Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009623.1 Hibiscus syriacus cultivar Beakdansim tig00117012_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: 3488723
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 18
Found at i:168375 original size:13 final size:13
Alignment explanation
Indices: 168357--168411 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
168347 GTCATAAATC
*
168357 TATGACGCGTATT
1 TATGACGCGCATT
*
168370 TATGACACGCATT
1 TATGACGCGCATT
*
168383 TATGACGCACATT
1 TATGACGCGCATT
*
168396 TATGACGCTCATT
1 TATGACGCGCATT
168409 TAT
1 TAT
168412 AATGCTCATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:168418 original size:13 final size:13
Alignment explanation
Indices: 168379--168421 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
168369 TTATGACACG
* *
168379 CATTTATGACGCA
1 CATTTATAACGCT
*
168392 CATTTATGACGCT
1 CATTTATAACGCT
*
168405 CATTTATAATGCT
1 CATTTATAACGCT
168418 CATT
1 CATT
168422 GCGCGTCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.40
Consensus pattern (13 bp):
CATTTATAACGCT
Found at i:168729 original size:15 final size:15
Alignment explanation
Indices: 168709--168738 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
168699 TATTGTACTC
168709 ATATGTCGATACAAA
1 ATATGTCGATACAAA
168724 ATATGTCGATACAAA
1 ATATGTCGATACAAA
168739 TTTTCAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (15 bp):
ATATGTCGATACAAA
Found at i:189453 original size:17 final size:17
Alignment explanation
Indices: 189431--189553 Score: 102
Period size: 17 Copynumber: 7.1 Consensus size: 17
189421 AATTAAGAGT
*
189431 TAGTTTAATAAATGAAC
1 TAGTTTAATGAATGAAC
*
189448 TAGTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
* *
189465 TAGTTTGATGAATGCAC
1 TAGTTTAATGAATGAAC
*
189482 TAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
* * *
189499 TAACTTTATTCAATGAAC
1 T-AGTTTAATGAATGAAC
* ** **
189517 TTGCAATCTTGAATGAAC
1 TAG-TTTAATGAATGAAC
*
189535 TAGTTTAATCAATGAAC
1 TAGTTTAATGAATGAAC
189552 TA
1 TA
189554 CTTACTTAAA
Statistics
Matches: 83, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
17 57 0.69
18 26 0.31
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:189592 original size:17 final size:17
Alignment explanation
Indices: 189545--189599 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
189535 TAGTTTAATC
*
189545 AATGAACTACTTA-CTTA
1 AATGAACTACATATC-TA
*
189562 AATGAAGTGA-ATATCTA
1 AATGAACT-ACATATCTA
*
189579 AATGAACTACATATGTA
1 AATGAACTACATATCTA
189596 AATG
1 AATG
189600 CAATGAATGC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 1 0.03
17 28 0.90
18 2 0.06
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (17 bp):
AATGAACTACATATCTA
Found at i:192161 original size:11 final size:12
Alignment explanation
Indices: 192107--192163 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 12
192097 AAAGTTCTTT
192107 TTTTATTTT-A-
1 TTTTATTTTAAG
*
192117 TTTTCTTTTCAAG
1 TTTTATTTT-AAG
*
192130 TTTTCATTTTTA-
1 TTTT-ATTTTAAG
192142 TTTTATTTTAAG
1 TTTTATTTTAAG
192154 TTTT-TTTTAA
1 TTTTATTTTAA
192164 ACATGCTAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
10 8 0.21
11 12 0.32
12 9 0.24
13 5 0.13
14 4 0.11
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.72
Consensus pattern (12 bp):
TTTTATTTTAAG
Found at i:199175 original size:12 final size:12
Alignment explanation
Indices: 199158--199197 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
199148 ATATGATTGT
*
199158 TAATTATATGAA
1 TAATTATAAGAA
199170 TAATTATAAGAA
1 TAATTATAAGAA
*
199182 TAATAATAAGAA
1 TAATTATAAGAA
199194 TAAT
1 TAAT
199198 GAAATGATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (12 bp):
TAATTATAAGAA
Found at i:203483 original size:48 final size:48
Alignment explanation
Indices: 203431--203527 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 48
203421 ATCTTATGGA
* *
203431 TTATTGTTATTGATTTGGTTATGTTATGCTTATTTTTGTGCAAGATCT
1 TTATTGTTACTGATTTGGTTATGTTATGCTTATTTTTGTACAAGATCT
* * * *
203479 TTATTGTTGCTGATTTGGTTGTGTTATTCTTATTTTTGTACAGGATCT
1 TTATTGTTACTGATTTGGTTATGTTATGCTTATTTTTGTACAAGATCT
203527 T
1 T
203528 ACTTTCAAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.16, C:0.07, G:0.20, T:0.57
Consensus pattern (48 bp):
TTATTGTTACTGATTTGGTTATGTTATGCTTATTTTTGTACAAGATCT
Found at i:203954 original size:24 final size:24
Alignment explanation
Indices: 203912--203964 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
203902 CTTTCTTTTC
* *
203912 TTTTCTTTTCTTTTCAAGTTTTCAT
1 TTTTATTTTATTTTCAAGTTTT-AT
203937 TTTTATTTTATTTT-AAGTTTTAT
1 TTTTATTTTATTTTCAAGTTTTAT
203960 TTTTA
1 TTTTA
203965 AACATGCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 7 0.27
24 7 0.27
25 12 0.46
ACGTcount: A:0.17, C:0.08, G:0.04, T:0.72
Consensus pattern (24 bp):
TTTTATTTTATTTTCAAGTTTTAT
Found at i:203965 original size:13 final size:13
Alignment explanation
Indices: 203917--203965 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
203907 TTTTCTTTTC
* *
203917 TTTTCTTTTCAAG
1 TTTTATTTTTAAG
203930 TTTTCATTTTT-A-
1 TTTT-ATTTTTAAG
203942 TTTTA-TTTTAAG
1 TTTTATTTTTAAG
203954 TTTTATTTTTAA
1 TTTTATTTTTAA
203966 ACATGCTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 4 0.13
11 2 0.07
12 9 0.30
13 11 0.37
14 4 0.13
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.69
Consensus pattern (13 bp):
TTTTATTTTTAAG
Found at i:205383 original size:75 final size:75
Alignment explanation
Indices: 205236--205386 Score: 266
Period size: 76 Copynumber: 2.0 Consensus size: 75
205226 ACACCGAAAC
205236 CCTTATGCATTTAAGAAACAAAATGCTAAAAAATACTAACTTCAAAATGCTTGTATTTGTTCTTG
1 CCTTATGCATTTAAGAAACAAAATGCTAAAAAATACTAACTTCAAAATGCTTGTATTTGTTCTTG
205301 CTGGAAAAAA
66 CTGGAAAAAA
*
205311 CCTTATGCATTTAAGAAACAAAATGCTAAAAAAATACTAACTTCAAAATGTTTGTATTTGTTCTT
1 CCTTATGCATTTAAGAAACAAAATGCT-AAAAAATACTAACTTCAAAATGCTTGTATTTGTTCTT
* *
205376 GTTGAAAAAAA
65 GCTGGAAAAAA
205387 AACCTCATTT
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
75 27 0.38
76 45 0.62
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.33
Consensus pattern (75 bp):
CCTTATGCATTTAAGAAACAAAATGCTAAAAAATACTAACTTCAAAATGCTTGTATTTGTTCTTG
CTGGAAAAAA
Found at i:206309 original size:2 final size:2
Alignment explanation
Indices: 206253--206295 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
206243 GATTTTCAAA
206253 AT AT -T 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 AT AT AT
206294 AT
1 AT
206296 TTTCAAACTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:206309 original size:17 final size:18
Alignment explanation
Indices: 206287--206320 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
206277 TATATATATA
206287 TATATA-TATTTTCAAAC
1 TATATACTATTTTCAAAC
206304 TATATACTATTTTCAAA
1 TATATACTATTTTCAAA
206321 ATATTTTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
TATATACTATTTTCAAAC
Found at i:206483 original size:23 final size:23
Alignment explanation
Indices: 206436--206503 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
206426 TCAAAAGGTT
* *
206436 TTTTCAAAACTATGTAATATGTAA
1 TTTT-AAAACTATATAATATTTAA
*
206460 TTTTAAAACTATATAGTATTTAA
1 TTTTAAAACTATATAATATTTAA
* *
206483 TGTTT-TAACTATATATTATTT
1 T-TTTAAAACTATATAATATTT
206504 TCAAAGTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
23 31 0.82
24 7 0.18
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (23 bp):
TTTTAAAACTATATAATATTTAA
Found at i:208419 original size:31 final size:27
Alignment explanation
Indices: 208359--208429 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 27
208349 AAACACATAT
208359 CTTTTAAAA-TTACT-CTTTTAGTCTAAA
1 CTTTTAAAATTTA-TAC-TTTAGTCTAAA
208386 CTTTTACAAACTTTATACTTTAGTCATTAAA
1 CTTTTA-AAA-TTTATACTTTAGTC--TAAA
208417 CTTTTAAAATTTA
1 CTTTTAAAATTTA
208430 CATTTTGGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
27 6 0.16
28 3 0.08
29 12 0.32
30 7 0.18
31 10 0.26
ACGTcount: A:0.35, C:0.14, G:0.03, T:0.48
Consensus pattern (27 bp):
CTTTTAAAATTTATACTTTAGTCTAAA
Found at i:216354 original size:75 final size:74
Alignment explanation
Indices: 216257--216445 Score: 216
Period size: 75 Copynumber: 2.5 Consensus size: 74
216247 TTAATATTTC
* * *
216257 TCTAGACTTAATATTATGGTTTGAGTCTTAAGATTTGATACTTTAATATTATGATTTGATTATGA
1 TCTAAACTTAATATTGTGGTTTGAGTCTTAA-ATTTGACACTTTAATATTATGATTTGATTATGA
*
216322 ATTTTATTAT
65 ATTTTACTAT
** * * * * * * *
216332 TCTGGAGTTAATATTGTGGTTTGAATCTTCAAATTTGACATTTTAATATTGTGGTTTGTTTATGG
1 TCTAAACTTAATATTGTGGTTTGAGTCTT-AAATTTGACACTTTAATATTATGATTTGATTATGA
216397 ATTTTACTAT
65 ATTTTACTAT
* *
216407 TCTAAACTTAATATTGCGGTTTGAGTCTTGATATTTGAC
1 TCTAAACTTAATATTGTGGTTTGAGTCTT-AAATTTGAC
216446 TTTATTTATG
Statistics
Matches: 95, Mismatches: 18, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
75 93 0.98
76 2 0.02
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.49
Consensus pattern (74 bp):
TCTAAACTTAATATTGTGGTTTGAGTCTTAAATTTGACACTTTAATATTATGATTTGATTATGAA
TTTTACTAT
Found at i:217313 original size:14 final size:14
Alignment explanation
Indices: 217294--217321 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
217284 TTGCCTTGGG
217294 CAATATTAGGGTTC
1 CAATATTAGGGTTC
217308 CAATATTAGGGTTC
1 CAATATTAGGGTTC
217322 AAGAGATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
CAATATTAGGGTTC
Found at i:224340 original size:10 final size:10
Alignment explanation
Indices: 224301--224340 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
224291 TTCATCACAC
224301 CAAATTCTCT
1 CAAATTCTCT
*
224311 CAATTTCTCT
1 CAAATTCTCT
*
224321 CAACTTCTCT
1 CAAATTCTCT
*
224331 CAAATACTCT
1 CAAATTCTCT
224341 TATAATCTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:224373 original size:10 final size:10
Alignment explanation
Indices: 224358--224394 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
224348 TCTTCTAAGG
224358 TATATTTTAT
1 TATATTTTAT
224368 TATATTTTAT
1 TATATTTTAT
224378 TATATTTT-T
1 TATATTTTAT
*
224387 AATATTTT
1 TATATTTT
224395 GTATTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TATATTTTAT
Found at i:224408 original size:9 final size:9
Alignment explanation
Indices: 224396--224447 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
224386 TAATATTTTG
224396 TATTTAATT
1 TATTTAATT
*
224405 TATTTAA-G
1 TATTTAATT
224413 TATTTAATT
1 TATTTAATT
224422 TATTTAA--
1 TATTTAATT
* *
224429 TATTTTACT
1 TATTTAATT
224438 TATTTAATT
1 TATTTAATT
224447 T
1 T
224448 TTTTGCAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:224417 original size:17 final size:17
Alignment explanation
Indices: 224395--224444 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
224385 TTAATATTTT
224395 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
224412 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
224429 -TATTTTACTTATTTAA
1 GTATTTAATTTATTTAA
224445 TTTTTTTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:224440 original size:16 final size:16
Alignment explanation
Indices: 224404--224449 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
224394 TGTATTTAAT
* *
224404 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTTAC
224421 TTATTTAATATTTTAC
1 TTATTTAATATTTTAC
224437 TTATTTAAT-TTTT
1 TTATTTAATATTTT
224450 TTGCAGATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTAATATTTTAC
Found at i:230275 original size:21 final size:20
Alignment explanation
Indices: 230229--230275 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
230219 GACTTGCTAG
230229 GGTTTTTGAAAATGAGTCTT
1 GGTTTTTGAAAATGAGTCTT
230249 GGTTTTTGAAAATGAGTCTT
1 GGTTTTTGAAAATGAGTCTT
230269 GGTTTTT
1 GGTTTTT
230276 ATTTTTGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.21, C:0.04, G:0.26, T:0.49
Consensus pattern (20 bp):
GGTTTTTGAAAATGAGTCTT
Found at i:232318 original size:21 final size:22
Alignment explanation
Indices: 232284--232324 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
232274 TTAAATATTA
232284 TAAAGGAGGTATCGATACTCAT
1 TAAAGGAGGTATCGATACTCAT
232306 TAAAGGA-GTATCGATACTC
1 TAAAGGAGGTATCGATACTC
232325 CTGTCCTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.27
Consensus pattern (22 bp):
TAAAGGAGGTATCGATACTCAT
Found at i:235062 original size:30 final size:30
Alignment explanation
Indices: 235028--235125 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 30
235018 GATAAACACC
235028 AAATAGTAAAAGGACTTGTCCACCAAGGTT
1 AAATAGTAAAAGGACTTGTCCACCAAGGTT
* * ** *
235058 AAATAGTACAAGGACTTGGCCAAAAAGTTT
1 AAATAGTAAAAGGACTTGTCCACCAAGGTT
*
235088 AAATAGTACAAA-GACTTGGT-CACCAATGTT
1 AAATAGTA-AAAGGACTT-GTCCACCAAGGTT
235118 AAATAGTA
1 AAATAGTA
235126 TAGGGACCAA
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
30 52 0.95
31 3 0.05
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.24
Consensus pattern (30 bp):
AAATAGTAAAAGGACTTGTCCACCAAGGTT
Found at i:236372 original size:3 final size:3
Alignment explanation
Indices: 236366--236397 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
236356 ATTATTATTA
236366 TTG TTG TTTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG -TTG TTG TTG TTG TTG TTG TTG TTG T
236398 AGGTTATAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:238085 original size:31 final size:31
Alignment explanation
Indices: 238049--238123 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
238039 CAAAAAATCA
* * *
238049 TAAGATGTTGTCACTTTCGTTTTAATTTAAT
1 TAAGATGTAGTCACTTTAGTTTTAATATAAT
* * *
238080 TAAGATATGGTCACTTTAGTTTTTATATAAT
1 TAAGATGTAGTCACTTTAGTTTTAATATAAT
238111 TAAGATGTAGTCA
1 TAAGATGTAGTCA
238124 TCACGGCTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.47
Consensus pattern (31 bp):
TAAGATGTAGTCACTTTAGTTTTAATATAAT
Found at i:238285 original size:25 final size:25
Alignment explanation
Indices: 238244--238313 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
238234 AAATTTTAAC
*
238244 ATAAAAT-ATATATTTTAAA-TGAAA
1 ATAAAATAAAATATTTTAAACT-AAA
*
238268 ATAAAATAAAATATTTTAAACTAAG
1 ATAAAATAAAATATTTTAAACTAAA
*
238293 TTAATAATAAAATATATTTAA
1 ATAA-AATAAAATAT-TTTAA
238314 TAAGTTAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
24 7 0.18
25 16 0.41
26 11 0.28
27 5 0.13
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (25 bp):
ATAAAATAAAATATTTTAAACTAAA
Found at i:238307 original size:26 final size:24
Alignment explanation
Indices: 238272--238346 Score: 91
Period size: 25 Copynumber: 3.0 Consensus size: 24
238262 ATGAAAATAA
238272 AATAAAATATTTTAAACTAAGTTAAT
1 AATAAAATATTTT-AA-TAAGTTAAT
238298 AATAAAATATATTTAATAAGTTAAT
1 AATAAAATAT-TTTAATAAGTTAAT
*
238323 -ATAAAAATATTTT-TTAAGTTAAT
1 AAT-AAAATATTTTAATAAGTTAAT
238346 A
1 A
238347 TATGTAAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
23 9 0.20
24 5 0.11
25 16 0.36
26 12 0.27
27 3 0.07
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.41
Consensus pattern (24 bp):
AATAAAATATTTTAATAAGTTAAT
Found at i:238340 original size:23 final size:24
Alignment explanation
Indices: 238273--238348 Score: 93
Period size: 23 Copynumber: 3.1 Consensus size: 24
238263 TGAAAATAAA
238273 ATAAAATAT-TTTAAACTAAGTTAAT
1 ATAAAATATATTT-AA-TAAGTTAAT
238298 AATAAAATATATTTAATAAGTTAAT
1 -ATAAAATATATTTAATAAGTTAAT
**
238323 ATAAAA-ATATTTTTTAAGTTAAT
1 ATAAAATATATTTAATAAGTTAAT
238346 ATA
1 ATA
238349 TGTAAAATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.38
24 6 0.13
25 9 0.19
26 11 0.23
27 3 0.06
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (24 bp):
ATAAAATATATTTAATAAGTTAAT
Found at i:238349 original size:25 final size:25
Alignment explanation
Indices: 238275--238359 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 25
238265 AAAATAAAAT
238275 AAAATATTTTAAACTAAGTTAATA-ATA
1 AAAATA-TTT-AA-TAAGTTAATATATA
238302 AAATATATTTAATAAGTT-A-ATATA
1 AAA-ATATTTAATAAGTTAATATATA
** *
238326 AAAATATTTTTTAAGTTAATATATGT
1 AAAATATTTAATAAGTTAATATAT-A
238352 AAAATATT
1 AAAATATT
238360 ATAAATTTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
23 13 0.26
24 8 0.16
25 10 0.20
26 10 0.20
27 6 0.12
28 3 0.06
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.42
Consensus pattern (25 bp):
AAAATATTTAATAAGTTAATATATA
Found at i:241091 original size:23 final size:23
Alignment explanation
Indices: 241045--241107 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 23
241035 TAAACGAAAG
*
241045 TAAACGAACACAAACAAACGAACATAA
1 TAAACGAACATAAACAAAC--AC--AA
*
241072 TAAATGAACATAAACAAACACAA
1 TAAACGAACATAAACAAACACAA
241095 TAAACGAACATAA
1 TAAACGAACATAA
241108 CGAACAACAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 14 0.42
25 2 0.06
27 17 0.52
ACGTcount: A:0.63, C:0.19, G:0.06, T:0.11
Consensus pattern (23 bp):
TAAACGAACATAAACAAACACAA
Found at i:246811 original size:2 final size:2
Alignment explanation
Indices: 246804--246838 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
246794 ATTAAATTTC
* *
246804 AT AT AT AT AT AT AT AT AT AT AT AT AG CT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
246839 ACACATGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:246999 original size:185 final size:188
Alignment explanation
Indices: 246716--247094 Score: 646
Period size: 185 Copynumber: 2.0 Consensus size: 188
246706 CAGAACTTGT
* *
246716 GCAATCACACCAAATTAGAGATGATTGAAATTATTTAAGTAATTATGGTAGGAGAAAAGAAAAGA
1 GCAATCACACCAAATTACAGATGATTGAAATTATTGAAGTAATTATGGTAGGAGAAAAGAAAAGA
246781 AAAAGCAAACCAAATTAAATTTCATATATATATATATATATATATATAGCTAT-ATA-TAACACA
66 AAAAGCAAACCAAATTAAATTTC----ATATATATATATATATATATAGCTATGATAGTAACACA
246844 T-GGTTGTG-AATGACTTGATTAAATATAAATGGA-AAACAA-CAAAATCCTTATGAC-AAC
127 TGGGTTGTGAAATGACTTGATTAAATATAAATGGAGAAACAACCAAAATCCTTATGACAAAC
246901 GCAATCACACCAAATTACAGATGATTGAAATTATTGAAGTAATTATGGTAGGAGAAAAGAAAAGA
1 GCAATCACACCAAATTACAGATGATTGAAATTATTGAAGTAATTATGGTAGGAGAAAAGAAAAGA
246966 AAAAGCAAACCAAATTAAATTTCATATATATATATATATATATAGCTATGGATAGTAACACATGG
66 AAAAGCAAACCAAATTAAATTTCATATATATATATATATATATAGCTAT-GATAGTAACACATGG
247031 GTTGTGAAATGACTTGATTAAATATAAATGGAGAAACAACCAAAATCCTTATGACAAAC
130 GTTGTGAAATGACTTGATTAAATATAAATGGAGAAACAACCAAAATCCTTATGACAAAC
247090 GCAAT
1 GCAAT
247095 TTAGACAAAC
Statistics
Matches: 184, Mismatches: 2, Indels: 12
0.93 0.01 0.06
Matches are distributed among these distances:
181 26 0.14
183 3 0.02
184 8 0.04
185 93 0.51
186 25 0.14
187 6 0.03
188 15 0.08
189 8 0.04
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.27
Consensus pattern (188 bp):
GCAATCACACCAAATTACAGATGATTGAAATTATTGAAGTAATTATGGTAGGAGAAAAGAAAAGA
AAAAGCAAACCAAATTAAATTTCATATATATATATATATATATAGCTATGATAGTAACACATGGG
TTGTGAAATGACTTGATTAAATATAAATGGAGAAACAACCAAAATCCTTATGACAAAC
Found at i:248932 original size:15 final size:15
Alignment explanation
Indices: 248912--248987 Score: 72
Period size: 14 Copynumber: 5.4 Consensus size: 15
248902 AAATAATTAA
248912 AATAATATATTTTAT
1 AATAATATATTTTAT
248927 AATAATATA-TTTAT
1 AATAATATATTTTAT
* * *
248941 AATTATTTATTATAT
1 AATAATATATTTTAT
*
248956 -TTAA-ATA-TTTA-
1 AATAATATATTTTAT
*
248967 ATTAATATATTTTAT
1 AATAATATATTTTAT
248982 AATAAT
1 AATAAT
248988 TTTTATATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
12 7 0.15
13 5 0.10
14 18 0.38
15 18 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:248955 original size:21 final size:21
Alignment explanation
Indices: 248931--249000 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 21
248921 TTTTATAATA
248931 ATATATTTATAATTATTTA-T
1 ATATATTTATAATTATTTATT
248951 -TATATTTA-AA-TATTTAATT
1 ATATATTTATAATTATTT-ATT
*
248970 AATATATTTTATAATAATTT-TT
1 -ATATA-TTTATAATTATTTATT
*
248992 ATATTTTTA
1 ATATATTTA
249001 ATAAACAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
17 5 0.12
18 3 0.07
19 9 0.22
20 4 0.10
21 8 0.20
22 6 0.15
23 2 0.05
24 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTATAATTATTTATT
Found at i:248955 original size:34 final size:34
Alignment explanation
Indices: 248917--249004 Score: 90
Period size: 40 Copynumber: 2.4 Consensus size: 34
248907 ATTAAAATAA
*
248917 TATATTTTATAATAATATA-TTTATAATTATTTAT
1 TATATTTTATAATAATATATTTTATAATAATTT-T
248951 TATATTTAAATATTTAATTAATATATTTTATAATAATTTT
1 TATATTT---TA--TAA-TAATATATTTTATAATAATTTT
248991 TATATTTT-TAATAA
1 TATATTTTATAATAA
249005 ACAAATAATA
Statistics
Matches: 46, Mismatches: 1, Indels: 15
0.74 0.02 0.24
Matches are distributed among these distances:
33 3 0.07
34 10 0.22
37 3 0.07
39 3 0.07
40 15 0.33
41 12 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
TATATTTTATAATAATATATTTTATAATAATTTT
Found at i:248966 original size:17 final size:19
Alignment explanation
Indices: 248932--249002 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 19
248922 TTTATAATAA
248932 TATATTTATAATTATTTAT
1 TATATTTATAATTATTTAT
* * *
248951 TATATTTAAATATTTAATTAA
1 TATATTT--ATAATTATTTAT
*
248972 TATATTTTATAATAATTT-T
1 TATA-TTTATAATTATTTAT
*
248991 TATATTTTTAAT
1 TATATTTATAAT
249003 AAACAAATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
18 7 0.17
19 11 0.27
20 7 0.17
21 13 0.32
22 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATATTTATAATTATTTAT
Found at i:249014 original size:41 final size:41
Alignment explanation
Indices: 248927--249026 Score: 114
Period size: 41 Copynumber: 2.5 Consensus size: 41
248917 TATATTTTAT
* ***
248927 AATAATATA-TTTATAATTATTTATTATATTTAAATATTTA
1 AATAATATATTTTATAATAATTTATTATATTTAAATAAACA
* *
248967 ATTAATATATTTTATAATAATTT-TTATATTTTTAATAAACA
1 AATAATATATTTTATAATAATTTATTATA-TTTAAATAAACA
*
249008 AATAATATATTTAATAATA
1 AATAATATATTTTATAATA
249027 TAAAAAATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 13 0.26
41 37 0.74
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (41 bp):
AATAATATATTTTATAATAATTTATTATATTTAAATAAACA
Found at i:249319 original size:23 final size:23
Alignment explanation
Indices: 249293--249336 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
249283 TTTCTTTAAC
249293 GACACATTTATCTATGCTTTTGT
1 GACACATTTATCTATGCTTTTGT
* * *
249316 GACATATTTTTCTTTGCTTTT
1 GACACATTTATCTATGCTTTT
249337 TGGTAGTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.55
Consensus pattern (23 bp):
GACACATTTATCTATGCTTTTGT
Found at i:250080 original size:21 final size:21
Alignment explanation
Indices: 250051--250097 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
250041 ATTCTGACTA
250051 TCGCATTGCGA-TTTTCCAAAT
1 TCGCATTGC-ACTTTTCCAAAT
* *
250072 TCGCGTTGCACTTTTCCTAAT
1 TCGCATTGCACTTTTCCAAAT
250093 TCGCA
1 TCGCA
250098 ATGCGAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.38
Consensus pattern (21 bp):
TCGCATTGCACTTTTCCAAAT
Found at i:250118 original size:20 final size:20
Alignment explanation
Indices: 250093--250158 Score: 123
Period size: 20 Copynumber: 3.3 Consensus size: 20
250083 TTTTCCTAAT
*
250093 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
250113 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
250133 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
250153 TCGCAA
1 TCGCAA
250159 CGCAAATCTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:250175 original size:20 final size:20
Alignment explanation
Indices: 250152--250238 Score: 140
Period size: 20 Copynumber: 4.3 Consensus size: 20
250142 GAATACGTAA
*
250152 ATCGCAACGCA-AATCTGACT
1 ATCGCAACG-AGATTCTGACT
250172 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
250192 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
250212 ATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
250232 ATCGCAA
1 ATCGCAA
250239 TACTTAATTT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
19 1 0.02
20 63 0.98
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:253596 original size:19 final size:19
Alignment explanation
Indices: 253508--253596 Score: 128
Period size: 19 Copynumber: 4.7 Consensus size: 19
253498 GACATTCATT
253508 TGACTATCGCAACGC--AA
1 TGACTATCGCAACGCGGAA
*
253525 TAGACTATCGCAACACGGAA
1 T-GACTATCGCAACGCGGAA
*
253545 TGACTATCGCAACACGGAA
1 TGACTATCGCAACGCGGAA
*
253564 TGACTATCGCAACGCGAAA
1 TGACTATCGCAACGCGGAA
253583 TGACTATCGCAACG
1 TGACTATCGCAACG
253597 AGAGAATTGC
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
17 1 0.02
18 13 0.20
19 49 0.74
20 3 0.05
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (19 bp):
TGACTATCGCAACGCGGAA
Found at i:253682 original size:34 final size:32
Alignment explanation
Indices: 253639--253735 Score: 126
Period size: 30 Copynumber: 3.0 Consensus size: 32
253629 CGCGAATTAG
*
253639 TTTCGCGTTGCGATTTTCATTTTCGCATTGCGA
1 TTTCTCGTTGCGATTTTCA-TTTCGCATTGCGA
253672 TTCTCTCGTTGCGATTTTCATTTCGCA-TGCGA
1 TT-TCTCGTTGCGATTTTCATTTCGCATTGCGA
* **
253704 -TTCTCATTGCGATAGTCATTTCGCATTGCGA
1 TTTCTCGTTGCGATTTTCATTTCGCATTGCGA
253735 T
1 T
253736 AGTCTGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
30 21 0.37
31 6 0.11
32 5 0.09
33 9 0.16
34 16 0.28
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
TTTCTCGTTGCGATTTTCATTTCGCATTGCGA
Found at i:255335 original size:42 final size:42
Alignment explanation
Indices: 255256--255348 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
255246 CCTCTTCAAC
* * *
255256 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
255298 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGTCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
255340 GATGACAGG
1 GATGACAGG
255349 TGAGTCGAGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.16, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:255957 original size:34 final size:34
Alignment explanation
Indices: 255913--256068 Score: 127
Period size: 34 Copynumber: 4.4 Consensus size: 34
255903 TGCGATTTTC
* *
255913 ATTTTGCATTGCGGTTCTTTCGTTGCGATAGTCA
1 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
* *
255947 AATTCGCATTGCGATAGTCATTTTTGCATTGCGATAGTCA
1 ATTTCGCATTGCGAT--TC---TTT-CGTTGCGATAGTCA
* * * * **
255987 TTTTCGCGTTACGATT-TTGTTGTTGCGATTTTC-
1 ATTTCGCATTGCGATTCTT-TCGTTGCGATAGTCA
*
256020 ATTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
1 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
*
256054 TTTTCGCATTGCGAT
1 ATTTCGCATTGCGAT
256069 AATCATTTTC
Statistics
Matches: 93, Mismatches: 20, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
33 24 0.26
34 38 0.41
35 1 0.01
36 2 0.02
38 1 0.01
39 3 0.03
40 24 0.26
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.44
Consensus pattern (34 bp):
ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
Found at i:255987 original size:20 final size:20
Alignment explanation
Indices: 255935--256091 Score: 126
Period size: 20 Copynumber: 8.5 Consensus size: 20
255925 GGTTCTTTCG
**
255935 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
255955 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
*
255975 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
255995 TTACGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
256009 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
256028 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
256042 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
256062 TTGCGATAATCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
256082 TTGCGATAGT
1 TTGCGATAGT
256092 AAACTATTCT
Statistics
Matches: 112, Mismatches: 11, Indels: 28
0.74 0.07 0.19
Matches are distributed among these distances:
14 13 0.12
16 12 0.11
17 6 0.05
18 5 0.04
19 7 0.06
20 69 0.62
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:258380 original size:22 final size:22
Alignment explanation
Indices: 258355--258429 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
258345 TGACCGTGAA
258355 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGCCGGAGATGGAGAC
* ** *
258377 TGATATCGTTGGAGAT-GAAAC
1 TGATTTCGCCGGAGATGGAGAC
* *
258398 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGCCGGAGATGGAGAC
* *
258420 GGATGTCGCC
1 TGATTTCGCC
258430 TTAGAGAGTG
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 18 0.44
22 23 0.56
ACGTcount: A:0.23, C:0.16, G:0.36, T:0.25
Consensus pattern (22 bp):
TGATTTCGCCGGAGATGGAGAC
Found at i:258401 original size:21 final size:21
Alignment explanation
Indices: 258355--258414 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
258345 TGACCGTGAA
* * *
258355 TGATTTCGCCGGAGATGGAGAC
1 TGATATCGTCGGAGAT-GAAAC
*
258377 TGATATCGTTGGAGATGAAAC
1 TGATATCGTCGGAGATGAAAC
*
258398 TGATTTCGTCGGAGATG
1 TGATATCGTCGGAGATG
258415 GGGACGGATG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 19 0.59
22 13 0.41
ACGTcount: A:0.25, C:0.13, G:0.33, T:0.28
Consensus pattern (21 bp):
TGATATCGTCGGAGATGAAAC
Found at i:258651 original size:20 final size:20
Alignment explanation
Indices: 258623--258690 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
258613 CAGATTTGCG
*
258623 TTGCGATTTACGTATTCACA
1 TTGCGATTTACGTATTCGCA
*
258643 TTACGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
258663 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
258683 TTGCGATT
1 TTGCGATT
258691 AGGAATATCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:258701 original size:20 final size:20
Alignment explanation
Indices: 258678--258730 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
258668 ATTTACGTAT
*
258678 TCGCATTGCGATTAGGAATA
1 TCGCAATGCGATTAGGAATA
* * *
258698 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCG-ATTAGGAATA
258719 TCGCAATGCGAT
1 TCGCAATGCGAT
258731 AGTCAGAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGATTAGGAATA
Found at i:258924 original size:10 final size:9
Alignment explanation
Indices: 258894--258958 Score: 53
Period size: 10 Copynumber: 7.1 Consensus size: 9
258884 TTATTTTCTC
258894 TATATATTA
1 TATATATTA
258903 TATATATT-
1 TATATATTA
258911 TATATATTA
1 TATATATTA
*
258920 -ATATATCA
1 TATATATTA
* *
258928 TATTTTATTT
1 TA-TATATTA
*
258938 TATTTTATTA
1 TA-TATATTA
258948 TATAGTATTA
1 TATA-TATTA
258958 T
1 T
258959 TATCTAATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
8 15 0.33
9 10 0.22
10 21 0.46
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (9 bp):
TATATATTA
Found at i:258956 original size:25 final size:24
Alignment explanation
Indices: 258884--258975 Score: 58
Period size: 27 Copynumber: 3.5 Consensus size: 24
258874 GGTCACTGAG
* *
258884 TTATTTTCTCTATATATTATATATATT
1 TTATTTTAT-TATATA-TAT-TTTATT
* *
258911 TATATATTAATATATCATATTTTATT
1 T-TATTTTATTATAT-ATATTTTATT
*
258937 TTATTTTATTATATAGTATTATTATC
1 TTATTTTATTATATA-TATT-TTATT
*
258963 TAATTATTATTAT
1 TTATT-TTATTAT
258976 TTATTTATAG
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
24 1 0.02
25 15 0.29
26 14 0.27
27 16 0.31
28 6 0.12
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (24 bp):
TTATTTTATTATATATATTTTATT
Found at i:260447 original size:66 final size:66
Alignment explanation
Indices: 260376--260587 Score: 408
Period size: 66 Copynumber: 3.2 Consensus size: 66
260366 TTTGAAATTT
260376 AAATTAGTTTAATTATTCAAATAAAATATTAAAATCTTTAGATTTAATGCTAGAGCCTCAATTTT
1 AAATTAGTTTAATTATTCAAATAAAATATTAAAATCTTTAGATTTAATGCTAGAGCCTCAATTTT
260441 A
66 A
260442 AAATTAGTTTAATTATTCAAATAAAATATTAAAATCTTTAGATTTAATGCTAGAGCCTCAATTTT
1 AAATTAGTTTAATTATTCAAATAAAATATTAAAATCTTTAGATTTAATGCTAGAGCCTCAATTTT
260507 -
66 A
260507 AAATTAGTTTAATTATTCAAATAAAATATTAAAATCTTTAGATTTAATGCTAGAGCCTCAATTTT
1 AAATTAGTTTAATTATTCAAATAAAATATTAAAATCTTTAGATTTAATGCTAGAGCCTCAATTTT
260572 A
66 A
*
260573 AAATTAGTTTTATTA
1 AAATTAGTTTAATTA
260588 AGTCCTTTAA
Statistics
Matches: 144, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
65 65 0.45
66 79 0.55
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (66 bp):
AAATTAGTTTAATTATTCAAATAAAATATTAAAATCTTTAGATTTAATGCTAGAGCCTCAATTTT
A
Found at i:260474 original size:31 final size:31
Alignment explanation
Indices: 260376--260476 Score: 78
Period size: 31 Copynumber: 3.1 Consensus size: 31
260366 TTTGAAATTT
260376 AAATTAGTTTAATTATTCAAATAAAATATTA
1 AAATTAGTTTAATTATTCAAATAAAATATTA
** ** ** * *
260407 AAATCTTTAGATTTAATGCTAGAGCCT-CAATTTTA
1 AAA---TTAG-TTTAATTATTCA-AATAAAATATTA
260442 AAATTAGTTTAATTATTCAAATAAAATATTA
1 AAATTAGTTTAATTATTCAAATAAAATATTA
260473 AAAT
1 AAAT
260477 CTTTAGATTT
Statistics
Matches: 48, Mismatches: 16, Indels: 12
0.63 0.21 0.16
Matches are distributed among these distances:
30 1 0.02
31 21 0.44
32 4 0.08
34 4 0.08
35 17 0.35
36 1 0.02
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.41
Consensus pattern (31 bp):
AAATTAGTTTAATTATTCAAATAAAATATTA
Found at i:263617 original size:2 final size:2
Alignment explanation
Indices: 263612--263654 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
263602 ATTTACACAA
263612 AT AT AT 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 AT AT AT
263654 A
1 A
263655 GTGGCGGATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:263617 original size:19 final size:21
Alignment explanation
Indices: 263579--263622 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
263569 ATAGTTTTAC
263579 TAATTAACACAAACATATATA
1 TAATTAACACAAACATATATA
* *
263600 TAATTTACACAAATATATATA
1 TAATTAACACAAACATATATA
263621 TA
1 TA
263623 TATATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (21 bp):
TAATTAACACAAACATATATA
Found at i:275889 original size:25 final size:25
Alignment explanation
Indices: 275855--275903 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
275845 CGTCTTGGCT
**
275855 CGGCACGACATGGCACGACTCGGCA
1 CGGCACGACACAGCACGACTCGGCA
*
275880 CGGCACGACACAGCACGGCTCGGC
1 CGGCACGACACAGCACGACTCGGC
275904 TCATCTCGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.22, C:0.39, G:0.33, T:0.06
Consensus pattern (25 bp):
CGGCACGACACAGCACGACTCGGCA
Found at i:276240 original size:22 final size:22
Alignment explanation
Indices: 276215--276269 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
276205 TCAGGAGTTA
* *
276215 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
276237 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
276259 CGGGAGTTATA
1 CAGGAGTTATA
276270 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:281731 original size:6 final size:6
Alignment explanation
Indices: 281720--281744 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
281710 TCGGCTCGGC
281720 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
281745 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:282260 original size:20 final size:19
Alignment explanation
Indices: 282222--282264 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
282212 AGGGCTATAT
*
282222 TCAACTTCTCAACTCACTC
1 TCAACTTCACAACTCACTC
*
282241 TCAACATTCACAATTCACTC
1 TCAAC-TTCACAACTCACTC
282261 TCAA
1 TCAA
282265 AGTGTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (19 bp):
TCAACTTCACAACTCACTC
Found at i:285844 original size:14 final size:14
Alignment explanation
Indices: 285825--285852 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
285815 CCCCCTCTCT
285825 GCGTTTGGATCTAA
1 GCGTTTGGATCTAA
285839 GCGTTTGGATCTAA
1 GCGTTTGGATCTAA
285853 AGAGCATCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (14 bp):
GCGTTTGGATCTAA
Found at i:287658 original size:105 final size:105
Alignment explanation
Indices: 287474--287678 Score: 340
Period size: 105 Copynumber: 2.0 Consensus size: 105
287464 CCGGATCCGG
*
287474 TTGCCTTCTCAAAGGCATAAAGATCCTGAAGTGCTACCCACCAAGGAGCAGCCTTGCTCTACCAC
1 TTGCCTTCTCAAAGGCATAAAGATCCTGAAGTGCTACCCACAAAGGAGCAGCCTTGCTCTACCAC
*
287539 AGGAAAGATTGATGAGGCCTTTGTTCAAGAGACGCTTGGA
66 AGGAAAGATAGATGAGGCCTTTGTTCAAGAGACGCTTGGA
* * *
287579 TTGCCTTCTCAAGGGCATAAAGATCCTGAAGTGCTACCCAGAAAGGAGCA-CCTTTGCTCTACCT
1 TTGCCTTCTCAAAGGCATAAAGATCCTGAAGTGCTACCCACAAAGGAGCAGCC-TTGCTCTACCA
*
287643 CAGGAAAGATAGATGAGGCCTTTGTTCAAGGGACGC
65 CAGGAAAGATAGATGAGGCCTTTGTTCAAGAGACGC
287679 ATGAGCATGT
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
104 2 0.02
105 91 0.98
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.23
Consensus pattern (105 bp):
TTGCCTTCTCAAAGGCATAAAGATCCTGAAGTGCTACCCACAAAGGAGCAGCCTTGCTCTACCAC
AGGAAAGATAGATGAGGCCTTTGTTCAAGAGACGCTTGGA
Found at i:291144 original size:30 final size:30
Alignment explanation
Indices: 291110--291279 Score: 101
Period size: 30 Copynumber: 5.2 Consensus size: 30
291100 TTTGTTTTGG
291110 GAGAAACAATCTCAAAAGTTTATGTTTCAA
1 GAGAAACAATCTCAAAAGTTTATGTTTCAA
** *
291140 GAGAAACTGTCTCAAGCGAGAGTAAATT-TGTTTAAA
1 GAGAAACAATCTCAA---A-AGT---TTATGTTTCAA
*
291176 GAGAAACAATCTCAAAGGTTTATGTTTCAA
1 GAGAAACAATCTCAAAAGTTTATGTTTCAA
** * *
291206 GAGAAACTGTCTCAAGTGAGATGAAACTT-TGTTTCGA
1 GAGAAACAATCTCAA---A-A-G---TTTATGTTTCAA
* *
291243 GAGAAACAATCTCAAAGGTTCATGTTTCAA
1 GAGAAACAATCTCAAAAGTTTATGTTTCAA
291273 GAGAAAC
1 GAGAAAC
291280 TGTATCAAAC
Statistics
Matches: 105, Mismatches: 18, Indels: 34
0.67 0.11 0.22
Matches are distributed among these distances:
29 3 0.03
30 47 0.45
32 3 0.03
33 3 0.03
34 4 0.04
35 1 0.01
36 20 0.19
37 22 0.21
38 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (30 bp):
GAGAAACAATCTCAAAAGTTTATGTTTCAA
Found at i:291146 original size:67 final size:66
Alignment explanation
Indices: 290999--291324 Score: 368
Period size: 66 Copynumber: 4.9 Consensus size: 66
290989 GAAAGAAATT
* * * * * * * * * * *
290999 TGTTTCAAGATAAGCTATCTCAAGTGAGATAAAATTTTATTTCGAGTGAAATAATTTCAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGA-GAAACTTTGTTTCAAGAGAAACAATCTCAAAAGTT
291063 TA
65 TA
* * ***
291065 TATTTCAAGGGAAACTGTCTCAAGCGAGACGAAACTTTGTTTTGGGAGAAACAATCTCAAAAGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGA-GAAACTTTGTTTCAAGAGAAACAATCTCAAAAGTT
291130 TA
65 TA
* *
291132 TGTTTCAAGAGAAACTGTCTCAAGCGAGAGTAAA-TTTGTTTAAAGAGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGAG-AAACTTTGTTTCAAGAGAAACAATCTCAAAAGTT
291196 TA
65 TA
* * *
291198 TGTTTCAAGAGAAACTGTCTCAAGTGAGATGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGA-GAAACTTTGTTTCAAGAGAAACAATCTCAAAAGTT
*
291263 CA
65 TA
* * * *
291265 TGTTTCAAGAGAAACTGTATCAAACGAGAAAAAATTTGTTTCAAGAGAAACAATCTCAAA
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGAGAAACTTTGTTTCAAGAGAAACAATCTCAAA
291325 GGAGACAAAA
Statistics
Matches: 225, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
66 135 0.60
67 90 0.40
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGAGAAACTTTGTTTCAAGAGAAACAATCTCAAAAGTTT
A
Found at i:291179 original size:36 final size:35
Alignment explanation
Indices: 291132--291361 Score: 160
Period size: 36 Copynumber: 6.7 Consensus size: 35
291122 CAAAAGTTTA
291132 TGTTTCAAGAGAAACTGTCTCAAGCGAGAGTAAATT
1 TGTTTCAAGAGAAACTGTCTCAAG-GAGAGTAAATT
* **
291168 TGTTTAAAGAGAAACAATCTCAA--AG-GT---TT
1 TGTTTCAAGAGAAACTGTCTCAAGGAGAGTAAATT
291197 ATGTTTCAAGAGAAACTGTCTCAAGTGAGA-TGAAACTT
1 -TGTTTCAAGAGAAACTGTCTCAAG-GAGAGT-AAA-TT
* ** **
291235 TGTTTCGAGAGAAACAATCTCAA--AG-GTTCA--
1 TGTTTCAAGAGAAACTGTCTCAAGGAGAGTAAATT
* * **
291265 TGTTTCAAGAGAAACTGTATCAAACGAGAAAAAATT
1 TGTTTCAAGAGAAACTGTCTC-AAGGAGAGTAAATT
** **
291301 TGTTTCAAGAGAAACAATCTCAAAGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTC-AAGGAGAGTAAATT
*
291337 TGTTTCAAGAGAAACTGACTCAAGG
1 TGTTTCAAGAGAAACTGTCTCAAGG
291362 GAGACAAACA
Statistics
Matches: 150, Mismatches: 27, Indels: 35
0.71 0.13 0.17
Matches are distributed among these distances:
29 2 0.01
30 37 0.25
31 2 0.01
32 2 0.01
33 8 0.05
34 4 0.03
35 4 0.03
36 69 0.46
37 20 0.13
38 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTGTCTCAAGGAGAGTAAATT
Found at i:291237 original size:133 final size:133
Alignment explanation
Indices: 291061--291326 Score: 415
Period size: 133 Copynumber: 2.0 Consensus size: 133
291051 AATTTCAAAA
* * *
291061 TTTATATTTCAAGGGAAACTGTCTCAAGCGAGACGAAACTTTGTTTTGGGAGAAACAATCTCAAA
1 TTTATATTTCAAGAGAAACTGTCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAAA
* * * **
291126 AGTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGAGTAAATTTGTTTAAAGAGAAACAATCTCAA
66 AGTTCATGTTTCAAGAGAAACTGTATCAAACGAGAAAAAATTTGTTTAAAGAGAAACAATCTCAA
291191 AGG
131 AGG
* * *
291194 TTTATGTTTCAAGAGAAACTGTCTCAAGTGAGATGAAACTTTGTTTCGAGAGAAACAATCTCAAA
1 TTTATATTTCAAGAGAAACTGTCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAAA
* *
291259 GGTTCATGTTTCAAGAGAAACTGTATCAAACGAGAAAAAATTTGTTTCAAGAGAAACAATCTCAA
66 AGTTCATGTTTCAAGAGAAACTGTATCAAACGAGAAAAAATTTGTTTAAAGAGAAACAATCTCAA
291324 AGG
131 AGG
291327 AGACAAAATT
Statistics
Matches: 120, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
133 120 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (133 bp):
TTTATATTTCAAGAGAAACTGTCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAAA
AGTTCATGTTTCAAGAGAAACTGTATCAAACGAGAAAAAATTTGTTTAAAGAGAAACAATCTCAA
AGG
Found at i:298750 original size:23 final size:21
Alignment explanation
Indices: 298713--298756 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 21
298703 TTTCCAACCC
298713 TATTATTATTATTATTAAAAA
1 TATTATTATTATTATTAAAAA
298734 TATTATTTATTTATTATTAAAAA
1 TATTA-TTA-TTATTATTAAAAA
298757 ATACCCAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.24
22 3 0.14
23 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTATTATTATTATTAAAAA
Found at i:302875 original size:18 final size:18
Alignment explanation
Indices: 302852--302887 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
302842 GGAGAATGAC
302852 AGTCAGATACTTATTCGA
1 AGTCAGATACTTATTCGA
302870 AGTCAGATACTTATTCGA
1 AGTCAGATACTTATTCGA
302888 TGGAGAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (18 bp):
AGTCAGATACTTATTCGA
Found at i:304024 original size:8 final size:7
Alignment explanation
Indices: 304011--304073 Score: 74
Period size: 7 Copynumber: 8.6 Consensus size: 7
304001 AAGAAAGAGA
304011 AAAAAAG
1 AAAAAAG
304018 TAAAAAAG
1 -AAAAAAG
304026 AAAAAAG
1 AAAAAAG
304033 AAAAAGAG
1 AAAAA-AG
304041 AAAAAAG
1 AAAAAAG
304048 AAAAAATG
1 AAAAAA-G
304056 ATAAAAA-
1 A-AAAAAG
*
304063 AAGAAAG
1 AAAAAAG
304070 AAAA
1 AAAA
304074 GAAAAGAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
6 4 0.08
7 24 0.49
8 16 0.33
9 5 0.10
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (7 bp):
AAAAAAG
Found at i:304024 original size:9 final size:8
Alignment explanation
Indices: 304008--304078 Score: 74
Period size: 8 Copynumber: 8.8 Consensus size: 8
303998 GAAAAGAAAG
304008 AGAAAAAA
1 AGAAAAAA
*
304016 AGTAAAAA
1 AGAAAAAA
304024 AG-AAAAA
1 AGAAAAAA
*
304031 AGAAAAAG
1 AGAAAAAA
304039 AG-AAAAA
1 AGAAAAAA
304046 AGAAAAAA
1 AGAAAAAA
*
304054 TGATAAAAAA
1 --AGAAAAAA
304064 AGAAAGAAA
1 AGAAA-AAA
304073 AGAAAA
1 AGAAAA
304079 GAAAATAATG
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
7 13 0.25
8 25 0.47
9 8 0.15
10 7 0.13
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.04
Consensus pattern (8 bp):
AGAAAAAA
Found at i:304025 original size:22 final size:21
Alignment explanation
Indices: 303999--304078 Score: 74
Period size: 22 Copynumber: 3.7 Consensus size: 21
303989 ATAAATGATG
*
303999 AAAAGAAAGAGAAAAAAAGTAA
1 AAAAGAAAAAGAAAAAAAG-AA
*
304021 AAAAGAAAAAAGAAAAAGAGAA
1 AAAAG-AAAAAGAAAAAAAGAA
*
304043 AAAAGAAAAAATGATAAAAA-AA
1 AAAAG-AAAAA-GAAAAAAAGAA
*
304065 GAAAG-AAAAGAAAA
1 AAAAGAAAAAGAAAA
304079 GAAAATAATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
19 4 0.08
20 4 0.08
22 24 0.48
23 18 0.36
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (21 bp):
AAAAGAAAAAGAAAAAAAGAA
Found at i:304031 original size:15 final size:14
Alignment explanation
Indices: 304011--304073 Score: 74
Period size: 15 Copynumber: 4.3 Consensus size: 14
304001 AAGAAAGAGA
304011 AAAAAAGTAAAAAAG
1 AAAAAAG-AAAAAAG
304026 AAAAAAGAAAAAGAG
1 AAAAAAGAAAAA-AG
304041 AAAAAAGAAAAAATG
1 AAAAAAGAAAAAA-G
*
304056 ATAAAAA-AAGAAAG
1 A-AAAAAGAAAAAAG
304070 AAAA
1 AAAA
304074 GAAAAGAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
13 3 0.07
14 8 0.18
15 28 0.64
16 5 0.11
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (14 bp):
AAAAAAGAAAAAAG
Found at i:304031 original size:29 final size:29
Alignment explanation
Indices: 303999--304092 Score: 102
Period size: 29 Copynumber: 3.1 Consensus size: 29
303989 ATAAATGATG
303999 AAAAGAAAGAGAAAAAAAGTAAAAAA-GAA
1 AAAAGAAAGAGAAAAAAAG-AAAAAATGAA
*
304028 AAAAGAAAAAGAGAAAAAAGAAAAAATGATAAA
1 AAAAGAAAGAGA-AAAAAAGAAAAAATG---AA
304061 AAAAGAAAGA-AAAGAAAAGAAAATAATGAA
1 AAAAGAAAGAGAAA-AAAAGAAAA-AATGAA
304091 AA
1 AA
304093 TGGAAAAGAA
Statistics
Matches: 56, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
29 17 0.30
30 12 0.21
31 2 0.04
32 10 0.18
33 15 0.27
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (29 bp):
AAAAGAAAGAGAAAAAAAGAAAAAATGAA
Found at i:304042 original size:31 final size:31
Alignment explanation
Indices: 303999--304092 Score: 115
Period size: 31 Copynumber: 3.0 Consensus size: 31
303989 ATAAATGATG
303999 AAAAGAAAGAGAAAAAAAGTAAAAAA-GAAAA
1 AAAAGAAAGAGAAAAAAAG-AAAAAATGAAAA
304030 AAGAA-AAAGAG-AAAAAAGAAAAAATGATAAA
1 AA-AAGAAAGAGAAAAAAAGAAAAAATGA-AAA
304061 AAAAGAAAGA-AAAGAAAAGAAAATAATGAAAA
1 AAAAGAAAGAGAAA-AAAAGAAAA-AATGAAAA
304093 TGGAAAAGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 13
0.81 0.00 0.19
Matches are distributed among these distances:
29 6 0.11
30 11 0.20
31 20 0.36
32 14 0.25
33 5 0.09
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (31 bp):
AAAAGAAAGAGAAAAAAAGAAAAAATGAAAA
Found at i:304078 original size:15 final size:14
Alignment explanation
Indices: 303999--304083 Score: 70
Period size: 15 Copynumber: 6.1 Consensus size: 14
303989 ATAAATGATG
*
303999 AAAAGAAAGAGAAA
1 AAAAGAAAAAGAAA
304013 AAAAGTAAAAA-AGAA
1 AAAAG-AAAAAGA-AA
304028 AAAAGAAAAAGAGAA
1 AAAAGAAAAAGA-AA
**
304043 AAAAGAAAAA-ATG
1 AAAAGAAAAAGAAA
*
304056 ATAA-AAAAAGAAA
1 AAAAGAAAAAGAAA
304069 GAAAAG-AAAAGAAA
1 -AAAAGAAAAAGAAA
304083 A
1 A
304084 TAATGAAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
12 5 0.09
13 5 0.09
14 23 0.40
15 25 0.43
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (14 bp):
AAAAGAAAAAGAAA
Found at i:304083 original size:22 final size:21
Alignment explanation
Indices: 303999--304092 Score: 63
Period size: 22 Copynumber: 4.4 Consensus size: 21
303989 ATAAATGATG
*
303999 AAAAGAAAGAGAAA-AAAAGTAA
1 AAAAGAAA-A-AAAGAAAAGAAA
304021 AAAAG-AAAAAAGAAAAAGAGAA
1 AAAAGAAAAAAAG-AAAAGA-AA
* *
304043 AAAAGAAAAAATG---ATAAA
1 AAAAGAAAAAAAGAAAAGAAA
304061 AAAAGAAAGAAAAGAAAAGAAA
1 AAAAGAAA-AAAAGAAAAGAAA
*
304083 ATAATGAAAA
1 A-AAAGAAAA
304093 TGGAAAAGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
18 10 0.18
19 9 0.16
20 1 0.02
21 7 0.12
22 18 0.32
23 12 0.21
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (21 bp):
AAAAGAAAAAAAGAAAAGAAA
Found at i:304092 original size:14 final size:14
Alignment explanation
Indices: 303998--304082 Score: 63
Period size: 14 Copynumber: 6.0 Consensus size: 14
303988 AATAAATGAT
303998 GAAAAGAAAGAGAAA
1 GAAAAGAAA-AGAAA
304013 -AAAAGTAAAA-AAGA
1 GAAAAG-AAAAGAA-A
*
304027 AAAAAGAAAAAGAGAA
1 GAAAAG-AAAAGA-AA
*
304043 -AAAAGAAAA-AAT
1 GAAAAGAAAAGAAA
304055 GATAAA-AAAAGAAA
1 GA-AAAGAAAAGAAA
304069 GAAAAGAAAAGAAA
1 GAAAAGAAAAGAAA
304083 ATAATGAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 19
0.73 0.04 0.24
Matches are distributed among these distances:
12 1 0.02
13 11 0.19
14 26 0.45
15 17 0.29
16 2 0.03
17 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (14 bp):
GAAAAGAAAAGAAA
Found at i:305718 original size:117 final size:116
Alignment explanation
Indices: 305492--305723 Score: 333
Period size: 117 Copynumber: 2.0 Consensus size: 116
305482 TCATCACTTT
*
305492 GTTCGATTCCATCATGAAGAAGGTGGATCAACATTTCTAGTGGAGAGTTCATAGTGAGAAGAACT
1 GTTCGATTCCATCATGAAGAAGGTGGATCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACT
* * * *
305557 CATCTGTTGAGGGAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTG
66 CATCCGATAAGGGAAAAGAAGTTCATAATGAAAAGAACTTGTTCAACCTTG
* *
305608 GTTCGATTCCATCACAT-AATG-AGGTGGATCGACATTTCTAGTGGAGAGTTCGTAATGAGAAGA
1 GTTCGATTCCAT--CATGAA-GAAGGTGGATCAACATTTCTAGTGGAGAGTTCATAATGAGAAGA
* * *
305671 ACTCATCCGATAAGGGAGAATAATTTCATAATGAAAAGAACTTGTTCAACCTT
63 ACTCATCCGATAAGGGAAAAGAAGTTCATAATGAAAAGAACTTGTTCAACCTT
305724 AGCTTGATCT
Statistics
Matches: 103, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
116 12 0.12
117 87 0.84
118 4 0.04
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (116 bp):
GTTCGATTCCATCATGAAGAAGGTGGATCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACT
CATCCGATAAGGGAAAAGAAGTTCATAATGAAAAGAACTTGTTCAACCTTG
Found at i:306096 original size:17 final size:17
Alignment explanation
Indices: 306074--306106 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
306064 ATTACAAAAT
306074 ACCCAAACC-AAACCCAA
1 ACCC-AACCTAAACCCAA
306091 ACCCAACCTAAACCCA
1 ACCCAACCTAAACCCA
306107 TTACCCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.48, C:0.48, G:0.00, T:0.03
Consensus pattern (17 bp):
ACCCAACCTAAACCCAA
Found at i:306105 original size:11 final size:11
Alignment explanation
Indices: 306074--306121 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
306064 ATTACAAAAT
*
306074 ACCCAAACCAA
1 ACCCAAACCCA
306085 ACCCAAACCCA
1 ACCCAAACCCA
*
306096 ACCTAAACCCA
1 ACCCAAACCCA
306107 TTACCCAATACCCA
1 --ACCCAA-ACCCA
306121 A
1 A
306122 ACATTCTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 20 0.65
12 1 0.03
13 5 0.16
14 5 0.16
ACGTcount: A:0.46, C:0.46, G:0.00, T:0.08
Consensus pattern (11 bp):
ACCCAAACCCA
Found at i:306118 original size:7 final size:6
Alignment explanation
Indices: 306074--306123 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
306064 ATTACAAAAT
* *
306074 ACCCAA A-CCAA ACCCAA ACCC-A ACCTAA ACCCATT ACCCAA TACCCAA
1 ACCCAA ACCCAA ACCCAA ACCCAA ACCCAA ACCCA-A ACCCAA -ACCCAA
306122 AC
1 AC
306124 ATTCTAACCC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
5 9 0.25
6 16 0.44
7 11 0.31
ACGTcount: A:0.46, C:0.46, G:0.00, T:0.08
Consensus pattern (6 bp):
ACCCAA
Found at i:306215 original size:6 final size:5
Alignment explanation
Indices: 306174--306217 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
306164 AAGCCCAAAT
*
306174 CCTAA CCTAA CCTAA CCTAA CTTAA CCATAA CCCTAAA CCTAA C
1 CCTAA CCTAA CCTAA CCTAA CCTAA CC-TAA -CCT-AA CCTAA C
306218 ACATCCTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 23 0.68
6 7 0.21
7 4 0.12
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (5 bp):
CCTAA
Found at i:309124 original size:13 final size:14
Alignment explanation
Indices: 309089--309132 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
309079 CCGGTCCAAC
*
309089 CCGACCCGACCTGGT
1 CCGACCCGACCT-GA
*
309104 CTGACCCGA-CTGA
1 CCGACCCGACCTGA
309117 CCGACCCGACCTGA
1 CCGACCCGACCTGA
309131 CC
1 CC
309133 CGTTGACCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 9 0.36
14 8 0.32
15 8 0.32
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.11
Consensus pattern (14 bp):
CCGACCCGACCTGA
Found at i:311502 original size:38 final size:38
Alignment explanation
Indices: 311451--311527 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
311441 TGAATCATGT
* * *
311451 TCTGATTTCTAATATGGATTCTGTTCTGATATATGATA
1 TCTGATATCTAATATGAATTATGTTCTGATATATGATA
* * * *
311489 TCTGATATGTAATATGAATTATGTTTTGATTTCTGATA
1 TCTGATATCTAATATGAATTATGTTCTGATATATGATA
311527 T
1 T
311528 GTCTGTTTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49
Consensus pattern (38 bp):
TCTGATATCTAATATGAATTATGTTCTGATATATGATA
Found at i:311783 original size:152 final size:153
Alignment explanation
Indices: 311545--311840 Score: 409
Period size: 152 Copynumber: 1.9 Consensus size: 153
311535 TATTGACAAA
* * *
311545 AAATATTTTATTTGGGGGTATTGTTGGAGGAAGAATATATACAGGCTCCTTGGCTTTGTGCTCGG
1 AAATATTTTATTTGGGGGTATTGTTGGAGGAAG-ATATATACAGACTCCTCGGCTTTGTGCTCAG
** * * * *
311610 GGCCTAACTGTTGTGTTGGGGTTGTATGGTTCTGGGAAACCTACACATTAT-TATGTGTTCGGTT
65 GGCCTAACTGTTGTGCAGGGGTTGTATGGTTATGGGAAACCTACACATTATGGACGTGTGCGGTT
* *
311674 GGGGGATTTACTATAGTTTTTAAT
130 GAGGGAATTACTATAGTTTTTAAT
*
311698 AAATGTTTTATTTGGGAGGTATTGTTGGAGGAAG-TATATGA-AGACTCCTCGGCTTTGTGCTCA
1 AAATATTTTATTTGGG-GGTATTGTTGGAGGAAGATATAT-ACAGACTCCTCGGCTTTGTGCTCA
* * *
311761 TGGCCTTACTGTTGTGCAGGGGTTGTATGGTTATGGGGAACCTACACATTATGGACGTGTGCGGT
64 GGGCCTAACTGTTGTGCAGGGGTTGTATGGTTATGGGAAACCTACACATTATGGACGTGTGCGGT
311826 TGAGGGAATTACTAT
129 TGAGGGAATTACTAT
311841 GATTTCTTAA
Statistics
Matches: 125, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
152 70 0.56
153 38 0.30
154 17 0.14
ACGTcount: A:0.21, C:0.12, G:0.30, T:0.37
Consensus pattern (153 bp):
AAATATTTTATTTGGGGGTATTGTTGGAGGAAGATATATACAGACTCCTCGGCTTTGTGCTCAGG
GCCTAACTGTTGTGCAGGGGTTGTATGGTTATGGGAAACCTACACATTATGGACGTGTGCGGTTG
AGGGAATTACTATAGTTTTTAAT
Found at i:322099 original size:18 final size:18
Alignment explanation
Indices: 322066--322104 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
322056 TTTTATTATT
* *
322066 TGGTCACGGCTAGAGACA
1 TGGTCACGACTAGAGAAA
*
322084 TGGTCACGACTGGAGAAA
1 TGGTCACGACTAGAGAAA
322102 TGG
1 TGG
322105 GCATGACGCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.18, G:0.36, T:0.18
Consensus pattern (18 bp):
TGGTCACGACTAGAGAAA
Found at i:322934 original size:15 final size:12
Alignment explanation
Indices: 322894--322928 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
322884 TATGCTCCTG
322894 ATGACGACGACA
1 ATGACGACGACA
322906 ATGACGACGACA
1 ATGACGACGACA
322918 ATGACGACGAC
1 ATGACGACGAC
322929 GACAATAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.40, C:0.26, G:0.26, T:0.09
Consensus pattern (12 bp):
ATGACGACGACA
Found at i:323225 original size:3 final size:3
Alignment explanation
Indices: 323217--323264 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
323207 TAATCGATTT
323217 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
323265 TATATGTATC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:328386 original size:19 final size:19
Alignment explanation
Indices: 328345--328386 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
328335 ATGACAAACA
*
328345 AATTCGCAAAGCAATCTCG
1 AATTCGCAAAGCAATCTCC
*
328364 AATTCGCAACGCGAA-CTCC
1 AATTCGCAAAGC-AATCTCC
328383 AATT
1 AATT
328387 TCGTAACTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (19 bp):
AATTCGCAAAGCAATCTCC
Found at i:328489 original size:20 final size:20
Alignment explanation
Indices: 328455--328694 Score: 140
Period size: 20 Copynumber: 12.0 Consensus size: 20
328445 AATTCGCGTT
328455 GCGATTTTCCAAATTCGCAAC
1 GCGATTTT-CAAATTCGCAAC
328476 GCGATTTTCAAATTCGCAAC
1 GCGATTTTCAAATTCGCAAC
*
328496 GCGAATATGT-AAA-TCGCAAC
1 GCG-AT-TTTCAAATTCGCAAC
* * *
328516 GCCAATCTGT-AAA-TCGTAAC
1 G-CGAT-TTTCAAATTCGCAAC
*
328536 GCGAATCTGT-AAA-TCGCAAC
1 GCG-AT-TTTCAAATTCGCAAC
* **
328556 ACAGA-AGTCAAATTCGCAAC
1 GC-GATTTTCAAATTCGCAAC
*
328576 GCGATTTCCAAATTCGCAAC
1 GCGATTTTCAAATTCGCAAC
* * * *
328596 GTGATTTACAAATTCGCCAT
1 GCGATTTTCAAATTCGCAAC
*
328616 GCGATTTACAAATTCGCAAC
1 GCGATTTTCAAATTCGCAAC
* *
328636 TCGA-TTTCTGAATTCGCAAC
1 GCGATTTTC-AAATTCGCAAC
* *
328656 TCGA-TTTCTGAATT-GCAAC
1 GCGATTTTC-AAATTCGCAAC
* *
328675 TCGATTTTCGAATTCGCAAC
1 GCGATTTTCAAATTCGCAAC
328695 ACGAATTTTA
Statistics
Matches: 186, Mismatches: 22, Indels: 23
0.81 0.10 0.10
Matches are distributed among these distances:
18 2 0.01
19 23 0.12
20 144 0.77
21 15 0.08
22 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (20 bp):
GCGATTTTCAAATTCGCAAC
Found at i:328515 original size:40 final size:40
Alignment explanation
Indices: 328402--328702 Score: 159
Period size: 40 Copynumber: 7.5 Consensus size: 40
328392 ACTCAGTTTC
* * ***
328402 CAAATTCGCAACGCGAATATGTAAATCGCATTACGATTTT
1 CAAATTCGCAACGCGAATTTCTAAATCGCAACGCGATTTT
* *** * *
328442 ACGAATTCGCGTTGCGATTTTCCAAATTCGCAACGCGATTTT
1 -CAAATTCGCAACGCGAATTTCTAAA-TCGCAACGCGATTTT
* * * *
328484 CAAATTCGCAACGCGAATATGTAAATCGCAACGCCAATCTGT
1 CAAATTCGCAACGCGAATTTCTAAATCGCAACG-CGAT-TTT
* * * * **
328526 -AAA-TCGTAACGCGAATCTGTAAATCGCAACACAGA-AGT
1 CAAATTCGCAACGCGAATTTCTAAATCGCAACGC-GATTTT
* * *
328564 CAAATTCGCAACGCG-ATTTCCAAATTCGCAACGTGATTTA
1 CAAATTCGCAACGCGAATTTCTAAA-TCGCAACGCGATTTT
* * *
328604 CAAATTCGCCATGCG-ATTTAC-AAATTCGCAACTCGA-TTT
1 CAAATTCGCAACGCGAATTT-CTAAA-TCGCAACGCGATTTT
* * * * *
328643 CTGAATTCGCAACTCG-ATTTCTGAATTGCAACTCGATTTT
1 C-AAATTCGCAACGCGAATTTCTAAATCGCAACGCGATTTT
* *
328683 CGAATTCGCAACACGAATTT
1 CAAATTCGCAACGCGAATTT
328703 TAATTTTGCA
Statistics
Matches: 200, Mismatches: 47, Indels: 27
0.73 0.17 0.10
Matches are distributed among these distances:
38 2 0.01
39 39 0.19
40 104 0.52
41 41 0.20
42 14 0.07
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (40 bp):
CAAATTCGCAACGCGAATTTCTAAATCGCAACGCGATTTT
Found at i:329527 original size:12 final size:12
Alignment explanation
Indices: 329506--329539 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
329496 ACCACATTTT
*
329506 CAATACCAAACA
1 CAATATCAAACA
329518 CAATATCAAACA
1 CAATATCAAACA
*
329530 CAATCTCAAA
1 CAATATCAAA
329540 ACTCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:329716 original size:24 final size:24
Alignment explanation
Indices: 329665--329718 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
329655 GTATTCGAAA
*
329665 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
329689 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
329713 TTTGAT
1 TTTGAT
329719 GATGTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:331997 original size:18 final size:18
Alignment explanation
Indices: 331974--332009 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
331964 AAGCAAAAGG
331974 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
331992 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
332010 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:332282 original size:20 final size:20
Alignment explanation
Indices: 332257--332295 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
332247 AAAATCACAA
332257 TGTGAATTTGACTTTCGCGT
1 TGTGAATTTGACTTTCGCGT
332277 TGTGAATTTGACTTTCGCG
1 TGTGAATTTGACTTTCGCG
332296 AAAATCGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.44
Consensus pattern (20 bp):
TGTGAATTTGACTTTCGCGT
Found at i:332506 original size:25 final size:25
Alignment explanation
Indices: 332465--332514 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
332455 AAATCAATTA
* *
332465 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGAGTACATTATTTG
332490 AACATTGTTATGAGTACATTATTTG
1 AACATTGTTATGAGTACATTATTTG
332515 GAAAATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGAGTACATTATTTG
Found at i:332921 original size:18 final size:18
Alignment explanation
Indices: 332900--332936 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
332890 GTAATTGGAG
332900 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
332918 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
332936 T
1 T
332937 ATAAATTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:332943 original size:24 final size:24
Alignment explanation
Indices: 332892--332944 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
332882 TTTCATATGT
* * *
332892 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
332916 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
332940 AATTT
1 AATTT
332945 CTGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:333636 original size:19 final size:19
Alignment explanation
Indices: 333588--333637 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
333578 ATAGTTTCTG
*
333588 AAACTTAAAATCGCAATGCA
1 AAAC-TAAAATCGCAACGCA
*
333608 AAAATGAAAATCGCAACGCA
1 AAACT-AAAATCGCAACGCA
333628 AAACTAAAAT
1 AAACTAAAAT
333638 TGCGTTGCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.56, C:0.18, G:0.10, T:0.16
Consensus pattern (19 bp):
AAACTAAAATCGCAACGCA
Found at i:334218 original size:20 final size:20
Alignment explanation
Indices: 334189--334237 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
334179 TAAACGCGCT
*
334189 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTCTG
*
334209 TTGTGAATTTGACTTCTCTG
1 TTGCGAATTTGACTTCTCTG
334229 TTGCGAATT
1 TTGCGAATT
334238 ACAAATTCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.14, G:0.22, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTCTG
Found at i:334251 original size:20 final size:20
Alignment explanation
Indices: 334228--334277 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
334218 TGACTTCTCT
334228 GTTGCGAATTACAAATTCGC
1 GTTGCGAATTACAAATTCGC
* *
334248 GTTGCGATTTACATATTCGC
1 GTTGCGAATTACAAATTCGC
*
334268 GTTACGAATT
1 GTTGCGAATT
334278 TGGAAAATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTACAAATTCGC
Found at i:334296 original size:21 final size:21
Alignment explanation
Indices: 334272--334337 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
334262 ATTCGCGTTA
* *
334272 CGAATTTGGAAAATCGCAACG
1 CGAATTCGTAAAATCGCAACG
334293 CGAATTCGTAAAATCGCAACG
1 CGAATTCGTAAAATCGCAACG
*
334314 CGAATTCGTAAAATCGCAATG
1 CGAATTCGTAAAATCGCAACG
334335 CGA
1 CGA
334338 TTTACATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (21 bp):
CGAATTCGTAAAATCGCAACG
Found at i:336645 original size:31 final size:31
Alignment explanation
Indices: 336610--336681 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
336600 AACTTTTAAA
336610 ATTTGCAATACCATCCCCCAACATTTAGTCC
1 ATTTGCAATACCATCCCCCAACATTTAGTCC
*** *
336641 ATTTGCAATATGGTCCCCCAACATTTAGTCT
1 ATTTGCAATACCATCCCCCAACATTTAGTCC
336672 ATTTGCAATA
1 ATTTGCAATA
336682 TGGCCCGACA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.29, C:0.28, G:0.10, T:0.33
Consensus pattern (31 bp):
ATTTGCAATACCATCCCCCAACATTTAGTCC
Found at i:336682 original size:31 final size:31
Alignment explanation
Indices: 336623--336684 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
336613 TGCAATACCA
336623 TCCCCCAACATTTAGTCCATTTGCAATATGG
1 TCCCCCAACATTTAGTCCATTTGCAATATGG
*
336654 TCCCCCAACATTTAGTCTATTTGCAATATGG
1 TCCCCCAACATTTAGTCCATTTGCAATATGG
336685 CCCGACATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCCATTTGCAATATGG
Found at i:340308 original size:20 final size:20
Alignment explanation
Indices: 340271--340308 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
340261 AAATAATTAA
*
340271 ATATATATAAATTTTAAACT
1 ATATATATAAATTATAAACT
340291 ATATATGATAAA-TATAAA
1 ATATAT-ATAAATTATAAA
340309 ATTTTATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (20 bp):
ATATATATAAATTATAAACT
Found at i:340517 original size:16 final size:16
Alignment explanation
Indices: 340496--340529 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
340486 TCAAAGATAC
340496 TTTTAGTAAAACATTA
1 TTTTAGTAAAACATTA
340512 TTTTAGTAAAACATTA
1 TTTTAGTAAAACATTA
340528 TT
1 TT
340530 CATACTAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (16 bp):
TTTTAGTAAAACATTA
Found at i:341157 original size:195 final size:195
Alignment explanation
Indices: 340809--341200 Score: 574
Period size: 195 Copynumber: 2.0 Consensus size: 195
340799 AAAATAAAAT
* * *
340809 TTAAGTATTAAAATAGGACAACAAATTATAAATTTAAGTACTAAATAGTTTATCTAATTTTTTAA
1 TTAAGTATCAAAATAGAACAACAAATAATAAATTTAAGTACTAAATAGTTTATCTAATTTTTTAA
* * *
340874 CAATTCTAAAAACTAAAATTTTAAGTTATAACAGGGGTTAGGGCCCCTTTGATCCCCAATGACCC
66 CAATACTAAAAACTAAAATTTTAAGTTATAACAGGGATTAGGGCCCCTTTGAGCCCCAATGACCC
* * * * *
340939 TTTGTCTATGATTGTTGATTAAAATAAATTTATCTCGTCAACGGTTGACGGTTCATCTCTTTTGA
131 TCTGCCTATGATTGTTGATTAAAATAAATTTATATCGTCAACGGATGACGGTTCATCTATTTTGA
* *
341004 TTAATGTATCAAAATAGAACAATAAATAAT-AATTTATGTACTAAATAGTTTATCTAATTTTTTT
1 TTAA-GTATCAAAATAGAACAACAAATAATAAATTTAAGTACTAAATAGTTTATCTAA-TTTTTT
* * * *
341068 AACAATACTAAAAACTAAAATTTTAAGTTATAACA-GGATTAGGGTCCCTTTGGGCCCTAATGGC
64 AACAATACTAAAAACTAAAATTTTAAGTTATAACAGGGATTAGGGCCCCTTTGAGCCCCAATGAC
*
341132 CCTCTGCCCT-TGATTGTTGATTAAAATAAATTTATATCGTCAACTGATGACGGTTCATCTATTT
129 CCTCTG-CCTATGATTGTTGATTAAAATAAATTTATATCGTCAACGGATGACGGTTCATCTATTT
341196 TGA
193 TGA
341199 TT
1 TT
341201 TAGATAGGGA
Statistics
Matches: 176, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
195 113 0.64
196 63 0.36
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (195 bp):
TTAAGTATCAAAATAGAACAACAAATAATAAATTTAAGTACTAAATAGTTTATCTAATTTTTTAA
CAATACTAAAAACTAAAATTTTAAGTTATAACAGGGATTAGGGCCCCTTTGAGCCCCAATGACCC
TCTGCCTATGATTGTTGATTAAAATAAATTTATATCGTCAACGGATGACGGTTCATCTATTTTGA
Found at i:341779 original size:2 final size:2
Alignment explanation
Indices: 341772--341811 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
341762 ACATAAATTC
341772 AT AT 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 AT AT
341812 TATTTATTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:341992 original size:21 final size:21
Alignment explanation
Indices: 341966--342164 Score: 207
Period size: 21 Copynumber: 9.6 Consensus size: 21
341956 GTTTCCAGAT
*
341966 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
341987 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
342008 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
342028 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
342049 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
342070 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
342091 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
342111 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
342132 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
342153 TCGCAATGCGAA
1 TCGCAATGCGAA
342165 TATGTAAATC
Statistics
Matches: 151, Mismatches: 15, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
20 34 0.23
21 117 0.77
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:342062 original size:83 final size:83
Alignment explanation
Indices: 341966--342164 Score: 362
Period size: 83 Copynumber: 2.4 Consensus size: 83
341956 GTTTCCAGAT
* * *
341966 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGTAAATCG
342031 CAATGCGATAGTCGACTA
66 CAATGCGATAGTCGACTA
*
342049 TCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCG
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGTAAATCG
342114 CAATGCGATAGTCGACTA
66 CAATGCGATAGTCGACTA
342132 TCGCAATGCGAACTTGGACTATCGCAATGCGAA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAA
342165 TATGTAAATC
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 111 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (83 bp):
TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGTAAATCG
CAATGCGATAGTCGACTA
Found at i:342114 original size:62 final size:61
Alignment explanation
Indices: 341986--342183 Score: 244
Period size: 62 Copynumber: 3.2 Consensus size: 61
341976 AACTTCGACT
*
341986 ATCGCAATGCGAACTTGGACTATCGCAATGCGAA-TATGTA-AATCGCAATGCG-ATA-GTCGAC
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAACT-TG-ACTATCGCAATGCGAATATGT--A-
*
342047 T
61 A
*
342048 ATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAACTT-GACTATCGCAATGCGAATATGTAA
* *
342110 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAACTT-GACTATCGCAATGCGAATATGTAA
342172 ATCGCAATGCGA
1 ATCGCAATGCGA
342184 TAGTCGAAGT
Statistics
Matches: 123, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
62 103 0.84
63 15 0.12
64 3 0.02
65 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.23
Consensus pattern (61 bp):
ATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGACTATCGCAATGCGAATATGTAA
Found at i:342203 original size:21 final size:21
Alignment explanation
Indices: 342179--342245 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
342169 TAAATCGCAA
342179 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
** * *
342200 TGCGATTTTCCAAATT--CGT
1 TGCGATAGTCGAAGTTCGCGT
*
342219 TACGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
342240 TGCGAT
1 TGCGAT
342246 TTATTCCAAA
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
19 14 0.41
21 20 0.59
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCGT
Found at i:342225 original size:40 final size:42
Alignment explanation
Indices: 342181--342270 Score: 157
Period size: 40 Copynumber: 2.2 Consensus size: 42
342171 AATCGCAATG
342181 CGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTA
1 CGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTA
*
342221 CGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
1 CGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTA
342263 CGATAGTC
1 CGATAGTC
342271 CAAAATCGCA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 24 0.51
41 2 0.04
42 21 0.45
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.34
Consensus pattern (42 bp):
CGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTA
Found at i:342274 original size:19 final size:19
Alignment explanation
Indices: 342197--342274 Score: 66
Period size: 19 Copynumber: 3.9 Consensus size: 19
342187 TCGAAGTTCG
**
342197 CGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAATT
* * *
342216 CGTTACGATAGTCGAAGTT
1 CGTTGCGATAGTCCAAATT
*
342235 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA--TAGTCCAAATT
342258 CGTTGCGATAGTCCAAA
1 CGTTGCGATAGTCCAAA
342275 ATCGCAACGA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
19 22 0.49
21 15 0.33
23 8 0.18
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (19 bp):
CGTTGCGATAGTCCAAATT
Found at i:342916 original size:6 final size:6
Alignment explanation
Indices: 342889--342943 Score: 80
Period size: 6 Copynumber: 9.7 Consensus size: 6
342879 CGTTCGTCTC
*
342889 TGGTCG -GGTCG -GGTTG -GGTCG TGGTCG TGGTCG TGGTCG TGGTCG
1 TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG
342934 TGGTCG TGGT
1 TGGTCG TGGT
342944 AATGGTAATG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
5 13 0.28
6 33 0.72
ACGTcount: A:0.00, C:0.15, G:0.53, T:0.33
Consensus pattern (6 bp):
TGGTCG
Found at i:342949 original size:6 final size:6
Alignment explanation
Indices: 342940--342994 Score: 74
Period size: 6 Copynumber: 9.2 Consensus size: 6
342930 GTCGTGGTCG
* * * *
342940 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAG TGGTAG TGGTAG TGGTAG
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA
342988 TGGTAA T
1 TGGTAA T
342995 ACGTGTCTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.25, C:0.00, G:0.40, T:0.35
Consensus pattern (6 bp):
TGGTAA
Found at i:342949 original size:12 final size:12
Alignment explanation
Indices: 342909--342992 Score: 87
Period size: 12 Copynumber: 7.0 Consensus size: 12
342899 GGGTTGGGTC
* *
342909 GTGGTCGTGGTC
1 GTGGTAGTGGTA
* *
342921 GTGGTCGTGGTC
1 GTGGTAGTGGTA
*
342933 GTGGTCGTGGTA
1 GTGGTAGTGGTA
* *
342945 ATGGTAATGGTA
1 GTGGTAGTGGTA
* *
342957 ATGGTAATGGTA
1 GTGGTAGTGGTA
342969 GTGGTAGTGGTA
1 GTGGTAGTGGTA
342981 GTGGTAGTGGTA
1 GTGGTAGTGGTA
342993 ATACGTGTCT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 66 1.00
ACGTcount: A:0.15, C:0.06, G:0.45, T:0.33
Consensus pattern (12 bp):
GTGGTAGTGGTA
Found at i:342949 original size:18 final size:18
Alignment explanation
Indices: 342928--342992 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
342918 GTCGTGGTCG
* *
342928 TGGTCGTGGTCGTGGTAA
1 TGGTAGTGGTAGTGGTAA
* *
342946 TGGTAATGGTAATGGTAA
1 TGGTAGTGGTAGTGGTAA
*
342964 TGGTAGTGGTAGTGGTAG
1 TGGTAGTGGTAGTGGTAA
342982 TGGTAGTGGTA
1 TGGTAGTGGTA
342993 ATACGTGTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.20, C:0.03, G:0.43, T:0.34
Consensus pattern (18 bp):
TGGTAGTGGTAGTGGTAA
Done.