Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008576.1 Hibiscus syriacus cultivar Beakdansim tig00111505_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: 399473
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:260004 original size:14 final size:14
Alignment explanation
Indices: 259981--260011 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
259971 ATATTTCTCC
*
259981 AAATACCAAAAAAA
1 AAATAACAAAAAAA
259995 AAATAACAAAAAAA
1 AAATAACAAAAAAA
260009 AAA
1 AAA
260012 GCAGAGAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.84, C:0.10, G:0.00, T:0.06
Consensus pattern (14 bp):
AAATAACAAAAAAA
Found at i:269068 original size:188 final size:188
Alignment explanation
Indices: 268740--269129 Score: 658
Period size: 188 Copynumber: 2.1 Consensus size: 188
268730 ATATTTTTTA
* * * *
268740 TTATTTTGGGTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAATCGGACCGACCCGAAAAT
1 TTATTTT-GTTCGGGTCGAGTCGGCTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAAT
*
268805 ATATATAATTCAGGTCGGGTCGGATTAAGTCATTGTTTTTATTAAATAAAAATATTTTTTTATTA
65 ATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTATTA
268870 TTTCGGGTCGGGTCGGGTTGGATTTCTAATTCATATATTCGAGTCAGGTCGGATGAAACT
130 TTTCGGGTC-GGTCGGGTTGGATTTCTAATTCATATATTCGAGTCAGGTCGGATGAAACT
*
268930 TTATTTTGTTCGGGTCGAGTCAGGCTT-GGGTTTAGGGTGAAAAAAACCGGATCG-CCCGAAAAT
1 TTATTTTGTTCGGGTCGAGTC-GGCTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAAT
*
268993 ATATATAATTCGGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTATTA
65 ATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTATTA
* *
269058 TTTCGGGTCGGTCGGGTTGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACT
130 TTTCGGGTCGGTCGGGTTGGATTTCTAATTCATATATTCGAGTCAGGTCGGATGAAACT
269117 TTATTTTGTTCGG
1 TTATTTTGTTCGG
269130 ATCGGATTGG
Statistics
Matches: 190, Mismatches: 9, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
187 61 0.32
188 81 0.43
189 37 0.19
190 11 0.06
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.37
Consensus pattern (188 bp):
TTATTTTGTTCGGGTCGAGTCGGCTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATA
TATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTATTAT
TTCGGGTCGGTCGGGTTGGATTTCTAATTCATATATTCGAGTCAGGTCGGATGAAACT
Found at i:269427 original size:33 final size:34
Alignment explanation
Indices: 269347--269429 Score: 89
Period size: 38 Copynumber: 2.4 Consensus size: 34
269337 TTTTGTCCGG
* *
269347 GTCGAATCGGGCTTTTTAAGTGTGATATTCGGGT
1 GTCGGATCGGGTTTTTTAAGTGTGATATTCGGGT
*
269381 CGAGTCGGGTCGGGTTCTTTTAAGTGTGATATTCGGGT
1 ---GTCGGATCGGGTT-TTTTAAGTGTGATATTCGGGT
269419 -T-GGATCGGGTT
1 GTCGGATCGGGTT
269430 AGGTTCGGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
33 9 0.22
34 1 0.02
37 10 0.24
38 21 0.51
ACGTcount: A:0.14, C:0.12, G:0.36, T:0.37
Consensus pattern (34 bp):
GTCGGATCGGGTTTTTTAAGTGTGATATTCGGGT
Found at i:269435 original size:38 final size:38
Alignment explanation
Indices: 269360--269435 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
269350 GAATCGGGCT
*
269360 TTTTAAGTGTGATATTCGGGTCGAGTCGGGTCGGGTTC
1 TTTTAAGTGTGATATTCGGGTCGAGTCGGGTCAGGTTC
* *
269398 TTTTAAGTGTGATATTCGGGTTG-GATCGGGTTAGGTTC
1 TTTTAAGTGTGATATTCGGGTCGAG-TCGGGTCAGGTTC
269436 GGGTTTAGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 33 0.97
ACGTcount: A:0.14, C:0.11, G:0.36, T:0.39
Consensus pattern (38 bp):
TTTTAAGTGTGATATTCGGGTCGAGTCGGGTCAGGTTC
Found at i:269539 original size:227 final size:217
Alignment explanation
Indices: 269094--269553 Score: 690
Period size: 217 Copynumber: 2.1 Consensus size: 217
269084 AATTCATATA
* * * *
269094 TTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGATCGGATTGGGTTTTTTAAGTGTGATATT
1 TTCGGGTCGGGTCGGATGAAACTTTATTTTGTCCGGATCGAATCGGGCTTTTTAAGTGTGATATT
* * *
269159 TGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGTTTGGGTTTAGGGTGAAAA
66 CGGGTCGAGTCGGGTCGGGTTCTTTTAAGTGTGATATTCGGGTCGGTTTGGGTTTAGGCTGAAAA
* * *
269224 AAACCGGACCGATCTGAAAATATATATAATTCGAGTCAGGTCGGATTAAGTCACTGTTTTTATTA
131 AAACCGGACCGACCCGAAAATATATATAATTCGAGTCAGGTCGGATTAAATCACTGTTTTTATTA
269289 AATAAAAATAATTTTTTATTAT
196 AATAAAAATAATTTTTTATTAT
* *
269311 TTTGGGTCGGGTCGGATGAAACTTTATTTTGTCCGGGTCGAATCGGGCTTTTTAAGTGTGATATT
1 TTCGGGTCGGGTCGGATGAAACTTTATTTTGTCCGGATCGAATCGGGCTTTTTAAGTGTGATATT
269376 CGGGTCGAGTCGGGTCGGGTTCTTTTAAGTGTGATATTCGGGTTGGATCGGGTTAGGTTCGGGTT
66 CGGGTCGAGTCGGGTCGGGTTCTTTTAAGTGTGATATTC--G--GG-TC-GG-T---TT-GGGTT
*
269441 TAGGCTG-AAAAAACCGGACCGACCCGAAAATATATATAATTCGGGTCAGGTCGGATTAAATCAC
120 TAGGCTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGAGTCAGGTCGGATTAAATCAC
269505 TGTTTTTATTAAATAAAAATAATTTTTTATTAT
185 TGTTTTTATTAAATAAAAATAATTTTTTATTAT
269538 TTCGGGTC-GGTCGGAT
1 TTCGGGTCGGGTCGGAT
269554 TTCTAATTCA
Statistics
Matches: 218, Mismatches: 14, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
217 96 0.44
219 1 0.00
221 2 0.01
222 2 0.01
223 2 0.01
224 1 0.00
226 8 0.04
227 95 0.44
228 11 0.05
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.37
Consensus pattern (217 bp):
TTCGGGTCGGGTCGGATGAAACTTTATTTTGTCCGGATCGAATCGGGCTTTTTAAGTGTGATATT
CGGGTCGAGTCGGGTCGGGTTCTTTTAAGTGTGATATTCGGGTCGGTTTGGGTTTAGGCTGAAAA
AAACCGGACCGACCCGAAAATATATATAATTCGAGTCAGGTCGGATTAAATCACTGTTTTTATTA
AATAAAAATAATTTTTTATTAT
Found at i:271087 original size:35 final size:35
Alignment explanation
Indices: 271041--271152 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
271031 AAAACAGTCC
* * *
271041 TCAATTTCATTCTAAACCCCAATTTCCAAAGTATT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
271076 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
** * *
271111 TCAATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
271146 TCAATTT
1 TCAATTT
271153 AAGGTTTAGA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.40, C:0.23, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:272806 original size:35 final size:35
Alignment explanation
Indices: 272765--272875 Score: 118
Period size: 35 Copynumber: 3.2 Consensus size: 35
272755 TCTAAACCTT
*
272765 AAATTGAAGCATTTTAGAATTTAGGGTTTAGAATT
1 AAATTGAAGCATTTTAGAATTTAGGGTTTAGAATG
* ** *
272800 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAAGCATTTTAGAATTTAGGGTTTAGAATG
** * *
272835 AAATTGAATTACTTT-GAAAATT-GGGTTTAGAATG
1 AAATTGAAGCATTTTAG-AATTTAGGGTTTAGAATG
272869 AAATTGA
1 AAATTGA
272876 GGATTGTTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
34 20 0.30
35 47 0.70
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.41
Consensus pattern (35 bp):
AAATTGAAGCATTTTAGAATTTAGGGTTTAGAATG
Found at i:272866 original size:34 final size:35
Alignment explanation
Indices: 272785--272875 Score: 130
Period size: 35 Copynumber: 2.6 Consensus size: 35
272775 ATTTTAGAAT
** * * *
272785 TTAGGGTTTAGAATTTAATTGAATTATTTTGGAAT
1 TTAGGGTTTAGAATGAAATTGAATTACTTTGAAAA
272820 TTAGGGTTTAGAATGAAATTGAATTACTTTGAAAA
1 TTAGGGTTTAGAATGAAATTGAATTACTTTGAAAA
272855 TT-GGGTTTAGAATGAAATTGA
1 TTAGGGTTTAGAATGAAATTGA
272876 GGATTGTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 19 0.37
35 32 0.63
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (35 bp):
TTAGGGTTTAGAATGAAATTGAATTACTTTGAAAA
Found at i:273902 original size:21 final size:21
Alignment explanation
Indices: 273876--273916 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
273866 GTGATGACGT
* *
273876 GACAATTCACAATGCTAACAC
1 GACAATCCACAATACTAACAC
*
273897 GACAATCCACAGTACTAACA
1 GACAATCCACAATACTAACA
273917 TTTCCATCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.29, G:0.10, T:0.17
Consensus pattern (21 bp):
GACAATCCACAATACTAACAC
Found at i:276853 original size:45 final size:45
Alignment explanation
Indices: 276804--276945 Score: 185
Period size: 45 Copynumber: 3.2 Consensus size: 45
276794 CTTCCTCTGT
* * *
276804 GATGCTTTCCATCAGCAGATCTTGATCTTGACCGCTTTCTATCCC
1 GATGCTTTCCATCAGCAGATCTTGACCTCGACCGCCTTCTATCCC
* *
276849 GATGCTTTCCTTCAGCAGATCTTGACCTCGACCGCCTTCTATCTC
1 GATGCTTTCCATCAGCAGATCTTGACCTCGACCGCCTTCTATCCC
* * ** **
276894 GATGCTTGCCGTCAGCAGATCTTGACCTCGAATGCCTTCTATTTC
1 GATGCTTTCCATCAGCAGATCTTGACCTCGACCGCCTTCTATCCC
276939 GATGCTT
1 GATGCTT
276946 AGATTTCTTA
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 87 1.00
ACGTcount: A:0.17, C:0.31, G:0.18, T:0.35
Consensus pattern (45 bp):
GATGCTTTCCATCAGCAGATCTTGACCTCGACCGCCTTCTATCCC
Found at i:281667 original size:3 final size:3
Alignment explanation
Indices: 281661--281726 Score: 107
Period size: 3 Copynumber: 22.0 Consensus size: 3
281651 TTATTAGAAG
*
281661 TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA T-A TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
281706 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
281727 ATATATTATT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 54 0.92
4 3 0.05
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:283030 original size:11 final size:11
Alignment explanation
Indices: 283014--283047 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
283004 CACTAACTTA
283014 TGGGCTTGGCT
1 TGGGCTTGGCT
283025 TGGGCTTGGCT
1 TGGGCTTGGCT
*
283036 T-GGCTTCGCT
1 TGGGCTTGGCT
283046 TG
1 TG
283048 TGGACTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.00, C:0.21, G:0.41, T:0.38
Consensus pattern (11 bp):
TGGGCTTGGCT
Found at i:288619 original size:477 final size:481
Alignment explanation
Indices: 287725--288688 Score: 1821
Period size: 477 Copynumber: 2.0 Consensus size: 481
287715 CATGGTTAGA
* *
287725 TGCTATGTCTACTTGGCAAGTTGCTTTGGTGGGTTACGGTAGTGGTTTGGTAGTTGGGCTATGTA
1 TGCTATGTCTACTTGGCAAGTTGCTTTGGTGGGCTACGGTAGTGGTTTGGTAGGTGGGCTATGTA
287790 TTTGATATACAGCGCTGAATGAGTTGGGAAACAGATGGGTTTACAAGTTGAAAAGGCATGGTAAA
66 TTTGATATACAGCGCTGAATGAGTTGGGAAACAGATGGGTTTACAAGTTGAAAAGGCATGGTAAA
287855 AGAAATAGAAGAAGAACAAGGTGACCCTATCAGAATCCATGTTTTAAAATCATCAGGTAAGCATT
131 AGAAATAGAAGAAGAACAAGGTGACCCTATCAGAATCCATGTTTTAAAATCATCAGGTAAGCATT
287920 TCCTTTTGAAACTAGAGTCTCTATAAACTGAAAGATAGTTGTTGTAAAGTGTGATAGATGTACAT
196 TCCTTTTGAAACTAGAGTCTCTATAAACTGAAAGATAGTTGTTGTAAAGTGTGATAGATGTACAT
287985 TTTCTTTTGAATTTTGGTCCCTGATCTTTTTTTCCTTGCAGGATGAATTTGAAACAGGACACAGA
261 TTTCTTTTGAATTTTGGTCCCTGATCTTTTTTTCCTTGCAGGATGAATTTGAAACAGGACACAGA
*
288050 ATCTGCAATATGAAATTATGACAACTTTCAAGTTACTGTGAATGATGTTGAAAAGATCATTGATT
326 ATCTGCAATATGAAATTATGACAACTTTCAAGCTACTGTGAATGATGTTGAAAAGATCATTGATT
288115 GGGAGAATACATCTCCGAAGCAAGTTGAAATCCTCTTCAAG-C-C-A-GCGGTTGATACAGATTC
391 GGGAGAATACATCTCCGAAGCAAGTTGAAATCCTCTTCAAGCCACTATGCGGTTGATACAGATTC
288176 ACATAACAATGCTAAGTGGATTAAAT
456 ACATAACAATGCTAAGTGGATTAAAT
288202 TGCTATGTCTACTTGGCAAGTTGCTTTGGTGGGCTACGGTAGTGGTTTGGTAGGTGGGCTATGTA
1 TGCTATGTCTACTTGGCAAGTTGCTTTGGTGGGCTACGGTAGTGGTTTGGTAGGTGGGCTATGTA
288267 TTTGATATACAGCGCTGAATGAGTTGGGAAACAGATGGGTTTACAAGTTGAAAAGGCATGGTAAA
66 TTTGATATACAGCGCTGAATGAGTTGGGAAACAGATGGGTTTACAAGTTGAAAAGGCATGGTAAA
288332 AGAAATAGAAGAAGAACAAGGTGACCCTATCAGAATCCATGTTTTAAAATCATCAGGTAAGCATT
131 AGAAATAGAAGAAGAACAAGGTGACCCTATCAGAATCCATGTTTTAAAATCATCAGGTAAGCATT
288397 TCCTTTTGAAACTAGAGTCTCTATAAACTGAAAGATAGTTGTTGTAAAGTGTGATAGATGTACAT
196 TCCTTTTGAAACTAGAGTCTCTATAAACTGAAAGATAGTTGTTGTAAAGTGTGATAGATGTACAT
**
288462 TTTCTTTTGAATTTTGGTCCCTG-TCCTTTTTTTCCTTGCAGGATGAATTTGAAACAGGACATGG
261 TTTCTTTTGAATTTTGGTCCCTGAT-CTTTTTTTCCTTGCAGGATGAATTTGAAACAGGACACAG
288526 AATCTGCAATATGAAATTATGACAACTTTCAAGCTACTGTGAATGATGTTGAAAAGATCATTGAT
325 AATCTGCAATATGAAATTATGACAACTTTCAAGCTACTGTGAATGATGTTGAAAAGATCATTGAT
288591 TGGGAGAATACATCTCCGAAGCAAGTTGAAATCCTCTTCAAGCCAGCTTATGCGGTTGATACAGA
390 TGGGAGAATACATCTCCGAAGCAAGTTGAAATCCTCTTCAAGCCA-C-TATGCGGTTGATACAGA
288656 TTCACATAACAATGCTAAGTGGATTAAAT
453 TTCACATAACAATGCTAAGTGGATTAAAT
288685 TGCT
1 TGCT
288689 GCCTGTTGGG
Statistics
Matches: 475, Mismatches: 5, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
476 1 0.00
477 424 0.89
478 1 0.00
480 1 0.00
482 1 0.00
483 47 0.10
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (481 bp):
TGCTATGTCTACTTGGCAAGTTGCTTTGGTGGGCTACGGTAGTGGTTTGGTAGGTGGGCTATGTA
TTTGATATACAGCGCTGAATGAGTTGGGAAACAGATGGGTTTACAAGTTGAAAAGGCATGGTAAA
AGAAATAGAAGAAGAACAAGGTGACCCTATCAGAATCCATGTTTTAAAATCATCAGGTAAGCATT
TCCTTTTGAAACTAGAGTCTCTATAAACTGAAAGATAGTTGTTGTAAAGTGTGATAGATGTACAT
TTTCTTTTGAATTTTGGTCCCTGATCTTTTTTTCCTTGCAGGATGAATTTGAAACAGGACACAGA
ATCTGCAATATGAAATTATGACAACTTTCAAGCTACTGTGAATGATGTTGAAAAGATCATTGATT
GGGAGAATACATCTCCGAAGCAAGTTGAAATCCTCTTCAAGCCACTATGCGGTTGATACAGATTC
ACATAACAATGCTAAGTGGATTAAAT
Found at i:291095 original size:17 final size:17
Alignment explanation
Indices: 291075--291110 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
291065 GATGTGGGAA
291075 ACAACATGATGCGTGAT
1 ACAACATGATGCGTGAT
291092 ACAACATGATGCGTGAT
1 ACAACATGATGCGTGAT
291109 AC
1 AC
291111 CTTCCCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (17 bp):
ACAACATGATGCGTGAT
Found at i:294740 original size:44 final size:45
Alignment explanation
Indices: 294676--294772 Score: 151
Period size: 44 Copynumber: 2.2 Consensus size: 45
294666 ATTTATTTTC
294676 ATTTTTCGAACAAGCATGCGAACTAGATATCATGCGGTTAGG-TTT
1 ATTTTT-GAACAAGCATGCGAACTAGATATCATGCGGTTAGGATTT
* *
294721 ATTTTTGAATAAGCATGCGAATTAGATATCATGCGGTTAGGATTT
1 ATTTTTGAACAAGCATGCGAACTAGATATCATGCGGTTAGGATTT
*
294766 CTTTTTG
1 ATTTTTG
294773 TGGATAACAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
44 33 0.69
45 15 0.31
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (45 bp):
ATTTTTGAACAAGCATGCGAACTAGATATCATGCGGTTAGGATTT
Found at i:302281 original size:18 final size:16
Alignment explanation
Indices: 302237--302303 Score: 66
Period size: 16 Copynumber: 4.1 Consensus size: 16
302227 AAGAAGAAAT
302237 AAAA-GAGAAAAAATGA
1 AAAATGAGAAAAAA-GA
302253 AAAATGAGAAAAAAGA
1 AAAATGAGAAAAAAGA
*
302269 AAAATGATGGAAAAAACA
1 AAAATGA--GAAAAAAGA
*
302287 AAAA-GAAAGAAAAAGA
1 AAAATGAGA-AAAAAGA
302303 A
1 A
302304 GAAAAAATGG
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
15 1 0.02
16 20 0.45
17 11 0.25
18 12 0.27
ACGTcount: A:0.75, C:0.01, G:0.18, T:0.06
Consensus pattern (16 bp):
AAAATGAGAAAAAAGA
Found at i:302283 original size:28 final size:26
Alignment explanation
Indices: 302252--302317 Score: 64
Period size: 28 Copynumber: 2.5 Consensus size: 26
302242 AGAAAAAATG
*
302252 AAAAATGAGAAAAAAGAAAAATGATGGA
1 AAAAATGAGAAAAAAGAAAAA-GA-AGA
* *
302280 AAAAA-CAAAAAGAAAGAAAAAGAAGA
1 AAAAATGAGAAA-AAAGAAAAAGAAGA
302306 AAAAATG-GAAAA
1 AAAAATGAGAAAA
302318 GGGAAGAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
25 1 0.03
26 10 0.32
27 6 0.19
28 14 0.45
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.06
Consensus pattern (26 bp):
AAAAATGAGAAAAAAGAAAAAGAAGA
Found at i:302318 original size:17 final size:16
Alignment explanation
Indices: 302243--302317 Score: 53
Period size: 17 Copynumber: 4.3 Consensus size: 16
302233 AAATAAAAGA
302243 GAAAAAATG-AAAAATG
1 GAAAAAA-GAAAAAATG
302259 AGAAAAAAGAAAAATGATG
1 -GAAAAAAGAAAAA--ATG
* *
302278 GAAAAAACAAAAAGAAAG
1 GAAAAAA-GAAAA-AATG
*
302296 AAAAAGAAGAAAAAATG
1 GAAAA-AAGAAAAAATG
302313 GAAAA
1 GAAAA
302318 GGGAAGAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
16 1 0.02
17 18 0.39
18 17 0.37
19 9 0.20
20 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.07
Consensus pattern (16 bp):
GAAAAAAGAAAAAATG
Found at i:303828 original size:55 final size:55
Alignment explanation
Indices: 303690--304321 Score: 727
Period size: 55 Copynumber: 11.6 Consensus size: 55
303680 GTTGAAGATT
* * **
303690 GAGTCCTATACTCTCTGAAGGAATAGGGAGTGGACAAGTTTTGTTGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCG-TTTGTTGAAGATTGTTC
* ** *
303742 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTC
*
303797 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCG-TTTGTTGAAGATTGTTC
* * *
303853 GAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTT-TATAAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGT-TGAAGATTGTTC
* *
303908 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCC-GTTTGTTGAAGATTGTTC
* * *
303964 GAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTATTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTC
* *
304019 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGCTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGT-TGAAGATTGTTC
* * *
304074 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTAAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTC
* * * *
304125 GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATT-TTCC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTT-C
* *
304180 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCG-TTTGTTGAAGATTGTTC
* * * * * * * *
304236 AAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACACATTT-TATGATGATGGTTC
1 GAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGT-TGAAGATTGTTC
*
304291 GAG-TCTTAAACT-TCCTGAAGGAATAGGGAGC
1 GAGTTC-TATACTCT-CTGAAGGAATAGGGAGC
304322 AGACTCGTCA
Statistics
Matches: 509, Mismatches: 52, Indels: 35
0.85 0.09 0.06
Matches are distributed among these distances:
51 52 0.10
52 38 0.07
53 2 0.00
54 6 0.01
55 264 0.52
56 144 0.28
57 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (55 bp):
GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTC
Found at i:303906 original size:111 final size:111
Alignment explanation
Indices: 303690--304321 Score: 749
Period size: 111 Copynumber: 5.8 Consensus size: 111
303680 GTTGAAGATT
* * * ** *
303690 GAGTCCTATACTCTCTGAAGGAATAGGGAGTGGACAAGTTTTGTTGAAGA---TT-GAGTCCTAT
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTCGAGTTCTAT
* ** *
303751 ACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGT-TGAAGATTGTTC
66 ACTCCCTGAAGGAATAGGGAGCGGACCCGTT-TTATGAAGATTGTTC
303797 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTCGAGTTCTAT
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTCGAGTTCTAT
* *
303862 ACTCCCTGAACGAATAGGGAGCGGACCCGTTTTATAAAGATTGTTC
66 ACTCCCTGAAGGAATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
*
303908 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTGTTGAAGATTGTTCGAGTTCTAT
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTCGAGTTCTAT
*
303973 ACTCCCTGAACGAATAGGGAGCGGACCCG-TTTATTGAAGATTGTTC
66 ACTCCCTGAAGGAATAGGGAGCGGACCCGTTTTA-TGAAGATTGTTC
* *
304019 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT-ATGAAGATTGCTCGAGTTCTAT
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTCGAGTTCTAT
* * * *
304083 ACTCTCTGAAGGAATAGGGAGCGAACACGTTTGT-TAAAGA---TT-
66 ACTCCCTGAAGGAATAGGGAGCGGACCCGTTT-TATGAAGATTGTTC
* * * * *
304125 GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTG-TTTATTGAAGATT-TTCCGAGTTCTA
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTT-CGAGTTCTA
* *
304188 TACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
65 TACTCCCTGAAGGAATAGGGAGCGGACCCGTTTTA-TGAAGATTGTTC
* * * * * * * *
304236 AAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTT-ATGATGATGGTTCGAG-TCTT
1 GAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTCGAGTTC-T
* *
304298 AAACTTCCTGAAGGAATAGGGAGC
64 ATACTCCCTGAAGGAATAGGGAGC
304322 AGACTCGTCA
Statistics
Matches: 458, Mismatches: 47, Indels: 36
0.85 0.09 0.07
Matches are distributed among these distances:
105 5 0.01
106 81 0.18
107 52 0.11
110 62 0.14
111 252 0.55
112 6 0.01
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (111 bp):
GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTCGAGTTCTAT
ACTCCCTGAAGGAATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
Found at i:304340 original size:272 final size:274
Alignment explanation
Indices: 303742--304341 Score: 759
Period size: 272 Copynumber: 2.2 Consensus size: 274
303732 GTTGAAGATT
* * * * *
303742 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTCGAGTTCTATA
1 GAGTTCTAAACTCTCTGAAGGAATAGGGAGCGGACACG-TCTTTGAAGATTGCTCGAGTTCTATA
* * * *
303807 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTCGAGTTCTATACTCCCTGAA
65 CTCTCTGAAGGAATAGAGAGCGAACACGTTTTGTTAAAGA-T-TTCGAGTCCTATACTCCCTGAA
*
303872 CGAATAGGGAGCGGACCCGTTTTATAAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGA
128 AGAATAGGGAGCGGACCCGTTTTATAAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGA
* * * * *
303937 GCGGACCCATTTTGTTGAAGATTGTTCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCG
193 GCGGACCCATTTTATTGAAGATTGTTCAAGTTCTATACTCCCTGAACGAATAGAGAGCAGACCAG
*
304002 TTTATTGAAGATTGTTC
258 TTTATTGAAGATGGTTC
* * * *
304019 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGCTCGAGTTCTATA
1 GAGTTCTAAACTCTCTGAAGGAATAGGGAGCGGACACGTCTT-TGAAGATTGCTCGAGTTCTATA
* *
304084 CTCTCTGAAGGAATAGGGAGCGAACACG-TTTGTTAAAGA-TT-GAGTCCTATACTCTCTGAAAG
65 CTCTCTGAAGGAATAGAGAGCGAACACGTTTTGTTAAAGATTTCGAGTCCTATACTCCCTGAAAG
* *
304146 AATAGGGAGCGGACCTG-TTTATTGAAGATT-TTCCGAGTTCTATACTCTCTGAAGGAATAGAGA
130 AATAGGGAGCGGACCCGTTTTA-TAAAGATTGTT-CGAGTTCTATACTCTCTGAAGGAATAGAGA
* * *
304209 GCGGACCCGTTTTATTGAAGATTGTTCAAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACAC
193 GCGGACCCATTTTATTGAAGATTGTTCAAGTTC-TATACTCCCTGAACGAATAGAGAGCAGAC-C
* *
304273 ATTTTA-TGATGATGGTTC
256 AGTTTATTGAAGATGGTTC
* *
304291 GAG-TCTTAAACT-TCCTGAAGGAATAGGGAGCAGACTCGTCATTTGAAGATT
1 GAGTTC-TAAACTCT-CTGAAGGAATAGGGAGCGGACACGTC-TTTGAAGATT
304342 TTTCAAGTTT
Statistics
Matches: 283, Mismatches: 32, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
271 11 0.04
272 171 0.60
273 9 0.03
276 12 0.04
277 80 0.28
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (274 bp):
GAGTTCTAAACTCTCTGAAGGAATAGGGAGCGGACACGTCTTTGAAGATTGCTCGAGTTCTATAC
TCTCTGAAGGAATAGAGAGCGAACACGTTTTGTTAAAGATTTCGAGTCCTATACTCCCTGAAAGA
ATAGGGAGCGGACCCGTTTTATAAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCG
GACCCATTTTATTGAAGATTGTTCAAGTTCTATACTCCCTGAACGAATAGAGAGCAGACCAGTTT
ATTGAAGATGGTTC
Found at i:309795 original size:21 final size:22
Alignment explanation
Indices: 309755--309795 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
309745 AATATATAGT
309755 AACCTAATACAATAATTTAATA
1 AACCTAATACAATAATTTAATA
309777 AACCTTAAT-CAAT-ATTTAA
1 AACC-TAATACAATAATTTAA
309796 AATAGTAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (22 bp):
AACCTAATACAATAATTTAATA
Found at i:310284 original size:19 final size:19
Alignment explanation
Indices: 310260--310298 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
310250 AACAACACTC
*
310260 TATAATCAAAGGACTATTT
1 TATAATCAAAGGACCATTT
*
310279 TATAATCAAATGACCATTT
1 TATAATCAAAGGACCATTT
310298 T
1 T
310299 GTAACAGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (19 bp):
TATAATCAAAGGACCATTT
Found at i:322450 original size:20 final size:21
Alignment explanation
Indices: 322425--322517 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
322415 TTTTCCCAAT
*
322425 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
322445 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
* *
322466 TAGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
322486 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
322507 TCGCAATGCGA
1 TCGCAATGCGA
322518 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:322531 original size:20 final size:20
Alignment explanation
Indices: 322506--322620 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
322496 AATTGGGAAA
*
322506 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
322526 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
322547 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
322567 TTTGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
322587 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
322607 TTCGCAACGCGATA
1 ATCGCAACGCGATA
322621 ATACATAATC
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.78
21 13 0.16
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:322532 original size:41 final size:41
Alignment explanation
Indices: 322427--322517 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 41
322417 TTCCCAATTC
322427 GCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATA
1 GCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATA
*
322468 GCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATC
1 GCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATA
322509 GCAATGCGA
1 GCAATGCGA
322518 TACTGACTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.42, C:0.16, G:0.25, T:0.16
Consensus pattern (41 bp):
GCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATA
Found at i:322548 original size:41 final size:41
Alignment explanation
Indices: 322503--322640 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
322493 GCGAATTGGG
* * *
322503 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * * *
322544 AAAATCGCAACGAGATACTTACTTTTGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
322586 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
322625 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
322641 TTTCAAAGCG
Statistics
Matches: 77, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
39 2 0.03
40 30 0.39
41 43 0.56
42 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:322836 original size:22 final size:22
Alignment explanation
Indices: 322808--322851 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
322798 CACTCTCTCA
*
322808 CCCATCTCCGATGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
322830 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
322852 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:323158 original size:20 final size:20
Alignment explanation
Indices: 323114--323173 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
323104 GCGATTATCT
** *
323114 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCA
323134 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCATTTTCA
* **
323154 TGTTGCGATTTTCATTTTCA
1 CGTTGCGATAGTCATTTTCA
323174 GAAACTATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCA
Found at i:323963 original size:13 final size:14
Alignment explanation
Indices: 323921--323978 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
323911 TTGTGTTTCG
*
323921 CGTTGTGATTTTGT
1 CGTTGCGATTTTGT
*
323935 CGTTGCGATTTCATTTT
1 CGTTGCGA-TT--TTGT
323952 GCGTTGCGATTTTGT
1 -CGTTGCGATTTTGT
323967 CGTTGCGATTTT
1 CGTTGCGATTTT
323979 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 19 0.51
15 5 0.14
17 5 0.14
18 8 0.22
ACGTcount: A:0.09, C:0.14, G:0.26, T:0.52
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:323963 original size:32 final size:33
Alignment explanation
Indices: 323916--323994 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
323906 GCGATTTGTG
*
323916 TTTCGCGTTGTGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
323948 TTTTGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
323981 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
323995 AGCCATTTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 25 0.60
33 17 0.40
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:323991 original size:19 final size:19
Alignment explanation
Indices: 323967--324033 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
323957 GCGATTTTGT
**
323967 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
323986 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
324006 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
324025 CGTTGCGAT
1 CGTTGCGAT
324034 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:324013 original size:20 final size:19
Alignment explanation
Indices: 323979--324033 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
323969 TTGCGATTTT
*
323979 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
323998 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
324018 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
324034 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:324130 original size:27 final size:26
Alignment explanation
Indices: 324061--324132 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
324051 GAAAGTAAAC
324061 TATTCTTCTTCTGGAATGTTTATATA
1 TATTCTTCTTCTGGAATGTTTATATA
* * **
324087 TATTGTCCTT-TTAAATGTTTATATA
1 TATTCTTCTTCTGGAATGTTTATATA
324112 -AGTTCTTACTTCTGGAATGTT
1 TA-TTCTT-CTTCTGGAATGTT
324133 ATCTGAGCAT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
24 1 0.03
25 16 0.46
26 11 0.31
27 7 0.20
ACGTcount: A:0.24, C:0.11, G:0.12, T:0.53
Consensus pattern (26 bp):
TATTCTTCTTCTGGAATGTTTATATA
Found at i:325930 original size:33 final size:33
Alignment explanation
Indices: 325893--325998 Score: 160
Period size: 33 Copynumber: 3.2 Consensus size: 33
325883 GGAAATTACT
325893 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
** *
325926 ATCGCAACGCTA-ATTTCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGA-ATCGCAATGCGAAATGAAA
*
325959 ATCGCAACGAGGGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
325992 ATCGCAA
1 ATCGCAA
325999 TGCGAATTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
32 1 0.02
33 62 0.97
34 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:326015 original size:19 final size:19
Alignment explanation
Indices: 325906--326004 Score: 83
Period size: 19 Copynumber: 5.7 Consensus size: 19
325896 GCAACGAGAG
325906 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
325925 AATCGCAA--CG--CT-AA
1 AATCGCAATGCGAAATGAA
**
325939 TTTCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
**
325958 AATCGCAA--CG--A-GGG
1 AATCGCAATGCGAAATGAA
325972 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
325991 AATCGCAATGCGAA
1 AATCGCAATGCGAA
326005 TTTAATTTCG
Statistics
Matches: 60, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
14 17 0.28
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 31 0.52
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:326021 original size:19 final size:20
Alignment explanation
Indices: 325999--326042 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
325989 AAAATCGCAA
325999 TGCGAATTT-AATTTCGCGT
1 TGCGAATTTCAATTTCGCGT
* *
326018 TGCGATTTTCATTTTCGCGT
1 TGCGAATTTCAATTTCGCGT
326038 TGCGA
1 TGCGA
326043 TTCTCTCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (20 bp):
TGCGAATTTCAATTTCGCGT
Found at i:326075 original size:19 final size:19
Alignment explanation
Indices: 325993--326076 Score: 70
Period size: 19 Copynumber: 4.6 Consensus size: 19
325983 GAAATGAAAA
* * *
325993 TCGCAATGCGAATTTAATT
1 TCGCATTGCGATTTTCATT
*
326012 TCGCGTTGCGATTTTCATTT
1 TCGCATTGCGATTTTCA-TT
* *
326032 TCGCGTTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
326048 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
326065 TCGCATTGCGAT
1 TCGCATTGCGAT
326077 AATATTTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
14 6 0.11
16 7 0.13
17 4 0.08
18 3 0.06
19 20 0.38
20 13 0.25
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:326204 original size:14 final size:14
Alignment explanation
Indices: 326183--326219 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
326173 CATCAATTAA
326183 ACAAATCAACTTTT
1 ACAAATCAACTTTT
* *
326197 ATAAATCACCTTTT
1 ACAAATCAACTTTT
326211 ACAAATCAA
1 ACAAATCAA
326220 TTAAACAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:327645 original size:21 final size:21
Alignment explanation
Indices: 327579--327645 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
327569 GTGAATCGGG
*
327579 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
327599 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
327621 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
327642 CTCT
1 CTCT
327646 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:327664 original size:42 final size:41
Alignment explanation
Indices: 327579--327701 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
327569 GTGAATCGGG
* * * *
327579 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
327621 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
327663 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
327702 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:329724 original size:20 final size:21
Alignment explanation
Indices: 329679--329735 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
329669 TCTTTTGGTT
329679 GAAATGAAAATCGC-A-ACGA
1 GAAATGAAAATCGCAACACGA
*
329698 GATAATGAGAATCGCAACACG-
1 GA-AATGAAAATCGCAACACGA
**
329719 GAAATGACTATCGCAAC
1 GAAATGAAAATCGCAAC
329736 GATAGAATCG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 2 0.06
20 24 0.75
21 3 0.09
22 3 0.09
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (21 bp):
GAAATGAAAATCGCAACACGA
Found at i:329747 original size:14 final size:14
Alignment explanation
Indices: 329728--329764 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
329718 GGAAATGACT
*
329728 ATCGCAACGATAGA
1 ATCGCAACGAGAGA
329742 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
329756 ACCGCAACG
1 ATCGCAACG
329765 CGAAATGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.27, G:0.24, T:0.08
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:329776 original size:47 final size:48
Alignment explanation
Indices: 329704--329797 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 48
329694 ACGAGATAAT
* * * *
329704 GAGAATCGCAACACGGAAATGACTATCGCAACGATAGAATCGCAACGA
1 GAGAACCGCAACACGGAAATGACTATCGCAACCAGACAATCGCAACGA
* *
329752 GAGAACCGCAACGC-GAAATGACTATCGCGACCAGACAATCGCAACG
1 GAGAACCGCAACACGGAAATGACTATCGCAACCAGACAATCGCAACG
329798 CGAAATGAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 28 0.70
48 12 0.30
ACGTcount: A:0.39, C:0.27, G:0.23, T:0.11
Consensus pattern (48 bp):
GAGAACCGCAACACGGAAATGACTATCGCAACCAGACAATCGCAACGA
Found at i:329810 original size:19 final size:19
Alignment explanation
Indices: 329788--329833 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
329778 GCGACCAGAC
329788 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
329807 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
329826 AATCGCAA
1 AATCGCAA
329834 TTTTTGTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:329862 original size:19 final size:19
Alignment explanation
Indices: 329834--329870 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
329824 AAAATCGCAA
*
329834 TTTTTGTTTCGCGTTGCGT
1 TTTTTATTTCGCGTTGCGT
329853 TTTTTATTTCGCGTTGCG
1 TTTTTATTTCGCGTTGCG
329871 ATTCTCTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.16, G:0.24, T:0.57
Consensus pattern (19 bp):
TTTTTATTTCGCGTTGCGT
Found at i:330506 original size:20 final size:20
Alignment explanation
Indices: 330421--330534 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
330411 CGCTATGTAA
* * *
330421 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
330441 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
330461 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
330482 ATCGCATTACGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
330502 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
330522 ATCGCATTGCGAT
1 ATCGCATTGCGAT
330535 TTTCCCAATT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 3 0.04
20 64 0.80
21 11 0.14
22 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:330645 original size:21 final size:21
Alignment explanation
Indices: 330605--330645 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
330595 ACTGTATACC
**
330605 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
330626 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
330646 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:331053 original size:21 final size:21
Alignment explanation
Indices: 331029--331089 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
331019 CCTAAAACCT
*
331029 TAAATTATAAACCCTAAACTC
1 TAAATCATAAACCCTAAACTC
*
331050 TAAATCAT-AACCCATAATCTC
1 TAAATCATAAACCC-TAAACTC
331071 TAAATCATAAACCCTAAAC
1 TAAATCATAAACCCTAAAC
331090 CTTAATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.14
21 25 0.71
22 5 0.14
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAATCATAAACCCTAAACTC
Found at i:333850 original size:2 final size:2
Alignment explanation
Indices: 333843--333872 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
333833 CCTTCAATGA
333843 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
333873 GGTATAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:337412 original size:25 final size:25
Alignment explanation
Indices: 337384--337433 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
337374 TTTATTTAAA
*
337384 AATATATATTCAGTAAATATTATAT
1 AATATATATTCAATAAATATTATAT
337409 AATATATATTCAATAAATATTATAT
1 AATATATATTCAATAAATATTATAT
337434 GAATTTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
AATATATATTCAATAAATATTATAT
Found at i:343009 original size:29 final size:29
Alignment explanation
Indices: 342975--343043 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
342965 GCAACACTCT
*
342975 ATAGTCAATGGACTATTTTATAACTTTTA
1 ATAGTCAATGGACCATTTTATAACTTTTA
*
343004 ATAGTCAGAT-GACCATTTTGTAACTTTTA
1 ATAGTCA-ATGGACCATTTTATAACTTTTA
*
343033 ATAGTCGATGG
1 ATAGTCAATGG
343044 GCTCAACAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.06
29 31 0.89
30 2 0.06
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.41
Consensus pattern (29 bp):
ATAGTCAATGGACCATTTTATAACTTTTA
Found at i:343077 original size:89 final size:89
Alignment explanation
Indices: 342924--343093 Score: 286
Period size: 89 Copynumber: 1.9 Consensus size: 89
342914 AATAACCGAG
* * *
342924 TGACCATTTTGTAACTTTTAATAGTCGGTGGATTCAACAAAGCAACACTCTATAGTCAATGGACT
1 TGACCATTTTGTAACTTTTAATAGTCGATGGACTCAACAAAGCAACACTCTATAGTCAAAGGACT
342989 ATTTTATAACTTTTAATAGTCAGA
66 ATTTTATAACTTTTAATAGTCAGA
* * *
343013 TGACCATTTTGTAACTTTTAATAGTCGATGGGCTCAACAAAGCAACTCTCTATTGTCAAAGGACT
1 TGACCATTTTGTAACTTTTAATAGTCGATGGACTCAACAAAGCAACACTCTATAGTCAAAGGACT
343078 ATTTTATAACTTTTAA
66 ATTTTATAACTTTTAA
343094 AATAATGTAA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 75 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (89 bp):
TGACCATTTTGTAACTTTTAATAGTCGATGGACTCAACAAAGCAACACTCTATAGTCAAAGGACT
ATTTTATAACTTTTAATAGTCAGA
Found at i:343318 original size:20 final size:18
Alignment explanation
Indices: 343277--343326 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
343267 TGAAAACACA
343277 TTAAATA-ATAAAAATAT
1 TTAAATATATAAAAATAT
*
343294 TTAAATATATGAAATAATGT
1 TTAAATATAT-AAA-AATAT
343314 TTAAATAT-TAAAA
1 TTAAATATATAAAA
343327 TAACATGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 8 0.28
18 5 0.17
19 4 0.14
20 12 0.41
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (18 bp):
TTAAATATATAAAAATAT
Found at i:343393 original size:22 final size:21
Alignment explanation
Indices: 343353--343393 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
343343 TATTTAATAA
* *
343353 TTATTTATTTCAAATAATTAG
1 TTATTTATTTAAAAAAATTAG
343374 TTATTTAATTTAAAAAAATT
1 TTATTT-ATTTAAAAAAATT
343394 GTACTACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TTATTTATTTAAAAAAATTAG
Found at i:344537 original size:48 final size:48
Alignment explanation
Indices: 344464--344665 Score: 280
Period size: 48 Copynumber: 4.2 Consensus size: 48
344454 TATTCCTAAC
* * * * *
344464 TGTTTGGTTGATGCTCATAATCTGGGAAAAAGTGAGCTTGCTGTGAAAA
1 TGTTTGGATGATGCTGAGAATCTGGGAAAAAGTGAGCTTGCTG-GGAAT
* *
344513 T-TTTGGGTGATGCTGAGAATCTGGGAAAAAGTGGGCTTGCTGGGAAT
1 TGTTTGGATGATGCTGAGAATCTGGGAAAAAGTGAGCTTGCTGGGAAT
* *
344560 TGTTTGGATGATGCTGATAATCTGGGAAAAAGTGAGCTTGCTGGGGAT
1 TGTTTGGATGATGCTGAGAATCTGGGAAAAAGTGAGCTTGCTGGGAAT
* * *
344608 TGTTTGGACGATGCTGAGAATCTGGGAAAAGGTGAGCTTTCTGGGAAT
1 TGTTTGGATGATGCTGAGAATCTGGGAAAAAGTGAGCTTGCTGGGAAT
344656 TGTTTGGATG
1 TGTTTGGATG
344666 GAAGGAAAGA
Statistics
Matches: 136, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
47 4 0.03
48 131 0.96
49 1 0.01
ACGTcount: A:0.25, C:0.09, G:0.35, T:0.32
Consensus pattern (48 bp):
TGTTTGGATGATGCTGAGAATCTGGGAAAAAGTGAGCTTGCTGGGAAT
Found at i:347589 original size:22 final size:22
Alignment explanation
Indices: 347564--347609 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
347554 TTTATTTACA
* *
347564 TTTGTTAATGTTCGATAATTCG
1 TTTGTTAATGTACAATAATTCG
*
347586 TTTGTTTATGTACAATAATTCG
1 TTTGTTAATGTACAATAATTCG
347608 TT
1 TT
347610 CGTTGACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (22 bp):
TTTGTTAATGTACAATAATTCG
Found at i:347770 original size:30 final size:30
Alignment explanation
Indices: 347718--347776 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
347708 AAATTACTCG
347718 TTTAGTACCTAAACTATTAATTTTTATTCAT
1 TTTAGTACCTAAACTATTAATTTTT-TTCAT
*
347749 TTTAGTACTTAAACT-TTAATTTTTTTCA
1 TTTAGTACCTAAACTATTAATTTTTTTCA
347777 AAATCATACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 9 0.33
31 14 0.52
ACGTcount: A:0.31, C:0.12, G:0.03, T:0.54
Consensus pattern (30 bp):
TTTAGTACCTAAACTATTAATTTTTTTCAT
Found at i:351614 original size:31 final size:31
Alignment explanation
Indices: 351576--351648 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
351566 AAATTATAGA
**
351576 TTTAGTATCTAAACTATCCGTTTT-GATTCGT
1 TTTAGTATCTAAACTATCAATTTTAG-TTCGT
*
351607 TTTAGTATCTAAATTATCAATTTTAGTTCGT
1 TTTAGTATCTAAACTATCAATTTTAGTTCGT
351638 TTTAGTA-CTAA
1 TTTAGTATCTAA
351649 CTTTTATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.11
31 33 0.87
32 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.49
Consensus pattern (31 bp):
TTTAGTATCTAAACTATCAATTTTAGTTCGT
Found at i:366983 original size:29 final size:29
Alignment explanation
Indices: 366938--367031 Score: 152
Period size: 29 Copynumber: 3.2 Consensus size: 29
366928 AACGTTTATA
* *
366938 ACTTTAGGTACTAGGATGAGTTAGAAAAT
1 ACTTTAGGCACTGGGATGAGTTAGAAAAT
366967 ACTTTAGGCACTGGGATGAGTTAGAAAAT
1 ACTTTAGGCACTGGGATGAGTTAGAAAAT
* *
366996 ACTTTAGGCACTGGGATAAGTCAGAAAAT
1 ACTTTAGGCACTGGGATGAGTTAGAAAAT
367025 ACTTTAG
1 ACTTTAG
367032 ACACCTATTC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 61 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (29 bp):
ACTTTAGGCACTGGGATGAGTTAGAAAAT
Found at i:367595 original size:18 final size:17
Alignment explanation
Indices: 367556--367598 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
367546 ATTATATGGA
367556 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
367572 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
367590 TATTATTAT
1 TATTATTAT
367599 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:367789 original size:18 final size:18
Alignment explanation
Indices: 367766--367800 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
367756 ATAGTTTATT
367766 TATATACATATTATTAAA
1 TATATACATATTATTAAA
* *
367784 TATATATATATTCTTAA
1 TATATACATATTATTAA
367801 TTATTTTTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
TATATACATATTATTAAA
Found at i:378798 original size:24 final size:24
Alignment explanation
Indices: 378735--378813 Score: 88
Period size: 25 Copynumber: 3.3 Consensus size: 24
378725 TCCATTTTAT
* *
378735 TTTAAACGAACATGTTCGCGAACG
1 TTTAAACGAACATGTTCGCTAACA
*
378759 TTATAAACGAAAATGTTCGCTAACA
1 TT-TAAACGAACATGTTCGCTAACA
* * *
378784 TTTAAACGGACATGTTCACTAATA
1 TTTAAACGAACATGTTCGCTAACA
378808 -TTAAAC
1 TTTAAAC
378814 TGACACGTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
23 6 0.13
24 20 0.43
25 21 0.45
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (24 bp):
TTTAAACGAACATGTTCGCTAACA
Found at i:378834 original size:23 final size:23
Alignment explanation
Indices: 378785--378835 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
378775 TCGCTAACAT
* *
378785 TTAAACGGACATGTTCACTAATA
1 TTAAACGGACACGTTCACGAATA
* * *
378808 TTAAACTGACACGTTTACGAATG
1 TTAAACGGACACGTTCACGAATA
378831 TTAAA
1 TTAAA
378836 TAAAAGAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (23 bp):
TTAAACGGACACGTTCACGAATA
Found at i:381381 original size:2 final size:2
Alignment explanation
Indices: 381369--381399 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
381359 TGTTTTGGTT
381369 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
381400 GGCAACAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:382518 original size:13 final size:13
Alignment explanation
Indices: 382502--382526 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
382492 TTGGGATCAG
382502 ATTTTATCATATA
1 ATTTTATCATATA
382515 ATTTTATCATAT
1 ATTTTATCATAT
382527 CTCATACAAT
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:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTTATCATATA
Found at i:385759 original size:8 final size:8
Alignment explanation
Indices: 385641--385757 Score: 209
Period size: 8 Copynumber: 14.8 Consensus size: 8
385631 TGATTTACAT
*
385641 ATACATAC
1 ATACATGC
385649 ATACATGC
1 ATACATGC
385657 ATACATGC
1 ATACATGC
385665 ATACATGC
1 ATACATGC
385673 ATACATGC
1 ATACATGC
385681 ATACATGC
1 ATACATGC
385689 ATACATGC
1 ATACATGC
385697 ATACATGC
1 ATACATGC
385705 ATACATGC
1 ATACATGC
385713 ATAC-TGC
1 ATACATGC
385720 ATACATGC
1 ATACATGC
385728 ATACATGC
1 ATACATGC
385736 ATACATGC
1 ATACATGC
*
385744 ATACATAC
1 ATACATGC
385752 ATACAT
1 ATACAT
385758 ACTATAAGAA
Statistics
Matches: 106, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
7 7 0.07
8 99 0.93
ACGTcount: A:0.39, C:0.25, G:0.10, T:0.26
Consensus pattern (8 bp):
ATACATGC
Found at i:387146 original size:18 final size:18
Alignment explanation
Indices: 387123--387159 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
387113 TCTTGTGGAG
387123 AATAATCTTACAATTTGC
1 AATAATCTTACAATTTGC
387141 AATAATCTTACAATTTGC
1 AATAATCTTACAATTTGC
387159 A
1 A
387160 GTGTTGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (18 bp):
AATAATCTTACAATTTGC
Found at i:388190 original size:3 final size:3
Alignment explanation
Indices: 388182--388210 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
388172 GAATAGAGTT
388182 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
388211 TAGGTACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:388275 original size:32 final size:31
Alignment explanation
Indices: 388225--388294 Score: 106
Period size: 32 Copynumber: 2.3 Consensus size: 31
388215 TACTTAGATG
*
388225 AAAAAA-ATATTTTAGGTACTTATTTTGACC
1 AAAAAATATATTTTAGGTACTTATTGTGACC
*
388255 AAAAAATATATATTTAGGTACTTATTGTGATC
1 AAAAAATATAT-TTTAGGTACTTATTGTGACC
388287 AAAAAATA
1 AAAAAATA
388295 CTTTTGGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 6 0.17
31 4 0.11
32 26 0.72
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (31 bp):
AAAAAATATATTTTAGGTACTTATTGTGACC
Found at i:393627 original size:60 final size:57
Alignment explanation
Indices: 393530--393654 Score: 146
Period size: 59 Copynumber: 2.1 Consensus size: 57
393520 GCATCATATG
* * * *
393530 TCCTCAAACTATGAATCATTTTAAATTGTTCTCTAAACTTTTGAATATACCAATTTCA
1 TCCTCAAACTATGAATCATTATAAATTGTCCTCTAAAC-TTTGAACATACCAAATTCA
*
393588 TCCTCAAACTAT-AATTTTCATTATAAATTAGTCCT-TAAACTTTGAACATTCCAAATTCA
1 TCCTCAAACTATGAA---TCATTATAAATT-GTCCTCTAAACTTTGAACATACCAAATTCA
393647 TCCTCAAA
1 TCCTCAAA
393655 ATTGACCCTC
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
57 2 0.03
58 12 0.21
59 24 0.41
60 16 0.28
61 4 0.07
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.39
Consensus pattern (57 bp):
TCCTCAAACTATGAATCATTATAAATTGTCCTCTAAACTTTGAACATACCAAATTCA
Found at i:394708 original size:18 final size:17
Alignment explanation
Indices: 394674--394712 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
394664 TTATAATTTG
**
394674 TTAAAAATAATTTTTAA
1 TTAAAAATAATAATTAA
394691 TTAAAAATACATAATTAA
1 TTAAAAATA-ATAATTAA
394709 TTAA
1 TTAA
394713 TCTTAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAAAATAATAATTAA
Found at i:398212 original size:29 final size:30
Alignment explanation
Indices: 398171--398237 Score: 102
Period size: 31 Copynumber: 2.3 Consensus size: 30
398161 GTAACTTTTA
398171 ATAGTCGAAGATTT-A-AAAGCAGTACCCT
1 ATAGTCGAAGATTTAATAAAGCAGTACCCT
*
398199 ATAGTTGAGAGATTTAATAAAGCAGTACCCT
1 ATAGTCGA-AGATTTAATAAAGCAGTACCCT
398230 ATAGTCGA
1 ATAGTCGA
398238 GGGACCATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 7 0.21
29 6 0.18
30 1 0.03
31 20 0.59
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (30 bp):
ATAGTCGAAGATTTAATAAAGCAGTACCCT
Done.