation
Indices: 2209--2267 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
2199 TTGTGTTTCG
2209 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2223 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
2240 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
2256 CGTTGCGATTTT
1 CGTTGCGATTTT
2268 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2241 original size:33 final size:33
Alignment explanation
Indices: 2204--2286 Score: 148
Period size: 33 Copynumber: 2.5 Consensus size: 33
2194 GCGATTTGTG
*
2204 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
2237 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
2270 TTTCGCATTGTGATTTT
1 TTTCGCATTGCGATTTT
2287 CATTTCGCGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.51
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:2249 original size:19 final size:19
Alignment explanation
Indices: 2225--2302 Score: 94
Period size: 19 Copynumber: 4.4 Consensus size: 19
2215 GATTTTGTCG
2225 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2244 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
2258 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
2277 TTGTGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2296 TTGCGAT
1 TTGCGAT
2303 AGCCATTTCC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 4 0.08
17 4 0.08
18 3 0.06
19 29 0.59
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2722 original size:21 final size:21
Alignment explanation
Indices: 2689--2749 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
2679 GACTCACATG
2689 TCATCCCTCAAGAGTCCCCT-
1 TCATCCCTCAAGAGTCCCCTA
** *
2709 TCAATCTTTCAAGAGGCCCCTA
1 TC-ATCCCTCAAGAGTCCCCTA
2731 TCATCCCTCAAGAGTCCCC
1 TCATCCCTCAAGAGTCCCC
2750 CCCACCGTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.23, C:0.41, G:0.11, T:0.25
Consensus pattern (21 bp):
TCATCCCTCAAGAGTCCCCTA
Found at i:4219 original size:14 final size:14
Alignment explanation
Indices: 4185--4223 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
4175 TTGATTGTTT
4185 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
4199 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
4213 TGTTGATTTGT
1 AATTGATTTGT
4224 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:4385 original size:19 final size:19
Alignment explanation
Indices: 4363--4434 Score: 126
Period size: 19 Copynumber: 3.8 Consensus size: 19
4353 GCAATGAGAG
*
4363 AATCGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
4382 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4401 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4420 AATCGCAATGAGAAA
1 AATCGCAATGCGAAA
4435 ATAGCAATGC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.50, C:0.15, G:0.19, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:4435 original size:33 final size:33
Alignment explanation
Indices: 4350--4446 Score: 122
Period size: 38 Copynumber: 2.8 Consensus size: 33
4340 GAAACTGACT
* *
4350 ATCGCAATGAGAGAATCGCAATGCAAAATGAAA
1 ATCGCAATGAGAAAATCGCAATGCGAAATGAAA
4383 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAAT--G--A-GAAAATCGCAATGCGAAATGAAA
*
4421 ATCGCAATGAGAAAATAGCAATGCGA
1 ATCGCAATGAGAAAATCGCAATGCGA
4447 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
33 23 0.41
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 29 0.52
ACGTcount: A:0.47, C:0.15, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGAGAAAATCGCAATGCGAAATGAAA
Found at i:4490 original size:20 final size:20
Alignment explanation
Indices: 4465--4539 Score: 132
Period size: 20 Copynumber: 3.8 Consensus size: 20
4455 TCGCATTACG
*
4465 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
4485 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
4505 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
4525 ATTTTCGCGTTGCGA
1 ATTTTCGCGTTGCGA
4540 ATTCCCCGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:5112 original size:20 final size:20
Alignment explanation
Indices: 5091--5178 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
5081 TGTATTATCT
* *
5091 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
5111 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
5131 CGTTGCGAAAGTCAGAATCA
1 CGTTGCGAAAGTCAGAATCG
* *
5151 CGTTACGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
*
5171 CATTGCGA
1 CGTTGCGA
5179 TTTTGTATTA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:5212 original size:20 final size:20
Alignment explanation
Indices: 5086--5220 Score: 119
Period size: 20 Copynumber: 6.7 Consensus size: 20
5076 GATTCTGTAT
*
5086 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
5106 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
5126 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * * *
5146 AATCACGTTACGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
5166 TATCGCATTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
5187 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
5207 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
5221 TTTCCAAATT
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
19 3 0.03
20 78 0.81
21 13 0.14
22 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:5239 original size:41 final size:41
Alignment explanation
Indices: 5160--5241 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
5150 ACGTTACGAA
** * *
5160 AGTCAGTATCGCATTGCGATTTTGTATTATCGCGTTGCGAT
1 AGTCAGTATCGCATTGCGATTTTCAAATATCGCATTGCGAT
5201 AGTCAGTATCGCATTGCGATTTTCCAAAT-TCGCATTGCGAT
1 AGTCAGTATCGCATTGCGATTTT-CAAATATCGCATTGCGAT
5242 TTACTTATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 34 0.94
42 2 0.06
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (41 bp):
AGTCAGTATCGCATTGCGATTTTCAAATATCGCATTGCGAT
Found at i:5253 original size:20 final size:21
Alignment explanation
Indices: 5209--5260 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
5199 ATAGTCAGTA
*
5209 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
5230 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
5250 TCGCATTGCGA
1 TCGCATTGCGA
5261 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:8903 original size:17 final size:17
Alignment explanation
Indices: 8864--8905 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
8854 AATAAATAAA
* *
8864 CAAGAAATGAATAGAAG
1 CAAGAAATGAAGAGAAC
*
8881 CGAGAAATGAAGAGAAC
1 CAAGAAATGAAGAGAAC
8898 CAAGAAAT
1 CAAGAAAT
8906 ATATCGATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.57, C:0.10, G:0.24, T:0.10
Consensus pattern (17 bp):
CAAGAAATGAAGAGAAC
Found at i:9279 original size:13 final size:13
Alignment explanation
Indices: 9257--9292 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
9247 TCTATTTATA
9257 TTTTTCCCTTTGT
1 TTTTTCCCTTTGT
*
9270 TTTTTTCCTTTGT
1 TTTTTCCCTTTGT
9283 TTTTTCCCTT
1 TTTTTCCCTT
9293 ACTACCCCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.00, C:0.22, G:0.06, T:0.72
Consensus pattern (13 bp):
TTTTTCCCTTTGT
Found at i:9430 original size:13 final size:13
Alignment explanation
Indices: 9412--9436 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9402 TATGACTGGA
9412 ATATAATATTATT
1 ATATAATATTATT
9425 ATATAATATTAT
1 ATATAATATTAT
9437 ATTATTTTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATAATATTATT
Found at i:9853 original size:17 final size:15
Alignment explanation
Indices: 9814--9855 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
9804 TTAAAGTTAT
9814 ATATTATTTTAAATA
1 ATATTATTTTAAATA
9829 AT-TATATTTGTACAATA
1 ATAT-TATTT-TA-AATA
9846 ATATTATTTT
1 ATATTATTTT
9856 TTCACATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.04
15 7 0.30
16 3 0.13
17 11 0.48
18 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
ATATTATTTTAAATA
Found at i:13630 original size:75 final size:75
Alignment explanation
Indices: 13537--13719 Score: 215
Period size: 75 Copynumber: 2.4 Consensus size: 75
13527 ATAAATAAAA
* * * * * *
13537 TCAAATATCAATACTCAAACTACAATATTAAGTTTAGAACAATAAAATCTATAAACAAA-TCACA
1 TCAAATCTCAAGACTCAAACTATAATATTAAGTCTAAAACAATAAAATCCATAAACAAACT-ACA
13601 ATATTAAAATG
65 ATATTAAAATG
* * * * *
13612 TCAAATCTCAAGATTCAAACTATAATATTAACTCTAAAATAATAAAATCCATAATCAAACTATAA
1 TCAAATCTCAAGACTCAAACTATAATATTAAGTCTAAAACAATAAAATCCATAAACAAACTACAA
*
13677 TATTAAAGTG
66 TATTAAAATG
* * *
13687 TCAAATCTTAAGACTGAAACCATAATATTAAGT
1 TCAAATCTCAAGACTCAAACTATAATATTAAGT
13720 ATATAAAAAT
Statistics
Matches: 90, Mismatches: 17, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
75 89 0.99
76 1 0.01
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.30
Consensus pattern (75 bp):
TCAAATCTCAAGACTCAAACTATAATATTAAGTCTAAAACAATAAAATCCATAAACAAACTACAA
TATTAAAATG
Found at i:13866 original size:16 final size:16
Alignment explanation
Indices: 13834--13873 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
13824 TATACTTCAT
13834 AATGATT-AAATGCTG
1 AATGATTCAAATGCTG
*
13849 AATGATTCAAATGTTG
1 AATGATTCAAATGCTG
13865 AATGATTCA
1 AATGATTCA
13874 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.35
Consensus pattern (16 bp):
AATGATTCAAATGCTG
Found at i:13955 original size:23 final size:23
Alignment explanation
Indices: 13925--13988 Score: 119
Period size: 23 Copynumber: 2.8 Consensus size: 23
13915 AATAACGGCT
13925 CTGAATCAGTTAGCACTGTTTTG
1 CTGAATCAGTTAGCACTGTTTTG
13948 CTGAATCAGTTAGCACTGTTTTG
1 CTGAATCAGTTAGCACTGTTTTG
*
13971 CTGAATCAGTCAGCACTG
1 CTGAATCAGTTAGCACTG
13989 AATCATTCAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (23 bp):
CTGAATCAGTTAGCACTGTTTTG
Found at i:16323 original size:20 final size:20
Alignment explanation
Indices: 16298--16343 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
16288 TATATATATC
*
16298 AAATAT-TTTTGAGTTAATTA
1 AAATATGTTTTAAGTT-ATTA
*
16318 AAATATGTTTTAAGTTTTTA
1 AAATATGTTTTAAGTTATTA
16338 AAATAT
1 AAATAT
16344 AAAAAATACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (20 bp):
AAATATGTTTTAAGTTATTA
Found at i:18418 original size:18 final size:18
Alignment explanation
Indices: 18374--18423 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
18364 GCTAAGCCTC
*
18374 CGTTGACCCGTTGACTGT
1 CGTTGACCTGTTGACTGT
18392 CGTTGACCTGTTGACTGT
1 CGTTGACCTGTTGACTGT
*
18410 CGTTGACCTATTGA
1 CGTTGACCTGTTGA
18424 TTATTATTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.14, C:0.24, G:0.26, T:0.36
Consensus pattern (18 bp):
CGTTGACCTGTTGACTGT
Found at i:20315 original size:39 final size:38
Alignment explanation
Indices: 20245--20363 Score: 121
Period size: 39 Copynumber: 3.1 Consensus size: 38
20235 TGTAAGACCA
* * ** * *
20245 TACCAAAAGCTCCTATTCTTTGTACATAGGGTAAATTCT
1 TACCATAA-CTCCTATACTTTGTGTACAGGGTAAATCCT
**
20284 TACCATAGACTCCTATACTTTGTGTACAGGGTAGGTCCT
1 TACCATA-ACTCCTATACTTTGTGTACAGGGTAAATCCT
* * *
20323 TACCATAACTCCTCTACTTTTTGTACAGGGTAAGTCCT
1 TACCATAACTCCTATACTTTGTGTACAGGGTAAATCCT
20361 TAC
1 TAC
20364 TACAGGCTCC
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
38 31 0.46
39 36 0.53
40 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (38 bp):
TACCATAACTCCTATACTTTGTGTACAGGGTAAATCCT
Found at i:20348 original size:38 final size:39
Alignment explanation
Indices: 20254--20363 Score: 132
Period size: 38 Copynumber: 2.8 Consensus size: 39
20244 ATACCAAAAG
* ** * * *
20254 CTCCTATTCTTTGTACATAGGGTAAATTCTTACCATAGA
1 CTCCTATACTTTGTGTACAGGGTAAGTCCTTACCATAGA
*
20293 CTCCTATACTTTGTGTACAGGGTAGGTCCTTACCATA-A
1 CTCCTATACTTTGTGTACAGGGTAAGTCCTTACCATAGA
* *
20331 CTCCTCTACTTTTTGTACAGGGTAAGTCCTTAC
1 CTCCTATACTTTGTGTACAGGGTAAGTCCTTAC
20364 TACAGGCTCC
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
38 31 0.51
39 30 0.49
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (39 bp):
CTCCTATACTTTGTGTACAGGGTAAGTCCTTACCATAGA
Found at i:21257 original size:19 final size:20
Alignment explanation
Indices: 21220--21258 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
21210 AGTGTTAATG
*
21220 AATTTTAAGATTTTATATTC
1 AATTTTAAGATTATATATTC
21240 AATTTTAA-ATTATATATTC
1 AATTTTAAGATTATATATTC
21259 GATTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (20 bp):
AATTTTAAGATTATATATTC
Found at i:25314 original size:12 final size:12
Alignment explanation
Indices: 25297--25321 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25287 TCACAAATAC
25297 ACATGACGTTGG
1 ACATGACGTTGG
25309 ACATGACGTTGG
1 ACATGACGTTGG
25321 A
1 A
25322 GAACAATCAT
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:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (12 bp):
ACATGACGTTGG
Found at i:26984 original size:204 final size:204
Alignment explanation
Indices: 26634--27041 Score: 807
Period size: 204 Copynumber: 2.0 Consensus size: 204
26624 TAGATAGGAA
26634 AAGAATCTCCGATACTTGTTAATTCATAGGAAATATGCTGATTTCTTGGTTTTCAAAGAAACAAA
1 AAGAATCTCCGATACTTGTTAATTCATAGGAAATATGCTGATTTCTTGGTTTTCAAAGAAACAAA
26699 ATAGTATAGCGTTATCTACCACTAAAGCAGAATACATTTCAACTGGTAGTTGTTGCACACAAGTT
66 ATAGTATAGCGTTATCTACCACTAAAGCAGAATACATTTCAACTGGTAGTTGTTGCACACAAGTT
26764 TTATGGATGAAACAACAACTTTTAGACTATGAAATTGAAGTTGGTACCATACCTATCAAGTGTGA
131 TTATGGATGAAACAACAACTTTTAGACTATGAAATTGAAGTTGGTACCATACCTATCAAGTGTGA
26829 CAATACTAG
196 CAATACTAG
*
26838 AAGAATCTCTGATACTTGTTAATTCATAGGAAATATGCTGATTTCTTGGTTTTCAAAGAAACAAA
1 AAGAATCTCCGATACTTGTTAATTCATAGGAAATATGCTGATTTCTTGGTTTTCAAAGAAACAAA
26903 ATAGTATAGCGTTATCTACCACTAAAGCAGAATACATTTCAACTGGTAGTTGTTGCACACAAGTT
66 ATAGTATAGCGTTATCTACCACTAAAGCAGAATACATTTCAACTGGTAGTTGTTGCACACAAGTT
26968 TTATGGATGAAACAACAACTTTTAGACTATGAAATTGAAGTTGGTACCATACCTATCAAGTGTGA
131 TTATGGATGAAACAACAACTTTTAGACTATGAAATTGAAGTTGGTACCATACCTATCAAGTGTGA
27033 CAATACTAG
196 CAATACTAG
27042 TACTATTTGT
Statistics
Matches: 203, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
204 203 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (204 bp):
AAGAATCTCCGATACTTGTTAATTCATAGGAAATATGCTGATTTCTTGGTTTTCAAAGAAACAAA
ATAGTATAGCGTTATCTACCACTAAAGCAGAATACATTTCAACTGGTAGTTGTTGCACACAAGTT
TTATGGATGAAACAACAACTTTTAGACTATGAAATTGAAGTTGGTACCATACCTATCAAGTGTGA
CAATACTAG
Found at i:29531 original size:21 final size:21
Alignment explanation
Indices: 29507--29549 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
29497 TGGGGAGTAA
29507 TTTATTTTCAAAGTATTAGAG
1 TTTATTTTCAAAGTATTAGAG
29528 TTTATTTTCAAAGTATTAGAG
1 TTTATTTTCAAAGTATTAGAG
29549 T
1 T
29550 AAGGGGGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTTATTTTCAAAGTATTAGAG
Found at i:29992 original size:20 final size:20
Alignment explanation
Indices: 29967--30019 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
29957 TTGCTCGGAG
29967 GGTACCGATACCCCCCAAGA
1 GGTACCGATACCCCCCAAGA
*
29987 GGTACCGATACCCCCCAGGA
1 GGTACCGATACCCCCCAAGA
30007 GGTACCGATACCC
1 GGTACCGATACCC
30020 TCTGTCTCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.40, G:0.23, T:0.11
Consensus pattern (20 bp):
GGTACCGATACCCCCCAAGA
Found at i:32224 original size:30 final size:30
Alignment explanation
Indices: 32166--32224 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
32156 TTTATCCACA
* *
32166 TAGAACACATTCACATAGAATATTTTCACG
1 TAGAACACATTCACATAGAACATATTCACG
*
32196 TAGAACACATTCACATATAACATATTCAC
1 TAGAACACATTCACATAGAACATATTCAC
32225 ATATTGATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29
Consensus pattern (30 bp):
TAGAACACATTCACATAGAACATATTCACG
Found at i:32228 original size:15 final size:15
Alignment explanation
Indices: 32162--32227 Score: 78
Period size: 15 Copynumber: 4.4 Consensus size: 15
32152 ATCTTTTATC
32162 CACATAGAACACATT
1 CACATAGAACACATT
* **
32177 CACATAGAATATTTT
1 CACATAGAACACATT
*
32192 CACGTAGAACACATT
1 CACATAGAACACATT
* *
32207 CACATATAACATATT
1 CACATAGAACACATT
32222 CACATA
1 CACATA
32228 TTGATAAAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.44, C:0.23, G:0.06, T:0.27
Consensus pattern (15 bp):
CACATAGAACACATT
Found at i:37021 original size:24 final size:24
Alignment explanation
Indices: 36994--37072 Score: 124
Period size: 24 Copynumber: 3.3 Consensus size: 24
36984 TCAAATTTGA
36994 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACATGACCTGG
* * *
37018 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATCTGATACATGACCTGG
37041 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACATGACCTGG
37065 ATTCTGAT
1 ATTCTGAT
37073 ATAATACTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
23 20 0.42
24 28 0.58
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATCTGATACATGACCTGG
Found at i:37047 original size:47 final size:48
Alignment explanation
Indices: 36994--37084 Score: 166
Period size: 47 Copynumber: 1.9 Consensus size: 48
36984 TCAAATTTGA
*
36994 ATTCTGATCTGATACATGACCTGGATTCTGATATGATA-TTGACATGG
1 ATTCTGATCTGATACATGACCTGGATTCTGATATAATACTTGACATGG
37041 ATTCTGATCTGATACATGACCTGGATTCTGATATAATACTTGAC
1 ATTCTGATCTGATACATGACCTGGATTCTGATATAATACTTGAC
37085 TTGAATTATG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
47 37 0.88
48 5 0.12
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (48 bp):
ATTCTGATCTGATACATGACCTGGATTCTGATATAATACTTGACATGG
Found at i:37079 original size:24 final size:24
Alignment explanation
Indices: 36994--37084 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
36984 TCAAATTTGA
*
36994 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACATGACCTGG
* *
37018 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGG
*
37041 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACATGACCTGG
* *
37065 ATTCTGATATAATACTTGAC
1 ATTCTGATATGATACATGAC
37085 TTGAATTATG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 20 0.35
24 37 0.65
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (24 bp):
ATTCTGATATGATACATGACCTGG
Found at i:41741 original size:24 final size:24
Alignment explanation
Indices: 41714--41792 Score: 124
Period size: 24 Copynumber: 3.3 Consensus size: 24
41704 TCAAATTTGA
41714 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACATGACCTGG
* * *
41738 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATCTGATACATGACCTGG
41761 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACATGACCTGG
41785 ATTCTGAT
1 ATTCTGAT
41793 ATAATACTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
23 20 0.42
24 28 0.58
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATCTGATACATGACCTGG
Found at i:41767 original size:47 final size:48
Alignment explanation
Indices: 41714--41804 Score: 166
Period size: 47 Copynumber: 1.9 Consensus size: 48
41704 TCAAATTTGA
*
41714 ATTCTGATCTGATACATGACCTGGATTCTGATATGATA-TTGACATGG
1 ATTCTGATCTGATACATGACCTGGATTCTGATATAATACTTGACATGG
41761 ATTCTGATCTGATACATGACCTGGATTCTGATATAATACTTGAC
1 ATTCTGATCTGATACATGACCTGGATTCTGATATAATACTTGAC
41805 TTGAATTATG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
47 37 0.88
48 5 0.12
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (48 bp):
ATTCTGATCTGATACATGACCTGGATTCTGATATAATACTTGACATGG
Found at i:41799 original size:24 final size:24
Alignment explanation
Indices: 41714--41804 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
41704 TCAAATTTGA
*
41714 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACATGACCTGG
* *
41738 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGG
*
41761 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACATGACCTGG
* *
41785 ATTCTGATATAATACTTGAC
1 ATTCTGATATGATACATGAC
41805 TTGAATTATG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 20 0.35
24 37 0.65
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (24 bp):
ATTCTGATATGATACATGACCTGG
Found at i:48045 original size:21 final size:20
Alignment explanation
Indices: 47998--48049 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
47988 TCTTTAATTA
47998 TAGTATCGATACCTCCACAT
1 TAGTATCGATACCTCCACAT
* *
48018 CAGTATCGATACTACTTCA-AT
1 TAGTATCGATAC--CTCCACAT
48039 TAGTATCGATA
1 TAGTATCGATA
48050 TTTTTCATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 11 0.41
21 12 0.44
22 4 0.15
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (20 bp):
TAGTATCGATACCTCCACAT
Found at i:51695 original size:29 final size:29
Alignment explanation
Indices: 51653--51712 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
51643 ATTCTACAGT
51653 GATCTCGTAGGACGCCATGCAATCCAGGC
1 GATCTCGTAGGACGCCATGCAATCCAGGC
*
51682 GATCTTGTAGGACGCCATGCAATCCAGGC
1 GATCTCGTAGGACGCCATGCAATCCAGGC
51711 GA
1 GA
51713 CATACGAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.18
Consensus pattern (29 bp):
GATCTCGTAGGACGCCATGCAATCCAGGC
Found at i:51727 original size:11 final size:11
Alignment explanation
Indices: 51711--51742 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
51701 CAATCCAGGC
51711 GACATACGAGA
1 GACATACGAGA
*
51722 GACATACGAGT
1 GACATACGAGA
51733 GACATACGAG
1 GACATACGAG
51743 CCATACAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.41, C:0.19, G:0.28, T:0.12
Consensus pattern (11 bp):
GACATACGAGA
Found at i:51847 original size:32 final size:32
Alignment explanation
Indices: 51806--51884 Score: 149
Period size: 32 Copynumber: 2.5 Consensus size: 32
51796 TATACGAGGT
51806 GAGGTCGCCATGCAGACGAGCCAGCCAATGGA
1 GAGGTCGCCATGCAGACGAGCCAGCCAATGGA
*
51838 GAGGTCGCCATGCAAACGAGCCAGCCAATGGA
1 GAGGTCGCCATGCAGACGAGCCAGCCAATGGA
51870 GAGGTCGCCATGCAG
1 GAGGTCGCCATGCAG
51885 TCTGGGCGAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.28, C:0.28, G:0.34, T:0.10
Consensus pattern (32 bp):
GAGGTCGCCATGCAGACGAGCCAGCCAATGGA
Found at i:51915 original size:29 final size:29
Alignment explanation
Indices: 51871--51965 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
51861 GCCAATGGAG
* **
51871 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
51900 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
51929 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
51958 AGGTCGCC
1 AGGTCGCC
51966 CCGGCGTCAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:52066 original size:50 final size:49
Alignment explanation
Indices: 52001--52097 Score: 185
Period size: 50 Copynumber: 2.0 Consensus size: 49
51991 ATGCATGCAC
52001 ATGCAGCCAAGATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTGT
1 ATGCAGCCAAGATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTGT
52050 ATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCT
1 ATGCA-GCCAAGATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCT
52098 ACAGCTATTG
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 5 0.11
50 42 0.89
ACGTcount: A:0.19, C:0.37, G:0.20, T:0.25
Consensus pattern (49 bp):
ATGCAGCCAAGATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTGT
Found at i:52349 original size:16 final size:18
Alignment explanation
Indices: 52328--52366 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
52318 GGAGATAAGG
*
52328 TAAATTTGTTTA-TATT-
1 TAAATTAGTTTATTATTA
52344 TAAATTAGTTTATTATTA
1 TAAATTAGTTTATTATTA
52362 TAAAT
1 TAAAT
52367 GTTAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TAAATTAGTTTATTATTA
Found at i:52529 original size:44 final size:48
Alignment explanation
Indices: 52471--52560 Score: 134
Period size: 44 Copynumber: 2.0 Consensus size: 48
52461 TTATATAGTT
52471 AAAAAATAATTAATTAGTTGTT-TT-GTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTGTTGTTAGTTAAATAGTTAAGTTATATAA
* *
52515 AAAAAATTATTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAATAATTAATTAGTTGTTGTTAGTTAAATAGTTAAGTTATAT
52561 TTGTTTGTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 20 0.50
45 2 0.05
46 3 0.08
47 7 0.17
48 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTGTTGTTAGTTAAATAGTTAAGTTATATAA
Found at i:52637 original size:32 final size:33
Alignment explanation
Indices: 52601--52677 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 33
52591 TTAGTTAGTA
*
52601 AGTTTATTAGTAG-TATA-TTATAATGAAAAAAT
1 AGTTTATTAGTAGTTATAGTTAT-ATAAAAAAAT
*
52633 AGTTTATTAGTTAGTTTTAGTTATATAAAAAAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAAAAT
*
52667 ATTTTATTAGT
1 AGTTTATTAGT
52678 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 10 0.26
33 4 0.10
34 21 0.54
35 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (33 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAAAAT
Found at i:52755 original size:16 final size:16
Alignment explanation
Indices: 52723--52769 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
52713 TTTAAAAAGT
*
52723 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
52739 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
52755 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
52770 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:52764 original size:15 final size:14
Alignment explanation
Indices: 52744--52774 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
52734 GTTTATTAGT
52744 TTATTATATTATAAG
1 TTATTATATTA-AAG
52759 TTATTATATTAAAG
1 TTATTATATTAAAG
52773 TT
1 TT
52775 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:54946 original size:17 final size:17
Alignment explanation
Indices: 54924--54956 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
54914 CAATGATGTT
*
54924 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
54941 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
54957 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:55185 original size:14 final size:14
Alignment explanation
Indices: 55166--55205 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
55156 TAGTAATAAT
55166 TATTAAATCATTAG
1 TATTAAATCATTAG
*
55180 TATTAAATCATTAT
1 TATTAAATCATTAG
*
55194 TA-TAAATAATTA
1 TATTAAATCATTA
55206 CTAAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (14 bp):
TATTAAATCATTAG
Found at i:55243 original size:14 final size:13
Alignment explanation
Indices: 55224--55267 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
55214 TAACATAATA
55224 ATTATTATAAAATC
1 ATTATTAT-AAATC
*
55238 ATTATTAT-AATG
1 ATTATTATAAATC
55250 ATTATTATCAAATC
1 ATTATTAT-AAATC
55264 ATTA
1 ATTA
55268 CTAAATCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 11 0.42
14 15 0.58
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (13 bp):
ATTATTATAAATC
Found at i:55255 original size:12 final size:12
Alignment explanation
Indices: 55148--55257 Score: 73
Period size: 13 Copynumber: 8.9 Consensus size: 12
55138 TTAGTATTCT
55148 ATAATTATTAGTA
1 ATAATTATTA-TA
55161 ATAATTATTA-A
1 ATAATTATTATA
* *
55172 ATCATTAGTATTAA
1 ATAATTATTA-T-A
*
55186 ATCATTATTATAA
1 ATAATTATTAT-A
*
55199 ATAATTACTA-A
1 ATAATTATTATA
**
55210 ATAA-TAACATA
1 ATAATTATTATA
55221 ATAATTATTATAAA
1 ATAATTATTAT--A
*
55235 ATCATTATTATA
1 ATAATTATTATA
*
55247 ATGATTATTAT
1 ATAATTATTAT
55258 CAAATCATTA
Statistics
Matches: 79, Mismatches: 11, Indels: 15
0.75 0.10 0.14
Matches are distributed among these distances:
10 3 0.04
11 19 0.24
12 15 0.19
13 21 0.27
14 21 0.27
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (12 bp):
ATAATTATTATA
Found at i:55426 original size:29 final size:29
Alignment explanation
Indices: 55384--55491 Score: 173
Period size: 29 Copynumber: 3.7 Consensus size: 29
55374 AAATAATGAT
*
55384 GGACGCTGGGCGTGCATGGCGTCCTTATA
1 GGACGCCGGGCGTGCATGGCGTCCTTATA
55413 GGACGCCGGGCGTGCATGGCGTCCTTATA
1 GGACGCCGGGCGTGCATGGCGTCCTTATA
* *
55442 GGACACCGGGCGTGCATGGCGACC-TATAA
1 GGACGCCGGGCGTGCATGGCGTCCTTAT-A
55471 GGACGCCGGGCGTGCATGGCG
1 GGACGCCGGGCGTGCATGGCG
55492 ACCTACGTTG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
28 3 0.04
29 71 0.96
ACGTcount: A:0.16, C:0.27, G:0.40, T:0.18
Consensus pattern (29 bp):
GGACGCCGGGCGTGCATGGCGTCCTTATA
Found at i:58680 original size:32 final size:31
Alignment explanation
Indices: 58644--58720 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
58634 CGGGGCCATG
*
58644 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
58676 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
58707 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
58721 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:59632 original size:22 final size:22
Alignment explanation
Indices: 59604--59668 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
59594 AACGGTCAAC
59604 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
59626 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
59648 GGTCAACGGTTGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
59669 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.09, C:0.22, G:0.49, T:0.20
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:59668 original size:5 final size:5
Alignment explanation
Indices: 59611--59651 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
59601 AACGGTCAAC
*
59611 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC
59652 AACGGTTGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:59683 original size:9 final size:9
Alignment explanation
Indices: 59665--59763 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
59655 GGTTGGGTCG
*
59665 GGTCAGACC
1 GGTCAAACC
59674 GGTCAAACC
1 GGTCAAACC
* *
59683 GATTCAGACC
1 G-GTCAAACC
59693 GGTCAAACC
1 GGTCAAACC
*
59702 GGTTCGAACC
1 GG-TCAAACC
*
59712 GGTTGAAACC
1 GG-TCAAACC
59722 GGTCAAACC
1 GGTCAAACC
59731 GGTCAGAACC
1 GGTCA-AACC
*
59741 GGTTGAAAACC
1 GG-T-CAAACC
59752 GGTCAAACC
1 GGTCAAACC
59761 GGT
1 GGT
59764 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:59689 original size:19 final size:19
Alignment explanation
Indices: 59667--59764 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
59657 TTGGGTCGGG
*
59667 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
59686 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
59705 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
59724 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* *
59744 TGAAAACCGGTCAAACCGGT
1 T-CAGACCGGTCAAACCGGT
59764 T
1 T
59765 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 38 0.56
20 17 0.25
21 10 0.15
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:59722 original size:29 final size:31
Alignment explanation
Indices: 59690--59764 Score: 129
Period size: 29 Copynumber: 2.5 Consensus size: 31
59680 ACCGATTCAG
59690 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
59719 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
59749 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
59765 TCCAGCAGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.56
30 16 0.37
31 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:63541 original size:43 final size:43
Alignment explanation
Indices: 63493--63768 Score: 385
Period size: 43 Copynumber: 6.4 Consensus size: 43
63483 CGGCGCTATG
*
63493 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCA
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCA
*
63536 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCA
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCA
* * *
63579 ACAAACGTCGCAATAGGTGTTGAGATTTAGCGGAGTTTTTCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCA
*
63622 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCA
*
63665 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCA
* * * * * **
63708 ACAAACACCGCAAAAGAT-CTG-GTATATAGCGGCGTTTTTTAGA
1 ACAAACGCCGCAATAGGTGTTGAG-ATTTAGCGGCG-TTTTTCCA
*
63751 ACAAACGCCGCAAAAGGT
1 ACAAACGCCGCAATAGGT
63769 CATATCTATA
Statistics
Matches: 215, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
41 1 0.00
42 12 0.06
43 202 0.94
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (43 bp):
ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCA
Found at i:63942 original size:21 final size:21
Alignment explanation
Indices: 63916--63974 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
63906 ATTTTAGAAT
*
63916 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* * *
63937 AAACTTAAAATCAATAACAAG
1 AAACTTGAAATCCATAACAAC
**
63958 AAAAATGAAATCCATAA
1 AAACTTGAAATCCATAA
63975 TAATAAATCA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.58, C:0.19, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:68190 original size:25 final size:25
Alignment explanation
Indices: 68131--68191 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
68121 TGGGCAAGAG
*
68131 GAAAAAGGGAATCGTGGGAACAGAT
1 GAAAAAGGGGATCGTGGGAACAGAT
68156 GAAAAAGGGGATCGTGGGAACAGAT
1 GAAAAAGGGGATCGTGGGAACAGAT
*
68181 GGAAAAGGGGA
1 GAAAAAGGGGA
68192 ATGGGATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.43, C:0.07, G:0.41, T:0.10
Consensus pattern (25 bp):
GAAAAAGGGGATCGTGGGAACAGAT
Found at i:68499 original size:81 final size:82
Alignment explanation
Indices: 68309--68504 Score: 225
Period size: 84 Copynumber: 2.4 Consensus size: 82
68299 TGTTTTTGCA
* * * * *
68309 GCGTTTGTGTAAAAATGCCGCTACAGTTCTAATATTTTGCGGCGTTTGTTGGAAAAATGCCACTA
1 GCGTTTGTATAAAAATGCCGCTAAAGTACTAATATGTTGCGGCGTTTGTT-GAAAAACGCCACTA
* **
68374 TAGGTGAACCCTATTGTG
65 TAGATGAACCCTATTACG
* * * *
68392 GCATTTTTTATAAAAATGCCGCTAAAGTACTAATATGTTGTGGCGTTTGTCT-ATAAACGCCACT
1 GC-GTTTGTATAAAAATGCCGCTAAAGTACTAATATGTTGCGGCGTTTGT-TGAAAAACGCCACT
*
68456 ATAGATGGA-CCTATTACG
64 ATAGATGAACCCTATTACG
*
68474 GCGTTTGTATAAAAACGCCGCTAAAGTACTA
1 GCGTTTGTATAAAAATGCCGCTAAAGTACTA
68505 CTCTATTACG
Statistics
Matches: 95, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
81 26 0.27
82 9 0.09
83 19 0.20
84 40 0.42
85 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (82 bp):
GCGTTTGTATAAAAATGCCGCTAAAGTACTAATATGTTGCGGCGTTTGTTGAAAAACGCCACTAT
AGATGAACCCTATTACG
Found at i:68526 original size:41 final size:41
Alignment explanation
Indices: 68400--68584 Score: 178
Period size: 41 Copynumber: 4.5 Consensus size: 41
68390 TGGCATTTTT
* * * * **
68400 TATAAAAATGCCGCTAAAGTACTAATATGTTGTGGCGTTTG
1 TATAAAAACGCCGCTAAAGTACTACTCTATTACGGCGTTTG
* * * *
68441 TCTATAAACGCCACTATAG-A-TGGAC-CTATTACGGCGTTTG
1 TATAAAAACGCCGCTAAAGTACT--ACTCTATTACGGCGTTTG
*
68481 TATAAAAACGCCGCTAAAGTACTACTCTATTACGGCGTTTA
1 TATAAAAACGCCGCTAAAGTACTACTCTATTACGGCGTTTG
** *
68522 TATAAAAACGCCGCTAAAGTACTACTCTATTGTGGCATTTG
1 TATAAAAACGCCGCTAAAGTACTACTCTATTACGGCGTTTG
* *
68563 TTTAAAAAACGACGCTAAAGTA
1 TAT-AAAAACGCCGCTAAAGTA
68585 TCATTTTGTG
Statistics
Matches: 117, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
39 1 0.01
40 29 0.25
41 69 0.59
42 18 0.15
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (41 bp):
TATAAAAACGCCGCTAAAGTACTACTCTATTACGGCGTTTG
Found at i:69251 original size:17 final size:18
Alignment explanation
Indices: 69218--69253 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
69208 AATTCCAAGA
69218 AAATATATTAATTTTTAT
1 AAATATATTAATTTTTAT
*
69236 AAATATA-TATTTTTTAT
1 AAATATATTAATTTTTAT
69253 A
1 A
69254 TTTTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATATATTAATTTTTAT
Found at i:69257 original size:25 final size:27
Alignment explanation
Indices: 69228--69279 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 27
69218 AAATATATTA
*
69228 ATTTTTATAAAT-ATATATTT-TTTAT
1 ATTTTTATAAATAAGATATTTATTTAT
69253 ATTTTTATAAATAAGATATTTATTTAT
1 ATTTTTATAAATAAGATATTTATTTAT
69280 TTAGAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 12 0.50
26 7 0.29
27 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
ATTTTTATAAATAAGATATTTATTTAT
Found at i:69280 original size:25 final size:24
Alignment explanation
Indices: 69223--69281 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
69213 CAAGAAAATA
* *
69223 TATTAATTTTTATAAATATATATT
1 TATTTATTTTTATAAATAGATATT
*
69247 TTTTATATTTTTATAAATAAGATATT
1 TATT-TATTTTTATAAAT-AGATATT
69273 TATTTATTT
1 TATTTATTT
69282 AGAAATATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 3 0.10
25 17 0.59
26 9 0.31
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
TATTTATTTTTATAAATAGATATT
Found at i:69543 original size:2 final size:2
Alignment explanation
Indices: 69536--69570 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
69526 AATGAAGTAA
*
69536 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
69571 AATAAGATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:71102 original size:122 final size:122
Alignment explanation
Indices: 70761--71446 Score: 790
Period size: 122 Copynumber: 5.7 Consensus size: 122
70751 GAATTAAAGC
* *
70761 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTCAGATGAGTTCTTCTCTTTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * ** *
70826 GAACTCTTTCTGGAAATGTTGATGTTGATCTATCTATTTCTGTGATAGAATC-ATTCAA
66 GAAATC-TTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGAATCGA-GCAA
* * * *
70884 ATGGTTGGACAAGTTCTTCTCATTATGAACTTATTCTT-CTCTTCAGATGAGTTATTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * * ** *
70948 GAACA-CTTCTGTAAATGTTGATGTTGATCTATCTCCTTCTGTGACAGCGTCGAGTAA
66 GAA-ATCTTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAA
*
71005 AAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * *
71070 GAAAACTTCTGGAAATGTTGGTGCTGATCTATCTCCTTTTGGGATAGAACCGAGCAA
66 GAAATCTTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAA
** * * *
71127 AATATTGAACAAGTTATTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTTATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * * *
71192 -AAATTCTTCTGGAAATGTTGGTGCTAATCTATCTTCTTTTGGGATAGAATTGAGCAA
66 GAAA-TCTTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAA
* *
71249 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCCTCTTCAGATGAGTTCTTTTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * ** *
71314 GAACTTCCTCTGGAAA---T-GT--TGATCCA--T-C--GAGTGATAGACTCGAGCAA
66 GAA-ATCTTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAA
* *
71361 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * *
71426 GAACTTCCTATGGAAATGTTG
66 GAA-ATCTTCTGGAAATGTTG
71447 ATCCATCGAG
Statistics
Matches: 490, Mismatches: 62, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
112 90 0.18
114 1 0.00
115 2 0.00
117 5 0.01
119 2 0.00
120 1 0.00
121 79 0.16
122 264 0.54
123 46 0.09
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.40
Consensus pattern (122 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAAATCTTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAA
Found at i:71431 original size:112 final size:112
Alignment explanation
Indices: 71234--71460 Score: 393
Period size: 112 Copynumber: 2.0 Consensus size: 112
71224 CTTCTTTTGG
* *
71234 GATAGAATTGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCCTCTTCAGATG
1 GATAGAATCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTCCTTCCTCTTCAGATG
*
71299 AGTTCTTTTCATTATGAACTTCCTCTGGAAATGTTGATCCATCGAGT
66 AGTTCTTTTCATTATGAACTTCCTATGGAAATGTTGATCCATCGAGT
* *
71346 GATAGACTCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
1 GATAGAATCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTCCTTCCTCTTCAGATG
71411 AGTTCTTCTT-ATTATGAACTTCCTATGGAAATGTTGATCCATCGAGT
66 AGTTCTT-TTCATTATGAACTTCCTATGGAAATGTTGATCCATCGAGT
71458 GAT
1 GAT
71461 GGAAATTTCT
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
112 107 0.98
113 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (112 bp):
GATAGAATCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTCCTTCCTCTTCAGATG
AGTTCTTTTCATTATGAACTTCCTATGGAAATGTTGATCCATCGAGT
Found at i:71526 original size:36 final size:36
Alignment explanation
Indices: 71486--71683 Score: 139
Period size: 37 Copynumber: 5.5 Consensus size: 36
71476 TAGTGAACTG
* * *
71486 TCTCAAGCGAGACGAATATTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGACAAATGTTGTTTTAAGAAAAACAA
* * ** ** **
71522 TCTCAAGTGAGATACATTGTTGTTTCGAGTGAAACTG
1 TCTCAAGTGAGACA-AATGTTGTTTTAAGAAAAACAA
* *
71559 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGACAAATGTTGTTTTAAGAAAAACAA
* ** ** **
71595 TCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTT
1 TCTCAAGTGAGACAAA-TGTTGTTTTAAGAAAAACAA
* * *
71632 TCTCAAGAGAGACGCAAT-TTGTTTTAAGAAAAATAA
1 TCTCAAGTGAGAC-AAATGTTGTTTTAAGAAAAACAA
*
71668 -CTCAAGTGAGATAAAT
1 TCTCAAGTGAGACAAAT
71684 TGTTATTTGA
Statistics
Matches: 116, Mismatches: 43, Indels: 8
0.69 0.26 0.05
Matches are distributed among these distances:
34 3 0.03
35 10 0.09
36 50 0.43
37 51 0.44
38 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (36 bp):
TCTCAAGTGAGACAAATGTTGTTTTAAGAAAAACAA
Found at i:71563 original size:37 final size:37
Alignment explanation
Indices: 71516--71643 Score: 141
Period size: 37 Copynumber: 3.5 Consensus size: 37
71506 GTTTTAAGAA
* *
71516 AAACAATCTCAAGTGAGATACATTGTTGTTTCGAGTG
1 AAACTATCTCAAGTGAGATAAATTGTTGTTTCGAGTG
* * * ** **
71553 AAACTGTCTCAAGCGAGACAAATT-TTGTTTTAAGAA
1 AAACTATCTCAAGTGAGATAAATTGTTGTTTCGAGTG
*
71589 AAACAATCTCAAGTGAGATAAATTGTTGTTTCGAGTG
1 AAACTATCTCAAGTGAGATAAATTGTTGTTTCGAGTG
* *
71626 AAACTTTCTCAAGAGAGA
1 AAACTATCTCAAGTGAGA
71644 CGCAATTTGT
Statistics
Matches: 70, Mismatches: 20, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
36 28 0.40
37 42 0.60
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (37 bp):
AAACTATCTCAAGTGAGATAAATTGTTGTTTCGAGTG
Found at i:71581 original size:73 final size:73
Alignment explanation
Indices: 71470--71687 Score: 334
Period size: 73 Copynumber: 3.0 Consensus size: 73
71460 TGGAAATTTC
* * *
71470 TGTTTCTAGTG-AACTGTCTCAAGCGAGACGAATATTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
*
71534 TACATTGT
66 TAAATTGT
71542 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
71607 TAAATTGT
66 TAAATTGT
* * * *
71615 TGTTTCGAGTGAAACTTTCTCAAGAGAGACGCAA-TTTGTTTTAAGAAAAATAA-CTCAAGTGAG
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGAC-AAATTTTGTTTTAAGAAAAACAATCTCAAGTGAG
71678 ATAAATTGT
65 ATAAATTGT
71687 T
1 T
71688 ATTTGAAAAC
Statistics
Matches: 136, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
72 30 0.22
73 104 0.76
74 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (73 bp):
TGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
TAAATTGT
Found at i:72467 original size:22 final size:22
Alignment explanation
Indices: 72413--72467 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
72403 TAAAGTTTTT
* *
72413 ATCTTTGAAAATAGAATCTATC
1 ATCTTTGAAGAGAGAATCTATC
72435 ATCTTTGAAGAGAGAATCTATC
1 ATCTTTGAAGAGAGAATCTATC
* *
72457 ATTTTTTAAGA
1 ATCTTTGAAGA
72468 ATGTAGATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (22 bp):
ATCTTTGAAGAGAGAATCTATC
Done.