Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008252.1 Hibiscus syriacus cultivar Beakdansim tig00110904_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: 2928487
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 13
Found at i:215280 original size:12 final size:12
Alignment explanation
Indices: 215250--215284 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
215240 ATCTAATATA
*
215250 TTTATATATTTA
1 TTTATATATTTT
215262 TTT-TATATTTT
1 TTTATATATTTT
215273 TTTATATATTTT
1 TTTATATATTTT
215285 ATATTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATATATTTT
Found at i:215313 original size:21 final size:20
Alignment explanation
Indices: 215245--215315 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
215235 ATTTAATCTA
*
215245 ATATATTTATATATTTATTTT
1 ATAT-TTTATATATATATTTT
*
215266 ATATTTT-TTTATATATTTT
1 ATATTTTATATATATATTTT
*
215285 ATATTTTTATATATGTATTTTT
1 ATA-TTTTATATATATA-TTTT
*
215307 TTATTTTAT
1 ATATTTTAT
215316 TTATTCAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
19 13 0.31
20 7 0.17
21 16 0.38
22 6 0.14
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.70
Consensus pattern (20 bp):
ATATTTTATATATATATTTT
Found at i:216669 original size:9 final size:9
Alignment explanation
Indices: 216655--216681 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
216645 ATTTTATTTT
216655 CATCATTCA
1 CATCATTCA
216664 CATCATTCA
1 CATCATTCA
216673 CATCATTCA
1 CATCATTCA
216682 AAAGAGGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (9 bp):
CATCATTCA
Found at i:220277 original size:85 final size:85
Alignment explanation
Indices: 220134--220447 Score: 465
Period size: 85 Copynumber: 3.7 Consensus size: 85
220124 TACATCTTAA
*
220134 CTCAAGGCA-AGAAGGGTTATCTATCAACAAAGACCTTCGAGTTTGATTACATTCAGCTCAAAGA
1 CTCAAGG-AGAGAAGGGTTATCTATCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGA
220198 CATATCAAATTTACAGCATAG
65 CATATCAAATTTACAGCATAG
* *
220219 CTCAAGGAGAGAAGGGTTATCTGTCAACCAAA-ACCTTCGAGTTCGATTATATTCAGCTCAAAGA
1 CTCAAGGAGAGAAGGGTTATCTATCAA-CAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGA
*
220283 CATATCAAATTTACAACATAG
65 CATATCAAATTTACAGCATAG
* *
220304 CTCAAGGTGAGAAGGGTTA--TATCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAATGAC
1 CTCAAGGAGAGAAGGGTTATCTATCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGAC
* * *
220367 ATATCAAAGTTGCAGCATAA
66 ATATCAAATTTACAGCATAG
* * * *
220387 CTCAAGGCGAGAAGGGTTATCTGTCAACAAATACCTTCGAGTTCGATTCCATTCAGCTCAA
1 CTCAAGGAGAGAAGGGTTATCTATCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAA
220448 GGGTATGTTG
Statistics
Matches: 208, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
82 4 0.02
83 70 0.34
84 1 0.00
85 129 0.62
86 4 0.02
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (85 bp):
CTCAAGGAGAGAAGGGTTATCTATCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGAC
ATATCAAATTTACAGCATAG
Found at i:220473 original size:168 final size:169
Alignment explanation
Indices: 220134--220447 Score: 506
Period size: 168 Copynumber: 1.9 Consensus size: 169
220124 TACATCTTAA
*
220134 CTCAAGGCAAGAAGGGTTATCTATCAACAAAGACCTTCGAGTTTGATTACATTCAGCTCAAAGAC
1 CTCAAGGCAAGAAGGGTTA-CTATCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGAC
* *
220199 ATATCAAATTTACAGCATAGCTCAAGGAGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCG
65 ATATCAAAGTTACAGCATAACTCAAGGAGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCG
*
220264 ATTATATTCAGCTCAAAGACATATCAAATTTACAACATAG
130 ATTACATTCAGCTCAAAGACATATCAAATTTACAACATAG
** *
220304 CTCAAGGTGAGAAGGGTTA-TATCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAATGACA
1 CTCAAGGCAAGAAGGGTTACTATCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGACA
* *
220368 TATCAAAGTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAA-CAAATACCTTCGAGTTCG
66 TATCAAAGTTACAGCATAACTCAAGGAGAGAAGGGTTATCTGTCAACCAAA-ACCTTCGAGTTCG
*
220432 ATTCCATTCAGCTCAA
130 ATTACATTCAGCTCAA
220448 GGGTATGTTG
Statistics
Matches: 133, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
167 4 0.03
168 112 0.84
170 17 0.13
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (169 bp):
CTCAAGGCAAGAAGGGTTACTATCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGACA
TATCAAAGTTACAGCATAACTCAAGGAGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGA
TTACATTCAGCTCAAAGACATATCAAATTTACAACATAG
Found at i:222163 original size:2 final size:2
Alignment explanation
Indices: 222156--222191 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
222146 ATTTAATCTA
222156 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
222192 TATCTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:222209 original size:8 final size:8
Alignment explanation
Indices: 222198--222238 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
222188 ATATTATCTT
222198 TTTTTATG
1 TTTTTATG
222206 TTTTTATG
1 TTTTTATG
*
222214 TTTTTATTT
1 TTTTTA-TG
222223 TTGTTTATG
1 TT-TTTATG
222232 TTTTTAT
1 TTTTTAT
222239 TATTGTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 19 0.66
9 6 0.21
10 4 0.14
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.78
Consensus pattern (8 bp):
TTTTTATG
Found at i:222217 original size:18 final size:16
Alignment explanation
Indices: 222198--222239 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
222188 ATATTATCTT
222198 TTTTTATGTT-TTTATG
1 TTTTTAT-TTGTTTATG
222214 TTTTTATTTTTGTTTATG
1 TTTTTA--TTTGTTTATG
222232 TTTTTATT
1 TTTTTATT
222240 ATTGTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 8 0.35
17 2 0.09
18 13 0.57
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.79
Consensus pattern (16 bp):
TTTTTATTTGTTTATG
Found at i:222244 original size:18 final size:18
Alignment explanation
Indices: 222208--222245 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
222198 TTTTTATGTT
*
222208 TTTATGTTTTTATTTTTG
1 TTTATGTTTTTATTATTG
222226 TTTATGTTTTTATTATTG
1 TTTATGTTTTTATTATTG
222244 TT
1 TT
222246 ATATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.11, T:0.76
Consensus pattern (18 bp):
TTTATGTTTTTATTATTG
Found at i:222388 original size:10 final size:10
Alignment explanation
Indices: 222373--222398 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
222363 ATTATATATA
222373 TGTGTATGTG
1 TGTGTATGTG
222383 TGTGTATGTG
1 TGTGTATGTG
222393 TGTGTA
1 TGTGTA
222399 GTATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (10 bp):
TGTGTATGTG
Found at i:222593 original size:12 final size:14
Alignment explanation
Indices: 222559--222595 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
222549 GGGTTAATAT
*
222559 TTATTATTATTATA
1 TTATTTTTATTATA
222573 TTATTTTTATTA-A
1 TTATTTTTATTATA
222586 TT-TTTTTATT
1 TTATTTTTATT
222596 TTAACATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 8 0.36
13 3 0.14
14 11 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTTTTATTATA
Found at i:224647 original size:21 final size:22
Alignment explanation
Indices: 224612--224654 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
224602 ATTTAAATAT
224612 ATTAAAGGAAGTACCGATACTC
1 ATTAAAGGAAGTACCGATACTC
224634 ATTAAAGG-AGTACCGATACTC
1 ATTAAAGGAAGTACCGATACTC
224655 CCTGTCCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (22 bp):
ATTAAAGGAAGTACCGATACTC
Found at i:234643 original size:3 final size:3
Alignment explanation
Indices: 234637--234728 Score: 121
Period size: 3 Copynumber: 30.0 Consensus size: 3
234627 AATAATTATT
* **
234637 TAA TAA TAA TATA TAA TAA TAA TATT TAA TAA TAA TAA TAA TTT TAA
1 TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
* *
234684 TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
234729 AACAAAAATA
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
3 72 0.94
4 5 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:234982 original size:76 final size:76
Alignment explanation
Indices: 234885--235120 Score: 463
Period size: 76 Copynumber: 3.1 Consensus size: 76
234875 GAGGTCTTAA
*
234885 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
234950 AGGCTTTTTGG
66 AGGCTTTTTGG
234961 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
235026 AGGCTTTTTGG
66 AGGCTTTTTGG
235037 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
235102 AGGCTTTTTGG
66 AGGCTTTTTGG
235113 AAACATCA
1 AAACATCA
235121 AAAAGCTCCC
Statistics
Matches: 159, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 159 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:235120 original size:31 final size:31
Alignment explanation
Indices: 235068--235151 Score: 145
Period size: 31 Copynumber: 2.8 Consensus size: 31
235058 TTACAGATGA
*
235068 CCCGAAGGC--TTTGAAAACATCAAAAAGCT
1 CCCGAAGGCTTTTTGGAAACATCAAAAAGCT
235097 CCCGAAGGCTTTTTGGAAACATCAAAAAGCT
1 CCCGAAGGCTTTTTGGAAACATCAAAAAGCT
235128 CCCGAAGGCTTTTTGGAAACATCA
1 CCCGAAGGCTTTTTGGAAACATCA
235152 TGCACTGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 9 0.17
31 43 0.83
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (31 bp):
CCCGAAGGCTTTTTGGAAACATCAAAAAGCT
Found at i:235126 original size:107 final size:107
Alignment explanation
Indices: 234992--235227 Score: 440
Period size: 107 Copynumber: 2.2 Consensus size: 107
234982 TTACAGATGA
*
234992 CCCGAAGGC--TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
1 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
*
235055 GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
66 GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAACT
235097 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
1 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
235162 GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAACT
66 GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAACT
235204 CCCGAAGGCTTTTTGGAAACATCA
1 CCCGAAGGCTTTTTGGAAACATCA
235228 TGCACTGTAG
Statistics
Matches: 127, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
105 9 0.07
107 118 0.93
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (107 bp):
CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAACT
Found at i:235193 original size:76 final size:76
Alignment explanation
Indices: 235097--235325 Score: 404
Period size: 76 Copynumber: 3.0 Consensus size: 76
235087 TCAAAAAGCT
* *
235097 CCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
1 CCCGAAGGC--TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAG
235162 GACTTACAGATGA
64 GACTTACAGATGA
*
235175 CCCGAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGA
235240 CTTACAGATGA
66 CTTACAGATGA
*
235251 CCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGA
1 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGA
235316 CTTACAGATG
66 CTTACAGATG
235326 TGGGAAGTAG
Statistics
Matches: 146, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
76 137 0.94
78 9 0.06
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (76 bp):
CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGA
CTTACAGATGA
Found at i:235242 original size:183 final size:183
Alignment explanation
Indices: 234925--235303 Score: 722
Period size: 183 Copynumber: 2.1 Consensus size: 183
234915 ACCCTAAGGC
*
234925 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
*
234990 GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
66 GACCCGAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
235055 GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
131 GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
235108 TTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
*
235173 GACCCGAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAG
66 GACCCGAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
*
235238 GACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
131 GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
235291 TTTGGAAACATCA
1 TTTGGAAACATCA
235304 TGCACTGTAG
Statistics
Matches: 192, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
183 192 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (183 bp):
TTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
GACCCGAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
Found at i:235558 original size:38 final size:37
Alignment explanation
Indices: 235498--235627 Score: 147
Period size: 35 Copynumber: 3.5 Consensus size: 37
235488 GAAATAACTG
*
235498 TCTCAAGCGAGACAAATCTTTGTTTTAAGAAAAAACAA
1 TCTCAAGCGAGACAAATTTTTGTTTTAAG-AAAAACAA
* * * ** **
235536 TCTCAAGTGAGATAAATTTTTGTTTCAAGTGAAACTG
1 TCTCAAGCGAGACAAATTTTTGTTTTAAGAAAAACAA
235573 TCTCAAGCGAGACAAA--TTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATTTTTGTTTTAAGAAAAACAA
* *
235608 TCTCAAGTGAGATAAATTTT
1 TCTCAAGCGAGACAAATTTT
235628 ATTTGAAAAC
Statistics
Matches: 73, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
35 28 0.38
37 20 0.27
38 25 0.34
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (37 bp):
TCTCAAGCGAGACAAATTTTTGTTTTAAGAAAAACAA
Found at i:235590 original size:37 final size:38
Alignment explanation
Indices: 235488--235627 Score: 126
Period size: 38 Copynumber: 3.8 Consensus size: 38
235478 AAAATAACTC
* * *
235488 GAAATAACTGTCTCAAGCGAGACAAATCTTTGTTTTAA
1 GAAAAAACTGTCTCAAGCGAGACAAATTTTTGTTTCAA
** * *
235526 GAAAAAACAATCTCAAGTGAGATAAATTTTTGTTTCAA
1 GAAAAAACTGTCTCAAGCGAGACAAATTTTTGTTTCAA
** *
235564 G-TGAAACTGTCTCAAGCGAGACAAA--TTTGTTTTAA
1 GAAAAAACTGTCTCAAGCGAGACAAATTTTTGTTTCAA
** * *
235599 G-AAAAACAATCTCAAGTGAGATAAATTTT
1 GAAAAAACTGTCTCAAGCGAGACAAATTTT
235628 ATTTGAAAAC
Statistics
Matches: 80, Mismatches: 20, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
35 28 0.35
37 20 0.25
38 32 0.40
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (38 bp):
GAAAAAACTGTCTCAAGCGAGACAAATTTTTGTTTCAA
Found at i:236366 original size:22 final size:22
Alignment explanation
Indices: 236341--236395 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
236331 AATAAAGCTT
*
236341 TCATCTTTGAAAATAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
236363 TCATCTTTAAAAAGATAATCTA
1 TCATCTTTGAAAAGAGAATCTA
236385 TCATCTTTGAA
1 TCATCTTTGAA
236396 GAGTGTAGAT
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:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:236880 original size:54 final size:54
Alignment explanation
Indices: 236760--236919 Score: 152
Period size: 54 Copynumber: 3.0 Consensus size: 54
236750 ATAATTACTG
* * * * * *
236760 GTTCGTAAAACATTTGACAATATATTCATC-TTTTCCTATGGTTTCTG-TC-GA-
1 GTTCGTAAAACATTTGAAAACACATTCATCATTTT-CTGTAGCTTCTGCTCAGAT
* * *
236811 GAT-GTAAAACATTTGAAAACACATTCTTC-CTTTCTTGTAGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGAAAACACATTCATCATTTTC-TGTAGCTTCTGCTCAGAT
* * *
236864 GTTCGTAAAGCATTTGACAACACATTCATCATTTTCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGAAAACACATTCATCATTTTCTGTAGCTTCTGCTCAGAT
236918 GT
1 GT
236920 CTTAATCATT
Statistics
Matches: 88, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
49 1 0.01
50 33 0.38
51 4 0.05
52 2 0.02
53 2 0.02
54 42 0.48
55 4 0.05
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (54 bp):
GTTCGTAAAACATTTGAAAACACATTCATCATTTTCTGTAGCTTCTGCTCAGAT
Found at i:240703 original size:20 final size:20
Alignment explanation
Indices: 240678--240715 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
240668 TTTTTTTTTT
240678 CAAAAAAAACAAAA-AAAAGG
1 CAAAAAAAA-AAAACAAAAGG
240698 CAAAAAAAAAAAACAAAA
1 CAAAAAAAAAAAACAAAA
240716 AATAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (20 bp):
CAAAAAAAAAAAACAAAAGG
Found at i:240726 original size:24 final size:24
Alignment explanation
Indices: 240679--240743 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
240669 TTTTTTTTTC
*
240679 AAAAAAAACAAAAAAAAGGCAAAA
1 AAAAAAAACAAAAAAAAGGAAAAA
*
240703 AAAAAAAACAAAAAATAA-TAAAAA
1 AAAAAAAACAAAAAA-AAGGAAAAA
**
240727 AGGAAAAA-AAAAAAAAG
1 AAAAAAAACAAAAAAAAG
240744 CCAAAATTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 2 0.06
23 6 0.17
24 25 0.71
25 2 0.06
ACGTcount: A:0.85, C:0.05, G:0.08, T:0.03
Consensus pattern (24 bp):
AAAAAAAACAAAAAAAAGGAAAAA
Found at i:240749 original size:24 final size:22
Alignment explanation
Indices: 240679--240749 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 22
240669 TTTTTTTTTC
* *
240679 AAAAAAAACAAAAAAAAGGCAA
1 AAAAAAAAAAAAAAAAAGACAA
*
240701 AAAAAAAAAACAAAAAATA-ATAA
1 AAAAAAAAAA-AAAAAA-AGACAA
*
240724 AAAAGGAAAAAAAAAAAAAGCCAA
1 AAAA--AAAAAAAAAAAAAGACAA
240748 AA
1 AA
240750 TTTCAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
22 9 0.23
23 13 0.33
24 11 0.28
25 6 0.15
ACGTcount: A:0.83, C:0.07, G:0.07, T:0.03
Consensus pattern (22 bp):
AAAAAAAAAAAAAAAAAGACAA
Found at i:240759 original size:32 final size:32
Alignment explanation
Indices: 240681--240742 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
240671 TTTTTTTCAA
* *
240681 AAAAAACAA-AAAAAAGGCAAAAAAAAAAAAC
1 AAAAAATAATAAAAAAGGAAAAAAAAAAAAAC
240712 AAAAAATAATAAAAAAGGAAAAAAAAAAAAA
1 AAAAAATAATAAAAAAGGAAAAAAAAAAAAA
240743 GCCAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 8 0.29
32 20 0.71
ACGTcount: A:0.85, C:0.05, G:0.06, T:0.03
Consensus pattern (32 bp):
AAAAAATAATAAAAAAGGAAAAAAAAAAAAAC
Found at i:245443 original size:11 final size:11
Alignment explanation
Indices: 245412--245499 Score: 90
Period size: 12 Copynumber: 7.7 Consensus size: 11
245402 CTATTTTTTT
**
245412 CAAAAAAAAAA
1 CAAAAAAAAGG
245423 CAAAAAAAAGG
1 CAAAAAAAAGG
245434 CAAAAAAAAGAGG
1 C-AAAAAAA-AGG
245447 CACAAAAAAAGG
1 CA-AAAAAAAGG
245459 CACAAAAAAA-G
1 CA-AAAAAAAGG
245470 C-AAAAAAAGG
1 CAAAAAAAAGG
*
245480 CACAAAAAAAAG
1 CA-AAAAAAAGG
245492 CAAAAAAA
1 CAAAAAAA
245500 GCCAAAATTT
Statistics
Matches: 68, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
9 7 0.10
10 2 0.03
11 18 0.26
12 31 0.46
13 10 0.15
ACGTcount: A:0.75, C:0.12, G:0.12, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAGG
Found at i:245475 original size:33 final size:32
Alignment explanation
Indices: 245414--245499 Score: 109
Period size: 33 Copynumber: 2.5 Consensus size: 32
245404 ATTTTTTTCA
*
245414 AAAAAAAAACAAAAAAAAGGCAAAAAAAAGAGGCAC
1 AAAAAAAAGCAAAAAAAA-GC--AAAAAA-AGGCAC
*
245450 AAAAAAAGGCACAAAAAAAGCAAAAAAAGGCAC
1 AAAAAAAAGCA-AAAAAAAGCAAAAAAAGGCAC
245483 AAAAAAAAGCAAAAAAA
1 AAAAAAAAGCAAAAAAA
245500 GCCAAAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
32 6 0.13
33 16 0.35
34 6 0.13
36 11 0.24
37 7 0.15
ACGTcount: A:0.76, C:0.12, G:0.13, T:0.00
Consensus pattern (32 bp):
AAAAAAAAGCAAAAAAAAGCAAAAAAAGGCAC
Found at i:245505 original size:10 final size:10
Alignment explanation
Indices: 245449--245506 Score: 57
Period size: 9 Copynumber: 5.5 Consensus size: 10
245439 AAAAGAGGCA
245449 CAAAAAAAGGC
1 CAAAAAAA-GC
245460 ACAAAAAAAG-
1 -CAAAAAAAGC
245470 CAAAAAAAGGC
1 CAAAAAAA-GC
245481 ACAAAAAAAAG-
1 -C-AAAAAAAGC
245492 CAAAAAAAGC
1 CAAAAAAAGC
245502 CAAAA
1 CAAAA
245507 TTTCAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
9 16 0.39
10 7 0.17
11 1 0.02
12 10 0.24
13 7 0.17
ACGTcount: A:0.72, C:0.16, G:0.12, T:0.00
Consensus pattern (10 bp):
CAAAAAAAGC
Found at i:251089 original size:11 final size:11
Alignment explanation
Indices: 251075--251136 Score: 54
Period size: 11 Copynumber: 5.3 Consensus size: 11
251065 CTTTTTTGGC
251075 TTTTTTTATTT
1 TTTTTTTATTT
251086 TTTTTTTATTT
1 TTTTTTTATTT
251097 TTTGTTTT-TTT
1 TTT-TTTTATTT
*
251108 GCCTTGTTTTTGTTT
1 ---TT-TTTTTATTT
*
251123 TTTTTTTGTTT
1 TTTTTTTATTT
251134 TTT
1 TTT
251137 GAAAAAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
11 29 0.64
12 6 0.13
14 6 0.13
15 4 0.09
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTTTTATTT
Found at i:251100 original size:37 final size:38
Alignment explanation
Indices: 251059--251137 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 38
251049 TTTTTTGAAA
*
251059 TTTTGGCTTTTTTGGCTT-TTTTTATTTTTTTTTTATT
1 TTTTGGCTTTTTTGCCTTGTTTTTATTTTTTTTTTATT
* * *
251096 TTTT-GTTTTTTTGCCTTGTTTTTGTTTTTTTTTTGTT
1 TTTTGGCTTTTTTGCCTTGTTTTTATTTTTTTTTTATT
251133 TTTTG
1 TTTTG
251138 AAAAAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 11 0.31
37 25 0.69
ACGTcount: A:0.03, C:0.05, G:0.13, T:0.80
Consensus pattern (38 bp):
TTTTGGCTTTTTTGCCTTGTTTTTATTTTTTTTTTATT
Found at i:253082 original size:9 final size:9
Alignment explanation
Indices: 253068--253094 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
253058 AAGTATGGGT
253068 AGAAATATC
1 AGAAATATC
253077 AGAAATATC
1 AGAAATATC
253086 AGAAATATC
1 AGAAATATC
253095 CGAGTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (9 bp):
AGAAATATC
Found at i:258801 original size:11 final size:11
Alignment explanation
Indices: 258787--258813 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
258777 GATTTTTTTG
258787 TTTTTTTGCCT
1 TTTTTTTGCCT
258798 TTTTTTTGCCT
1 TTTTTTTGCCT
258809 TTTTT
1 TTTTT
258814 GTTTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (11 bp):
TTTTTTTGCCT
Found at i:260382 original size:15 final size:16
Alignment explanation
Indices: 260355--260391 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
260345 CTTTATTATC
260355 TTATTTCATCTTTCGT
1 TTATTTCATCTTTCGT
*
260371 TTATTT-ATCTTTTGT
1 TTATTTCATCTTTCGT
260386 TTATTT
1 TTATTT
260392 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTTCGT
Found at i:260757 original size:11 final size:10
Alignment explanation
Indices: 260741--260785 Score: 58
Period size: 11 Copynumber: 4.5 Consensus size: 10
260731 TTATTTTTTT
260741 CAAAAAAAAGG
1 CAAAAAAAA-G
260752 CAAAAAAAA-
1 CAAAAAAAAG
260761 -AAAAAAAAG
1 CAAAAAAAAG
260770 CAAAAAAAAG
1 CAAAAAAAAG
260780 CCAAAA
1 -CAAAA
260786 TTTCAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.26
10 9 0.29
11 14 0.45
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAG
Found at i:260785 original size:18 final size:19
Alignment explanation
Indices: 260742--260778 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
260732 TATTTTTTTC
260742 AAAAAAAAGGCAAAAAAAA
1 AAAAAAAAGGCAAAAAAAA
260761 AAAAAAAA-GCAAAAAAAA
1 AAAAAAAAGGCAAAAAAAA
260779 GCCAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.86, C:0.05, G:0.08, T:0.00
Consensus pattern (19 bp):
AAAAAAAAGGCAAAAAAAA
Found at i:273794 original size:3 final size:3
Alignment explanation
Indices: 273788--273888 Score: 139
Period size: 3 Copynumber: 33.0 Consensus size: 3
273778 AATAATTATT
* **
273788 TAA TAA TAA TATA TAA TAA TAA TATT TAA TAA TAA TAA TAA TTT TAA
1 TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
* *
273835 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
273883 TAA TAA
1 TAA TAA
273889 AAACAAAAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
3 81 0.94
4 5 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:288639 original size:20 final size:20
Alignment explanation
Indices: 288587--288673 Score: 63
Period size: 20 Copynumber: 4.3 Consensus size: 20
288577 TAAAAGTTCG
* *
288587 ATAATATAATAATTATTTTA
1 ATAATTTAATAAATATTTTA
* *
288607 TTGTATTTAATAAAT-TTATTA
1 AT-AATTTAATAAATATT-TTA
* *
288628 ATAATTTTAT-AATCTTTTA
1 ATAATTTAATAAATATTTTA
*
288647 ATAAATTTAATAAGTATTTT-
1 AT-AATTTAATAAATATTTTA
288667 ATAATTT
1 ATAATTT
288674 TTTAAACTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
19 13 0.25
20 20 0.38
21 19 0.37
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (20 bp):
ATAATTTAATAAATATTTTA
Found at i:288650 original size:31 final size:31
Alignment explanation
Indices: 288612--288678 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
288602 TTTTATTGTA
*
288612 TTTAATAAATTTATTAA-TAATTTTATAATCT
1 TTTAATAAATTTAATAAGT-ATTTTATAATCT
*
288643 TTTAATAAATTTAATAAGTATTTTATAATTT
1 TTTAATAAATTTAATAAGTATTTTATAATCT
288674 TTTAA
1 TTTAA
288679 ACTTTATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (31 bp):
TTTAATAAATTTAATAAGTATTTTATAATCT
Found at i:289108 original size:21 final size:21
Alignment explanation
Indices: 289079--289131 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
289069 ATTCTGACTA
289079 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
289100 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
289121 TCGCAATGCGA
1 TCGCATTGCGA
289132 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:289146 original size:20 final size:20
Alignment explanation
Indices: 289121--289171 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
289111 TTTTCCTAAT
289121 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
289141 TCGCAATGCAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
289161 TCGCAATGCGA
1 TCGCAATGCGA
289172 TTTACATATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:289810 original size:20 final size:20
Alignment explanation
Indices: 289785--289828 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
289775 TCTTGCATTA
289785 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
** *
289805 CGATAGTCATTTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
289825 CGAT
1 CGAT
289829 TTAAAGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
CGATAGTCAAATTCGCGTTG
Found at i:291738 original size:20 final size:20
Alignment explanation
Indices: 291713--291836 Score: 170
Period size: 20 Copynumber: 6.5 Consensus size: 20
291703 AGAATAGTTT
291713 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
291733 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
291753 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
291769 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
291787 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
291807 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
291827 ACTATCGCAA
1 ACTATCGCAA
291837 CGAAAGAATC
Statistics
Matches: 93, Mismatches: 5, Indels: 12
0.85 0.05 0.11
Matches are distributed among these distances:
14 7 0.08
16 4 0.04
17 4 0.04
18 4 0.04
20 74 0.80
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:291782 original size:34 final size:34
Alignment explanation
Indices: 291736--291857 Score: 154
Period size: 34 Copynumber: 3.4 Consensus size: 34
291726 GAAAATGACT
* *
291736 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
291770 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGA
1 ATCGCAATGCGAAAATGACTATCGCAA--CG-AAA-GA
**
291808 CTATCGCAATGCGAATTTGACTATCGCAACGAAAGA
1 --ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
291844 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
291858 TGAAAATCGC
Statistics
Matches: 77, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
34 39 0.51
36 4 0.05
37 5 0.06
38 4 0.05
40 25 0.32
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
Found at i:291834 original size:74 final size:74
Alignment explanation
Indices: 291713--291857 Score: 254
Period size: 74 Copynumber: 2.0 Consensus size: 74
291703 AGAATAGTTT
*
291713 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAAT
1 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAAT
291778 GCGAAAATG
66 GCGAAAATG
* **
291787 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAAAGAATCGCAAT
1 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAAT
291852 GCGAAA
66 GCGAAA
291858 TGAAAATCGC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 67 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (74 bp):
ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAAT
GCGAAAATG
Found at i:292014 original size:20 final size:20
Alignment explanation
Indices: 291971--292016 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
291961 ATTCTCTCGT
* **
291971 TGCGATAGTAATTTTCGCTT
1 TGCGATAGTAATTTTCACGA
*
291991 TGCGATAGTCATTTTCACGA
1 TGCGATAGTAATTTTCACGA
292011 TGCGAT
1 TGCGAT
292017 TTTAAGTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (20 bp):
TGCGATAGTAATTTTCACGA
Found at i:292591 original size:21 final size:21
Alignment explanation
Indices: 292500--292591 Score: 78
Period size: 21 Copynumber: 4.4 Consensus size: 21
292490 GACTCACCTG
* *
292500 TCATCGTTAAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
292522 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
292542 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
292563 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
292584 TCATCGTT
1 TCATCGTT
292592 GTAGAGGTCG
Statistics
Matches: 53, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.06
21 49 0.92
22 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:293984 original size:14 final size:14
Alignment explanation
Indices: 293965--294000 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
293955 ATTGTTTAAT
293965 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
293979 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
293993 TGATTTGT
1 TGATTTGT
294001 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:294195 original size:34 final size:33
Alignment explanation
Indices: 294113--294197 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
294103 TCGCAACGTG
** *
294113 GAAATGACTATCGTAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
* *
294146 GAAATGAAAAGCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
294179 GAAAATGAAAATCGCAACG
1 G-AAATGAAAATCGCAACG
294198 CGAAATTAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 29 0.64
34 16 0.36
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:294278 original size:19 final size:19
Alignment explanation
Indices: 294207--294293 Score: 103
Period size: 19 Copynumber: 4.8 Consensus size: 19
294197 GCGAAATTAG
294207 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
294226 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
* * *
294244 -CTCG--TTGAGCTTTTCA
1 TTTCGCATTGCGATTTTCA
294260 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
294279 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
294294 CTCTCGTTGC
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
14 4 0.07
16 7 0.12
17 3 0.05
18 4 0.07
19 25 0.45
20 13 0.23
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:294323 original size:20 final size:20
Alignment explanation
Indices: 294298--294386 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
294288 GCGATTCTCT
*
294298 CGTTGCGATAGTTATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
294318 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
294338 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
294358 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
294378 CGTTGCGAT
1 CGTTGCGAT
294387 TTCCACGTTG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 61 0.97
21 2 0.03
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:294324 original size:53 final size:53
Alignment explanation
Indices: 294207--294326 Score: 163
Period size: 53 Copynumber: 2.3 Consensus size: 53
294197 GCGAAATTAG
* *
294207 TTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGAGCTTTTCA
1 TTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGAGATGTTCA
* *
294260 TTTCGCATTGCGATTTTCA-TTTCGCATTGCGATTCTCTCGTTGCGATAGTT-A
1 TTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGAGAT-GTTCA
*
294312 TTTCCGCGTTGCGAT
1 TTT-CGCATTGCGAT
294327 AGTCAATTCC
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
52 29 0.48
53 31 0.52
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (53 bp):
TTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGAGATGTTCA
Found at i:296117 original size:24 final size:24
Alignment explanation
Indices: 296083--296136 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
296073 CTGAAAAATC
296083 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
296107 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
296131 ATCAAA
1 ATCAAA
296137 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:296150 original size:24 final size:24
Alignment explanation
Indices: 296083--296151 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
296073 CTGAAAAATC
* * *
296083 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
296107 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
296131 ATCAAATTTCGAATACTGACC
1 ATCAAAGTCCGAATACTGACC
296152 CAACTTCACT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:296776 original size:20 final size:20
Alignment explanation
Indices: 296753--296958 Score: 267
Period size: 20 Copynumber: 10.3 Consensus size: 20
296743 CAGAATCTCG
296753 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
296773 TTGCGATTTACGTAATT-GCA
1 TTGCGATTTACGT-ATTCGCA
* *
296793 TTGCGATTTACGTAATCACA
1 TTGCGATTTACGTATTCGCA
* *
296813 TTGTGATTTACGTATTCACA
1 TTGCGATTTACGTATTCGCA
296833 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
296853 TTGCGATTTACGT-TTCGCA
1 TTGCGATTTACGTATTCGCA
*
296872 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
296892 TTGCGATTTACGTAATT-GCA
1 TTGCGATTTACGT-ATTCGCA
* ** *
296912 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
296933 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
296953 TTGCGA
1 TTGCGA
296959 ATTAGGAAAA
Statistics
Matches: 163, Mismatches: 16, Indels: 14
0.84 0.08 0.07
Matches are distributed among these distances:
19 22 0.13
20 124 0.76
21 17 0.10
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:296979 original size:21 final size:21
Alignment explanation
Indices: 296955--297000 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
296945 TATTCGCATT
296955 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
296976 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
296997 GCGA
1 GCGA
297001 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:297703 original size:31 final size:31
Alignment explanation
Indices: 297661--297723 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
297651 TCAATAAAAT
*
297661 TTAAAAAATTATAAAA-TACTTATTAAATTTA
1 TTAAAAAATTATAAAATTA-TTAATAAATTTA
*
297692 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAATTATTAATAAATTTA
297723 T
1 T
297724 CTCAATACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (31 bp):
TTAAAAAATTATAAAATTATTAATAAATTTA
Found at i:303633 original size:29 final size:28
Alignment explanation
Indices: 303575--303636 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
303565 TGATAACCTG
* **
303575 AAAATCATCAATTCATGATTTTATAAAA
1 AAAATCATCAATTCATCATTAAATAAAA
* *
303603 AAAATCATGTAATTCATCATTAAATATAA
1 AAAATCAT-CAATTCATCATTAAATAAAA
303632 AAAAT
1 AAAAT
303637 AACTTATGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAATCATCAATTCATCATTAAATAAAA
Found at i:304113 original size:18 final size:18
Alignment explanation
Indices: 304014--304113 Score: 100
Period size: 18 Copynumber: 5.7 Consensus size: 18
304004 TCTATGTTTC
* *
304014 ATAACTGTAAAACATCTG
1 ATAACTATAAATCATCTG
*
304032 ATAACTGTAAA-CATCTG
1 ATAACTATAAATCATCTG
*
304049 ATAACTA-AAATTCATCTA
1 ATAACTATAAA-TCATCTG
* *
304067 ATAACTGTAAAT-ATATG
1 ATAACTATAAATCATCTG
304084 ATAACTGA-AAATCATCTG
1 ATAACT-ATAAATCATCTG
304102 ATAACTATAAAT
1 ATAACTATAAAT
304114 ATTTAGAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
16 3 0.04
17 26 0.38
18 37 0.54
19 3 0.04
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (18 bp):
ATAACTATAAATCATCTG
Found at i:304113 original size:35 final size:35
Alignment explanation
Indices: 304014--304115 Score: 136
Period size: 35 Copynumber: 2.9 Consensus size: 35
304004 TCTATGTTTC
* *
304014 ATAACTGTAAAA-CATCTGATAACTGTAAACATCTG
1 ATAACTG-AAAATCATCTGATAACTGTAAATATATG
*
304049 ATAACT-AAAATTCATCTAATAACTGTAAATATATG
1 ATAACTGAAAA-TCATCTGATAACTGTAAATATATG
*
304084 ATAACTGAAAATCATCTGATAACTATAAATAT
1 ATAACTGAAAATCATCTGATAACTGTAAATAT
304116 TTAGAATTCA
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
33 4 0.07
35 51 0.86
36 4 0.07
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (35 bp):
ATAACTGAAAATCATCTGATAACTGTAAATATATG
Found at i:305831 original size:24 final size:24
Alignment explanation
Indices: 305804--305857 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
305794 TTCGGGACTA
*
305804 TCTATGTGGCACTTCAGTGCATAT
1 TCTATGTGGCACTTCAGTGCAAAT
* * *
305828 TCTACGTGGCATTTCGGTGCAAAT
1 TCTATGTGGCACTTCAGTGCAAAT
*
305852 TATATG
1 TCTATG
305858 AGCAGTGGTG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (24 bp):
TCTATGTGGCACTTCAGTGCAAAT
Found at i:306425 original size:16 final size:17
Alignment explanation
Indices: 306393--306425 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
306383 ATTTTCAATG
306393 AGTTTTAAAAGAGTCAA
1 AGTTTTAAAAGAGTCAA
*
306410 AGTTTTGAAA-AGTCAA
1 AGTTTTAAAAGAGTCAA
306426 TGTGACACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (17 bp):
AGTTTTAAAAGAGTCAA
Found at i:307976 original size:17 final size:17
Alignment explanation
Indices: 307954--308006 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
307944 AATTAAGAGT
307954 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
307971 TAGTTTGATGAATGAAA
1 TAGTTTAATAAATGAAC
* *
307988 TAGTTTACTTAATGAAC
1 TAGTTTAATAAATGAAC
308005 TA
1 TA
308007 CTTCCCTAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:311165 original size:23 final size:23
Alignment explanation
Indices: 311104--311168 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
311094 CACCACAGGT
* *
311104 CGTATAATTGCACCGAAGTGCAA
1 CGTAGAATTGCACCGCAGTGCAA
**
311127 CGTAGAATTGCACCGCAGTGCCG
1 CGTAGAATTGCACCGCAGTGCAA
311150 CGTAGAATTGCACCGCAGT
1 CGTAGAATTGCACCGCAGT
311169 TCCATATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGCAGTGCAA
Found at i:313228 original size:17 final size:17
Alignment explanation
Indices: 313206--313244 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
313196 TTTCGGTTTG
*
313206 AAAAAAACCAATTTTAA
1 AAAAAAACCAATTATAA
*
313223 AAAAAAACCGATTATAA
1 AAAAAAACCAATTATAA
313240 AAAAA
1 AAAAA
313245 TTGATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.69, C:0.10, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAAAACCAATTATAA
Found at i:313343 original size:33 final size:33
Alignment explanation
Indices: 313296--313399 Score: 174
Period size: 33 Copynumber: 3.2 Consensus size: 33
313286 ACAAAGTTTA
* *
313296 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
313328 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
313361 CGATAAATTCAAATACTTAAAAACTTACAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
313394 CGATAA
1 CGATAA
313400 TTGAAACAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 4 0.06
33 64 0.94
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:313419 original size:21 final size:21
Alignment explanation
Indices: 313394--313435 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
313384 CTTACAAGTT
313394 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
313415 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
313436 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:322282 original size:23 final size:24
Alignment explanation
Indices: 322233--322321 Score: 137
Period size: 24 Copynumber: 3.8 Consensus size: 24
322223 CTTCGTGGTC
322233 CTTCGGGACAAATTCTATGCGGTA
1 CTTCGGGACAAATTCTATGCGGTA
* *
322257 CTTCGAGACAAATT-TATACGGTA
1 CTTCGGGACAAATTCTATGCGGTA
322280 CTTCGGGACAAATTCTATGCGGTA
1 CTTCGGGACAAATTCTATGCGGTA
*
322304 CTTCGGGACATA-TCTATG
1 CTTCGGGACAAATTCTATG
322322 TAGCACTACG
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
23 27 0.46
24 32 0.54
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.30
Consensus pattern (24 bp):
CTTCGGGACAAATTCTATGCGGTA
Found at i:325006 original size:54 final size:54
Alignment explanation
Indices: 324922--325041 Score: 150
Period size: 54 Copynumber: 2.2 Consensus size: 54
324912 GTTACACCGA
* * * *
324922 AGTGCCGAAATGGAAATTCACAAACTCATTATGAATTCCATGGATTGCAGACAT
1 AGTGCCAAAATGGAAATTCACAAACACATTATGAATACCATGGATTGCACACAT
** * * **
324976 AGTGCCAAAATGGTCATTCATAAACACATTATGAATACCATGGGTTGCACATTT
1 AGTGCCAAAATGGAAATTCACAAACACATTATGAATACCATGGATTGCACACAT
325030 AGTGCCAAAATG
1 AGTGCCAAAATG
325042 CACCGTTATG
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (54 bp):
AGTGCCAAAATGGAAATTCACAAACACATTATGAATACCATGGATTGCACACAT
Found at i:325779 original size:20 final size:21
Alignment explanation
Indices: 325744--325799 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
325734 AGGTTCAATA
*
325744 GTATCGATACCCCTAT-TATG
1 GTATCGATACTCCTATATATG
*
325764 GTATCGATACTTCTATACTATG
1 GTATCGATACTCCTATA-TATG
*
325786 GTACCGATACTCCT
1 GTATCGATACTCCT
325800 TTCAGTATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 14 0.47
22 16 0.53
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (21 bp):
GTATCGATACTCCTATATATG
Found at i:327141 original size:19 final size:20
Alignment explanation
Indices: 327096--327147 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
327086 CCACGTGAAG
327096 AGTAT-GATACTGTTCATGC
1 AGTATCGATACTGTTCATGC
* *
327115 AGTATCGATATTGTTCGTGC
1 AGTATCGATACTGTTCATGC
327135 A-TATCGATACTGT
1 AGTATCGATACTGT
327148 AAGAACAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.38
Consensus pattern (20 bp):
AGTATCGATACTGTTCATGC
Found at i:328233 original size:17 final size:17
Alignment explanation
Indices: 328211--328243 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
328201 GATATATTGT
328211 TTTTTAAATTTTAAATA
1 TTTTTAAATTTTAAATA
*
328228 TTTTTAACTTTTAAAT
1 TTTTTAAATTTTAAAT
328244 GATACAATCG
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:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTTAAATTTTAAATA
Found at i:334907 original size:14 final size:14
Alignment explanation
Indices: 334890--334919 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
334880 TATTGGATTC
334890 TTTATGTGATTGGA
1 TTTATGTGATTGGA
334904 TTTATGTGATTGGA
1 TTTATGTGATTGGA
334918 TT
1 TT
334920 AGATAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (14 bp):
TTTATGTGATTGGA
Found at i:337991 original size:22 final size:22
Alignment explanation
Indices: 337944--337991 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
337934 TGGTATAAAT
** * *
337944 TTTAAAATTATTTATTTGAGTT
1 TTTAAAATTATTTACATCAGTA
337966 TTTAAAATTATTTACATCAGTA
1 TTTAAAATTATTTACATCAGTA
337988 TTTA
1 TTTA
337992 GAGAGCCCGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.54
Consensus pattern (22 bp):
TTTAAAATTATTTACATCAGTA
Found at i:340694 original size:16 final size:15
Alignment explanation
Indices: 340649--340694 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
340639 AAAAAACTGG
*
340649 AATAAAATGCAGCAA
1 AATAAAATGCAGAAA
*
340664 AATAAAAGGGCAGAAA
1 AATAAAA-TGCAGAAA
340680 AATAAAATGCTAGAA
1 AATAAAATGC-AGAA
340695 TTTAAAGTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 9 0.35
16 17 0.65
ACGTcount: A:0.61, C:0.09, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAAAATGCAGAAA
Found at i:341038 original size:202 final size:201
Alignment explanation
Indices: 340744--341131 Score: 546
Period size: 202 Copynumber: 1.9 Consensus size: 201
340734 GAAATAAATT
* * * **
340744 AAATAAATTTAAAAGTTAGGGGTTGTTTTTAACCATTTAACATGAACCATAAATAATGTGGATCA
1 AAATAAATATAAAAGTTAGGGATTGTTTTTAACCATTTAACACGAACCATAAATAATGCAGATCA
*
340809 TCCCCCAGGGCAGGTCACCACAAGGTCGTTGAATATTCGAATGTTAGAAAATTAGCAGATTAGTT
66 TCCCCCAGGGCAGGTCACCACAAGGTCGTTGAATATTCGAATATTAGAAAATTAGCAGATTAGTT
*
340874 TGTGCAATAAAATAAAATAAAATGTTAGTAAGTAAGAACAATAAAAATAAAAAGTTAGTATGCTA
131 TGTGCAATAAAATAAAATAAAA-GTAAGTAAGTAAGAACAATAAAAAT-AAAAGTTAGTATGCTA
340939 ATATAAAC
194 ATATAAAC
* * * * *
340947 AAATAAA-ATAAAAGTTAGGGATTGTTTTTAATCGTTTAACCCGGACCATAAATAATGCAGATCG
1 AAATAAATATAAAAGTTAGGGATTGTTTTTAACCATTTAACACGAACCATAAATAATGCAGATCA
* ** * *
341011 TCCCCCAGGG-TGAGTCACCGTAAGGTCGTTGAATATTCGAATATTAGAAAATTAGCGGGTTAGT
66 TCCCCCAGGGCAG-GTCACCACAAGGTCGTTGAATATTCGAATATTAGAAAATTAGCAGATTAGT
*** *
341075 TTGTGCAATAAAATAAAATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAAGTTAG
130 TTGTGCAATAAAATAAAATAAAAGTAAGTAAGTAAGAACAATAAAAATAAAAGTTAG
341132 AAAAATTAGC
Statistics
Matches: 163, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
200 9 0.06
201 24 0.15
202 123 0.75
203 7 0.04
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (201 bp):
AAATAAATATAAAAGTTAGGGATTGTTTTTAACCATTTAACACGAACCATAAATAATGCAGATCA
TCCCCCAGGGCAGGTCACCACAAGGTCGTTGAATATTCGAATATTAGAAAATTAGCAGATTAGTT
TGTGCAATAAAATAAAATAAAAGTAAGTAAGTAAGAACAATAAAAATAAAAGTTAGTATGCTAAT
ATAAAC
Found at i:342604 original size:103 final size:104
Alignment explanation
Indices: 342415--342607 Score: 239
Period size: 103 Copynumber: 1.9 Consensus size: 104
342405 GAGGATTTAA
** * * *
342415 AGATGACATTGTTCCTTCATGTGGAGGACTTCTGGTCAATCTAGATATAATTTGGTGTTGAAGAC
1 AGATGACATTGTTCCTTCATGTGGAGGAAATCTGGTCAATCTAGAGATAATATAGTGTTGAAGAC
*
342480 GACACTGCTCATCCATGTTGAAGAGATCTGGCCACTTTT
66 GACACTGCTCATCCATATTGAAGAGATCTGGCCACTTTT
* *
342519 AGATGACGTTGTTCCTTC-TCGTTGAGGAAAT-TGGTCAATCATA-AGATAATATAGTGTTGAAG
1 AGATGACATTGTTCCTTCAT-GTGGAGGAAATCTGGTCAATC-TAGAGATAATATAGTGTTGAAG
* * **
342581 ATGACTCTGCTCATCTGTATTGAAGAG
64 ACGACACTGCTCATCCATATTGAAGAG
342608 TTCTAGCTAC
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
103 48 0.64
104 27 0.36
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (104 bp):
AGATGACATTGTTCCTTCATGTGGAGGAAATCTGGTCAATCTAGAGATAATATAGTGTTGAAGAC
GACACTGCTCATCCATATTGAAGAGATCTGGCCACTTTT
Found at i:342973 original size:139 final size:139
Alignment explanation
Indices: 342723--343265 Score: 703
Period size: 139 Copynumber: 3.9 Consensus size: 139
342713 AGTATTTGGG
* * * * * *
342723 TAATTTGGAGAGAATACGGTTCCTTCGCGTTGAGGAAGTTTGATTGTCTAAGGATGGCACTGCTC
1 TAATTTGGAGACAACACGGTTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACACTACTC
* * * * * *
342788 ATTCGCATTGAGGAGATCTTGTCGGTGGATGACATTGTTCATTCGTGTTGAGGAAGTCTAGCAGT
66 CTTCACATTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGAAGTCTAGCCGT
342853 TTTAGAAGA
131 TTTAGAAGA
* *
342862 TAATTTGGAGACAACACGGTTTCTTCACGTTGAGGAAGTCTGATTGTCTGAGGATGACACTACTC
1 TAATTTGGAGACAACACGGTTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACACTACTC
* * * *
342927 CTTCGCGTTGAGGAGATCTGGTCGGTGGACAACATTGTTCCTTCGTGTTAAGGAAGTCTAGCCGT
66 CTTCACATTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGAAGTCTAGCCGT
342992 TTTAGAAGA
131 TTTAGAAGA
* *
343001 TAATTTGGAGACAACACGGTTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGATATTGA-T
1 TAATTTGGAGACAACACGGTTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACACT-ACT
** * * * * * *
343065 CCTTCATGTTGAGGAGATCTGGTCAGTGAAGGGCATTGTTTCTTCGTGTTGAAGAAGT-TAAGCC
65 CCTTCACATTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGAAGTCT-AGCC
343129 GTTTTAGAAGA
129 GTTTTAGAAGA
* * ** * * *
343140 TAATTTGGAGACAACATGGTTCATTCTTGTTGAGAAAGTCTGATTATCTGAGGATGACACTGCTC
1 TAATTTGGAGACAACACGGTTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACACTACTC
* * * *
343205 CTTCACATTTAGGAGTTATGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGACGTCTAG
66 CTTCACATTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGAAGTCTAG
343266 TCATCTGGAG
Statistics
Matches: 349, Mismatches: 51, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
138 1 0.00
139 346 0.99
140 2 0.01
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (139 bp):
TAATTTGGAGACAACACGGTTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACACTACTC
CTTCACATTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGAAGTCTAGCCGT
TTTAGAAGA
Found at i:343627 original size:103 final size:104
Alignment explanation
Indices: 343484--343724 Score: 387
Period size: 103 Copynumber: 2.3 Consensus size: 104
343474 AAGTGAGATA
** **
343484 AATTTTTGTTTTGAGTGAAAC-ATTTCAAAATTTGTGTTTCAAGAGAAAACTGTCTCAAGCGAGA
1 AATTTTTGTTTCAAGTGAAACAATTTCAAAATTTGCATTTCAAGAGAAAACTGTCTCAAGCGAGA
*
343548 CAAAATTTATTTTTAAGAAAAACAATCTCAAATGTTATT
66 CAAAATTTATTTTTAAGAAAAACAATCTCAAATGTTATC
* *
343587 AA-TTTTGTTTCAAGTGAAACAATTTCAAAATTTGCATTTCAAGGGAAAATTGTCTCAAGCGAGA
1 AATTTTTGTTTCAAGTGAAACAATTTCAAAATTTGCATTTCAAGAGAAAACTGTCTCAAGCGAGA
* *
343651 TAAAATTTGTTTTTAAGAAAAACAATCTCAAATGTTATC
66 CAAAATTTATTTTTAAGAAAAACAATCTCAAATGTTATC
343690 AATTTTTGTTTCAAGTGAAACAATTTCAAAATTTG
1 AATTTTTGTTTCAAGTGAAACAATTTCAAAATTTG
343725 GGGAAAACTG
Statistics
Matches: 127, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
102 16 0.13
103 79 0.62
104 32 0.25
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (104 bp):
AATTTTTGTTTCAAGTGAAACAATTTCAAAATTTGCATTTCAAGAGAAAACTGTCTCAAGCGAGA
CAAAATTTATTTTTAAGAAAAACAATCTCAAATGTTATC
Found at i:350494 original size:123 final size:124
Alignment explanation
Indices: 350275--350521 Score: 478
Period size: 123 Copynumber: 2.0 Consensus size: 124
350265 CCAGGTGTTG
350275 TTGAAAGTCAGAAAATCTTATAGTTATAGTTCAATTTCCAAGCAACTAACCCAAACTAGATTCAG
1 TTGAAAGTCAGAAAATCTTATAGTTATAGTTCAATTTCCAAGCAACTAACCCAAACTAGATTCAG
350340 CTACATGACTATTCCATCTGTGAAGATCATGATCATCATTGAACGTCATC-ACAGAAGT
66 CTACATGACTATTCCATCTGTGAAGATCATGATCATCATTGAACGTCATCAACAGAAGT
*
350398 TTGAAAGTCAGAAAATCTTATCGTTATAGTTCAATTTCCAAGCAACTAACCCAAACTAGATTCAG
1 TTGAAAGTCAGAAAATCTTATAGTTATAGTTCAATTTCCAAGCAACTAACCCAAACTAGATTCAG
350463 CTACATGACTATTCCATCTGTGAAGATCATGATCATCATTGAACGTCATCAACAGAAGT
66 CTACATGACTATTCCATCTGTGAAGATCATGATCATCATTGAACGTCATCAACAGAAGT
350522 AAAAACCAAT
Statistics
Matches: 122, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
123 114 0.93
124 8 0.07
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (124 bp):
TTGAAAGTCAGAAAATCTTATAGTTATAGTTCAATTTCCAAGCAACTAACCCAAACTAGATTCAG
CTACATGACTATTCCATCTGTGAAGATCATGATCATCATTGAACGTCATCAACAGAAGT
Found at i:355217 original size:207 final size:200
Alignment explanation
Indices: 354967--355342 Score: 538
Period size: 207 Copynumber: 1.8 Consensus size: 200
354957 AACCCGGATA
* * * *
354967 ATAAATAATGTTGATCGACCCCCAGGGCGGGTCACCACAAGGTCGTTGAATATTTAAATATTAGA
1 ATAAATAATGTGGATCGACCCCCAAGACGGGTCACCACAAGGTCGTTGAATATTCAAATATTAGA
355032 AAATTAACGGATTAGTTTGTGCAATAAAATAAAATAAAATGTTAGTAAATTAGTAAGAACAATAA
66 AAATTAACGGATTAGTTTGTGC-----AATAAAATAAAATGTTAGTAAATTA-TAAGAACAATAA
* *
355097 AAATAAAAAGTTAATATGTTAGTATAAATAAATAAAATAACAGTTAGGGATTGTTTTTAACCGTT
125 AAAT-AAAAGTTAAAATGTTAGTATAAA-AAATAAAATAAAAGTTAGGGATTGTTTTTAACCGTT
355162 TATAGACCGAACC
188 TATAGACCGAACC
* * *
355175 ATAAATAATGTGGATCGTCCCCCAAGAC-GGTCACCTCAAGGTCGTTGAATATTCGAATATTAGA
1 ATAAATAATGTGGATCGACCCCCAAGACGGGTCACCACAAGGTCGTTGAATATTCAAATATTAGA
** * *
355239 AAATTAGTGGGTTAGTTTGTGCAATAAAATAAAATGTTAGTAAGTTATAAGAACAATAAAAATAA
66 AAATTAACGGATTAGTTTGTGCAATAAAATAAAATGTTAGTAAATTATAAGAACAATAAAAATAA
* *
355304 AAGTTAAAATGTTAGTATGAACAATAAAATAAAAGTTAG
131 AAGTTAAAATGTTAGTATAAAAAATAAAATAAAAGTTAG
355343 AATGTTAGTA
Statistics
Matches: 153, Mismatches: 15, Indels: 9
0.86 0.08 0.05
Matches are distributed among these distances:
199 16 0.10
200 21 0.14
201 16 0.10
202 24 0.16
207 52 0.34
208 24 0.16
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (200 bp):
ATAAATAATGTGGATCGACCCCCAAGACGGGTCACCACAAGGTCGTTGAATATTCAAATATTAGA
AAATTAACGGATTAGTTTGTGCAATAAAATAAAATGTTAGTAAATTATAAGAACAATAAAAATAA
AAGTTAAAATGTTAGTATAAAAAATAAAATAAAAGTTAGGGATTGTTTTTAACCGTTTATAGACC
GAACC
Found at i:355301 original size:33 final size:33
Alignment explanation
Indices: 355260--355354 Score: 126
Period size: 32 Copynumber: 2.9 Consensus size: 33
355250 TTAGTTTGTG
*
355260 CAATAAAATAAAATGTTAGTAA-GTTA-TAAGAA
1 CAATAAAATAAAA-GTTAGAAATGTTAGTAAGAA
*
355292 CAATAAAAATAAAAGTTA-AAATGTTAGTATGAA
1 CAAT-AAAATAAAAGTTAGAAATGTTAGTAAGAA
355325 CAATAAAATAAAAGTTAG-AATGTTAGTAAG
1 CAATAAAATAAAAGTTAGAAATGTTAGTAAG
355355 TTAGAAAAGT
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
31 2 0.04
32 36 0.64
33 18 0.32
ACGTcount: A:0.56, C:0.03, G:0.14, T:0.27
Consensus pattern (33 bp):
CAATAAAATAAAAGTTAGAAATGTTAGTAAGAA
Found at i:355454 original size:19 final size:19
Alignment explanation
Indices: 355430--355469 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
355420 ACCATAAGGT
*
355430 TGAATAATATGAA-AAACAA
1 TGAATAA-ATAAATAAACAA
355449 TGAATAAATAAATAAACAA
1 TGAATAAATAAATAAACAA
355468 TG
1 TG
355470 GTTAGAATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (19 bp):
TGAATAAATAAATAAACAA
Found at i:356323 original size:26 final size:26
Alignment explanation
Indices: 356290--356339 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
356280 TATTCATGCT
356290 AAAAAGAAAGA-AGAAAACAAACATAA
1 AAAAAGAAAGATA-AAAACAAACATAA
*
356316 AAAAAGAAAGATAAAAACCAACAT
1 AAAAAGAAAGATAAAAACAAACAT
356340 GAAGGAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.74, C:0.10, G:0.10, T:0.06
Consensus pattern (26 bp):
AAAAAGAAAGATAAAAACAAACATAA
Found at i:356968 original size:21 final size:21
Alignment explanation
Indices: 356926--356968 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
356916 CAAAAGTATT
*
356926 AAAATTAAATTATAATAAATA
1 AAAATTAAATTATAAGAAATA
*
356947 AAAATTAAAATT-TAAGATATA
1 AAAATT-AAATTATAAGAAATA
356968 A
1 A
356969 TCATGTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAATTAAATTATAAGAAATA
Found at i:357570 original size:18 final size:18
Alignment explanation
Indices: 357547--357590 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
357537 ACTTCTTAAA
*
357547 ATTTTTAGGT-TTTCTTAT
1 ATTTTTAGATATTT-TTAT
357565 ATTTTTAGATATTTTTAT
1 ATTTTTAGATATTTTTAT
357583 ATCTTTTA
1 AT-TTTTA
357591 TTGATTATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.66
Consensus pattern (18 bp):
ATTTTTAGATATTTTTAT
Found at i:357775 original size:6 final size:6
Alignment explanation
Indices: 357764--357812 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
357754 ATAAAATTAT
*
357764 ATTTTA ATTTTA ATTTTA A-TTAA ATTTATA ATTTT- ATTTTA TATTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTT-TA ATTTTA ATTTTA -ATTTTA
357812 A
1 A
357813 AAAGTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 9 0.24
6 17 0.46
7 11 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
ATTTTA
Found at i:357790 original size:23 final size:23
Alignment explanation
Indices: 357758--357804 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
357748 TTAATGATAA
*
357758 AATTATATTT-TAATTTTAATTTT
1 AATTAAATTTATAATTTT-ATTTT
357781 AATTAAATTTATAATTTTATTTT
1 AATTAAATTTATAATTTTATTTT
357804 A
1 A
357805 TATTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
AATTAAATTTATAATTTTATTTT
Found at i:357793 original size:29 final size:30
Alignment explanation
Indices: 357755--357812 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
357745 AATTTAATGA
357755 TAAAATTAT-ATTTTAATTTTA-ATTTTAAT
1 TAAAATTATAATTTT-ATTTTATATTTTAAT
*
357784 TAAATTTATAATTTTATTTTATATTTTAA
1 TAAAATTATAATTTTATTTTATATTTTAA
357813 AAAGTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TAAAATTATAATTTTATTTTATATTTTAAT
Found at i:362673 original size:19 final size:20
Alignment explanation
Indices: 362627--362674 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
362617 AAACCACGTG
* *
362627 TCTTCCTTTCTTTTCAGCTA
1 TCTTCCTTTCTTTCCAACTA
362647 TCTT-CTTTCTTTCCAACT-
1 TCTTCCTTTCTTTCCAACTA
362665 TCTTCCTTTC
1 TCTTCCTTTC
362675 ATCTCAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.16
19 17 0.68
20 4 0.16
ACGTcount: A:0.08, C:0.33, G:0.02, T:0.56
Consensus pattern (20 bp):
TCTTCCTTTCTTTCCAACTA
Found at i:364987 original size:21 final size:21
Alignment explanation
Indices: 364963--365003 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
364953 CCAAAGAAGC
364963 ATGTATTATGAACCCTGGTGG
1 ATGTATTATGAACCCTGGTGG
364984 ATGTATTATGAACCCTGGTG
1 ATGTATTATGAACCCTGGTG
365004 CATTTATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (21 bp):
ATGTATTATGAACCCTGGTGG
Found at i:366367 original size:64 final size:63
Alignment explanation
Indices: 366299--366528 Score: 230
Period size: 64 Copynumber: 3.6 Consensus size: 63
366289 ATGGAACACT
* ***
366299 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
366363 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * * *
366427 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGAAATGCATTCGATG-TTCAATTAAT-TC
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATAGC
*
366490 A
63 C
* *
366491 TAGATGCATCGATGCATGGACTGATGCATCGGTGCATG
1 T-GATGCATCGATGCATGGAGTG-TGCATCGATGCATG
366529 CCTTTGAATA
Statistics
Matches: 139, Mismatches: 21, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
63 4 0.03
64 70 0.50
65 65 0.47
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:366451 original size:19 final size:19
Alignment explanation
Indices: 366427--366463 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
366417 GAAAATATTC
366427 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
366446 AGAGTGCATCGGTGCATG
1 AGAGTGCATCGATGCATG
366464 AAATGCATTC
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:0.24, C:0.16, G:0.38, T:0.22
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:366519 original size:65 final size:65
Alignment explanation
Indices: 366321--366528 Score: 241
Period size: 65 Copynumber: 3.2 Consensus size: 65
366311 GCACCAAGTG
* *
366321 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCT-GATGCATCGATGCATGG-CTT
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATAGATGCATCGATGCATGGAC-T
366384 G-
64 GA
* *
366385 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAG-TGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATAGATGCATCGATGCATGGACT
366447 GA
64 GA
* * *
366449 GTGCATCGGTGCATGAAATGCATTCGATG-TTCAATTAATTCATAGATGCATCGATGCATGGACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCATAGATGCATCGATGCATGGACT
366513 GA
64 GA
*
366515 TGCATCGGTGCATG
1 TGCATCGATGCATG
366529 CCTTTGAATA
Statistics
Matches: 125, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
63 12 0.10
64 44 0.35
65 64 0.51
66 5 0.04
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (65 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATAGATGCATCGATGCATGGACTGA
Found at i:374954 original size:64 final size:64
Alignment explanation
Indices: 374886--375115 Score: 230
Period size: 64 Copynumber: 3.6 Consensus size: 64
374876 TTGGAACACT
* ***
374886 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
** * * **
374950 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTAAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
* * * * * * *
375014 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAAT-TC
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATAGC
*
375077 A
64 C
* *
375078 TAGATGCATCGATGCATGGACTGATGCATCGGTGCATG
1 T-GATGCATCGATGCATGGAGTG-TGCATCGATGCATG
375116 CCTTTGAATA
Statistics
Matches: 138, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
64 78 0.57
65 60 0.43
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (64 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
Found at i:375038 original size:19 final size:19
Alignment explanation
Indices: 375014--375064 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
375004 AAAAATATTC
375014 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
375033 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
375052 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
375065 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:386611 original size:46 final size:45
Alignment explanation
Indices: 386550--386720 Score: 281
Period size: 46 Copynumber: 3.8 Consensus size: 45
386540 TATAAAATCT
*
386550 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
386595 CTTACCATTTAATCCCATAAGCTAGTAAGCTTATTTTACCAATATA
1 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
386641 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
386687 CTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
386721 GCCAGTTTAT
Statistics
Matches: 120, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
44 24 0.20
45 12 0.10
46 84 0.70
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:386881 original size:40 final size:40
Alignment explanation
Indices: 386802--386881 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
386792 ATATGAGTCA
* * * *
386802 AATATTGCACCGAAGTGCTGAGGTCGAGCTTTGCTCACCT
1 AATAATGCACCGAACTGCTGAGGTCGAGCTTTACCCACCT
* *
386842 AATAATGCACCGTACTGCTGAGGTCGGGCTTTACCCACCT
1 AATAATGCACCGAACTGCTGAGGTCGAGCTTTACCCACCT
386882 GATACACCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.26
Consensus pattern (40 bp):
AATAATGCACCGAACTGCTGAGGTCGAGCTTTACCCACCT
Found at i:387992 original size:12 final size:12
Alignment explanation
Indices: 387975--388001 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
387965 GGGAATAGGG
387975 TTTTGTTGTTGT
1 TTTTGTTGTTGT
387987 TTTTGTTGTTGT
1 TTTTGTTGTTGT
387999 TTT
1 TTT
388002 AGATCGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (12 bp):
TTTTGTTGTTGT
Found at i:393373 original size:21 final size:20
Alignment explanation
Indices: 393346--393403 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
393336 TTATCCAATA
393346 AACTTGACATCCATAACAA-C
1 AACTTGA-ATCCATAACAACC
393366 AGACTTGAAATCCATAACAACC
1 A-ACTTG-AATCCATAACAACC
393388 AACTTGAACTCCATAA
1 AACTTGAA-TCCATAA
393404 TAATAAATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.09
21 28 0.82
22 3 0.09
ACGTcount: A:0.45, C:0.28, G:0.07, T:0.21
Consensus pattern (20 bp):
AACTTGAATCCATAACAACC
Found at i:402706 original size:83 final size:83
Alignment explanation
Indices: 402619--402930 Score: 281
Period size: 83 Copynumber: 3.8 Consensus size: 83
402609 ACAAAAAATG
* * * * *
402619 CCACTATAGATGAATCTTATTGCGGCATTTGTATAAAAATGCCACTAAAGTAATACTATGTTGCG
1 CCACTATAGATGAACCCTATTGCGGCATTTGTATAAAAACGCCACTAAAGTACTACTCTGTTGCG
*
402684 GTGTTTGTTGAGAAAAAA
66 GTATTTGTTGAGAAAAAA
* * * *
402702 CCACTATAAATGAACCCTATTGTGG-AGTTTGCAT-AAAACGCCGCTAAAGTACTACTCTGTTGC
1 CCACTATAGATGAACCCTATTGCGGCA-TTTGTATAAAAACGCCACTAAAGTACTACTCTGTTGC
* *
402765 GGTATTTGTTGAGACAACA
65 GGTATTTGTTGAGAAAAAA
* * ** ** ** *
402784 TCAATATAGATGAACCCTATTATGGTGTTACTATAAAAACGCCACTAACGTACTACTCTGTTGCG
1 CCACTATAGATGAACCCTATTGCGGCATTTGTATAAAAACGCCACTAAAGTACTACTCTGTTGCG
* * *
402849 GCATTTGTTTA-AAAAATG
66 GTATTTGTTGAGAAAAA-A
* * * * * * * *
402867 TCACTATAGATTAACTCTATTGCGGCGTTTTTGT-AAAACTGCCGCTAAAGTACTACTCTATTGC
1 CCACTATAGATGAACCCTATTGCGGCATTTGTATAAAAAC-GCCACTAAAGTACTACTCTGTTGC
402931 AGTGTTTATA
Statistics
Matches: 185, Mismatches: 39, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
82 75 0.41
83 110 0.59
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (83 bp):
CCACTATAGATGAACCCTATTGCGGCATTTGTATAAAAACGCCACTAAAGTACTACTCTGTTGCG
GTATTTGTTGAGAAAAAA
Found at i:402945 original size:41 final size:41
Alignment explanation
Indices: 402880--402958 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
402870 CTATAGATTA
* * *
402880 ACTCTATTGCGGCGTTTTTGT-AAAACTGCCGCTAAAGTACT
1 ACTCTATTGCAGCGTTTATATAAAAAC-GCCGCTAAAGTACT
* *
402921 ACTCTATTGCAGTGTTTATATAAAAACGCGGCTAAAGT
1 ACTCTATTGCAGCGTTTATATAAAAACGCCGCTAAAGT
402959 TACCATTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 27 0.84
42 5 0.16
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (41 bp):
ACTCTATTGCAGCGTTTATATAAAAACGCCGCTAAAGTACT
Found at i:408322 original size:59 final size:59
Alignment explanation
Indices: 408249--408401 Score: 261
Period size: 59 Copynumber: 2.6 Consensus size: 59
408239 ATACAATCAA
* **
408249 TATGATTTTCTTACCATTTTAGCACACAAAGTGCCATATATGGAAATTGATACACTTAG
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCATATATGGAAATCCATACACTTAG
* *
408308 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCTTATCTGGAAATCCATACACTTAG
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCATATATGGAAATCCATACACTTAG
408367 TATGATTTCCTTACCATTTTAGCACACAAAGTGCC
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCC
408402 CTTTGGTAAT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 89 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (59 bp):
TATGATTTCCTTACCATTTTAGCACACAAAGTGCCATATATGGAAATCCATACACTTAG
Found at i:414018 original size:16 final size:16
Alignment explanation
Indices: 413997--414036 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
413987 TTTCTTCTCC
413997 CCTAAACTCAGGAGCT
1 CCTAAACTCAGGAGCT
**
414013 CCTAAACTTTGGAGCT
1 CCTAAACTCAGGAGCT
*
414029 CCCAAACT
1 CCTAAACT
414037 TCTTAACTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.23
Consensus pattern (16 bp):
CCTAAACTCAGGAGCT
Found at i:415113 original size:59 final size:59
Alignment explanation
Indices: 415015--415245 Score: 363
Period size: 59 Copynumber: 3.9 Consensus size: 59
415005 TAAATTCAAT
* * * * *
415015 TGGAATTTCATACAATCAATATGATTTTCTTACCATTTTAGCACACAAAGTGCCATATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCATATC
* *
415074 TAGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCACATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCATATC
** *
415133 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGTGCACAAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCATATC
*
415192 TGGAAATTTATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCC
415246 CTTTGGTAAT
Statistics
Matches: 157, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 157 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (59 bp):
TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCATATC
Found at i:420353 original size:18 final size:19
Alignment explanation
Indices: 420313--420353 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
420303 TTTATAATAA
*
420313 AAATTAATTTACTTTTTTT
1 AAATTAATTTAATTTTTTT
420332 -AATTAA-TTAATTTTTTT
1 AAATTAATTTAATTTTTTT
420349 AAATT
1 AAATT
420354 TAATCCGACC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
AAATTAATTTAATTTTTTT
Found at i:422718 original size:125 final size:125
Alignment explanation
Indices: 422177--422854 Score: 1127
Period size: 125 Copynumber: 5.4 Consensus size: 125
422167 TAATCCTCCA
* * *
422177 GTCAGAGAATATTATCTTTGCCCTATTATGTCACCCATATCCCTCGGGGACACTAGATATATCAG
1 GTCAGAGAATATTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAG
422242 TACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTC
66 TACCTATTATTTCACTATTCACATGAAGGCGCGTT-CCGGGGGCGCGCCTTCCATTATTTC
*
422303 GTCAGAGAATATTATCATTGCCCTATTATGTCATTCATG-CCCTC-GGGACACTAGATATATCAG
1 GTCAGAGAATATTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAG
422366 TACCTATTATTTCACTATTC-CATGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTC
66 TACCTATTATTTCACTATTCACATGAAGGCGCGTTC-CGGGGGCGCGCCTTCCATTATTTC
422426 GTCAGAGAATATTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAG
1 GTCAGAGAATATTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAG
* *
422491 TACCTA-TATTTCACTATTCACGTGAAGGCGCGTTCCCGGGG-GCGCCTTCCATTATTTTTATTT
66 TACCTATTATTTCACTATTCACATGAAGGCGCGTTCCGGGGGCGCGCCTTCC---A---TTATTT
422554 C
125 C
*
422555 GTCAGAGAATATTATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGGACACTAGATATATCA
1 GTCAGAGAATATTATCATTGCCCTATTATGTCACTCATGTCCCTC-GGGGACACTAGATATATCA
*
422620 GTACCTATTATTTCACTATTCACATGAAGGCGCGTTCC-AGGGCGCGCCTTCCATTATTTC
65 GTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCGGGGGCGCGCCTTCCATTATTTC
422680 GTCAGAGAATATTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAG
1 GTCAGAGAATATTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAG
*
422745 TACCTATTATTTCACTATTCACCTGAAGGCGCGTTCCGGGGGCGCGCCTTCCATTATTTC
66 TACCTATTATTTCACTATTCACATGAAGGCGCGTTCCGGGGGCGCGCCTTCCATTATTTC
*
422805 GTCAGAGAATATGTATCATTGCCCTATTATGTCACTCA-GTCCCTTGGGGA
1 GTCAGAGAATAT-TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
422855 ATAACTTAAA
Statistics
Matches: 523, Mismatches: 14, Indels: 31
0.92 0.02 0.05
Matches are distributed among these distances:
122 1 0.00
123 85 0.16
124 118 0.23
125 139 0.27
126 61 0.12
128 1 0.00
129 51 0.10
130 29 0.06
131 38 0.07
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (125 bp):
GTCAGAGAATATTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAG
TACCTATTATTTCACTATTCACATGAAGGCGCGTTCCGGGGGCGCGCCTTCCATTATTTC
Found at i:423317 original size:34 final size:33
Alignment explanation
Indices: 423239--423322 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
423229 AAATTTAATG
*
423239 TTAAATTTCGAATACTA-ATTTATATTTTAAAT
1 TTAAATTTCGAATAATATATTTATATTTTAAAT
* * *
423271 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATA-TATTTATATTTTAAAT
423304 TTAAATTTCGAATAATATA
1 TTAAATTTCGAATAATATA
423323 ATGTTTTTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
31 7 0.16
32 8 0.18
33 22 0.49
34 8 0.18
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (33 bp):
TTAAATTTCGAATAATATATTTATATTTTAAAT
Found at i:423931 original size:21 final size:21
Alignment explanation
Indices: 423844--423936 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
423834 TATGGTATAA
*
423844 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
423865 AA-CCTG-GCGGCTAGGCATGT
1 AACCCTGCG-GGCTAGGAATGT
423885 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
423906 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
423927 AACCCTGCGG
1 AACCCTGCGG
423937 AGATGGCATA
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
19 1 0.02
20 21 0.32
21 40 0.61
22 4 0.06
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:425730 original size:32 final size:32
Alignment explanation
Indices: 425679--425751 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
425669 AATTCTAAAT
* * * *
425679 AAATAATAATTATATAAATATTATTTTAATAA
1 AAATAATAATTACATAAATATTAATATAAAAA
425711 AAA-AATAATTTACATAAATATTAATATAAAAA
1 AAATAATAA-TTACATAAATATTAATATAAAAA
425743 AAATAATAA
1 AAATAATAA
425752 CTATTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 5 0.14
32 25 0.71
33 5 0.14
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (32 bp):
AAATAATAATTACATAAATATTAATATAAAAA
Found at i:425746 original size:17 final size:17
Alignment explanation
Indices: 425726--425779 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
425716 TAATTTACAT
*
425726 AAATATTAATATAAAAA
1 AAATAATAATATAAAAA
425743 AAATAATAACTATTTAAAAA
1 AAATAATAA-TA--TAAAAA
* *
425763 AAATACTAACATAAAAA
1 AAATAATAATATAAAAA
425780 TAATTTCTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 14 0.45
18 2 0.06
19 1 0.03
20 14 0.45
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAATAATATAAAAA
Found at i:429673 original size:208 final size:204
Alignment explanation
Indices: 429308--429721 Score: 749
Period size: 208 Copynumber: 2.0 Consensus size: 204
429298 ATACTCTGAT
429308 TACATTACACGATAATGGCATCTAGACAAACTGCATAAATTTGGTCAACTTTGACATGCATGTAT
1 TACATTACACGATAATGGCATCTAGACAAACTGCATAAATTTGGTCAACTTTGACATGCATGTAT
* *
429373 GCTCATAATATTATTATCGTGTTCTTAAGGATTCAACTGGAAAAAGAACTACAACGAATAAGATA
66 GCTCAAAATAATATTATCGTGTTCTTAAGGATTCAACTGGAAAAAGAACTACAACGAATAAGATA
429438 CTTTTAGATACATTCGAGATAAAAAAGGACAGACTAATACAACAACAAAATTCAGTTGCAAAAAA
131 CTTTTAGATACATTCGAGATAAAAAAGGACAGACTAATACAACAACAAAATTCAGTTGCAAAAAA
429503 TAGAACTCA
196 TAGAACTCA
*
429512 TACATTACACGATAATGGCATCTAGACAAACTGCATAAATTTGGTCATCACTTTTTACATGCCAT
1 TACATTACACGATAATGGCATCTAGACAAACTGCATAAATTTGGTCA--AC-TTTGACATG-CAT
429577 GTATGCTCAAAATAATATTATCGTGTTCTTAAGGATTCAACTGGAAAAAGAACTACAAACGAATA
62 GTATGCTCAAAATAATATTATCGTGTTCTTAAGGATTCAACTGGAAAAAGAACTAC-AACGAATA
429642 AGATACTTTTAGATACATTCGAGAT-AAAAAGGACAGACTAATACAACAACAAAATTCAGTTGCA
126 AGATACTTTTAGATACATTCGAGATAAAAAAGGACAGACTAATACAACAACAAAATTCAGTTGCA
429706 AAAAATAGAACTCA
191 AAAAATAGAACTCA
429720 TA
1 TA
429722 AAGTTTACAA
Statistics
Matches: 202, Mismatches: 3, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
204 47 0.23
206 2 0.01
207 8 0.04
208 112 0.55
209 33 0.16
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (204 bp):
TACATTACACGATAATGGCATCTAGACAAACTGCATAAATTTGGTCAACTTTGACATGCATGTAT
GCTCAAAATAATATTATCGTGTTCTTAAGGATTCAACTGGAAAAAGAACTACAACGAATAAGATA
CTTTTAGATACATTCGAGATAAAAAAGGACAGACTAATACAACAACAAAATTCAGTTGCAAAAAA
TAGAACTCA
Found at i:437155 original size:3 final size:3
Alignment explanation
Indices: 437147--437192 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
437137 AATATTATAA
*
437147 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
437193 CAATTTTTGC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:437167 original size:23 final size:23
Alignment explanation
Indices: 437139--437186 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
437129 CTACCAAAAA
437139 TATTATAATATTATTATTATTAT
1 TATTATAATATTATTATTATTAT
*
437162 TATTATTATATTATTATTATTAT
1 TATTATAATATTATTATTATTAT
437185 TA
1 TA
437187 ATATTACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTATAATATTATTATTATTAT
Found at i:438937 original size:21 final size:21
Alignment explanation
Indices: 438912--438961 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
438902 TTTTATTTCA
438912 TTATTATTCCTATATTT-ATAT
1 TTATTATTCCTAT-TTTAATAT
* *
438933 TTATTAATCTTATTTTAAATAT
1 TTATTATTCCTATTTT-AATAT
438955 TTATTAT
1 TTATTAT
438962 CCAATATCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 11 0.46
22 10 0.42
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTATTCCTATTTTAATAT
Found at i:439678 original size:19 final size:19
Alignment explanation
Indices: 439632--439719 Score: 87
Period size: 19 Copynumber: 4.8 Consensus size: 19
439622 AGGGTGTCAA
* *
439632 AGTGCATCCATACACCCCGT
1 AGTGCATCCATGCA-CCTGT
*
439652 AGTACATCCATGCACCTGT
1 AGTGCATCCATGCACCTGT
439671 AGTGCATCCATGCA--T-T
1 AGTGCATCCATGCACCTGT
*
439687 -GTGCATCGATGCACCCTG-
1 AGTGCATCCATGCA-CCTGT
439705 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
439720 TCCATTTCGA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
15 12 0.21
16 1 0.02
17 1 0.02
18 2 0.04
19 29 0.51
20 12 0.21
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (19 bp):
AGTGCATCCATGCACCTGT
Found at i:443116 original size:17 final size:18
Alignment explanation
Indices: 443075--443126 Score: 79
Period size: 17 Copynumber: 2.9 Consensus size: 18
443065 AGGATGTCAA
443075 AGTGCATCCATGCACCTGC
1 AGTGCATCCATGCA-CTGC
443094 AGTGCATCCATGCACTG-
1 AGTGCATCCATGCACTGC
*
443111 AGTGCACCCATGCACT
1 AGTGCATCCATGCACT
443127 CTATTTCGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 15 0.47
18 3 0.09
19 14 0.44
ACGTcount: A:0.23, C:0.35, G:0.21, T:0.21
Consensus pattern (18 bp):
AGTGCATCCATGCACTGC
Found at i:443170 original size:20 final size:20
Alignment explanation
Indices: 443145--443240 Score: 147
Period size: 20 Copynumber: 4.8 Consensus size: 20
443135 AATGCAATTA
443145 GTGCATCCATGCACCCTGCT
1 GTGCATCCATGCACCCTGCT
*
443165 GTGCATCCATGCACCCTGTT
1 GTGCATCCATGCACCCTGCT
* *
443185 GTGTATCCATGCACCTTGCT
1 GTGCATCCATGCACCCTGCT
*
443205 GTGCATCCATGCACCCTGTT
1 GTGCATCCATGCACCCTGCT
*
443225 GTGTATCCATGCACCC
1 GTGCATCCATGCACCC
443241 AGGCTACAAC
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.16, C:0.35, G:0.20, T:0.29
Consensus pattern (20 bp):
GTGCATCCATGCACCCTGCT
Found at i:443195 original size:40 final size:40
Alignment explanation
Indices: 443149--443240 Score: 175
Period size: 40 Copynumber: 2.3 Consensus size: 40
443139 CAATTAGTGC
443149 ATCCATGCACCCTGCTGTGCATCCATGCACCCTGTTGTGT
1 ATCCATGCACCCTGCTGTGCATCCATGCACCCTGTTGTGT
*
443189 ATCCATGCACCTTGCTGTGCATCCATGCACCCTGTTGTGT
1 ATCCATGCACCCTGCTGTGCATCCATGCACCCTGTTGTGT
443229 ATCCATGCACCC
1 ATCCATGCACCC
443241 AGGCTACAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.16, C:0.36, G:0.18, T:0.29
Consensus pattern (40 bp):
ATCCATGCACCCTGCTGTGCATCCATGCACCCTGTTGTGT
Found at i:445510 original size:13 final size:13
Alignment explanation
Indices: 445492--445524 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
445482 CATTTTCAAT
445492 GACGAAGATCCGA
1 GACGAAGATCCGA
445505 GACGAAGATCCGA
1 GACGAAGATCCGA
445518 GACGAAG
1 GACGAAG
445525 CAGTGATCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.21, G:0.33, T:0.06
Consensus pattern (13 bp):
GACGAAGATCCGA
Done.